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

Testicular Germ Cell Tumors (Primary solid tumor)

21 August 2015 | analyses__2015_08_21

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 (2015): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1SX6CJH

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 47 focal events and 10 molecular subtypes across 150 patients, 246 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q21.2 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
amp_2p24.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3q27.3 cnv correlated to 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_4q12 cnv correlated to 'CN_CNMF'.
amp_7p22.1 cnv correlated to 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q11.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q11.23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q23.3 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12p13.33 cnv correlated to 'RPPA_CHIERARCHICAL'.
amp_12p12.1 cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12p11.21 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_16q21 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20q11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_22q11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.31 cnv correlated to 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p31.1 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_1q42.12 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q37.3 cnv correlated to 'METHLYATION_CNMF'.
del_3p26.2 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5p14.3 cnv correlated to 'RPPA_CNMF'.
del_5q12.1 cnv correlated to 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6p22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q26 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7q11.22 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7q36.1 cnv correlated to 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p23 cnv correlated to 'CN_CNMF'.
del_9q33.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_9q34.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_10p15.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q26.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p15.5 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p12 cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q12.3 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q24.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q34 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q23.1 cnv correlated to 'CN_CNMF'.
del_18p11.32 cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
del_18q22.2 cnv correlated to 'MIRSEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19q13.41 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_20p12.1 cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp21.1 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xq27.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 47 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, 246 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
