Correlation between copy number variation genes and molecular subtypes

Skin Cutaneous Melanoma (Metastatic)

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/C1D798G6

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 54 peak regions and 10 molecular subtypes across 260 patients, 33 significant findings detected with Q value < 0.25.

Amp Peak 2(1q44) cnvs correlated to 'CN_CNMF'.
Amp Peak 5(5p15.33) cnvs correlated to 'CN_CNMF'.
Amp Peak 6(5q35.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 7(6p25.1) cnvs correlated to 'CN_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 9(7p22.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 10(7q34) cnvs correlated to 'CN_CNMF'.
Amp Peak 11(8q11.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 12(8q24.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 16(12q14.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 19(17q25.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 21(20q13.33) cnvs correlated to 'CN_CNMF'.
Amp Peak 22(22q13.2) cnvs correlated to 'CN_CNMF'.
Del Peak 1(1p36.31) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 2(1p22.1) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 8(5q11.2) cnvs correlated to 'CN_CNMF'.
Del Peak 9(5q31.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 10(6q22.31) cnvs correlated to 'CN_CNMF'.
Del Peak 11(6q25.3) cnvs correlated to 'CN_CNMF'.
Del Peak 12(6q26) cnvs correlated to 'CN_CNMF'.
Del Peak 14(9p23) cnvs correlated to 'CN_CNMF'.
Del Peak 15(9p21.3) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 16(10p15.3) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 17(10q23.31) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 18(10q26.3) cnvs correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 19(11q23.3) 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 54 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 33 significant findings detected.


