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 27 peak regions and 8 molecular subtypes across 470 patients, 52 significant findings detected with Q value < 0.25.

Amp Peak 1(Xq22.3) cnvs correlated to 'CN_CNMF'.
Del Peak 2(2p23.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 3(2q35) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 6(6q22.31) cnvs correlated to 'CN_CNMF'.
Del Peak 9(8p12) cnvs correlated to 'CN_CNMF'.
Del Peak 10(8q24.22) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 11(9q21.13) cnvs correlated to 'CN_CNMF'.
Del Peak 12(10q21.2) cnvs correlated to 'CN_CNMF'.
Del Peak 13(10q23.31) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 14(11p15.1) cnvs correlated to 'CN_CNMF'.
Del Peak 15(13q12.3) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 17(15q25.3) cnvs correlated to 'CN_CNMF'.
Del Peak 21(18p11.21) cnvs correlated to 'CN_CNMF'.
Del Peak 22(18q22.2) cnvs correlated to 'CN_CNMF'.
Del Peak 23(19p13.2) cnvs correlated to 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 26(21q21.1) cnvs correlated to 'CN_CNMF'.
Del Peak 27(22q13.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 28(22q13.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 29(22q13.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 30(22q13.32) 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 27 regions and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 52 significant findings detected.


		Molecular subtypes	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Del Peak 2(2p23 1)	12 (3%)	458	4.94e-10 (9.88e-08)	2.89e-05 (0.00515)	0.772 (1.00)	0.0179 (1.00)	1.83e-05 (0.00341)	1.93e-05 (0.00356)	1.19e-06 (0.000229)	5.09e-07 (9.87e-05)
Del Peak 3(2q35)	11 (2%)	459	1.04e-11 (2.1e-09)	2.47e-05 (0.00442)	0.562 (1.00)	0.00287 (0.425)	1.83e-05 (0.00341)	1.93e-05 (0.00356)	1.19e-06 (0.000229)	5.09e-07 (9.87e-05)
Del Peak 27(22q13 1)	81 (17%)	389	5.8e-86 (1.19e-83)	0.000321 (0.0548)	0.205 (1.00)	0.0795 (1.00)	3.11e-07 (6.12e-05)	2e-05 (0.00365)	0.00371 (0.545)	0.00144 (0.228)
Del Peak 28(22q13 2)	81 (17%)	389	5.8e-86 (1.19e-83)	0.000321 (0.0548)	0.205 (1.00)	0.0795 (1.00)	3.11e-07 (6.12e-05)	2e-05 (0.00365)	0.00371 (0.545)	0.00144 (0.228)
Del Peak 29(22q13 31)	81 (17%)	389	5.8e-86 (1.19e-83)	0.000321 (0.0548)	0.205 (1.00)	0.0795 (1.00)	3.11e-07 (6.12e-05)	2e-05 (0.00365)	0.00371 (0.545)	0.00144 (0.228)
Del Peak 30(22q13 32)	82 (17%)	388	4.47e-84 (9.08e-82)	0.000162 (0.0282)	0.205 (1.00)	0.0795 (1.00)	1.64e-07 (3.25e-05)	1.17e-05 (0.00222)	0.00209 (0.322)	0.000846 (0.139)
Del Peak 10(8q24 22)	7 (1%)	463	5.43e-05 (0.00962)	0.00247 (0.373)	0.837 (1.00)	0.0549 (1.00)	0.00213 (0.324)	0.00122 (0.196)	0.000185 (0.0319)	0.000108 (0.019)
