Correlation between copy number variation genes (focal events) and molecular subtypes

Rectum Adenocarcinoma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

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 (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1W37V79

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 59 focal events and 12 molecular subtypes across 165 patients, 12 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_8p11.23 cnv correlated to 'CN_CNMF'.
amp_8p11.21 cnv correlated to 'CN_CNMF'.
amp_8q24.21 cnv correlated to 'CN_CNMF'.
amp_13q12.13 cnv correlated to 'CN_CNMF'.
amp_13q12.2 cnv correlated to 'CN_CNMF'.
amp_13q22.1 cnv correlated to 'CN_CNMF'.
del_2p12 cnv correlated to 'CN_CNMF'.
del_8p23.2 cnv correlated to 'CN_CNMF'.
del_14q11.2 cnv correlated to 'CN_CNMF'.
del_15q22.33 cnv correlated to 'CN_CNMF'.
del_18q21.2 cnv correlated to 'CN_CNMF'.
del_18q22.1 cnv correlated to 'CN_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 59 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 12 significant findings detected.


		Clinical Features	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	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	Fisher's exact test	Fisher's exact test
amp 8p11 23	53 (32%)	112	0.00353 (1.00)	0.208 (1.00)	1e-05 (0.00699)	0.266 (1.00)	0.377 (1.00)	0.129 (1.00)	0.125 (1.00)	0.0343 (1.00)	0.0487 (1.00)	0.0272 (1.00)	0.979 (1.00)	0.119 (1.00)
amp 8p11 21	70 (42%)	95	0.0119 (1.00)	0.211 (1.00)	1e-05 (0.00699)	0.234 (1.00)	0.37 (1.00)	0.52 (1.00)	0.227 (1.00)	0.134 (1.00)	0.182 (1.00)	0.274 (1.00)	0.226 (1.00)	0.322 (1.00)
amp 8q24 21	109 (66%)	56	0.0169 (1.00)	0.242 (1.00)	1e-05 (0.00699)	0.127 (1.00)	0.628 (1.00)	0.887 (1.00)	0.0307 (1.00)	0.00726 (1.00)	0.54 (1.00)	0.263 (1.00)	0.0748 (1.00)	0.443 (1.00)
amp 13q12 13	126 (76%)	39	0.416 (1.00)	0.176 (1.00)	2e-05 (0.0139)	0.173 (1.00)	0.325 (1.00)	0.436 (1.00)	0.00165 (1.00)	0.00223 (1.00)	0.00269 (1.00)	0.00397 (1.00)	0.939 (1.00)	0.782 (1.00)
amp 13q12 2	125 (76%)	40	0.363 (1.00)	0.235 (1.00)	1e-05 (0.00699)	0.115 (1.00)	0.592 (1.00)	0.589 (1.00)	0.0158 (1.00)	0.0119 (1.00)	0.0213 (1.00)	0.0218 (1.00)	0.824 (1.00)	0.636 (1.00)
amp 13q22 1	120 (73%)	45	0.265 (1.00)	0.0644 (1.00)	2e-05 (0.0139)	0.0343 (1.00)	0.907 (1.00)	0.271 (1.00)	0.00461 (1.00)	0.00105 (0.712)	0.00442 (1.00)	0.0104 (1.00)	1 (1.00)	0.4 (1.00)