		Molecular subtypes	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Amp Peak 7(6p25 1)	0 (0%)	113	2.06e-06 (0.00109)	0.000693 (0.35)	0.00798 (1.00)	0.542 (1.00)	0.0856 (1.00)	0.00485 (1.00)	0.00153 (0.757)	1.05e-05 (0.00547)	0.0258 (1.00)	5.92e-06 (0.00311)
Del Peak 16(10p15 3)	0 (0%)	119	0.000162 (0.083)	0.00716 (1.00)	0.481 (1.00)	0.787 (1.00)	2.76e-06 (0.00145)	0.000289 (0.147)	0.116 (1.00)	0.259 (1.00)	0.856 (1.00)	0.369 (1.00)
Del Peak 9(5q31 3)	0 (0%)	165	7.86e-08 (4.2e-05)	0.000111 (0.0574)	0.125 (1.00)	0.823 (1.00)	0.916 (1.00)	0.751 (1.00)	0.511 (1.00)	0.334 (1.00)	0.264 (1.00)	0.339 (1.00)
Del Peak 15(9p21 3)	0 (0%)	60	6.73e-07 (0.000357)	0.000596 (0.302)	0.749 (1.00)	0.127 (1.00)	0.000146 (0.0753)	0.0102 (1.00)	0.961 (1.00)	0.602 (1.00)	0.907 (1.00)	0.918 (1.00)
Del Peak 17(10q23 31)	0 (0%)	101	2.83e-05 (0.0147)	0.0428 (1.00)	0.214 (1.00)	0.732 (1.00)	0.000165 (0.0845)	0.00158 (0.781)	0.739 (1.00)	0.713 (1.00)	0.723 (1.00)	0.708 (1.00)
Del Peak 18(10q26 3)	0 (0%)	98	0.00312 (1.00)	0.175 (1.00)	0.4 (1.00)	0.83 (1.00)	3.59e-06 (0.00189)	0.000195 (0.0997)	0.207 (1.00)	0.852 (1.00)	0.543 (1.00)	0.877 (1.00)
Amp Peak 2(1q44)	0 (0%)	123	5.77e-05 (0.0299)	0.00339 (1.00)	0.943 (1.00)	0.95 (1.00)	0.209 (1.00)	0.566 (1.00)	0.153 (1.00)	0.0745 (1.00)	0.196 (1.00)	0.0472 (1.00)
Amp Peak 5(5p15 33)	0 (0%)	181	1.93e-07 (0.000103)	0.244 (1.00)	0.0548 (1.00)	0.559 (1.00)	0.525 (1.00)	0.209 (1.00)	0.0125 (1.00)	0.174 (1.00)	0.00122 (0.606)	0.204 (1.00)
Amp Peak 6(5q35 3)	0 (0%)	219	4.25e-07 (0.000226)	0.000886 (0.446)	0.564 (1.00)	0.342 (1.00)	0.253 (1.00)	0.0985 (1.00)	0.104 (1.00)	0.195 (1.00)	0.195 (1.00)	0.202 (1.00)
Amp Peak 9(7p22 3)	0 (0%)	122	7.75e-10 (4.16e-07)	0.327 (1.00)	0.65 (1.00)	0.924 (1.00)	0.0979 (1.00)	0.25 (1.00)	0.958 (1.00)	0.468 (1.00)	0.932 (1.00)	0.765 (1.00)
Amp Peak 10(7q34)	0 (0%)	107	9.15e-07 (0.000484)	0.239 (1.00)	0.249 (1.00)	0.546 (1.00)	0.217 (1.00)	0.359 (1.00)	0.343 (1.00)	0.302 (1.00)	0.309 (1.00)	0.353 (1.00)
Amp Peak 11(8q11 21)	0 (0%)	148	9.71e-06 (0.00509)	0.00343 (1.00)	0.687 (1.00)	0.645 (1.00)	0.0367 (1.00)	0.32 (1.00)	0.35 (1.00)	0.872 (1.00)	0.103 (1.00)	0.845 (1.00)
Amp Peak 12(8q24 21)	0 (0%)	130	1.14e-07 (6.1e-05)	0.00315 (1.00)	0.529 (1.00)	0.89 (1.00)	0.0357 (1.00)	0.678 (1.00)	0.476 (1.00)	0.386 (1.00)	0.276 (1.00)	0.832 (1.00)
Amp Peak 16(12q14 1)	0 (0%)	217	0.000259 (0.132)	0.485 (1.00)	0.62 (1.00)	0.508 (1.00)	0.4 (1.00)	0.0473 (1.00)	0.905 (1.00)	0.695 (1.00)	0.864 (1.00)	0.725 (1.00)
Amp Peak 19(17q25 3)	0 (0%)	169	9.53e-05 (0.0493)	0.00273 (1.00)	0.0204 (1.00)	0.149 (1.00)	0.257 (1.00)	0.233 (1.00)	0.088 (1.00)	0.033 (1.00)	0.0167 (1.00)	0.00964 (1.00)
Amp Peak 21(20q13 33)	0 (0%)	128	3.41e-05 (0.0177)	0.0195 (1.00)	0.771 (1.00)	1 (1.00)	0.0123 (1.00)	0.321 (1.00)	0.623 (1.00)	0.249 (1.00)	0.0561 (1.00)	0.156 (1.00)
Amp Peak 22(22q13 2)	0 (0%)	153	1.79e-10 (9.61e-08)	0.0285 (1.00)	0.745 (1.00)	0.789 (1.00)	0.809 (1.00)	0.884 (1.00)	0.419 (1.00)	0.536 (1.00)	0.307 (1.00)	0.378 (1.00)
