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 30 peak regions and 10 molecular subtypes across 493 patients, 118 significant findings detected with Q value < 0.25.

Amp Peak 1(1q24.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Amp Peak 2(1q32.1) cnvs correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Amp Peak 3(3q26.32) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Amp Peak 5(5q35.1) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 6(7q36.3) cnvs correlated to 'CN_CNMF', 'RPPA_CNMF', and 'MRNASEQ_CNMF'.
Amp Peak 7(8q24.22) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 1(1p36.23) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 2(1p31.1) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 3(1q43) cnvs correlated to 'MIRSEQ_CHIERARCHICAL'.
Del Peak 4(2q37.3) cnvs correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 5(3p25.3) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 6(3p21.32) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 7(3p12.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 8(3q11.2) cnvs correlated to 'CN_CNMF'.
Del Peak 9(4q34.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 10(6q26) cnvs correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
Del Peak 11(6q26) cnvs correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
Del Peak 12(8p23.2) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
Del Peak 13(9p23) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 14(9p21.3) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 15(10q23.31) cnvs correlated to 'CN_CNMF'.
Del Peak 16(13q13.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 17(14q31.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Del Peak 18(Xq23) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 30 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 118 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
Del Peak 1(1p36 23)	98 (20%)	395	0.000181 (0.0378)	7.87e-05 (0.0171)	1.28e-09 (3.44e-07)	0.0201 (1.00)	4.28e-05 (0.00949)	0.000753 (0.143)	0.000118 (0.0251)	0.000449 (0.0903)	1.09e-07 (2.82e-05)	2.73e-08 (7.19e-06)
Del Peak 14(9p21 3)	152 (31%)	341	0.00125 (0.23)	0.000662 (0.128)	1.96e-29 (5.78e-27)	2.24e-21 (6.46e-19)	1.86e-07 (4.74e-05)	0.00673 (1.00)	2.08e-23 (6.02e-21)	1.15e-27 (3.37e-25)	5.17e-15 (1.45e-12)	2.78e-07 (7.06e-05)
Del Peak 17(14q31 1)	218 (44%)	275	5.92e-05 (0.0129)	2.77e-05 (0.00627)	2.06e-13 (5.7e-11)	6.79e-08 (1.78e-05)	2.81e-09 (7.52e-07)	2.31e-05 (0.00527)	6.67e-20 (1.91e-17)	6.4e-15 (1.79e-12)	2.51e-09 (6.74e-07)	0.0712 (1.00)
Amp Peak 7(8q24 22)	73 (15%)	420	0.226 (1.00)	0.278 (1.00)	2.35e-15 (6.61e-13)	1.18e-06 (0.00029)	4.06e-07 (0.000102)	0.000883 (0.166)	2.78e-12 (7.68e-10)	2.89e-11 (7.92e-09)	6.2e-09 (1.65e-06)	0.000181 (0.0378)
Del Peak 5(3p25 3)	432 (88%)	61	1.55e-07 (3.99e-05)	1.19e-08 (3.16e-06)	5.54e-30 (1.65e-27)	0.000657 (0.128)	0.00265 (0.443)	0.00232 (0.399)	2.88e-12 (7.91e-10)	7.52e-16 (2.13e-13)	8.36e-07 (0.000209)	1.13e-09 (3.07e-07)
Del Peak 6(3p21 32)	435 (88%)	58	1.55e-07 (3.99e-05)	1.19e-08 (3.16e-06)	1.74e-29 (5.14e-27)	0.00169 (0.301)	0.0114 (1.00)	0.000819 (0.155)	1.15e-13 (3.21e-11)	3.21e-16 (9.12e-14)	2.3e-06 (0.000551)	1.02e-09 (2.77e-07)
Amp Peak 3(3q26 32)	80 (16%)	413	0.0484 (1.00)	0.0372 (1.00)	1.5e-06 (0.000363)	6.37e-06 (0.00151)	0.00103 (0.191)	0.000218 (0.0447)	1.41e-06 (0.000342)	9.53e-08 (2.48e-05)	1.35e-06 (0.000328)	0.0086 (1.00)
Del Peak 13(9p23)	144 (29%)	349	0.00362 (0.598)	0.0023 (0.399)	3.36e-30 (1e-27)	3.43e-20 (9.85e-18)	3.33e-07 (8.42e-05)	0.0164 (1.00)	3.59e-23 (1.04e-20)	9.21e-24 (2.68e-21)	1.81e-14 (5.05e-12)	1.15e-05 (0.00266)
Del Peak 16(13q13 3)	76 (15%)	417	0.0144 (1.00)	0.0117 (1.00)	4.05e-06 (0.000963)	0.000675 (0.13)	3.61e-05 (0.00809)	0.0618 (1.00)	1.24e-06 (0.000303)	9.39e-08 (2.45e-05)	3.56e-07 (8.97e-05)	4.74e-05 (0.0105)
Amp Peak 2(1q32 1)	59 (12%)	434	0.41 (1.00)	0.724 (1.00)	7.5e-10 (2.05e-07)	0.172 (1.00)	0.00062 (0.122)	0.245 (1.00)	7.94e-06 (0.00186)	0.000588 (0.116)	2.13e-05 (0.00488)	1 (1.00)
Del Peak 10(6q26)	142 (29%)	351	0.015 (1.00)	0.00364 (0.598)	1.84e-25 (5.4e-23)	0.0171 (1.00)	1.07e-06 (0.000264)	0.000939 (0.175)	0.000478 (0.0956)	0.0191 (1.00)	2.1e-05 (0.00484)	0.0216 (1.00)
Del Peak 11(6q26)	142 (29%)	351	0.015 (1.00)	0.00364 (0.598)	1.84e-25 (5.4e-23)	0.0171 (1.00)	1.07e-06 (0.000264)	0.00135 (0.244)	0.000159 (0.0336)	0.0191 (1.00)	6.59e-06 (0.00155)	0.0257 (1.00)
Amp Peak 1(1q24 1)	60 (12%)	433	0.259 (1.00)	0.491 (1.00)	1.06e-07 (2.75e-05)	0.359 (1.00)	0.00247 (0.42)	0.382 (1.00)	3.88e-05 (0.00865)	0.00128 (0.235)	2.39e-05 (0.00543)	0.978 (1.00)
Del Peak 2(1p31 1)	72 (15%)	421	0.00167 (0.299)	0.000542 (0.107)	2.84e-05 (0.00639)	0.0474 (1.00)	0.00253 (0.427)	0.00763 (1.00)	0.0596 (1.00)	0.00727 (1.00)	4.74e-05 (0.0105)	3.38e-06 (0.000808)
Del Peak 9(4q34 3)	76 (15%)	417	0.314 (1.00)	0.292 (1.00)	5.47e-09 (1.46e-06)	0.000408 (0.0825)	0.0109 (1.00)	0.136 (1.00)	0.000344 (0.0698)	1.18e-05 (0.00272)	0.845 (1.00)	0.0122 (1.00)
Del Peak 18(Xq23)	55 (11%)	438	0.109 (1.00)	0.0776 (1.00)	6.53e-06 (0.00154)	0.000715 (0.136)	0.00215 (0.376)	0.00131 (0.239)	0.208 (1.00)	0.0183 (1.00)	0.00173 (0.307)	0.000111 (0.0237)
Amp Peak 6(7q36 3)	163 (33%)	330	0.667 (1.00)	0.639 (1.00)	1.25e-06 (0.000305)	0.0283 (1.00)	0.000218 (0.0447)	0.0198 (1.00)	0.00013 (0.0275)	0.00373 (0.604)	0.0305 (1.00)	0.0817 (1.00)
Del Peak 4(2q37 3)	48 (10%)	445	0.00156 (0.281)	0.00222 (0.386)	0.396 (1.00)	0.757 (1.00)	0.282 (1.00)	0.356 (1.00)	0.000109 (0.0234)	0.00019 (0.0393)	0.276 (1.00)	0.000161 (0.0338)
Amp Peak 5(5q35 1)	311 (63%)	182	0.0174 (1.00)	0.00729 (1.00)	5.53e-05 (0.0121)	0.888 (1.00)	0.0536 (1.00)	0.00237 (0.406)	0.0134 (1.00)	0.000701 (0.135)	0.0256 (1.00)	0.00393 (0.633)
Del Peak 7(3p12 2)	283 (57%)	210	0.0404 (1.00)	0.0145 (1.00)	2.28e-17 (6.51e-15)	0.349 (1.00)	0.316 (1.00)	0.0864 (1.00)	0.00398 (0.637)	0.000211 (0.0435)	0.0304 (1.00)	0.159 (1.00)
Del Peak 12(8p23 2)	146 (30%)	347	0.502 (1.00)	0.475 (1.00)	9.42e-06 (0.0022)	0.0223 (1.00)	0.0872 (1.00)	0.316 (1.00)	0.00256 (0.43)	0.00869 (1.00)	0.000511 (0.102)	0.00696 (1.00)
Del Peak 3(1q43)	38 (8%)	455	0.0107 (1.00)	0.0123 (1.00)	0.00529 (0.835)	0.697 (1.00)	0.879 (1.00)	0.0168 (1.00)	0.00846 (1.00)	0.00476 (0.757)	0.0748 (1.00)	0.000102 (0.022)
Del Peak 8(3q11 2)	150 (30%)	343	0.183 (1.00)	0.0989 (1.00)	0.000919 (0.172)	0.687 (1.00)	0.808 (1.00)	0.17 (1.00)	0.523 (1.00)	0.106 (1.00)	0.00914 (1.00)	0.0412 (1.00)
Del Peak 15(10q23 31)	90 (18%)	403	0.441 (1.00)	0.643 (1.00)	9.29e-07 (0.000231)	0.00202 (0.355)	0.16 (1.00)	0.192 (1.00)	0.0578 (1.00)	0.0344 (1.00)	0.047 (1.00)	0.0922 (1.00)
Amp Peak 4(4q32 1)	14 (3%)	479			0.698 (1.00)	1 (1.00)	0.0366 (1.00)	0.385 (1.00)	0.0813 (1.00)	0.466 (1.00)	0.0206 (1.00)	0.0805 (1.00)
Amp Peak 8(10p14)	16 (3%)	477	0.189 (1.00)	0.197 (1.00)	0.00753 (1.00)	0.342 (1.00)	0.0436 (1.00)	0.0264 (1.00)	0.0321 (1.00)	0.00295 (0.49)	0.199 (1.00)	0.0611 (1.00)
Amp Peak 9(17q24 3)	37 (8%)	456	0.0692 (1.00)	0.0971 (1.00)	0.00541 (0.85)	0.163 (1.00)	0.0779 (1.00)	0.424 (1.00)	0.197 (1.00)	0.0204 (1.00)	0.042 (1.00)	0.0198 (1.00)
Amp Peak 10(Xp22 2)	35 (7%)	458	1 (1.00)	1 (1.00)	0.00655 (1.00)	0.137 (1.00)	0.0167 (1.00)	0.0767 (1.00)	0.1 (1.00)	0.166 (1.00)	0.0205 (1.00)	0.17 (1.00)
Amp Peak 11(Xp11 4)	36 (7%)	457	0.843 (1.00)	0.845 (1.00)	0.0113 (1.00)	0.0575 (1.00)	0.0526 (1.00)	0.0226 (1.00)	0.0321 (1.00)	0.0469 (1.00)	0.0205 (1.00)	0.17 (1.00)
Amp Peak 12(Xq11 2)	32 (6%)	461	0.172 (1.00)	0.182 (1.00)	0.253 (1.00)	0.233 (1.00)	0.462 (1.00)	0.0883 (1.00)	0.104 (1.00)	0.391 (1.00)	0.372 (1.00)	0.116 (1.00)

