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 43 peak regions and 8 molecular subtypes across 220 patients, 64 significant findings detected with Q value < 0.25.

Amp Peak 1(1q32.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Amp Peak 3(7p11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Amp Peak 4(7q32.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Amp Peak 5(8q24.21) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 6(10p15.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.
Amp Peak 9(12p13.32) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 12(19p13.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 13(19q13.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Amp Peak 15(Xq11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 1(1p36.31) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Del Peak 2(1p32.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 4(2q37.3) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 7(4q33) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 8(4q35.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 9(5q35.2) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 13(9p21.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 14(10q26.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 15(11p15.5) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 17(12q24.11) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 25(19q13.42) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Del Peak 26(22q13.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 28(Xq21.1) cnvs correlated to 'MIRSEQ_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 43 regions and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 64 significant findings detected.


		Molecular subtypes	MRNA CNMF	MRNA CHIERARCHICAL	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	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Del Peak 1(1p36 31)	83 (38%)	137	0.000549 (0.146)	0.00201 (0.508)	3.69e-31 (1.19e-28)	3.02e-37 (9.77e-35)	4.44e-17 (1.4e-14)	7.5e-20 (2.39e-17)	4.56e-11 (1.4e-08)	0.00939 (1.00)
Del Peak 2(1p32 3)	77 (35%)	143	0.0286 (1.00)	0.0635 (1.00)	2.88e-37 (9.35e-35)	1.25e-40 (4.07e-38)	2.7e-18 (8.55e-16)	2.09e-23 (6.71e-21)	3.51e-13 (1.09e-10)	0.0009 (0.237)
Del Peak 14(10q26 2)	70 (32%)	150	0.179 (1.00)	0.257 (1.00)	1.05e-17 (3.33e-15)	1.53e-16 (4.78e-14)	1.09e-13 (3.39e-11)	2.8e-08 (8.42e-06)	3.44e-06 (0.001)	0.000724 (0.191)
Del Peak 25(19q13 42)	116 (53%)	104	0.0353 (1.00)	0.0105 (1.00)	4.4e-29 (1.42e-26)	1.12e-22 (3.57e-20)	4.81e-11 (1.48e-08)	3.35e-12 (1.03e-09)	6.67e-10 (2.04e-07)	0.112 (1.00)
Amp Peak 1(1q32 1)	23 (10%)	197			7.81e-07 (0.000231)	8.15e-05 (0.0225)	1.9e-05 (0.00537)	0.378 (1.00)	0.639 (1.00)	0.416 (1.00)
Amp Peak 3(7p11 2)	55 (25%)	165	0.864 (1.00)	0.86 (1.00)	1.1e-18 (3.49e-16)	1.17e-12 (3.64e-10)	1.17e-09 (3.55e-07)	0.0172 (1.00)	0.00108 (0.282)	0.0182 (1.00)
Amp Peak 4(7q32 3)	77 (35%)	143	0.764 (1.00)	0.575 (1.00)	8.39e-17 (2.63e-14)	5.43e-07 (0.000161)	2.53e-05 (0.0071)	0.0286 (1.00)	0.0551 (1.00)	0.207 (1.00)
Amp Peak 6(10p15 1)	35 (16%)	185	0.467 (1.00)	0.468 (1.00)	2.61e-09 (7.9e-07)	9.16e-08 (2.75e-05)	0.00335 (0.82)	0.00473 (1.00)	0.000613 (0.162)	0.869 (1.00)
Amp Peak 13(19q13 2)	15 (7%)	205	0.369 (1.00)	0.327 (1.00)	1.02e-06 (3e-04)	0.000382 (0.103)	0.000267 (0.0728)	0.0101 (1.00)	0.0341 (1.00)	0.0081 (1.00)
Amp Peak 15(Xq11 2)	31 (14%)	189	0.282 (1.00)	0.803 (1.00)	3.63e-06 (0.00105)	1.97e-06 (0.000578)	0.0118 (1.00)	0.000397 (0.107)	0.124 (1.00)	0.373 (1.00)
Del Peak 15(11p15 5)	48 (22%)	172	0.642 (1.00)	0.184 (1.00)	1.98e-07 (5.91e-05)	1.03e-09 (3.15e-07)	0.0248 (1.00)	0.000283 (0.0768)	0.206 (1.00)	0.428 (1.00)
Del Peak 26(22q13 31)	31 (14%)	189	0.25 (1.00)	0.144 (1.00)	2.21e-06 (0.000646)	1.75e-05 (0.00496)	4.5e-05 (0.0126)	0.00189 (0.484)	0.00961 (1.00)	0.119 (1.00)
Amp Peak 5(8q24 21)	44 (20%)	176	0.37 (1.00)	1 (1.00)	6.87e-06 (0.00198)	1.72e-06 (0.000504)	0.00114 (0.297)	0.00189 (0.484)	0.0201 (1.00)	0.11 (1.00)