Del Peak 1(1p36 31)	0 (0%)	199	0.143 (1.00)	0.000116 (0.0595)	0.134 (1.00)	0.419 (1.00)	0.206 (1.00)	0.00631 (1.00)	0.442 (1.00)	0.338 (1.00)	0.634 (1.00)	0.276 (1.00)
Del Peak 2(1p22 1)	0 (0%)	195	0.0206 (1.00)	0.000312 (0.158)	0.76 (1.00)	0.301 (1.00)	0.00151 (0.75)	0.0525 (1.00)	0.512 (1.00)	0.709 (1.00)	0.28 (1.00)	0.474 (1.00)
Del Peak 8(5q11 2)	0 (0%)	190	3.16e-08 (1.69e-05)	0.0827 (1.00)	0.0465 (1.00)	0.227 (1.00)	0.687 (1.00)	0.703 (1.00)	0.777 (1.00)	0.524 (1.00)	0.244 (1.00)	0.496 (1.00)
Del Peak 10(6q22 31)	0 (0%)	104	1.33e-13 (7.2e-11)	0.0426 (1.00)	0.292 (1.00)	0.453 (1.00)	0.00107 (0.534)	0.688 (1.00)	0.835 (1.00)	0.836 (1.00)	0.704 (1.00)	0.372 (1.00)
Del Peak 11(6q25 3)	0 (0%)	95	1.4e-11 (7.54e-09)	0.136 (1.00)	0.187 (1.00)	0.734 (1.00)	0.0012 (0.596)	0.623 (1.00)	0.94 (1.00)	0.98 (1.00)	0.955 (1.00)	0.627 (1.00)
Del Peak 12(6q26)	0 (0%)	98	1.71e-14 (9.26e-12)	0.09 (1.00)	0.367 (1.00)	0.782 (1.00)	0.000949 (0.477)	0.726 (1.00)	0.703 (1.00)	0.941 (1.00)	0.811 (1.00)	0.768 (1.00)
Del Peak 14(9p23)	0 (0%)	83	2.6e-05 (0.0136)	0.0133 (1.00)	0.842 (1.00)	0.555 (1.00)	0.00592 (1.00)	0.0364 (1.00)	0.877 (1.00)	0.398 (1.00)	0.509 (1.00)	0.889 (1.00)
Del Peak 19(11q23 3)	0 (0%)	119	1.76e-05 (0.0092)	0.095 (1.00)	0.227 (1.00)	0.464 (1.00)	0.282 (1.00)	0.599 (1.00)	0.145 (1.00)	0.13 (1.00)	0.0924 (1.00)	0.0531 (1.00)
Amp Peak 1(1p12)	0 (0%)	182	0.0467 (1.00)	0.357 (1.00)	0.379 (1.00)	0.404 (1.00)	0.109 (1.00)	0.396 (1.00)	0.72 (1.00)	0.744 (1.00)	0.409 (1.00)	0.58 (1.00)
Amp Peak 3(3p13)	0 (0%)	193	0.456 (1.00)	0.679 (1.00)	0.376 (1.00)	0.123 (1.00)	0.821 (1.00)	0.546 (1.00)	1 (1.00)	0.49 (1.00)	1 (1.00)	0.436 (1.00)
Amp Peak 4(4q12)	0 (0%)	212	0.00675 (1.00)	0.259 (1.00)	0.293 (1.00)	0.313 (1.00)	0.816 (1.00)	0.358 (1.00)	0.0688 (1.00)	0.0136 (1.00)	0.0546 (1.00)	0.0186 (1.00)
Amp Peak 8(6q12)	0 (0%)	201	0.734 (1.00)	0.566 (1.00)	0.587 (1.00)	0.427 (1.00)	0.0688 (1.00)	0.428 (1.00)	0.327 (1.00)	0.238 (1.00)	0.89 (1.00)	0.124 (1.00)
Amp Peak 13(9p24 1)	0 (0%)	238	0.752 (1.00)	0.516 (1.00)	0.711 (1.00)	0.815 (1.00)	0.613 (1.00)	0.56 (1.00)	0.262 (1.00)	0.841 (1.00)	0.192 (1.00)	0.53 (1.00)
Amp Peak 14(11q13 3)	0 (0%)	210	0.00115 (0.574)	0.209 (1.00)	0.733 (1.00)	0.956 (1.00)	0.896 (1.00)	1 (1.00)	0.499 (1.00)	0.326 (1.00)	0.778 (1.00)	0.567 (1.00)
Amp Peak 15(11q13 4)	0 (0%)	214	0.000564 (0.286)	0.0549 (1.00)	0.968 (1.00)	0.968 (1.00)	0.532 (1.00)	0.602 (1.00)	0.263 (1.00)	0.137 (1.00)	0.411 (1.00)	0.78 (1.00)
Amp Peak 17(12q15)	0 (0%)	219	0.00425 (1.00)	1 (1.00)	0.408 (1.00)	0.52 (1.00)	0.716 (1.00)	0.588 (1.00)	0.95 (1.00)	0.615 (1.00)	0.951 (1.00)	0.894 (1.00)
Amp Peak 18(15q26 2)	0 (0%)	171	0.0025 (1.00)	0.698 (1.00)	0.861 (1.00)	0.641 (1.00)	0.544 (1.00)	0.245 (1.00)	0.801 (1.00)	0.269 (1.00)	0.42 (1.00)	0.506 (1.00)
Amp Peak 20(19p13 2)	0 (0%)	208	0.0685 (1.00)	0.211 (1.00)	0.758 (1.00)	0.33 (1.00)	0.0265 (1.00)	0.0109 (1.00)	0.351 (1.00)	0.09 (1.00)	0.0427 (1.00)	0.0305 (1.00)
Del Peak 3(2q37 3)	0 (0%)	193	0.0655 (1.00)	0.0472 (1.00)	0.433 (1.00)	0.246 (1.00)	0.0448 (1.00)	0.0271 (1.00)	0.0717 (1.00)	0.0346 (1.00)	0.0656 (1.00)	0.0313 (1.00)
