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 44 peak regions and 8 molecular subtypes across 65 patients, 61 significant findings detected with Q value < 0.25.

Amp Peak 3(7q22.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 4(8q24.21) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Amp Peak 7(12p13.33) cnvs correlated to 'CN_CNMF'.
Amp Peak 8(12p11.21) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 12(18q11.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 14(20q13.2) cnvs correlated to 'CN_CNMF'.
Del Peak 2(1p36.11) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 3(1p21.2) cnvs correlated to 'CN_CNMF'.
Del Peak 4(5q14.2) cnvs correlated to 'CN_CNMF'.
Del Peak 5(5q15) cnvs correlated to 'CN_CNMF'.
Del Peak 6(6p25.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 7(6p22.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 8(6q22.33) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 10(8p21.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 12(9p21.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 13(10q23.2) cnvs correlated to 'CN_CNMF'.
Del Peak 15(12p12.3) cnvs correlated to 'CN_CNMF'.
Del Peak 16(12q12) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 17(12q24.31) cnvs correlated to 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 18(15q15.1) cnvs correlated to 'CN_CNMF'.
Del Peak 19(17p11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 20(17q22) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 28(Xq21.1) cnvs correlated to 'CN_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 44 regions and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 61 significant findings detected.


		Molecular subtypes	CN CNMF	METHLYATION CNMF	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Chi-square 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 12(9p21 3)	0 (0%)	24	1.43e-06 (0.000496)	9.11e-08 (3.2e-05)	2.16e-05 (0.00726)	4.09e-06 (0.00141)	2.95e-05 (0.00987)	4.02e-05 (0.0133)	2.78e-07 (9.69e-05)	4.88e-06 (0.00167)
Del Peak 8(6q22 33)	0 (0%)	34	0.000728 (0.216)	3.79e-05 (0.0126)	0.00218 (0.607)	4.39e-06 (0.00151)	0.000693 (0.207)	0.000148 (0.0477)	0.000163 (0.052)	0.000466 (0.143)
Del Peak 10(8p21 3)	0 (0%)	46	2.52e-05 (0.00847)	0.000211 (0.0666)	8.93e-05 (0.0292)	0.000538 (0.165)	0.000789 (0.233)	0.00201 (0.561)	0.000163 (0.052)	0.00115 (0.328)
Del Peak 19(17p11 2)	0 (0%)	39	5.43e-05 (0.0179)	1.13e-08 (3.99e-06)	0.000809 (0.238)	0.000824 (0.241)	0.00233 (0.643)	0.000332 (0.104)	0.000246 (0.0774)	0.00165 (0.467)
Amp Peak 12(18q11 2)	0 (0%)	46	0.000293 (0.0919)	0.00369 (0.983)	0.000369 (0.115)	0.00807 (1.00)	0.00589 (1.00)	0.00109 (0.313)	0.000478 (0.147)	0.000556 (0.17)
Del Peak 6(6p25 2)	0 (0%)	39	4.12e-05 (0.0136)	1.76e-05 (0.00596)	0.000193 (0.0611)	0.00724 (1.00)	0.0226 (1.00)	0.00597 (1.00)	0.00737 (1.00)	0.018 (1.00)
Del Peak 7(6p22 3)	0 (0%)	40	0.000854 (0.249)	6.32e-05 (0.0207)	0.000119 (0.0386)	0.00228 (0.63)	0.00633 (1.00)	0.00252 (0.694)	0.00497 (1.00)	0.0134 (1.00)
Del Peak 17(12q24 31)	0 (0%)	49	0.000948 (0.275)	9.01e-05 (0.0294)	0.0138 (1.00)	0.000169 (0.0538)	0.00107 (0.31)	0.00541 (1.00)	0.000454 (0.14)	0.00402 (1.00)
Amp Peak 3(7q22 1)	0 (0%)	47	0.000766 (0.227)	0.000101 (0.0328)	0.27 (1.00)	0.191 (1.00)	0.125 (1.00)	0.218 (1.00)	0.109 (1.00)	0.162 (1.00)
Amp Peak 4(8q24 21)	0 (0%)	40	7.91e-06 (0.0027)	0.00287 (0.778)	0.000579 (0.176)	0.00333 (0.895)	0.0284 (1.00)	0.0744 (1.00)	0.00983 (1.00)	0.0358 (1.00)
Amp Peak 8(12p11 21)	0 (0%)	51	1.52e-05 (0.00514)	0.000696 (0.208)	0.00328 (0.885)	0.0824 (1.00)	0.00428 (1.00)	0.017 (1.00)	0.00584 (1.00)	0.0135 (1.00)
Del Peak 2(1p36 11)	0 (0%)	47	0.00068 (0.205)	0.000619 (0.187)	0.00953 (1.00)	0.26 (1.00)	0.0801 (1.00)	0.0769 (1.00)	0.00911 (1.00)	0.0518 (1.00)
Del Peak 16(12q12)	0 (0%)	55	0.00014 (0.0453)	3.91e-05 (0.013)	0.0244 (1.00)	0.0185 (1.00)	0.108 (1.00)	0.0614 (1.00)	0.0138 (1.00)	0.0413 (1.00)
Del Peak 20(17q22)	0 (0%)	47	9.68e-06 (0.00329)	3.54e-05 (0.0118)	0.0403 (1.00)	0.00272 (0.74)	0.0142 (1.00)	0.0299 (1.00)	0.00822 (1.00)	0.0183 (1.00)
