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

Bladder Urothelial Carcinoma (Primary solid tumor)

16 April 2014 | analyses__2014_04_16

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/C1GT5KRG

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 69 focal events and 10 molecular subtypes across 250 patients, 66 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p34.2 cnv correlated to 'CN_CNMF'.
amp_1q21.3 cnv correlated to 'CN_CNMF'.
amp_1q23.3 cnv correlated to 'CN_CNMF'.
amp_3p25.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3q26.32 cnv correlated to 'CN_CNMF'.
amp_4q13.3 cnv correlated to 'CN_CNMF'.
amp_5p15.33 cnv correlated to 'CN_CNMF'.
amp_6p22.3 cnv correlated to 'CN_CNMF'.
amp_7p21.1 cnv correlated to 'CN_CNMF'.
amp_7p11.2 cnv correlated to 'CN_CNMF'.
amp_8p11.23 cnv correlated to 'CN_CNMF'.
amp_9p24.1 cnv correlated to 'CN_CNMF'.
amp_10p14 cnv correlated to 'CN_CNMF'.
amp_11q13.3 cnv correlated to 'CN_CNMF'.
amp_12p13.32 cnv correlated to 'CN_CNMF'.
amp_14q11.2 cnv correlated to 'CN_CNMF'.
amp_16q22.1 cnv correlated to 'CN_CNMF'.
amp_17q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
amp_17q12 cnv correlated to 'CN_CNMF'.
amp_19q12 cnv correlated to 'CN_CNMF'.
amp_19q13.43 cnv correlated to 'CN_CNMF'.
amp_20q11.21 cnv correlated to 'CN_CNMF'.
amp_22q11.23 cnv correlated to 'CN_CNMF'.
del_2q22.1 cnv correlated to 'CN_CNMF'.
del_2q37.1 cnv correlated to 'CN_CNMF'.
del_3p21.31 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_3p14.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_3p13 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_4q22.1 cnv correlated to 'CN_CNMF'.
del_4q34.2 cnv correlated to 'CN_CNMF'.
del_5q11.2 cnv correlated to 'CN_CNMF'.
del_6p25.3 cnv correlated to 'CN_CNMF'.
del_6q21 cnv correlated to 'CN_CNMF'.
del_6q27 cnv correlated to 'CN_CNMF'.
del_8p23.3 cnv correlated to 'CN_CNMF'.
del_8p12 cnv correlated to 'CN_CNMF'.
del_8p11.21 cnv correlated to 'CN_CNMF'.
del_9p23 cnv correlated to 'CN_CNMF'.
del_9p21.3 cnv correlated to 'CN_CNMF'.
del_9q33.2 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'CN_CNMF'.
del_10q26.13 cnv correlated to 'CN_CNMF'.
del_11p15.5 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_11q25 cnv correlated to 'CN_CNMF'.
del_13q14.2 cnv correlated to 'CN_CNMF'.
del_14q12 cnv correlated to 'CN_CNMF'.
del_14q24.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_15q13.1 cnv correlated to 'CN_CNMF'.
del_16p13.3 cnv correlated to 'CN_CNMF'.
del_16q23.1 cnv correlated to 'CN_CNMF'.
del_17p12 cnv correlated to 'CN_CNMF'.
del_18q23 cnv correlated to 'MIRSEQ_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'CN_CNMF'.
del_22q13.31 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 69 focal 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	Chi-square 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	Fisher's exact test
amp 3p25 2	122 (49%)	128	2.16e-11 (1.48e-08)	0.00258 (1.00)	0.0772 (1.00)	0.0256 (1.00)	1.98e-05 (0.0127)	2.7e-05 (0.0174)	8.4e-05 (0.0535)	0.00165 (1.00)	1.7e-05 (0.011)	0.000179 (0.113)
amp 17q11 2	111 (44%)	139	8.52e-07 (0.000562)	2.45e-05 (0.0158)	0.0338 (1.00)	0.0753 (1.00)	0.000328 (0.206)	0.00162 (0.991)	0.0207 (1.00)	0.161 (1.00)	0.000886 (0.55)	0.0016 (0.98)
del 3p21 31	72 (29%)	178	1.28e-06 (0.00084)	0.26 (1.00)	0.0296 (1.00)	0.0311 (1.00)	7.98e-06 (0.0052)	0.0103 (1.00)	0.236 (1.00)	0.147 (1.00)	0.463 (1.00)	0.159 (1.00)
del 3p14 2	71 (28%)	179	2.18e-08 (1.47e-05)	0.418 (1.00)	0.0413 (1.00)	0.032 (1.00)	8.04e-05 (0.0513)	0.037 (1.00)	0.643 (1.00)	0.411 (1.00)	0.343 (1.00)	0.144 (1.00)
