Correlation between copy number variation genes and molecular subtypes

Liver Hepatocellular Carcinoma (Primary solid tumor)

23 May 2013 | analyses__2013_05_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/C1QV3JKK

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 52 peak regions and 8 molecular subtypes across 108 patients, 23 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 8(5p15.33) cnvs correlated to 'CN_CNMF'.
Amp Peak 11(6p21.1) cnvs correlated to 'METHLYATION_CNMF'.
Amp Peak 14(8q11.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 15(8q24.13) cnvs correlated to 'CN_CNMF'.
Amp Peak 23(17q25.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 24(19p13.12) cnvs correlated to 'MIRSEQ_MATURE_CNMF'.
Del Peak 5(3p13) cnvs correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CNMF'.
Del Peak 6(4q24) cnvs correlated to 'CN_CNMF'.
Del Peak 7(4q35.1) cnvs correlated to 'CN_CNMF'.
Del Peak 10(8p23.3) cnvs correlated to 'CN_CNMF'.
Del Peak 11(8p23.2) cnvs correlated to 'CN_CNMF'.
Del Peak 12(8p21.1) cnvs correlated to 'CN_CNMF'.
Del Peak 15(10q24.33) cnvs correlated to 'MIRSEQ_MATURE_CNMF'.
Del Peak 19(13q14.2) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
Del Peak 20(14q23.3) cnvs correlated to 'CN_CNMF'.
Del Peak 21(14q32.33) cnvs correlated to 'CN_CNMF'.
Del Peak 23(17p12) cnvs correlated to 'MIRSEQ_MATURE_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 52 regions and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 23 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	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test
Amp Peak 2(1q22)	0 (0%)	30	0.000625 (0.246)	3.41e-05 (0.0137)	0.131 (1.00)	0.581 (1.00)	0.412 (1.00)	0.723 (1.00)	0.269 (1.00)	0.3 (1.00)
Del Peak 5(3p13)	0 (0%)	90	0.131 (1.00)	0.0925 (1.00)	0.00238 (0.919)	0.000163 (0.0653)	0.0355 (1.00)	1 (1.00)	3.78e-06 (0.00155)	0.264 (1.00)
Del Peak 19(13q14 2)	0 (0%)	61	1.24e-05 (0.00504)	0.185 (1.00)	0.0283 (1.00)	0.0938 (1.00)	0.0531 (1.00)	0.525 (1.00)	0.000299 (0.119)	0.12 (1.00)
Del Peak 23(17p12)	0 (0%)	46	0.00534 (1.00)	0.239 (1.00)	0.121 (1.00)	0.139 (1.00)	0.00447 (1.00)	0.0258 (1.00)	0.000473 (0.187)	0.000433 (0.171)
