Correlation between copy number variations of arm-level result and molecular subtypes

Prostate Adenocarcinoma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

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 variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1NK3CVQ

Overview

Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 77 arm-level events and 10 molecular subtypes across 419 patients, 66 significant findings detected with P value < 0.05 and Q value < 0.25.

1p gain cnv correlated to 'CN_CNMF'.
1q gain cnv correlated to 'CN_CNMF'.
3p gain cnv correlated to 'CN_CNMF'.
3q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
5p gain cnv correlated to 'CN_CNMF'.
5q gain cnv correlated to 'CN_CNMF'.
7p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
7q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
8p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
8q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
9p gain cnv correlated to 'CN_CNMF'.
9q gain cnv correlated to 'CN_CNMF'.
11p gain cnv correlated to 'CN_CNMF'.
11q gain cnv correlated to 'CN_CNMF'.
16p gain cnv correlated to 'CN_CNMF'.
19p gain cnv correlated to 'CN_CNMF'.
19q gain cnv correlated to 'CN_CNMF'.
20p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
20q gain cnv correlated to 'CN_CNMF'.
21q gain cnv correlated to 'CN_CNMF'.
1p loss cnv correlated to 'CN_CNMF'.
2q loss cnv correlated to 'CN_CNMF'.
4p loss cnv correlated to 'CN_CNMF'.
4q loss cnv correlated to 'CN_CNMF'.
5q loss cnv correlated to 'CN_CNMF'.
6p loss cnv correlated to 'CN_CNMF'.
6q loss cnv correlated to 'CN_CNMF'.
8p loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
9p loss cnv correlated to 'CN_CNMF'.
10p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
10q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
12p loss cnv correlated to 'CN_CNMF'.
12q loss cnv correlated to 'CN_CNMF'.
13q loss cnv correlated to 'CN_CNMF'.
14q loss cnv correlated to 'CN_CNMF'.
15q loss cnv correlated to 'CN_CNMF'.
16q loss cnv correlated to 'CN_CNMF'.
17p loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
17q loss cnv correlated to 'CN_CNMF'.
18p loss cnv correlated to 'CN_CNMF'.
18q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
22q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
xq loss 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 77 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 66 significant findings detected.