del 3p13	66 (26%)	184	3.81e-07 (0.000253)	0.395 (1.00)	0.156 (1.00)	0.00489 (1.00)	4.28e-05 (0.0274)	0.0706 (1.00)	0.84 (1.00)	0.912 (1.00)	0.457 (1.00)	0.0208 (1.00)
del 11p15 5	123 (49%)	127	3.7e-08 (2.48e-05)	0.000276 (0.173)	0.348 (1.00)	0.767 (1.00)	0.0734 (1.00)	0.00179 (1.00)	0.00492 (1.00)	0.00523 (1.00)	0.00376 (1.00)	0.0372 (1.00)
del 14q24 1	83 (33%)	167	3.29e-09 (2.24e-06)	0.0202 (1.00)	0.432 (1.00)	0.355 (1.00)	0.0148 (1.00)	8.01e-06 (0.0052)	0.0497 (1.00)	0.355 (1.00)	0.0553 (1.00)	0.234 (1.00)
amp 1p34 2	68 (27%)	182	0.000224 (0.141)	0.233 (1.00)	0.153 (1.00)	0.609 (1.00)	0.903 (1.00)	0.509 (1.00)	0.0889 (1.00)	0.721 (1.00)	0.89 (1.00)	0.73 (1.00)
amp 1q21 3	123 (49%)	127	7.21e-13 (4.96e-10)	0.0318 (1.00)	0.368 (1.00)	0.486 (1.00)	0.0129 (1.00)	0.0571 (1.00)	0.111 (1.00)	0.151 (1.00)	0.381 (1.00)	0.14 (1.00)
amp 1q23 3	129 (52%)	121	8.39e-09 (5.7e-06)	0.0153 (1.00)	0.518 (1.00)	0.452 (1.00)	0.0898 (1.00)	0.486 (1.00)	0.00155 (0.952)	0.00109 (0.674)	0.0279 (1.00)	0.0125 (1.00)
amp 3q26 32	136 (54%)	114	3.64e-05 (0.0234)	0.754 (1.00)	0.389 (1.00)	0.162 (1.00)	0.521 (1.00)	0.434 (1.00)	0.39 (1.00)	0.051 (1.00)	0.3 (1.00)	0.106 (1.00)
amp 4q13 3	45 (18%)	205	0.000396 (0.247)	0.0254 (1.00)	0.499 (1.00)	0.806 (1.00)	0.368 (1.00)	0.339 (1.00)	0.372 (1.00)	0.219 (1.00)	0.169 (1.00)	0.118 (1.00)
amp 5p15 33	128 (51%)	122	1.35e-08 (9.14e-06)	0.215 (1.00)	0.0241 (1.00)	0.0452 (1.00)	0.348 (1.00)	0.0228 (1.00)	0.0584 (1.00)	0.0472 (1.00)	0.305 (1.00)	0.0157 (1.00)
amp 6p22 3	107 (43%)	143	1.23e-13 (8.46e-11)	0.116 (1.00)	0.299 (1.00)	0.536 (1.00)	1 (1.00)	0.834 (1.00)	0.35 (1.00)	0.0783 (1.00)	0.481 (1.00)	0.609 (1.00)
amp 7p21 1	130 (52%)	120	7.2e-08 (4.82e-05)	0.067 (1.00)	0.128 (1.00)	0.717 (1.00)	0.687 (1.00)	0.425 (1.00)	0.164 (1.00)	0.135 (1.00)	0.701 (1.00)	0.699 (1.00)
amp 7p11 2	127 (51%)	123	1.04e-07 (6.91e-05)	0.0549 (1.00)	0.0872 (1.00)	0.943 (1.00)	0.77 (1.00)	0.717 (1.00)	0.27 (1.00)	0.515 (1.00)	0.639 (1.00)	0.702 (1.00)
amp 8p11 23	77 (31%)	173	1.67e-05 (0.0108)	0.19 (1.00)	0.711 (1.00)	0.817 (1.00)	0.97 (1.00)	0.963 (1.00)	0.487 (1.00)	0.604 (1.00)	0.249 (1.00)	0.36 (1.00)
amp 9p24 1	49 (20%)	201	1.85e-06 (0.00121)	0.424 (1.00)	0.581 (1.00)	0.499 (1.00)	0.0594 (1.00)	0.00641 (1.00)	0.886 (1.00)	1 (1.00)	0.781 (1.00)	0.331 (1.00)
amp 10p14	112 (45%)	138	2.51e-16 (1.73e-13)	0.159 (1.00)	0.331 (1.00)	0.406 (1.00)	0.842 (1.00)	0.136 (1.00)	0.337 (1.00)	0.324 (1.00)	0.376 (1.00)	0.467 (1.00)
amp 11q13 3	95 (38%)	155	2.35e-08 (1.58e-05)	0.473 (1.00)	0.237 (1.00)	0.0685 (1.00)	0.18 (1.00)	1 (1.00)	0.125 (1.00)	0.171 (1.00)	0.479 (1.00)	0.848 (1.00)
amp 12p13 32	87 (35%)	163	2.83e-06 (0.00185)	0.127 (1.00)	0.761 (1.00)	0.723 (1.00)	0.748 (1.00)	0.742 (1.00)	0.967 (1.00)	0.00119 (0.737)	0.888 (1.00)	0.344 (1.00)
amp 14q11 2	60 (24%)	190	0.000215 (0.135)	0.158 (1.00)	0.524 (1.00)	0.223 (1.00)	0.104 (1.00)	0.0107 (1.00)	0.307 (1.00)	0.424 (1.00)	0.656 (1.00)	0.383 (1.00)
amp 16q22 1	74 (30%)	176	1.43e-05 (0.00928)	0.551 (1.00)	0.07 (1.00)	0.47 (1.00)	0.078 (1.00)	0.0402 (1.00)	0.609 (1.00)	0.081 (1.00)	0.265 (1.00)	0.65 (1.00)
amp 17q12	103 (41%)	147	0.000214 (0.135)	0.00614 (1.00)	0.0765 (1.00)	0.0166 (1.00)	0.0161 (1.00)	0.102 (1.00)	0.00162 (0.991)	0.019 (1.00)	0.00157 (0.966)	0.002 (1.00)
amp 19q12	104 (42%)	146	5.93e-07 (0.000393)	0.0492 (1.00)	0.721 (1.00)	0.805 (1.00)	0.358 (1.00)	0.208 (1.00)	0.286 (1.00)	0.0705 (1.00)	0.578 (1.00)	0.208 (1.00)