Del Peak 4(3q23)	0 (0%)	220	0.785 (1.00)	0.0284 (1.00)	0.845 (1.00)	0.903 (1.00)	0.576 (1.00)	0.519 (1.00)	0.607 (1.00)	0.692 (1.00)	1 (1.00)	0.45 (1.00)
Del Peak 5(4p16 3)	0 (0%)	198	0.884 (1.00)	0.5 (1.00)	0.406 (1.00)	0.91 (1.00)	0.0214 (1.00)	0.22 (1.00)	0.584 (1.00)	0.385 (1.00)	0.121 (1.00)	0.3 (1.00)
Del Peak 6(4q34 3)	0 (0%)	190	0.0164 (1.00)	0.183 (1.00)	0.658 (1.00)	0.769 (1.00)	0.0124 (1.00)	0.00771 (1.00)	0.0142 (1.00)	0.00324 (1.00)	0.00797 (1.00)	0.00242 (1.00)
Del Peak 7(5p15 31)	0 (0%)	206	0.0958 (1.00)	0.153 (1.00)	0.377 (1.00)	0.179 (1.00)	0.286 (1.00)	0.421 (1.00)	0.365 (1.00)	0.219 (1.00)	0.473 (1.00)	0.0597 (1.00)
Del Peak 13(8p22)	0 (0%)	196	0.0468 (1.00)	0.27 (1.00)	0.0923 (1.00)	0.335 (1.00)	0.17 (1.00)	0.838 (1.00)	0.351 (1.00)	0.589 (1.00)	0.18 (1.00)	0.285 (1.00)
Del Peak 20(12p13 31)	0 (0%)	220	0.403 (1.00)	0.274 (1.00)	0.363 (1.00)	0.787 (1.00)	0.197 (1.00)	0.481 (1.00)	0.716 (1.00)	0.864 (1.00)	0.582 (1.00)	0.788 (1.00)
Del Peak 21(12q23 3)	0 (0%)	198	0.208 (1.00)	0.0133 (1.00)	0.589 (1.00)	0.492 (1.00)	0.845 (1.00)	0.353 (1.00)	0.669 (1.00)	0.499 (1.00)	0.805 (1.00)	0.42 (1.00)
Del Peak 22(13q12 11)	0 (0%)	202	0.00198 (0.975)	0.457 (1.00)	0.532 (1.00)	0.555 (1.00)	0.981 (1.00)	0.726 (1.00)	0.0833 (1.00)	0.0166 (1.00)	0.175 (1.00)	0.0702 (1.00)
Del Peak 23(13q34)	0 (0%)	201	0.00851 (1.00)	0.00395 (1.00)	0.078 (1.00)	0.785 (1.00)	0.963 (1.00)	0.215 (1.00)	0.82 (1.00)	0.106 (1.00)	0.793 (1.00)	0.368 (1.00)
Del Peak 24(14q32 2)	0 (0%)	172	0.000975 (0.489)	0.718 (1.00)	0.162 (1.00)	0.419 (1.00)	0.0184 (1.00)	0.662 (1.00)	0.786 (1.00)	0.682 (1.00)	0.939 (1.00)	0.778 (1.00)
Del Peak 25(15q13 3)	0 (0%)	200	0.333 (1.00)	0.103 (1.00)	0.393 (1.00)	0.656 (1.00)	0.623 (1.00)	0.218 (1.00)	0.41 (1.00)	0.405 (1.00)	0.494 (1.00)	0.68 (1.00)
Del Peak 26(15q15 1)	0 (0%)	196	0.184 (1.00)	0.0285 (1.00)	0.382 (1.00)	0.501 (1.00)	0.722 (1.00)	0.471 (1.00)	0.247 (1.00)	0.0921 (1.00)	0.569 (1.00)	0.474 (1.00)
Del Peak 27(16p13 3)	0 (0%)	211	0.503 (1.00)	0.0496 (1.00)	0.199 (1.00)	0.408 (1.00)	0.329 (1.00)	0.681 (1.00)	0.373 (1.00)	0.555 (1.00)	0.248 (1.00)	0.417 (1.00)
Del Peak 28(16q12 1)	0 (0%)	176	0.227 (1.00)	0.506 (1.00)	0.0151 (1.00)	0.547 (1.00)	0.179 (1.00)	0.348 (1.00)	0.147 (1.00)	0.143 (1.00)	0.301 (1.00)	0.0543 (1.00)
Del Peak 29(16q24 3)	0 (0%)	168	0.0372 (1.00)	0.619 (1.00)	0.331 (1.00)	0.828 (1.00)	0.0122 (1.00)	0.18 (1.00)	0.0713 (1.00)	0.0543 (1.00)	0.142 (1.00)	0.0474 (1.00)
Del Peak 30(17q21 31)	0 (0%)	202	0.133 (1.00)	0.275 (1.00)	0.107 (1.00)	0.5 (1.00)	0.623 (1.00)	0.695 (1.00)	0.641 (1.00)	0.362 (1.00)	0.537 (1.00)	0.398 (1.00)
Del Peak 31(19p13 3)	0 (0%)	185	0.000956 (0.48)	0.509 (1.00)	0.00607 (1.00)	0.0213 (1.00)	0.00451 (1.00)	0.156 (1.00)	0.856 (1.00)	0.401 (1.00)	0.345 (1.00)	0.187 (1.00)
Del Peak 32(22q12 1)	0 (0%)	222	0.333 (1.00)	0.584 (1.00)	0.364 (1.00)	0.355 (1.00)	0.431 (1.00)	0.71 (1.00)	0.0101 (1.00)	0.253 (1.00)	0.0857 (1.00)	0.25 (1.00)

