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 6 molecular subtypes across 177 patients, 35 significant findings detected with Q value < 0.25.

Amp Peak 4(8p11.22) cnvs correlated to 'CN_CNMF'.
Amp Peak 5(8q21.13) cnvs correlated to 'CN_CNMF'.
Amp Peak 7(12q24.32) cnvs correlated to 'CN_CNMF'.
Del Peak 5(2q22.1) cnvs correlated to 'CN_CNMF'.
Del Peak 6(2q22.3) cnvs correlated to 'CN_CNMF'.
Del Peak 10(5q11.2) cnvs correlated to 'CN_CNMF'.
Del Peak 11(5q21.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 12(6q15) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
Del Peak 14(8p21.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 15(8p11.21) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 16(10q23.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 18(12p13.2) cnvs correlated to 'CN_CNMF'.
Del Peak 19(13q14.13) cnvs correlated to 'CN_CNMF'.
Del Peak 20(16q22.3) cnvs correlated to 'CN_CNMF'.
Del Peak 21(16q24.1) cnvs correlated to 'CN_CNMF'.
Del Peak 22(17p13.1) cnvs correlated to 'CN_CNMF'.
Del Peak 23(17q21.31) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 24(18q22.1) cnvs correlated to 'CN_CNMF'.
Del Peak 25(18q23) cnvs correlated to 'CN_CNMF'.
Del Peak 26(21q22.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 27(21q22.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 44 regions and 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 35 significant findings detected.