amp 19q13 43	97 (39%)	153	6.37e-06 (0.00415)	0.0128 (1.00)	0.185 (1.00)	0.337 (1.00)	0.567 (1.00)	0.946 (1.00)	0.637 (1.00)	0.0359 (1.00)	0.301 (1.00)	0.0223 (1.00)
amp 20q11 21	163 (65%)	87	6.91e-07 (0.000457)	0.0768 (1.00)	0.688 (1.00)	0.0689 (1.00)	1 (1.00)	0.303 (1.00)	0.127 (1.00)	0.0725 (1.00)	0.121 (1.00)	0.488 (1.00)
amp 22q11 23	52 (21%)	198	1.29e-06 (0.000846)	0.00674 (1.00)	0.568 (1.00)	0.561 (1.00)	0.101 (1.00)	0.127 (1.00)	0.111 (1.00)	0.655 (1.00)	0.503 (1.00)	0.281 (1.00)
del 2q22 1	78 (31%)	172	0.000144 (0.0914)	0.0871 (1.00)	0.249 (1.00)	0.529 (1.00)	0.252 (1.00)	0.066 (1.00)	0.231 (1.00)	0.68 (1.00)	0.055 (1.00)	0.283 (1.00)
del 2q37 1	126 (50%)	124	2.81e-08 (1.89e-05)	0.00125 (0.769)	0.565 (1.00)	0.286 (1.00)	0.459 (1.00)	0.0799 (1.00)	0.0942 (1.00)	0.113 (1.00)	0.0527 (1.00)	0.0519 (1.00)
del 4q22 1	105 (42%)	145	0.0002 (0.127)	0.109 (1.00)	0.513 (1.00)	0.421 (1.00)	0.0327 (1.00)	0.0367 (1.00)	0.438 (1.00)	0.694 (1.00)	0.0481 (1.00)	0.075 (1.00)
del 4q34 2	113 (45%)	137	3.64e-07 (0.000242)	0.594 (1.00)	0.429 (1.00)	0.911 (1.00)	0.707 (1.00)	0.363 (1.00)	0.0744 (1.00)	0.154 (1.00)	0.191 (1.00)	0.166 (1.00)
del 5q11 2	128 (51%)	122	3.71e-09 (2.52e-06)	0.132 (1.00)	0.954 (1.00)	0.304 (1.00)	0.508 (1.00)	0.304 (1.00)	0.316 (1.00)	0.642 (1.00)	0.617 (1.00)	0.303 (1.00)
del 6p25 3	67 (27%)	183	7.06e-05 (0.0451)	0.0681 (1.00)	0.808 (1.00)	0.662 (1.00)	0.641 (1.00)	0.122 (1.00)	0.513 (1.00)	0.882 (1.00)	0.837 (1.00)	0.748 (1.00)
del 6q21	111 (44%)	139	2.32e-09 (1.58e-06)	0.0157 (1.00)	0.843 (1.00)	0.627 (1.00)	0.871 (1.00)	0.0716 (1.00)	0.374 (1.00)	0.569 (1.00)	0.337 (1.00)	0.425 (1.00)
del 6q27	113 (45%)	137	3.54e-10 (2.42e-07)	0.0025 (1.00)	0.657 (1.00)	0.627 (1.00)	0.634 (1.00)	0.0362 (1.00)	0.106 (1.00)	0.139 (1.00)	0.182 (1.00)	0.323 (1.00)
del 8p23 3	143 (57%)	107	2.89e-10 (1.98e-07)	0.00923 (1.00)	0.523 (1.00)	0.231 (1.00)	0.0773 (1.00)	0.133 (1.00)	0.00228 (1.00)	0.0727 (1.00)	0.0431 (1.00)	0.00976 (1.00)
del 8p12	123 (49%)	127	1.22e-08 (8.23e-06)	0.075 (1.00)	0.548 (1.00)	0.507 (1.00)	0.098 (1.00)	0.379 (1.00)	0.0446 (1.00)	0.0317 (1.00)	0.192 (1.00)	0.034 (1.00)
del 8p11 21	66 (26%)	184	1.09e-05 (0.0071)	0.717 (1.00)	0.217 (1.00)	0.108 (1.00)	0.213 (1.00)	0.0293 (1.00)	0.148 (1.00)	0.827 (1.00)	0.146 (1.00)	0.0154 (1.00)
del 9p23	112 (45%)	138	3.81e-06 (0.00249)	0.539 (1.00)	0.204 (1.00)	0.137 (1.00)	0.957 (1.00)	0.117 (1.00)	0.485 (1.00)	0.372 (1.00)	0.64 (1.00)	0.783 (1.00)
del 9p21 3	148 (59%)	102	1.2e-06 (0.000789)	0.97 (1.00)	0.415 (1.00)	0.00249 (1.00)	0.708 (1.00)	0.517 (1.00)	0.769 (1.00)	0.514 (1.00)	0.576 (1.00)	0.791 (1.00)
del 9q33 2	99 (40%)	151	0.398 (1.00)	0.00782 (1.00)	0.073 (1.00)	0.00257 (1.00)	0.0277 (1.00)	9.48e-05 (0.0603)	0.391 (1.00)	0.32 (1.00)	0.0714 (1.00)	0.243 (1.00)
del 10q23 31	100 (40%)	150	4.91e-07 (0.000325)	0.0165 (1.00)	0.6 (1.00)	0.735 (1.00)	0.264 (1.00)	0.468 (1.00)	0.656 (1.00)	0.343 (1.00)	0.748 (1.00)	0.664 (1.00)
del 10q26 13	102 (41%)	148	1.9e-07 (0.000127)	0.0283 (1.00)	0.384 (1.00)	0.662 (1.00)	0.463 (1.00)	0.393 (1.00)	0.412 (1.00)	0.371 (1.00)	0.366 (1.00)	0.476 (1.00)
del 11q25	91 (36%)	159	1.03e-07 (6.89e-05)	0.00412 (1.00)	0.853 (1.00)	0.785 (1.00)	0.123 (1.00)	0.0371 (1.00)	0.69 (1.00)	0.104 (1.00)	0.269 (1.00)	0.411 (1.00)
del 13q14 2	100 (40%)	150	9.85e-09 (6.68e-06)	0.633 (1.00)	0.00849 (1.00)	0.00343 (1.00)	0.013 (1.00)	0.133 (1.00)	0.88 (1.00)	0.214 (1.00)	0.551 (1.00)	0.731 (1.00)
del 14q12	79 (32%)	171	1.86e-08 (1.25e-05)	0.366 (1.00)	0.149 (1.00)	0.0906 (1.00)	0.165 (1.00)	0.00181 (1.00)	0.0663 (1.00)	0.241 (1.00)	0.0645 (1.00)	0.248 (1.00)