'Amp Peak 2(1q44)' versus 'CN_CNMF'

P value = 5.77e-05 (Fisher's exact test), Q value = 0.03

Table S1. Gene #2: 'Amp Peak 2(1q44)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
AMP PEAK 2(1Q44) CNV	46	60	31
AMP PEAK 2(1Q44) WILD-TYPE	26	37	60

Figure S1. Get High-res Image Gene #2: 'Amp Peak 2(1q44)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 1.93e-07 (Fisher's exact test), Q value = 1e-04

Table S2. Gene #5: 'Amp Peak 5(5p15.33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
AMP PEAK 5(5P15.33) CNV	30	40	9
AMP PEAK 5(5P15.33) WILD-TYPE	42	57	82

Figure S2. Get High-res Image Gene #5: 'Amp Peak 5(5p15.33)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 6(5q35.3)' versus 'CN_CNMF'

P value = 4.25e-07 (Fisher's exact test), Q value = 0.00023

Table S3. Gene #6: 'Amp Peak 6(5q35.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
AMP PEAK 6(5Q35.3) CNV	8	30	3
AMP PEAK 6(5Q35.3) WILD-TYPE	64	67	88

Figure S3. Get High-res Image Gene #6: 'Amp Peak 6(5q35.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 7(6p25.1)' versus 'CN_CNMF'

P value = 2.06e-06 (Fisher's exact test), Q value = 0.0011

Table S4. Gene #7: 'Amp Peak 7(6p25.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
AMP PEAK 7(6P25.1) CNV	35	74	38
AMP PEAK 7(6P25.1) WILD-TYPE	37	23	53

Figure S4. Get High-res Image Gene #7: 'Amp Peak 7(6p25.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 7(6p25.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.05e-05 (Fisher's exact test), Q value = 0.0055