		Molecular subtypes	CN CNMF	METHLYATION CNMF	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Del Peak 27(21q22 3)	57 (32%)	120	6.11e-08 (1.53e-05)	8.77e-11 (2.29e-08)	1.26e-09 (3.21e-07)	2.38e-07 (5.9e-05)	0.0567 (1.00)	0.00017 (0.0402)
Del Peak 12(6q15)	56 (32%)	121	5.01e-16 (1.32e-13)	7.81e-10 (2e-07)	0.000903 (0.208)	0.00209 (0.466)	0.000276 (0.0647)	0.824 (1.00)
Del Peak 26(21q22 2)	58 (33%)	119	2.8e-08 (7.05e-06)	2.5e-12 (6.54e-10)	5.24e-09 (1.33e-06)	2.68e-07 (6.61e-05)	0.138 (1.00)	0.00284 (0.629)
Del Peak 16(10q23 31)	63 (36%)	114	1.59e-07 (3.95e-05)	1.88e-05 (0.00457)	6.89e-05 (0.0165)	0.0214 (1.00)	0.0408 (1.00)	0.0472 (1.00)
Del Peak 11(5q21 1)	31 (18%)	146	1.7e-10 (4.41e-08)	7.32e-06 (0.00179)	0.149 (1.00)	0.47 (1.00)	0.299 (1.00)	0.538 (1.00)
Del Peak 14(8p21 3)	106 (60%)	71	2.84e-08 (7.12e-06)	4.63e-05 (0.0112)	0.0474 (1.00)	0.0594 (1.00)	0.00184 (0.415)	0.0562 (1.00)
Amp Peak 4(8p11 22)	16 (9%)	161	0.000449 (0.105)	0.481 (1.00)	0.286 (1.00)	0.491 (1.00)	0.587 (1.00)	0.454 (1.00)
Amp Peak 5(8q21 13)	44 (25%)	133	3.78e-10 (9.71e-08)	0.0101 (1.00)	0.0655 (1.00)	0.04 (1.00)	0.372 (1.00)	0.313 (1.00)
Amp Peak 7(12q24 32)	7 (4%)	170	0.000749 (0.173)	0.264 (1.00)	0.675 (1.00)	1 (1.00)	0.456 (1.00)	0.864 (1.00)
Del Peak 5(2q22 1)	21 (12%)	156	9.66e-05 (0.0231)	0.00421 (0.914)	0.586 (1.00)	0.313 (1.00)	0.0121 (1.00)	0.00772 (1.00)
Del Peak 6(2q22 3)	23 (13%)	154	4.5e-05 (0.0109)	0.0319 (1.00)	0.0398 (1.00)	0.0112 (1.00)	0.0038 (0.832)	0.0855 (1.00)
Del Peak 10(5q11 2)	29 (16%)	148	2.4e-06 (0.000587)	0.0294 (1.00)	0.798 (1.00)	0.956 (1.00)	0.599 (1.00)	0.68 (1.00)
Del Peak 15(8p11 21)	59 (33%)	118	0.0116 (1.00)	0.000204 (0.048)	0.0647 (1.00)	0.0193 (1.00)	0.281 (1.00)	0.207 (1.00)
Del Peak 18(12p13 2)	38 (21%)	139	0.000529 (0.123)	0.031 (1.00)	0.702 (1.00)	0.651 (1.00)	0.0527 (1.00)	0.856 (1.00)
Del Peak 19(13q14 13)	81 (46%)	96	0.000113 (0.0269)	0.00503 (1.00)	0.0245 (1.00)	0.0251 (1.00)	0.306 (1.00)	0.363 (1.00)
Del Peak 20(16q22 3)	57 (32%)	120	6.54e-07 (0.000161)	0.0146 (1.00)	0.015 (1.00)	0.154 (1.00)	0.0185 (1.00)	0.0792 (1.00)
Del Peak 21(16q24 1)	72 (41%)	105	2.18e-10 (5.61e-08)	0.00797 (1.00)	0.0605 (1.00)	0.373 (1.00)	0.0395 (1.00)	0.0325 (1.00)
Del Peak 22(17p13 1)	45 (25%)	132	3.97e-09 (1.01e-06)	0.216 (1.00)	0.0694 (1.00)	0.00328 (0.723)	0.286 (1.00)	0.0611 (1.00)
Del Peak 23(17q21 31)	34 (19%)	143	0.00156 (0.357)	0.000275 (0.0645)	0.00426 (0.921)	0.00464 (0.993)	0.533 (1.00)	0.289 (1.00)
Del Peak 24(18q22 1)	44 (25%)	133	9.08e-11 (2.36e-08)	0.625 (1.00)	0.667 (1.00)	0.108 (1.00)	0.0534 (1.00)	0.152 (1.00)