Amp Peak 7(12p13 33)	0 (0%)	55	2.52e-07 (8.8e-05)	0.00565 (1.00)	0.0587 (1.00)	0.0562 (1.00)	0.0436 (1.00)	0.113 (1.00)	0.0158 (1.00)	0.0791 (1.00)
Amp Peak 14(20q13 2)	0 (0%)	48	2.88e-06 (0.000992)	0.121 (1.00)	0.053 (1.00)	0.191 (1.00)	0.146 (1.00)	0.218 (1.00)	0.0368 (1.00)	0.162 (1.00)
Del Peak 3(1p21 2)	0 (0%)	54	0.000152 (0.0489)	0.0382 (1.00)	0.153 (1.00)	0.252 (1.00)	0.0668 (1.00)	0.316 (1.00)	0.0137 (1.00)	0.209 (1.00)
Del Peak 4(5q14 2)	0 (0%)	53	0.000601 (0.182)	0.329 (1.00)	0.234 (1.00)	0.245 (1.00)	0.184 (1.00)	0.5 (1.00)	0.0517 (1.00)	0.467 (1.00)
Del Peak 5(5q15)	0 (0%)	51	0.000688 (0.206)	0.0877 (1.00)	0.546 (1.00)	0.113 (1.00)	0.124 (1.00)	0.331 (1.00)	0.029 (1.00)	0.256 (1.00)
Del Peak 13(10q23 2)	0 (0%)	51	1.2e-07 (4.2e-05)	0.0371 (1.00)	0.0892 (1.00)	0.0209 (1.00)	0.0421 (1.00)	0.0149 (1.00)	0.00118 (0.336)	0.0107 (1.00)
Del Peak 15(12p12 3)	0 (0%)	54	0.000408 (0.127)	0.00266 (0.729)	0.125 (1.00)	0.134 (1.00)	0.0436 (1.00)	0.00989 (1.00)	0.0181 (1.00)	0.00739 (1.00)
Del Peak 18(15q15 1)	0 (0%)	51	1.29e-06 (0.000446)	0.00359 (0.962)	0.0414 (1.00)	0.00942 (1.00)	0.0194 (1.00)	0.0346 (1.00)	0.000994 (0.287)	0.0159 (1.00)
Del Peak 28(Xq21 1)	0 (0%)	58	0.00041 (0.127)	0.0299 (1.00)	0.365 (1.00)	0.782 (1.00)	0.252 (1.00)	0.554 (1.00)	0.0704 (1.00)	0.396 (1.00)
Amp Peak 1(1p34 2)	0 (0%)	60	0.173 (1.00)	0.729 (1.00)	1 (1.00)	1 (1.00)	0.656 (1.00)	1 (1.00)	0.821 (1.00)	1 (1.00)
Amp Peak 2(1p12)	0 (0%)	54	0.0445 (1.00)	0.251 (1.00)	0.952 (1.00)	0.746 (1.00)	0.889 (1.00)	0.885 (1.00)	0.474 (1.00)	0.791 (1.00)
Amp Peak 5(9p13 3)	0 (0%)	58	0.077 (1.00)	0.404 (1.00)	0.133 (1.00)	0.119 (1.00)	0.305 (1.00)	0.226 (1.00)	0.161 (1.00)	0.166 (1.00)
Amp Peak 6(11p11 2)	0 (0%)	59	0.0888 (1.00)	0.059 (1.00)	0.314 (1.00)	0.195 (1.00)	0.571 (1.00)	0.195 (1.00)	0.312 (1.00)	0.206 (1.00)
Amp Peak 9(12q15)	0 (0%)	57	0.00549 (1.00)	0.0311 (1.00)	0.237 (1.00)	0.0355 (1.00)	0.0225 (1.00)	0.0131 (1.00)	0.00463 (1.00)	0.00874 (1.00)
Amp Peak 10(17p11 2)	0 (0%)	62	0.635 (1.00)	0.338 (1.00)	0.885 (1.00)	0.683 (1.00)	0.577 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
Amp Peak 11(17q21 33)	0 (0%)	58	0.0162 (1.00)	0.239 (1.00)	0.609 (1.00)	0.72 (1.00)	1 (1.00)	0.756 (1.00)	0.67 (1.00)	0.768 (1.00)
Amp Peak 13(19q13 13)	0 (0%)	51	0.0229 (1.00)	0.0745 (1.00)	0.309 (1.00)	0.0443 (1.00)	0.286 (1.00)	0.22 (1.00)	0.286 (1.00)	0.434 (1.00)
Amp Peak 15(Xp22 11)	0 (0%)	61	0.248 (1.00)	0.667 (1.00)	0.885 (1.00)	0.312 (1.00)	1 (1.00)	0.818 (1.00)	0.821 (1.00)	0.816 (1.00)
Amp Peak 16(Xq27 1)	0 (0%)	59	0.0165 (1.00)	0.873 (1.00)	0.391 (1.00)	0.615 (1.00)	0.463 (1.00)	1 (1.00)	0.624 (1.00)	0.744 (1.00)
Del Peak 1(1p36 22)	0 (0%)	51	0.0207 (1.00)	0.00361 (0.964)	0.0753 (1.00)	0.134 (1.00)	0.0339 (1.00)	0.186 (1.00)	0.0686 (1.00)	0.107 (1.00)
Del Peak 9(7q36 1)	0 (0%)	58	0.00189 (0.533)	0.0439 (1.00)	0.133 (1.00)	0.119 (1.00)	0.305 (1.00)	0.74 (1.00)	0.461 (1.00)	0.643 (1.00)
Del Peak 11(8q12 1)	0 (0%)	60	0.0349 (1.00)	0.077 (1.00)	0.314 (1.00)	0.257 (1.00)	0.571 (1.00)	0.195 (1.00)	0.312 (1.00)	0.206 (1.00)
Del Peak 14(11p15 4)	0 (0%)	53	0.0304 (1.00)	0.467 (1.00)	0.761 (1.00)	0.592 (1.00)	0.525 (1.00)	1 (1.00)	0.732 (1.00)	1 (1.00)
Del Peak 21(18p11 32)	0 (0%)	44	0.124 (1.00)	1 (1.00)	0.542 (1.00)	1 (1.00)	0.218 (1.00)	0.935 (1.00)	0.664 (1.00)	1 (1.00)
Del Peak 22(18q12 1)	0 (0%)	28	0.02 (1.00)	0.0844 (1.00)	0.113 (1.00)	0.338 (1.00)	0.0835 (1.00)	0.0889 (1.00)	0.0632 (1.00)	0.141 (1.00)
Del Peak 23(18q21 2)	0 (0%)	20	0.00267 (0.729)	0.000946 (0.275)	0.00907 (1.00)	0.0226 (1.00)	0.00861 (1.00)	0.00197 (0.551)	0.00115 (0.328)	0.00436 (1.00)
Del Peak 24(19q13 33)	0 (0%)	58	0.00189 (0.533)	0.0851 (1.00)	0.819 (1.00)	1 (1.00)	0.848 (1.00)	0.74 (1.00)	0.461 (1.00)	0.643 (1.00)
Del Peak 25(21q22 11)	0 (0%)	43	0.0192 (1.00)	0.158 (1.00)	0.154 (1.00)	0.00376 (0.996)	0.0379 (1.00)	0.265 (1.00)	0.0685 (1.00)	0.181 (1.00)
Del Peak 26(21q22 11)	0 (0%)	43	0.0192 (1.00)	0.158 (1.00)	0.154 (1.00)	0.00376 (0.996)	0.0379 (1.00)	0.265 (1.00)	0.0685 (1.00)	0.181 (1.00)
Del Peak 27(22q13 31)	0 (0%)	49	0.006 (1.00)	0.15 (1.00)	0.358 (1.00)	0.26 (1.00)	0.38 (1.00)	0.424 (1.00)	0.286 (1.00)	0.326 (1.00)

