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 34 peak regions and 8 molecular subtypes across 158 patients, 56 significant findings detected with Q value < 0.25.

Amp Peak 1(2q32.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 2(2q32.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 3(3p14.1) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Amp Peak 4(3q22.3) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Amp Peak 5(5q35.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 7(7q22.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 8(16p11.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 9(17q25.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 1(1p36.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 3(3p22.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 4(4q32.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 6(5q15) cnvs correlated to 'MRNASEQ_CHIERARCHICAL'.
Del Peak 7(5q35.2) cnvs correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 10(6q25.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 11(9p21.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 12(11q22.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 13(11q24.2) cnvs correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 14(14q11.2) cnvs correlated to 'CN_CNMF'.
Del Peak 15(14q32.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 16(14q32.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 17(15q15.1) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 19(19p13.3) cnvs correlated to 'CN_CNMF'.
Del Peak 22(22q12.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 23(Xq21.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 24(Xq28) 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 34 regions and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 56 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	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Amp Peak 7(7q22 1)	0 (0%)	69	2.75e-09 (7.27e-07)	4.13e-07 (0.000104)	1.08e-10 (2.87e-08)	2.64e-08 (6.85e-06)	0.00385 (0.769)	0.0787 (1.00)	0.186 (1.00)	0.0719 (1.00)
Del Peak 3(3p22 1)	0 (0%)	145	1.26e-05 (0.00311)	1.98e-07 (5.04e-05)	0.00157 (0.335)	3.76e-05 (0.00907)	0.00815 (1.00)	0.0732 (1.00)	0.124 (1.00)	0.000844 (0.185)
Del Peak 11(9p21 3)	0 (0%)	134	1.68e-06 (0.000423)	2.99e-08 (7.74e-06)	1.22e-08 (3.21e-06)	0.000149 (0.0352)	0.0474 (1.00)	0.112 (1.00)	0.1 (1.00)	0.00232 (0.485)
Del Peak 12(11q22 3)	0 (0%)	142	0.000468 (0.105)	0.000577 (0.129)	0.000441 (0.0996)	0.000153 (0.0359)	0.502 (1.00)	0.123 (1.00)	0.473 (1.00)	0.0315 (1.00)
Del Peak 1(1p36 31)	0 (0%)	124	4.51e-11 (1.2e-08)	0.000877 (0.191)	3.14e-06 (0.000782)	0.0166 (1.00)	0.214 (1.00)	0.492 (1.00)	0.701 (1.00)	0.67 (1.00)
Del Peak 4(4q32 1)	0 (0%)	135	1.57e-08 (4.11e-06)	1.95e-08 (5.09e-06)	2.91e-07 (7.39e-05)	0.00146 (0.315)	0.11 (1.00)	0.516 (1.00)	0.895 (1.00)	0.0806 (1.00)
Del Peak 7(5q35 2)	0 (0%)	147	0.0171 (1.00)	5.45e-05 (0.013)	0.000644 (0.144)	6.21e-06 (0.00154)	0.179 (1.00)	0.0376 (1.00)	0.57 (1.00)	0.0979 (1.00)
Del Peak 22(22q12 2)	0 (0%)	118	1.76e-06 (0.000439)	1.43e-05 (0.00351)	0.000111 (0.0262)	0.00354 (0.718)	0.126 (1.00)	0.0507 (1.00)	0.278 (1.00)	0.498 (1.00)
Del Peak 23(Xq21 31)	0 (0%)	136	8.01e-08 (2.07e-05)	3.67e-05 (0.00889)	5.16e-05 (0.0124)	0.00164 (0.347)	0.154 (1.00)	0.141 (1.00)	0.151 (1.00)	0.0087 (1.00)
Amp Peak 3(3p14 1)	0 (0%)	115	1.3e-18 (3.53e-16)	0.0179 (1.00)	2.97e-05 (0.00722)	0.00357 (0.722)	0.00305 (0.632)	0.202 (1.00)	0.365 (1.00)	0.0292 (1.00)