del 15q13 1	103 (41%)	147	2.01e-06 (0.00131)	0.0116 (1.00)	0.286 (1.00)	0.45 (1.00)	0.826 (1.00)	0.147 (1.00)	0.134 (1.00)	0.18 (1.00)	0.251 (1.00)	0.326 (1.00)
del 16p13 3	99 (40%)	151	7.13e-10 (4.87e-07)	0.129 (1.00)	0.192 (1.00)	0.204 (1.00)	0.73 (1.00)	0.572 (1.00)	0.922 (1.00)	0.751 (1.00)	0.589 (1.00)	0.718 (1.00)
del 16q23 1	69 (28%)	181	4.91e-08 (3.29e-05)	0.0112 (1.00)	0.427 (1.00)	0.11 (1.00)	0.225 (1.00)	0.526 (1.00)	0.0354 (1.00)	0.393 (1.00)	0.104 (1.00)	0.126 (1.00)
del 17p12	130 (52%)	120	2.81e-05 (0.0181)	0.0191 (1.00)	0.201 (1.00)	0.448 (1.00)	0.348 (1.00)	0.068 (1.00)	0.611 (1.00)	0.829 (1.00)	0.736 (1.00)	0.486 (1.00)
del 18q23	104 (42%)	146	0.00082 (0.511)	0.551 (1.00)	0.599 (1.00)	1 (1.00)	1 (1.00)	0.94 (1.00)	0.00113 (0.699)	0.000331 (0.207)	0.00523 (1.00)	0.111 (1.00)
del 19p13 3	93 (37%)	157	0.000295 (0.186)	0.757 (1.00)	0.865 (1.00)	0.813 (1.00)	0.0888 (1.00)	0.321 (1.00)	0.498 (1.00)	0.305 (1.00)	0.268 (1.00)	0.391 (1.00)
del 22q13 31	114 (46%)	136	1.33e-10 (9.15e-08)	0.00859 (1.00)	0.42 (1.00)	0.0181 (1.00)	0.0111 (1.00)	0.00631 (1.00)	0.971 (1.00)	0.538 (1.00)	0.0912 (1.00)	0.198 (1.00)
amp 4p16 3	52 (21%)	198	0.207 (1.00)	0.00674 (1.00)	0.0275 (1.00)	0.00827 (1.00)	0.00349 (1.00)	0.00166 (1.00)	0.016 (1.00)	0.0169 (1.00)	0.00847 (1.00)	0.00814 (1.00)
amp 6q21	23 (9%)	227	0.272 (1.00)	0.54 (1.00)	0.451 (1.00)	0.195 (1.00)	0.441 (1.00)	0.209 (1.00)	0.529 (1.00)	0.608 (1.00)	0.687 (1.00)	0.725 (1.00)
amp 8q22 3	160 (64%)	90	0.00198 (1.00)	0.02 (1.00)	0.0247 (1.00)	0.128 (1.00)	0.48 (1.00)	0.471 (1.00)	0.0565 (1.00)	0.197 (1.00)	0.00562 (1.00)	0.0649 (1.00)
amp 11q22 2	46 (18%)	204	0.00924 (1.00)	0.606 (1.00)	0.641 (1.00)	0.276 (1.00)	0.0946 (1.00)	0.0748 (1.00)	0.0657 (1.00)	0.00755 (1.00)	0.0631 (1.00)	0.167 (1.00)
amp 12q15	75 (30%)	175	0.000875 (0.544)	0.207 (1.00)	0.0497 (1.00)	0.027 (1.00)	0.108 (1.00)	0.106 (1.00)	0.108 (1.00)	0.0111 (1.00)	0.0835 (1.00)	0.00354 (1.00)
amp 13q22 1	77 (31%)	173	0.0519 (1.00)	0.56 (1.00)	0.962 (1.00)	0.871 (1.00)	0.881 (1.00)	0.694 (1.00)	0.319 (1.00)	0.665 (1.00)	0.713 (1.00)	0.451 (1.00)
amp 16p13 13	56 (22%)	194	0.00651 (1.00)	0.588 (1.00)	0.462 (1.00)	0.827 (1.00)	0.218 (1.00)	0.78 (1.00)	0.79 (1.00)	0.839 (1.00)	0.668 (1.00)	0.444 (1.00)
del 1p36 11	49 (20%)	201	0.638 (1.00)	0.278 (1.00)	0.335 (1.00)	0.027 (1.00)	0.0526 (1.00)	0.172 (1.00)	0.877 (1.00)	0.385 (1.00)	0.643 (1.00)	0.74 (1.00)
del 1p21 3	42 (17%)	208	0.024 (1.00)	0.0764 (1.00)	0.345 (1.00)	0.937 (1.00)	0.441 (1.00)	0.0165 (1.00)	0.306 (1.00)	0.217 (1.00)	0.764 (1.00)	0.458 (1.00)
del 1q32 1	45 (18%)	205	0.226 (1.00)	0.672 (1.00)	0.426 (1.00)	0.614 (1.00)	0.509 (1.00)	0.0134 (1.00)	0.195 (1.00)	0.327 (1.00)	0.154 (1.00)	0.311 (1.00)
del 7q36 3	38 (15%)	212	0.143 (1.00)	0.117 (1.00)	0.287 (1.00)	0.222 (1.00)	0.151 (1.00)	0.389 (1.00)	0.58 (1.00)	0.11 (1.00)	0.842 (1.00)	0.74 (1.00)
del 10p12 1	40 (16%)	210	0.000553 (0.345)	0.0614 (1.00)	0.769 (1.00)	0.646 (1.00)	0.00936 (1.00)	0.127 (1.00)	0.286 (1.00)	0.064 (1.00)	0.544 (1.00)	0.464 (1.00)
del 18q21 2	110 (44%)	140	0.00133 (0.818)	0.702 (1.00)	0.862 (1.00)	0.982 (1.00)	0.827 (1.00)	0.848 (1.00)	0.00393 (1.00)	0.00223 (1.00)	0.023 (1.00)	0.172 (1.00)
del xp11 3	57 (23%)	193	0.00684 (1.00)	0.367 (1.00)	0.644 (1.00)	0.718 (1.00)	0.408 (1.00)	0.961 (1.00)	0.11 (1.00)	0.449 (1.00)	0.118 (1.00)	0.537 (1.00)
del xq21 33	50 (20%)	200	0.0102 (1.00)	0.00957 (1.00)	0.981 (1.00)	0.0974 (1.00)	0.0177 (1.00)	0.609 (1.00)	0.031 (1.00)	0.834 (1.00)	0.0565 (1.00)	0.0903 (1.00)