Del Peak 25(18q23)	50 (28%)	127	1.2e-13 (3.16e-11)	0.525 (1.00)	0.423 (1.00)	0.13 (1.00)	0.104 (1.00)	0.447 (1.00)
Amp Peak 1(1q21 3)	10 (6%)	167	0.0731 (1.00)	0.361 (1.00)	0.534 (1.00)	0.726 (1.00)	0.0787 (1.00)	1 (1.00)
Amp Peak 2(3q26 2)	25 (14%)	152	0.00195 (0.437)	0.267 (1.00)	0.73 (1.00)	0.631 (1.00)	0.932 (1.00)	0.377 (1.00)
Amp Peak 3(7p15 3)	33 (19%)	144	0.00185 (0.417)	0.107 (1.00)	0.0633 (1.00)	0.113 (1.00)	0.87 (1.00)	0.55 (1.00)
Amp Peak 6(10q21 2)	10 (6%)	167	0.00948 (1.00)	0.434 (1.00)	0.119 (1.00)	0.0962 (1.00)	0.278 (1.00)	1 (1.00)
Amp Peak 8(14q21 1)	8 (5%)	169	0.107 (1.00)	0.543 (1.00)	0.132 (1.00)	0.298 (1.00)	0.828 (1.00)	0.265 (1.00)
Amp Peak 9(Xp22 11)	5 (3%)	172	0.325 (1.00)	0.863 (1.00)	0.858 (1.00)	0.863 (1.00)	0.21 (1.00)	0.396 (1.00)
Amp Peak 10(Xp22 11)	5 (3%)	172	0.62 (1.00)	0.619 (1.00)	0.551 (1.00)	0.688 (1.00)	0.755 (1.00)	0.325 (1.00)
Amp Peak 11(Xp21 1)	4 (2%)	173	0.693 (1.00)	0.387 (1.00)	0.839 (1.00)	1 (1.00)	0.266 (1.00)	0.666 (1.00)
Amp Peak 12(Xq21 1)	7 (4%)	170	0.351 (1.00)	0.203 (1.00)	0.212 (1.00)	0.438 (1.00)	0.406 (1.00)	0.771 (1.00)
Amp Peak 13(Xq21 1)	5 (3%)	172	0.0712 (1.00)	0.00434 (0.934)	0.51 (1.00)	0.377 (1.00)	0.869 (1.00)	0.845 (1.00)
Amp Peak 14(Xq21 31)	5 (3%)	172	0.0904 (1.00)	0.275 (1.00)	0.551 (1.00)	0.234 (1.00)	0.703 (1.00)	1 (1.00)
Amp Peak 15(Xq25)	4 (2%)	173	0.0327 (1.00)	0.237 (1.00)	0.29 (1.00)	0.631 (1.00)	0.404 (1.00)	0.133 (1.00)
Amp Peak 16(Xq25)	6 (3%)	171	1 (1.00)	0.322 (1.00)	0.193 (1.00)	0.327 (1.00)	0.197 (1.00)	0.405 (1.00)
Amp Peak 17(Xq27 1)	9 (5%)	168	0.00408 (0.89)	0.434 (1.00)	1 (1.00)	0.815 (1.00)	0.0648 (1.00)	0.0234 (1.00)
Del Peak 1(1p31 3)	21 (12%)	156	0.0431 (1.00)	0.00225 (0.499)	0.0189 (1.00)	0.00182 (0.412)	0.187 (1.00)	0.152 (1.00)
Del Peak 2(1p21 3)	17 (10%)	160	0.00593 (1.00)	0.745 (1.00)	0.867 (1.00)	0.518 (1.00)	0.0741 (1.00)	0.89 (1.00)
Del Peak 3(1q23 1)	8 (5%)	169	0.0635 (1.00)	0.127 (1.00)	0.212 (1.00)	0.043 (1.00)	0.0579 (1.00)	0.707 (1.00)
Del Peak 4(1q42 13)	17 (10%)	160	0.114 (1.00)	0.0123 (1.00)	0.875 (1.00)	0.713 (1.00)	0.27 (1.00)	0.791 (1.00)
Del Peak 7(3p13)	28 (16%)	149	0.387 (1.00)	0.087 (1.00)	0.48 (1.00)	0.885 (1.00)	0.195 (1.00)	0.117 (1.00)
Del Peak 8(3q29)	12 (7%)	165	0.406 (1.00)	0.212 (1.00)	0.0981 (1.00)	0.15 (1.00)	0.579 (1.00)	1 (1.00)
Del Peak 9(4q28 1)	12 (7%)	165	0.0172 (1.00)	0.00141 (0.324)	0.189 (1.00)	0.622 (1.00)	0.263 (1.00)	0.181 (1.00)
Del Peak 13(7q36 1)	8 (5%)	169	0.538 (1.00)	0.348 (1.00)	0.534 (1.00)	0.726 (1.00)	0.69 (1.00)	0.564 (1.00)
Del Peak 17(11q23 2)	20 (11%)	157	0.121 (1.00)	0.222 (1.00)	0.754 (1.00)	0.753 (1.00)	0.387 (1.00)	0.602 (1.00)