Amp Peak 4(3q22 3)	0 (0%)	105	1.67e-19 (4.54e-17)	0.0484 (1.00)	0.000169 (0.0394)	0.0596 (1.00)	0.0231 (1.00)	0.268 (1.00)	0.324 (1.00)	0.0449 (1.00)
Amp Peak 5(5q35 2)	0 (0%)	134	1.92e-05 (0.00471)	0.0226 (1.00)	0.0703 (1.00)	0.000813 (0.18)	0.033 (1.00)	0.218 (1.00)	0.0706 (1.00)	0.394 (1.00)
Amp Peak 9(17q25 2)	0 (0%)	46	2.17e-05 (0.0053)	0.0343 (1.00)	0.000751 (0.167)	0.0037 (0.743)	0.642 (1.00)	0.869 (1.00)	0.553 (1.00)	0.602 (1.00)
Del Peak 10(6q25 3)	0 (0%)	141	0.000426 (0.0968)	0.000179 (0.0415)	0.0142 (1.00)	0.0852 (1.00)	0.764 (1.00)	0.296 (1.00)	0.774 (1.00)	0.134 (1.00)
Del Peak 13(11q24 2)	0 (0%)	141	0.00322 (0.658)	0.000179 (0.0415)	0.00174 (0.366)	0.00114 (0.248)	0.279 (1.00)	0.0646 (1.00)	0.619 (1.00)	0.0519 (1.00)
Del Peak 15(14q32 2)	0 (0%)	123	5.24e-13 (1.4e-10)	0.0508 (1.00)	0.000837 (0.184)	0.0147 (1.00)	0.901 (1.00)	0.354 (1.00)	0.855 (1.00)	0.346 (1.00)
Del Peak 16(14q32 2)	0 (0%)	123	1.29e-14 (3.49e-12)	0.0141 (1.00)	0.000376 (0.086)	0.00519 (1.00)	0.901 (1.00)	0.354 (1.00)	0.855 (1.00)	0.346 (1.00)
Del Peak 17(15q15 1)	0 (0%)	137	5.22e-05 (0.0125)	0.00311 (0.64)	0.000415 (0.0946)	0.0293 (1.00)	0.277 (1.00)	0.223 (1.00)	0.4 (1.00)	0.0758 (1.00)
Amp Peak 1(2q32 2)	0 (0%)	124	1.75e-07 (4.51e-05)	0.0102 (1.00)	0.058 (1.00)	1 (1.00)	0.511 (1.00)	0.83 (1.00)	0.293 (1.00)	0.327 (1.00)
Amp Peak 2(2q32 2)	0 (0%)	124	1.75e-07 (4.51e-05)	0.0102 (1.00)	0.058 (1.00)	1 (1.00)	0.511 (1.00)	0.83 (1.00)	0.293 (1.00)	0.327 (1.00)
Amp Peak 8(16p11 2)	0 (0%)	73	2.1e-12 (5.62e-10)	0.431 (1.00)	0.0149 (1.00)	0.0117 (1.00)	0.0896 (1.00)	0.0546 (1.00)	0.0261 (1.00)	0.0538 (1.00)
Del Peak 6(5q15)	0 (0%)	147	0.0628 (1.00)	0.00811 (1.00)	0.015 (1.00)	0.000285 (0.0656)	0.732 (1.00)	0.0376 (1.00)	0.656 (1.00)	0.056 (1.00)
Del Peak 14(14q11 2)	0 (0%)	123	2.48e-13 (6.67e-11)	0.0813 (1.00)	0.00492 (0.965)	0.0433 (1.00)	0.917 (1.00)	0.527 (1.00)	0.855 (1.00)	0.346 (1.00)
Del Peak 19(19p13 3)	0 (0%)	142	0.000168 (0.0393)	0.00731 (1.00)	0.056 (1.00)	0.0148 (1.00)	0.801 (1.00)	0.115 (1.00)	0.258 (1.00)	0.141 (1.00)
Del Peak 24(Xq28)	0 (0%)	137	3.2e-07 (8.11e-05)	0.00123 (0.266)	0.00151 (0.323)	0.0185 (1.00)	0.277 (1.00)	0.519 (1.00)	0.451 (1.00)	0.0519 (1.00)
Amp Peak 6(6p12 3)	0 (0%)	152	0.2 (1.00)	0.0204 (1.00)	0.556 (1.00)	0.152 (1.00)	0.534 (1.00)	0.386 (1.00)	0.32 (1.00)	0.516 (1.00)
Amp Peak 10(19p13 2)	0 (0%)	142	0.705 (1.00)	0.0407 (1.00)	0.0497 (1.00)	0.321 (1.00)	0.981 (1.00)	0.889 (1.00)	0.927 (1.00)	0.368 (1.00)
Del Peak 2(2q36 3)	0 (0%)	151	0.0183 (1.00)	0.00312 (0.64)	0.497 (1.00)	0.138 (1.00)	0.461 (1.00)	1 (1.00)	0.257 (1.00)	0.375 (1.00)
Del Peak 5(5p14 2)	0 (0%)	147	0.0196 (1.00)	0.00811 (1.00)	0.15 (1.00)	0.00585 (1.00)	0.228 (1.00)	0.427 (1.00)	0.57 (1.00)	0.567 (1.00)
Del Peak 8(6p12 3)	0 (0%)	143	0.0043 (0.855)	0.00301 (0.626)	0.177 (1.00)	0.448 (1.00)	0.766 (1.00)	0.933 (1.00)	1 (1.00)	0.361 (1.00)
Del Peak 9(6q22 31)	0 (0%)	142	0.00747 (1.00)	0.0043 (0.855)	0.0084 (1.00)	0.0527 (1.00)	0.401 (1.00)	0.259 (1.00)	0.33 (1.00)	0.0496 (1.00)
Del Peak 18(16q24 1)	0 (0%)	151	0.0729 (1.00)	0.00448 (0.882)	0.0352 (1.00)	0.00212 (0.445)	0.102 (1.00)	0.378 (1.00)	1 (1.00)	0.181 (1.00)
Del Peak 20(19q13 2)	0 (0%)	144	0.00962 (1.00)	0.0176 (1.00)	0.0147 (1.00)	0.00832 (1.00)	0.133 (1.00)	0.383 (1.00)	0.034 (1.00)	0.408 (1.00)
Del Peak 21(19q13 42)	0 (0%)	143	0.0185 (1.00)	0.029 (1.00)	0.0454 (1.00)	0.0311 (1.00)	0.537 (1.00)	0.383 (1.00)	0.152 (1.00)	0.9 (1.00)