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

P value = 1.06e-07 (Fisher's exact test), Q value = 2.7e-05

Table S1. Gene #1: 'Amp Peak 1(1q24.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	197	164
AMP PEAK 1(1Q24.1) MUTATED	35	11	14
AMP PEAK 1(1Q24.1) WILD-TYPE	97	186	150

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1q24.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 3.88e-05 (Fisher's exact test), Q value = 0.0086

Table S2. Gene #1: 'Amp Peak 1(1q24.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
AMP PEAK 1(1Q24.1) MUTATED	18	36	3
AMP PEAK 1(1Q24.1) WILD-TYPE	179	143	94

Figure S2. Get High-res Image Gene #1: 'Amp Peak 1(1q24.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 1(1q24.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00128 (Fisher's exact test), Q value = 0.24

Table S3. Gene #1: 'Amp Peak 1(1q24.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
AMP PEAK 1(1Q24.1) MUTATED	2	21	34
AMP PEAK 1(1Q24.1) WILD-TYPE	67	193	156

Figure S3. Get High-res Image Gene #1: 'Amp Peak 1(1q24.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 1(1q24.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.39e-05 (Fisher's exact test), Q value = 0.0054

Table S4. Gene #1: 'Amp Peak 1(1q24.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	104	184	143	44
AMP PEAK 1(1Q24.1) MUTATED	4	16	33	5
AMP PEAK 1(1Q24.1) WILD-TYPE	100	168	110	39

Figure S4. Get High-res Image Gene #1: 'Amp Peak 1(1q24.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 7.5e-10 (Fisher's exact test), Q value = 2e-07

Table S5. Gene #2: 'Amp Peak 2(1q32.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	197	164
AMP PEAK 2(1Q32.1) MUTATED	37	8	14
AMP PEAK 2(1Q32.1) WILD-TYPE	95	189	150

Figure S5. Get High-res Image Gene #2: 'Amp Peak 2(1q32.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 2(1q32.1) mutation analysis' versus 'RPPA_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.12

Table S6. Gene #2: 'Amp Peak 2(1q32.1) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	147	141
AMP PEAK 2(1Q32.1) MUTATED	32	13	9
AMP PEAK 2(1Q32.1) WILD-TYPE	127	134	132

Figure S6. Get High-res Image Gene #2: 'Amp Peak 2(1q32.1) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Amp Peak 2(1q32.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.94e-06 (Fisher's exact test), Q value = 0.0019

Table S7. Gene #2: 'Amp Peak 2(1q32.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
AMP PEAK 2(1Q32.1) MUTATED	18	36	2
AMP PEAK 2(1Q32.1) WILD-TYPE	179	143	95

Figure S7. Get High-res Image Gene #2: 'Amp Peak 2(1q32.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 2(1q32.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000588 (Fisher's exact test), Q value = 0.12

Table S8. Gene #2: 'Amp Peak 2(1q32.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
AMP PEAK 2(1Q32.1) MUTATED	1	22	33
AMP PEAK 2(1Q32.1) WILD-TYPE	68	192	157

Figure S8. Get High-res Image Gene #2: 'Amp Peak 2(1q32.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 2(1q32.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.13e-05 (Fisher's exact test), Q value = 0.0049

