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 62 peak regions and 12 molecular subtypes across 162 patients, 16 significant findings detected with Q value < 0.25.

Amp Peak 4(6p21.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 5(8p11.23) cnvs correlated to 'CN_CNMF'.
Amp Peak 6(8p11.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 7(8q24.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 13(13q12.13) cnvs correlated to 'CN_CNMF'.
Amp Peak 14(13q12.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 15(13q22.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 17(16p11.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 18(17q12) cnvs correlated to 'CN_CNMF'.
Amp Peak 19(17q24.1) cnvs correlated to 'CN_CNMF'.
Del Peak 3(1p13.2) cnvs correlated to 'CN_CNMF'.
Del Peak 8(4q22.1) cnvs correlated to 'CN_CNMF'.
Del Peak 15(8p23.2) cnvs correlated to 'CN_CNMF'.
Del Peak 24(15q22.33) cnvs correlated to 'CN_CNMF'.
Del Peak 30(18q21.2) cnvs correlated to 'CN_CNMF'.
Del Peak 31(18q22.1) 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 62 regions and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 16 significant findings detected.


		Molecular subtypes	MRNA CNMF	MRNA CHIERARCHICAL	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	Chi-square test	Fisher's exact test	Fisher's exact test	Chi-square test	Chi-square test	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Chi-square test
Amp Peak 4(6p21 1)	0 (0%)	110	0.0305 (1.00)	0.0161 (1.00)	0.000112 (0.0812)	0.0497 (1.00)	0.912 (1.00)	0.1 (1.00)	0.738 (1.00)	0.747 (1.00)	0.163 (1.00)	0.413 (1.00)	0.677 (1.00)	0.987 (1.00)
Amp Peak 5(8p11 23)	0 (0%)	110	0.00313 (1.00)	0.283 (1.00)	2.54e-08 (1.86e-05)	0.306 (1.00)	0.376 (1.00)	0.376 (1.00)	0.662 (1.00)	0.823 (1.00)	0.0568 (1.00)	0.00668 (1.00)	0.492 (1.00)	0.191 (1.00)
Amp Peak 6(8p11 21)	0 (0%)	93	0.0123 (1.00)	0.0875 (1.00)	2.38e-13 (1.75e-10)	0.0935 (1.00)	0.371 (1.00)	0.5 (1.00)	0.377 (1.00)	0.935 (1.00)	0.173 (1.00)	0.084 (1.00)	0.39 (1.00)	0.11 (1.00)
Amp Peak 7(8q24 21)	0 (0%)	55	0.0165 (1.00)	0.0726 (1.00)	1.7e-09 (1.25e-06)	0.0452 (1.00)	0.629 (1.00)	0.59 (1.00)	0.444 (1.00)	0.627 (1.00)	0.566 (1.00)	0.144 (1.00)	0.638 (1.00)	0.153 (1.00)