		Clinical Features	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
8q gain	96 (23%)	323	1e-05 (0.00722)	9e-05 (0.0601)	0.00216 (1.00)	0.00527 (1.00)	1e-05 (0.00722)	0.00016 (0.106)	0.00032 (0.211)	0.00128 (0.818)	2e-05 (0.0137)	0.00107 (0.691)
8p loss	140 (33%)	279	0.00239 (1.00)	1e-05 (0.00722)	0.547 (1.00)	0.934 (1.00)	1e-05 (0.00722)	2e-05 (0.0137)	2e-05 (0.0137)	0.0114 (1.00)	0.00556 (1.00)	0.0313 (1.00)
7p gain	82 (20%)	337	1e-05 (0.00722)	1e-05 (0.00722)	0.557 (1.00)	0.726 (1.00)	1e-05 (0.00722)	0.00588 (1.00)	0.0434 (1.00)	0.00125 (0.802)	0.00487 (1.00)	0.0115 (1.00)
7q gain	78 (19%)	341	1e-05 (0.00722)	1e-05 (0.00722)	0.62 (1.00)	0.713 (1.00)	1e-05 (0.00722)	0.00804 (1.00)	0.027 (1.00)	0.00162 (1.00)	0.00663 (1.00)	0.0277 (1.00)
8p gain	54 (13%)	365	1e-05 (0.00722)	1e-05 (0.00722)	0.00593 (1.00)	0.00832 (1.00)	1e-05 (0.00722)	0.00291 (1.00)	0.139 (1.00)	0.0351 (1.00)	0.00134 (0.854)	0.139 (1.00)
10p loss	31 (7%)	388	1e-05 (0.00722)	0.00024 (0.159)	0.00666 (1.00)	0.0128 (1.00)	0.0001 (0.0667)	0.00133 (0.849)	0.00449 (1.00)	0.00101 (0.655)	0.355 (1.00)	0.00302 (1.00)
17p loss	60 (14%)	359	1e-05 (0.00722)	0.00925 (1.00)	0.00353 (1.00)	0.00933 (1.00)	8e-05 (0.0536)	7e-05 (0.047)	0.179 (1.00)	0.077 (1.00)	0.0744 (1.00)	0.267 (1.00)
3q gain	45 (11%)	374	1e-05 (0.00722)	0.0368 (1.00)	0.0421 (1.00)	0.18 (1.00)	0.00014 (0.0932)	0.0129 (1.00)	0.388 (1.00)	0.282 (1.00)	0.106 (1.00)	0.0128 (1.00)
20p gain	17 (4%)	402	2e-05 (0.0137)	0.0219 (1.00)	0.371 (1.00)	0.187 (1.00)	0.0188 (1.00)	0.0347 (1.00)	0.075 (1.00)	0.332 (1.00)	0.00033 (0.217)	0.0152 (1.00)
10q loss	34 (8%)	385	1e-05 (0.00722)	0.0163 (1.00)	0.04 (1.00)	0.0392 (1.00)	0.0187 (1.00)	0.0196 (1.00)	0.004 (1.00)	0.00022 (0.146)	0.175 (1.00)	0.0912 (1.00)
18q loss	82 (20%)	337	1e-05 (0.00722)	0.0278 (1.00)	0.0156 (1.00)	0.0193 (1.00)	0.0088 (1.00)	0.0207 (1.00)	0.265 (1.00)	8e-05 (0.0536)	0.0477 (1.00)	0.129 (1.00)
22q loss	37 (9%)	382	1e-05 (0.00722)	0.0563 (1.00)	0.44 (1.00)	0.805 (1.00)	0.106 (1.00)	0.0646 (1.00)	0.0614 (1.00)	0.012 (1.00)	0.394 (1.00)	3e-05 (0.0204)
1p gain	11 (3%)	408	6e-05 (0.0404)	0.0694 (1.00)	0.0399 (1.00)	0.338 (1.00)	0.0754 (1.00)	0.332 (1.00)	0.14 (1.00)	0.596 (1.00)	0.182 (1.00)	0.115 (1.00)
1q gain	19 (5%)	400	1e-05 (0.00722)	0.00541 (1.00)	0.0216 (1.00)	0.18 (1.00)	0.00306 (1.00)	0.0713 (1.00)	0.102 (1.00)	0.666 (1.00)	0.0712 (1.00)	0.0919 (1.00)
3p gain	32 (8%)	387	1e-05 (0.00722)	0.00845 (1.00)	0.0835 (1.00)	0.465 (1.00)	0.00375 (1.00)	0.0274 (1.00)	0.51 (1.00)	0.133 (1.00)	0.0658 (1.00)	0.0633 (1.00)
5p gain	17 (4%)	402	1e-05 (0.00722)	0.07 (1.00)	0.298 (1.00)	0.308 (1.00)	0.018 (1.00)	0.514 (1.00)	0.793 (1.00)	0.176 (1.00)	0.0089 (1.00)	0.00328 (1.00)
5q gain	12 (3%)	407	3e-05 (0.0204)	0.123 (1.00)			0.0612 (1.00)	0.305 (1.00)	0.813 (1.00)	0.735 (1.00)	0.353 (1.00)	0.16 (1.00)