'Amp Peak 4(8p11.22) mutation analysis' versus 'CN_CNMF'

P value = 0.000449 (Fisher's exact test), Q value = 0.1

Table S1. Gene #4: 'Amp Peak 4(8p11.22) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	83	54	1
AMP PEAK 4(8P11.22) MUTATED	4	1	11	0
AMP PEAK 4(8P11.22) WILD-TYPE	35	82	43	1

Figure S1. Get High-res Image Gene #4: 'Amp Peak 4(8p11.22) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 5(8q21.13) mutation analysis' versus 'CN_CNMF'

P value = 3.78e-10 (Fisher's exact test), Q value = 9.7e-08

Table S2. Gene #5: 'Amp Peak 5(8q21.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	83	54	1
AMP PEAK 5(8Q21.13) MUTATED	9	5	30	0
AMP PEAK 5(8Q21.13) WILD-TYPE	30	78	24	1

Figure S2. Get High-res Image Gene #5: 'Amp Peak 5(8q21.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 7(12q24.32) mutation analysis' versus 'CN_CNMF'

P value = 0.000749 (Fisher's exact test), Q value = 0.17

Table S3. Gene #7: 'Amp Peak 7(12q24.32) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	83	54	1
AMP PEAK 7(12Q24.32) MUTATED	0	0	7	0
AMP PEAK 7(12Q24.32) WILD-TYPE	39	83	47	1

Figure S3. Get High-res Image Gene #7: 'Amp Peak 7(12q24.32) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 5(2q22.1) mutation analysis' versus 'CN_CNMF'

P value = 9.66e-05 (Fisher's exact test), Q value = 0.023

Table S4. Gene #22: 'Del Peak 5(2q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	83	54	1
DEL PEAK 5(2Q22.1) MUTATED	9	2	9	1
DEL PEAK 5(2Q22.1) WILD-TYPE	30	81	45	0

Figure S4. Get High-res Image Gene #22: 'Del Peak 5(2q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 6(2q22.3) mutation analysis' versus 'CN_CNMF'

P value = 4.5e-05 (Fisher's exact test), Q value = 0.011

Table S5. Gene #23: 'Del Peak 6(2q22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	83	54	1
DEL PEAK 6(2Q22.3) MUTATED	8	2	12	1
DEL PEAK 6(2Q22.3) WILD-TYPE	31	81	42	0

Figure S5. Get High-res Image Gene #23: 'Del Peak 6(2q22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 10(5q11.2) mutation analysis' versus 'CN_CNMF'

P value = 2.4e-06 (Fisher's exact test), Q value = 0.00059

Table S6. Gene #27: 'Del Peak 10(5q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	83	54	1
DEL PEAK 10(5Q11.2) MUTATED	12	2	15	0
DEL PEAK 10(5Q11.2) WILD-TYPE	27	81	39	1

Figure S6. Get High-res Image Gene #27: 'Del Peak 10(5q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 11(5q21.1) mutation analysis' versus 'CN_CNMF'

P value = 1.7e-10 (Fisher's exact test), Q value = 4.4e-08

Table S7. Gene #28: 'Del Peak 11(5q21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	83	54	1
DEL PEAK 11(5Q21.1) MUTATED	16	0	15	0
DEL PEAK 11(5Q21.1) WILD-TYPE	23	83	39	1

Figure S7. Get High-res Image Gene #28: 'Del Peak 11(5q21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 11(5q21.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.32e-06 (Fisher's exact test), Q value = 0.0018

Table S8. Gene #28: 'Del Peak 11(5q21.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	50	68
DEL PEAK 11(5Q21.1) MUTATED	20	3	5
DEL PEAK 11(5Q21.1) WILD-TYPE	33	47	63

Figure S8. Get High-res Image Gene #28: 'Del Peak 11(5q21.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 12(6q15) mutation analysis' versus 'CN_CNMF'

P value = 5.01e-16 (Fisher's exact test), Q value = 1.3e-13

Table S9. Gene #29: 'Del Peak 12(6q15) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	83	54	1
DEL PEAK 12(6Q15) MUTATED	29	4	22	1
DEL PEAK 12(6Q15) WILD-TYPE	10	79	32	0