Amp Peak 9(12p13 32)	34 (15%)	186	0.864 (1.00)	0.86 (1.00)	1e-05 (0.00285)	6.33e-05 (0.0176)	0.0134 (1.00)	0.000959 (0.251)	0.00802 (1.00)	0.00986 (1.00)
Amp Peak 12(19p13 3)	51 (23%)	169	0.186 (1.00)	0.272 (1.00)	1.69e-09 (5.13e-07)	5.84e-06 (0.00169)	0.00459 (1.00)	0.00296 (0.732)	0.113 (1.00)	0.546 (1.00)
Del Peak 7(4q33)	61 (28%)	159	1 (1.00)	0.784 (1.00)	0.000502 (0.134)	0.000365 (0.0989)	0.0319 (1.00)	0.0186 (1.00)	0.00194 (0.492)	0.362 (1.00)
Del Peak 8(4q35 2)	62 (28%)	158	1 (1.00)	0.784 (1.00)	8.18e-05 (0.0225)	6.46e-05 (0.0179)	0.019 (1.00)	0.0166 (1.00)	0.00505 (1.00)	0.262 (1.00)
Del Peak 13(9p21 3)	78 (35%)	142	0.333 (1.00)	0.272 (1.00)	2.4e-07 (7.15e-05)	8.35e-06 (0.0024)	0.00679 (1.00)	0.0465 (1.00)	0.256 (1.00)	0.15 (1.00)
Del Peak 17(12q24 11)	30 (14%)	190	1 (1.00)	0.388 (1.00)	4.97e-05 (0.0139)	1.48e-05 (0.00421)	0.312 (1.00)	0.00896 (1.00)	0.0154 (1.00)	0.766 (1.00)
Del Peak 4(2q37 3)	32 (15%)	188	0.18 (1.00)	0.547 (1.00)	0.00134 (0.347)	9.19e-06 (0.00263)	0.0218 (1.00)	0.0217 (1.00)	0.063 (1.00)	0.204 (1.00)
Del Peak 9(5q35 2)	28 (13%)	192	0.446 (1.00)	0.61 (1.00)	0.00261 (0.646)	0.000447 (0.12)	0.0301 (1.00)	0.0054 (1.00)	0.0269 (1.00)	0.0798 (1.00)
Del Peak 28(Xq21 1)	30 (14%)	190	0.73 (1.00)	0.504 (1.00)	0.468 (1.00)	0.0585 (1.00)	0.00838 (1.00)	0.0258 (1.00)	0.000193 (0.0529)	0.363 (1.00)
Amp Peak 2(4q12)	10 (5%)	210			0.503 (1.00)	0.523 (1.00)	0.393 (1.00)	0.543 (1.00)	0.812 (1.00)	0.393 (1.00)
Amp Peak 7(10q11 21)	5 (2%)	215			0.2 (1.00)	0.443 (1.00)	0.213 (1.00)	0.176 (1.00)	0.00949 (1.00)	0.556 (1.00)
Amp Peak 8(11q23 3)	38 (17%)	182	0.0708 (1.00)	0.0162 (1.00)	0.922 (1.00)	0.0277 (1.00)	0.217 (1.00)	0.23 (1.00)	0.479 (1.00)	0.591 (1.00)
Amp Peak 10(12p11 22)	21 (10%)	199	1 (1.00)	0.388 (1.00)	0.0212 (1.00)	0.0474 (1.00)	0.142 (1.00)	0.00329 (0.81)	0.00209 (0.527)	0.0355 (1.00)
Amp Peak 11(12q14 1)	14 (6%)	206			0.122 (1.00)	0.398 (1.00)	0.029 (1.00)	0.328 (1.00)	0.94 (1.00)	0.909 (1.00)
Amp Peak 14(Xp22 33)	15 (7%)	205			0.00248 (0.617)	0.0073 (1.00)	0.323 (1.00)	0.0905 (1.00)	0.121 (1.00)	1 (1.00)
Del Peak 3(1q43)	13 (6%)	207			0.666 (1.00)	0.33 (1.00)	0.202 (1.00)	0.0861 (1.00)	0.343 (1.00)	0.296 (1.00)
Del Peak 5(3p21 1)	20 (9%)	200	1 (1.00)	0.413 (1.00)	0.359 (1.00)	0.0288 (1.00)	0.94 (1.00)	0.0143 (1.00)	0.0566 (1.00)	0.00812 (1.00)
Del Peak 6(3q29)	21 (10%)	199	0.175 (1.00)	1 (1.00)	0.00982 (1.00)	0.00218 (0.547)	0.114 (1.00)	0.074 (1.00)	0.54 (1.00)	0.136 (1.00)
Del Peak 10(6p24 1)	21 (10%)	199			0.131 (1.00)	0.371 (1.00)	0.436 (1.00)	0.233 (1.00)	0.252 (1.00)	0.45 (1.00)
Del Peak 11(6q24 3)	33 (15%)	187	0.0479 (1.00)	0.0407 (1.00)	0.0158 (1.00)	0.0015 (0.386)	0.269 (1.00)	0.0519 (1.00)	0.0189 (1.00)	0.449 (1.00)
Del Peak 12(8p23 2)	11 (5%)	209	1 (1.00)	0.388 (1.00)	0.00696 (1.00)	0.0127 (1.00)	0.136 (1.00)	0.36 (1.00)	0.634 (1.00)	0.23 (1.00)
Del Peak 16(11q25)	15 (7%)	205			0.00183 (0.471)	0.0165 (1.00)	0.126 (1.00)	0.0905 (1.00)	0.633 (1.00)	0.118 (1.00)
Del Peak 18(13q14 2)	65 (30%)	155	0.18 (1.00)	0.0733 (1.00)	0.054 (1.00)	0.00902 (1.00)	0.482 (1.00)	0.202 (1.00)	0.214 (1.00)	0.548 (1.00)
Del Peak 19(13q34)	50 (23%)	170	0.508 (1.00)	0.526 (1.00)	0.244 (1.00)	0.0929 (1.00)	0.242 (1.00)	0.156 (1.00)	0.106 (1.00)	0.316 (1.00)
Del Peak 20(14q24 3)	51 (23%)	169	0.303 (1.00)	0.341 (1.00)	0.00236 (0.589)	0.0151 (1.00)	0.0253 (1.00)	0.118 (1.00)	0.00879 (1.00)	0.0141 (1.00)
Del Peak 21(15q21 3)	27 (12%)	193	0.839 (1.00)	0.828 (1.00)	0.0596 (1.00)	0.0592 (1.00)	0.00699 (1.00)	0.247 (1.00)	0.34 (1.00)	0.841 (1.00)
Del Peak 22(17q25 3)	15 (7%)	205			0.0206 (1.00)	0.164 (1.00)	0.658 (1.00)	0.367 (1.00)	0.354 (1.00)	0.755 (1.00)
Del Peak 23(18p11 32)	32 (15%)	188	0.321 (1.00)	0.388 (1.00)	0.552 (1.00)	0.137 (1.00)	0.481 (1.00)	0.648 (1.00)	0.68 (1.00)	0.38 (1.00)
Del Peak 24(18q23)	35 (16%)	185	0.321 (1.00)	0.388 (1.00)	0.918 (1.00)	0.108 (1.00)	0.489 (1.00)	0.875 (1.00)	0.756 (1.00)	0.54 (1.00)
Del Peak 27(Xp22 31)	51 (23%)	169	0.73 (1.00)	0.61 (1.00)	0.517 (1.00)	0.201 (1.00)	0.548 (1.00)	0.0926 (1.00)	0.0789 (1.00)	0.0865 (1.00)