del 2p12	13 (8%)	152	0.394 (1.00)	0.837 (1.00)	2e-05 (0.0139)	1 (1.00)	0.344 (1.00)	0.149 (1.00)	0.251 (1.00)	0.0996 (1.00)	0.15 (1.00)	0.145 (1.00)
del 8p23 2	100 (61%)	65	0.111 (1.00)	0.0885 (1.00)	0.00015 (0.103)	0.461 (1.00)	1 (1.00)	0.271 (1.00)	0.064 (1.00)	0.0265 (1.00)	0.779 (1.00)	0.331 (1.00)	0.557 (1.00)	0.506 (1.00)
del 14q11 2	70 (42%)	95	0.483 (1.00)	0.128 (1.00)	0.00021 (0.144)	0.932 (1.00)	0.703 (1.00)	0.693 (1.00)	0.0686 (1.00)	0.276 (1.00)	0.11 (1.00)	0.342 (1.00)	0.751 (1.00)	0.785 (1.00)
del 15q22 33	77 (47%)	88	0.624 (1.00)	0.155 (1.00)	9e-05 (0.0621)	0.596 (1.00)	0.148 (1.00)	0.0587 (1.00)	0.786 (1.00)	0.184 (1.00)	0.421 (1.00)	0.746 (1.00)	0.856 (1.00)	0.522 (1.00)
del 18q21 2	145 (88%)	20	0.131 (1.00)	0.337 (1.00)	2e-05 (0.0139)	0.0458 (1.00)	1 (1.00)	0.77 (1.00)	0.936 (1.00)	0.811 (1.00)	0.401 (1.00)	0.122 (1.00)	0.902 (1.00)	0.866 (1.00)
del 18q22 1	141 (85%)	24	0.0665 (1.00)	0.0887 (1.00)	1e-05 (0.00699)	0.0275 (1.00)	0.777 (1.00)	0.651 (1.00)	0.622 (1.00)	0.68 (1.00)	0.829 (1.00)	0.299 (1.00)	0.785 (1.00)	1 (1.00)
amp 1q21 3	48 (29%)	117	1 (1.00)	0.851 (1.00)	0.00332 (1.00)	0.926 (1.00)	0.532 (1.00)	0.226 (1.00)	0.506 (1.00)	0.362 (1.00)	0.0567 (1.00)	0.15 (1.00)	0.928 (1.00)	0.395 (1.00)
amp 1q32 2	48 (29%)	117	0.827 (1.00)	0.937 (1.00)	0.0387 (1.00)	0.513 (1.00)	0.187 (1.00)	0.0276 (1.00)	0.507 (1.00)	0.543 (1.00)	0.0811 (1.00)	0.651 (1.00)	0.297 (1.00)	0.119 (1.00)
amp 5q22 3	20 (12%)	145	0.022 (1.00)	0.174 (1.00)	0.00859 (1.00)	0.224 (1.00)	0.106 (1.00)	0.658 (1.00)	0.721 (1.00)	0.681 (1.00)	0.453 (1.00)	0.663 (1.00)	1 (1.00)	0.285 (1.00)
amp 6p21 1	54 (33%)	111	0.0587 (1.00)	0.106 (1.00)	0.00062 (0.425)	0.0598 (1.00)	0.808 (1.00)	0.0458 (1.00)	0.574 (1.00)	0.337 (1.00)	0.192 (1.00)	0.39 (1.00)	0.367 (1.00)	0.783 (1.00)
amp 10q22 2	11 (7%)	154	0.501 (1.00)	0.931 (1.00)	0.536 (1.00)	1 (1.00)	1 (1.00)	0.972 (1.00)	0.22 (1.00)	0.191 (1.00)	0.377 (1.00)	0.189 (1.00)
amp 11p15 5	45 (27%)	120	0.381 (1.00)	0.0961 (1.00)	0.0789 (1.00)	0.621 (1.00)	0.72 (1.00)	0.586 (1.00)	0.137 (1.00)	0.0338 (1.00)	0.0972 (1.00)	0.538 (1.00)	0.452 (1.00)	0.0897 (1.00)
amp 11q13 3	28 (17%)	137	0.327 (1.00)	0.332 (1.00)	0.0351 (1.00)	0.00418 (1.00)	0.912 (1.00)	0.731 (1.00)	0.142 (1.00)	0.00189 (1.00)	0.0142 (1.00)	0.338 (1.00)	0.0783 (1.00)	0.135 (1.00)