Amp Peak 13(13q12 13)	0 (0%)	41	0.416 (1.00)	1 (1.00)	3.06e-05 (0.0222)	0.456 (1.00)	0.424 (1.00)	0.427 (1.00)	0.0118 (1.00)	0.241 (1.00)	0.0122 (1.00)	0.00847 (1.00)	0.31 (1.00)	0.458 (1.00)
Amp Peak 14(13q12 2)	0 (0%)	42	0.363 (1.00)	0.889 (1.00)	4.86e-06 (0.00355)	0.311 (1.00)	0.736 (1.00)	0.548 (1.00)	0.0325 (1.00)	0.423 (1.00)	0.0737 (1.00)	0.0227 (1.00)	0.0371 (1.00)	0.425 (1.00)
Amp Peak 15(13q22 1)	0 (0%)	45	0.265 (1.00)	0.645 (1.00)	1.02e-07 (7.48e-05)	0.0811 (1.00)	0.907 (1.00)	0.14 (1.00)	0.372 (1.00)	0.418 (1.00)	0.00712 (1.00)	0.00304 (1.00)	0.0306 (1.00)	0.0945 (1.00)
Amp Peak 17(16p11 2)	0 (0%)	117	0.0674 (1.00)	0.59 (1.00)	2.96e-05 (0.0215)	0.252 (1.00)	0.3 (1.00)	0.306 (1.00)	0.388 (1.00)	0.789 (1.00)	0.178 (1.00)	0.816 (1.00)	0.202 (1.00)	0.123 (1.00)
Amp Peak 18(17q12)	0 (0%)	119	0.00641 (1.00)	0.196 (1.00)	0.0002 (0.145)	0.502 (1.00)	0.176 (1.00)	0.895 (1.00)	0.356 (1.00)	0.146 (1.00)	0.171 (1.00)	0.898 (1.00)	0.469 (1.00)	0.816 (1.00)
Amp Peak 19(17q24 1)	0 (0%)	125	0.291 (1.00)	0.942 (1.00)	0.000331 (0.238)	0.121 (1.00)	0.608 (1.00)	0.63 (1.00)	0.569 (1.00)	0.236 (1.00)	0.599 (1.00)	0.668 (1.00)	0.786 (1.00)	0.699 (1.00)
Del Peak 3(1p13 2)	0 (0%)	111	0.697 (1.00)	0.0287 (1.00)	0.000178 (0.129)	0.353 (1.00)	0.544 (1.00)	0.739 (1.00)	0.181 (1.00)	0.5 (1.00)	0.404 (1.00)	0.104 (1.00)	0.883 (1.00)	0.827 (1.00)
Del Peak 8(4q22 1)	0 (0%)	90	0.787 (1.00)	0.1 (1.00)	9.65e-05 (0.07)	0.114 (1.00)	0.702 (1.00)	0.711 (1.00)	0.0246 (1.00)	0.0556 (1.00)	0.917 (1.00)	0.0816 (1.00)	0.952 (1.00)	0.403 (1.00)
Del Peak 15(8p23 2)	0 (0%)	62	0.111 (1.00)	0.0638 (1.00)	6.4e-06 (0.00466)	0.0456 (1.00)	1 (1.00)	0.582 (1.00)	0.0289 (1.00)	0.23 (1.00)	0.643 (1.00)	0.863 (1.00)	0.544 (1.00)	0.45 (1.00)
Del Peak 24(15q22 33)	0 (0%)	87	0.72 (1.00)	0.0793 (1.00)	0.000218 (0.157)	0.605 (1.00)	0.194 (1.00)	0.215 (1.00)	0.26 (1.00)	0.51 (1.00)	0.384 (1.00)	0.777 (1.00)	0.683 (1.00)	0.735 (1.00)
Del Peak 30(18q21 2)	0 (0%)	19	0.132 (1.00)	0.123 (1.00)	5.18e-06 (0.00378)	0.152 (1.00)	1 (1.00)	0.573 (1.00)	0.12 (1.00)	0.423 (1.00)	0.433 (1.00)	0.231 (1.00)	0.581 (1.00)	0.861 (1.00)