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

P value = 1.75e-07 (Fisher's exact test), Q value = 4.5e-05

Table S1. Gene #1: 'Amp Peak 1(2q32.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	52	70
AMP PEAK 1(2Q32.2) CNV	12	20	2
AMP PEAK 1(2Q32.2) WILD-TYPE	24	32	68

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(2q32.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 2(2q32.2)' versus 'CN_CNMF'

P value = 1.75e-07 (Fisher's exact test), Q value = 4.5e-05

Table S2. Gene #2: 'Amp Peak 2(2q32.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	52	70
AMP PEAK 2(2Q32.2) CNV	12	20	2
AMP PEAK 2(2Q32.2) WILD-TYPE	24	32	68

Figure S2. Get High-res Image Gene #2: 'Amp Peak 2(2q32.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 3(3p14.1)' versus 'CN_CNMF'

P value = 1.3e-18 (Fisher's exact test), Q value = 3.5e-16

Table S3. Gene #3: 'Amp Peak 3(3p14.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	52	70
AMP PEAK 3(3P14.1) CNV	31	8	4
AMP PEAK 3(3P14.1) WILD-TYPE	5	44	66

Figure S3. Get High-res Image Gene #3: 'Amp Peak 3(3p14.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 3(3p14.1)' versus 'MRNASEQ_CNMF'

P value = 2.97e-05 (Fisher's exact test), Q value = 0.0072

Table S4. Gene #3: 'Amp Peak 3(3p14.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	42	25	23
AMP PEAK 3(3P14.1) CNV	3	18	11	7
AMP PEAK 3(3P14.1) WILD-TYPE	48	24	14	16

Figure S4. Get High-res Image Gene #3: 'Amp Peak 3(3p14.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Amp Peak 4(3q22.3)' versus 'CN_CNMF'

P value = 1.67e-19 (Fisher's exact test), Q value = 4.5e-17

Table S5. Gene #4: 'Amp Peak 4(3q22.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	52	70
AMP PEAK 4(3Q22.3) CNV	34	13	6
AMP PEAK 4(3Q22.3) WILD-TYPE	2	39	64

Figure S5. Get High-res Image Gene #4: 'Amp Peak 4(3q22.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 4(3q22.3)' versus 'MRNASEQ_CNMF'

P value = 0.000169 (Fisher's exact test), Q value = 0.039

Table S6. Gene #4: 'Amp Peak 4(3q22.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	42	25	23
AMP PEAK 4(3Q22.3) CNV	6	18	12	12
AMP PEAK 4(3Q22.3) WILD-TYPE	45	24	13	11