Amp Peak 6(3q26 31)	0 (0%)	87	2.91e-05 (0.0118)	0.0486 (1.00)	0.126 (1.00)	1 (1.00)	0.378 (1.00)	0.224 (1.00)	0.375 (1.00)	0.0461 (1.00)
Amp Peak 8(5p15 33)	0 (0%)	55	0.000135 (0.0543)	0.254 (1.00)	0.165 (1.00)	0.0938 (1.00)	0.3 (1.00)	0.523 (1.00)	0.642 (1.00)	0.14 (1.00)
Amp Peak 11(6p21 1)	0 (0%)	63	0.00445 (1.00)	2.01e-05 (0.00816)	0.00623 (1.00)	0.332 (1.00)	0.346 (1.00)	1 (1.00)	0.247 (1.00)	0.384 (1.00)
Amp Peak 14(8q11 21)	0 (0%)	63	8.87e-07 (0.000366)	0.653 (1.00)	0.321 (1.00)	0.806 (1.00)	0.261 (1.00)	0.751 (1.00)	0.89 (1.00)	0.469 (1.00)
Amp Peak 15(8q24 13)	0 (0%)	44	1.51e-06 (0.000622)	0.398 (1.00)	0.178 (1.00)	0.623 (1.00)	0.4 (1.00)	0.743 (1.00)	0.559 (1.00)	0.961 (1.00)
Amp Peak 23(17q25 3)	0 (0%)	60	3.57e-06 (0.00147)	0.019 (1.00)	0.388 (1.00)	0.811 (1.00)	0.929 (1.00)	0.533 (1.00)	0.126 (1.00)	0.511 (1.00)
Amp Peak 24(19p13 12)	0 (0%)	80	0.0073 (1.00)	0.00177 (0.688)	0.0391 (1.00)	0.0464 (1.00)	0.412 (1.00)	0.723 (1.00)	0.000221 (0.0885)	0.262 (1.00)
Del Peak 6(4q24)	0 (0%)	61	6.98e-06 (0.00286)	0.0123 (1.00)	0.412 (1.00)	0.809 (1.00)	0.141 (1.00)	1 (1.00)	0.229 (1.00)	0.203 (1.00)
Del Peak 7(4q35 1)	0 (0%)	62	3.25e-05 (0.0131)	0.00145 (0.564)	0.116 (1.00)	0.337 (1.00)	0.181 (1.00)	0.532 (1.00)	0.42 (1.00)	0.0746 (1.00)
Del Peak 10(8p23 3)	0 (0%)	42	2.99e-15 (1.24e-12)	0.422 (1.00)	0.224 (1.00)	0.623 (1.00)	0.626 (1.00)	0.518 (1.00)	0.16 (1.00)	0.144 (1.00)
Del Peak 11(8p23 2)	0 (0%)	41	1.54e-16 (6.4e-14)	0.145 (1.00)	0.234 (1.00)	0.46 (1.00)	0.492 (1.00)	0.195 (1.00)	0.186 (1.00)	0.0725 (1.00)
Del Peak 12(8p21 1)	0 (0%)	37	3.2e-15 (1.32e-12)	0.292 (1.00)	0.273 (1.00)	0.623 (1.00)	0.29 (1.00)	0.318 (1.00)	0.119 (1.00)	0.182 (1.00)
Del Peak 15(10q24 33)	0 (0%)	76	0.0037 (1.00)	0.861 (1.00)	0.0056 (1.00)	0.0647 (1.00)	0.0152 (1.00)	0.0881 (1.00)	0.000322 (0.128)	0.00419 (1.00)
Del Peak 20(14q23 3)	0 (0%)	68	0.000302 (0.12)	0.168 (1.00)	0.401 (1.00)	0.0482 (1.00)	0.726 (1.00)	0.017 (1.00)	0.045 (1.00)	0.305 (1.00)
Del Peak 21(14q32 33)	0 (0%)	68	1.14e-05 (0.00463)	0.0948 (1.00)	0.218 (1.00)	0.325 (1.00)	0.334 (1.00)	0.197 (1.00)	0.0482 (1.00)	0.378 (1.00)
Amp Peak 1(1p22 3)	0 (0%)	79	0.0302 (1.00)	0.125 (1.00)	0.218 (1.00)	0.112 (1.00)	0.206 (1.00)	0.279 (1.00)	0.156 (1.00)	0.522 (1.00)