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

P value = 7.81e-07 (Fisher's exact test), Q value = 0.00023

Table S1. Gene #1: 'Amp Peak 1(1q32.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
AMP PEAK 1(1Q32.1) MUTATED	5	16	2
AMP PEAK 1(1Q32.1) WILD-TYPE	89	34	74

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1q32.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 1(1q32.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.15e-05 (Fisher's exact test), Q value = 0.023

Table S2. Gene #1: 'Amp Peak 1(1q32.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
AMP PEAK 1(1Q32.1) MUTATED	8	12	2	1
AMP PEAK 1(1Q32.1) WILD-TYPE	92	22	56	22

Figure S2. Get High-res Image Gene #1: 'Amp Peak 1(1q32.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 1.9e-05 (Chi-square test), Q value = 0.0054

Table S3. Gene #1: 'Amp Peak 1(1q32.1) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
AMP PEAK 1(1Q32.1) MUTATED	1	13	1	8	0
AMP PEAK 1(1Q32.1) WILD-TYPE	59	29	34	62	11

Figure S3. Get High-res Image Gene #1: 'Amp Peak 1(1q32.1) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Amp Peak 3(7p11.2) mutation analysis' versus 'CN_CNMF'

P value = 1.1e-18 (Fisher's exact test), Q value = 3.5e-16

Table S4. Gene #3: 'Amp Peak 3(7p11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
AMP PEAK 3(7P11.2) MUTATED	9	38	8
AMP PEAK 3(7P11.2) WILD-TYPE	85	12	68

Figure S4. Get High-res Image Gene #3: 'Amp Peak 3(7p11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 3(7p11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.17e-12 (Fisher's exact test), Q value = 3.6e-10

Table S5. Gene #3: 'Amp Peak 3(7p11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
AMP PEAK 3(7P11.2) MUTATED	17	27	6	3
AMP PEAK 3(7P11.2) WILD-TYPE	83	7	52	20

Figure S5. Get High-res Image Gene #3: 'Amp Peak 3(7p11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 3(7p11.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.17e-09 (Chi-square test), Q value = 3.6e-07

Table S6. Gene #3: 'Amp Peak 3(7p11.2) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
AMP PEAK 3(7P11.2) MUTATED	14	27	4	9	0
AMP PEAK 3(7P11.2) WILD-TYPE	46	15	31	61	11