Table S5. Gene #7: 'Amp Peak 7(6p25.1)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	26	141	72
AMP PEAK 7(6P25.1) CNV	14	97	25
AMP PEAK 7(6P25.1) WILD-TYPE	12	44	47

Figure S5. Get High-res Image Gene #7: 'Amp Peak 7(6p25.1)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 7(6p25.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.92e-06 (Fisher's exact test), Q value = 0.0031

Table S6. Gene #7: 'Amp Peak 7(6p25.1)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	82	20
AMP PEAK 7(6P25.1) CNV	94	29	13
AMP PEAK 7(6P25.1) WILD-TYPE	43	53	7

Figure S6. Get High-res Image Gene #7: 'Amp Peak 7(6p25.1)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 9(7p22.3)' versus 'CN_CNMF'

P value = 7.75e-10 (Fisher's exact test), Q value = 4.2e-07

Table S7. Gene #9: 'Amp Peak 9(7p22.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
AMP PEAK 9(7P22.3) CNV	60	46	32
AMP PEAK 9(7P22.3) WILD-TYPE	12	51	59

Figure S7. Get High-res Image Gene #9: 'Amp Peak 9(7p22.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 10(7q34)' versus 'CN_CNMF'

P value = 9.15e-07 (Fisher's exact test), Q value = 0.00048

Table S8. Gene #10: 'Amp Peak 10(7q34)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
AMP PEAK 10(7Q34) CNV	60	52	41
AMP PEAK 10(7Q34) WILD-TYPE	12	45	50

Figure S8. Get High-res Image Gene #10: 'Amp Peak 10(7q34)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 11(8q11.21)' versus 'CN_CNMF'

P value = 9.71e-06 (Fisher's exact test), Q value = 0.0051

Table S9. Gene #11: 'Amp Peak 11(8q11.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
AMP PEAK 11(8Q11.21) CNV	43	47	22
AMP PEAK 11(8Q11.21) WILD-TYPE	29	50	69

Figure S9. Get High-res Image Gene #11: 'Amp Peak 11(8q11.21)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 12(8q24.21)' versus 'CN_CNMF'

P value = 1.14e-07 (Fisher's exact test), Q value = 6.1e-05

Table S10. Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
AMP PEAK 12(8Q24.21) CNV	46	60	24
AMP PEAK 12(8Q24.21) WILD-TYPE	26	37	67

Figure S10. Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 16(12q14.1)' versus 'CN_CNMF'

P value = 0.000259 (Fisher's exact test), Q value = 0.13

Table S11. Gene #16: 'Amp Peak 16(12q14.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
AMP PEAK 16(12Q14.1) CNV	22	15	6
AMP PEAK 16(12Q14.1) WILD-TYPE	50	82	85

Figure S11. Get High-res Image Gene #16: 'Amp Peak 16(12q14.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 19(17q25.3)' versus 'CN_CNMF'

P value = 9.53e-05 (Fisher's exact test), Q value = 0.049

Table S12. Gene #19: 'Amp Peak 19(17q25.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
AMP PEAK 19(17Q25.3) CNV	25	48	18
AMP PEAK 19(17Q25.3) WILD-TYPE	47	49	73

Figure S12. Get High-res Image Gene #19: 'Amp Peak 19(17q25.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 21(20q13.33)' versus 'CN_CNMF'

P value = 3.41e-05 (Fisher's exact test), Q value = 0.018

Table S13. Gene #21: 'Amp Peak 21(20q13.33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
AMP PEAK 21(20Q13.33) CNV	50	51	31
AMP PEAK 21(20Q13.33) WILD-TYPE	22	46	60

Figure S13. Get High-res Image Gene #21: 'Amp Peak 21(20q13.33)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 22(22q13.2)' versus 'CN_CNMF'

P value = 1.79e-10 (Fisher's exact test), Q value = 9.6e-08

Table S14. Gene #22: 'Amp Peak 22(22q13.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
AMP PEAK 22(22Q13.2) CNV	53	32	22
AMP PEAK 22(22Q13.2) WILD-TYPE	19	65	69

Figure S14. Get High-res Image Gene #22: 'Amp Peak 22(22q13.2)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 0.000116 (Fisher's exact test), Q value = 0.06