Amp Peak 3(1q42 3)	0 (0%)	36	0.159 (1.00)	0.00313 (1.00)	0.0429 (1.00)	0.802 (1.00)	0.532 (1.00)	0.496 (1.00)	0.719 (1.00)	0.312 (1.00)
Amp Peak 4(2p24 1)	0 (0%)	84	0.158 (1.00)	0.688 (1.00)	0.702 (1.00)	0.25 (1.00)	0.164 (1.00)	0.705 (1.00)	0.145 (1.00)	0.0434 (1.00)
Amp Peak 5(2q31 2)	0 (0%)	83	0.0983 (1.00)	0.638 (1.00)	0.626 (1.00)	0.778 (1.00)	0.304 (1.00)	1 (1.00)	0.457 (1.00)	0.0767 (1.00)
Amp Peak 7(4q13 3)	0 (0%)	95	0.325 (1.00)	0.646 (1.00)	0.707 (1.00)	0.302 (1.00)	0.403 (1.00)	0.348 (1.00)	0.0719 (1.00)	0.579 (1.00)
Amp Peak 9(5q35 3)	0 (0%)	68	0.0189 (1.00)	0.336 (1.00)	0.358 (1.00)	0.443 (1.00)	1 (1.00)	1 (1.00)	0.822 (1.00)	0.866 (1.00)
Amp Peak 10(6p22 3)	0 (0%)	66	0.0039 (1.00)	0.00116 (0.454)	0.0579 (1.00)	1 (1.00)	0.477 (1.00)	1 (1.00)	0.371 (1.00)	0.961 (1.00)
Amp Peak 12(6q12)	0 (0%)	74	0.0544 (1.00)	0.0418 (1.00)	0.101 (1.00)	1 (1.00)	0.0695 (1.00)	0.322 (1.00)	0.0782 (1.00)	0.417 (1.00)
Amp Peak 13(7q21 2)	0 (0%)	69	0.101 (1.00)	0.164 (1.00)	0.397 (1.00)	0.2 (1.00)	0.665 (1.00)	0.317 (1.00)	0.247 (1.00)	0.872 (1.00)
Amp Peak 16(10p15 1)	0 (0%)	86	0.0189 (1.00)	0.0357 (1.00)	0.273 (1.00)	0.0167 (1.00)	0.447 (1.00)	0.689 (1.00)	0.0101 (1.00)	0.0904 (1.00)
Amp Peak 17(11q13 3)	0 (0%)	88	0.147 (1.00)	0.949 (1.00)	0.16 (1.00)	0.732 (1.00)	0.116 (1.00)	0.108 (1.00)	0.133 (1.00)	0.0467 (1.00)
Amp Peak 18(12q23 1)	0 (0%)	86	0.0428 (1.00)	0.314 (1.00)	0.668 (1.00)	0.131 (1.00)	0.472 (1.00)	0.452 (1.00)	0.124 (1.00)	0.921 (1.00)
Amp Peak 19(13q32 3)	0 (0%)	85	0.00127 (0.498)	0.0718 (1.00)	0.372 (1.00)	0.144 (1.00)	0.536 (1.00)	0.121 (1.00)	0.0717 (1.00)	0.199 (1.00)
Amp Peak 20(15q26 3)	0 (0%)	92	0.708 (1.00)	1 (1.00)	0.61 (1.00)	0.542 (1.00)	0.932 (1.00)	1 (1.00)	0.736 (1.00)	0.861 (1.00)
Amp Peak 21(17p11 2)	0 (0%)	92	0.552 (1.00)	0.937 (1.00)	0.39 (1.00)	0.302 (1.00)	1 (1.00)	1 (1.00)	0.885 (1.00)	0.659 (1.00)
Amp Peak 22(17q23 1)	0 (0%)	64	0.0114 (1.00)	0.115 (1.00)	0.301 (1.00)	0.22 (1.00)	0.892 (1.00)	0.754 (1.00)	0.336 (1.00)	0.545 (1.00)
Amp Peak 25(19q13 11)	0 (0%)	73	0.00681 (1.00)	0.192 (1.00)	0.686 (1.00)	0.302 (1.00)	0.462 (1.00)	0.32 (1.00)	0.00695 (1.00)	0.287 (1.00)