Table S9. Gene #2: 'Amp Peak 2(1q32.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	104	184	143	44
AMP PEAK 2(1Q32.1) MUTATED	4	16	33	4
AMP PEAK 2(1Q32.1) WILD-TYPE	100	168	110	40

Figure S9. Get High-res Image Gene #2: 'Amp Peak 2(1q32.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 3(3q26.32) mutation analysis' versus 'CN_CNMF'

P value = 1.5e-06 (Fisher's exact test), Q value = 0.00036

Table S10. Gene #3: 'Amp Peak 3(3q26.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	197	164
AMP PEAK 3(3Q26.32) MUTATED	35	13	32
AMP PEAK 3(3Q26.32) WILD-TYPE	97	184	132

Figure S10. Get High-res Image Gene #3: 'Amp Peak 3(3q26.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 3(3q26.32) mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.37e-06 (Fisher's exact test), Q value = 0.0015

Table S11. Gene #3: 'Amp Peak 3(3q26.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	118	64
AMP PEAK 3(3Q26.32) MUTATED	28	6	11
AMP PEAK 3(3Q26.32) WILD-TYPE	68	112	53

Figure S11. Get High-res Image Gene #3: 'Amp Peak 3(3q26.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 3(3q26.32) mutation analysis' versus 'RPPA_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.19

Table S12. Gene #3: 'Amp Peak 3(3q26.32) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	147	141
AMP PEAK 3(3Q26.32) MUTATED	40	14	21
AMP PEAK 3(3Q26.32) WILD-TYPE	119	133	120

Figure S12. Get High-res Image Gene #3: 'Amp Peak 3(3q26.32) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Amp Peak 3(3q26.32) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.000218 (Fisher's exact test), Q value = 0.045

Table S13. Gene #3: 'Amp Peak 3(3q26.32) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	211	104
AMP PEAK 3(3Q26.32) MUTATED	21	23	31
AMP PEAK 3(3Q26.32) WILD-TYPE	111	188	73

Figure S13. Get High-res Image Gene #3: 'Amp Peak 3(3q26.32) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 3(3q26.32) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.41e-06 (Fisher's exact test), Q value = 0.00034

Table S14. Gene #3: 'Amp Peak 3(3q26.32) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
AMP PEAK 3(3Q26.32) MUTATED	18	51	11
AMP PEAK 3(3Q26.32) WILD-TYPE	179	128	86

Figure S14. Get High-res Image Gene #3: 'Amp Peak 3(3q26.32) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 3(3q26.32) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.53e-08 (Fisher's exact test), Q value = 2.5e-05

Table S15. Gene #3: 'Amp Peak 3(3q26.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
AMP PEAK 3(3Q26.32) MUTATED	7	18	55
AMP PEAK 3(3Q26.32) WILD-TYPE	62	196	135

Figure S15. Get High-res Image Gene #3: 'Amp Peak 3(3q26.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 3(3q26.32) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.35e-06 (Fisher's exact test), Q value = 0.00033

Table S16. Gene #3: 'Amp Peak 3(3q26.32) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	104	184	143	44
AMP PEAK 3(3Q26.32) MUTATED	10	16	43	8
AMP PEAK 3(3Q26.32) WILD-TYPE	94	168	100	36

Figure S16. Get High-res Image Gene #3: 'Amp Peak 3(3q26.32) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 5(5q35.1) mutation analysis' versus 'CN_CNMF'

P value = 5.53e-05 (Fisher's exact test), Q value = 0.012

Table S17. Gene #5: 'Amp Peak 5(5q35.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	197	164
AMP PEAK 5(5Q35.1) MUTATED	94	136	81
AMP PEAK 5(5Q35.1) WILD-TYPE	38	61	83

Figure S17. Get High-res Image Gene #5: 'Amp Peak 5(5q35.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 5(5q35.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000701 (Fisher's exact test), Q value = 0.13

Table S18. Gene #5: 'Amp Peak 5(5q35.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
AMP PEAK 5(5Q35.1) MUTATED	30	148	122
AMP PEAK 5(5Q35.1) WILD-TYPE	39	66	68

Figure S18. Get High-res Image Gene #5: 'Amp Peak 5(5q35.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 6(7q36.3) mutation analysis' versus 'CN_CNMF'

P value = 1.25e-06 (Fisher's exact test), Q value = 3e-04

Table S19. Gene #6: 'Amp Peak 6(7q36.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	197	164
AMP PEAK 6(7Q36.3) MUTATED	63	41	59
AMP PEAK 6(7Q36.3) WILD-TYPE	69	156	105

Figure S19. Get High-res Image Gene #6: 'Amp Peak 6(7q36.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 6(7q36.3) mutation analysis' versus 'RPPA_CNMF'

P value = 0.000218 (Fisher's exact test), Q value = 0.045

Table S20. Gene #6: 'Amp Peak 6(7q36.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	147	141
AMP PEAK 6(7Q36.3) MUTATED	68	31	49
AMP PEAK 6(7Q36.3) WILD-TYPE	91	116	92

Figure S20. Get High-res Image Gene #6: 'Amp Peak 6(7q36.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Amp Peak 6(7q36.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.027

Table S21. Gene #6: 'Amp Peak 6(7q36.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
AMP PEAK 6(7Q36.3) MUTATED	48	80	29
AMP PEAK 6(7Q36.3) WILD-TYPE	149	99	68

Figure S21. Get High-res Image Gene #6: 'Amp Peak 6(7q36.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 7(8q24.22) mutation analysis' versus 'CN_CNMF'

P value = 2.35e-15 (Fisher's exact test), Q value = 6.6e-13

Table S22. Gene #7: 'Amp Peak 7(8q24.22) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	197	164
AMP PEAK 7(8Q24.22) MUTATED	42	3	28
AMP PEAK 7(8Q24.22) WILD-TYPE	90	194	136

Figure S22. Get High-res Image Gene #7: 'Amp Peak 7(8q24.22) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 7(8q24.22) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.18e-06 (Fisher's exact test), Q value = 0.00029

Table S23. Gene #7: 'Amp Peak 7(8q24.22) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	118	64
AMP PEAK 7(8Q24.22) MUTATED	30	6	11
AMP PEAK 7(8Q24.22) WILD-TYPE	66	112	53

Figure S23. Get High-res Image Gene #7: 'Amp Peak 7(8q24.22) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 7(8q24.22) mutation analysis' versus 'RPPA_CNMF'

P value = 4.06e-07 (Fisher's exact test), Q value = 1e-04

Table S24. Gene #7: 'Amp Peak 7(8q24.22) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	147	141
AMP PEAK 7(8Q24.22) MUTATED	42	7	19
AMP PEAK 7(8Q24.22) WILD-TYPE	117	140	122

Figure S24. Get High-res Image Gene #7: 'Amp Peak 7(8q24.22) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Amp Peak 7(8q24.22) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.000883 (Fisher's exact test), Q value = 0.17

Table S25. Gene #7: 'Amp Peak 7(8q24.22) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	211	104
AMP PEAK 7(8Q24.22) MUTATED	18	22	28
AMP PEAK 7(8Q24.22) WILD-TYPE	114	189	76

Figure S25. Get High-res Image Gene #7: 'Amp Peak 7(8q24.22) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 7(8q24.22) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.78e-12 (Fisher's exact test), Q value = 7.7e-10

Table S26. Gene #7: 'Amp Peak 7(8q24.22) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
AMP PEAK 7(8Q24.22) MUTATED	8	53	8
AMP PEAK 7(8Q24.22) WILD-TYPE	189	126	89