Del Peak 31(18q22 1)	0 (0%)	24	0.0671 (1.00)	0.0605 (1.00)	2.38e-07 (0.000174)	0.0366 (1.00)	0.776 (1.00)	0.484 (1.00)	0.00538 (1.00)	0.475 (1.00)	0.805 (1.00)	0.493 (1.00)	0.0159 (1.00)	0.435 (1.00)
Amp Peak 1(1q21 3)	0 (0%)	114	1 (1.00)	0.63 (1.00)	0.000676 (0.483)	0.619 (1.00)	0.531 (1.00)	0.18 (1.00)	0.776 (1.00)	0.0138 (1.00)	0.0805 (1.00)	0.646 (1.00)	0.0818 (1.00)	0.893 (1.00)
Amp Peak 2(1q32 2)	0 (0%)	114	0.827 (1.00)	0.88 (1.00)	0.00918 (1.00)	0.575 (1.00)	0.185 (1.00)	0.0535 (1.00)	0.912 (1.00)	0.0667 (1.00)	0.11 (1.00)	0.39 (1.00)	0.0179 (1.00)	0.696 (1.00)
Amp Peak 3(5q22 3)	0 (0%)	143	0.0141 (1.00)	0.566 (1.00)	0.118 (1.00)	0.254 (1.00)	0.159 (1.00)	0.445 (1.00)	0.0738 (1.00)	0.215 (1.00)	0.485 (1.00)	0.65 (1.00)	0.0569 (1.00)	0.278 (1.00)
Amp Peak 8(10q22 2)	0 (0%)	151	0.502 (1.00)	0.865 (1.00)	0.912 (1.00)	1 (1.00)	1 (1.00)	0.694 (1.00)			0.387 (1.00)	0.28 (1.00)	0.594 (1.00)	0.861 (1.00)
Amp Peak 9(11p15 5)	0 (0%)	119	0.536 (1.00)	0.775 (1.00)	0.0286 (1.00)	0.873 (1.00)	0.697 (1.00)	0.696 (1.00)	0.00835 (1.00)	0.00295 (1.00)	0.0902 (1.00)	0.47 (1.00)	0.6 (1.00)	0.00644 (1.00)
Amp Peak 10(11q13 3)	0 (0%)	136	0.0613 (1.00)	0.0402 (1.00)	0.000568 (0.408)	0.00267 (1.00)	0.906 (1.00)	0.861 (1.00)	0.105 (1.00)	0.67 (1.00)	0.0151 (1.00)	0.136 (1.00)	0.674 (1.00)	0.66 (1.00)
Amp Peak 11(12p13 33)	0 (0%)	121	0.69 (1.00)	1 (1.00)	0.0385 (1.00)	0.512 (1.00)	0.113 (1.00)	0.0558 (1.00)	0.452 (1.00)	0.241 (1.00)	0.593 (1.00)	0.84 (1.00)	0.18 (1.00)	0.463 (1.00)
Amp Peak 12(12p12 1)	0 (0%)	122	0.697 (1.00)	1 (1.00)	0.036 (1.00)	0.488 (1.00)	0.0503 (1.00)	0.0273 (1.00)	0.605 (1.00)	0.197 (1.00)	0.681 (1.00)	0.42 (1.00)	0.0552 (1.00)	0.515 (1.00)
Amp Peak 16(15q26 1)	0 (0%)	147	0.183 (1.00)	0.155 (1.00)	0.314 (1.00)	0.49 (1.00)	0.101 (1.00)	0.244 (1.00)	0.189 (1.00)	0.215 (1.00)	0.503 (1.00)	0.919 (1.00)	0.454 (1.00)	0.278 (1.00)
Amp Peak 20(19p13 2)	0 (0%)	130	0.0202 (1.00)	0.00871 (1.00)	0.000599 (0.429)	0.673 (1.00)	0.389 (1.00)	0.259 (1.00)	0.153 (1.00)	0.531 (1.00)	0.643 (1.00)	0.916 (1.00)	0.606 (1.00)	0.602 (1.00)
Amp Peak 21(20q11 21)	0 (0%)	19	0.00777 (1.00)	0.376 (1.00)	0.00116 (0.824)	0.0342 (1.00)	0.194 (1.00)	0.0766 (1.00)	0.552 (1.00)	0.271 (1.00)	0.0283 (1.00)	0.0916 (1.00)	0.0125 (1.00)	0.309 (1.00)