9p gain	23 (5%)	396	1e-05 (0.00722)	0.348 (1.00)	0.484 (1.00)	0.176 (1.00)	0.471 (1.00)	0.381 (1.00)	0.251 (1.00)	0.463 (1.00)	0.713 (1.00)	0.251 (1.00)
9q gain	37 (9%)	382	1e-05 (0.00722)	0.0837 (1.00)	0.0261 (1.00)	0.0132 (1.00)	0.145 (1.00)	0.0322 (1.00)	0.123 (1.00)	0.0153 (1.00)	0.366 (1.00)	0.0967 (1.00)
11p gain	17 (4%)	402	1e-05 (0.00722)	0.209 (1.00)	0.768 (1.00)	0.664 (1.00)	0.0136 (1.00)	0.399 (1.00)	0.83 (1.00)	0.457 (1.00)	0.474 (1.00)	0.121 (1.00)
11q gain	20 (5%)	399	1e-05 (0.00722)	0.164 (1.00)	0.768 (1.00)	0.666 (1.00)	0.00739 (1.00)	0.241 (1.00)	0.503 (1.00)	0.489 (1.00)	0.408 (1.00)	0.118 (1.00)
16p gain	23 (5%)	396	5e-05 (0.0338)	0.333 (1.00)	0.818 (1.00)	0.659 (1.00)	0.272 (1.00)	0.0664 (1.00)	0.173 (1.00)	0.00543 (1.00)	0.0101 (1.00)	0.0713 (1.00)
19p gain	8 (2%)	411	5e-05 (0.0338)	0.314 (1.00)			0.289 (1.00)	0.348 (1.00)	0.161 (1.00)	0.0725 (1.00)	0.399 (1.00)	0.0563 (1.00)
19q gain	9 (2%)	410	2e-05 (0.0137)	0.33 (1.00)	0.781 (1.00)	0.78 (1.00)	0.185 (1.00)	0.21 (1.00)	0.128 (1.00)	0.0519 (1.00)	0.232 (1.00)	0.0216 (1.00)
20q gain	18 (4%)	401	1e-05 (0.00722)	0.0705 (1.00)	0.619 (1.00)	0.888 (1.00)	0.212 (1.00)	0.165 (1.00)	0.312 (1.00)	0.284 (1.00)	0.0218 (1.00)	0.0733 (1.00)
21q gain	16 (4%)	403	1e-05 (0.00722)	0.0694 (1.00)	0.442 (1.00)	0.449 (1.00)	0.0324 (1.00)	0.108 (1.00)	0.0593 (1.00)	0.0161 (1.00)	0.0191 (1.00)	0.0159 (1.00)
1p loss	16 (4%)	403	1e-05 (0.00722)	0.07 (1.00)	0.255 (1.00)	0.228 (1.00)	0.0395 (1.00)	0.0525 (1.00)	0.0586 (1.00)	0.0178 (1.00)	0.0302 (1.00)	0.0521 (1.00)
2q loss	12 (3%)	407	0.00025 (0.165)	0.355 (1.00)			0.368 (1.00)	0.0673 (1.00)	0.231 (1.00)	0.738 (1.00)	0.813 (1.00)	0.0825 (1.00)
4p loss	15 (4%)	404	6e-05 (0.0404)	0.258 (1.00)	0.297 (1.00)	0.307 (1.00)	0.0343 (1.00)	0.0743 (1.00)	0.00577 (1.00)	0.0823 (1.00)	0.00885 (1.00)	0.0153 (1.00)
4q loss	10 (2%)	409	0.00016 (0.106)	0.585 (1.00)	0.785 (1.00)	0.781 (1.00)	0.102 (1.00)	0.156 (1.00)	0.372 (1.00)	0.258 (1.00)	0.283 (1.00)	0.238 (1.00)
5q loss	14 (3%)	405	1e-05 (0.00722)	0.361 (1.00)	0.254 (1.00)	0.228 (1.00)	0.213 (1.00)	0.32 (1.00)	0.13 (1.00)	0.00388 (1.00)	0.00745 (1.00)	0.0168 (1.00)
6p loss	21 (5%)	398	1e-05 (0.00722)	0.00444 (1.00)	0.254 (1.00)	0.227 (1.00)	0.00627 (1.00)	0.0117 (1.00)	0.535 (1.00)	0.0194 (1.00)	0.164 (1.00)	0.0234 (1.00)
6q loss	32 (8%)	387	1e-05 (0.00722)	0.00073 (0.477)	0.0768 (1.00)	0.163 (1.00)	0.00512 (1.00)	0.0052 (1.00)	0.355 (1.00)	0.0111 (1.00)	0.0627 (1.00)	0.0771 (1.00)
9p loss	18 (4%)	401	0.00025 (0.165)	0.62 (1.00)	0.0854 (1.00)	0.0726 (1.00)	0.0588 (1.00)	0.0282 (1.00)	0.496 (1.00)	0.542 (1.00)	0.0407 (1.00)	0.312 (1.00)
12p loss	40 (10%)	379	1e-05 (0.00722)	0.127 (1.00)	0.192 (1.00)	0.436 (1.00)	0.208 (1.00)	0.135 (1.00)	0.0193 (1.00)	0.0079 (1.00)	0.081 (1.00)	0.0261 (1.00)
12q loss	17 (4%)	402	7e-05 (0.047)	0.618 (1.00)	0.175 (1.00)	0.122 (1.00)	0.304 (1.00)	0.425 (1.00)	0.175 (1.00)	0.164 (1.00)	0.266 (1.00)	0.208 (1.00)