Figure S26. Get High-res Image Gene #7: 'Amp Peak 7(8q24.22) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 7(8q24.22) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.89e-11 (Fisher's exact test), Q value = 7.9e-09

Table S27. Gene #7: 'Amp Peak 7(8q24.22) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
AMP PEAK 7(8Q24.22) MUTATED	3	12	54
AMP PEAK 7(8Q24.22) WILD-TYPE	66	202	136

Figure S27. Get High-res Image Gene #7: 'Amp Peak 7(8q24.22) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 7(8q24.22) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 6.2e-09 (Fisher's exact test), Q value = 1.6e-06

Table S28. Gene #7: 'Amp Peak 7(8q24.22) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	104	184	143	44
AMP PEAK 7(8Q24.22) MUTATED	12	10	44	5
AMP PEAK 7(8Q24.22) WILD-TYPE	92	174	99	39

Figure S28. Get High-res Image Gene #7: 'Amp Peak 7(8q24.22) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 7(8q24.22) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000181 (Fisher's exact test), Q value = 0.038

Table S29. Gene #7: 'Amp Peak 7(8q24.22) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	259	51
AMP PEAK 7(8Q24.22) MUTATED	38	23	10
AMP PEAK 7(8Q24.22) WILD-TYPE	127	236	41

Figure S29. Get High-res Image Gene #7: 'Amp Peak 7(8q24.22) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 1(1p36.23) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000181 (Fisher's exact test), Q value = 0.038

Table S30. Gene #13: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	24	13
DEL PEAK 1(1P36.23) MUTATED	2	8	8
DEL PEAK 1(1P36.23) WILD-TYPE	31	16	5

Figure S30. Get High-res Image Gene #13: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 1(1p36.23) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 7.87e-05 (Fisher's exact test), Q value = 0.017

Table S31. Gene #13: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	23	33
DEL PEAK 1(1P36.23) MUTATED	9	7	2
DEL PEAK 1(1P36.23) WILD-TYPE	5	16	31

Figure S31. Get High-res Image Gene #13: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 1(1p36.23) mutation analysis' versus 'CN_CNMF'

P value = 1.28e-09 (Fisher's exact test), Q value = 3.4e-07

Table S32. Gene #13: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	197	164
DEL PEAK 1(1P36.23) MUTATED	36	13	49
DEL PEAK 1(1P36.23) WILD-TYPE	96	184	115

Figure S32. Get High-res Image Gene #13: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 1(1p36.23) mutation analysis' versus 'RPPA_CNMF'

P value = 4.28e-05 (Fisher's exact test), Q value = 0.0095

Table S33. Gene #13: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	147	141
DEL PEAK 1(1P36.23) MUTATED	48	15	24
DEL PEAK 1(1P36.23) WILD-TYPE	111	132	117

Figure S33. Get High-res Image Gene #13: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 1(1p36.23) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.000753 (Fisher's exact test), Q value = 0.14

Table S34. Gene #13: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	211	104
DEL PEAK 1(1P36.23) MUTATED	31	26	30
DEL PEAK 1(1P36.23) WILD-TYPE	101	185	74

Figure S34. Get High-res Image Gene #13: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 1(1p36.23) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000118 (Fisher's exact test), Q value = 0.025

Table S35. Gene #13: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
DEL PEAK 1(1P36.23) MUTATED	24	53	17
DEL PEAK 1(1P36.23) WILD-TYPE	173	126	80

Figure S35. Get High-res Image Gene #13: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 1(1p36.23) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000449 (Fisher's exact test), Q value = 0.09

Table S36. Gene #13: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
DEL PEAK 1(1P36.23) MUTATED	18	26	50
DEL PEAK 1(1P36.23) WILD-TYPE	51	188	140

Figure S36. Get High-res Image Gene #13: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 1(1p36.23) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.09e-07 (Fisher's exact test), Q value = 2.8e-05

Table S37. Gene #13: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	104	184	143	44
DEL PEAK 1(1P36.23) MUTATED	22	20	52	4
DEL PEAK 1(1P36.23) WILD-TYPE	82	164	91	40

Figure S37. Get High-res Image Gene #13: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 1(1p36.23) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.73e-08 (Fisher's exact test), Q value = 7.2e-06

Table S38. Gene #13: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	259	51
DEL PEAK 1(1P36.23) MUTATED	41	32	25
DEL PEAK 1(1P36.23) WILD-TYPE	124	227	26

Figure S38. Get High-res Image Gene #13: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 2(1p31.1) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000542 (Fisher's exact test), Q value = 0.11

Table S39. Gene #14: 'Del Peak 2(1p31.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	23	33
DEL PEAK 2(1P31.1) MUTATED	8	4	2
DEL PEAK 2(1P31.1) WILD-TYPE	6	19	31

Figure S39. Get High-res Image Gene #14: 'Del Peak 2(1p31.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 2(1p31.1) mutation analysis' versus 'CN_CNMF'

P value = 2.84e-05 (Fisher's exact test), Q value = 0.0064

Table S40. Gene #14: 'Del Peak 2(1p31.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	197	164
DEL PEAK 2(1P31.1) MUTATED	27	12	33
DEL PEAK 2(1P31.1) WILD-TYPE	105	185	131

Figure S40. Get High-res Image Gene #14: 'Del Peak 2(1p31.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 2(1p31.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.74e-05 (Fisher's exact test), Q value = 0.01

Table S41. Gene #14: 'Del Peak 2(1p31.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	104	184	143	44
DEL PEAK 2(1P31.1) MUTATED	13	17	39	3
DEL PEAK 2(1P31.1) WILD-TYPE	91	167	104	41

Figure S41. Get High-res Image Gene #14: 'Del Peak 2(1p31.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 2(1p31.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.38e-06 (Fisher's exact test), Q value = 0.00081

Table S42. Gene #14: 'Del Peak 2(1p31.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	259	51
DEL PEAK 2(1P31.1) MUTATED	23	28	21
DEL PEAK 2(1P31.1) WILD-TYPE	142	231	30

Figure S42. Get High-res Image Gene #14: 'Del Peak 2(1p31.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 3(1q43) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000102 (Fisher's exact test), Q value = 0.022

Table S43. Gene #15: 'Del Peak 3(1q43) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	259	51
DEL PEAK 3(1Q43) MUTATED	8	17	13
DEL PEAK 3(1Q43) WILD-TYPE	157	242	38

Figure S43. Get High-res Image Gene #15: 'Del Peak 3(1q43) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 4(2q37.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000109 (Fisher's exact test), Q value = 0.023

Table S44. Gene #16: 'Del Peak 4(2q37.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
DEL PEAK 4(2Q37.3) MUTATED	7	19	18
DEL PEAK 4(2Q37.3) WILD-TYPE	190	160	79

Figure S44. Get High-res Image Gene #16: 'Del Peak 4(2q37.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 4(2q37.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.039

Table S45. Gene #16: 'Del Peak 4(2q37.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
DEL PEAK 4(2Q37.3) MUTATED	12	8	24
DEL PEAK 4(2Q37.3) WILD-TYPE	57	206	166

Figure S45. Get High-res Image Gene #16: 'Del Peak 4(2q37.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 4(2q37.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000161 (Fisher's exact test), Q value = 0.034

Table S46. Gene #16: 'Del Peak 4(2q37.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	259	51
DEL PEAK 4(2Q37.3) MUTATED	15	17	14
DEL PEAK 4(2Q37.3) WILD-TYPE	150	242	37

Figure S46. Get High-res Image Gene #16: 'Del Peak 4(2q37.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 5(3p25.3) mutation analysis' versus 'MRNA_CNMF'