amp 8q11 23	122 (81%)	28	0.00012 (0.00134)	0.0102 (0.0291)	0.00055 (0.0041)	0.00013 (0.00142)	2e-05 (0.000392)	1e-05 (0.000336)	7e-05 (0.000914)	2e-05 (0.000392)	2e-05 (0.000392)	2e-05 (0.000392)
amp 20q11 21	51 (34%)	99	0.00497 (0.0181)	0.00288 (0.0125)	0.0191 (0.0466)	0.0145 (0.0367)	0.00288 (0.0125)	0.034 (0.0708)	0.017 (0.042)	0.00696 (0.0229)	0.00969 (0.0281)	0.00799 (0.0245)
amp 22q11 21	57 (38%)	93	4e-05 (0.000696)	0.00665 (0.0222)	0.0119 (0.0321)	0.00528 (0.0182)	0.00017 (0.0016)	1e-05 (0.000336)	0.0132 (0.0346)	0.00015 (0.00147)	0.00028 (0.00244)	2e-05 (0.000392)
del 6p22 3	24 (16%)	126	6e-05 (0.00091)	0.0156 (0.0388)	0.00021 (0.0019)	0.00062 (0.00435)	0.00408 (0.0157)	0.0118 (0.0321)	0.00519 (0.0182)	0.00351 (0.0145)	0.00384 (0.0154)	0.00757 (0.0239)
del 6q26	26 (17%)	124	0.0328 (0.0685)	0.00077 (0.00503)	0.0237 (0.054)	0.0143 (0.0366)	0.00612 (0.021)	0.00149 (0.00783)	0.0139 (0.036)	0.00519 (0.0182)	0.00502 (0.0181)	0.0156 (0.0388)
del 10p15 3	84 (56%)	66	0.00134 (0.0075)	0.00038 (0.00298)	0.00391 (0.0154)	0.00306 (0.0128)	0.00015 (0.00147)	0.0012 (0.00688)	0.0204 (0.0491)	0.00067 (0.00456)	0.00034 (0.00276)	0.00038 (0.00298)
del 10q23 1	71 (47%)	79	0.00509 (0.0181)	2e-05 (0.000392)	0.0235 (0.0539)	0.0136 (0.0355)	3e-05 (0.000542)	0.00029 (0.00248)	0.018 (0.0444)	3e-05 (0.000542)	8e-05 (0.00102)	0.00014 (0.00143)
del 10q26 3	76 (51%)	74	0.0004 (0.00308)	1e-05 (0.000336)	0.0118 (0.0321)	0.00291 (0.0125)	2e-05 (0.000392)	0.00011 (0.00126)	0.0216 (0.0507)	7e-05 (0.000914)	2e-05 (0.000392)	7e-05 (0.000914)
del 19q13 41	58 (39%)	92	1e-05 (0.000336)	1e-05 (0.000336)	1e-05 (0.000336)	1e-05 (0.000336)	1e-05 (0.000336)	1e-05 (0.000336)	1e-05 (0.000336)	1e-05 (0.000336)	1e-05 (0.000336)	1e-05 (0.000336)
amp 7q11 22	120 (80%)	30	0.00056 (0.00411)	0.0383 (0.0773)	0.0123 (0.033)	0.057 (0.104)	0.0001 (0.00117)	0.00233 (0.0111)	0.00014 (0.00143)	0.0002 (0.00184)	0.00014 (0.00143)	0.00081 (0.00508)
amp 8q23 3	108 (72%)	42	0.184 (0.261)	0.00365 (0.0148)	0.025 (0.0564)	0.0109 (0.0305)	0.00031 (0.0026)	0.00076 (0.00503)	5e-05 (0.000783)	0.0001 (0.00117)	0.00054 (0.00409)	0.00164 (0.00838)
amp 16q21	21 (14%)	129	0.00017 (0.0016)	0.372 (0.455)	0.00306 (0.0128)	0.00141 (0.00762)	0.00295 (0.0126)	0.00758 (0.0239)	0.00116 (0.00681)	0.0083 (0.0252)	0.0025 (0.0115)	0.00884 (0.0263)
del 11q12 3	114 (76%)	36	5e-05 (0.000783)	0.185 (0.262)	0.0322 (0.0681)	0.0222 (0.0516)	9e-05 (0.00111)	2e-05 (0.000392)	5e-05 (0.000783)	1e-05 (0.000336)	7e-05 (0.000914)	2e-05 (0.000392)
amp 2p24 1	62 (41%)	88	0.0034 (0.0141)	0.00063 (0.00435)	0.194 (0.272)	0.127 (0.192)	0.0205 (0.0491)	0.0441 (0.086)	0.0289 (0.063)	0.0388 (0.0779)	0.0436 (0.0853)	0.0323 (0.0681)