Del Peak 23(19p13 2)	6 (1%)	464	0.00498 (0.707)	0.00102 (0.165)	0.682 (1.00)	0.256 (1.00)	0.00664 (0.922)	0.00259 (0.387)	0.000641 (0.106)	0.000407 (0.0684)
Del Peak 13(10q23 31)	11 (2%)	459	6.4e-05 (0.0113)	0.0184 (1.00)	0.0336 (1.00)	0.0641 (1.00)	0.00424 (0.611)	0.00115 (0.187)	0.0315 (1.00)	0.0136 (1.00)
Amp Peak 1(Xq22 3)	16 (3%)	454	2.56e-06 (0.000486)	0.461 (1.00)	0.856 (1.00)	0.129 (1.00)	0.0422 (1.00)	0.0361 (1.00)	0.0704 (1.00)	0.0468 (1.00)
Del Peak 6(6q22 31)	6 (1%)	464	0.000427 (0.0712)	0.00547 (0.772)	0.0379 (1.00)	0.798 (1.00)	0.0173 (1.00)	0.00933 (1.00)	0.00877 (1.00)	0.00798 (1.00)
Del Peak 9(8p12)	4 (1%)	466	2.31e-05 (0.00416)	0.0474 (1.00)			0.0371 (1.00)	0.0346 (1.00)	0.00761 (1.00)	0.00564 (0.789)
Del Peak 11(9q21 13)	22 (5%)	448	4.31e-14 (8.7e-12)	0.155 (1.00)	0.182 (1.00)	0.0136 (1.00)	0.245 (1.00)	0.788 (1.00)	0.0282 (1.00)	0.0542 (1.00)
Del Peak 12(10q21 2)	11 (2%)	459	0.000788 (0.13)	0.0668 (1.00)	0.162 (1.00)	1 (1.00)	0.0513 (1.00)	0.148 (1.00)	0.373 (1.00)	0.609 (1.00)
Del Peak 14(11p15 1)	6 (1%)	464	9.28e-08 (1.85e-05)	0.0202 (1.00)	0.499 (1.00)	1 (1.00)	0.0495 (1.00)	0.166 (1.00)	0.0256 (1.00)	0.0361 (1.00)
Del Peak 15(13q12 3)	15 (3%)	455	0.0258 (1.00)	0.00123 (0.197)	0.388 (1.00)	0.44 (1.00)	0.00963 (1.00)	0.0448 (1.00)	0.0541 (1.00)	0.0258 (1.00)
Del Peak 17(15q25 3)	7 (1%)	463	0.00134 (0.213)	0.032 (1.00)	0.444 (1.00)	0.0817 (1.00)	0.0841 (1.00)	0.0672 (1.00)	0.0046 (0.658)	0.00247 (0.373)
Del Peak 21(18p11 21)	4 (1%)	466	0.000241 (0.0414)	0.191 (1.00)	1 (1.00)	0.369 (1.00)	0.242 (1.00)	0.0893 (1.00)	0.111 (1.00)	0.0414 (1.00)
Del Peak 22(18q22 2)	5 (1%)	465	0.00151 (0.233)	0.0616 (1.00)	1 (1.00)	0.256 (1.00)	0.12 (1.00)	0.0427 (1.00)	0.0395 (1.00)	0.0134 (1.00)
Del Peak 26(21q21 1)	8 (2%)	462	1.29e-05 (0.00242)	0.172 (1.00)	0.147 (1.00)	0.206 (1.00)	0.289 (1.00)	0.459 (1.00)	0.0516 (1.00)	0.0866 (1.00)
Del Peak 4(5p15 2)	3 (1%)	467	0.261 (1.00)	0.728 (1.00)
Del Peak 8(7q34)	4 (1%)	466	0.646 (1.00)	0.635 (1.00)			0.747 (1.00)	0.589 (1.00)	1 (1.00)	1 (1.00)
Del Peak 16(13q14 3)	18 (4%)	452	0.00717 (0.989)	0.0318 (1.00)	0.0908 (1.00)	1 (1.00)	0.0103 (1.00)	0.0249 (1.00)	0.0279 (1.00)	0.021 (1.00)
Del Peak 19(16q23 3)	6 (1%)	464	0.0518 (1.00)	0.126 (1.00)	0.444 (1.00)	0.103 (1.00)	0.127 (1.00)	0.111 (1.00)	0.194 (1.00)	0.292 (1.00)
Del Peak 20(17p13 1)	8 (2%)	462	0.0021 (0.322)	0.884 (1.00)	1 (1.00)	1 (1.00)	0.71 (1.00)	0.642 (1.00)	0.294 (1.00)	0.308 (1.00)
Del Peak 31(Xq22 1)	6 (1%)	464	0.0793 (1.00)	0.437 (1.00)	0.0993 (1.00)	0.12 (1.00)	0.671 (1.00)	0.861 (1.00)	0.522 (1.00)	0.386 (1.00)
Del Peak 32(Xq22 3)	4 (1%)	466	0.0568 (1.00)	0.0474 (1.00)	0.281 (1.00)	0.369 (1.00)	0.129 (1.00)	0.4 (1.00)	0.111 (1.00)	0.0414 (1.00)