'Amp Peak 3(7q22.1)' versus 'CN_CNMF'

P value = 0.000766 (Chi-square test), Q value = 0.23

Table S1. Gene #3: 'Amp Peak 3(7q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	11	35	9	9	1
AMP PEAK 3(7Q22.1) CNV	4	4	7	2	1
AMP PEAK 3(7Q22.1) WILD-TYPE	7	31	2	7	0

Figure S1. Get High-res Image Gene #3: 'Amp Peak 3(7q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 3(7q22.1)' versus 'METHLYATION_CNMF'

P value = 0.000101 (Fisher's exact test), Q value = 0.033

Table S2. Gene #3: 'Amp Peak 3(7q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	24	25	15
AMP PEAK 3(7Q22.1) CNV	10	0	7
AMP PEAK 3(7Q22.1) WILD-TYPE	14	25	8

Figure S2. Get High-res Image Gene #3: 'Amp Peak 3(7q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 4(8q24.21)' versus 'CN_CNMF'

P value = 7.91e-06 (Chi-square test), Q value = 0.0027

Table S3. Gene #4: 'Amp Peak 4(8q24.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	11	35	9	9	1
AMP PEAK 4(8Q24.21) CNV	11	6	6	2	0
AMP PEAK 4(8Q24.21) WILD-TYPE	0	29	3	7	1

Figure S3. Get High-res Image Gene #4: 'Amp Peak 4(8q24.21)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 4(8q24.21)' versus 'MRNASEQ_CNMF'

P value = 0.000579 (Fisher's exact test), Q value = 0.18

Table S4. Gene #4: 'Amp Peak 4(8q24.21)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	21	12	12	10
AMP PEAK 4(8Q24.21) CNV	14	5	2	0
AMP PEAK 4(8Q24.21) WILD-TYPE	7	7	10	10

Figure S4. Get High-res Image Gene #4: 'Amp Peak 4(8q24.21)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Amp Peak 7(12p13.33)' versus 'CN_CNMF'