amp 3q27 3	49 (33%)	101	0.0765 (0.134)	0.102 (0.167)	0.00255 (0.0116)	0.00119 (0.00688)	0.00243 (0.0113)	0.00784 (0.0242)	0.00085 (0.00519)	0.00261 (0.0118)	0.00077 (0.00503)	0.00389 (0.0154)
del 4q22 2	110 (73%)	40	0.0199 (0.0482)	0.0326 (0.0684)	0.679 (0.735)	0.56 (0.622)	0.00907 (0.0268)	0.0015 (0.00783)	0.00287 (0.0125)	0.00469 (0.0174)	0.0305 (0.0652)	0.00995 (0.0287)
del 7q11 22	4 (3%)	146	0.314 (0.4)	0.00755 (0.0239)	0.119 (0.184)	0.0286 (0.0628)	0.00948 (0.0277)	0.0303 (0.0651)	0.0048 (0.0176)	0.00936 (0.0275)	0.0103 (0.0291)	0.0144 (0.0367)
del 3p26 2	41 (27%)	109	0.759 (0.798)	0.0209 (0.0495)	0.0873 (0.148)	0.504 (0.577)	0.00138 (0.00754)	0.00396 (0.0154)	0.00661 (0.0222)	0.00364 (0.0148)	0.00166 (0.00839)	0.00058 (0.00419)
del 11p15 5	94 (63%)	56	0.0256 (0.0575)	0.254 (0.336)	0.158 (0.229)	0.447 (0.527)	0.00281 (0.0125)	0.00418 (0.016)	0.00524 (0.0182)	0.00241 (0.0113)	0.00624 (0.0213)	0.00709 (0.023)
del 11q24 2	122 (81%)	28	7e-05 (0.000914)	0.722 (0.768)	0.594 (0.655)	0.31 (0.397)	0.00882 (0.0263)	0.00059 (0.0042)	0.0125 (0.0332)	0.0067 (0.0222)	0.015 (0.038)	0.00081 (0.00508)
amp 12p11 21	144 (96%)	6	0.108 (0.173)	0.0381 (0.0772)	0.153 (0.223)	0.0352 (0.073)	0.0365 (0.0753)	0.498 (0.573)	0.206 (0.285)	0.0377 (0.077)	0.0392 (0.0785)	0.0243 (0.0551)
del 5q12 1	105 (70%)	45	0.088 (0.148)	0.104 (0.169)	0.0114 (0.0316)	0.335 (0.421)	0.032 (0.0681)	0.00755 (0.0239)	0.39 (0.468)	0.023 (0.0533)	0.0289 (0.063)	0.0126 (0.0332)
del 11p12	99 (66%)	51	0.0554 (0.103)	0.111 (0.177)	0.138 (0.205)	0.486 (0.562)	0.0016 (0.00826)	0.00508 (0.0181)	0.00209 (0.0101)	0.00137 (0.00754)	0.00652 (0.022)	0.00422 (0.016)
amp 7p22 1	126 (84%)	24	0.0863 (0.147)	0.08 (0.139)	0.124 (0.19)	0.0911 (0.152)	0.0283 (0.0624)	0.105 (0.169)	0.00775 (0.0242)	0.0114 (0.0316)	0.0221 (0.0516)	0.021 (0.0495)
del 1p36 31	34 (23%)	116	0.283 (0.368)	0.734 (0.775)	0.156 (0.226)	0.0572 (0.104)	0.00232 (0.0111)	0.0515 (0.0973)	0.00441 (0.0166)	0.00462 (0.0172)	0.0017 (0.0085)	0.0139 (0.036)
del xp21 1	28 (19%)	122	0.0578 (0.105)	0.00087 (0.00524)	0.9 (0.923)	0.62 (0.681)	0.0445 (0.0861)	0.0509 (0.0965)	0.0433 (0.0851)	0.0719 (0.126)	0.0491 (0.0942)	0.00085 (0.00519)
del xq27 3	30 (20%)	120	0.00113 (0.00672)	0.00147 (0.00783)	0.119 (0.184)	0.743 (0.783)	0.0928 (0.154)	0.0636 (0.113)	0.0109 (0.0305)	0.0116 (0.0319)	0.102 (0.167)	0.0589 (0.106)
del 1p31 1	27 (18%)	123	0.00702 (0.0229)	0.6 (0.66)	0.353 (0.436)	0.0493 (0.0942)	0.246 (0.328)	0.728 (0.772)	0.00819 (0.025)	0.152 (0.223)	0.0651 (0.115)	0.239 (0.321)
del 7q36 1	15 (10%)	135	0.0506 (0.0964)	0.889 (0.917)	0.386 (0.466)	0.0292 (0.063)	0.2 (0.277)	0.0102 (0.0291)	0.167 (0.239)	0.831 (0.864)	0.384 (0.466)	0.0292 (0.063)
del 9q34 2	60 (40%)	90	0.00034 (0.00276)	0.28 (0.365)	0.127 (0.192)	0.0566 (0.104)	0.0942 (0.155)	0.00394 (0.0154)	0.502 (0.576)	0.0276 (0.0611)	0.139 (0.205)	0.123 (0.188)