'Amp Peak 1(Xq22.3) mutation analysis' versus 'CN_CNMF'

P value = 2.56e-06 (Fisher's exact test), Q value = 0.00049

Table S1. Gene #1: 'Amp Peak 1(Xq22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	363	73
AMP PEAK 1(XQ22.3) MUTATED	8	8	0
AMP PEAK 1(XQ22.3) WILD-TYPE	26	355	73

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(Xq22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 2(2p23.1) mutation analysis' versus 'CN_CNMF'

P value = 4.94e-10 (Fisher's exact test), Q value = 9.9e-08

Table S2. Gene #2: 'Del Peak 2(2p23.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	363	73
DEL PEAK 2(2P23.1) MUTATED	9	1	2
DEL PEAK 2(2P23.1) WILD-TYPE	25	362	71

Figure S2. Get High-res Image Gene #2: 'Del Peak 2(2p23.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 2(2p23.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.89e-05 (Fisher's exact test), Q value = 0.0052

Table S3. Gene #2: 'Del Peak 2(2p23.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	71	259
DEL PEAK 2(2P23.1) MUTATED	10	2	0
DEL PEAK 2(2P23.1) WILD-TYPE	130	69	259

Figure S3. Get High-res Image Gene #2: 'Del Peak 2(2p23.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 2(2p23.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.83e-05 (Fisher's exact test), Q value = 0.0034

Table S4. Gene #2: 'Del Peak 2(2p23.1) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	130	50	89	138
DEL PEAK 2(2P23.1) MUTATED	11	0	0	0
DEL PEAK 2(2P23.1) WILD-TYPE	119	50	89	138

Figure S4. Get High-res Image Gene #2: 'Del Peak 2(2p23.1) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 2(2p23.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.93e-05 (Fisher's exact test), Q value = 0.0036

Table S5. Gene #2: 'Del Peak 2(2p23.1) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	191	74
DEL PEAK 2(2P23.1) MUTATED	11	0	0
DEL PEAK 2(2P23.1) WILD-TYPE	131	191	74

Figure S5. Get High-res Image Gene #2: 'Del Peak 2(2p23.1) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 2(2p23.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.19e-06 (Fisher's exact test), Q value = 0.00023

Table S6. Gene #2: 'Del Peak 2(2p23.1) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	153	144
DEL PEAK 2(2P23.1) MUTATED	11	0	0
DEL PEAK 2(2P23.1) WILD-TYPE	115	153	144

Figure S6. Get High-res Image Gene #2: 'Del Peak 2(2p23.1) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'Del Peak 2(2p23.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.09e-07 (Fisher's exact test), Q value = 9.9e-05

Table S7. Gene #2: 'Del Peak 2(2p23.1) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	133	117
DEL PEAK 2(2P23.1) MUTATED	0	0	11
DEL PEAK 2(2P23.1) WILD-TYPE	173	133	106

Figure S7. Get High-res Image Gene #2: 'Del Peak 2(2p23.1) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 3(2q35) mutation analysis' versus 'CN_CNMF'

P value = 1.04e-11 (Fisher's exact test), Q value = 2.1e-09

Table S8. Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	363	73
DEL PEAK 3(2Q35) MUTATED	10	1	0
DEL PEAK 3(2Q35) WILD-TYPE	24	362	73

Figure S8. Get High-res Image Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 3(2q35) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.47e-05 (Fisher's exact test), Q value = 0.0044

Table S9. Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	71	259
DEL PEAK 3(2Q35) MUTATED	10	1	0
DEL PEAK 3(2Q35) WILD-TYPE	130	70	259

Figure S9. Get High-res Image Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 3(2q35) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.83e-05 (Fisher's exact test), Q value = 0.0034

Table S10. Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	130	50	89	138
DEL PEAK 3(2Q35) MUTATED	11	0	0	0
DEL PEAK 3(2Q35) WILD-TYPE	119	50	89	138

Figure S10. Get High-res Image Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 3(2q35) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.93e-05 (Fisher's exact test), Q value = 0.0036

Table S11. Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	191	74
DEL PEAK 3(2Q35) MUTATED	11	0	0
DEL PEAK 3(2Q35) WILD-TYPE	131	191	74

Figure S11. Get High-res Image Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 3(2q35) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.19e-06 (Fisher's exact test), Q value = 0.00023