Figure S9. Get High-res Image Gene #29: 'Del Peak 12(6q15) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 12(6q15) mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.81e-10 (Fisher's exact test), Q value = 2e-07

Table S10. Gene #29: 'Del Peak 12(6q15) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	50	68
DEL PEAK 12(6Q15) MUTATED	32	2	19
DEL PEAK 12(6Q15) WILD-TYPE	21	48	49

Figure S10. Get High-res Image Gene #29: 'Del Peak 12(6q15) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 12(6q15) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000903 (Fisher's exact test), Q value = 0.21

Table S11. Gene #29: 'Del Peak 12(6q15) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	41	49
DEL PEAK 12(6Q15) MUTATED	24	5	14
DEL PEAK 12(6Q15) WILD-TYPE	26	36	35

Figure S11. Get High-res Image Gene #29: 'Del Peak 12(6q15) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

'Del Peak 12(6q15) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000276 (Fisher's exact test), Q value = 0.065

Table S12. Gene #29: 'Del Peak 12(6q15) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	46	25	60
DEL PEAK 12(6Q15) MUTATED	23	5	6	21
DEL PEAK 12(6Q15) WILD-TYPE	22	41	19	39

Figure S12. Get High-res Image Gene #29: 'Del Peak 12(6q15) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

'Del Peak 14(8p21.3) mutation analysis' versus 'CN_CNMF'

P value = 2.84e-08 (Fisher's exact test), Q value = 7.1e-06

Table S13. Gene #31: 'Del Peak 14(8p21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	83	54	1
DEL PEAK 14(8P21.3) MUTATED	18	38	49	1
DEL PEAK 14(8P21.3) WILD-TYPE	21	45	5	0

Figure S13. Get High-res Image Gene #31: 'Del Peak 14(8p21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 14(8p21.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.63e-05 (Fisher's exact test), Q value = 0.011

Table S14. Gene #31: 'Del Peak 14(8p21.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	50	68
DEL PEAK 14(8P21.3) MUTATED	29	19	53
DEL PEAK 14(8P21.3) WILD-TYPE	24	31	15

Figure S14. Get High-res Image Gene #31: 'Del Peak 14(8p21.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 15(8p11.21) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000204 (Fisher's exact test), Q value = 0.048

Table S15. Gene #32: 'Del Peak 15(8p11.21) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	50	68
DEL PEAK 15(8P11.21) MUTATED	17	6	32
DEL PEAK 15(8P11.21) WILD-TYPE	36	44	36

Figure S15. Get High-res Image Gene #32: 'Del Peak 15(8p11.21) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 16(10q23.31) mutation analysis' versus 'CN_CNMF'

P value = 1.59e-07 (Fisher's exact test), Q value = 3.9e-05

Table S16. Gene #33: 'Del Peak 16(10q23.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	83	54	1
DEL PEAK 16(10Q23.31) MUTATED	6	21	35	1
DEL PEAK 16(10Q23.31) WILD-TYPE	33	62	19	0

Figure S16. Get High-res Image Gene #33: 'Del Peak 16(10q23.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 16(10q23.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.88e-05 (Fisher's exact test), Q value = 0.0046

Table S17. Gene #33: 'Del Peak 16(10q23.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	50	68
DEL PEAK 16(10Q23.31) MUTATED	13	10	39
DEL PEAK 16(10Q23.31) WILD-TYPE	40	40	29

Figure S17. Get High-res Image Gene #33: 'Del Peak 16(10q23.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 16(10q23.31) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.89e-05 (Fisher's exact test), Q value = 0.017

Table S18. Gene #33: 'Del Peak 16(10q23.31) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	41	49
DEL PEAK 16(10Q23.31) MUTATED	12	11	31
DEL PEAK 16(10Q23.31) WILD-TYPE	38	30	18

Figure S18. Get High-res Image Gene #33: 'Del Peak 16(10q23.31) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

'Del Peak 18(12p13.2) mutation analysis' versus 'CN_CNMF'