Figure S6. Get High-res Image Gene #4: 'Amp Peak 4(3q22.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Amp Peak 5(5q35.2)' versus 'CN_CNMF'

P value = 1.92e-05 (Fisher's exact test), Q value = 0.0047

Table S7. Gene #5: 'Amp Peak 5(5q35.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	52	70
AMP PEAK 5(5Q35.2) CNV	1	18	5
AMP PEAK 5(5Q35.2) WILD-TYPE	35	34	65

Figure S7. Get High-res Image Gene #5: 'Amp Peak 5(5q35.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 5(5q35.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000813 (Fisher's exact test), Q value = 0.18

Table S8. Gene #5: 'Amp Peak 5(5q35.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	23	74	44
AMP PEAK 5(5Q35.2) CNV	1	7	15
AMP PEAK 5(5Q35.2) WILD-TYPE	22	67	29

Figure S8. Get High-res Image Gene #5: 'Amp Peak 5(5q35.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

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

P value = 2.75e-09 (Fisher's exact test), Q value = 7.3e-07

Table S9. Gene #7: 'Amp Peak 7(7q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	52	70
AMP PEAK 7(7Q22.1) CNV	34	16	39
AMP PEAK 7(7Q22.1) WILD-TYPE	2	36	31

Figure S9. Get High-res Image Gene #7: 'Amp Peak 7(7q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 4.13e-07 (Fisher's exact test), Q value = 1e-04

Table S10. Gene #7: 'Amp Peak 7(7q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	43	62
AMP PEAK 7(7Q22.1) CNV	17	12	49
AMP PEAK 7(7Q22.1) WILD-TYPE	20	31	13

Figure S10. Get High-res Image Gene #7: 'Amp Peak 7(7q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 7(7q22.1)' versus 'MRNASEQ_CNMF'

P value = 1.08e-10 (Fisher's exact test), Q value = 2.9e-08

Table S11. Gene #7: 'Amp Peak 7(7q22.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	42	25	23
AMP PEAK 7(7Q22.1) CNV	14	38	11	19
AMP PEAK 7(7Q22.1) WILD-TYPE	37	4	14	4

Figure S11. Get High-res Image Gene #7: 'Amp Peak 7(7q22.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Amp Peak 7(7q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.64e-08 (Fisher's exact test), Q value = 6.9e-06

Table S12. Gene #7: 'Amp Peak 7(7q22.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	23	74	44
AMP PEAK 7(7Q22.1) CNV	8	60	14
AMP PEAK 7(7Q22.1) WILD-TYPE	15	14	30

Figure S12. Get High-res Image Gene #7: 'Amp Peak 7(7q22.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 8(16p11.2)' versus 'CN_CNMF'

P value = 2.1e-12 (Fisher's exact test), Q value = 5.6e-10

Table S13. Gene #8: 'Amp Peak 8(16p11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	52	70
AMP PEAK 8(16P11.2) CNV	36	26	23
AMP PEAK 8(16P11.2) WILD-TYPE	0	26	47

Figure S13. Get High-res Image Gene #8: 'Amp Peak 8(16p11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 9(17q25.2)' versus 'CN_CNMF'

P value = 2.17e-05 (Fisher's exact test), Q value = 0.0053

Table S14. Gene #9: 'Amp Peak 9(17q25.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	52	70
AMP PEAK 9(17Q25.2) CNV	35	29	48
AMP PEAK 9(17Q25.2) WILD-TYPE	1	23	22

Figure S14. Get High-res Image Gene #9: 'Amp Peak 9(17q25.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 9(17q25.2)' versus 'MRNASEQ_CNMF'

P value = 0.000751 (Fisher's exact test), Q value = 0.17

Table S15. Gene #9: 'Amp Peak 9(17q25.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	42	25	23
AMP PEAK 9(17Q25.2) CNV	27	38	19	17
AMP PEAK 9(17Q25.2) WILD-TYPE	24	4	6	6

Figure S15. Get High-res Image Gene #9: 'Amp Peak 9(17q25.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

P value = 4.51e-11 (Fisher's exact test), Q value = 1.2e-08

Table S16. Gene #11: 'Del Peak 1(1p36.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	52	70
DEL PEAK 1(1P36.31) CNV	1	28	5
DEL PEAK 1(1P36.31) WILD-TYPE	35	24	65

Figure S16. Get High-res Image Gene #11: 'Del Peak 1(1p36.31)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 0.000877 (Fisher's exact test), Q value = 0.19