Amp Peak 22(20q11 23)	0 (0%)	18	0.00777 (1.00)	0.376 (1.00)	0.00257 (1.00)	0.094 (1.00)	0.194 (1.00)	0.0766 (1.00)	0.552 (1.00)	0.271 (1.00)	0.0504 (1.00)	0.0697 (1.00)	0.0332 (1.00)	0.493 (1.00)
Amp Peak 23(20q13 31)	0 (0%)	17	0.00462 (1.00)	0.31 (1.00)	0.00544 (1.00)	0.094 (1.00)	0.194 (1.00)	0.0766 (1.00)	0.552 (1.00)	0.271 (1.00)	0.0728 (1.00)	0.109 (1.00)	0.0332 (1.00)	0.493 (1.00)
Amp Peak 24(Xp22 2)	0 (0%)	129	0.0247 (1.00)	0.056 (1.00)	0.644 (1.00)	0.504 (1.00)	0.795 (1.00)	0.66 (1.00)	0.991 (1.00)	1 (1.00)	0.775 (1.00)	0.955 (1.00)	0.166 (1.00)	0.28 (1.00)
Amp Peak 25(Xq27 3)	0 (0%)	124	0.209 (1.00)	0.564 (1.00)	0.0252 (1.00)	0.0389 (1.00)	0.586 (1.00)	0.182 (1.00)	0.252 (1.00)	0.702 (1.00)	0.56 (1.00)	0.442 (1.00)	0.185 (1.00)	0.424 (1.00)
Del Peak 1(1p36 11)	0 (0%)	91	0.24 (1.00)	0.0255 (1.00)	0.429 (1.00)	0.0677 (1.00)	0.803 (1.00)	0.801 (1.00)	0.569 (1.00)	1 (1.00)	0.467 (1.00)	0.755 (1.00)	0.9 (1.00)	0.938 (1.00)
Del Peak 2(1p33)	0 (0%)	113	0.626 (1.00)	0.00289 (1.00)	0.00196 (1.00)	0.0563 (1.00)	0.88 (1.00)	0.247 (1.00)	0.661 (1.00)	1 (1.00)	0.369 (1.00)	0.187 (1.00)	0.937 (1.00)	0.691 (1.00)
Del Peak 4(2p12)	0 (0%)	145	0.393 (1.00)	0.467 (1.00)	0.0623 (1.00)	0.884 (1.00)	0.344 (1.00)	0.171 (1.00)	0.655 (1.00)	1 (1.00)	0.37 (1.00)	0.62 (1.00)	0.515 (1.00)	0.568 (1.00)
Del Peak 5(3p14 2)	0 (0%)	133	0.8 (1.00)	0.491 (1.00)	0.606 (1.00)	0.833 (1.00)	0.217 (1.00)	0.694 (1.00)	0.268 (1.00)	0.319 (1.00)	0.832 (1.00)	1 (1.00)	0.519 (1.00)	0.651 (1.00)
Del Peak 6(3q26 31)	0 (0%)	145	1 (1.00)	0.383 (1.00)	0.604 (1.00)	1 (1.00)	0.746 (1.00)	0.703 (1.00)	0.242 (1.00)	1 (1.00)	0.0981 (1.00)	0.933 (1.00)	0.0822 (1.00)	0.807 (1.00)
Del Peak 7(4p13)	0 (0%)	104	0.78 (1.00)	0.228 (1.00)	0.000895 (0.639)	0.024 (1.00)	0.787 (1.00)	0.313 (1.00)	0.503 (1.00)	0.293 (1.00)	0.975 (1.00)	0.0616 (1.00)	0.626 (1.00)	0.226 (1.00)
Del Peak 9(4q35 1)	0 (0%)	90	0.609 (1.00)	0.334 (1.00)	0.000537 (0.386)	0.0525 (1.00)	0.506 (1.00)	0.688 (1.00)	0.452 (1.00)	0.038 (1.00)	0.431 (1.00)	0.0369 (1.00)	0.899 (1.00)	0.349 (1.00)