13q loss	62 (15%)	357	1e-05 (0.00722)	0.31 (1.00)	0.554 (1.00)	0.457 (1.00)	0.263 (1.00)	0.3 (1.00)	0.414 (1.00)	0.155 (1.00)	0.145 (1.00)	0.00358 (1.00)
14q loss	19 (5%)	400	0.00014 (0.0932)	0.1 (1.00)	0.466 (1.00)	0.487 (1.00)	0.0856 (1.00)	0.196 (1.00)	0.00841 (1.00)	0.127 (1.00)	0.0681 (1.00)	0.0263 (1.00)
15q loss	24 (6%)	395	1e-05 (0.00722)	0.0182 (1.00)	0.0394 (1.00)	0.0937 (1.00)	0.0121 (1.00)	0.0831 (1.00)	0.0225 (1.00)	0.00751 (1.00)	0.00105 (0.679)	0.572 (1.00)
16q loss	87 (21%)	332	1e-05 (0.00722)	0.00113 (0.728)	0.505 (1.00)	0.197 (1.00)	0.0515 (1.00)	0.0345 (1.00)	0.0324 (1.00)	0.00095 (0.617)	0.0036 (1.00)	0.164 (1.00)
17q loss	14 (3%)	405	3e-05 (0.0204)	0.0279 (1.00)	0.45 (1.00)	0.387 (1.00)	0.0098 (1.00)	0.0122 (1.00)	0.0534 (1.00)	0.00274 (1.00)	0.0456 (1.00)	0.0101 (1.00)
18p loss	55 (13%)	364	1e-05 (0.00722)	0.00725 (1.00)	0.0628 (1.00)	0.0673 (1.00)	0.0222 (1.00)	0.142 (1.00)	0.265 (1.00)	0.0207 (1.00)	0.0571 (1.00)	0.273 (1.00)
xq loss	27 (6%)	392	1e-05 (0.00722)	0.00125 (0.802)	0.111 (1.00)	0.196 (1.00)	0.00071 (0.464)	0.00059 (0.387)	0.0465 (1.00)	0.00191 (1.00)	0.00176 (1.00)	0.00255 (1.00)
2p gain	8 (2%)	411	0.00746 (1.00)	0.109 (1.00)			0.0304 (1.00)	0.0783 (1.00)	0.256 (1.00)	0.398 (1.00)	0.00291 (1.00)	0.249 (1.00)
2q gain	4 (1%)	415	0.0467 (1.00)	0.384 (1.00)			0.648 (1.00)	0.787 (1.00)	0.33 (1.00)	0.826 (1.00)	0.0214 (1.00)	0.475 (1.00)
4p gain	8 (2%)	411	0.00693 (1.00)	0.33 (1.00)			0.206 (1.00)	0.898 (1.00)	0.983 (1.00)	1 (1.00)	1 (1.00)	0.282 (1.00)
4q gain	7 (2%)	412	0.0191 (1.00)	0.315 (1.00)			0.224 (1.00)	0.589 (1.00)	0.919 (1.00)	1 (1.00)	0.796 (1.00)	0.22 (1.00)
6p gain	6 (1%)	413	0.0187 (1.00)	0.381 (1.00)			0.0637 (1.00)	0.783 (1.00)	0.512 (1.00)	0.278 (1.00)	0.339 (1.00)	0.319 (1.00)
6q gain	3 (1%)	416	0.0254 (1.00)						0.779 (1.00)	0.292 (1.00)	0.392 (1.00)	0.777 (1.00)
10p gain	10 (2%)	409	0.0107 (1.00)	0.317 (1.00)	0.785 (1.00)	0.779 (1.00)	0.497 (1.00)	0.183 (1.00)	0.068 (1.00)	0.0935 (1.00)	0.123 (1.00)	0.283 (1.00)
10q gain	12 (3%)	407	0.00185 (1.00)	0.361 (1.00)	0.0401 (1.00)	0.0399 (1.00)	0.485 (1.00)	0.134 (1.00)	0.309 (1.00)	0.083 (1.00)	0.333 (1.00)	0.245 (1.00)
12p gain	11 (3%)	408	0.00393 (1.00)	0.038 (1.00)			0.332 (1.00)	0.244 (1.00)	0.0999 (1.00)	0.272 (1.00)	0.0829 (1.00)	0.607 (1.00)
12q gain	12 (3%)	407	0.0178 (1.00)	0.0365 (1.00)	0.469 (1.00)	0.63 (1.00)	0.0877 (1.00)	0.491 (1.00)	0.0802 (1.00)	0.449 (1.00)	0.212 (1.00)	0.903 (1.00)
13q gain	5 (1%)	414	0.0587 (1.00)	0.114 (1.00)			0.393 (1.00)	0.141 (1.00)	0.577 (1.00)	0.121 (1.00)	0.138 (1.00)	0.376 (1.00)
14q gain	7 (2%)	412	0.00074 (0.482)	0.0804 (1.00)	0.786 (1.00)	0.783 (1.00)	0.17 (1.00)	0.245 (1.00)	0.268 (1.00)	0.293 (1.00)	0.567 (1.00)	0.262 (1.00)
15q gain	5 (1%)	414	0.131 (1.00)	1 (1.00)			1 (1.00)	0.839 (1.00)	0.761 (1.00)	0.717 (1.00)	1 (1.00)	0.448 (1.00)