Figure S6. Get High-res Image Gene #3: 'Amp Peak 3(7p11.2) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Amp Peak 4(7q32.3) mutation analysis' versus 'CN_CNMF'

P value = 8.39e-17 (Fisher's exact test), Q value = 2.6e-14

Table S7. Gene #4: 'Amp Peak 4(7q32.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
AMP PEAK 4(7Q32.3) MUTATED	20	43	14
AMP PEAK 4(7Q32.3) WILD-TYPE	74	7	62

Figure S7. Get High-res Image Gene #4: 'Amp Peak 4(7q32.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 4(7q32.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.43e-07 (Fisher's exact test), Q value = 0.00016

Table S8. Gene #4: 'Amp Peak 4(7q32.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
AMP PEAK 4(7Q32.3) MUTATED	35	25	12	3
AMP PEAK 4(7Q32.3) WILD-TYPE	65	9	46	20

Figure S8. Get High-res Image Gene #4: 'Amp Peak 4(7q32.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 4(7q32.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.53e-05 (Chi-square test), Q value = 0.0071

Table S9. Gene #4: 'Amp Peak 4(7q32.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
AMP PEAK 4(7Q32.3) MUTATED	26	26	7	16	1
AMP PEAK 4(7Q32.3) WILD-TYPE	34	16	28	54	10

Figure S9. Get High-res Image Gene #4: 'Amp Peak 4(7q32.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Amp Peak 5(8q24.21) mutation analysis' versus 'CN_CNMF'

P value = 6.87e-06 (Fisher's exact test), Q value = 0.002

Table S10. Gene #5: 'Amp Peak 5(8q24.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
AMP PEAK 5(8Q24.21) MUTATED	32	8	4
AMP PEAK 5(8Q24.21) WILD-TYPE	62	42	72

Figure S10. Get High-res Image Gene #5: 'Amp Peak 5(8q24.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 5(8q24.21) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.72e-06 (Fisher's exact test), Q value = 5e-04

Table S11. Gene #5: 'Amp Peak 5(8q24.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
AMP PEAK 5(8Q24.21) MUTATED	36	4	3	1
AMP PEAK 5(8Q24.21) WILD-TYPE	64	30	55	22

Figure S11. Get High-res Image Gene #5: 'Amp Peak 5(8q24.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 6(10p15.1) mutation analysis' versus 'CN_CNMF'

P value = 2.61e-09 (Fisher's exact test), Q value = 7.9e-07

Table S12. Gene #6: 'Amp Peak 6(10p15.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
AMP PEAK 6(10P15.1) MUTATED	31	3	1
AMP PEAK 6(10P15.1) WILD-TYPE	63	47	75

Figure S12. Get High-res Image Gene #6: 'Amp Peak 6(10p15.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 6(10p15.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.16e-08 (Fisher's exact test), Q value = 2.7e-05

Table S13. Gene #6: 'Amp Peak 6(10p15.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
AMP PEAK 6(10P15.1) MUTATED	31	2	0	2
AMP PEAK 6(10P15.1) WILD-TYPE	69	32	58	21

Figure S13. Get High-res Image Gene #6: 'Amp Peak 6(10p15.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 6(10p15.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000613 (Fisher's exact test), Q value = 0.16

Table S14. Gene #6: 'Amp Peak 6(10p15.1) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	50	50	32	87
AMP PEAK 6(10P15.1) MUTATED	8	16	0	11
AMP PEAK 6(10P15.1) WILD-TYPE	42	34	32	76

Figure S14. Get High-res Image Gene #6: 'Amp Peak 6(10p15.1) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'Amp Peak 9(12p13.32) mutation analysis' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0029

Table S15. Gene #9: 'Amp Peak 9(12p13.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
AMP PEAK 9(12P13.32) MUTATED	27	4	3
AMP PEAK 9(12P13.32) WILD-TYPE	67	46	73

Figure S15. Get High-res Image Gene #9: 'Amp Peak 9(12p13.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 9(12p13.32) mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.33e-05 (Fisher's exact test), Q value = 0.018

Table S16. Gene #9: 'Amp Peak 9(12p13.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
AMP PEAK 9(12P13.32) MUTATED	28	3	2	1
AMP PEAK 9(12P13.32) WILD-TYPE	72	31	56	22

Figure S16. Get High-res Image Gene #9: 'Amp Peak 9(12p13.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 12(19p13.3) mutation analysis' versus 'CN_CNMF'

P value = 1.69e-09 (Fisher's exact test), Q value = 5.1e-07

Table S17. Gene #12: 'Amp Peak 12(19p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
AMP PEAK 12(19P13.3) MUTATED	4	15	32
AMP PEAK 12(19P13.3) WILD-TYPE	90	35	44

Figure S17. Get High-res Image Gene #12: 'Amp Peak 12(19p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 12(19p13.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.84e-06 (Fisher's exact test), Q value = 0.0017

Table S18. Gene #12: 'Amp Peak 12(19p13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
AMP PEAK 12(19P13.3) MUTATED	10	10	25	2
AMP PEAK 12(19P13.3) WILD-TYPE	90	24	33	21