Amp Peak 26(20q13 13)	0 (0%)	70	0.0192 (1.00)	0.401 (1.00)	0.00449 (1.00)	0.461 (1.00)	0.885 (1.00)	0.519 (1.00)	0.165 (1.00)	0.163 (1.00)
Del Peak 1(1p36 32)	0 (0%)	58	0.032 (1.00)	0.0124 (1.00)	0.276 (1.00)	0.631 (1.00)	0.661 (1.00)	0.218 (1.00)	0.202 (1.00)	0.163 (1.00)
Del Peak 2(1p35 2)	0 (0%)	69	0.331 (1.00)	0.00189 (0.731)	0.0744 (1.00)	0.127 (1.00)	0.0792 (1.00)	0.318 (1.00)	0.268 (1.00)	0.0585 (1.00)
Del Peak 3(2q22 1)	0 (0%)	97	0.0493 (1.00)	0.19 (1.00)	0.751 (1.00)	0.69 (1.00)	0.0432 (1.00)	0.0911 (1.00)	0.198 (1.00)	0.00221 (0.854)
Del Peak 4(2q37 3)	0 (0%)	89	0.109 (1.00)	0.807 (1.00)	0.442 (1.00)	0.75 (1.00)	0.0724 (1.00)	0.0886 (1.00)	0.282 (1.00)	0.0353 (1.00)
Del Peak 8(5q23 1)	0 (0%)	91	0.945 (1.00)	0.133 (1.00)	0.335 (1.00)	0.152 (1.00)	0.266 (1.00)	0.208 (1.00)	0.156 (1.00)	0.335 (1.00)
Del Peak 9(6q26)	0 (0%)	65	0.249 (1.00)	0.246 (1.00)	0.669 (1.00)	0.127 (1.00)	0.294 (1.00)	0.747 (1.00)	0.667 (1.00)	0.32 (1.00)
Del Peak 13(9p21 3)	0 (0%)	64	0.00992 (1.00)	0.611 (1.00)	0.781 (1.00)	0.337 (1.00)	0.365 (1.00)	0.342 (1.00)	0.137 (1.00)	0.0704 (1.00)
Del Peak 14(10q23 31)	0 (0%)	74	0.00518 (1.00)	0.774 (1.00)	0.00548 (1.00)	0.0722 (1.00)	0.082 (1.00)	0.169 (1.00)	0.000857 (0.337)	0.00832 (1.00)
Del Peak 16(11q14 1)	0 (0%)	87	0.563 (1.00)	0.862 (1.00)	0.429 (1.00)	0.554 (1.00)	0.94 (1.00)	1 (1.00)	0.776 (1.00)	0.505 (1.00)
Del Peak 17(12p12 1)	0 (0%)	83	0.602 (1.00)	0.33 (1.00)	0.248 (1.00)	0.177 (1.00)	0.12 (1.00)	0.018 (1.00)	0.00249 (0.961)	0.102 (1.00)
Del Peak 18(12q24 33)	0 (0%)	89	0.121 (1.00)	0.32 (1.00)	0.352 (1.00)	1 (1.00)	0.0498 (1.00)	0.391 (1.00)	0.41 (1.00)	1 (1.00)
Del Peak 22(16q23 1)	0 (0%)	63	0.0138 (1.00)	0.0163 (1.00)	0.0114 (1.00)	0.0538 (1.00)	0.305 (1.00)	0.338 (1.00)	0.123 (1.00)	0.0602 (1.00)
Del Peak 24(19p13 3)	0 (0%)	83	0.0177 (1.00)	0.0138 (1.00)	0.503 (1.00)	0.267 (1.00)	0.146 (1.00)	0.0521 (1.00)	0.0118 (1.00)	0.196 (1.00)
Del Peak 25(22q12 1)	0 (0%)	86	0.153 (1.00)	0.33 (1.00)	0.123 (1.00)	0.235 (1.00)	0.943 (1.00)	0.435 (1.00)	0.452 (1.00)	0.9 (1.00)
Del Peak 26(22q13 32)	0 (0%)	80	0.0338 (1.00)	0.422 (1.00)	0.0415 (1.00)	1 (1.00)	0.455 (1.00)	0.463 (1.00)	0.867 (1.00)	0.33 (1.00)