Table S15. Gene #23: 'Del Peak 1(1p36.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	97	97
DEL PEAK 1(1P36.31) CNV	28	20	13
DEL PEAK 1(1P36.31) WILD-TYPE	38	77	84

Figure S15. Get High-res Image Gene #23: 'Del Peak 1(1p36.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 2(1p22.1)' versus 'METHLYATION_CNMF'

P value = 0.000312 (Fisher's exact test), Q value = 0.16

Table S16. Gene #24: 'Del Peak 2(1p22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	97	97
DEL PEAK 2(1P22.1) CNV	29	16	20
DEL PEAK 2(1P22.1) WILD-TYPE	37	81	77

Figure S16. Get High-res Image Gene #24: 'Del Peak 2(1p22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 8(5q11.2)' versus 'CN_CNMF'

P value = 3.16e-08 (Fisher's exact test), Q value = 1.7e-05

Table S17. Gene #30: 'Del Peak 8(5q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
DEL PEAK 8(5Q11.2) CNV	38	12	20
DEL PEAK 8(5Q11.2) WILD-TYPE	34	85	71

Figure S17. Get High-res Image Gene #30: 'Del Peak 8(5q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 9(5q31.3)' versus 'CN_CNMF'

P value = 7.86e-08 (Fisher's exact test), Q value = 4.2e-05

Table S18. Gene #31: 'Del Peak 9(5q31.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
DEL PEAK 9(5Q31.3) CNV	44	18	33
DEL PEAK 9(5Q31.3) WILD-TYPE	28	79	58

Figure S18. Get High-res Image Gene #31: 'Del Peak 9(5q31.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 9(5q31.3)' versus 'METHLYATION_CNMF'

P value = 0.000111 (Fisher's exact test), Q value = 0.057

Table S19. Gene #31: 'Del Peak 9(5q31.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	97	97
DEL PEAK 9(5Q31.3) CNV	13	50	32
DEL PEAK 9(5Q31.3) WILD-TYPE	53	47	65

Figure S19. Get High-res Image Gene #31: 'Del Peak 9(5q31.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 10(6q22.31)' versus 'CN_CNMF'

P value = 1.33e-13 (Fisher's exact test), Q value = 7.2e-11

Table S20. Gene #32: 'Del Peak 10(6q22.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
DEL PEAK 10(6Q22.31) CNV	44	83	29
DEL PEAK 10(6Q22.31) WILD-TYPE	28	14	62

Figure S20. Get High-res Image Gene #32: 'Del Peak 10(6q22.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 11(6q25.3)' versus 'CN_CNMF'

P value = 1.4e-11 (Fisher's exact test), Q value = 7.5e-09

Table S21. Gene #33: 'Del Peak 11(6q25.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
DEL PEAK 11(6Q25.3) CNV	44	85	36
DEL PEAK 11(6Q25.3) WILD-TYPE	28	12	55

Figure S21. Get High-res Image Gene #33: 'Del Peak 11(6q25.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 12(6q26)' versus 'CN_CNMF'

P value = 1.71e-14 (Fisher's exact test), Q value = 9.3e-12

Table S22. Gene #34: 'Del Peak 12(6q26)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
DEL PEAK 12(6Q26) CNV	45	86	31
DEL PEAK 12(6Q26) WILD-TYPE	27	11	60

Figure S22. Get High-res Image Gene #34: 'Del Peak 12(6q26)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 14(9p23)' versus 'CN_CNMF'

P value = 2.6e-05 (Fisher's exact test), Q value = 0.014

Table S23. Gene #36: 'Del Peak 14(9p23)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
DEL PEAK 14(9P23) CNV	61	69	47
DEL PEAK 14(9P23) WILD-TYPE	11	28	44

Figure S23. Get High-res Image Gene #36: 'Del Peak 14(9p23)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 15(9p21.3)' versus 'CN_CNMF'

P value = 6.73e-07 (Fisher's exact test), Q value = 0.00036

Table S24. Gene #37: 'Del Peak 15(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
DEL PEAK 15(9P21.3) CNV	66	81	53
DEL PEAK 15(9P21.3) WILD-TYPE	6	16	38