P value = 1.55e-07 (Fisher's exact test), Q value = 4e-05

Table S47. Gene #17: 'Del Peak 5(3p25.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	24	13
DEL PEAK 5(3P25.3) MUTATED	32	22	3
DEL PEAK 5(3P25.3) WILD-TYPE	1	2	10

Figure S47. Get High-res Image Gene #17: 'Del Peak 5(3p25.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 5(3p25.3) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.19e-08 (Fisher's exact test), Q value = 3.2e-06

Table S48. Gene #17: 'Del Peak 5(3p25.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	23	33
DEL PEAK 5(3P25.3) MUTATED	3	22	32
DEL PEAK 5(3P25.3) WILD-TYPE	11	1	1

Figure S48. Get High-res Image Gene #17: 'Del Peak 5(3p25.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 5(3p25.3) mutation analysis' versus 'CN_CNMF'

P value = 5.54e-30 (Fisher's exact test), Q value = 1.6e-27

Table S49. Gene #17: 'Del Peak 5(3p25.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	197	164
DEL PEAK 5(3P25.3) MUTATED	130	197	105
DEL PEAK 5(3P25.3) WILD-TYPE	2	0	59

Figure S49. Get High-res Image Gene #17: 'Del Peak 5(3p25.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 5(3p25.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000657 (Fisher's exact test), Q value = 0.13

Table S50. Gene #17: 'Del Peak 5(3p25.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	118	64
DEL PEAK 5(3P25.3) MUTATED	91	108	48
DEL PEAK 5(3P25.3) WILD-TYPE	5	10	16

Figure S50. Get High-res Image Gene #17: 'Del Peak 5(3p25.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 5(3p25.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.88e-12 (Fisher's exact test), Q value = 7.9e-10

Table S51. Gene #17: 'Del Peak 5(3p25.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
DEL PEAK 5(3P25.3) MUTATED	190	160	63
DEL PEAK 5(3P25.3) WILD-TYPE	7	19	34

Figure S51. Get High-res Image Gene #17: 'Del Peak 5(3p25.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 5(3p25.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.52e-16 (Fisher's exact test), Q value = 2.1e-13

Table S52. Gene #17: 'Del Peak 5(3p25.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
DEL PEAK 5(3P25.3) MUTATED	37	206	170
DEL PEAK 5(3P25.3) WILD-TYPE	32	8	20

Figure S52. Get High-res Image Gene #17: 'Del Peak 5(3p25.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 5(3p25.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 8.36e-07 (Fisher's exact test), Q value = 0.00021

Table S53. Gene #17: 'Del Peak 5(3p25.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	104	184	143	44
DEL PEAK 5(3P25.3) MUTATED	86	177	111	41
DEL PEAK 5(3P25.3) WILD-TYPE	18	7	32	3

Figure S53. Get High-res Image Gene #17: 'Del Peak 5(3p25.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 5(3p25.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.13e-09 (Fisher's exact test), Q value = 3.1e-07

Table S54. Gene #17: 'Del Peak 5(3p25.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	259	51
DEL PEAK 5(3P25.3) MUTATED	141	244	30
DEL PEAK 5(3P25.3) WILD-TYPE	24	15	21

Figure S54. Get High-res Image Gene #17: 'Del Peak 5(3p25.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 6(3p21.32) mutation analysis' versus 'MRNA_CNMF'

P value = 1.55e-07 (Fisher's exact test), Q value = 4e-05

Table S55. Gene #18: 'Del Peak 6(3p21.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	24	13
DEL PEAK 6(3P21.32) MUTATED	32	22	3
DEL PEAK 6(3P21.32) WILD-TYPE	1	2	10

Figure S55. Get High-res Image Gene #18: 'Del Peak 6(3p21.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 6(3p21.32) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.19e-08 (Fisher's exact test), Q value = 3.2e-06

Table S56. Gene #18: 'Del Peak 6(3p21.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	23	33
DEL PEAK 6(3P21.32) MUTATED	3	22	32
DEL PEAK 6(3P21.32) WILD-TYPE	11	1	1

Figure S56. Get High-res Image Gene #18: 'Del Peak 6(3p21.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 6(3p21.32) mutation analysis' versus 'CN_CNMF'

P value = 1.74e-29 (Fisher's exact test), Q value = 5.1e-27

Table S57. Gene #18: 'Del Peak 6(3p21.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	197	164
DEL PEAK 6(3P21.32) MUTATED	132	196	107
DEL PEAK 6(3P21.32) WILD-TYPE	0	1	57

Figure S57. Get High-res Image Gene #18: 'Del Peak 6(3p21.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 6(3p21.32) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.000819 (Fisher's exact test), Q value = 0.15

Table S58. Gene #18: 'Del Peak 6(3p21.32) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	211	104
DEL PEAK 6(3P21.32) MUTATED	124	193	82
DEL PEAK 6(3P21.32) WILD-TYPE	8	18	22

Figure S58. Get High-res Image Gene #18: 'Del Peak 6(3p21.32) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 6(3p21.32) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.15e-13 (Fisher's exact test), Q value = 3.2e-11

Table S59. Gene #18: 'Del Peak 6(3p21.32) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
DEL PEAK 6(3P21.32) MUTATED	192	161	63
DEL PEAK 6(3P21.32) WILD-TYPE	5	18	34

Figure S59. Get High-res Image Gene #18: 'Del Peak 6(3p21.32) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 6(3p21.32) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.21e-16 (Fisher's exact test), Q value = 9.1e-14

Table S60. Gene #18: 'Del Peak 6(3p21.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
DEL PEAK 6(3P21.32) MUTATED	38	208	170
DEL PEAK 6(3P21.32) WILD-TYPE	31	6	20

Figure S60. Get High-res Image Gene #18: 'Del Peak 6(3p21.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 6(3p21.32) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.3e-06 (Fisher's exact test), Q value = 0.00055

Table S61. Gene #18: 'Del Peak 6(3p21.32) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	104	184	143	44
DEL PEAK 6(3P21.32) MUTATED	86	178	114	40
DEL PEAK 6(3P21.32) WILD-TYPE	18	6	29	4

Figure S61. Get High-res Image Gene #18: 'Del Peak 6(3p21.32) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 6(3p21.32) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.02e-09 (Fisher's exact test), Q value = 2.8e-07

Table S62. Gene #18: 'Del Peak 6(3p21.32) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	259	51
DEL PEAK 6(3P21.32) MUTATED	139	247	32
DEL PEAK 6(3P21.32) WILD-TYPE	26	12	19

Figure S62. Get High-res Image Gene #18: 'Del Peak 6(3p21.32) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 7(3p12.2) mutation analysis' versus 'CN_CNMF'

P value = 2.28e-17 (Fisher's exact test), Q value = 6.5e-15

Table S63. Gene #19: 'Del Peak 7(3p12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	197	164
DEL PEAK 7(3P12.2) MUTATED	115	102	66
DEL PEAK 7(3P12.2) WILD-TYPE	17	95	98

Figure S63. Get High-res Image Gene #19: 'Del Peak 7(3p12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 7(3p12.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000211 (Fisher's exact test), Q value = 0.043

Table S64. Gene #19: 'Del Peak 7(3p12.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
DEL PEAK 7(3P12.2) MUTATED	24	125	120
DEL PEAK 7(3P12.2) WILD-TYPE	45	89	70

Figure S64. Get High-res Image Gene #19: 'Del Peak 7(3p12.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 8(3q11.2) mutation analysis' versus 'CN_CNMF'