16q gain	7 (2%)	412	0.267 (1.00)	0.862 (1.00)	0.677 (1.00)	0.558 (1.00)	0.876 (1.00)	0.773 (1.00)	0.333 (1.00)	0.183 (1.00)	0.348 (1.00)	0.976 (1.00)
17p gain	5 (1%)	414	0.06 (1.00)						0.653 (1.00)	0.484 (1.00)	0.11 (1.00)	0.158 (1.00)
17q gain	8 (2%)	411	0.00192 (1.00)	0.828 (1.00)	0.472 (1.00)	0.78 (1.00)	0.381 (1.00)	1 (1.00)	0.892 (1.00)	0.359 (1.00)	0.205 (1.00)	0.266 (1.00)
18p gain	13 (3%)	406	0.00085 (0.553)	1 (1.00)	0.899 (1.00)	0.663 (1.00)	0.209 (1.00)	0.935 (1.00)	0.841 (1.00)	0.93 (1.00)	0.774 (1.00)	0.459 (1.00)
18q gain	7 (2%)	412	0.05 (1.00)	1 (1.00)	1 (1.00)	0.491 (1.00)	0.224 (1.00)	0.778 (1.00)	0.531 (1.00)	0.768 (1.00)	0.567 (1.00)	0.218 (1.00)
xq gain	4 (1%)	415	0.0107 (1.00)	0.382 (1.00)			0.647 (1.00)	0.633 (1.00)	0.177 (1.00)	0.827 (1.00)	0.0215 (1.00)	0.518 (1.00)
1q loss	4 (1%)	415	0.0933 (1.00)				0.648 (1.00)	0.631 (1.00)	0.0837 (1.00)	0.124 (1.00)	0.0711 (1.00)	0.0777 (1.00)
2p loss	9 (2%)	410	0.00268 (1.00)	0.22 (1.00)			0.205 (1.00)	0.0133 (1.00)	0.422 (1.00)	0.732 (1.00)	0.297 (1.00)	0.271 (1.00)
3p loss	7 (2%)	412	0.436 (1.00)	0.158 (1.00)			0.136 (1.00)	0.16 (1.00)	0.072 (1.00)	0.471 (1.00)	0.0208 (1.00)	0.186 (1.00)
3q loss	4 (1%)	415	0.631 (1.00)	0.634 (1.00)			0.778 (1.00)	0.63 (1.00)	0.0318 (1.00)	0.0768 (1.00)	0.391 (1.00)	0.0298 (1.00)
5p loss	6 (1%)	413	0.00104 (0.674)	0.232 (1.00)	0.783 (1.00)	1 (1.00)	0.331 (1.00)	0.0533 (1.00)	0.694 (1.00)	0.486 (1.00)	0.744 (1.00)	0.155 (1.00)
8q loss	20 (5%)	399	0.462 (1.00)	0.0385 (1.00)	1 (1.00)	1 (1.00)	0.00283 (1.00)	0.0677 (1.00)	0.452 (1.00)	0.138 (1.00)	0.158 (1.00)	0.0845 (1.00)
9q loss	7 (2%)	412	0.0523 (1.00)	0.453 (1.00)	0.443 (1.00)	0.45 (1.00)	0.533 (1.00)	1 (1.00)	0.554 (1.00)	0.768 (1.00)	0.348 (1.00)	0.529 (1.00)
11p loss	6 (1%)	413	0.0192 (1.00)	1 (1.00)			0.33 (1.00)	0.295 (1.00)	0.51 (1.00)	0.656 (1.00)	0.339 (1.00)	0.843 (1.00)
11q loss	3 (1%)	416	0.26 (1.00)				0.406 (1.00)	0.785 (1.00)	0.779 (1.00)	0.76 (1.00)	1 (1.00)	1 (1.00)
16p loss	29 (7%)	390	0.0006 (0.393)	0.0828 (1.00)	0.45 (1.00)	0.351 (1.00)	0.125 (1.00)	0.653 (1.00)	0.0118 (1.00)	0.62 (1.00)	0.0417 (1.00)	0.291 (1.00)
19p loss	13 (3%)	406	0.00126 (0.806)	0.606 (1.00)	0.625 (1.00)	0.487 (1.00)	0.347 (1.00)	0.927 (1.00)	0.121 (1.00)	0.183 (1.00)	0.0451 (1.00)	0.12 (1.00)
19q loss	13 (3%)	406	0.00124 (0.797)	0.607 (1.00)	0.622 (1.00)	0.491 (1.00)	0.348 (1.00)	0.927 (1.00)	0.121 (1.00)	0.183 (1.00)	0.0453 (1.00)	0.121 (1.00)
20p loss	15 (4%)	404	0.262 (1.00)	0.11 (1.00)	0.896 (1.00)	1 (1.00)	0.27 (1.00)	0.489 (1.00)	0.156 (1.00)	0.289 (1.00)	0.571 (1.00)	0.118 (1.00)
20q loss	8 (2%)	411	0.077 (1.00)	0.0822 (1.00)	1 (1.00)	1 (1.00)	0.166 (1.00)	0.245 (1.00)	0.0199 (1.00)	0.0282 (1.00)	0.364 (1.00)	0.0193 (1.00)
21q loss	16 (4%)	403	0.0011 (0.709)	0.35 (1.00)	0.506 (1.00)	0.508 (1.00)	0.191 (1.00)	0.109 (1.00)	0.576 (1.00)	0.0837 (1.00)	0.166 (1.00)	0.777 (1.00)