Table S17. Gene #11: 'Del Peak 1(1p36.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	43	62
DEL PEAK 1(1P36.31) CNV	6	18	7
DEL PEAK 1(1P36.31) WILD-TYPE	31	25	55

Figure S17. Get High-res Image Gene #11: 'Del Peak 1(1p36.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 3.14e-06 (Fisher's exact test), Q value = 0.00078

Table S18. Gene #11: 'Del Peak 1(1p36.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	42	25	23
DEL PEAK 1(1P36.31) CNV	22	4	2	0
DEL PEAK 1(1P36.31) WILD-TYPE	29	38	23	23

Figure S18. Get High-res Image Gene #11: 'Del Peak 1(1p36.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 3(3p22.1)' versus 'CN_CNMF'

P value = 1.26e-05 (Fisher's exact test), Q value = 0.0031

Table S19. Gene #13: 'Del Peak 3(3p22.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	52	70
DEL PEAK 3(3P22.1) CNV	0	12	1
DEL PEAK 3(3P22.1) WILD-TYPE	36	40	69

Figure S19. Get High-res Image Gene #13: 'Del Peak 3(3p22.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 3(3p22.1)' versus 'METHLYATION_CNMF'

P value = 1.98e-07 (Fisher's exact test), Q value = 5e-05

Table S20. Gene #13: 'Del Peak 3(3p22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	43	62
DEL PEAK 3(3P22.1) CNV	0	12	0
DEL PEAK 3(3P22.1) WILD-TYPE	37	31	62

Figure S20. Get High-res Image Gene #13: 'Del Peak 3(3p22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 3(3p22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.76e-05 (Fisher's exact test), Q value = 0.0091

Table S21. Gene #13: 'Del Peak 3(3p22.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	23	74	44
DEL PEAK 3(3P22.1) CNV	2	0	10
DEL PEAK 3(3P22.1) WILD-TYPE	21	74	34

Figure S21. Get High-res Image Gene #13: 'Del Peak 3(3p22.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 3(3p22.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000844 (Fisher's exact test), Q value = 0.18

Table S22. Gene #13: 'Del Peak 3(3p22.1)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	10	52	64
DEL PEAK 3(3P22.1) CNV	4	5	1
DEL PEAK 3(3P22.1) WILD-TYPE	6	47	63

Figure S22. Get High-res Image Gene #13: 'Del Peak 3(3p22.1)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 4(4q32.1)' versus 'CN_CNMF'

P value = 1.57e-08 (Fisher's exact test), Q value = 4.1e-06

Table S23. Gene #14: 'Del Peak 4(4q32.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	52	70
DEL PEAK 4(4Q32.1) CNV	0	20	3
DEL PEAK 4(4Q32.1) WILD-TYPE	36	32	67

Figure S23. Get High-res Image Gene #14: 'Del Peak 4(4q32.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 4(4q32.1)' versus 'METHLYATION_CNMF'

P value = 1.95e-08 (Fisher's exact test), Q value = 5.1e-06

Table S24. Gene #14: 'Del Peak 4(4q32.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	43	62
DEL PEAK 4(4Q32.1) CNV	1	17	1
DEL PEAK 4(4Q32.1) WILD-TYPE	36	26	61

Figure S24. Get High-res Image Gene #14: 'Del Peak 4(4q32.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 4(4q32.1)' versus 'MRNASEQ_CNMF'

P value = 2.91e-07 (Fisher's exact test), Q value = 7.4e-05

Table S25. Gene #14: 'Del Peak 4(4q32.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	42	25	23
DEL PEAK 4(4Q32.1) CNV	18	1	0	0
DEL PEAK 4(4Q32.1) WILD-TYPE	33	41	25	23

Figure S25. Get High-res Image Gene #14: 'Del Peak 4(4q32.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 6(5q15)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000285 (Fisher's exact test), Q value = 0.066

Table S26. Gene #16: 'Del Peak 6(5q15)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	23	74	44
DEL PEAK 6(5Q15) CNV	6	1	1
DEL PEAK 6(5Q15) WILD-TYPE	17	73	43

Figure S26. Get High-res Image Gene #16: 'Del Peak 6(5q15)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 7(5q35.2)' versus 'METHLYATION_CNMF'

P value = 5.45e-05 (Fisher's exact test), Q value = 0.013

Table S27. Gene #17: 'Del Peak 7(5q35.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	43	62
DEL PEAK 7(5Q35.2) CNV	1	9	0
DEL PEAK 7(5Q35.2) WILD-TYPE	36	34	62