amp 12p13 33	41 (25%)	124	0.689 (1.00)	0.483 (1.00)	0.0332 (1.00)	0.724 (1.00)	0.114 (1.00)	0.215 (1.00)	0.81 (1.00)	0.832 (1.00)	0.578 (1.00)	0.817 (1.00)	0.437 (1.00)	0.23 (1.00)
amp 12p12 1	40 (24%)	125	0.7 (1.00)	0.468 (1.00)	0.0302 (1.00)	0.366 (1.00)	0.0493 (1.00)	0.00868 (1.00)	0.704 (1.00)	0.511 (1.00)	0.692 (1.00)	0.759 (1.00)	0.436 (1.00)	0.147 (1.00)
amp 15q26 1	13 (8%)	152	0.111 (1.00)	0.211 (1.00)	1 (1.00)	0.42 (1.00)	0.153 (1.00)	0.346 (1.00)	0.0908 (1.00)	0.122 (1.00)	0.907 (1.00)	1 (1.00)	0.744 (1.00)	0.641 (1.00)
amp 16p11 2	47 (28%)	118	0.123 (1.00)	0.577 (1.00)	0.0005 (0.343)	0.128 (1.00)	0.343 (1.00)	0.666 (1.00)	0.153 (1.00)	0.119 (1.00)	0.0968 (1.00)	0.851 (1.00)	0.643 (1.00)	0.987 (1.00)
amp 17q12	46 (28%)	119	0.00642 (1.00)	0.129 (1.00)	0.00152 (1.00)	0.376 (1.00)	0.176 (1.00)	0.916 (1.00)	0.434 (1.00)	0.0253 (1.00)	0.149 (1.00)	0.597 (1.00)	0.119 (1.00)	0.637 (1.00)
amp 17q24 1	39 (24%)	126	0.294 (1.00)	0.707 (1.00)	0.00085 (0.578)	0.148 (1.00)	0.61 (1.00)	0.748 (1.00)	0.64 (1.00)	0.17 (1.00)	0.61 (1.00)	0.206 (1.00)	0.496 (1.00)	0.938 (1.00)
amp 19p13 2	36 (22%)	129	0.02 (1.00)	0.249 (1.00)	0.00104 (0.706)	0.531 (1.00)	0.544 (1.00)	0.0853 (1.00)	0.0592 (1.00)	0.704 (1.00)	0.588 (1.00)	0.695 (1.00)	0.87 (1.00)	0.87 (1.00)
amp 20q11 21	146 (88%)	19	0.00684 (1.00)	0.164 (1.00)	0.00067 (0.458)	0.0203 (1.00)	0.192 (1.00)	0.367 (1.00)	0.0587 (1.00)	0.003 (1.00)	0.0074 (1.00)	0.397 (1.00)	0.496 (1.00)	0.592 (1.00)
amp 20q11 23	147 (89%)	18	0.00789 (1.00)	0.163 (1.00)	0.00137 (0.926)	0.0485 (1.00)	0.194 (1.00)	0.372 (1.00)	0.0402 (1.00)	0.00244 (1.00)	0.0149 (1.00)	0.278 (1.00)	0.361 (1.00)	1 (1.00)
amp 20q13 31	148 (90%)	17	0.0045 (1.00)	0.106 (1.00)	0.00248 (1.00)	0.0467 (1.00)	0.195 (1.00)	0.371 (1.00)	0.0603 (1.00)	0.00629 (1.00)	0.0215 (1.00)	0.382 (1.00)	0.363 (1.00)	1 (1.00)
amp xp22 2	32 (19%)	133	0.0526 (1.00)	0.221 (1.00)	0.595 (1.00)	0.275 (1.00)	0.961 (1.00)	0.235 (1.00)	0.709 (1.00)	0.173 (1.00)	0.813 (1.00)	0.869 (1.00)	0.183 (1.00)	0.95 (1.00)
del 1p36 11	75 (45%)	90	0.113 (1.00)	0.0639 (1.00)	0.196 (1.00)	0.145 (1.00)	0.703 (1.00)	0.923 (1.00)	0.729 (1.00)	0.0215 (1.00)	0.495 (1.00)	0.0646 (1.00)	0.356 (1.00)	0.798 (1.00)
del 1p33	53 (32%)	112	0.365 (1.00)	0.00398 (1.00)	0.0163 (1.00)	0.139 (1.00)	0.8 (1.00)	0.31 (1.00)	0.698 (1.00)	0.162 (1.00)	0.445 (1.00)	0.266 (1.00)	0.558 (1.00)	0.567 (1.00)