Figure S18. Get High-res Image Gene #12: 'Amp Peak 12(19p13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 13(19q13.2) mutation analysis' versus 'CN_CNMF'

P value = 1.02e-06 (Fisher's exact test), Q value = 3e-04

Table S19. Gene #13: 'Amp Peak 13(19q13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
AMP PEAK 13(19Q13.2) MUTATED	1	12	2
AMP PEAK 13(19Q13.2) WILD-TYPE	93	38	74

Figure S19. Get High-res Image Gene #13: 'Amp Peak 13(19q13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 13(19q13.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000382 (Fisher's exact test), Q value = 0.1

Table S20. Gene #13: 'Amp Peak 13(19q13.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
AMP PEAK 13(19Q13.2) MUTATED	5	8	0	1
AMP PEAK 13(19Q13.2) WILD-TYPE	95	26	58	22

Figure S20. Get High-res Image Gene #13: 'Amp Peak 13(19q13.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 13(19q13.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000267 (Chi-square test), Q value = 0.073

Table S21. Gene #13: 'Amp Peak 13(19q13.2) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
AMP PEAK 13(19Q13.2) MUTATED	3	9	0	1	1
AMP PEAK 13(19Q13.2) WILD-TYPE	57	33	35	69	10

Figure S21. Get High-res Image Gene #13: 'Amp Peak 13(19q13.2) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Amp Peak 15(Xq11.2) mutation analysis' versus 'CN_CNMF'

P value = 3.63e-06 (Fisher's exact test), Q value = 0.0011

Table S22. Gene #15: 'Amp Peak 15(Xq11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
AMP PEAK 15(XQ11.2) MUTATED	26	2	3
AMP PEAK 15(XQ11.2) WILD-TYPE	68	48	73

Figure S22. Get High-res Image Gene #15: 'Amp Peak 15(Xq11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 15(Xq11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.97e-06 (Fisher's exact test), Q value = 0.00058

Table S23. Gene #15: 'Amp Peak 15(Xq11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
AMP PEAK 15(XQ11.2) MUTATED	27	3	0	1
AMP PEAK 15(XQ11.2) WILD-TYPE	73	31	58	22

Figure S23. Get High-res Image Gene #15: 'Amp Peak 15(Xq11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 15(Xq11.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000397 (Fisher's exact test), Q value = 0.11

Table S24. Gene #15: 'Amp Peak 15(Xq11.2) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	117	69
AMP PEAK 15(XQ11.2) MUTATED	0	26	5
AMP PEAK 15(XQ11.2) WILD-TYPE	32	91	64

Figure S24. Get High-res Image Gene #15: 'Amp Peak 15(Xq11.2) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 1(1p36.31) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000549 (Fisher's exact test), Q value = 0.15

Table S25. Gene #16: 'Del Peak 1(1p36.31) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	10	8
DEL PEAK 1(1P36.31) MUTATED	0	8	2
DEL PEAK 1(1P36.31) WILD-TYPE	9	2	6

Figure S25. Get High-res Image Gene #16: 'Del Peak 1(1p36.31) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 1(1p36.31) mutation analysis' versus 'CN_CNMF'

P value = 3.69e-31 (Fisher's exact test), Q value = 1.2e-28

Table S26. Gene #16: 'Del Peak 1(1p36.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
DEL PEAK 1(1P36.31) MUTATED	7	9	67
DEL PEAK 1(1P36.31) WILD-TYPE	87	41	9

Figure S26. Get High-res Image Gene #16: 'Del Peak 1(1p36.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 1(1p36.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.02e-37 (Fisher's exact test), Q value = 9.8e-35

Table S27. Gene #16: 'Del Peak 1(1p36.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
DEL PEAK 1(1P36.31) MUTATED	6	8	58	7
DEL PEAK 1(1P36.31) WILD-TYPE	94	26	0	16

Figure S27. Get High-res Image Gene #16: 'Del Peak 1(1p36.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 1(1p36.31) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.44e-17 (Chi-square test), Q value = 1.4e-14

Table S28. Gene #16: 'Del Peak 1(1p36.31) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
DEL PEAK 1(1P36.31) MUTATED	4	10	34	32	3
DEL PEAK 1(1P36.31) WILD-TYPE	56	32	1	38	8

Figure S28. Get High-res Image Gene #16: 'Del Peak 1(1p36.31) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 1(1p36.31) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.5e-20 (Fisher's exact test), Q value = 2.4e-17

Table S29. Gene #16: 'Del Peak 1(1p36.31) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	117	69
DEL PEAK 1(1P36.31) MUTATED	32	19	32
DEL PEAK 1(1P36.31) WILD-TYPE	0	98	37

Figure S29. Get High-res Image Gene #16: 'Del Peak 1(1p36.31) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 1(1p36.31) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.56e-11 (Fisher's exact test), Q value = 1.4e-08