Figure S27. Get High-res Image Gene #17: 'Del Peak 7(5q35.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 7(5q35.2)' versus 'MRNASEQ_CNMF'

P value = 0.000644 (Fisher's exact test), Q value = 0.14

Table S28. Gene #17: 'Del Peak 7(5q35.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	42	25	23
DEL PEAK 7(5Q35.2) CNV	9	0	0	0
DEL PEAK 7(5Q35.2) WILD-TYPE	42	42	25	23

Figure S28. Get High-res Image Gene #17: 'Del Peak 7(5q35.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 7(5q35.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.21e-06 (Fisher's exact test), Q value = 0.0015

Table S29. Gene #17: 'Del Peak 7(5q35.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	23	74	44
DEL PEAK 7(5Q35.2) CNV	7	0	2
DEL PEAK 7(5Q35.2) WILD-TYPE	16	74	42

Figure S29. Get High-res Image Gene #17: 'Del Peak 7(5q35.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 10(6q25.3)' versus 'CN_CNMF'

P value = 0.000426 (Fisher's exact test), Q value = 0.097

Table S30. Gene #20: 'Del Peak 10(6q25.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	52	70
DEL PEAK 10(6Q25.3) CNV	1	13	3
DEL PEAK 10(6Q25.3) WILD-TYPE	35	39	67

Figure S30. Get High-res Image Gene #20: 'Del Peak 10(6q25.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 10(6q25.3)' versus 'METHLYATION_CNMF'

P value = 0.000179 (Fisher's exact test), Q value = 0.041

Table S31. Gene #20: 'Del Peak 10(6q25.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	43	62
DEL PEAK 10(6Q25.3) CNV	2	12	2
DEL PEAK 10(6Q25.3) WILD-TYPE	35	31	60

Figure S31. Get High-res Image Gene #20: 'Del Peak 10(6q25.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 11(9p21.3)' versus 'CN_CNMF'

P value = 1.68e-06 (Fisher's exact test), Q value = 0.00042

Table S32. Gene #21: 'Del Peak 11(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	52	70
DEL PEAK 11(9P21.3) CNV	1	19	4
DEL PEAK 11(9P21.3) WILD-TYPE	35	33	66

Figure S32. Get High-res Image Gene #21: 'Del Peak 11(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 11(9p21.3)' versus 'METHLYATION_CNMF'

P value = 2.99e-08 (Fisher's exact test), Q value = 7.7e-06

Table S33. Gene #21: 'Del Peak 11(9p21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	43	62
DEL PEAK 11(9P21.3) CNV	4	17	0
DEL PEAK 11(9P21.3) WILD-TYPE	33	26	62

Figure S33. Get High-res Image Gene #21: 'Del Peak 11(9p21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 11(9p21.3)' versus 'MRNASEQ_CNMF'

P value = 1.22e-08 (Fisher's exact test), Q value = 3.2e-06

Table S34. Gene #21: 'Del Peak 11(9p21.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	42	25	23
DEL PEAK 11(9P21.3) CNV	20	0	1	0
DEL PEAK 11(9P21.3) WILD-TYPE	31	42	24	23

Figure S34. Get High-res Image Gene #21: 'Del Peak 11(9p21.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 11(9p21.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000149 (Fisher's exact test), Q value = 0.035

Table S35. Gene #21: 'Del Peak 11(9p21.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	23	74	44
DEL PEAK 11(9P21.3) CNV	8	3	10
DEL PEAK 11(9P21.3) WILD-TYPE	15	71	34

Figure S35. Get High-res Image Gene #21: 'Del Peak 11(9p21.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 12(11q22.3)' versus 'CN_CNMF'

P value = 0.000468 (Fisher's exact test), Q value = 0.11

Table S36. Gene #22: 'Del Peak 12(11q22.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	52	70
DEL PEAK 12(11Q22.3) CNV	0	12	4
DEL PEAK 12(11Q22.3) WILD-TYPE	36	40	66

Figure S36. Get High-res Image Gene #22: 'Del Peak 12(11q22.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 12(11q22.3)' versus 'METHLYATION_CNMF'

P value = 0.000577 (Fisher's exact test), Q value = 0.13

Table S37. Gene #22: 'Del Peak 12(11q22.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	43	62
DEL PEAK 12(11Q22.3) CNV	2	11	2
DEL PEAK 12(11Q22.3) WILD-TYPE	35	32	60