del 1p13 2	54 (33%)	111	0.473 (1.00)	0.0241 (1.00)	0.00276 (1.00)	0.576 (1.00)	0.546 (1.00)	0.572 (1.00)	0.244 (1.00)	0.029 (1.00)	0.505 (1.00)	0.211 (1.00)	0.648 (1.00)	0.615 (1.00)
del 3p14 2	31 (19%)	134	0.8 (1.00)	0.701 (1.00)	0.776 (1.00)	1 (1.00)	0.216 (1.00)	0.716 (1.00)	0.345 (1.00)	0.764 (1.00)	0.809 (1.00)	0.96 (1.00)	0.257 (1.00)	0.248 (1.00)
del 3q26 31	18 (11%)	147	1 (1.00)	0.868 (1.00)	0.151 (1.00)	0.477 (1.00)	0.448 (1.00)	0.239 (1.00)	0.111 (1.00)	0.529 (1.00)	0.264 (1.00)	0.0575 (1.00)	0.785 (1.00)	0.367 (1.00)
del 4p13	60 (36%)	105	0.782 (1.00)	0.0386 (1.00)	0.00076 (0.518)	0.0691 (1.00)	0.838 (1.00)	0.505 (1.00)	0.711 (1.00)	0.254 (1.00)	0.978 (1.00)	0.219 (1.00)	0.165 (1.00)	0.499 (1.00)
del 4q22 1	73 (44%)	92	0.616 (1.00)	0.0247 (1.00)	0.00041 (0.282)	0.235 (1.00)	0.701 (1.00)	0.477 (1.00)	0.394 (1.00)	0.312 (1.00)	0.987 (1.00)	0.254 (1.00)	0.615 (1.00)	0.706 (1.00)
del 4q35 1	72 (44%)	93	0.61 (1.00)	0.0634 (1.00)	0.00195 (1.00)	0.106 (1.00)	0.383 (1.00)	0.656 (1.00)	0.251 (1.00)	0.031 (1.00)	0.484 (1.00)	0.0505 (1.00)	0.549 (1.00)	0.851 (1.00)
del 5q12 1	53 (32%)	112	0.0677 (1.00)	0.00196 (1.00)	0.204 (1.00)	0.00378 (1.00)	0.782 (1.00)	0.276 (1.00)	0.595 (1.00)	0.0296 (1.00)	0.534 (1.00)	0.289 (1.00)	0.0276 (1.00)	0.236 (1.00)
del 5q22 2	59 (36%)	106	0.185 (1.00)	0.00079 (0.538)	0.178 (1.00)	0.189 (1.00)	0.549 (1.00)	0.73 (1.00)	1 (1.00)	0.0983 (1.00)	0.74 (1.00)	0.24 (1.00)	0.0199 (1.00)	0.194 (1.00)
del 6p25 3	24 (15%)	141	1 (1.00)	0.941 (1.00)	0.812 (1.00)	0.0199 (1.00)	0.653 (1.00)	0.985 (1.00)	0.949 (1.00)	0.867 (1.00)	0.753 (1.00)	0.786 (1.00)	0.569 (1.00)	0.756 (1.00)
del 6q26	30 (18%)	135	0.157 (1.00)	0.745 (1.00)	0.0141 (1.00)	0.633 (1.00)	0.0992 (1.00)	0.199 (1.00)	0.264 (1.00)	0.12 (1.00)	0.0534 (1.00)	0.333 (1.00)	0.0786 (1.00)	0.949 (1.00)
del 7q31 1	4 (2%)	161			0.105 (1.00)		1 (1.00)	0.952 (1.00)	0.759 (1.00)	0.765 (1.00)	1 (1.00)	1 (1.00)
del 8p11 21	45 (27%)	120	0.745 (1.00)	0.469 (1.00)	0.00964 (1.00)	0.235 (1.00)	0.0701 (1.00)	0.368 (1.00)	0.0216 (1.00)	0.0121 (1.00)	0.0589 (1.00)	0.00765 (1.00)	0.339 (1.00)	0.742 (1.00)
del 10q21 1	41 (25%)	124	0.28 (1.00)	0.711 (1.00)	0.257 (1.00)	0.485 (1.00)	0.0172 (1.00)	0.067 (1.00)	0.196 (1.00)	0.67 (1.00)	0.861 (1.00)	0.191 (1.00)	0.963 (1.00)	0.392 (1.00)
del 10q25 2	48 (29%)	117	0.759 (1.00)	0.774 (1.00)	0.737 (1.00)	0.488 (1.00)	0.457 (1.00)	0.239 (1.00)	0.688 (1.00)	0.223 (1.00)	0.621 (1.00)	0.275 (1.00)	0.443 (1.00)	0.3 (1.00)