'1p gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.04

Table S1. Gene #1: '1p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
1P GAIN MUTATED	1	10	0
1P GAIN WILD-TYPE	234	106	68

Figure S1. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #1: 'CN_CNMF'

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S2. Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
1Q GAIN MUTATED	3	16	0
1Q GAIN WILD-TYPE	232	100	68

Figure S2. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S3. Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
3P GAIN MUTATED	1	25	6
3P GAIN WILD-TYPE	234	91	62

Figure S3. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S4. Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
3Q GAIN MUTATED	6	33	6
3Q GAIN WILD-TYPE	229	83	62

Figure S4. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.093

Table S5. Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	112	134
3Q GAIN MUTATED	23	3	12
3Q GAIN WILD-TYPE	101	109	122

Figure S5. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S6. Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
5P GAIN MUTATED	1	16	0
5P GAIN WILD-TYPE	234	100	68

Figure S6. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S7. Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
5Q GAIN MUTATED	1	11	0
5Q GAIN WILD-TYPE	234	105	68

Figure S7. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S8. Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
7P GAIN MUTATED	14	50	18
7P GAIN WILD-TYPE	221	66	50

Figure S8. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S9. Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	106	129
7P GAIN MUTATED	34	5	19
7P GAIN WILD-TYPE	62	101	110

Figure S9. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S10. Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	112	134
7P GAIN MUTATED	42	6	20
7P GAIN WILD-TYPE	82	106	114

Figure S10. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S11. Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
7Q GAIN MUTATED	14	46	18
7Q GAIN WILD-TYPE	221	70	50

Figure S11. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S12. Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	106	129
7Q GAIN MUTATED	34	5	17
7Q GAIN WILD-TYPE	62	101	112

Figure S12. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S13. Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	112	134
7Q GAIN MUTATED	41	6	18
7Q GAIN WILD-TYPE	83	106	116

Figure S13. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S14. Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
8P GAIN MUTATED	11	37	6
8P GAIN WILD-TYPE	224	79	62

Figure S14. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S15. Gene #15: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	106	129
8P GAIN MUTATED	26	4	8
8P GAIN WILD-TYPE	70	102	121

Figure S15. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S16. Gene #15: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	112	134
8P GAIN MUTATED	31	5	10
8P GAIN WILD-TYPE	93	107	124

Figure S16. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S17. Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
8Q GAIN MUTATED	29	57	10
8Q GAIN WILD-TYPE	206	59	58