'amp_1p34.2' versus 'CN_CNMF'

P value = 0.000224 (Chi-square test), Q value = 0.14

Table S1. Gene #1: 'amp_1p34.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
AMP PEAK 1(1P34.2) MUTATED	3	8	5	9	16	13	10	4
AMP PEAK 1(1P34.2) WILD-TYPE	12	80	12	11	22	19	14	12

Figure S1. Get High-res Image Gene #1: 'amp_1p34.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q21.3' versus 'CN_CNMF'

P value = 7.21e-13 (Chi-square test), Q value = 5e-10

Table S2. Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
AMP PEAK 2(1Q21.3) MUTATED	7	16	11	19	17	23	20	10
AMP PEAK 2(1Q21.3) WILD-TYPE	8	72	6	1	21	9	4	6

Figure S2. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q23.3' versus 'CN_CNMF'

P value = 8.39e-09 (Chi-square test), Q value = 5.7e-06

Table S3. Gene #3: 'amp_1q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
AMP PEAK 3(1Q23.3) MUTATED	8	22	13	18	18	24	16	10
AMP PEAK 3(1Q23.3) WILD-TYPE	7	66	4	2	20	8	8	6

Figure S3. Get High-res Image Gene #3: 'amp_1q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3p25.2' versus 'CN_CNMF'

P value = 2.16e-11 (Chi-square test), Q value = 1.5e-08

Table S4. Gene #4: 'amp_3p25.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
AMP PEAK 4(3P25.2) MUTATED	14	20	10	10	15	22	23	8
AMP PEAK 4(3P25.2) WILD-TYPE	1	68	7	10	23	10	1	8

Figure S4. Get High-res Image Gene #4: 'amp_3p25.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3p25.2' versus 'MRNASEQ_CNMF'

P value = 1.98e-05 (Fisher's exact test), Q value = 0.013

Table S5. Gene #4: 'amp_3p25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	104	70	64
AMP PEAK 4(3P25.2) MUTATED	63	38	16
AMP PEAK 4(3P25.2) WILD-TYPE	41	32	48

Figure S5. Get High-res Image Gene #4: 'amp_3p25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3p25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.7e-05 (Fisher's exact test), Q value = 0.017

Table S6. Gene #4: 'amp_3p25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	48	92
AMP PEAK 4(3P25.2) MUTATED	31	31	55
AMP PEAK 4(3P25.2) WILD-TYPE	67	17	37

Figure S6. Get High-res Image Gene #4: 'amp_3p25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3p25.2' versus 'MIRSEQ_CNMF'

P value = 8.4e-05 (Fisher's exact test), Q value = 0.054

Table S7. Gene #4: 'amp_3p25.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	108	82
AMP PEAK 4(3P25.2) MUTATED	43	46	32
AMP PEAK 4(3P25.2) WILD-TYPE	16	62	50

Figure S7. Get High-res Image Gene #4: 'amp_3p25.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_3p25.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.7e-05 (Fisher's exact test), Q value = 0.011

Table S8. Gene #4: 'amp_3p25.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	100	101
AMP PEAK 4(3P25.2) MUTATED	37	47	37
AMP PEAK 4(3P25.2) WILD-TYPE	11	53	64

Figure S8. Get High-res Image Gene #4: 'amp_3p25.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_3p25.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000179 (Fisher's exact test), Q value = 0.11

Table S9. Gene #4: 'amp_3p25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	133	45
AMP PEAK 4(3P25.2) MUTATED	37	51	33
AMP PEAK 4(3P25.2) WILD-TYPE	34	82	12

Figure S9. Get High-res Image Gene #4: 'amp_3p25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.32' versus 'CN_CNMF'

P value = 3.64e-05 (Chi-square test), Q value = 0.023

Table S10. Gene #5: 'amp_3q26.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
AMP PEAK 5(3Q26.32) MUTATED	11	30	13	12	26	23	16	5
AMP PEAK 5(3Q26.32) WILD-TYPE	4	58	4	8	12	9	8	11

Figure S10. Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4q13.3' versus 'CN_CNMF'

P value = 0.000396 (Chi-square test), Q value = 0.25

Table S11. Gene #7: 'amp_4q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
AMP PEAK 7(4Q13.3) MUTATED	2	5	3	9	12	4	7	3
AMP PEAK 7(4Q13.3) WILD-TYPE	13	83	14	11	26	28	17	13

Figure S11. Get High-res Image Gene #7: 'amp_4q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1.35e-08 (Chi-square test), Q value = 9.1e-06

Table S12. Gene #8: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
AMP PEAK 8(5P15.33) MUTATED	9	22	8	9	27	26	19	8
AMP PEAK 8(5P15.33) WILD-TYPE	6	66	9	11	11	6	5	8

Figure S12. Get High-res Image Gene #8: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p22.3' versus 'CN_CNMF'

P value = 1.23e-13 (Chi-square test), Q value = 8.5e-11

Table S13. Gene #9: 'amp_6p22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
AMP PEAK 9(6P22.3) MUTATED	10	14	7	12	14	32	11	7
AMP PEAK 9(6P22.3) WILD-TYPE	5	74	10	8	24	0	13	9

Figure S13. Get High-res Image Gene #9: 'amp_6p22.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p21.1' versus 'CN_CNMF'

P value = 7.2e-08 (Chi-square test), Q value = 4.8e-05

Table S14. Gene #11: 'amp_7p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
AMP PEAK 11(7P21.1) MUTATED	6	24	11	13	25	28	16	7
AMP PEAK 11(7P21.1) WILD-TYPE	9	64	6	7	13	4	8	9

Figure S14. Get High-res Image Gene #11: 'amp_7p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1.04e-07 (Chi-square test), Q value = 6.9e-05

Table S15. Gene #12: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
AMP PEAK 12(7P11.2) MUTATED	9	21	10	12	26	25	17	7
AMP PEAK 12(7P11.2) WILD-TYPE	6	67	7	8	12	7	7	9

Figure S15. Get High-res Image Gene #12: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p11.23' versus 'CN_CNMF'

P value = 1.67e-05 (Chi-square test), Q value = 0.011

Table S16. Gene #13: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
AMP PEAK 13(8P11.23) MUTATED	6	16	15	6	12	11	6	5
AMP PEAK 13(8P11.23) WILD-TYPE	9	72	2	14	26	21	18	11

Figure S16. Get High-res Image Gene #13: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p24.1' versus 'CN_CNMF'

P value = 1.85e-06 (Chi-square test), Q value = 0.0012

Table S17. Gene #15: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
AMP PEAK 15(9P24.1) MUTATED	3	6	5	4	2	13	7	9
AMP PEAK 15(9P24.1) WILD-TYPE	12	82	12	16	36	19	17	7

Figure S17. Get High-res Image Gene #15: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10p14' versus 'CN_CNMF'

P value = 2.51e-16 (Chi-square test), Q value = 1.7e-13

Table S18. Gene #16: 'amp_10p14' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
AMP PEAK 16(10P14) MUTATED	11	9	5	15	19	26	20	7
AMP PEAK 16(10P14) WILD-TYPE	4	79	12	5	19	6	4	9

Figure S18. Get High-res Image Gene #16: 'amp_10p14' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'CN_CNMF'