del 13q34	113 (75%)	37	0.0444 (0.0861)	0.556 (0.622)	0.113 (0.18)	0.161 (0.232)	0.0838 (0.144)	0.00207 (0.0101)	0.122 (0.188)	0.13 (0.196)	0.217 (0.297)	0.00207 (0.0101)
del 1q42 12	9 (6%)	141	0.0401 (0.0799)	0.519 (0.59)	0.833 (0.864)	0.291 (0.376)	0.559 (0.622)	0.196 (0.274)	0.125 (0.191)	0.127 (0.192)	0.499 (0.573)	0.0084 (0.0253)
del 9q33 3	60 (40%)	90	0.00028 (0.00244)	0.39 (0.468)	0.128 (0.192)	0.0562 (0.104)	0.116 (0.184)	0.0151 (0.038)	0.578 (0.639)	0.055 (0.103)	0.165 (0.237)	0.187 (0.263)
del 18p11 32	118 (79%)	32	0.698 (0.751)	0.131 (0.196)	0.712 (0.763)	0.959 (0.965)	0.0486 (0.0935)	0.248 (0.329)	0.119 (0.184)	0.0189 (0.0463)	0.278 (0.364)	0.145 (0.214)
del 18q22 2	125 (83%)	25	0.059 (0.106)	0.143 (0.212)	0.72 (0.767)	0.953 (0.961)	0.109 (0.174)	0.135 (0.201)	0.0924 (0.154)	0.0412 (0.0814)	0.236 (0.317)	0.0257 (0.0575)
del 20p12 1	29 (19%)	121	0.336 (0.421)	0.337 (0.421)	0.414 (0.492)	0.453 (0.53)	0.311 (0.397)	0.0942 (0.155)	0.0261 (0.0582)	0.245 (0.327)	0.0624 (0.112)	0.0124 (0.0332)
amp 1q21 2	69 (46%)	81	0.0796 (0.139)	0.719 (0.767)	0.323 (0.409)	0.916 (0.932)	0.871 (0.899)	0.0008 (0.00508)	0.0806 (0.139)	0.934 (0.944)	0.676 (0.735)	0.0702 (0.124)
amp 4q12	20 (13%)	130	0.00778 (0.0242)	0.655 (0.716)	0.803 (0.84)	0.451 (0.529)	0.396 (0.471)	0.396 (0.471)	0.352 (0.435)	0.332 (0.418)	0.275 (0.362)	0.375 (0.456)
amp 12p13 33	145 (97%)	5	0.0524 (0.0985)	0.102 (0.167)	0.153 (0.223)	0.0378 (0.077)	0.0832 (0.143)	0.683 (0.736)	0.373 (0.455)	0.0844 (0.144)	0.0869 (0.147)	0.0637 (0.113)
amp 12p12 1	147 (98%)	3	0.0553 (0.103)	0.108 (0.173)	0.291 (0.376)	0.235 (0.317)	0.448 (0.527)	0.559 (0.622)	0.0592 (0.106)	0.338 (0.421)	0.328 (0.415)	0.0232 (0.0534)
del 2q37 3	15 (10%)	135	0.459 (0.534)	0.041 (0.0812)	0.416 (0.493)	0.253 (0.335)	0.0561 (0.104)	0.172 (0.246)	0.216 (0.296)	0.118 (0.184)	0.107 (0.173)	0.119 (0.184)
del 5p14 3	103 (69%)	47	0.264 (0.348)	0.317 (0.403)	0.0208 (0.0495)	0.704 (0.755)	0.182 (0.259)	0.297 (0.381)	0.646 (0.708)	0.151 (0.222)	0.197 (0.274)	0.179 (0.256)
del 9p23	66 (44%)	84	0.0372 (0.0764)	0.916 (0.932)	0.522 (0.591)	0.343 (0.426)	0.913 (0.932)	0.525 (0.591)	0.523 (0.591)	0.911 (0.932)	0.932 (0.944)	0.838 (0.867)
del 16q23 1	66 (44%)	84	0.00134 (0.0075)	0.235 (0.317)	0.683 (0.736)	0.382 (0.464)	0.36 (0.441)	0.393 (0.471)	0.117 (0.184)	0.208 (0.286)	0.572 (0.634)	0.223 (0.304)
amp 12q15	100 (67%)	50	0.526 (0.591)	0.928 (0.942)	0.39 (0.468)	1 (1.00)	0.816 (0.85)	0.732 (0.775)	0.296 (0.381)	0.514 (0.586)	0.52 (0.591)	0.227 (0.308)
del 5p15 2	101 (67%)	49	0.187 (0.263)	0.487 (0.562)	0.118 (0.184)	0.486 (0.562)	0.212 (0.291)	0.457 (0.533)	0.546 (0.612)	0.243 (0.325)	0.283 (0.368)	0.357 (0.44)
del 9p24 3	70 (47%)	80	0.089 (0.149)	0.896 (0.921)	0.667 (0.727)	0.425 (0.502)	1 (1.00)	0.804 (0.84)	0.338 (0.421)	0.678 (0.735)	1 (1.00)	0.794 (0.833)