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

P value = 0.000625 (Fisher's exact test), Q value = 0.25

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	37	34
AMP PEAK 2(1Q22) CNV	31	18	29
AMP PEAK 2(1Q22) WILD-TYPE	6	19	5

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 = 3.41e-05 (Fisher's exact test), Q value = 0.014

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	31	48
AMP PEAK 2(1Q22) CNV	11	25	42
AMP PEAK 2(1Q22) WILD-TYPE	17	6	6

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 = 2.91e-05 (Fisher's exact test), Q value = 0.012

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	37	34
AMP PEAK 6(3Q26.31) CNV	5	1	15
AMP PEAK 6(3Q26.31) WILD-TYPE	32	36	19

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

'Amp Peak 8(5p15.33)' versus 'CN_CNMF'

P value = 0.000135 (Fisher's exact test), Q value = 0.054

Table S4. Gene #8: 'Amp Peak 8(5p15.33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	37	34
AMP PEAK 8(5P15.33) CNV	22	8	23
AMP PEAK 8(5P15.33) WILD-TYPE	15	29	11

Figure S4. Get High-res Image Gene #8: 'Amp Peak 8(5p15.33)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 11(6p21.1)' versus 'METHLYATION_CNMF'

P value = 2.01e-05 (Fisher's exact test), Q value = 0.0082

Table S5. Gene #11: 'Amp Peak 11(6p21.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	31	48
AMP PEAK 11(6P21.1) CNV	2	14	28
AMP PEAK 11(6P21.1) WILD-TYPE	26	17	20

Figure S5. Get High-res Image Gene #11: 'Amp Peak 11(6p21.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 14(8q11.21)' versus 'CN_CNMF'

P value = 8.87e-07 (Fisher's exact test), Q value = 0.00037

Table S6. Gene #14: 'Amp Peak 14(8q11.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	37	34
AMP PEAK 14(8Q11.21) CNV	28	7	10
AMP PEAK 14(8Q11.21) WILD-TYPE	9	30	24

Figure S6. Get High-res Image Gene #14: 'Amp Peak 14(8q11.21)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 15(8q24.13)' versus 'CN_CNMF'

P value = 1.51e-06 (Fisher's exact test), Q value = 0.00062

Table S7. Gene #15: 'Amp Peak 15(8q24.13)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	37	34
AMP PEAK 15(8Q24.13) CNV	33	12	19
AMP PEAK 15(8Q24.13) WILD-TYPE	4	25	15

Figure S7. Get High-res Image Gene #15: 'Amp Peak 15(8q24.13)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 23(17q25.3)' versus 'CN_CNMF'

P value = 3.57e-06 (Fisher's exact test), Q value = 0.0015

Table S8. Gene #23: 'Amp Peak 23(17q25.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	37	34
AMP PEAK 23(17Q25.3) CNV	10	11	27
AMP PEAK 23(17Q25.3) WILD-TYPE	27	26	7

Figure S8. Get High-res Image Gene #23: 'Amp Peak 23(17q25.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 24(19p13.12)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000221 (Chi-square test), Q value = 0.088

Table S9. Gene #24: 'Amp Peak 24(19p13.12)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	10	15	15	25	14	15
AMP PEAK 24(19P13.12) CNV	0	4	11	4	3	2
AMP PEAK 24(19P13.12) WILD-TYPE	10	11	4	21	11	13

Figure S9. Get High-res Image Gene #24: 'Amp Peak 24(19p13.12)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

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

P value = 0.000163 (Fisher's exact test), Q value = 0.065

Table S10. Gene #31: 'Del Peak 5(3p13)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	29	40
DEL PEAK 5(3P13) CNV	11	1
DEL PEAK 5(3P13) WILD-TYPE	18	39

Figure S10. Get High-res Image Gene #31: 'Del Peak 5(3p13)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

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

P value = 3.78e-06 (Chi-square test), Q value = 0.0016

Table S11. Gene #31: 'Del Peak 5(3p13)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	10	15	15	25	14	15
DEL PEAK 5(3P13) CNV	0	2	9	0	0	3
DEL PEAK 5(3P13) WILD-TYPE	10	13	6	25	14	12

Figure S11. Get High-res Image Gene #31: 'Del Peak 5(3p13)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'Del Peak 6(4q24)' versus 'CN_CNMF'

P value = 6.98e-06 (Fisher's exact test), Q value = 0.0029

Table S12. Gene #32: 'Del Peak 6(4q24)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	37	34
DEL PEAK 6(4Q24) CNV	13	8	26
DEL PEAK 6(4Q24) WILD-TYPE	24	29	8

Figure S12. Get High-res Image Gene #32: 'Del Peak 6(4q24)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 7(4q35.1)' versus 'CN_CNMF'

P value = 3.25e-05 (Fisher's exact test), Q value = 0.013

Table S13. Gene #33: 'Del Peak 7(4q35.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	37	34
DEL PEAK 7(4Q35.1) CNV	13	8	25
DEL PEAK 7(4Q35.1) WILD-TYPE	24	29	9

Figure S13. Get High-res Image Gene #33: 'Del Peak 7(4q35.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 10(8p23.3)' versus 'CN_CNMF'

P value = 2.99e-15 (Fisher's exact test), Q value = 1.2e-12

Table S14. Gene #36: 'Del Peak 10(8p23.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	37	34
DEL PEAK 10(8P23.3) CNV	37	6	23
DEL PEAK 10(8P23.3) WILD-TYPE	0	31	11