P value = 0.000919 (Fisher's exact test), Q value = 0.17

Table S65. Gene #20: 'Del Peak 8(3q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	197	164
DEL PEAK 8(3Q11.2) MUTATED	57	54	39
DEL PEAK 8(3Q11.2) WILD-TYPE	75	143	125

Figure S65. Get High-res Image Gene #20: 'Del Peak 8(3q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 9(4q34.3) mutation analysis' versus 'CN_CNMF'

P value = 5.47e-09 (Fisher's exact test), Q value = 1.5e-06

Table S66. Gene #21: 'Del Peak 9(4q34.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	197	164
DEL PEAK 9(4Q34.3) MUTATED	37	9	30
DEL PEAK 9(4Q34.3) WILD-TYPE	95	188	134

Figure S66. Get High-res Image Gene #21: 'Del Peak 9(4q34.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 9(4q34.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000408 (Fisher's exact test), Q value = 0.083

Table S67. Gene #21: 'Del Peak 9(4q34.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	118	64
DEL PEAK 9(4Q34.3) MUTATED	30	12	10
DEL PEAK 9(4Q34.3) WILD-TYPE	66	106	54

Figure S67. Get High-res Image Gene #21: 'Del Peak 9(4q34.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 9(4q34.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000344 (Fisher's exact test), Q value = 0.07

Table S68. Gene #21: 'Del Peak 9(4q34.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
DEL PEAK 9(4Q34.3) MUTATED	24	41	6
DEL PEAK 9(4Q34.3) WILD-TYPE	173	138	91

Figure S68. Get High-res Image Gene #21: 'Del Peak 9(4q34.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 9(4q34.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.18e-05 (Fisher's exact test), Q value = 0.0027

Table S69. Gene #21: 'Del Peak 9(4q34.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
DEL PEAK 9(4Q34.3) MUTATED	2	24	45
DEL PEAK 9(4Q34.3) WILD-TYPE	67	190	145

Figure S69. Get High-res Image Gene #21: 'Del Peak 9(4q34.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 10(6q26) mutation analysis' versus 'CN_CNMF'

P value = 1.84e-25 (Fisher's exact test), Q value = 5.4e-23

Table S70. Gene #22: 'Del Peak 10(6q26) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	197	164
DEL PEAK 10(6Q26) MUTATED	84	19	39
DEL PEAK 10(6Q26) WILD-TYPE	48	178	125

Figure S70. Get High-res Image Gene #22: 'Del Peak 10(6q26) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 10(6q26) mutation analysis' versus 'RPPA_CNMF'

P value = 1.07e-06 (Fisher's exact test), Q value = 0.00026

Table S71. Gene #22: 'Del Peak 10(6q26) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	147	141
DEL PEAK 10(6Q26) MUTATED	69	35	24
DEL PEAK 10(6Q26) WILD-TYPE	90	112	117

Figure S71. Get High-res Image Gene #22: 'Del Peak 10(6q26) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 10(6q26) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.000939 (Fisher's exact test), Q value = 0.17

Table S72. Gene #22: 'Del Peak 10(6q26) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	211	104
DEL PEAK 10(6Q26) MUTATED	42	44	42
DEL PEAK 10(6Q26) WILD-TYPE	90	167	62

Figure S72. Get High-res Image Gene #22: 'Del Peak 10(6q26) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 10(6q26) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000478 (Fisher's exact test), Q value = 0.096

Table S73. Gene #22: 'Del Peak 10(6q26) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
DEL PEAK 10(6Q26) MUTATED	48	68	17
DEL PEAK 10(6Q26) WILD-TYPE	149	111	80

Figure S73. Get High-res Image Gene #22: 'Del Peak 10(6q26) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 10(6q26) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.1e-05 (Fisher's exact test), Q value = 0.0048

Table S74. Gene #22: 'Del Peak 10(6q26) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	104	184	143	44
DEL PEAK 10(6Q26) MUTATED	21	41	64	12
DEL PEAK 10(6Q26) WILD-TYPE	83	143	79	32

Figure S74. Get High-res Image Gene #22: 'Del Peak 10(6q26) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 11(6q26) mutation analysis' versus 'CN_CNMF'

P value = 1.84e-25 (Fisher's exact test), Q value = 5.4e-23

Table S75. Gene #23: 'Del Peak 11(6q26) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	197	164
DEL PEAK 11(6Q26) MUTATED	84	19	39
DEL PEAK 11(6Q26) WILD-TYPE	48	178	125

Figure S75. Get High-res Image Gene #23: 'Del Peak 11(6q26) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 11(6q26) mutation analysis' versus 'RPPA_CNMF'

P value = 1.07e-06 (Fisher's exact test), Q value = 0.00026

Table S76. Gene #23: 'Del Peak 11(6q26) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	147	141
DEL PEAK 11(6Q26) MUTATED	69	35	24
DEL PEAK 11(6Q26) WILD-TYPE	90	112	117

Figure S76. Get High-res Image Gene #23: 'Del Peak 11(6q26) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 11(6q26) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.00135 (Fisher's exact test), Q value = 0.24

Table S77. Gene #23: 'Del Peak 11(6q26) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	211	104
DEL PEAK 11(6Q26) MUTATED	43	44	41
DEL PEAK 11(6Q26) WILD-TYPE	89	167	63

Figure S77. Get High-res Image Gene #23: 'Del Peak 11(6q26) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 11(6q26) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000159 (Fisher's exact test), Q value = 0.034

Table S78. Gene #23: 'Del Peak 11(6q26) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
DEL PEAK 11(6Q26) MUTATED	48	69	16
DEL PEAK 11(6Q26) WILD-TYPE	149	110	81

Figure S78. Get High-res Image Gene #23: 'Del Peak 11(6q26) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 11(6q26) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 6.59e-06 (Fisher's exact test), Q value = 0.0015

Table S79. Gene #23: 'Del Peak 11(6q26) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	104	184	143	44
DEL PEAK 11(6Q26) MUTATED	20	41	65	12
DEL PEAK 11(6Q26) WILD-TYPE	84	143	78	32

Figure S79. Get High-res Image Gene #23: 'Del Peak 11(6q26) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 12(8p23.2) mutation analysis' versus 'CN_CNMF'

P value = 9.42e-06 (Fisher's exact test), Q value = 0.0022

Table S80. Gene #24: 'Del Peak 12(8p23.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	197	164
DEL PEAK 12(8P23.2) MUTATED	51	35	60
DEL PEAK 12(8P23.2) WILD-TYPE	81	162	104

Figure S80. Get High-res Image Gene #24: 'Del Peak 12(8p23.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 12(8p23.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000511 (Fisher's exact test), Q value = 0.1

Table S81. Gene #24: 'Del Peak 12(8p23.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	104	184	143	44
DEL PEAK 12(8P23.2) MUTATED	33	38	60	12
DEL PEAK 12(8P23.2) WILD-TYPE	71	146	83	32

Figure S81. Get High-res Image Gene #24: 'Del Peak 12(8p23.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 13(9p23) mutation analysis' versus 'CN_CNMF'

P value = 3.36e-30 (Fisher's exact test), Q value = 1e-27

Table S82. Gene #25: 'Del Peak 13(9p23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	197	164
DEL PEAK 13(9P23) MUTATED	80	9	55
DEL PEAK 13(9P23) WILD-TYPE	52	188	109

Figure S82. Get High-res Image Gene #25: 'Del Peak 13(9p23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 13(9p23) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.43e-20 (Fisher's exact test), Q value = 9.9e-18