Figure S37. Get High-res Image Gene #22: 'Del Peak 12(11q22.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 12(11q22.3)' versus 'MRNASEQ_CNMF'

P value = 0.000441 (Fisher's exact test), Q value = 0.1

Table S38. Gene #22: 'Del Peak 12(11q22.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	42	25	23
DEL PEAK 12(11Q22.3) CNV	13	1	1	0
DEL PEAK 12(11Q22.3) WILD-TYPE	38	41	24	23

Figure S38. Get High-res Image Gene #22: 'Del Peak 12(11q22.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 12(11q22.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000153 (Fisher's exact test), Q value = 0.036

Table S39. Gene #22: 'Del Peak 12(11q22.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	23	74	44
DEL PEAK 12(11Q22.3) CNV	6	1	8
DEL PEAK 12(11Q22.3) WILD-TYPE	17	73	36

Figure S39. Get High-res Image Gene #22: 'Del Peak 12(11q22.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 13(11q24.2)' versus 'METHLYATION_CNMF'

P value = 0.000179 (Fisher's exact test), Q value = 0.041

Table S40. Gene #23: 'Del Peak 13(11q24.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	43	62
DEL PEAK 13(11Q24.2) CNV	2	12	2
DEL PEAK 13(11Q24.2) WILD-TYPE	35	31	60

Figure S40. Get High-res Image Gene #23: 'Del Peak 13(11q24.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 13(11q24.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00114 (Fisher's exact test), Q value = 0.25

Table S41. Gene #23: 'Del Peak 13(11q24.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	23	74	44
DEL PEAK 13(11Q24.2) CNV	5	2	9
DEL PEAK 13(11Q24.2) WILD-TYPE	18	72	35

Figure S41. Get High-res Image Gene #23: 'Del Peak 13(11q24.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 14(14q11.2)' versus 'CN_CNMF'

P value = 2.48e-13 (Fisher's exact test), Q value = 6.7e-11

Table S42. Gene #24: 'Del Peak 14(14q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	52	70
DEL PEAK 14(14Q11.2) CNV	3	30	2
DEL PEAK 14(14Q11.2) WILD-TYPE	33	22	68

Figure S42. Get High-res Image Gene #24: 'Del Peak 14(14q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 15(14q32.2)' versus 'CN_CNMF'

P value = 5.24e-13 (Fisher's exact test), Q value = 1.4e-10

Table S43. Gene #25: 'Del Peak 15(14q32.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	52	70
DEL PEAK 15(14Q32.2) CNV	2	30	3
DEL PEAK 15(14Q32.2) WILD-TYPE	34	22	67

Figure S43. Get High-res Image Gene #25: 'Del Peak 15(14q32.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 15(14q32.2)' versus 'MRNASEQ_CNMF'

P value = 0.000837 (Fisher's exact test), Q value = 0.18

Table S44. Gene #25: 'Del Peak 15(14q32.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	42	25	23
DEL PEAK 15(14Q32.2) CNV	19	2	5	3
DEL PEAK 15(14Q32.2) WILD-TYPE	32	40	20	20

Figure S44. Get High-res Image Gene #25: 'Del Peak 15(14q32.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 16(14q32.2)' versus 'CN_CNMF'

P value = 1.29e-14 (Fisher's exact test), Q value = 3.5e-12

Table S45. Gene #26: 'Del Peak 16(14q32.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	52	70
DEL PEAK 16(14Q32.2) CNV	2	31	2
DEL PEAK 16(14Q32.2) WILD-TYPE	34	21	68

Figure S45. Get High-res Image Gene #26: 'Del Peak 16(14q32.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 16(14q32.2)' versus 'MRNASEQ_CNMF'

P value = 0.000376 (Fisher's exact test), Q value = 0.086

Table S46. Gene #26: 'Del Peak 16(14q32.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	42	25	23
DEL PEAK 16(14Q32.2) CNV	20	2	5	3
DEL PEAK 16(14Q32.2) WILD-TYPE	31	40	20	20

Figure S46. Get High-res Image Gene #26: 'Del Peak 16(14q32.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 17(15q15.1)' versus 'CN_CNMF'

P value = 5.22e-05 (Fisher's exact test), Q value = 0.012

Table S47. Gene #27: 'Del Peak 17(15q15.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	52	70
DEL PEAK 17(15Q15.1) CNV	2	16	3
DEL PEAK 17(15Q15.1) WILD-TYPE	34	36	67