Table S12. Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	153	144
DEL PEAK 3(2Q35) MUTATED	11	0	0
DEL PEAK 3(2Q35) WILD-TYPE	115	153	144

Figure S12. Get High-res Image Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'Del Peak 3(2q35) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.09e-07 (Fisher's exact test), Q value = 9.9e-05

Table S13. Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	133	117
DEL PEAK 3(2Q35) MUTATED	0	0	11
DEL PEAK 3(2Q35) WILD-TYPE	173	133	106

Figure S13. Get High-res Image Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 6(6q22.31) mutation analysis' versus 'CN_CNMF'

P value = 0.000427 (Fisher's exact test), Q value = 0.071

Table S14. Gene #5: 'Del Peak 6(6q22.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	363	73
DEL PEAK 6(6Q22.31) MUTATED	4	2	0
DEL PEAK 6(6Q22.31) WILD-TYPE	30	361	73

Figure S14. Get High-res Image Gene #5: 'Del Peak 6(6q22.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 9(8p12) mutation analysis' versus 'CN_CNMF'

P value = 2.31e-05 (Fisher's exact test), Q value = 0.0042

Table S15. Gene #7: 'Del Peak 9(8p12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	363	73
DEL PEAK 9(8P12) MUTATED	4	0	0
DEL PEAK 9(8P12) WILD-TYPE	30	363	73

Figure S15. Get High-res Image Gene #7: 'Del Peak 9(8p12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 10(8q24.22) mutation analysis' versus 'CN_CNMF'

P value = 5.43e-05 (Fisher's exact test), Q value = 0.0096

Table S16. Gene #8: 'Del Peak 10(8q24.22) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	363	73
DEL PEAK 10(8Q24.22) MUTATED	5	2	0
DEL PEAK 10(8Q24.22) WILD-TYPE	29	361	73

Figure S16. Get High-res Image Gene #8: 'Del Peak 10(8q24.22) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 10(8q24.22) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00122 (Fisher's exact test), Q value = 0.2

Table S17. Gene #8: 'Del Peak 10(8q24.22) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	191	74
DEL PEAK 10(8Q24.22) MUTATED	7	0	0
DEL PEAK 10(8Q24.22) WILD-TYPE	135	191	74

Figure S17. Get High-res Image Gene #8: 'Del Peak 10(8q24.22) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 10(8q24.22) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000185 (Fisher's exact test), Q value = 0.032

Table S18. Gene #8: 'Del Peak 10(8q24.22) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	153	144
DEL PEAK 10(8Q24.22) MUTATED	7	0	0
DEL PEAK 10(8Q24.22) WILD-TYPE	119	153	144

Figure S18. Get High-res Image Gene #8: 'Del Peak 10(8q24.22) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'Del Peak 10(8q24.22) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000108 (Fisher's exact test), Q value = 0.019

Table S19. Gene #8: 'Del Peak 10(8q24.22) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	133	117
DEL PEAK 10(8Q24.22) MUTATED	0	0	7
DEL PEAK 10(8Q24.22) WILD-TYPE	173	133	110

Figure S19. Get High-res Image Gene #8: 'Del Peak 10(8q24.22) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 11(9q21.13) mutation analysis' versus 'CN_CNMF'

P value = 4.31e-14 (Fisher's exact test), Q value = 8.7e-12

Table S20. Gene #9: 'Del Peak 11(9q21.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	363	73
DEL PEAK 11(9Q21.13) MUTATED	15	7	0
DEL PEAK 11(9Q21.13) WILD-TYPE	19	356	73

Figure S20. Get High-res Image Gene #9: 'Del Peak 11(9q21.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 12(10q21.2) mutation analysis' versus 'CN_CNMF'

P value = 0.000788 (Fisher's exact test), Q value = 0.13

Table S21. Gene #10: 'Del Peak 12(10q21.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	363	73
DEL PEAK 12(10Q21.2) MUTATED	5	6	0
DEL PEAK 12(10Q21.2) WILD-TYPE	29	357	73

Figure S21. Get High-res Image Gene #10: 'Del Peak 12(10q21.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 13(10q23.31) mutation analysis' versus 'CN_CNMF'

P value = 6.4e-05 (Fisher's exact test), Q value = 0.011

Table S22. Gene #11: 'Del Peak 13(10q23.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	363	73
DEL PEAK 13(10Q23.31) MUTATED	6	5	0
DEL PEAK 13(10Q23.31) WILD-TYPE	28	358	73

Figure S22. Get High-res Image Gene #11: 'Del Peak 13(10q23.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 13(10q23.31) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00115 (Fisher's exact test), Q value = 0.19

Table S23. Gene #11: 'Del Peak 13(10q23.31) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	191	74
DEL PEAK 13(10Q23.31) MUTATED	8	0	2
DEL PEAK 13(10Q23.31) WILD-TYPE	134	191	72

Figure S23. Get High-res Image Gene #11: 'Del Peak 13(10q23.31) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 14(11p15.1) mutation analysis' versus 'CN_CNMF'

P value = 9.28e-08 (Fisher's exact test), Q value = 1.8e-05

Table S24. Gene #12: 'Del Peak 14(11p15.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	363	73
DEL PEAK 14(11P15.1) MUTATED	6	0	0
DEL PEAK 14(11P15.1) WILD-TYPE	28	363	73

Figure S24. Get High-res Image Gene #12: 'Del Peak 14(11p15.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 15(13q12.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.00123 (Fisher's exact test), Q value = 0.2

Table S25. Gene #13: 'Del Peak 15(13q12.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	71	259
DEL PEAK 15(13Q12.3) MUTATED	10	3	2
DEL PEAK 15(13Q12.3) WILD-TYPE	130	68	257

Figure S25. Get High-res Image Gene #13: 'Del Peak 15(13q12.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 17(15q25.3) mutation analysis' versus 'CN_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.21

Table S26. Gene #15: 'Del Peak 17(15q25.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	363	73
DEL PEAK 17(15Q25.3) MUTATED	4	3	0
DEL PEAK 17(15Q25.3) WILD-TYPE	30	360	73

Figure S26. Get High-res Image Gene #15: 'Del Peak 17(15q25.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 21(18p11.21) mutation analysis' versus 'CN_CNMF'

P value = 0.000241 (Fisher's exact test), Q value = 0.041

Table S27. Gene #18: 'Del Peak 21(18p11.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	363	73
DEL PEAK 21(18P11.21) MUTATED	3	0	1
DEL PEAK 21(18P11.21) WILD-TYPE	31	363	72

Figure S27. Get High-res Image Gene #18: 'Del Peak 21(18p11.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 22(18q22.2) mutation analysis' versus 'CN_CNMF'

P value = 0.00151 (Fisher's exact test), Q value = 0.23

Table S28. Gene #19: 'Del Peak 22(18q22.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	363	73
DEL PEAK 22(18Q22.2) MUTATED	3	1	1
DEL PEAK 22(18Q22.2) WILD-TYPE	31	362	72

Figure S28. Get High-res Image Gene #19: 'Del Peak 22(18q22.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 23(19p13.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.17

Table S29. Gene #20: 'Del Peak 23(19p13.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	71	259
DEL PEAK 23(19P13.2) MUTATED	6	0	0
DEL PEAK 23(19P13.2) WILD-TYPE	134	71	259

Figure S29. Get High-res Image Gene #20: 'Del Peak 23(19p13.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 23(19p13.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000641 (Fisher's exact test), Q value = 0.11

Table S30. Gene #20: 'Del Peak 23(19p13.2) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	126	153	144
DEL PEAK 23(19P13.2) MUTATED	6	0	0
DEL PEAK 23(19P13.2) WILD-TYPE	120	153	144

Figure S30. Get High-res Image Gene #20: 'Del Peak 23(19p13.2) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'Del Peak 23(19p13.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000407 (Fisher's exact test), Q value = 0.068

Table S31. Gene #20: 'Del Peak 23(19p13.2) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	133	117
DEL PEAK 23(19P13.2) MUTATED	0	0	6
DEL PEAK 23(19P13.2) WILD-TYPE	173	133	111

Figure S31. Get High-res Image Gene #20: 'Del Peak 23(19p13.2) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 26(21q21.1) mutation analysis' versus 'CN_CNMF'

P value = 1.29e-05 (Fisher's exact test), Q value = 0.0024

Table S32. Gene #21: 'Del Peak 26(21q21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	363	73
DEL PEAK 26(21Q21.1) MUTATED	5	1	2
DEL PEAK 26(21Q21.1) WILD-TYPE	29	362	71

Figure S32. Get High-res Image Gene #21: 'Del Peak 26(21q21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 27(22q13.1) mutation analysis' versus 'CN_CNMF'

P value = 5.8e-86 (Fisher's exact test), Q value = 1.2e-83

Table S33. Gene #22: 'Del Peak 27(22q13.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	363	73
DEL PEAK 27(22Q13.1) MUTATED	8	0	73
DEL PEAK 27(22Q13.1) WILD-TYPE	26	363	0

Figure S33. Get High-res Image Gene #22: 'Del Peak 27(22q13.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 27(22q13.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000321 (Fisher's exact test), Q value = 0.055

Table S34. Gene #22: 'Del Peak 27(22q13.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	71	259
DEL PEAK 27(22Q13.1) MUTATED	39	6	36
DEL PEAK 27(22Q13.1) WILD-TYPE	101	65	223

Figure S34. Get High-res Image Gene #22: 'Del Peak 27(22q13.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 27(22q13.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.11e-07 (Fisher's exact test), Q value = 6.1e-05

Table S35. Gene #22: 'Del Peak 27(22q13.1) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	130	50	89	138
DEL PEAK 27(22Q13.1) MUTATED	36	4	21	7
DEL PEAK 27(22Q13.1) WILD-TYPE	94	46	68	131

Figure S35. Get High-res Image Gene #22: 'Del Peak 27(22q13.1) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 27(22q13.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0037

Table S36. Gene #22: 'Del Peak 27(22q13.1) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	191	74
DEL PEAK 27(22Q13.1) MUTATED	36	15	17
DEL PEAK 27(22Q13.1) WILD-TYPE	106	176	57

Figure S36. Get High-res Image Gene #22: 'Del Peak 27(22q13.1) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 27(22q13.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00144 (Fisher's exact test), Q value = 0.23

Table S37. Gene #22: 'Del Peak 27(22q13.1) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	133	117
DEL PEAK 27(22Q13.1) MUTATED	21	19	33
DEL PEAK 27(22Q13.1) WILD-TYPE	152	114	84

Figure S37. Get High-res Image Gene #22: 'Del Peak 27(22q13.1) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 28(22q13.2) mutation analysis' versus 'CN_CNMF'

P value = 5.8e-86 (Fisher's exact test), Q value = 1.2e-83

Table S38. Gene #23: 'Del Peak 28(22q13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	363	73
DEL PEAK 28(22Q13.2) MUTATED	8	0	73
DEL PEAK 28(22Q13.2) WILD-TYPE	26	363	0

Figure S38. Get High-res Image Gene #23: 'Del Peak 28(22q13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 28(22q13.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000321 (Fisher's exact test), Q value = 0.055

Table S39. Gene #23: 'Del Peak 28(22q13.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	71	259
DEL PEAK 28(22Q13.2) MUTATED	39	6	36
DEL PEAK 28(22Q13.2) WILD-TYPE	101	65	223

Figure S39. Get High-res Image Gene #23: 'Del Peak 28(22q13.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 28(22q13.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.11e-07 (Fisher's exact test), Q value = 6.1e-05

Table S40. Gene #23: 'Del Peak 28(22q13.2) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	130	50	89	138
DEL PEAK 28(22Q13.2) MUTATED	36	4	21	7
DEL PEAK 28(22Q13.2) WILD-TYPE	94	46	68	131

Figure S40. Get High-res Image Gene #23: 'Del Peak 28(22q13.2) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 28(22q13.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0037

Table S41. Gene #23: 'Del Peak 28(22q13.2) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	191	74
DEL PEAK 28(22Q13.2) MUTATED	36	15	17
DEL PEAK 28(22Q13.2) WILD-TYPE	106	176	57

Figure S41. Get High-res Image Gene #23: 'Del Peak 28(22q13.2) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 28(22q13.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00144 (Fisher's exact test), Q value = 0.23

Table S42. Gene #23: 'Del Peak 28(22q13.2) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	133	117
DEL PEAK 28(22Q13.2) MUTATED	21	19	33
DEL PEAK 28(22Q13.2) WILD-TYPE	152	114	84

Figure S42. Get High-res Image Gene #23: 'Del Peak 28(22q13.2) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 29(22q13.31) mutation analysis' versus 'CN_CNMF'

P value = 5.8e-86 (Fisher's exact test), Q value = 1.2e-83

Table S43. Gene #24: 'Del Peak 29(22q13.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	363	73
DEL PEAK 29(22Q13.31) MUTATED	8	0	73
DEL PEAK 29(22Q13.31) WILD-TYPE	26	363	0

Figure S43. Get High-res Image Gene #24: 'Del Peak 29(22q13.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 29(22q13.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000321 (Fisher's exact test), Q value = 0.055

Table S44. Gene #24: 'Del Peak 29(22q13.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	71	259
DEL PEAK 29(22Q13.31) MUTATED	39	6	36
DEL PEAK 29(22Q13.31) WILD-TYPE	101	65	223

Figure S44. Get High-res Image Gene #24: 'Del Peak 29(22q13.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 29(22q13.31) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.11e-07 (Fisher's exact test), Q value = 6.1e-05

Table S45. Gene #24: 'Del Peak 29(22q13.31) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	130	50	89	138
DEL PEAK 29(22Q13.31) MUTATED	36	4	21	7
DEL PEAK 29(22Q13.31) WILD-TYPE	94	46	68	131

Figure S45. Get High-res Image Gene #24: 'Del Peak 29(22q13.31) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 29(22q13.31) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0037

Table S46. Gene #24: 'Del Peak 29(22q13.31) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	191	74
DEL PEAK 29(22Q13.31) MUTATED	36	15	17
DEL PEAK 29(22Q13.31) WILD-TYPE	106	176	57

Figure S46. Get High-res Image Gene #24: 'Del Peak 29(22q13.31) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 29(22q13.31) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00144 (Fisher's exact test), Q value = 0.23

Table S47. Gene #24: 'Del Peak 29(22q13.31) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	133	117
DEL PEAK 29(22Q13.31) MUTATED	21	19	33
DEL PEAK 29(22Q13.31) WILD-TYPE	152	114	84

Figure S47. Get High-res Image Gene #24: 'Del Peak 29(22q13.31) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 30(22q13.32) mutation analysis' versus 'CN_CNMF'

P value = 4.47e-84 (Fisher's exact test), Q value = 9.1e-82

Table S48. Gene #25: 'Del Peak 30(22q13.32) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	363	73
DEL PEAK 30(22Q13.32) MUTATED	8	1	73
DEL PEAK 30(22Q13.32) WILD-TYPE	26	362	0

Figure S48. Get High-res Image Gene #25: 'Del Peak 30(22q13.32) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 30(22q13.32) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000162 (Fisher's exact test), Q value = 0.028

Table S49. Gene #25: 'Del Peak 30(22q13.32) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	71	259
DEL PEAK 30(22Q13.32) MUTATED	40	6	36
DEL PEAK 30(22Q13.32) WILD-TYPE	100	65	223

Figure S49. Get High-res Image Gene #25: 'Del Peak 30(22q13.32) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 30(22q13.32) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.64e-07 (Fisher's exact test), Q value = 3.3e-05

Table S50. Gene #25: 'Del Peak 30(22q13.32) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	130	50	89	138
DEL PEAK 30(22Q13.32) MUTATED	37	4	21	7
DEL PEAK 30(22Q13.32) WILD-TYPE	93	46	68	131

Figure S50. Get High-res Image Gene #25: 'Del Peak 30(22q13.32) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 30(22q13.32) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.17e-05 (Fisher's exact test), Q value = 0.0022

Table S51. Gene #25: 'Del Peak 30(22q13.32) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	191	74
DEL PEAK 30(22Q13.32) MUTATED	37	15	17
DEL PEAK 30(22Q13.32) WILD-TYPE	105	176	57

Figure S51. Get High-res Image Gene #25: 'Del Peak 30(22q13.32) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 30(22q13.32) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000846 (Fisher's exact test), Q value = 0.14

Table S52. Gene #25: 'Del Peak 30(22q13.32) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	133	117
DEL PEAK 30(22Q13.32) MUTATED	21	19	34
DEL PEAK 30(22Q13.32) WILD-TYPE	152	114	83

Figure S52. Get High-res Image Gene #25: 'Del Peak 30(22q13.32) mutation analysis' versus Clinical Feature #8: '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 = THCA-TP.transferedmergedcluster.txt
Number of patients = 470
Number of copy number variation regions = 27
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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