Figure S24. Get High-res Image Gene #37: 'Del Peak 15(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 15(9p21.3)' versus 'MRNASEQ_CNMF'

P value = 0.000146 (Fisher's exact test), Q value = 0.075

Table S25. Gene #37: 'Del Peak 15(9p21.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	70	92
DEL PEAK 15(9P21.3) CNV	73	46	69
DEL PEAK 15(9P21.3) WILD-TYPE	6	24	23

Figure S25. Get High-res Image Gene #37: 'Del Peak 15(9p21.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 16(10p15.3)' versus 'CN_CNMF'

P value = 0.000162 (Fisher's exact test), Q value = 0.083

Table S26. Gene #38: 'Del Peak 16(10p15.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
DEL PEAK 16(10P15.3) CNV	52	53	36
DEL PEAK 16(10P15.3) WILD-TYPE	20	44	55

Figure S26. Get High-res Image Gene #38: 'Del Peak 16(10p15.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 16(10p15.3)' versus 'MRNASEQ_CNMF'

P value = 2.76e-06 (Fisher's exact test), Q value = 0.0015

Table S27. Gene #38: 'Del Peak 16(10p15.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	70	92
DEL PEAK 16(10P15.3) CNV	61	30	40
DEL PEAK 16(10P15.3) WILD-TYPE	18	40	52

Figure S27. Get High-res Image Gene #38: 'Del Peak 16(10p15.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 16(10p15.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000289 (Fisher's exact test), Q value = 0.15

Table S28. Gene #38: 'Del Peak 16(10p15.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	57	122
DEL PEAK 16(10P15.3) CNV	30	44	57
DEL PEAK 16(10P15.3) WILD-TYPE	32	13	65

Figure S28. Get High-res Image Gene #38: 'Del Peak 16(10p15.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 17(10q23.31)' versus 'CN_CNMF'

P value = 2.83e-05 (Fisher's exact test), Q value = 0.015

Table S29. Gene #39: 'Del Peak 17(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
DEL PEAK 17(10Q23.31) CNV	59	56	44
DEL PEAK 17(10Q23.31) WILD-TYPE	13	41	47

Figure S29. Get High-res Image Gene #39: 'Del Peak 17(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 17(10q23.31)' versus 'MRNASEQ_CNMF'

P value = 0.000165 (Fisher's exact test), Q value = 0.084

Table S30. Gene #39: 'Del Peak 17(10q23.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	70	92
DEL PEAK 17(10Q23.31) CNV	63	37	48
DEL PEAK 17(10Q23.31) WILD-TYPE	16	33	44

Figure S30. Get High-res Image Gene #39: 'Del Peak 17(10q23.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 18(10q26.3)' versus 'MRNASEQ_CNMF'

P value = 3.59e-06 (Fisher's exact test), Q value = 0.0019

Table S31. Gene #40: 'Del Peak 18(10q26.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	70	92
DEL PEAK 18(10Q26.3) CNV	66	37	46
DEL PEAK 18(10Q26.3) WILD-TYPE	13	33	46

Figure S31. Get High-res Image Gene #40: 'Del Peak 18(10q26.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 18(10q26.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000195 (Fisher's exact test), Q value = 0.1

Table S32. Gene #40: 'Del Peak 18(10q26.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	57	122
DEL PEAK 18(10Q26.3) CNV	29	47	73
DEL PEAK 18(10Q26.3) WILD-TYPE	33	10	49

Figure S32. Get High-res Image Gene #40: 'Del Peak 18(10q26.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 19(11q23.3)' versus 'CN_CNMF'

P value = 1.76e-05 (Fisher's exact test), Q value = 0.0092

Table S33. Gene #41: 'Del Peak 19(11q23.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	97	91
DEL PEAK 19(11Q23.3) CNV	50	59	32
DEL PEAK 19(11Q23.3) WILD-TYPE	22	38	59

Figure S33. Get High-res Image Gene #41: 'Del Peak 19(11q23.3)' 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 = SKCM-TM.transferedmergedcluster.txt
Number of patients = 260
Number of copy number variation regions = 54
Number of molecular subtypes = 10
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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