'amp_1q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-04 (Fisher's exact test), Q value = 0.0051

Table S1. Gene #1: 'amp_1q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
AMP PEAK 1(1Q21.2) MUTATED	12	19	3	16	3	13	3
AMP PEAK 1(1Q21.2) WILD-TYPE	31	8	9	8	5	10	10

Figure S1. Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_2p24.1' versus 'CN_CNMF'

P value = 0.0034 (Fisher's exact test), Q value = 0.014

Table S2. Gene #2: 'amp_2p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
AMP PEAK 2(2P24.1) MUTATED	12	17	33
AMP PEAK 2(2P24.1) WILD-TYPE	36	27	25

Figure S2. Get High-res Image Gene #2: 'amp_2p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2p24.1' versus 'METHLYATION_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.0044

Table S3. Gene #2: 'amp_2p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	49	45
AMP PEAK 2(2P24.1) MUTATED	14	20	28
AMP PEAK 2(2P24.1) WILD-TYPE	42	29	17

Figure S3. Get High-res Image Gene #2: 'amp_2p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_2p24.1' versus 'MRNASEQ_CNMF'

P value = 0.0205 (Fisher's exact test), Q value = 0.049

Table S4. Gene #2: 'amp_2p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
AMP PEAK 2(2P24.1) MUTATED	23	15	24
AMP PEAK 2(2P24.1) WILD-TYPE	47	25	16

Figure S4. Get High-res Image Gene #2: 'amp_2p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_2p24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0441 (Fisher's exact test), Q value = 0.086

Table S5. Gene #2: 'amp_2p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
AMP PEAK 2(2P24.1) MUTATED	10	13	6	14	2	9	8
AMP PEAK 2(2P24.1) WILD-TYPE	33	14	6	10	6	14	5

Figure S5. Get High-res Image Gene #2: 'amp_2p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_2p24.1' versus 'MIRSEQ_CNMF'

P value = 0.0289 (Fisher's exact test), Q value = 0.063

Table S6. Gene #2: 'amp_2p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	57	41
AMP PEAK 2(2P24.1) MUTATED	15	24	23
AMP PEAK 2(2P24.1) WILD-TYPE	37	33	18

Figure S6. Get High-res Image Gene #2: 'amp_2p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_2p24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0388 (Fisher's exact test), Q value = 0.078

Table S7. Gene #2: 'amp_2p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
AMP PEAK 2(2P24.1) MUTATED	23	15	24
AMP PEAK 2(2P24.1) WILD-TYPE	47	23	18

Figure S7. Get High-res Image Gene #2: 'amp_2p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_2p24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0436 (Fisher's exact test), Q value = 0.085

Table S8. Gene #2: 'amp_2p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
AMP PEAK 2(2P24.1) MUTATED	22	15	25
AMP PEAK 2(2P24.1) WILD-TYPE	47	21	20

Figure S8. Get High-res Image Gene #2: 'amp_2p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_2p24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0323 (Fisher's exact test), Q value = 0.068

Table S9. Gene #2: 'amp_2p24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
AMP PEAK 2(2P24.1) MUTATED	9	14	15	24
AMP PEAK 2(2P24.1) WILD-TYPE	28	19	23	18

Figure S9. Get High-res Image Gene #2: 'amp_2p24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q27.3' versus 'RPPA_CNMF'