P value = 2.52e-07 (Chi-square test), Q value = 8.8e-05

Table S5. Gene #7: 'Amp Peak 7(12p13.33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	11	35	9	9	1
AMP PEAK 7(12P13.33) CNV	8	0	2	0	0
AMP PEAK 7(12P13.33) WILD-TYPE	3	35	7	9	1

Figure S5. Get High-res Image Gene #7: 'Amp Peak 7(12p13.33)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 8(12p11.21)' versus 'CN_CNMF'

P value = 1.52e-05 (Chi-square test), Q value = 0.0051

Table S6. Gene #8: 'Amp Peak 8(12p11.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	11	35	9	9	1
AMP PEAK 8(12P11.21) CNV	7	0	2	4	1
AMP PEAK 8(12P11.21) WILD-TYPE	4	35	7	5	0

Figure S6. Get High-res Image Gene #8: 'Amp Peak 8(12p11.21)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 8(12p11.21)' versus 'METHLYATION_CNMF'

P value = 0.000696 (Fisher's exact test), Q value = 0.21

Table S7. Gene #8: 'Amp Peak 8(12p11.21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	24	25	15
AMP PEAK 8(12P11.21) CNV	8	0	6
AMP PEAK 8(12P11.21) WILD-TYPE	16	25	9

Figure S7. Get High-res Image Gene #8: 'Amp Peak 8(12p11.21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 12(18q11.2)' versus 'CN_CNMF'

P value = 0.000293 (Chi-square test), Q value = 0.092

Table S8. Gene #12: 'Amp Peak 12(18q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	11	35	9	9	1
AMP PEAK 12(18Q11.2) CNV	4	3	5	7	0
AMP PEAK 12(18Q11.2) WILD-TYPE	7	32	4	2	1

Figure S8. Get High-res Image Gene #12: 'Amp Peak 12(18q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 12(18q11.2)' versus 'MRNASEQ_CNMF'

P value = 0.000369 (Fisher's exact test), Q value = 0.11

Table S9. Gene #12: 'Amp Peak 12(18q11.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	21	12	12	10
AMP PEAK 12(18Q11.2) CNV	13	3	0	1
AMP PEAK 12(18Q11.2) WILD-TYPE	8	9	12	9

Figure S9. Get High-res Image Gene #12: 'Amp Peak 12(18q11.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Amp Peak 12(18q11.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000478 (Fisher's exact test), Q value = 0.15

Table S10. Gene #12: 'Amp Peak 12(18q11.2)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	25	10	23
AMP PEAK 12(18Q11.2) CNV	14	1	2
AMP PEAK 12(18Q11.2) WILD-TYPE	11	9	21

Figure S10. Get High-res Image Gene #12: 'Amp Peak 12(18q11.2)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 12(18q11.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000556 (Fisher's exact test), Q value = 0.17

Table S11. Gene #12: 'Amp Peak 12(18q11.2)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	12	26	20
AMP PEAK 12(18Q11.2) CNV	0	14	3
AMP PEAK 12(18Q11.2) WILD-TYPE	12	12	17

Figure S11. Get High-res Image Gene #12: 'Amp Peak 12(18q11.2)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 14(20q13.2)' versus 'CN_CNMF'

P value = 2.88e-06 (Chi-square test), Q value = 0.00099

Table S12. Gene #14: 'Amp Peak 14(20q13.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	11	35	9	9	1
AMP PEAK 14(20Q13.2) CNV	10	3	3	1	0
AMP PEAK 14(20Q13.2) WILD-TYPE	1	32	6	8	1

Figure S12. Get High-res Image Gene #14: 'Amp Peak 14(20q13.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 2(1p36.11)' versus 'CN_CNMF'

P value = 0.00068 (Chi-square test), Q value = 0.2

Table S13. Gene #18: 'Del Peak 2(1p36.11)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	11	35	9	9	1
DEL PEAK 2(1P36.11) CNV	8	3	3	4	0
DEL PEAK 2(1P36.11) WILD-TYPE	3	32	6	5	1

Figure S13. Get High-res Image Gene #18: 'Del Peak 2(1p36.11)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 2(1p36.11)' versus 'METHLYATION_CNMF'

P value = 0.000619 (Fisher's exact test), Q value = 0.19

Table S14. Gene #18: 'Del Peak 2(1p36.11)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	24	25	15
DEL PEAK 2(1P36.11) CNV	9	1	8
DEL PEAK 2(1P36.11) WILD-TYPE	15	24	7

Figure S14. Get High-res Image Gene #18: 'Del Peak 2(1p36.11)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 3(1p21.2)' versus 'CN_CNMF'

P value = 0.000152 (Chi-square test), Q value = 0.049

Table S15. Gene #19: 'Del Peak 3(1p21.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	11	35	9	9	1
DEL PEAK 3(1P21.2) CNV	7	1	2	1	0
DEL PEAK 3(1P21.2) WILD-TYPE	4	34	7	8	1

Figure S15. Get High-res Image Gene #19: 'Del Peak 3(1p21.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 4(5q14.2)' versus 'CN_CNMF'