Del Peak 10(5q11 2)	0 (0%)	113	0.168 (1.00)	0.0498 (1.00)	0.102 (1.00)	0.00391 (1.00)	0.94 (1.00)	0.24 (1.00)	0.117 (1.00)	0.93 (1.00)	0.458 (1.00)	0.0378 (1.00)	0.142 (1.00)	0.157 (1.00)
Del Peak 11(5q22 2)	0 (0%)	107	0.313 (1.00)	0.019 (1.00)	0.0844 (1.00)	0.397 (1.00)	0.684 (1.00)	0.987 (1.00)	0.468 (1.00)	0.675 (1.00)	0.66 (1.00)	0.191 (1.00)	0.0623 (1.00)	0.104 (1.00)
Del Peak 12(6p25 3)	0 (0%)	138	1 (1.00)	0.826 (1.00)	0.648 (1.00)	0.0338 (1.00)	0.654 (1.00)	0.988 (1.00)	0.68 (1.00)	0.554 (1.00)	0.69 (1.00)	0.568 (1.00)	0.698 (1.00)	0.476 (1.00)
Del Peak 13(6q26)	0 (0%)	132	0.158 (1.00)	0.0354 (1.00)	0.159 (1.00)	0.799 (1.00)	0.0993 (1.00)	0.343 (1.00)	0.89 (1.00)	0.648 (1.00)	0.0771 (1.00)	0.0645 (1.00)	0.302 (1.00)	0.566 (1.00)
Del Peak 14(7q31 1)	0 (0%)	158			0.311 (1.00)		1 (1.00)	0.459 (1.00)			0.749 (1.00)	1 (1.00)
Del Peak 16(8p11 21)	0 (0%)	138	0.317 (1.00)	0.69 (1.00)	0.14 (1.00)	0.324 (1.00)	0.112 (1.00)	0.56 (1.00)	0.408 (1.00)	0.423 (1.00)	0.0753 (1.00)	0.117 (1.00)	0.17 (1.00)	0.0408 (1.00)
Del Peak 17(10q21 1)	0 (0%)	125	0.218 (1.00)	0.228 (1.00)	0.0716 (1.00)	0.246 (1.00)	0.0595 (1.00)	0.0237 (1.00)	0.183 (1.00)	0.62 (1.00)	0.747 (1.00)	0.892 (1.00)	0.864 (1.00)	0.594 (1.00)
Del Peak 18(10q25 2)	0 (0%)	115	0.57 (1.00)	0.626 (1.00)	0.806 (1.00)	0.595 (1.00)	0.455 (1.00)	0.203 (1.00)	0.129 (1.00)	0.928 (1.00)	0.703 (1.00)	0.742 (1.00)	0.983 (1.00)	0.615 (1.00)
Del Peak 19(11q22 3)	0 (0%)	125	0.00481 (1.00)	0.0127 (1.00)	0.0015 (1.00)	0.09 (1.00)	0.826 (1.00)	0.0557 (1.00)	0.0198 (1.00)	0.000489 (0.352)	0.444 (1.00)	0.617 (1.00)	0.725 (1.00)	0.543 (1.00)
Del Peak 20(12p13 1)	0 (0%)	129	1 (1.00)	1 (1.00)	0.657 (1.00)	0.224 (1.00)	0.535 (1.00)	0.311 (1.00)	0.391 (1.00)	0.00666 (1.00)	0.287 (1.00)	0.224 (1.00)	0.794 (1.00)	0.155 (1.00)
Del Peak 21(12q21 33)	0 (0%)	134	0.671 (1.00)	0.92 (1.00)	0.0206 (1.00)	0.69 (1.00)	0.606 (1.00)	0.775 (1.00)	0.383 (1.00)	0.0422 (1.00)	0.467 (1.00)	0.247 (1.00)	0.617 (1.00)	0.368 (1.00)
Del Peak 22(14q11 2)	0 (0%)	95	0.678 (1.00)	0.666 (1.00)	0.00346 (1.00)	1 (1.00)	0.803 (1.00)	0.888 (1.00)	0.395 (1.00)	0.39 (1.00)	0.0858 (1.00)	0.141 (1.00)	0.702 (1.00)	0.632 (1.00)