P value = 0.000529 (Fisher's exact test), Q value = 0.12

Table S19. Gene #35: 'Del Peak 18(12p13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	83	54	1
DEL PEAK 18(12P13.2) MUTATED	6	10	22	0
DEL PEAK 18(12P13.2) WILD-TYPE	33	73	32	1

Figure S19. Get High-res Image Gene #35: 'Del Peak 18(12p13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 19(13q14.13) mutation analysis' versus 'CN_CNMF'

P value = 0.000113 (Fisher's exact test), Q value = 0.027

Table S20. Gene #36: 'Del Peak 19(13q14.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	83	54	1
DEL PEAK 19(13Q14.13) MUTATED	25	24	31	1
DEL PEAK 19(13Q14.13) WILD-TYPE	14	59	23	0

Figure S20. Get High-res Image Gene #36: 'Del Peak 19(13q14.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 20(16q22.3) mutation analysis' versus 'CN_CNMF'

P value = 6.54e-07 (Fisher's exact test), Q value = 0.00016

Table S21. Gene #37: 'Del Peak 20(16q22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	83	54	1
DEL PEAK 20(16Q22.3) MUTATED	6	18	33	0
DEL PEAK 20(16Q22.3) WILD-TYPE	33	65	21	1

Figure S21. Get High-res Image Gene #37: 'Del Peak 20(16q22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 21(16q24.1) mutation analysis' versus 'CN_CNMF'

P value = 2.18e-10 (Fisher's exact test), Q value = 5.6e-08

Table S22. Gene #38: 'Del Peak 21(16q24.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	83	54	1
DEL PEAK 21(16Q24.1) MUTATED	8	22	42	0
DEL PEAK 21(16Q24.1) WILD-TYPE	31	61	12	1

Figure S22. Get High-res Image Gene #38: 'Del Peak 21(16q24.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 22(17p13.1) mutation analysis' versus 'CN_CNMF'

P value = 3.97e-09 (Fisher's exact test), Q value = 1e-06

Table S23. Gene #39: 'Del Peak 22(17p13.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	83	54	1
DEL PEAK 22(17P13.1) MUTATED	3	11	30	1
DEL PEAK 22(17P13.1) WILD-TYPE	36	72	24	0

Figure S23. Get High-res Image Gene #39: 'Del Peak 22(17p13.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 23(17q21.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000275 (Fisher's exact test), Q value = 0.065

Table S24. Gene #40: 'Del Peak 23(17q21.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	50	68
DEL PEAK 23(17Q21.31) MUTATED	4	5	23
DEL PEAK 23(17Q21.31) WILD-TYPE	49	45	45

Figure S24. Get High-res Image Gene #40: 'Del Peak 23(17q21.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 24(18q22.1) mutation analysis' versus 'CN_CNMF'

P value = 9.08e-11 (Fisher's exact test), Q value = 2.4e-08

Table S25. Gene #41: 'Del Peak 24(18q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	83	54	1
DEL PEAK 24(18Q22.1) MUTATED	3	9	32	0
DEL PEAK 24(18Q22.1) WILD-TYPE	36	74	22	1

Figure S25. Get High-res Image Gene #41: 'Del Peak 24(18q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 25(18q23) mutation analysis' versus 'CN_CNMF'

P value = 1.2e-13 (Fisher's exact test), Q value = 3.2e-11

Table S26. Gene #42: 'Del Peak 25(18q23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	83	54	1
DEL PEAK 25(18Q23) MUTATED	4	9	37	0
DEL PEAK 25(18Q23) WILD-TYPE	35	74	17	1

Figure S26. Get High-res Image Gene #42: 'Del Peak 25(18q23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 26(21q22.2) mutation analysis' versus 'CN_CNMF'

P value = 2.8e-08 (Fisher's exact test), Q value = 7e-06

Table S27. Gene #43: 'Del Peak 26(21q22.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	83	54	1
DEL PEAK 26(21Q22.2) MUTATED	0	38	19	1
DEL PEAK 26(21Q22.2) WILD-TYPE	39	45	35	0