Figure S17. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.06

Table S18. Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	106	129
8Q GAIN MUTATED	34	10	25
8Q GAIN WILD-TYPE	62	96	104

Figure S18. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S19. Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	112	134
8Q GAIN MUTATED	47	10	26
8Q GAIN WILD-TYPE	77	102	108

Figure S19. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.11

Table S20. Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	97	135
8Q GAIN MUTATED	42	8	33
8Q GAIN WILD-TYPE	96	89	102

Figure S20. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.21

Table S21. Gene #16: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	88	40	123	73	91
8Q GAIN MUTATED	7	8	41	17	21
8Q GAIN WILD-TYPE	81	32	82	56	70

Figure S21. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S22. Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	118	151
8Q GAIN MUTATED	50	28	16
8Q GAIN WILD-TYPE	96	90	135

Figure S22. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S23. Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
9P GAIN MUTATED	2	20	1
9P GAIN WILD-TYPE	233	96	67

Figure S23. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S24. Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
9Q GAIN MUTATED	5	31	1
9Q GAIN WILD-TYPE	230	85	67

Figure S24. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S25. Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
11P GAIN MUTATED	1	14	2
11P GAIN WILD-TYPE	234	102	66

Figure S25. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S26. Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
11Q GAIN MUTATED	1	17	2
11Q GAIN WILD-TYPE	234	99	66

Figure S26. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.034

Table S27. Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
16P GAIN MUTATED	7	16	0
16P GAIN WILD-TYPE	228	100	68

Figure S27. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.034

Table S28. Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
19P GAIN MUTATED	0	8	0
19P GAIN WILD-TYPE	235	108	68

Figure S28. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

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

Table S29. Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
19Q GAIN MUTATED	0	9	0
19Q GAIN WILD-TYPE	235	107	68

Figure S29. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'CN_CNMF'

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

Table S30. Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
20P GAIN MUTATED	2	14	1
20P GAIN WILD-TYPE	233	102	67

Figure S30. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.22

Table S31. Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	118	151
20P GAIN MUTATED	13	2	1
20P GAIN WILD-TYPE	133	116	150

Figure S31. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S32. Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
20Q GAIN MUTATED	2	15	1
20Q GAIN WILD-TYPE	233	101	67

Figure S32. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S33. Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
21Q GAIN MUTATED	0	16	0
21Q GAIN WILD-TYPE	235	100	68

Figure S33. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S34. Gene #40: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
1P LOSS MUTATED	1	15	0
1P LOSS WILD-TYPE	234	101	68

Figure S34. Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.16

Table S35. Gene #43: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
2Q LOSS MUTATED	1	9	2
2Q LOSS WILD-TYPE	234	107	66

Figure S35. Get High-res Image Gene #43: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.04

Table S36. Gene #46: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
4P LOSS MUTATED	2	12	1
4P LOSS WILD-TYPE	233	104	67

Figure S36. Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.11

Table S37. Gene #47: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
4Q LOSS MUTATED	1	9	0
4Q LOSS WILD-TYPE	234	107	68

Figure S37. Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S38. Gene #49: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
5Q LOSS MUTATED	0	13	1
5Q LOSS WILD-TYPE	235	103	67

Figure S38. Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S39. Gene #50: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
6P LOSS MUTATED	3	18	0
6P LOSS WILD-TYPE	232	98	68

Figure S39. Get High-res Image Gene #50: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S40. Gene #51: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
6Q LOSS MUTATED	5	24	3
6Q LOSS WILD-TYPE	230	92	65

Figure S40. Get High-res Image Gene #51: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S41. Gene #52: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	106	129
8P LOSS MUTATED	29	13	63
8P LOSS WILD-TYPE	67	93	66

Figure S41. Get High-res Image Gene #52: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S42. Gene #52: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	112	134
8P LOSS MUTATED	35	20	65
8P LOSS WILD-TYPE	89	92	69

Figure S42. Get High-res Image Gene #52: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S43. Gene #52: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	97	135
8P LOSS MUTATED	37	19	64
8P LOSS WILD-TYPE	101	78	71

Figure S43. Get High-res Image Gene #52: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

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

Table S44. Gene #52: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	88	40	123	73	91
8P LOSS MUTATED	17	5	47	35	35
8P LOSS WILD-TYPE	71	35	76	38	56

Figure S44. Get High-res Image Gene #52: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.16