P value = 0.00255 (Fisher's exact test), Q value = 0.012

Table S10. Gene #3: 'amp_3q27.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
AMP PEAK 3(3Q27.3) MUTATED	6	1	5	18	7
AMP PEAK 3(3Q27.3) WILD-TYPE	39	7	5	19	11

Figure S10. Get High-res Image Gene #3: 'amp_3q27.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_3q27.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00119 (Fisher's exact test), Q value = 0.0069

Table S11. Gene #3: 'amp_3q27.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
AMP PEAK 3(3Q27.3) MUTATED	7	11	19
AMP PEAK 3(3Q27.3) WILD-TYPE	44	14	23

Figure S11. Get High-res Image Gene #3: 'amp_3q27.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_3q27.3' versus 'MRNASEQ_CNMF'

P value = 0.00243 (Fisher's exact test), Q value = 0.011

Table S12. Gene #3: 'amp_3q27.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
AMP PEAK 3(3Q27.3) MUTATED	13	18	18
AMP PEAK 3(3Q27.3) WILD-TYPE	57	22	22

Figure S12. Get High-res Image Gene #3: 'amp_3q27.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3q27.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00784 (Fisher's exact test), Q value = 0.024

Table S13. Gene #3: 'amp_3q27.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
AMP PEAK 3(3Q27.3) MUTATED	5	8	6	9	4	10	7
AMP PEAK 3(3Q27.3) WILD-TYPE	38	19	6	15	4	13	6

Figure S13. Get High-res Image Gene #3: 'amp_3q27.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3q27.3' versus 'MIRSEQ_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.0052

Table S14. Gene #3: 'amp_3q27.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	57	41
AMP PEAK 3(3Q27.3) MUTATED	7	24	18
AMP PEAK 3(3Q27.3) WILD-TYPE	45	33	23

Figure S14. Get High-res Image Gene #3: 'amp_3q27.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_3q27.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00261 (Fisher's exact test), Q value = 0.012

Table S15. Gene #3: 'amp_3q27.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
AMP PEAK 3(3Q27.3) MUTATED	13	18	18
AMP PEAK 3(3Q27.3) WILD-TYPE	57	20	24

Figure S15. Get High-res Image Gene #3: 'amp_3q27.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3q27.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.005

Table S16. Gene #3: 'amp_3q27.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
AMP PEAK 3(3Q27.3) MUTATED	12	17	20
AMP PEAK 3(3Q27.3) WILD-TYPE	57	19	25

Figure S16. Get High-res Image Gene #3: 'amp_3q27.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_3q27.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00389 (Fisher's exact test), Q value = 0.015

Table S17. Gene #3: 'amp_3q27.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
AMP PEAK 3(3Q27.3) MUTATED	5	8	17	19
AMP PEAK 3(3Q27.3) WILD-TYPE	32	25	21	23

Figure S17. Get High-res Image Gene #3: 'amp_3q27.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q12' versus 'CN_CNMF'

P value = 0.00778 (Fisher's exact test), Q value = 0.024

Table S18. Gene #4: 'amp_4q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
AMP PEAK 4(4Q12) MUTATED	3	12	5
AMP PEAK 4(4Q12) WILD-TYPE	45	32	53

Figure S18. Get High-res Image Gene #4: 'amp_4q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p22.1' versus 'MRNASEQ_CNMF'

P value = 0.0283 (Fisher's exact test), Q value = 0.062

Table S19. Gene #5: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
AMP PEAK 5(7P22.1) MUTATED	62	36	28
AMP PEAK 5(7P22.1) WILD-TYPE	8	4	12

Figure S19. Get High-res Image Gene #5: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p22.1' versus 'MIRSEQ_CNMF'

P value = 0.00775 (Fisher's exact test), Q value = 0.024

Table S20. Gene #5: 'amp_7p22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	57	41
AMP PEAK 5(7P22.1) MUTATED	46	52	28
AMP PEAK 5(7P22.1) WILD-TYPE	6	5	13

Figure S20. Get High-res Image Gene #5: 'amp_7p22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7p22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0114 (Fisher's exact test), Q value = 0.032