Table S30. Gene #16: 'Del Peak 1(1p36.31) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	50	50	32	87
DEL PEAK 1(1P36.31) MUTATED	9	7	26	41
DEL PEAK 1(1P36.31) WILD-TYPE	41	43	6	46

Figure S30. Get High-res Image Gene #16: 'Del Peak 1(1p36.31) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'Del Peak 2(1p32.3) mutation analysis' versus 'CN_CNMF'

P value = 2.88e-37 (Fisher's exact test), Q value = 9.4e-35

Table S31. Gene #17: 'Del Peak 2(1p32.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
DEL PEAK 2(1P32.3) MUTATED	5	4	68
DEL PEAK 2(1P32.3) WILD-TYPE	89	46	8

Figure S31. Get High-res Image Gene #17: 'Del Peak 2(1p32.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 2(1p32.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.25e-40 (Fisher's exact test), Q value = 4.1e-38

Table S32. Gene #17: 'Del Peak 2(1p32.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
DEL PEAK 2(1P32.3) MUTATED	4	5	58	7
DEL PEAK 2(1P32.3) WILD-TYPE	96	29	0	16

Figure S32. Get High-res Image Gene #17: 'Del Peak 2(1p32.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 2(1p32.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.7e-18 (Chi-square test), Q value = 8.6e-16

Table S33. Gene #17: 'Del Peak 2(1p32.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
DEL PEAK 2(1P32.3) MUTATED	4	5	33	32	3
DEL PEAK 2(1P32.3) WILD-TYPE	56	37	2	38	8

Figure S33. Get High-res Image Gene #17: 'Del Peak 2(1p32.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 2(1p32.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.09e-23 (Fisher's exact test), Q value = 6.7e-21

Table S34. Gene #17: 'Del Peak 2(1p32.3) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	117	69
DEL PEAK 2(1P32.3) MUTATED	32	13	32
DEL PEAK 2(1P32.3) WILD-TYPE	0	104	37

Figure S34. Get High-res Image Gene #17: 'Del Peak 2(1p32.3) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 2(1p32.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.51e-13 (Fisher's exact test), Q value = 1.1e-10

Table S35. Gene #17: 'Del Peak 2(1p32.3) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	50	50	32	87
DEL PEAK 2(1P32.3) MUTATED	7	4	25	41
DEL PEAK 2(1P32.3) WILD-TYPE	43	46	7	46

Figure S35. Get High-res Image Gene #17: 'Del Peak 2(1p32.3) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'Del Peak 2(1p32.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-04 (Fisher's exact test), Q value = 0.24

Table S36. Gene #17: 'Del Peak 2(1p32.3) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	13	118
DEL PEAK 2(1P32.3) MUTATED	44	3	30
DEL PEAK 2(1P32.3) WILD-TYPE	44	10	88

Figure S36. Get High-res Image Gene #17: 'Del Peak 2(1p32.3) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

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

P value = 9.19e-06 (Fisher's exact test), Q value = 0.0026

Table S37. Gene #19: 'Del Peak 4(2q37.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
DEL PEAK 4(2Q37.3) MUTATED	28	1	2	1
DEL PEAK 4(2Q37.3) WILD-TYPE	72	33	56	22

Figure S37. Get High-res Image Gene #19: 'Del Peak 4(2q37.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 7(4q33) mutation analysis' versus 'CN_CNMF'

P value = 0.000502 (Fisher's exact test), Q value = 0.13

Table S38. Gene #22: 'Del Peak 7(4q33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
DEL PEAK 7(4Q33) MUTATED	25	5	31
DEL PEAK 7(4Q33) WILD-TYPE	69	45	45

Figure S38. Get High-res Image Gene #22: 'Del Peak 7(4q33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 7(4q33) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000365 (Fisher's exact test), Q value = 0.099

Table S39. Gene #22: 'Del Peak 7(4q33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
DEL PEAK 7(4Q33) MUTATED	31	3	25	2
DEL PEAK 7(4Q33) WILD-TYPE	69	31	33	21

Figure S39. Get High-res Image Gene #22: 'Del Peak 7(4q33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 8(4q35.2) mutation analysis' versus 'CN_CNMF'

P value = 8.18e-05 (Fisher's exact test), Q value = 0.023

Table S40. Gene #23: 'Del Peak 8(4q35.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
DEL PEAK 8(4Q35.2) MUTATED	26	4	32
DEL PEAK 8(4Q35.2) WILD-TYPE	68	46	44

Figure S40. Get High-res Image Gene #23: 'Del Peak 8(4q35.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 8(4q35.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.46e-05 (Fisher's exact test), Q value = 0.018

Table S41. Gene #23: 'Del Peak 8(4q35.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
DEL PEAK 8(4Q35.2) MUTATED	33	2	25	2
DEL PEAK 8(4Q35.2) WILD-TYPE	67	32	33	21

Figure S41. Get High-res Image Gene #23: 'Del Peak 8(4q35.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 9(5q35.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000447 (Fisher's exact test), Q value = 0.12