P value = 0.000601 (Chi-square test), Q value = 0.18

Table S16. Gene #20: 'Del Peak 4(5q14.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	11	35	9	9	1
DEL PEAK 4(5Q14.2) CNV	6	2	4	0	0
DEL PEAK 4(5Q14.2) WILD-TYPE	5	33	5	9	1

Figure S16. Get High-res Image Gene #20: 'Del Peak 4(5q14.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 5(5q15)' versus 'CN_CNMF'

P value = 0.000688 (Chi-square test), Q value = 0.21

Table S17. Gene #21: 'Del Peak 5(5q15)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	11	35	9	9	1
DEL PEAK 5(5Q15) CNV	6	2	5	1	0
DEL PEAK 5(5Q15) WILD-TYPE	5	33	4	8	1

Figure S17. Get High-res Image Gene #21: 'Del Peak 5(5q15)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 6(6p25.2)' versus 'CN_CNMF'

P value = 4.12e-05 (Chi-square test), Q value = 0.014

Table S18. Gene #22: 'Del Peak 6(6p25.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	11	35	9	9	1
DEL PEAK 6(6P25.2) CNV	9	6	8	3	0
DEL PEAK 6(6P25.2) WILD-TYPE	2	29	1	6	1

Figure S18. Get High-res Image Gene #22: 'Del Peak 6(6p25.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 6(6p25.2)' versus 'METHLYATION_CNMF'

P value = 1.76e-05 (Fisher's exact test), Q value = 0.006

Table S19. Gene #22: 'Del Peak 6(6p25.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	24	25	15
DEL PEAK 6(6P25.2) CNV	17	2	6
DEL PEAK 6(6P25.2) WILD-TYPE	7	23	9

Figure S19. Get High-res Image Gene #22: 'Del Peak 6(6p25.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 6(6p25.2)' versus 'MRNASEQ_CNMF'

P value = 0.000193 (Fisher's exact test), Q value = 0.061

Table S20. Gene #22: 'Del Peak 6(6p25.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	21	12	12	10
DEL PEAK 6(6P25.2) CNV	15	4	2	0
DEL PEAK 6(6P25.2) WILD-TYPE	6	8	10	10

Figure S20. Get High-res Image Gene #22: 'Del Peak 6(6p25.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 7(6p22.3)' versus 'CN_CNMF'

P value = 0.000854 (Chi-square test), Q value = 0.25

Table S21. Gene #23: 'Del Peak 7(6p22.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	11	35	9	9	1
DEL PEAK 7(6P22.3) CNV	8	6	7	4	0
DEL PEAK 7(6P22.3) WILD-TYPE	3	29	2	5	1

Figure S21. Get High-res Image Gene #23: 'Del Peak 7(6p22.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 7(6p22.3)' versus 'METHLYATION_CNMF'

P value = 6.32e-05 (Fisher's exact test), Q value = 0.021

Table S22. Gene #23: 'Del Peak 7(6p22.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	24	25	15
DEL PEAK 7(6P22.3) CNV	16	2	6
DEL PEAK 7(6P22.3) WILD-TYPE	8	23	9

Figure S22. Get High-res Image Gene #23: 'Del Peak 7(6p22.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 7(6p22.3)' versus 'MRNASEQ_CNMF'

P value = 0.000119 (Fisher's exact test), Q value = 0.039

Table S23. Gene #23: 'Del Peak 7(6p22.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	21	12	12	10
DEL PEAK 7(6P22.3) CNV	15	3	2	0
DEL PEAK 7(6P22.3) WILD-TYPE	6	9	10	10

Figure S23. Get High-res Image Gene #23: 'Del Peak 7(6p22.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 8(6q22.33)' versus 'CN_CNMF'

P value = 0.000728 (Chi-square test), Q value = 0.22

Table S24. Gene #24: 'Del Peak 8(6q22.33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	11	35	9	9	1
DEL PEAK 8(6Q22.33) CNV	9	9	8	5	0
DEL PEAK 8(6Q22.33) WILD-TYPE	2	26	1	4	1

Figure S24. Get High-res Image Gene #24: 'Del Peak 8(6q22.33)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 8(6q22.33)' versus 'METHLYATION_CNMF'

P value = 3.79e-05 (Fisher's exact test), Q value = 0.013

Table S25. Gene #24: 'Del Peak 8(6q22.33)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	24	25	15
DEL PEAK 8(6Q22.33) CNV	19	4	7
DEL PEAK 8(6Q22.33) WILD-TYPE	5	21	8

Figure S25. Get High-res Image Gene #24: 'Del Peak 8(6q22.33)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 8(6q22.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.39e-06 (Fisher's exact test), Q value = 0.0015

Table S26. Gene #24: 'Del Peak 8(6q22.33)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	5	22	28
DEL PEAK 8(6Q22.33) CNV	0	18	6
DEL PEAK 8(6Q22.33) WILD-TYPE	5	4	22

Figure S26. Get High-res Image Gene #24: 'Del Peak 8(6q22.33)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 8(6q22.33)' versus 'MIRSEQ_CNMF'