Del Peak 23(14q31 1)	0 (0%)	93	0.678 (1.00)	0.666 (1.00)	0.0115 (1.00)	1 (1.00)	0.633 (1.00)	0.316 (1.00)	0.261 (1.00)	0.442 (1.00)	0.161 (1.00)	0.2 (1.00)	0.853 (1.00)	0.798 (1.00)
Del Peak 25(16p13 3)	0 (0%)	149	0.886 (1.00)	0.778 (1.00)	0.535 (1.00)	0.0269 (1.00)	0.725 (1.00)	0.667 (1.00)	0.747 (1.00)	1 (1.00)	0.237 (1.00)	0.317 (1.00)	0.913 (1.00)	0.693 (1.00)
Del Peak 26(16q23 1)	0 (0%)	139	0.153 (1.00)	0.191 (1.00)	0.0873 (1.00)	0.202 (1.00)	0.589 (1.00)	0.711 (1.00)	0.44 (1.00)	1 (1.00)	0.619 (1.00)	0.103 (1.00)	0.613 (1.00)	0.237 (1.00)
Del Peak 27(17p12)	0 (0%)	52	0.165 (1.00)	0.485 (1.00)	0.0299 (1.00)	0.555 (1.00)	0.521 (1.00)	0.756 (1.00)	0.206 (1.00)	0.0314 (1.00)	0.87 (1.00)	0.446 (1.00)	0.479 (1.00)	0.697 (1.00)
Del Peak 28(17p11 2)	0 (0%)	60	0.331 (1.00)	0.52 (1.00)	0.0494 (1.00)	0.797 (1.00)	0.919 (1.00)	0.379 (1.00)	0.0582 (1.00)	0.0696 (1.00)	0.999 (1.00)	0.915 (1.00)	1 (1.00)	0.767 (1.00)
Del Peak 29(17q25 3)	0 (0%)	138	0.544 (1.00)	0.236 (1.00)	0.192 (1.00)	0.0232 (1.00)	0.457 (1.00)	0.171 (1.00)	0.0483 (1.00)	0.015 (1.00)	0.352 (1.00)	0.155 (1.00)	0.409 (1.00)	0.175 (1.00)
Del Peak 32(19p13 3)	0 (0%)	124	0.198 (1.00)	0.491 (1.00)	0.0671 (1.00)	0.0528 (1.00)	0.893 (1.00)	0.958 (1.00)	0.409 (1.00)	0.0191 (1.00)	0.492 (1.00)	0.0125 (1.00)	0.323 (1.00)	0.215 (1.00)
Del Peak 33(20p12 1)	0 (0%)	102	0.621 (1.00)	0.782 (1.00)	0.0361 (1.00)	0.724 (1.00)	0.54 (1.00)	0.28 (1.00)	0.233 (1.00)	0.93 (1.00)	0.0474 (1.00)	0.234 (1.00)	0.777 (1.00)	0.957 (1.00)
Del Peak 34(20p12 1)	0 (0%)	102	0.621 (1.00)	0.782 (1.00)	0.0361 (1.00)	0.724 (1.00)	0.54 (1.00)	0.28 (1.00)	0.233 (1.00)	0.93 (1.00)	0.0474 (1.00)	0.234 (1.00)	0.777 (1.00)	0.957 (1.00)
Del Peak 35(21q11 2)	0 (0%)	92	0.486 (1.00)	0.12 (1.00)	0.304 (1.00)	0.964 (1.00)	0.924 (1.00)	0.41 (1.00)	0.55 (1.00)	0.937 (1.00)	0.052 (1.00)	0.465 (1.00)	0.348 (1.00)	0.53 (1.00)
Del Peak 36(22q13 31)	0 (0%)	96	0.952 (1.00)	0.513 (1.00)	0.222 (1.00)	0.695 (1.00)	0.532 (1.00)	0.462 (1.00)	0.264 (1.00)	0.194 (1.00)	0.00619 (1.00)	0.337 (1.00)	0.198 (1.00)	0.183 (1.00)
Del Peak 37(Xp22 33)	0 (0%)	129	0.778 (1.00)	0.775 (1.00)	0.266 (1.00)	0.00204 (1.00)	0.724 (1.00)	0.801 (1.00)	0.91 (1.00)	1 (1.00)	0.643 (1.00)	0.819 (1.00)	0.977 (1.00)	0.699 (1.00)