Table S45. Gene #54: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
9P LOSS MUTATED	5	13	0
9P LOSS WILD-TYPE	230	103	68

Figure S45. Get High-res Image Gene #54: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S46. Gene #56: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
10P LOSS MUTATED	7	23	1
10P LOSS WILD-TYPE	228	93	67

Figure S46. Get High-res Image Gene #56: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.16

Table S47. Gene #56: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	106	129
10P LOSS MUTATED	8	0	15
10P LOSS WILD-TYPE	88	106	114

Figure S47. Get High-res Image Gene #56: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.067

Table S48. Gene #56: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	112	134
10P LOSS MUTATED	9	0	16
10P LOSS WILD-TYPE	115	112	118

Figure S48. Get High-res Image Gene #56: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S49. Gene #57: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
10Q LOSS MUTATED	8	23	3
10Q LOSS WILD-TYPE	227	93	65

Figure S49. Get High-res Image Gene #57: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.15

Table S50. Gene #57: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	70	196
10Q LOSS MUTATED	5	1	26
10Q LOSS WILD-TYPE	144	69	170

Figure S50. Get High-res Image Gene #57: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S51. Gene #60: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
12P LOSS MUTATED	15	25	0
12P LOSS WILD-TYPE	220	91	68

Figure S51. Get High-res Image Gene #60: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.047

Table S52. Gene #61: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
12Q LOSS MUTATED	4	13	0
12Q LOSS WILD-TYPE	231	103	68

Figure S52. Get High-res Image Gene #61: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S53. Gene #62: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
13Q LOSS MUTATED	14	41	7
13Q LOSS WILD-TYPE	221	75	61

Figure S53. Get High-res Image Gene #62: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.093

Table S54. Gene #63: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
14Q LOSS MUTATED	4	14	1
14Q LOSS WILD-TYPE	231	102	67

Figure S54. Get High-res Image Gene #63: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S55. Gene #64: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
15Q LOSS MUTATED	4	20	0
15Q LOSS WILD-TYPE	231	96	68

Figure S55. Get High-res Image Gene #64: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S56. Gene #66: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
16Q LOSS MUTATED	30	54	3
16Q LOSS WILD-TYPE	205	62	65

Figure S56. Get High-res Image Gene #66: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S57. Gene #67: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
17P LOSS MUTATED	15	43	2
17P LOSS WILD-TYPE	220	73	66

Figure S57. Get High-res Image Gene #67: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.054

Table S58. Gene #67: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	112	134
17P LOSS MUTATED	14	6	33
17P LOSS WILD-TYPE	110	106	101

Figure S58. Get High-res Image Gene #67: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.047

Table S59. Gene #67: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	97	135
17P LOSS MUTATED	10	9	34
17P LOSS WILD-TYPE	128	88	101

Figure S59. Get High-res Image Gene #67: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S60. Gene #68: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
17Q LOSS MUTATED	1	12	1
17Q LOSS WILD-TYPE	234	104	67

Figure S60. Get High-res Image Gene #68: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S61. Gene #69: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
18P LOSS MUTATED	16	36	3
18P LOSS WILD-TYPE	219	80	65

Figure S61. Get High-res Image Gene #69: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S62. Gene #70: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
18Q LOSS MUTATED	24	52	6
18Q LOSS WILD-TYPE	211	64	62

Figure S62. Get High-res Image Gene #70: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.054

Table S63. Gene #70: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	70	196
18Q LOSS MUTATED	16	9	55
18Q LOSS WILD-TYPE	133	61	141

Figure S63. Get High-res Image Gene #70: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S64. Gene #76: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
22Q LOSS MUTATED	7	28	2
22Q LOSS WILD-TYPE	228	88	66

Figure S64. Get High-res Image Gene #76: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S65. Gene #76: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	95	37	125	61	97
22Q LOSS MUTATED	1	5	22	3	4
22Q LOSS WILD-TYPE	94	32	103	58	93

Figure S65. Get High-res Image Gene #76: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0072

Table S66. Gene #77: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	116	68
XQ LOSS MUTATED	4	22	1
XQ LOSS WILD-TYPE	231	94	67

Figure S66. Get High-res Image Gene #77: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtypes file = PRAD-TP.transferedmergedcluster.txt
Number of patients = 419
Number of significantly arm-level cnvs = 77
Number of molecular subtypes = 10
Exclude genes that fewer than K tumors have mutations, 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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