P value = 2.35e-08 (Chi-square test), Q value = 1.6e-05

Table S19. Gene #17: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
AMP PEAK 17(11Q13.3) MUTATED	11	15	12	7	25	15	7	3
AMP PEAK 17(11Q13.3) WILD-TYPE	4	73	5	13	13	17	17	13

Figure S19. Get High-res Image Gene #17: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p13.32' versus 'CN_CNMF'

P value = 2.83e-06 (Chi-square test), Q value = 0.0019

Table S20. Gene #19: 'amp_12p13.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
AMP PEAK 19(12P13.32) MUTATED	8	13	8	8	19	21	6	4
AMP PEAK 19(12P13.32) WILD-TYPE	7	75	9	12	19	11	18	12

Figure S20. Get High-res Image Gene #19: 'amp_12p13.32' versus Molecular Subtype #1: 'CN_CNMF'

'amp_14q11.2' versus 'CN_CNMF'

P value = 0.000215 (Chi-square test), Q value = 0.14

Table S21. Gene #22: 'amp_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
AMP PEAK 22(14Q11.2) MUTATED	7	10	8	2	15	6	5	7
AMP PEAK 22(14Q11.2) WILD-TYPE	8	78	9	18	23	26	19	9

Figure S21. Get High-res Image Gene #22: 'amp_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_16q22.1' versus 'CN_CNMF'

P value = 1.43e-05 (Chi-square test), Q value = 0.0093

Table S22. Gene #24: 'amp_16q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
AMP PEAK 24(16Q22.1) MUTATED	3	16	6	14	18	12	3	2
AMP PEAK 24(16Q22.1) WILD-TYPE	12	72	11	6	20	20	21	14

Figure S22. Get High-res Image Gene #24: 'amp_16q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q11.2' versus 'CN_CNMF'

P value = 8.52e-07 (Chi-square test), Q value = 0.00056

Table S23. Gene #25: 'amp_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
AMP PEAK 25(17Q11.2) MUTATED	9	20	14	12	15	23	12	6
AMP PEAK 25(17Q11.2) WILD-TYPE	6	68	3	8	23	9	12	10

Figure S23. Get High-res Image Gene #25: 'amp_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q11.2' versus 'METHLYATION_CNMF'

P value = 2.45e-05 (Fisher's exact test), Q value = 0.016

Table S24. Gene #25: 'amp_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	103	49
AMP PEAK 25(17Q11.2) MUTATED	60	30	21
AMP PEAK 25(17Q11.2) WILD-TYPE	38	73	28

Figure S24. Get High-res Image Gene #25: 'amp_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q11.2' versus 'MRNASEQ_CNMF'

P value = 0.000328 (Fisher's exact test), Q value = 0.21

Table S25. Gene #25: 'amp_17q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	104	70	64
AMP PEAK 25(17Q11.2) MUTATED	63	27	20
AMP PEAK 25(17Q11.2) WILD-TYPE	41	43	44

Figure S25. Get High-res Image Gene #25: 'amp_17q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q12' versus 'CN_CNMF'

P value = 0.000214 (Chi-square test), Q value = 0.14

Table S26. Gene #26: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
AMP PEAK 26(17Q12) MUTATED	11	24	13	9	11	15	14	6
AMP PEAK 26(17Q12) WILD-TYPE	4	64	4	11	27	17	10	10

Figure S26. Get High-res Image Gene #26: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'CN_CNMF'

P value = 5.93e-07 (Chi-square test), Q value = 0.00039

Table S27. Gene #27: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
AMP PEAK 27(19Q12) MUTATED	10	18	5	11	20	24	12	4
AMP PEAK 27(19Q12) WILD-TYPE	5	70	12	9	18	8	12	12

Figure S27. Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q13.43' versus 'CN_CNMF'

P value = 6.37e-06 (Chi-square test), Q value = 0.0042

Table S28. Gene #28: 'amp_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
AMP PEAK 28(19Q13.43) MUTATED	9	15	7	10	25	17	9	5
AMP PEAK 28(19Q13.43) WILD-TYPE	6	73	10	10	13	15	15	11

Figure S28. Get High-res Image Gene #28: 'amp_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q11.21' versus 'CN_CNMF'

P value = 6.91e-07 (Chi-square test), Q value = 0.00046

Table S29. Gene #29: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
AMP PEAK 29(20Q11.21) MUTATED	12	35	15	18	29	25	17	12
AMP PEAK 29(20Q11.21) WILD-TYPE	3	53	2	2	9	7	7	4

Figure S29. Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_22q11.23' versus 'CN_CNMF'

P value = 1.29e-06 (Chi-square test), Q value = 0.00085

Table S30. Gene #30: 'amp_22q11.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
AMP PEAK 30(22Q11.23) MUTATED	10	5	7	3	6	10	7	4
AMP PEAK 30(22Q11.23) WILD-TYPE	5	83	10	17	32	22	17	12

Figure S30. Get High-res Image Gene #30: 'amp_22q11.23' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'CN_CNMF'

P value = 0.000144 (Chi-square test), Q value = 0.091

Table S31. Gene #34: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
DEL PEAK 4(2Q22.1) MUTATED	3	12	6	8	13	14	15	7
DEL PEAK 4(2Q22.1) WILD-TYPE	12	76	11	12	25	18	9	9

Figure S31. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.1' versus 'CN_CNMF'

P value = 2.81e-08 (Chi-square test), Q value = 1.9e-05

Table S32. Gene #35: 'del_2q37.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
DEL PEAK 5(2Q37.1) MUTATED	7	20	8	14	27	21	19	10
DEL PEAK 5(2Q37.1) WILD-TYPE	8	68	9	6	11	11	5	6

Figure S32. Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p21.31' versus 'CN_CNMF'

P value = 1.28e-06 (Chi-square test), Q value = 0.00084

Table S33. Gene #36: 'del_3p21.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
DEL PEAK 6(3P21.31) MUTATED	8	14	7	8	21	12	0	2
DEL PEAK 6(3P21.31) WILD-TYPE	7	74	10	12	17	20	24	14

Figure S33. Get High-res Image Gene #36: 'del_3p21.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p21.31' versus 'MRNASEQ_CNMF'

P value = 7.98e-06 (Fisher's exact test), Q value = 0.0052

Table S34. Gene #36: 'del_3p21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	104	70	64
DEL PEAK 6(3P21.31) MUTATED	26	11	34
DEL PEAK 6(3P21.31) WILD-TYPE	78	59	30