'Amp Peak 4(6p21.1)' versus 'CN_CNMF'

P value = 0.000112 (Chi-square test), Q value = 0.081

Table S1. Gene #4: 'Amp Peak 4(6p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	7	32	46	55	22
AMP PEAK 4(6P21.1) CNV	4	16	11	8	13
AMP PEAK 4(6P21.1) WILD-TYPE	3	16	35	47	9

Figure S1. Get High-res Image Gene #4: 'Amp Peak 4(6p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 5(8p11.23)' versus 'CN_CNMF'

P value = 2.54e-08 (Chi-square test), Q value = 1.9e-05

Table S2. Gene #5: 'Amp Peak 5(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	7	32	46	55	22
AMP PEAK 5(8P11.23) CNV	2	12	29	2	7
AMP PEAK 5(8P11.23) WILD-TYPE	5	20	17	53	15

Figure S2. Get High-res Image Gene #5: 'Amp Peak 5(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 6(8p11.21)' versus 'CN_CNMF'

P value = 2.38e-13 (Chi-square test), Q value = 1.7e-10

Table S3. Gene #6: 'Amp Peak 6(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	7	32	46	55	22
AMP PEAK 6(8P11.21) CNV	3	13	40	4	9
AMP PEAK 6(8P11.21) WILD-TYPE	4	19	6	51	13

Figure S3. Get High-res Image Gene #6: 'Amp Peak 6(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 7(8q24.21)' versus 'CN_CNMF'

P value = 1.7e-09 (Chi-square test), Q value = 1.2e-06

Table S4. Gene #7: 'Amp Peak 7(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	7	32	46	55	22
AMP PEAK 7(8Q24.21) CNV	4	25	46	22	10
AMP PEAK 7(8Q24.21) WILD-TYPE	3	7	0	33	12

Figure S4. Get High-res Image Gene #7: 'Amp Peak 7(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 13(13q12.13)' versus 'CN_CNMF'

P value = 3.06e-05 (Chi-square test), Q value = 0.022

Table S5. Gene #13: 'Amp Peak 13(13q12.13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	7	32	46	55	22
AMP PEAK 13(13Q12.13) CNV	6	30	33	30	22
AMP PEAK 13(13Q12.13) WILD-TYPE	1	2	13	25	0

Figure S5. Get High-res Image Gene #13: 'Amp Peak 13(13q12.13)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 14(13q12.2)' versus 'CN_CNMF'

P value = 4.86e-06 (Chi-square test), Q value = 0.0036

Table S6. Gene #14: 'Amp Peak 14(13q12.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	7	32	46	55	22
AMP PEAK 14(13Q12.2) CNV	6	30	34	28	22
AMP PEAK 14(13Q12.2) WILD-TYPE	1	2	12	27	0

Figure S6. Get High-res Image Gene #14: 'Amp Peak 14(13q12.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 15(13q22.1)' versus 'CN_CNMF'

P value = 1.02e-07 (Chi-square test), Q value = 7.5e-05

Table S7. Gene #15: 'Amp Peak 15(13q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	7	32	46	55	22
AMP PEAK 15(13Q22.1) CNV	7	30	33	25	22
AMP PEAK 15(13Q22.1) WILD-TYPE	0	2	13	30	0

Figure S7. Get High-res Image Gene #15: 'Amp Peak 15(13q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 17(16p11.2)' versus 'CN_CNMF'

P value = 2.96e-05 (Chi-square test), Q value = 0.021

Table S8. Gene #17: 'Amp Peak 17(16p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	7	32	46	55	22
AMP PEAK 17(16P11.2) CNV	2	16	10	5	12
AMP PEAK 17(16P11.2) WILD-TYPE	5	16	36	50	10