Figure S27. Get High-res Image Gene #43: 'Del Peak 26(21q22.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 26(21q22.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.5e-12 (Fisher's exact test), Q value = 6.5e-10

Table S28. Gene #43: 'Del Peak 26(21q22.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	50	68
DEL PEAK 26(21Q22.2) MUTATED	4	9	44
DEL PEAK 26(21Q22.2) WILD-TYPE	49	41	24

Figure S28. Get High-res Image Gene #43: 'Del Peak 26(21q22.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 26(21q22.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.24e-09 (Fisher's exact test), Q value = 1.3e-06

Table S29. Gene #43: 'Del Peak 26(21q22.2) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	41	49
DEL PEAK 26(21Q22.2) MUTATED	4	14	32
DEL PEAK 26(21Q22.2) WILD-TYPE	46	27	17

Figure S29. Get High-res Image Gene #43: 'Del Peak 26(21q22.2) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

'Del Peak 26(21q22.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.68e-07 (Fisher's exact test), Q value = 6.6e-05

Table S30. Gene #43: 'Del Peak 26(21q22.2) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	41	43	56
DEL PEAK 26(21Q22.2) MUTATED	3	27	20
DEL PEAK 26(21Q22.2) WILD-TYPE	38	16	36

Figure S30. Get High-res Image Gene #43: 'Del Peak 26(21q22.2) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 27(21q22.3) mutation analysis' versus 'CN_CNMF'

P value = 6.11e-08 (Fisher's exact test), Q value = 1.5e-05

Table S31. Gene #44: 'Del Peak 27(21q22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	83	54	1
DEL PEAK 27(21Q22.3) MUTATED	0	38	19	0
DEL PEAK 27(21Q22.3) WILD-TYPE	39	45	35	1

Figure S31. Get High-res Image Gene #44: 'Del Peak 27(21q22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 27(21q22.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.77e-11 (Fisher's exact test), Q value = 2.3e-08

Table S32. Gene #44: 'Del Peak 27(21q22.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	50	68
DEL PEAK 27(21Q22.3) MUTATED	5	8	42
DEL PEAK 27(21Q22.3) WILD-TYPE	48	42	26

Figure S32. Get High-res Image Gene #44: 'Del Peak 27(21q22.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 27(21q22.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.26e-09 (Fisher's exact test), Q value = 3.2e-07

Table S33. Gene #44: 'Del Peak 27(21q22.3) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	41	49
DEL PEAK 27(21Q22.3) MUTATED	4	12	33
DEL PEAK 27(21Q22.3) WILD-TYPE	46	29	16

Figure S33. Get High-res Image Gene #44: 'Del Peak 27(21q22.3) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

'Del Peak 27(21q22.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.38e-07 (Fisher's exact test), Q value = 5.9e-05

Table S34. Gene #44: 'Del Peak 27(21q22.3) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	41	43	56
DEL PEAK 27(21Q22.3) MUTATED	3	27	19
DEL PEAK 27(21Q22.3) WILD-TYPE	38	16	37

Figure S34. Get High-res Image Gene #44: 'Del Peak 27(21q22.3) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 27(21q22.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.04

Table S35. Gene #44: 'Del Peak 27(21q22.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	30	69	77
DEL PEAK 27(21Q22.3) MUTATED	3	34	20
DEL PEAK 27(21Q22.3) WILD-TYPE	27	35	57

Figure S35. Get High-res Image Gene #44: 'Del Peak 27(21q22.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
Molecular subtype file = PRAD-TP.transferedmergedcluster.txt
Number of patients = 177
Number of copy number variation regions = 44
Number of molecular subtypes = 6
Exclude regions that fewer than K tumors have alterations, K = 3

Fisher's exact test

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

Q value calculation

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

References

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

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

[3] GISTIC_version2

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