Figure S34. Get High-res Image Gene #36: 'del_3p21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'CN_CNMF'

P value = 2.18e-08 (Chi-square test), Q value = 1.5e-05

Table S35. Gene #37: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
DEL PEAK 7(3P14.2) MUTATED	8	12	6	8	22	14	0	1
DEL PEAK 7(3P14.2) WILD-TYPE	7	76	11	12	16	18	24	15

Figure S35. Get High-res Image Gene #37: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.2' versus 'MRNASEQ_CNMF'

P value = 8.04e-05 (Fisher's exact test), Q value = 0.051

Table S36. Gene #37: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	104	70	64
DEL PEAK 7(3P14.2) MUTATED	25	12	32
DEL PEAK 7(3P14.2) WILD-TYPE	79	58	32

Figure S36. Get High-res Image Gene #37: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p13' versus 'CN_CNMF'

P value = 3.81e-07 (Chi-square test), Q value = 0.00025

Table S37. Gene #38: 'del_3p13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
DEL PEAK 8(3P13) MUTATED	7	13	4	6	21	14	0	1
DEL PEAK 8(3P13) WILD-TYPE	8	75	13	14	17	18	24	15

Figure S37. Get High-res Image Gene #38: 'del_3p13' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p13' versus 'MRNASEQ_CNMF'

P value = 4.28e-05 (Fisher's exact test), Q value = 0.027

Table S38. Gene #38: 'del_3p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	104	70	64
DEL PEAK 8(3P13) MUTATED	22	11	31
DEL PEAK 8(3P13) WILD-TYPE	82	59	33

Figure S38. Get High-res Image Gene #38: 'del_3p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'CN_CNMF'

P value = 2e-04 (Chi-square test), Q value = 0.13

Table S39. Gene #39: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
DEL PEAK 9(4Q22.1) MUTATED	6	19	11	10	24	17	10	8
DEL PEAK 9(4Q22.1) WILD-TYPE	9	69	6	10	14	15	14	8

Figure S39. Get High-res Image Gene #39: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.2' versus 'CN_CNMF'

P value = 3.64e-07 (Chi-square test), Q value = 0.00024

Table S40. Gene #40: 'del_4q34.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
DEL PEAK 10(4Q34.2) MUTATED	10	17	8	11	27	18	11	11
DEL PEAK 10(4Q34.2) WILD-TYPE	5	71	9	9	11	14	13	5

Figure S40. Get High-res Image Gene #40: 'del_4q34.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q11.2' versus 'CN_CNMF'

P value = 3.71e-09 (Chi-square test), Q value = 2.5e-06

Table S41. Gene #41: 'del_5q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
DEL PEAK 11(5Q11.2) MUTATED	6	22	7	19	26	23	15	10
DEL PEAK 11(5Q11.2) WILD-TYPE	9	66	10	1	12	9	9	6

Figure S41. Get High-res Image Gene #41: 'del_5q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.3' versus 'CN_CNMF'

P value = 7.06e-05 (Chi-square test), Q value = 0.045

Table S42. Gene #42: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
DEL PEAK 12(6P25.3) MUTATED	8	9	9	6	7	12	9	7
DEL PEAK 12(6P25.3) WILD-TYPE	7	79	8	14	31	20	15	9

Figure S42. Get High-res Image Gene #42: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q21' versus 'CN_CNMF'

P value = 2.32e-09 (Chi-square test), Q value = 1.6e-06

Table S43. Gene #43: 'del_6q21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
DEL PEAK 13(6Q21) MUTATED	9	15	10	13	25	11	19	9
DEL PEAK 13(6Q21) WILD-TYPE	6	73	7	7	13	21	5	7

Figure S43. Get High-res Image Gene #43: 'del_6q21' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q27' versus 'CN_CNMF'

P value = 3.54e-10 (Chi-square test), Q value = 2.4e-07

Table S44. Gene #44: 'del_6q27' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
DEL PEAK 14(6Q27) MUTATED	12	15	11	11	22	12	20	10
DEL PEAK 14(6Q27) WILD-TYPE	3	73	6	9	16	20	4	6

Figure S44. Get High-res Image Gene #44: 'del_6q27' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.3' versus 'CN_CNMF'

P value = 2.89e-10 (Chi-square test), Q value = 2e-07

Table S45. Gene #46: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
DEL PEAK 16(8P23.3) MUTATED	11	32	1	18	25	26	17	13
DEL PEAK 16(8P23.3) WILD-TYPE	4	56	16	2	13	6	7	3

Figure S45. Get High-res Image Gene #46: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p12' versus 'CN_CNMF'

P value = 1.22e-08 (Chi-square test), Q value = 8.2e-06

Table S46. Gene #47: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
DEL PEAK 17(8P12) MUTATED	10	26	0	13	22	23	17	12
DEL PEAK 17(8P12) WILD-TYPE	5	62	17	7	16	9	7	4

Figure S46. Get High-res Image Gene #47: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p11.21' versus 'CN_CNMF'

P value = 1.09e-05 (Chi-square test), Q value = 0.0071

Table S47. Gene #48: 'del_8p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
DEL PEAK 18(8P11.21) MUTATED	5	12	0	10	15	5	10	9
DEL PEAK 18(8P11.21) WILD-TYPE	10	76	17	10	23	27	14	7

Figure S47. Get High-res Image Gene #48: 'del_8p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'CN_CNMF'

P value = 3.81e-06 (Chi-square test), Q value = 0.0025

Table S48. Gene #49: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
DEL PEAK 19(9P23) MUTATED	7	39	6	9	30	8	13	0
DEL PEAK 19(9P23) WILD-TYPE	8	49	11	11	8	24	11	16

Figure S48. Get High-res Image Gene #49: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 1.2e-06 (Chi-square test), Q value = 0.00079

Table S49. Gene #50: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
DEL PEAK 20(9P21.3) MUTATED	11	56	8	13	33	12	14	1
DEL PEAK 20(9P21.3) WILD-TYPE	4	32	9	7	5	20	10	15

Figure S49. Get High-res Image Gene #50: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q33.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.48e-05 (Fisher's exact test), Q value = 0.06

Table S50. Gene #51: 'del_9q33.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	48	92
DEL PEAK 21(9Q33.2) MUTATED	24	27	45
DEL PEAK 21(9Q33.2) WILD-TYPE	74	21	47

Figure S50. Get High-res Image Gene #51: 'del_9q33.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 4.91e-07 (Chi-square test), Q value = 0.00033