P value = 0.000693 (Fisher's exact test), Q value = 0.21

Table S27. Gene #24: 'Del Peak 8(6q22.33)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	11	18
DEL PEAK 8(6Q22.33) CNV	20	3	3
DEL PEAK 8(6Q22.33) WILD-TYPE	9	8	15

Figure S27. Get High-res Image Gene #24: 'Del Peak 8(6q22.33)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 8(6q22.33)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000148 (Fisher's exact test), Q value = 0.048

Table S28. Gene #24: 'Del Peak 8(6q22.33)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	20	27
DEL PEAK 8(6Q22.33) CNV	2	4	20
DEL PEAK 8(6Q22.33) WILD-TYPE	9	16	7

Figure S28. Get High-res Image Gene #24: 'Del Peak 8(6q22.33)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 8(6q22.33)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000163 (Fisher's exact test), Q value = 0.052

Table S29. Gene #24: 'Del Peak 8(6q22.33)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	25	10	23
DEL PEAK 8(6Q22.33) CNV	19	2	5
DEL PEAK 8(6Q22.33) WILD-TYPE	6	8	18

Figure S29. Get High-res Image Gene #24: 'Del Peak 8(6q22.33)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'Del Peak 8(6q22.33)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000466 (Fisher's exact test), Q value = 0.14

Table S30. Gene #24: 'Del Peak 8(6q22.33)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	12	26	20
DEL PEAK 8(6Q22.33) CNV	3	19	4
DEL PEAK 8(6Q22.33) WILD-TYPE	9	7	16

Figure S30. Get High-res Image Gene #24: 'Del Peak 8(6q22.33)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 10(8p21.3)' versus 'CN_CNMF'

P value = 2.52e-05 (Chi-square test), Q value = 0.0085

Table S31. Gene #26: 'Del Peak 10(8p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	11	35	9	9	1
DEL PEAK 10(8P21.3) CNV	9	2	4	4	0
DEL PEAK 10(8P21.3) WILD-TYPE	2	33	5	5	1

Figure S31. Get High-res Image Gene #26: 'Del Peak 10(8p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 10(8p21.3)' versus 'METHLYATION_CNMF'

P value = 0.000211 (Fisher's exact test), Q value = 0.067

Table S32. Gene #26: 'Del Peak 10(8p21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	24	25	15
DEL PEAK 10(8P21.3) CNV	13	1	4
DEL PEAK 10(8P21.3) WILD-TYPE	11	24	11

Figure S32. Get High-res Image Gene #26: 'Del Peak 10(8p21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 10(8p21.3)' versus 'MRNASEQ_CNMF'

P value = 8.93e-05 (Fisher's exact test), Q value = 0.029

Table S33. Gene #26: 'Del Peak 10(8p21.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	21	12	12	10
DEL PEAK 10(8P21.3) CNV	13	1	1	0
DEL PEAK 10(8P21.3) WILD-TYPE	8	11	11	10

Figure S33. Get High-res Image Gene #26: 'Del Peak 10(8p21.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 10(8p21.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000538 (Fisher's exact test), Q value = 0.16

Table S34. Gene #26: 'Del Peak 10(8p21.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	5	22	28
DEL PEAK 10(8P21.3) CNV	1	12	2
DEL PEAK 10(8P21.3) WILD-TYPE	4	10	26

Figure S34. Get High-res Image Gene #26: 'Del Peak 10(8p21.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 10(8p21.3)' versus 'MIRSEQ_CNMF'

P value = 0.000789 (Fisher's exact test), Q value = 0.23

Table S35. Gene #26: 'Del Peak 10(8p21.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	11	18
DEL PEAK 10(8P21.3) CNV	15	1	1
DEL PEAK 10(8P21.3) WILD-TYPE	14	10	17

Figure S35. Get High-res Image Gene #26: 'Del Peak 10(8p21.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 10(8p21.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000163 (Fisher's exact test), Q value = 0.052

Table S36. Gene #26: 'Del Peak 10(8p21.3)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	25	10	23
DEL PEAK 10(8P21.3) CNV	14	2	1
DEL PEAK 10(8P21.3) WILD-TYPE	11	8	22

Figure S36. Get High-res Image Gene #26: 'Del Peak 10(8p21.3)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'Del Peak 12(9p21.3)' versus 'CN_CNMF'

P value = 1.43e-06 (Chi-square test), Q value = 5e-04

Table S37. Gene #28: 'Del Peak 12(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	11	35	9	9	1
DEL PEAK 12(9P21.3) CNV	11	11	9	9	1
DEL PEAK 12(9P21.3) WILD-TYPE	0	24	0	0	0

Figure S37. Get High-res Image Gene #28: 'Del Peak 12(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 12(9p21.3)' versus 'METHLYATION_CNMF'

P value = 9.11e-08 (Fisher's exact test), Q value = 3.2e-05

Table S38. Gene #28: 'Del Peak 12(9p21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	24	25	15
DEL PEAK 12(9P21.3) CNV	24	7	9
DEL PEAK 12(9P21.3) WILD-TYPE	0	18	6

Figure S38. Get High-res Image Gene #28: 'Del Peak 12(9p21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 12(9p21.3)' versus 'MRNASEQ_CNMF'