Table S83. Gene #25: 'Del Peak 13(9p23) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	118	64
DEL PEAK 13(9P23) MUTATED	60	6	21
DEL PEAK 13(9P23) WILD-TYPE	36	112	43

Figure S83. Get High-res Image Gene #25: 'Del Peak 13(9p23) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 13(9p23) mutation analysis' versus 'RPPA_CNMF'

P value = 3.33e-07 (Fisher's exact test), Q value = 8.4e-05

Table S84. Gene #25: 'Del Peak 13(9p23) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	147	141
DEL PEAK 13(9P23) MUTATED	73	27	35
DEL PEAK 13(9P23) WILD-TYPE	86	120	106

Figure S84. Get High-res Image Gene #25: 'Del Peak 13(9p23) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 13(9p23) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.59e-23 (Fisher's exact test), Q value = 1e-20

Table S85. Gene #25: 'Del Peak 13(9p23) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
DEL PEAK 13(9P23) MUTATED	24	101	13
DEL PEAK 13(9P23) WILD-TYPE	173	78	84

Figure S85. Get High-res Image Gene #25: 'Del Peak 13(9p23) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 13(9p23) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.21e-24 (Fisher's exact test), Q value = 2.7e-21

Table S86. Gene #25: 'Del Peak 13(9p23) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
DEL PEAK 13(9P23) MUTATED	9	24	105
DEL PEAK 13(9P23) WILD-TYPE	60	190	85

Figure S86. Get High-res Image Gene #25: 'Del Peak 13(9p23) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 13(9p23) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.81e-14 (Fisher's exact test), Q value = 5.1e-12

Table S87. Gene #25: 'Del Peak 13(9p23) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	104	184	143	44
DEL PEAK 13(9P23) MUTATED	25	23	76	15
DEL PEAK 13(9P23) WILD-TYPE	79	161	67	29

Figure S87. Get High-res Image Gene #25: 'Del Peak 13(9p23) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 13(9p23) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.15e-05 (Fisher's exact test), Q value = 0.0027

Table S88. Gene #25: 'Del Peak 13(9p23) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	259	51
DEL PEAK 13(9P23) MUTATED	69	53	17
DEL PEAK 13(9P23) WILD-TYPE	96	206	34

Figure S88. Get High-res Image Gene #25: 'Del Peak 13(9p23) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 14(9p21.3) mutation analysis' versus 'MRNA_CNMF'

P value = 0.00125 (Fisher's exact test), Q value = 0.23

Table S89. Gene #26: 'Del Peak 14(9p21.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	24	13
DEL PEAK 14(9P21.3) MUTATED	5	13	1
DEL PEAK 14(9P21.3) WILD-TYPE	28	11	12

Figure S89. Get High-res Image Gene #26: 'Del Peak 14(9p21.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 14(9p21.3) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000662 (Fisher's exact test), Q value = 0.13

Table S90. Gene #26: 'Del Peak 14(9p21.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	23	33
DEL PEAK 14(9P21.3) MUTATED	1	13	5
DEL PEAK 14(9P21.3) WILD-TYPE	13	10	28

Figure S90. Get High-res Image Gene #26: 'Del Peak 14(9p21.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 14(9p21.3) mutation analysis' versus 'CN_CNMF'

P value = 1.96e-29 (Fisher's exact test), Q value = 5.8e-27

Table S91. Gene #26: 'Del Peak 14(9p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	197	164
DEL PEAK 14(9P21.3) MUTATED	81	11	60
DEL PEAK 14(9P21.3) WILD-TYPE	51	186	104

Figure S91. Get High-res Image Gene #26: 'Del Peak 14(9p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 14(9p21.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.24e-21 (Fisher's exact test), Q value = 6.5e-19

Table S92. Gene #26: 'Del Peak 14(9p21.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	118	64
DEL PEAK 14(9P21.3) MUTATED	62	6	23
DEL PEAK 14(9P21.3) WILD-TYPE	34	112	41

Figure S92. Get High-res Image Gene #26: 'Del Peak 14(9p21.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 14(9p21.3) mutation analysis' versus 'RPPA_CNMF'

P value = 1.86e-07 (Fisher's exact test), Q value = 4.7e-05

Table S93. Gene #26: 'Del Peak 14(9p21.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	147	141
DEL PEAK 14(9P21.3) MUTATED	76	28	38
DEL PEAK 14(9P21.3) WILD-TYPE	83	119	103

Figure S93. Get High-res Image Gene #26: 'Del Peak 14(9p21.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 14(9p21.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.08e-23 (Fisher's exact test), Q value = 6e-21

Table S94. Gene #26: 'Del Peak 14(9p21.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
DEL PEAK 14(9P21.3) MUTATED	26	105	15
DEL PEAK 14(9P21.3) WILD-TYPE	171	74	82

Figure S94. Get High-res Image Gene #26: 'Del Peak 14(9p21.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 14(9p21.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.15e-27 (Fisher's exact test), Q value = 3.4e-25

Table S95. Gene #26: 'Del Peak 14(9p21.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
DEL PEAK 14(9P21.3) MUTATED	8	25	113
DEL PEAK 14(9P21.3) WILD-TYPE	61	189	77

Figure S95. Get High-res Image Gene #26: 'Del Peak 14(9p21.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 14(9p21.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 5.17e-15 (Fisher's exact test), Q value = 1.5e-12

Table S96. Gene #26: 'Del Peak 14(9p21.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	104	184	143	44
DEL PEAK 14(9P21.3) MUTATED	28	24	79	15
DEL PEAK 14(9P21.3) WILD-TYPE	76	160	64	29

Figure S96. Get High-res Image Gene #26: 'Del Peak 14(9p21.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 14(9p21.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.78e-07 (Fisher's exact test), Q value = 7.1e-05

Table S97. Gene #26: 'Del Peak 14(9p21.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	259	51
DEL PEAK 14(9P21.3) MUTATED	75	53	18
DEL PEAK 14(9P21.3) WILD-TYPE	90	206	33

Figure S97. Get High-res Image Gene #26: 'Del Peak 14(9p21.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 15(10q23.31) mutation analysis' versus 'CN_CNMF'

P value = 9.29e-07 (Fisher's exact test), Q value = 0.00023

Table S98. Gene #27: 'Del Peak 15(10q23.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	197	164
DEL PEAK 15(10Q23.31) MUTATED	36	15	39
DEL PEAK 15(10Q23.31) WILD-TYPE	96	182	125

Figure S98. Get High-res Image Gene #27: 'Del Peak 15(10q23.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 16(13q13.3) mutation analysis' versus 'CN_CNMF'

P value = 4.05e-06 (Fisher's exact test), Q value = 0.00096

Table S99. Gene #28: 'Del Peak 16(13q13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	197	164
DEL PEAK 16(13Q13.3) MUTATED	31	12	33
DEL PEAK 16(13Q13.3) WILD-TYPE	101	185	131

Figure S99. Get High-res Image Gene #28: 'Del Peak 16(13q13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 16(13q13.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000675 (Fisher's exact test), Q value = 0.13

Table S100. Gene #28: 'Del Peak 16(13q13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	118	64
DEL PEAK 16(13Q13.3) MUTATED	21	8	16
DEL PEAK 16(13Q13.3) WILD-TYPE	75	110	48

Figure S100. Get High-res Image Gene #28: 'Del Peak 16(13q13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 16(13q13.3) mutation analysis' versus 'RPPA_CNMF'