Table S51. Gene #53: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
DEL PEAK 23(10Q23.31) MUTATED	5	13	8	9	21	20	13	11
DEL PEAK 23(10Q23.31) WILD-TYPE	10	75	9	11	17	12	11	5

Figure S51. Get High-res Image Gene #53: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q26.13' versus 'CN_CNMF'

P value = 1.9e-07 (Chi-square test), Q value = 0.00013

Table S52. Gene #54: 'del_10q26.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
DEL PEAK 24(10Q26.13) MUTATED	5	14	9	8	19	21	14	12
DEL PEAK 24(10Q26.13) WILD-TYPE	10	74	8	12	19	11	10	4

Figure S52. Get High-res Image Gene #54: 'del_10q26.13' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.5' versus 'CN_CNMF'

P value = 3.7e-08 (Chi-square test), Q value = 2.5e-05

Table S53. Gene #55: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
DEL PEAK 25(11P15.5) MUTATED	12	24	9	17	28	14	15	4
DEL PEAK 25(11P15.5) WILD-TYPE	3	64	8	3	10	18	9	12

Figure S53. Get High-res Image Gene #55: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 0.000276 (Fisher's exact test), Q value = 0.17

Table S54. Gene #55: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	103	49
DEL PEAK 25(11P15.5) MUTATED	59	35	29
DEL PEAK 25(11P15.5) WILD-TYPE	39	68	20

Figure S54. Get High-res Image Gene #55: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q25' versus 'CN_CNMF'

P value = 1.03e-07 (Chi-square test), Q value = 6.9e-05

Table S55. Gene #56: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
DEL PEAK 26(11Q25) MUTATED	7	12	10	9	26	12	12	3
DEL PEAK 26(11Q25) WILD-TYPE	8	76	7	11	12	20	12	13

Figure S55. Get High-res Image Gene #56: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'CN_CNMF'

P value = 9.85e-09 (Chi-square test), Q value = 6.7e-06

Table S56. Gene #57: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
DEL PEAK 27(13Q14.2) MUTATED	5	11	12	8	21	19	13	11
DEL PEAK 27(13Q14.2) WILD-TYPE	10	77	5	12	17	13	11	5

Figure S56. Get High-res Image Gene #57: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q12' versus 'CN_CNMF'

P value = 1.86e-08 (Chi-square test), Q value = 1.3e-05

Table S57. Gene #58: 'del_14q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
DEL PEAK 28(14Q12) MUTATED	6	17	3	13	7	17	16	0
DEL PEAK 28(14Q12) WILD-TYPE	9	71	14	7	31	15	8	16

Figure S57. Get High-res Image Gene #58: 'del_14q12' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q24.1' versus 'CN_CNMF'

P value = 3.29e-09 (Chi-square test), Q value = 2.2e-06

Table S58. Gene #59: 'del_14q24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
DEL PEAK 29(14Q24.1) MUTATED	8	16	3	15	8	16	16	1
DEL PEAK 29(14Q24.1) WILD-TYPE	7	72	14	5	30	16	8	15

Figure S58. Get High-res Image Gene #59: 'del_14q24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.01e-06 (Fisher's exact test), Q value = 0.0052

Table S59. Gene #59: 'del_14q24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	48	92
DEL PEAK 29(14Q24.1) MUTATED	18	28	32
DEL PEAK 29(14Q24.1) WILD-TYPE	80	20	60

Figure S59. Get High-res Image Gene #59: 'del_14q24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q13.1' versus 'CN_CNMF'

P value = 2.01e-06 (Chi-square test), Q value = 0.0013

Table S60. Gene #60: 'del_15q13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
DEL PEAK 30(15Q13.1) MUTATED	9	14	7	9	22	19	13	10
DEL PEAK 30(15Q13.1) WILD-TYPE	6	74	10	11	16	13	11	6

Figure S60. Get High-res Image Gene #60: 'del_15q13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16p13.3' versus 'CN_CNMF'

P value = 7.13e-10 (Chi-square test), Q value = 4.9e-07

Table S61. Gene #61: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
DEL PEAK 31(16P13.3) MUTATED	6	12	5	7	27	16	13	13
DEL PEAK 31(16P13.3) WILD-TYPE	9	76	12	13	11	16	11	3

Figure S61. Get High-res Image Gene #61: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 4.91e-08 (Chi-square test), Q value = 3.3e-05

Table S62. Gene #62: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
DEL PEAK 32(16Q23.1) MUTATED	7	7	9	2	10	11	13	10
DEL PEAK 32(16Q23.1) WILD-TYPE	8	81	8	18	28	21	11	6

Figure S62. Get High-res Image Gene #62: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p12' versus 'CN_CNMF'

P value = 2.81e-05 (Chi-square test), Q value = 0.018

Table S63. Gene #63: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
DEL PEAK 33(17P12) MUTATED	13	29	10	15	24	22	12	5
DEL PEAK 33(17P12) WILD-TYPE	2	59	7	5	14	10	12	11

Figure S63. Get High-res Image Gene #63: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000331 (Fisher's exact test), Q value = 0.21

Table S64. Gene #65: 'del_18q23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	15	58
DEL PEAK 35(18Q23) MUTATED	60	11	33
DEL PEAK 35(18Q23) WILD-TYPE	116	4	25

Figure S64. Get High-res Image Gene #65: 'del_18q23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 0.000295 (Chi-square test), Q value = 0.19

Table S65. Gene #66: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
DEL PEAK 36(19P13.3) MUTATED	3	18	8	14	19	16	9	6
DEL PEAK 36(19P13.3) WILD-TYPE	12	70	9	6	19	16	15	10

Figure S65. Get High-res Image Gene #66: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.31' versus 'CN_CNMF'

P value = 1.33e-10 (Chi-square test), Q value = 9.2e-08

Table S66. Gene #67: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	15	88	17	20	38	32	24	16
DEL PEAK 37(22Q13.31) MUTATED	5	15	7	14	22	24	13	14
DEL PEAK 37(22Q13.31) WILD-TYPE	10	73	10	6	16	8	11	2

Figure S66. Get High-res Image Gene #67: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = BLCA-TP.transferedmergedcluster.txt
Number of patients = 250
Number of significantly focal cnvs = 69
Number of molecular subtypes = 10
Exclude genes that fewer than K tumors have alterations, K = 3

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

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[2] 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)

[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)

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