del 11q22 3	38 (23%)	127	0.0334 (1.00)	0.0306 (1.00)	0.00293 (1.00)	0.0349 (1.00)	0.689 (1.00)	0.134 (1.00)	0.071 (1.00)	0.0716 (1.00)	0.45 (1.00)	0.966 (1.00)	0.416 (1.00)	0.664 (1.00)
del 12p13 1	33 (20%)	132	1 (1.00)	0.263 (1.00)	0.602 (1.00)	0.197 (1.00)	0.537 (1.00)	0.275 (1.00)	0.53 (1.00)	0.149 (1.00)	0.292 (1.00)	0.526 (1.00)	0.814 (1.00)	0.831 (1.00)
del 12q22	26 (16%)	139	0.354 (1.00)	0.477 (1.00)	0.0341 (1.00)	0.773 (1.00)	0.824 (1.00)	0.513 (1.00)	0.879 (1.00)	0.498 (1.00)	0.514 (1.00)	0.706 (1.00)	0.492 (1.00)	0.387 (1.00)
del 14q31 1	72 (44%)	93	0.482 (1.00)	0.237 (1.00)	0.0531 (1.00)	0.966 (1.00)	0.707 (1.00)	0.201 (1.00)	0.0805 (1.00)	0.142 (1.00)	0.198 (1.00)	0.235 (1.00)	0.391 (1.00)	0.658 (1.00)
del 15q21 1	79 (48%)	86	0.572 (1.00)	0.111 (1.00)	0.00075 (0.512)	0.788 (1.00)	0.0319 (1.00)	0.325 (1.00)	0.539 (1.00)	0.701 (1.00)	0.81 (1.00)	0.437 (1.00)	0.424 (1.00)	0.586 (1.00)
del 16p13 3	13 (8%)	152	0.886 (1.00)	0.677 (1.00)	0.204 (1.00)	0.0209 (1.00)	0.727 (1.00)	0.595 (1.00)	0.914 (1.00)	0.83 (1.00)	0.357 (1.00)	0.635 (1.00)	0.254 (1.00)	0.489 (1.00)
del 16q23 1	23 (14%)	142	0.154 (1.00)	0.351 (1.00)	0.00335 (1.00)	0.127 (1.00)	0.589 (1.00)	0.952 (1.00)	0.589 (1.00)	0.656 (1.00)	0.76 (1.00)	0.845 (1.00)	0.889 (1.00)	0.869 (1.00)
del 17p11 2	113 (68%)	52	0.0829 (1.00)	0.756 (1.00)	0.0706 (1.00)	0.29 (1.00)	0.831 (1.00)	0.357 (1.00)	0.864 (1.00)	0.973 (1.00)	0.934 (1.00)	0.352 (1.00)	0.633 (1.00)	0.704 (1.00)
del 19p13 3	37 (22%)	128	0.198 (1.00)	0.886 (1.00)	0.675 (1.00)	0.0416 (1.00)	0.961 (1.00)	0.832 (1.00)	0.901 (1.00)	0.532 (1.00)	0.354 (1.00)	0.00134 (0.907)	0.529 (1.00)	0.33 (1.00)
del 20p12 1	49 (30%)	116	0.942 (1.00)	0.336 (1.00)	0.015 (1.00)	0.494 (1.00)	0.263 (1.00)	0.383 (1.00)	0.679 (1.00)	0.969 (1.00)	0.357 (1.00)	0.253 (1.00)	0.439 (1.00)	0.44 (1.00)
del 21q11 2	73 (44%)	92	0.313 (1.00)	0.0593 (1.00)	0.0837 (1.00)	0.875 (1.00)	0.923 (1.00)	0.213 (1.00)	0.249 (1.00)	0.485 (1.00)	0.0636 (1.00)	0.724 (1.00)	0.221 (1.00)	0.19 (1.00)
del 22q13 31	68 (41%)	97	0.907 (1.00)	0.29 (1.00)	0.00786 (1.00)	0.87 (1.00)	0.409 (1.00)	0.35 (1.00)	0.0644 (1.00)	0.123 (1.00)	0.00627 (1.00)	0.115 (1.00)	0.1 (1.00)	0.0137 (1.00)
del xp22 33	34 (21%)	131	0.778 (1.00)	0.916 (1.00)	0.0534 (1.00)	0.0015 (1.00)	0.725 (1.00)	0.896 (1.00)	0.673 (1.00)	0.502 (1.00)	0.695 (1.00)	1 (1.00)	0.627 (1.00)	0.586 (1.00)