P value = 2.16e-05 (Fisher's exact test), Q value = 0.0073

Table S39. Gene #28: 'Del Peak 12(9p21.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	21	12	12	10
DEL PEAK 12(9P21.3) CNV	20	6	3	3
DEL PEAK 12(9P21.3) WILD-TYPE	1	6	9	7

Figure S39. Get High-res Image Gene #28: 'Del Peak 12(9p21.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 12(9p21.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.09e-06 (Fisher's exact test), Q value = 0.0014

Table S40. Gene #28: 'Del Peak 12(9p21.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	5	22	28
DEL PEAK 12(9P21.3) CNV	1	21	10
DEL PEAK 12(9P21.3) WILD-TYPE	4	1	18

Figure S40. Get High-res Image Gene #28: 'Del Peak 12(9p21.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 12(9p21.3)' versus 'MIRSEQ_CNMF'

P value = 2.95e-05 (Fisher's exact test), Q value = 0.0099

Table S41. Gene #28: 'Del Peak 12(9p21.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	11	18
DEL PEAK 12(9P21.3) CNV	25	5	4
DEL PEAK 12(9P21.3) WILD-TYPE	4	6	14

Figure S41. Get High-res Image Gene #28: 'Del Peak 12(9p21.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 12(9p21.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.02e-05 (Fisher's exact test), Q value = 0.013

Table S42. Gene #28: 'Del Peak 12(9p21.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	20	27
DEL PEAK 12(9P21.3) CNV	3	7	24
DEL PEAK 12(9P21.3) WILD-TYPE	8	13	3

Figure S42. Get High-res Image Gene #28: 'Del Peak 12(9p21.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 12(9p21.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.78e-07 (Fisher's exact test), Q value = 9.7e-05

Table S43. Gene #28: 'Del Peak 12(9p21.3)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	25	10	23
DEL PEAK 12(9P21.3) CNV	24	4	6
DEL PEAK 12(9P21.3) WILD-TYPE	1	6	17

Figure S43. Get High-res Image Gene #28: 'Del Peak 12(9p21.3)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'Del Peak 12(9p21.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.88e-06 (Fisher's exact test), Q value = 0.0017

Table S44. Gene #28: 'Del Peak 12(9p21.3)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	12	26	20
DEL PEAK 12(9P21.3) CNV	3	24	7
DEL PEAK 12(9P21.3) WILD-TYPE	9	2	13

Figure S44. Get High-res Image Gene #28: 'Del Peak 12(9p21.3)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 13(10q23.2)' versus 'CN_CNMF'

P value = 1.2e-07 (Chi-square test), Q value = 4.2e-05

Table S45. Gene #29: 'Del Peak 13(10q23.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	11	35	9	9	1
DEL PEAK 13(10Q23.2) CNV	5	1	8	0	0
DEL PEAK 13(10Q23.2) WILD-TYPE	6	34	1	9	1

Figure S45. Get High-res Image Gene #29: 'Del Peak 13(10q23.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 15(12p12.3)' versus 'CN_CNMF'

P value = 0.000408 (Chi-square test), Q value = 0.13

Table S46. Gene #31: 'Del Peak 15(12p12.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	11	35	9	9	1
DEL PEAK 15(12P12.3) CNV	3	1	1	5	1
DEL PEAK 15(12P12.3) WILD-TYPE	8	34	8	4	0

Figure S46. Get High-res Image Gene #31: 'Del Peak 15(12p12.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 16(12q12)' versus 'CN_CNMF'

P value = 0.00014 (Chi-square test), Q value = 0.045

Table S47. Gene #32: 'Del Peak 16(12q12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	11	35	9	9	1
DEL PEAK 16(12Q12) CNV	2	1	6	1	0
DEL PEAK 16(12Q12) WILD-TYPE	9	34	3	8	1

Figure S47. Get High-res Image Gene #32: 'Del Peak 16(12q12)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 16(12q12)' versus 'METHLYATION_CNMF'

P value = 3.91e-05 (Fisher's exact test), Q value = 0.013

Table S48. Gene #32: 'Del Peak 16(12q12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	24	25	15
DEL PEAK 16(12Q12) CNV	10	0	0
DEL PEAK 16(12Q12) WILD-TYPE	14	25	15

Figure S48. Get High-res Image Gene #32: 'Del Peak 16(12q12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 17(12q24.31)' versus 'METHLYATION_CNMF'

P value = 9.01e-05 (Fisher's exact test), Q value = 0.029

Table S49. Gene #33: 'Del Peak 17(12q24.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	24	25	15
DEL PEAK 17(12Q24.31) CNV	13	1	2
DEL PEAK 17(12Q24.31) WILD-TYPE	11	24	13

Figure S49. Get High-res Image Gene #33: 'Del Peak 17(12q24.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 17(12q24.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000169 (Fisher's exact test), Q value = 0.054

Table S50. Gene #33: 'Del Peak 17(12q24.31)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	5	22	28
DEL PEAK 17(12Q24.31) CNV	0	11	1
DEL PEAK 17(12Q24.31) WILD-TYPE	5	11	27

Figure S50. Get High-res Image Gene #33: 'Del Peak 17(12q24.31)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 17(12q24.31)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000454 (Fisher's exact test), Q value = 0.14