Table S42. Gene #24: 'Del Peak 9(5q35.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
DEL PEAK 9(5Q35.2) MUTATED	20	5	0	3
DEL PEAK 9(5Q35.2) WILD-TYPE	80	29	58	20

Figure S42. Get High-res Image Gene #24: 'Del Peak 9(5q35.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 13(9p21.3) mutation analysis' versus 'CN_CNMF'

P value = 2.4e-07 (Fisher's exact test), Q value = 7.1e-05

Table S43. Gene #28: 'Del Peak 13(9p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
DEL PEAK 13(9P21.3) MUTATED	28	34	16
DEL PEAK 13(9P21.3) WILD-TYPE	66	16	60

Figure S43. Get High-res Image Gene #28: 'Del Peak 13(9p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 13(9p21.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.35e-06 (Fisher's exact test), Q value = 0.0024

Table S44. Gene #28: 'Del Peak 13(9p21.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
DEL PEAK 13(9P21.3) MUTATED	38	23	12	3
DEL PEAK 13(9P21.3) WILD-TYPE	62	11	46	20

Figure S44. Get High-res Image Gene #28: 'Del Peak 13(9p21.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 14(10q26.2) mutation analysis' versus 'CN_CNMF'

P value = 1.05e-17 (Fisher's exact test), Q value = 3.3e-15

Table S45. Gene #29: 'Del Peak 14(10q26.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
DEL PEAK 14(10Q26.2) MUTATED	27	39	4
DEL PEAK 14(10Q26.2) WILD-TYPE	67	11	72

Figure S45. Get High-res Image Gene #29: 'Del Peak 14(10q26.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 14(10q26.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.53e-16 (Fisher's exact test), Q value = 4.8e-14

Table S46. Gene #29: 'Del Peak 14(10q26.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
DEL PEAK 14(10Q26.2) MUTATED	33	30	3	3
DEL PEAK 14(10Q26.2) WILD-TYPE	67	4	55	20

Figure S46. Get High-res Image Gene #29: 'Del Peak 14(10q26.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 14(10q26.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.09e-13 (Chi-square test), Q value = 3.4e-11

Table S47. Gene #29: 'Del Peak 14(10q26.2) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
DEL PEAK 14(10Q26.2) MUTATED	18	34	2	13	1
DEL PEAK 14(10Q26.2) WILD-TYPE	42	8	33	57	10

Figure S47. Get High-res Image Gene #29: 'Del Peak 14(10q26.2) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 14(10q26.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.8e-08 (Fisher's exact test), Q value = 8.4e-06

Table S48. Gene #29: 'Del Peak 14(10q26.2) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	117	69
DEL PEAK 14(10Q26.2) MUTATED	1	55	12
DEL PEAK 14(10Q26.2) WILD-TYPE	31	62	57

Figure S48. Get High-res Image Gene #29: 'Del Peak 14(10q26.2) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 14(10q26.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.44e-06 (Fisher's exact test), Q value = 0.001

Table S49. Gene #29: 'Del Peak 14(10q26.2) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	50	50	32	87
DEL PEAK 14(10Q26.2) MUTATED	20	29	5	16
DEL PEAK 14(10Q26.2) WILD-TYPE	30	21	27	71

Figure S49. Get High-res Image Gene #29: 'Del Peak 14(10q26.2) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'Del Peak 14(10q26.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000724 (Fisher's exact test), Q value = 0.19

Table S50. Gene #29: 'Del Peak 14(10q26.2) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	88	13	118
DEL PEAK 14(10Q26.2) MUTATED	16	4	50
DEL PEAK 14(10Q26.2) WILD-TYPE	72	9	68

Figure S50. Get High-res Image Gene #29: 'Del Peak 14(10q26.2) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 15(11p15.5) mutation analysis' versus 'CN_CNMF'

P value = 1.98e-07 (Fisher's exact test), Q value = 5.9e-05

Table S51. Gene #30: 'Del Peak 15(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
DEL PEAK 15(11P15.5) MUTATED	35	10	3
DEL PEAK 15(11P15.5) WILD-TYPE	59	40	73

Figure S51. Get High-res Image Gene #30: 'Del Peak 15(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 15(11p15.5) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.03e-09 (Fisher's exact test), Q value = 3.1e-07

Table S52. Gene #30: 'Del Peak 15(11p15.5) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
DEL PEAK 15(11P15.5) MUTATED	40	5	0	3
DEL PEAK 15(11P15.5) WILD-TYPE	60	29	58	20

Figure S52. Get High-res Image Gene #30: 'Del Peak 15(11p15.5) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 15(11p15.5) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000283 (Fisher's exact test), Q value = 0.077

Table S53. Gene #30: 'Del Peak 15(11p15.5) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	117	69
DEL PEAK 15(11P15.5) MUTATED	0	34	13
DEL PEAK 15(11P15.5) WILD-TYPE	32	83	56

Figure S53. Get High-res Image Gene #30: 'Del Peak 15(11p15.5) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 17(12q24.11) mutation analysis' versus 'CN_CNMF'