'amp_8p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S1. Gene #5: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	32	31	36
AMP PEAK 5(8P11.23) MUTATED	6	9	10	28
AMP PEAK 5(8P11.23) WILD-TYPE	60	23	21	8

Figure S1. Get High-res Image Gene #5: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S2. Gene #6: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	32	31	36
AMP PEAK 6(8P11.21) MUTATED	12	13	13	32
AMP PEAK 6(8P11.21) WILD-TYPE	54	19	18	4

Figure S2. Get High-res Image Gene #6: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S3. Gene #7: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	32	31	36
AMP PEAK 7(8Q24.21) MUTATED	35	14	25	35
AMP PEAK 7(8Q24.21) WILD-TYPE	31	18	6	1

Figure S3. Get High-res Image Gene #7: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q12.13' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S4. Gene #13: 'amp_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	32	31	36
AMP PEAK 13(13Q12.13) MUTATED	38	32	29	27
AMP PEAK 13(13Q12.13) WILD-TYPE	28	0	2	9

Figure S4. Get High-res Image Gene #13: 'amp_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S5. Gene #14: 'amp_13q12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	32	31	36
AMP PEAK 14(13Q12.2) MUTATED	36	32	29	28
AMP PEAK 14(13Q12.2) WILD-TYPE	30	0	2	8

Figure S5. Get High-res Image Gene #14: 'amp_13q12.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q22.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S6. Gene #15: 'amp_13q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	32	31	36
AMP PEAK 15(13Q22.1) MUTATED	34	32	28	26
AMP PEAK 15(13Q22.1) WILD-TYPE	32	0	3	10

Figure S6. Get High-res Image Gene #15: 'amp_13q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_2p12' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S7. Gene #28: 'del_2p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	32	31	36
DEL PEAK 4(2P12) MUTATED	0	8	0	5
DEL PEAK 4(2P12) WILD-TYPE	66	24	31	31

Figure S7. Get High-res Image Gene #28: 'del_2p12' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.1

Table S8. Gene #39: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	32	31	36
DEL PEAK 15(8P23.2) MUTATED	28	21	20	31
DEL PEAK 15(8P23.2) WILD-TYPE	38	11	11	5

Figure S8. Get High-res Image Gene #39: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q11.2' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.14

Table S9. Gene #46: 'del_14q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	32	31	36
DEL PEAK 22(14Q11.2) MUTATED	19	22	18	11
DEL PEAK 22(14Q11.2) WILD-TYPE	47	10	13	25

Figure S9. Get High-res Image Gene #46: 'del_14q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q22.33' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.062

Table S10. Gene #49: 'del_15q22.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	32	31	36
DEL PEAK 25(15Q22.33) MUTATED	17	22	17	21
DEL PEAK 25(15Q22.33) WILD-TYPE	49	10	14	15

Figure S10. Get High-res Image Gene #49: 'del_15q22.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q21.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S11. Gene #53: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	32	31	36
DEL PEAK 29(18Q21.2) MUTATED	48	30	31	36
DEL PEAK 29(18Q21.2) WILD-TYPE	18	2	0	0

Figure S11. Get High-res Image Gene #53: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S12. Gene #54: 'del_18q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	66	32	31	36
DEL PEAK 30(18Q22.1) MUTATED	44	30	31	36
DEL PEAK 30(18Q22.1) WILD-TYPE	22	2	0	0

Figure S12. Get High-res Image Gene #54: 'del_18q22.1' versus Molecular Subtype #3: 'CN_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = READ-TP.transferedmergedcluster.txt
Number of patients = 165
Number of significantly focal cnvs = 59
Number of molecular subtypes = 12
Exclude genes 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.

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] 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)

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