Figure S47. Get High-res Image Gene #27: 'Del Peak 17(15q15.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 17(15q15.1)' versus 'MRNASEQ_CNMF'

P value = 0.000415 (Fisher's exact test), Q value = 0.095

Table S48. Gene #27: 'Del Peak 17(15q15.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	42	25	23
DEL PEAK 17(15Q15.1) CNV	14	1	3	0
DEL PEAK 17(15Q15.1) WILD-TYPE	37	41	22	23

Figure S48. Get High-res Image Gene #27: 'Del Peak 17(15q15.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 19(19p13.3)' versus 'CN_CNMF'

P value = 0.000168 (Fisher's exact test), Q value = 0.039

Table S49. Gene #29: 'Del Peak 19(19p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	52	70
DEL PEAK 19(19P13.3) CNV	1	13	2
DEL PEAK 19(19P13.3) WILD-TYPE	35	39	68

Figure S49. Get High-res Image Gene #29: 'Del Peak 19(19p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 22(22q12.2)' versus 'CN_CNMF'

P value = 1.76e-06 (Fisher's exact test), Q value = 0.00044

Table S50. Gene #32: 'Del Peak 22(22q12.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	52	70
DEL PEAK 22(22Q12.2) CNV	2	26	12
DEL PEAK 22(22Q12.2) WILD-TYPE	34	26	58

Figure S50. Get High-res Image Gene #32: 'Del Peak 22(22q12.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 22(22q12.2)' versus 'METHLYATION_CNMF'

P value = 1.43e-05 (Fisher's exact test), Q value = 0.0035

Table S51. Gene #32: 'Del Peak 22(22q12.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	43	62
DEL PEAK 22(22Q12.2) CNV	5	23	9
DEL PEAK 22(22Q12.2) WILD-TYPE	32	20	53

Figure S51. Get High-res Image Gene #32: 'Del Peak 22(22q12.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 22(22q12.2)' versus 'MRNASEQ_CNMF'

P value = 0.000111 (Fisher's exact test), Q value = 0.026

Table S52. Gene #32: 'Del Peak 22(22q12.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	42	25	23
DEL PEAK 22(22Q12.2) CNV	23	5	5	1
DEL PEAK 22(22Q12.2) WILD-TYPE	28	37	20	22

Figure S52. Get High-res Image Gene #32: 'Del Peak 22(22q12.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 23(Xq21.31)' versus 'CN_CNMF'

P value = 8.01e-08 (Fisher's exact test), Q value = 2.1e-05

Table S53. Gene #33: 'Del Peak 23(Xq21.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	52	70
DEL PEAK 23(XQ21.31) CNV	1	19	2
DEL PEAK 23(XQ21.31) WILD-TYPE	35	33	68

Figure S53. Get High-res Image Gene #33: 'Del Peak 23(Xq21.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 23(Xq21.31)' versus 'METHLYATION_CNMF'

P value = 3.67e-05 (Fisher's exact test), Q value = 0.0089

Table S54. Gene #33: 'Del Peak 23(Xq21.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	43	62
DEL PEAK 23(XQ21.31) CNV	2	15	3
DEL PEAK 23(XQ21.31) WILD-TYPE	35	28	59

Figure S54. Get High-res Image Gene #33: 'Del Peak 23(Xq21.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 23(Xq21.31)' versus 'MRNASEQ_CNMF'

P value = 5.16e-05 (Fisher's exact test), Q value = 0.012

Table S55. Gene #33: 'Del Peak 23(Xq21.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	51	42	25	23
DEL PEAK 23(XQ21.31) CNV	15	1	1	0
DEL PEAK 23(XQ21.31) WILD-TYPE	36	41	24	23

Figure S55. Get High-res Image Gene #33: 'Del Peak 23(Xq21.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 24(Xq28)' versus 'CN_CNMF'

P value = 3.2e-07 (Fisher's exact test), Q value = 8.1e-05

Table S56. Gene #34: 'Del Peak 24(Xq28)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	52	70
DEL PEAK 24(XQ28) CNV	1	18	2
DEL PEAK 24(XQ28) WILD-TYPE	35	34	68

Figure S56. Get High-res Image Gene #34: 'Del Peak 24(Xq28)' 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 = KIRP-TP.transferedmergedcluster.txt
Number of patients = 158
Number of copy number variation regions = 34
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

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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