Table S51. Gene #33: 'Del Peak 17(12q24.31)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	25	10	23
DEL PEAK 17(12Q24.31) CNV	11	2	0
DEL PEAK 17(12Q24.31) WILD-TYPE	14	8	23

Figure S51. Get High-res Image Gene #33: 'Del Peak 17(12q24.31)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'Del Peak 18(15q15.1)' versus 'CN_CNMF'

P value = 1.29e-06 (Chi-square test), Q value = 0.00045

Table S52. Gene #34: 'Del Peak 18(15q15.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	11	35	9	9	1
DEL PEAK 18(15Q15.1) CNV	7	0	6	1	0
DEL PEAK 18(15Q15.1) WILD-TYPE	4	35	3	8	1

Figure S52. Get High-res Image Gene #34: 'Del Peak 18(15q15.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 19(17p11.2)' versus 'CN_CNMF'

P value = 5.43e-05 (Chi-square test), Q value = 0.018

Table S53. Gene #35: 'Del Peak 19(17p11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	11	35	9	9	1
DEL PEAK 19(17P11.2) CNV	10	5	5	5	1
DEL PEAK 19(17P11.2) WILD-TYPE	1	30	4	4	0

Figure S53. Get High-res Image Gene #35: 'Del Peak 19(17p11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 19(17p11.2)' versus 'METHLYATION_CNMF'

P value = 1.13e-08 (Fisher's exact test), Q value = 4e-06

Table S54. Gene #35: 'Del Peak 19(17p11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	24	25	15
DEL PEAK 19(17P11.2) CNV	18	0	8
DEL PEAK 19(17P11.2) WILD-TYPE	6	25	7

Figure S54. Get High-res Image Gene #35: 'Del Peak 19(17p11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 19(17p11.2)' versus 'MRNASEQ_CNMF'

P value = 0.000809 (Fisher's exact test), Q value = 0.24

Table S55. Gene #35: 'Del Peak 19(17p11.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	21	12	12	10
DEL PEAK 19(17P11.2) CNV	15	3	2	1
DEL PEAK 19(17P11.2) WILD-TYPE	6	9	10	9

Figure S55. Get High-res Image Gene #35: 'Del Peak 19(17p11.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 19(17p11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000824 (Fisher's exact test), Q value = 0.24

Table S56. Gene #35: 'Del Peak 19(17p11.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	5	22	28
DEL PEAK 19(17P11.2) CNV	1	15	5
DEL PEAK 19(17P11.2) WILD-TYPE	4	7	23

Figure S56. Get High-res Image Gene #35: 'Del Peak 19(17p11.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 19(17p11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000332 (Fisher's exact test), Q value = 0.1

Table S57. Gene #35: 'Del Peak 19(17p11.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	20	27
DEL PEAK 19(17P11.2) CNV	1	4	18
DEL PEAK 19(17P11.2) WILD-TYPE	10	16	9

Figure S57. Get High-res Image Gene #35: 'Del Peak 19(17p11.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 19(17p11.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000246 (Fisher's exact test), Q value = 0.077

Table S58. Gene #35: 'Del Peak 19(17p11.2)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	25	10	23
DEL PEAK 19(17P11.2) CNV	17	3	3
DEL PEAK 19(17P11.2) WILD-TYPE	8	7	20

Figure S58. Get High-res Image Gene #35: 'Del Peak 19(17p11.2)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'Del Peak 20(17q22)' versus 'CN_CNMF'

P value = 9.68e-06 (Chi-square test), Q value = 0.0033

Table S59. Gene #36: 'Del Peak 20(17q22)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	11	35	9	9	1
DEL PEAK 20(17Q22) CNV	9	2	2	4	1
DEL PEAK 20(17Q22) WILD-TYPE	2	33	7	5	0

Figure S59. Get High-res Image Gene #36: 'Del Peak 20(17q22)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 20(17q22)' versus 'METHLYATION_CNMF'

P value = 3.54e-05 (Fisher's exact test), Q value = 0.012

Table S60. Gene #36: 'Del Peak 20(17q22)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	24	25	15
DEL PEAK 20(17Q22) CNV	12	0	6
DEL PEAK 20(17Q22) WILD-TYPE	12	25	9

Figure S60. Get High-res Image Gene #36: 'Del Peak 20(17q22)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 28(Xq21.1)' versus 'CN_CNMF'

P value = 0.00041 (Chi-square test), Q value = 0.13

Table S61. Gene #44: 'Del Peak 28(Xq21.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	11	35	9	9	1
DEL PEAK 28(XQ21.1) CNV	5	0	2	0	0
DEL PEAK 28(XQ21.1) WILD-TYPE	6	35	7	9	1

Figure S61. Get High-res Image Gene #44: 'Del Peak 28(Xq21.1)' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data

Input

Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
Molecular subtype file = PAAD-TP.transferedmergedcluster.txt
Number of patients = 65
Number of copy number variation regions = 44
Number of molecular subtypes = 8
Exclude regions that fewer than K tumors have alterations, K = 3

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

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

[2] 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)

[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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