Table S21. Gene #5: 'amp_7p22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
AMP PEAK 5(7P22.1) MUTATED	62	35	29
AMP PEAK 5(7P22.1) WILD-TYPE	8	3	13

Figure S21. Get High-res Image Gene #5: 'amp_7p22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7p22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.052

Table S22. Gene #5: 'amp_7p22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
AMP PEAK 5(7P22.1) MUTATED	61	33	32
AMP PEAK 5(7P22.1) WILD-TYPE	8	3	13

Figure S22. Get High-res Image Gene #5: 'amp_7p22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7p22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.021 (Fisher's exact test), Q value = 0.05

Table S23. Gene #5: 'amp_7p22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
AMP PEAK 5(7P22.1) MUTATED	34	28	35	29
AMP PEAK 5(7P22.1) WILD-TYPE	3	5	3	13

Figure S23. Get High-res Image Gene #5: 'amp_7p22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q11.22' versus 'CN_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0041

Table S24. Gene #6: 'amp_7q11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
AMP PEAK 6(7Q11.22) MUTATED	35	43	42
AMP PEAK 6(7Q11.22) WILD-TYPE	13	1	16

Figure S24. Get High-res Image Gene #6: 'amp_7q11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q11.22' versus 'METHLYATION_CNMF'

P value = 0.0383 (Fisher's exact test), Q value = 0.077

Table S25. Gene #6: 'amp_7q11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	49	45
AMP PEAK 6(7Q11.22) MUTATED	48	42	30
AMP PEAK 6(7Q11.22) WILD-TYPE	8	7	15

Figure S25. Get High-res Image Gene #6: 'amp_7q11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q11.22' versus 'RPPA_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.033

Table S26. Gene #6: 'amp_7q11.22' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
AMP PEAK 6(7Q11.22) MUTATED	39	8	7	22	16
AMP PEAK 6(7Q11.22) WILD-TYPE	6	0	3	15	2

Figure S26. Get High-res Image Gene #6: 'amp_7q11.22' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_7q11.22' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.0012

Table S27. Gene #6: 'amp_7q11.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
AMP PEAK 6(7Q11.22) MUTATED	63	35	22
AMP PEAK 6(7Q11.22) WILD-TYPE	7	5	18

Figure S27. Get High-res Image Gene #6: 'amp_7q11.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7q11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00233 (Fisher's exact test), Q value = 0.011

Table S28. Gene #6: 'amp_7q11.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
AMP PEAK 6(7Q11.22) MUTATED	39	24	8	14	7	21	7
AMP PEAK 6(7Q11.22) WILD-TYPE	4	3	4	10	1	2	6

Figure S28. Get High-res Image Gene #6: 'amp_7q11.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q11.22' versus 'MIRSEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0014

Table S29. Gene #6: 'amp_7q11.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	57	41
AMP PEAK 6(7Q11.22) MUTATED	46	51	23
AMP PEAK 6(7Q11.22) WILD-TYPE	6	6	18

Figure S29. Get High-res Image Gene #6: 'amp_7q11.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7q11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.0018

Table S30. Gene #6: 'amp_7q11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
AMP PEAK 6(7Q11.22) MUTATED	63	33	24
AMP PEAK 6(7Q11.22) WILD-TYPE	7	5	18

Figure S30. Get High-res Image Gene #6: 'amp_7q11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q11.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0014

Table S31. Gene #6: 'amp_7q11.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
AMP PEAK 6(7Q11.22) MUTATED	62	32	26
AMP PEAK 6(7Q11.22) WILD-TYPE	7	4	19

Figure S31. Get High-res Image Gene #6: 'amp_7q11.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7q11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00081 (Fisher's exact test), Q value = 0.0051

Table S32. Gene #6: 'amp_7q11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
AMP PEAK 6(7Q11.22) MUTATED	33	30	33	24
AMP PEAK 6(7Q11.22) WILD-TYPE	4	3	5	18

Figure S32. