Correlation between copy number variation genes and molecular subtypes

Liver Hepatocellular Carcinoma (Primary solid tumor)

23 September 2013 | analyses__2013_09_23

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1QC01V0

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 53 peak regions and 8 molecular subtypes across 139 patients, 20 significant findings detected with Q value < 0.25.

Amp Peak 2(1q22) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 6(3q26.31) cnvs correlated to 'CN_CNMF'.
Amp Peak 10(6p21.1) cnvs correlated to 'METHLYATION_CNMF'.
Amp Peak 12(8q13.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 13(8q24.13) cnvs correlated to 'CN_CNMF'.
Amp Peak 18(13q32.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 23(19p13.12) cnvs correlated to 'MIRSEQ_MATURE_CNMF'.
Del Peak 5(3p13) cnvs correlated to 'MRNASEQ_CNMF'.
Del Peak 7(4q25) cnvs correlated to 'CN_CNMF'.
Del Peak 8(4q35.1) cnvs correlated to 'CN_CNMF'.
Del Peak 12(8p23.2) cnvs correlated to 'CN_CNMF'.
Del Peak 13(8p11.22) cnvs correlated to 'CN_CNMF'.
Del Peak 16(10q23.31) cnvs correlated to 'MRNASEQ_CNMF'.
Del Peak 20(13q14.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 21(13q22.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 22(14q23.3) cnvs correlated to 'MRNASEQ_CNMF'.
Del Peak 24(17p13.3) 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 53 regions and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 20 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	Chi-square test	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Amp Peak 2(1q22)	0 (0%)	39	9.39e-07 (0.000394)	7.03e-05 (0.0292)	0.215 (1.00)	0.603 (1.00)	0.13 (1.00)	0.0591 (1.00)	0.0908 (1.00)	0.459 (1.00)
Del Peak 20(13q14 2)	0 (0%)	76	2.03e-06 (0.000847)	0.23 (1.00)	9.13e-05 (0.0378)	0.0169 (1.00)	0.00181 (0.715)	0.109 (1.00)	0.00652 (1.00)	0.179 (1.00)
Del Peak 21(13q22 2)	0 (0%)	88	0.000431 (0.176)	0.148 (1.00)	0.000493 (0.2)	0.188 (1.00)	0.0328 (1.00)	0.486 (1.00)	0.0595 (1.00)	0.475 (1.00)
Amp Peak 6(3q26 31)	0 (0%)	113	0.000317 (0.13)	0.0256 (1.00)	0.109 (1.00)	0.079 (1.00)	0.0385 (1.00)	0.0212 (1.00)	0.654 (1.00)	0.0206 (1.00)
Amp Peak 10(6p21 1)	0 (0%)	82	0.00467 (1.00)	0.000112 (0.0461)	0.00375 (1.00)	0.973 (1.00)	0.93 (1.00)	0.653 (1.00)	0.338 (1.00)	0.822 (1.00)
Amp Peak 12(8q13 1)	0 (0%)	70	3.51e-09 (1.48e-06)	0.574 (1.00)	0.00322 (1.00)	0.347 (1.00)	0.229 (1.00)	0.803 (1.00)	0.39 (1.00)	0.882 (1.00)
Amp Peak 13(8q24 13)	0 (0%)	58	1.75e-08 (7.36e-06)	0.306 (1.00)	0.00317 (1.00)	0.409 (1.00)	0.336 (1.00)	0.773 (1.00)	0.571 (1.00)	0.826 (1.00)
Amp Peak 18(13q32 3)	0 (0%)	113	0.000372 (0.152)	0.0405 (1.00)	0.0714 (1.00)	0.0373 (1.00)	0.19 (1.00)	0.346 (1.00)	0.846 (1.00)	0.451 (1.00)
Amp Peak 23(19p13 12)	0 (0%)	104	0.0418 (1.00)	0.00125 (0.495)	0.000869 (0.347)	0.00566 (1.00)	0.0126 (1.00)	0.0865 (1.00)	0.000159 (0.0655)	0.23 (1.00)
Del Peak 5(3p13)	0 (0%)	117	0.0258 (1.00)	0.127 (1.00)	3.88e-05 (0.0161)	0.00117 (0.464)	0.0961 (1.00)	0.329 (1.00)	0.064 (1.00)	0.0387 (1.00)
Del Peak 7(4q25)	0 (0%)	75	6.25e-07 (0.000263)	0.00812 (1.00)	0.00584 (1.00)	0.147 (1.00)	0.767 (1.00)	0.91 (1.00)	0.506 (1.00)	0.827 (1.00)
Del Peak 8(4q35 1)	0 (0%)	80	0.000487 (0.198)	0.00279 (1.00)	0.0074 (1.00)	0.263 (1.00)	0.923 (1.00)	0.682 (1.00)	1 (1.00)	0.548 (1.00)
Del Peak 12(8p23 2)	0 (0%)	55	1.28e-15 (5.43e-13)	0.0693 (1.00)	0.584 (1.00)	0.617 (1.00)	0.568 (1.00)	0.504 (1.00)	1 (1.00)	0.456 (1.00)
Del Peak 13(8p11 22)	0 (0%)	72	7.27e-15 (3.07e-12)	0.367 (1.00)	0.816 (1.00)	0.507 (1.00)	0.754 (1.00)	0.338 (1.00)	0.626 (1.00)	0.17 (1.00)
Del Peak 16(10q23 31)	0 (0%)	92	0.00192 (0.755)	0.622 (1.00)	0.000277 (0.114)	0.0419 (1.00)	0.0407 (1.00)	0.131 (1.00)	0.0549 (1.00)	0.381 (1.00)
Del Peak 22(14q23 3)	0 (0%)	90	0.134 (1.00)	0.0609 (1.00)	0.000548 (0.222)	0.00495 (1.00)	0.247 (1.00)	0.101 (1.00)	0.196 (1.00)	0.0615 (1.00)
Del Peak 24(17p13 3)	0 (0%)	62	3.32e-06 (0.00138)	0.216 (1.00)	0.00553 (1.00)	0.0665 (1.00)	0.00315 (1.00)	0.00225 (0.877)	0.0313 (1.00)	0.00203 (0.792)
Amp Peak 1(1p22 3)	0 (0%)	102	0.00189 (0.744)	0.0813 (1.00)	0.0213 (1.00)	0.0347 (1.00)	0.529 (1.00)	0.669 (1.00)	0.534 (1.00)	0.727 (1.00)
Amp Peak 3(1q42 3)	0 (0%)	44	0.00324 (1.00)	0.00801 (1.00)	0.885 (1.00)	0.284 (1.00)	0.733 (1.00)	0.27 (1.00)	0.405 (1.00)	0.302 (1.00)
Amp Peak 4(2p24 1)	0 (0%)	110	0.000838 (0.336)	0.814 (1.00)	0.0376 (1.00)	0.0394 (1.00)	0.316 (1.00)	0.511 (1.00)	0.73 (1.00)	0.366 (1.00)
Amp Peak 5(2q31 2)	0 (0%)	110	0.00924 (1.00)	0.583 (1.00)	0.399 (1.00)	0.48 (1.00)	0.419 (1.00)	1 (1.00)	0.73 (1.00)	0.721 (1.00)
Amp Peak 7(5p15 33)	0 (0%)	71	0.00296 (1.00)	0.241 (1.00)	0.525 (1.00)	0.947 (1.00)	0.239 (1.00)	0.0901 (1.00)	0.52 (1.00)	0.234 (1.00)
Amp Peak 8(5q35 3)	0 (0%)	92	0.02 (1.00)	0.653 (1.00)	0.859 (1.00)	0.377 (1.00)	0.254 (1.00)	0.473 (1.00)	0.314 (1.00)	0.198 (1.00)
Amp Peak 9(6p25 2)	0 (0%)	81	0.00262 (1.00)	0.00335 (1.00)	0.0282 (1.00)	0.194 (1.00)	0.941 (1.00)	0.936 (1.00)	0.454 (1.00)	0.968 (1.00)
Amp Peak 11(7q21 2)	0 (0%)	89	0.18 (1.00)	0.153 (1.00)	0.192 (1.00)	0.342 (1.00)	0.151 (1.00)	0.0914 (1.00)	0.842 (1.00)	0.231 (1.00)
Amp Peak 14(9q34 2)	0 (0%)	121	0.165 (1.00)	0.0488 (1.00)	0.285 (1.00)	0.0679 (1.00)	0.373 (1.00)	0.193 (1.00)	0.64 (1.00)	0.0109 (1.00)
Amp Peak 15(10p15 1)	0 (0%)	109	0.517 (1.00)	0.15 (1.00)	0.294 (1.00)	0.329 (1.00)	0.815 (1.00)	0.835 (1.00)	0.162 (1.00)	0.915 (1.00)
Amp Peak 16(11q13 3)	0 (0%)	114	0.0611 (1.00)	1 (1.00)	0.0497 (1.00)	0.623 (1.00)	0.0576 (1.00)	0.255 (1.00)	0.0333 (1.00)	0.395 (1.00)
Amp Peak 17(12q23 1)	0 (0%)	113	0.0232 (1.00)	0.391 (1.00)	0.237 (1.00)	0.0626 (1.00)	0.839 (1.00)	0.819 (1.00)	0.883 (1.00)	0.951 (1.00)
Amp Peak 19(15q26 3)	0 (0%)	117	0.0245 (1.00)	0.819 (1.00)	0.433 (1.00)	0.197 (1.00)	0.458 (1.00)	0.436 (1.00)	0.908 (1.00)	0.384 (1.00)
Amp Peak 20(17p11 2)	0 (0%)	120	0.61 (1.00)	0.938 (1.00)	0.132 (1.00)	0.0768 (1.00)	0.872 (1.00)	0.938 (1.00)	1 (1.00)	0.939 (1.00)
Amp Peak 21(17q23 1)	0 (0%)	82	0.00811 (1.00)	0.195 (1.00)	0.129 (1.00)	0.281 (1.00)	0.509 (1.00)	0.635 (1.00)	0.707 (1.00)	0.431 (1.00)
Amp Peak 22(17q25 3)	0 (0%)	79	0.000934 (0.373)	0.0398 (1.00)	0.13 (1.00)	0.801 (1.00)	0.339 (1.00)	0.492 (1.00)	0.364 (1.00)	0.325 (1.00)
Amp Peak 24(19q13 11)	0 (0%)	96	0.0717 (1.00)	0.155 (1.00)	0.0151 (1.00)	0.183 (1.00)	0.255 (1.00)	0.162 (1.00)	0.0666 (1.00)	0.318 (1.00)
Amp Peak 25(20q13 33)	0 (0%)	87	0.00196 (0.767)	0.0464 (1.00)	0.0202 (1.00)	0.0603 (1.00)	0.585 (1.00)	0.906 (1.00)	0.319 (1.00)	0.821 (1.00)
Del Peak 1(1p36 32)	0 (0%)	78	0.0165 (1.00)	0.0105 (1.00)	0.041 (1.00)	0.263 (1.00)	0.819 (1.00)	0.774 (1.00)	0.948 (1.00)	0.619 (1.00)
Del Peak 2(1p35 2)	0 (0%)	90	0.0324 (1.00)	0.00625 (1.00)	0.0599 (1.00)	0.0319 (1.00)	0.424 (1.00)	0.165 (1.00)	0.649 (1.00)	0.0969 (1.00)
Del Peak 3(2q22 1)	0 (0%)	123	0.119 (1.00)	0.0872 (1.00)	0.0442 (1.00)	0.643 (1.00)	0.0316 (1.00)	0.00855 (1.00)	0.526 (1.00)	0.0181 (1.00)
Del Peak 4(2q37 3)	0 (0%)	112	0.00333 (1.00)	0.804 (1.00)	0.000708 (0.285)	0.251 (1.00)	0.0704 (1.00)	0.0421 (1.00)	0.437 (1.00)	0.114 (1.00)
Del Peak 6(4p16 1)	0 (0%)	111	0.308 (1.00)	0.0298 (1.00)	0.316 (1.00)	0.391 (1.00)	0.64 (1.00)	0.582 (1.00)	0.157 (1.00)	0.217 (1.00)
Del Peak 9(5q23 1)	0 (0%)	120	0.284 (1.00)	0.149 (1.00)	0.91 (1.00)	0.211 (1.00)	0.336 (1.00)	0.643 (1.00)	0.621 (1.00)	0.461 (1.00)
Del Peak 10(6q16 3)	0 (0%)	91	0.00903 (1.00)	0.525 (1.00)	0.00239 (0.924)	0.134 (1.00)	0.137 (1.00)	0.41 (1.00)	0.701 (1.00)	0.33 (1.00)
Del Peak 11(6q26)	0 (0%)	86	0.00211 (0.824)	0.165 (1.00)	0.00894 (1.00)	0.0504 (1.00)	0.00496 (1.00)	0.111 (1.00)	0.481 (1.00)	0.0643 (1.00)
Del Peak 14(9p21 3)	0 (0%)	89	0.00656 (1.00)	0.766 (1.00)	0.0777 (1.00)	0.239 (1.00)	0.679 (1.00)	0.581 (1.00)	1 (1.00)	0.359 (1.00)
Del Peak 15(9q34 3)	0 (0%)	91	0.00082 (0.33)	0.0839 (1.00)	0.0348 (1.00)	0.235 (1.00)	0.94 (1.00)	0.297 (1.00)	0.792 (1.00)	0.152 (1.00)
Del Peak 17(11q23 3)	0 (0%)	109	0.219 (1.00)	0.445 (1.00)	0.155 (1.00)	0.165 (1.00)	0.777 (1.00)	0.659 (1.00)	0.0172 (1.00)	0.55 (1.00)
Del Peak 18(12p12 1)	0 (0%)	107	0.0145 (1.00)	0.382 (1.00)	0.00276 (1.00)	0.329 (1.00)	0.312 (1.00)	0.214 (1.00)	0.268 (1.00)	0.323 (1.00)
Del Peak 19(12q24 33)	0 (0%)	115	0.00496 (1.00)	0.204 (1.00)	0.0968 (1.00)	0.322 (1.00)	0.891 (1.00)	0.724 (1.00)	0.768 (1.00)	0.621 (1.00)
Del Peak 23(16q23 1)	0 (0%)	81	0.0139 (1.00)	0.00936 (1.00)	0.00233 (0.905)	0.0198 (1.00)	0.283 (1.00)	0.0998 (1.00)	0.746 (1.00)	0.105 (1.00)
Del Peak 25(17p11 2)	0 (0%)	62	0.0013 (0.515)	0.298 (1.00)	0.0641 (1.00)	0.0252 (1.00)	0.000628 (0.254)	0.00349 (1.00)	0.177 (1.00)	0.0025 (0.964)
Del Peak 26(18q21 2)	0 (0%)	111	0.0163 (1.00)	0.0151 (1.00)	0.0777 (1.00)	0.695 (1.00)	0.321 (1.00)	0.582 (1.00)	0.641 (1.00)	0.459 (1.00)
Del Peak 27(19p13 3)	0 (0%)	107	0.0789 (1.00)	0.0169 (1.00)	0.00841 (1.00)	0.41 (1.00)	0.157 (1.00)	0.191 (1.00)	0.6 (1.00)	0.105 (1.00)
Del Peak 28(22q13 32)	0 (0%)	100	0.0549 (1.00)	0.55 (1.00)	0.0844 (1.00)	0.629 (1.00)	0.879 (1.00)	0.265 (1.00)	0.968 (1.00)	0.763 (1.00)

'Amp Peak 2(1q22)' versus 'CN_CNMF'

P value = 9.39e-07 (Fisher's exact test), Q value = 0.00039

Table S1. Gene #2: 'Amp Peak 2(1q22)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	48	52
AMP PEAK 2(1Q22) CNV	33	21	46
AMP PEAK 2(1Q22) WILD-TYPE	6	27	6

Figure S1. Get High-res Image Gene #2: 'Amp Peak 2(1q22)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 2(1q22)' versus 'METHLYATION_CNMF'

P value = 7.03e-05 (Fisher's exact test), Q value = 0.029

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	35	56
AMP PEAK 2(1Q22) CNV	14	29	48
AMP PEAK 2(1Q22) WILD-TYPE	18	6	8

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

'Amp Peak 6(3q26.31)' versus 'CN_CNMF'

P value = 0.000317 (Fisher's exact test), Q value = 0.13

Table S3. Gene #6: 'Amp Peak 6(3q26.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	48	52
AMP PEAK 6(3Q26.31) CNV	3	4	19
AMP PEAK 6(3Q26.31) WILD-TYPE	36	44	33

Figure S3. Get High-res Image Gene #6: 'Amp Peak 6(3q26.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 10(6p21.1)' versus 'METHLYATION_CNMF'

P value = 0.000112 (Fisher's exact test), Q value = 0.046

Table S4. Gene #10: 'Amp Peak 10(6p21.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	35	56
AMP PEAK 10(6P21.1) CNV	4	16	32
AMP PEAK 10(6P21.1) WILD-TYPE	28	19	24

Figure S4. Get High-res Image Gene #10: 'Amp Peak 10(6p21.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 12(8q13.1)' versus 'CN_CNMF'

P value = 3.51e-09 (Fisher's exact test), Q value = 1.5e-06

Table S5. Gene #12: 'Amp Peak 12(8q13.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	48	52
AMP PEAK 12(8Q13.1) CNV	35	14	20
AMP PEAK 12(8Q13.1) WILD-TYPE	4	34	32

Figure S5. Get High-res Image Gene #12: 'Amp Peak 12(8q13.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 13(8q24.13)' versus 'CN_CNMF'

P value = 1.75e-08 (Fisher's exact test), Q value = 7.4e-06

Table S6. Gene #13: 'Amp Peak 13(8q24.13)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	48	52
AMP PEAK 13(8Q24.13) CNV	37	19	25
AMP PEAK 13(8Q24.13) WILD-TYPE	2	29	27

Figure S6. Get High-res Image Gene #13: 'Amp Peak 13(8q24.13)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 18(13q32.3)' versus 'CN_CNMF'

P value = 0.000372 (Fisher's exact test), Q value = 0.15

Table S7. Gene #18: 'Amp Peak 18(13q32.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	48	52
AMP PEAK 18(13Q32.3) CNV	6	2	18
AMP PEAK 18(13Q32.3) WILD-TYPE	33	46	34

Figure S7. Get High-res Image Gene #18: 'Amp Peak 18(13q32.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 23(19p13.12)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000159 (Fisher's exact test), Q value = 0.065

Table S8. Gene #23: 'Amp Peak 23(19p13.12)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	62	43
AMP PEAK 23(19P13.12) CNV	4	9	21
AMP PEAK 23(19P13.12) WILD-TYPE	25	53	22

Figure S8. Get High-res Image Gene #23: 'Amp Peak 23(19p13.12)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'Del Peak 5(3p13)' versus 'MRNASEQ_CNMF'

P value = 3.88e-05 (Chi-square test), Q value = 0.016

Table S9. Gene #30: 'Del Peak 5(3p13)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	18	27	25	31
DEL PEAK 5(3P13) CNV	14	2	1	1	3
DEL PEAK 5(3P13) WILD-TYPE	18	16	26	24	28

Figure S9. Get High-res Image Gene #30: 'Del Peak 5(3p13)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 7(4q25)' versus 'CN_CNMF'

P value = 6.25e-07 (Fisher's exact test), Q value = 0.00026

Table S10. Gene #32: 'Del Peak 7(4q25)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	48	52
DEL PEAK 7(4Q25) CNV	12	13	39
DEL PEAK 7(4Q25) WILD-TYPE	27	35	13

Figure S10. Get High-res Image Gene #32: 'Del Peak 7(4q25)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 8(4q35.1)' versus 'CN_CNMF'

P value = 0.000487 (Fisher's exact test), Q value = 0.2

Table S11. Gene #33: 'Del Peak 8(4q35.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	48	52
DEL PEAK 8(4Q35.1) CNV	13	13	33
DEL PEAK 8(4Q35.1) WILD-TYPE	26	35	19

Figure S11. Get High-res Image Gene #33: 'Del Peak 8(4q35.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 12(8p23.2)' versus 'CN_CNMF'

P value = 1.28e-15 (Fisher's exact test), Q value = 5.4e-13

Table S12. Gene #37: 'Del Peak 12(8p23.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	48	52
DEL PEAK 12(8P23.2) CNV	39	10	35
DEL PEAK 12(8P23.2) WILD-TYPE	0	38	17

Figure S12. Get High-res Image Gene #37: 'Del Peak 12(8p23.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 13(8p11.22)' versus 'CN_CNMF'

P value = 7.27e-15 (Fisher's exact test), Q value = 3.1e-12

Table S13. Gene #38: 'Del Peak 13(8p11.22)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	48	52
DEL PEAK 13(8P11.22) CNV	33	3	31
DEL PEAK 13(8P11.22) WILD-TYPE	6	45	21

Figure S13. Get High-res Image Gene #38: 'Del Peak 13(8p11.22)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 0.000277 (Chi-square test), Q value = 0.11

Table S14. Gene #41: 'Del Peak 16(10q23.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	18	27	25	31
DEL PEAK 16(10Q23.31) CNV	11	12	4	3	15
DEL PEAK 16(10Q23.31) WILD-TYPE	21	6	23	22	16

Figure S14. Get High-res Image Gene #41: 'Del Peak 16(10q23.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 20(13q14.2)' versus 'CN_CNMF'

P value = 2.03e-06 (Fisher's exact test), Q value = 0.00085

Table S15. Gene #45: 'Del Peak 20(13q14.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	48	52
DEL PEAK 20(13Q14.2) CNV	12	13	38
DEL PEAK 20(13Q14.2) WILD-TYPE	27	35	14

Figure S15. Get High-res Image Gene #45: 'Del Peak 20(13q14.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 20(13q14.2)' versus 'MRNASEQ_CNMF'

P value = 9.13e-05 (Chi-square test), Q value = 0.038

Table S16. Gene #45: 'Del Peak 20(13q14.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	18	27	25	31
DEL PEAK 20(13Q14.2) CNV	23	10	7	4	17
DEL PEAK 20(13Q14.2) WILD-TYPE	9	8	20	21	14

Figure S16. Get High-res Image Gene #45: 'Del Peak 20(13q14.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 21(13q22.2)' versus 'CN_CNMF'

P value = 0.000431 (Fisher's exact test), Q value = 0.18

Table S17. Gene #46: 'Del Peak 21(13q22.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	48	52
DEL PEAK 21(13Q22.2) CNV	9	12	30
DEL PEAK 21(13Q22.2) WILD-TYPE	30	36	22

Figure S17. Get High-res Image Gene #46: 'Del Peak 21(13q22.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 21(13q22.2)' versus 'MRNASEQ_CNMF'

P value = 0.000493 (Chi-square test), Q value = 0.2

Table S18. Gene #46: 'Del Peak 21(13q22.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	18	27	25	31
DEL PEAK 21(13Q22.2) CNV	20	5	5	4	15
DEL PEAK 21(13Q22.2) WILD-TYPE	12	13	22	21	16

Figure S18. Get High-res Image Gene #46: 'Del Peak 21(13q22.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 22(14q23.3)' versus 'MRNASEQ_CNMF'

P value = 0.000548 (Chi-square test), Q value = 0.22

Table S19. Gene #47: 'Del Peak 22(14q23.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	32	18	27	25	31
DEL PEAK 22(14Q23.3) CNV	15	13	5	4	11
DEL PEAK 22(14Q23.3) WILD-TYPE	17	5	22	21	20

Figure S19. Get High-res Image Gene #47: 'Del Peak 22(14q23.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 24(17p13.3)' versus 'CN_CNMF'

P value = 3.32e-06 (Fisher's exact test), Q value = 0.0014

Table S20. Gene #49: 'Del Peak 24(17p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	48	52
DEL PEAK 24(17P13.3) CNV	12	23	42
DEL PEAK 24(17P13.3) WILD-TYPE	27	25	10

Figure S20. Get High-res Image Gene #49: 'Del Peak 24(17p13.3)' 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 = LIHC-TP.transferedmergedcluster.txt
Number of patients = 139
Number of copy number variation regions = 53
Number of molecular subtypes = 8
Exclude regions that fewer than K tumors have alterations, K = 3

Fisher's exact test

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

Chi-square test

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

Q value calculation

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

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

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

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

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

[4] GISTIC_version2

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