P value = 3.61e-05 (Fisher's exact test), Q value = 0.0081

Table S101. Gene #28: 'Del Peak 16(13q13.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	147	141
DEL PEAK 16(13Q13.3) MUTATED	40	10	19
DEL PEAK 16(13Q13.3) WILD-TYPE	119	137	122

Figure S101. Get High-res Image Gene #28: 'Del Peak 16(13q13.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 16(13q13.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.24e-06 (Fisher's exact test), Q value = 3e-04

Table S102. Gene #28: 'Del Peak 16(13q13.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
DEL PEAK 16(13Q13.3) MUTATED	15	48	11
DEL PEAK 16(13Q13.3) WILD-TYPE	182	131	86

Figure S102. Get High-res Image Gene #28: 'Del Peak 16(13q13.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 16(13q13.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.39e-08 (Fisher's exact test), Q value = 2.5e-05

Table S103. Gene #28: 'Del Peak 16(13q13.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
DEL PEAK 16(13Q13.3) MUTATED	9	14	51
DEL PEAK 16(13Q13.3) WILD-TYPE	60	200	139

Figure S103. Get High-res Image Gene #28: 'Del Peak 16(13q13.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 16(13q13.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.56e-07 (Fisher's exact test), Q value = 9e-05

Table S104. Gene #28: 'Del Peak 16(13q13.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	104	184	143	44
DEL PEAK 16(13Q13.3) MUTATED	14	14	43	3
DEL PEAK 16(13Q13.3) WILD-TYPE	90	170	100	41

Figure S104. Get High-res Image Gene #28: 'Del Peak 16(13q13.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 16(13q13.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.74e-05 (Fisher's exact test), Q value = 0.01

Table S105. Gene #28: 'Del Peak 16(13q13.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	259	51
DEL PEAK 16(13Q13.3) MUTATED	32	25	17
DEL PEAK 16(13Q13.3) WILD-TYPE	133	234	34

Figure S105. Get High-res Image Gene #28: 'Del Peak 16(13q13.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 17(14q31.1) mutation analysis' versus 'MRNA_CNMF'

P value = 5.92e-05 (Fisher's exact test), Q value = 0.013

Table S106. Gene #29: 'Del Peak 17(14q31.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	24	13
DEL PEAK 17(14Q31.1) MUTATED	10	19	2
DEL PEAK 17(14Q31.1) WILD-TYPE	23	5	11

Figure S106. Get High-res Image Gene #29: 'Del Peak 17(14q31.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 17(14q31.1) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 2.77e-05 (Fisher's exact test), Q value = 0.0063

Table S107. Gene #29: 'Del Peak 17(14q31.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	23	33
DEL PEAK 17(14Q31.1) MUTATED	3	19	9
DEL PEAK 17(14Q31.1) WILD-TYPE	11	4	24

Figure S107. Get High-res Image Gene #29: 'Del Peak 17(14q31.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 17(14q31.1) mutation analysis' versus 'CN_CNMF'

P value = 2.06e-13 (Fisher's exact test), Q value = 5.7e-11

Table S108. Gene #29: 'Del Peak 17(14q31.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	197	164
DEL PEAK 17(14Q31.1) MUTATED	92	54	72
DEL PEAK 17(14Q31.1) WILD-TYPE	40	143	92

Figure S108. Get High-res Image Gene #29: 'Del Peak 17(14q31.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 17(14q31.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.79e-08 (Fisher's exact test), Q value = 1.8e-05

Table S109. Gene #29: 'Del Peak 17(14q31.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	118	64
DEL PEAK 17(14Q31.1) MUTATED	61	30	32
DEL PEAK 17(14Q31.1) WILD-TYPE	35	88	32

Figure S109. Get High-res Image Gene #29: 'Del Peak 17(14q31.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 17(14q31.1) mutation analysis' versus 'RPPA_CNMF'

P value = 2.81e-09 (Fisher's exact test), Q value = 7.5e-07

Table S110. Gene #29: 'Del Peak 17(14q31.1) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	147	141
DEL PEAK 17(14Q31.1) MUTATED	102	57	42
DEL PEAK 17(14Q31.1) WILD-TYPE	57	90	99

Figure S110. Get High-res Image Gene #29: 'Del Peak 17(14q31.1) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 17(14q31.1) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 2.31e-05 (Fisher's exact test), Q value = 0.0053

Table S111. Gene #29: 'Del Peak 17(14q31.1) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	211	104
DEL PEAK 17(14Q31.1) MUTATED	79	73	49
DEL PEAK 17(14Q31.1) WILD-TYPE	53	138	55

Figure S111. Get High-res Image Gene #29: 'Del Peak 17(14q31.1) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 17(14q31.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.67e-20 (Fisher's exact test), Q value = 1.9e-17

Table S112. Gene #29: 'Del Peak 17(14q31.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
DEL PEAK 17(14Q31.1) MUTATED	68	126	17
DEL PEAK 17(14Q31.1) WILD-TYPE	129	53	80

Figure S112. Get High-res Image Gene #29: 'Del Peak 17(14q31.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 17(14q31.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.4e-15 (Fisher's exact test), Q value = 1.8e-12

Table S113. Gene #29: 'Del Peak 17(14q31.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
DEL PEAK 17(14Q31.1) MUTATED	11	76	124
DEL PEAK 17(14Q31.1) WILD-TYPE	58	138	66

Figure S113. Get High-res Image Gene #29: 'Del Peak 17(14q31.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 17(14q31.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.51e-09 (Fisher's exact test), Q value = 6.7e-07

Table S114. Gene #29: 'Del Peak 17(14q31.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	104	184	143	44
DEL PEAK 17(14Q31.1) MUTATED	39	64	96	13
DEL PEAK 17(14Q31.1) WILD-TYPE	65	120	47	31

Figure S114. Get High-res Image Gene #29: 'Del Peak 17(14q31.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 18(Xq23) mutation analysis' versus 'CN_CNMF'

P value = 6.53e-06 (Fisher's exact test), Q value = 0.0015

Table S115. Gene #30: 'Del Peak 18(Xq23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	197	164
DEL PEAK 18(XQ23) MUTATED	28	8	19
DEL PEAK 18(XQ23) WILD-TYPE	104	189	145

Figure S115. Get High-res Image Gene #30: 'Del Peak 18(Xq23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 18(Xq23) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000715 (Fisher's exact test), Q value = 0.14

Table S116. Gene #30: 'Del Peak 18(Xq23) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	118	64
DEL PEAK 18(XQ23) MUTATED	18	5	3
DEL PEAK 18(XQ23) WILD-TYPE	78	113	61

Figure S116. Get High-res Image Gene #30: 'Del Peak 18(Xq23) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 18(Xq23) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.00131 (Fisher's exact test), Q value = 0.24

Table S117. Gene #30: 'Del Peak 18(Xq23) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	211	104
DEL PEAK 18(XQ23) MUTATED	14	13	21
DEL PEAK 18(XQ23) WILD-TYPE	118	198	83

Figure S117. Get High-res Image Gene #30: 'Del Peak 18(Xq23) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 18(Xq23) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000111 (Fisher's exact test), Q value = 0.024

Table S118. Gene #30: 'Del Peak 18(Xq23) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	259	51
DEL PEAK 18(XQ23) MUTATED	16	22	16
DEL PEAK 18(XQ23) WILD-TYPE	149	237	35

Figure S118. Get High-res Image Gene #30: 'Del Peak 18(Xq23) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
Molecular subtype file = KIRC-TP.transferedmergedcluster.txt
Number of patients = 493
Number of copy number variation regions = 30
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.

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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