Figure S8. Get High-res Image Gene #17: 'Amp Peak 17(16p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 18(17q12)' versus 'CN_CNMF'

P value = 2e-04 (Chi-square test), Q value = 0.14

Table S9. Gene #18: 'Amp Peak 18(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	7	32	46	55	22
AMP PEAK 18(17Q12) CNV	2	17	15	8	1
AMP PEAK 18(17Q12) WILD-TYPE	5	15	31	47	21

Figure S9. Get High-res Image Gene #18: 'Amp Peak 18(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 19(17q24.1)' versus 'CN_CNMF'

P value = 0.000331 (Chi-square test), Q value = 0.24

Table S10. Gene #19: 'Amp Peak 19(17q24.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	7	32	46	55	22
AMP PEAK 19(17Q24.1) CNV	1	16	10	10	0
AMP PEAK 19(17Q24.1) WILD-TYPE	6	16	36	45	22

Figure S10. Get High-res Image Gene #19: 'Amp Peak 19(17q24.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 3(1p13.2)' versus 'CN_CNMF'

P value = 0.000178 (Chi-square test), Q value = 0.13

Table S11. Gene #28: 'Del Peak 3(1p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	7	32	46	55	22
DEL PEAK 3(1P13.2) CNV	6	15	16	7	7
DEL PEAK 3(1P13.2) WILD-TYPE	1	17	30	48	15

Figure S11. Get High-res Image Gene #28: 'Del Peak 3(1p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 8(4q22.1)' versus 'CN_CNMF'

P value = 9.65e-05 (Chi-square test), Q value = 0.07

Table S12. Gene #33: 'Del Peak 8(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	7	32	46	55	22
DEL PEAK 8(4Q22.1) CNV	6	18	19	13	16
DEL PEAK 8(4Q22.1) WILD-TYPE	1	14	27	42	6

Figure S12. Get High-res Image Gene #33: 'Del Peak 8(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 15(8p23.2)' versus 'CN_CNMF'

P value = 6.4e-06 (Chi-square test), Q value = 0.0047

Table S13. Gene #40: 'Del Peak 15(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	7	32	46	55	22
DEL PEAK 15(8P23.2) CNV	6	25	37	19	13
DEL PEAK 15(8P23.2) WILD-TYPE	1	7	9	36	9

Figure S13. Get High-res Image Gene #40: 'Del Peak 15(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 24(15q22.33)' versus 'CN_CNMF'

P value = 0.000218 (Chi-square test), Q value = 0.16

Table S14. Gene #49: 'Del Peak 24(15q22.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	7	32	46	55	22
DEL PEAK 24(15Q22.33) CNV	6	20	22	13	14
DEL PEAK 24(15Q22.33) WILD-TYPE	1	12	24	42	8

Figure S14. Get High-res Image Gene #49: 'Del Peak 24(15q22.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 30(18q21.2)' versus 'CN_CNMF'

P value = 5.18e-06 (Chi-square test), Q value = 0.0038

Table S15. Gene #55: 'Del Peak 30(18q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	7	32	46	55	22
DEL PEAK 30(18Q21.2) CNV	7	32	45	38	21
DEL PEAK 30(18Q21.2) WILD-TYPE	0	0	1	17	1

Figure S15. Get High-res Image Gene #55: 'Del Peak 30(18q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 31(18q22.1)' versus 'CN_CNMF'

P value = 2.38e-07 (Chi-square test), Q value = 0.00017

Table S16. Gene #56: 'Del Peak 31(18q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	7	32	46	55	22
DEL PEAK 31(18Q22.1) CNV	7	32	44	34	21
DEL PEAK 31(18Q22.1) WILD-TYPE	0	0	2	21	1

Figure S16. Get High-res Image Gene #56: 'Del Peak 31(18q22.1)' versus Molecular Subtype #3: '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 = READ-TP.transferedmergedcluster.txt
Number of patients = 162
Number of copy number variation regions = 62
Number of molecular subtypes = 12
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.

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

Made with Nozzle