Figure S14. Get High-res Image Gene #36: 'Del Peak 10(8p23.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 11(8p23.2)' versus 'CN_CNMF'

P value = 1.54e-16 (Fisher's exact test), Q value = 6.4e-14

Table S15. Gene #37: 'Del Peak 11(8p23.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	37	34
DEL PEAK 11(8P23.2) CNV	37	5	25
DEL PEAK 11(8P23.2) WILD-TYPE	0	32	9

Figure S15. Get High-res Image Gene #37: 'Del Peak 11(8p23.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 12(8p21.1)' versus 'CN_CNMF'

P value = 3.2e-15 (Fisher's exact test), Q value = 1.3e-12

Table S16. Gene #38: 'Del Peak 12(8p21.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	37	34
DEL PEAK 12(8P21.1) CNV	37	7	27
DEL PEAK 12(8P21.1) WILD-TYPE	0	30	7

Figure S16. Get High-res Image Gene #38: 'Del Peak 12(8p21.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 15(10q24.33)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000322 (Chi-square test), Q value = 0.13

Table S17. Gene #41: 'Del Peak 15(10q24.33)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	10	15	15	25	14	15
DEL PEAK 15(10Q24.33) CNV	2	7	10	0	4	6
DEL PEAK 15(10Q24.33) WILD-TYPE	8	8	5	25	10	9

Figure S17. Get High-res Image Gene #41: 'Del Peak 15(10q24.33)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'Del Peak 19(13q14.2)' versus 'CN_CNMF'

P value = 1.24e-05 (Fisher's exact test), Q value = 0.005

Table S18. Gene #45: 'Del Peak 19(13q14.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	37	34
DEL PEAK 19(13Q14.2) CNV	12	9	26
DEL PEAK 19(13Q14.2) WILD-TYPE	25	28	8

Figure S18. Get High-res Image Gene #45: 'Del Peak 19(13q14.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 19(13q14.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000299 (Chi-square test), Q value = 0.12

Table S19. Gene #45: 'Del Peak 19(13q14.2)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	10	15	15	25	14	15
DEL PEAK 19(13Q14.2) CNV	2	9	13	4	7	6
DEL PEAK 19(13Q14.2) WILD-TYPE	8	6	2	21	7	9

Figure S19. Get High-res Image Gene #45: 'Del Peak 19(13q14.2)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'Del Peak 20(14q23.3)' versus 'CN_CNMF'

P value = 0.000302 (Fisher's exact test), Q value = 0.12

Table S20. Gene #46: 'Del Peak 20(14q23.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	37	34
DEL PEAK 20(14Q23.3) CNV	13	6	21
DEL PEAK 20(14Q23.3) WILD-TYPE	24	31	13

Figure S20. Get High-res Image Gene #46: 'Del Peak 20(14q23.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 21(14q32.33)' versus 'CN_CNMF'

P value = 1.14e-05 (Fisher's exact test), Q value = 0.0046

Table S21. Gene #47: 'Del Peak 21(14q32.33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	37	34
DEL PEAK 21(14Q32.33) CNV	12	5	23
DEL PEAK 21(14Q32.33) WILD-TYPE	25	32	11

Figure S21. Get High-res Image Gene #47: 'Del Peak 21(14q32.33)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 23(17p12)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000473 (Chi-square test), Q value = 0.19

Table S22. Gene #49: 'Del Peak 23(17p12)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	10	15	15	25	14	15
DEL PEAK 23(17P12) CNV	4	14	6	9	10	13
DEL PEAK 23(17P12) WILD-TYPE	6	1	9	16	4	2

Figure S22. Get High-res Image Gene #49: 'Del Peak 23(17p12)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'Del Peak 23(17p12)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000433 (Fisher's exact test), Q value = 0.17

Table S23. Gene #49: 'Del Peak 23(17p12)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	16	39	24	15
DEL PEAK 23(17P12) CNV	14	19	19	4
DEL PEAK 23(17P12) WILD-TYPE	2	20	5	11

Figure S23. Get High-res Image Gene #49: 'Del Peak 23(17p12)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_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 = LIHC-TP.transferedmergedcluster.txt
Number of patients = 108
Number of copy number variation regions = 52
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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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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