P value = 4.97e-05 (Fisher's exact test), Q value = 0.014

Table S54. Gene #32: 'Del Peak 17(12q24.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
DEL PEAK 17(12Q24.11) MUTATED	24	3	3
DEL PEAK 17(12Q24.11) WILD-TYPE	70	47	73

Figure S54. Get High-res Image Gene #32: 'Del Peak 17(12q24.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 17(12q24.11) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.48e-05 (Fisher's exact test), Q value = 0.0042

Table S55. Gene #32: 'Del Peak 17(12q24.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
DEL PEAK 17(12Q24.11) MUTATED	26	1	1	2
DEL PEAK 17(12Q24.11) WILD-TYPE	74	33	57	21

Figure S55. Get High-res Image Gene #32: 'Del Peak 17(12q24.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 25(19q13.42) mutation analysis' versus 'CN_CNMF'

P value = 4.4e-29 (Fisher's exact test), Q value = 1.4e-26

Table S56. Gene #40: 'Del Peak 25(19q13.42) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
DEL PEAK 25(19Q13.42) MUTATED	26	14	76
DEL PEAK 25(19Q13.42) WILD-TYPE	68	36	0

Figure S56. Get High-res Image Gene #40: 'Del Peak 25(19q13.42) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 25(19q13.42) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.12e-22 (Fisher's exact test), Q value = 3.6e-20

Table S57. Gene #40: 'Del Peak 25(19q13.42) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
DEL PEAK 25(19Q13.42) MUTATED	44	4	58	7
DEL PEAK 25(19Q13.42) WILD-TYPE	56	30	0	16

Figure S57. Get High-res Image Gene #40: 'Del Peak 25(19q13.42) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 25(19q13.42) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.81e-11 (Chi-square test), Q value = 1.5e-08

Table S58. Gene #40: 'Del Peak 25(19q13.42) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
DEL PEAK 25(19Q13.42) MUTATED	24	9	35	43	5
DEL PEAK 25(19Q13.42) WILD-TYPE	36	33	0	27	6

Figure S58. Get High-res Image Gene #40: 'Del Peak 25(19q13.42) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 25(19q13.42) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.35e-12 (Fisher's exact test), Q value = 1e-09

Table S59. Gene #40: 'Del Peak 25(19q13.42) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	117	69
DEL PEAK 25(19Q13.42) MUTATED	32	42	42
DEL PEAK 25(19Q13.42) WILD-TYPE	0	75	27

Figure S59. Get High-res Image Gene #40: 'Del Peak 25(19q13.42) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 25(19q13.42) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 6.67e-10 (Fisher's exact test), Q value = 2e-07

Table S60. Gene #40: 'Del Peak 25(19q13.42) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	50	50	32	87
DEL PEAK 25(19Q13.42) MUTATED	22	12	30	52
DEL PEAK 25(19Q13.42) WILD-TYPE	28	38	2	35

Figure S60. Get High-res Image Gene #40: 'Del Peak 25(19q13.42) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'Del Peak 26(22q13.31) mutation analysis' versus 'CN_CNMF'

P value = 2.21e-06 (Fisher's exact test), Q value = 0.00065

Table S61. Gene #41: 'Del Peak 26(22q13.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
DEL PEAK 26(22Q13.31) MUTATED	14	16	1
DEL PEAK 26(22Q13.31) WILD-TYPE	80	34	75

Figure S61. Get High-res Image Gene #41: 'Del Peak 26(22q13.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 26(22q13.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.75e-05 (Fisher's exact test), Q value = 0.005

Table S62. Gene #41: 'Del Peak 26(22q13.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	100	34	58	23
DEL PEAK 26(22Q13.31) MUTATED	19	10	0	1
DEL PEAK 26(22Q13.31) WILD-TYPE	81	24	58	22

Figure S62. Get High-res Image Gene #41: 'Del Peak 26(22q13.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 26(22q13.31) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.5e-05 (Chi-square test), Q value = 0.013

Table S63. Gene #41: 'Del Peak 26(22q13.31) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
DEL PEAK 26(22Q13.31) MUTATED	8	15	0	7	0
DEL PEAK 26(22Q13.31) WILD-TYPE	52	27	35	63	11

Figure S63. Get High-res Image Gene #41: 'Del Peak 26(22q13.31) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 28(Xq21.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000193 (Fisher's exact test), Q value = 0.053

Table S64. Gene #43: 'Del Peak 28(Xq21.1) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	50	50	32	87
DEL PEAK 28(XQ21.1) MUTATED	3	9	12	6
DEL PEAK 28(XQ21.1) WILD-TYPE	47	41	20	81

Figure S64. Get High-res Image Gene #43: 'Del Peak 28(Xq21.1) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_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 = LGG-TP.transferedmergedcluster.txt
Number of patients = 220
Number of copy number variation regions = 43
Number of molecular subtypes = 8
Exclude regions that fewer than K tumors have alterations, K = 3

Fisher's exact test

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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

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

References

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

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

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

[4] GISTIC_version2

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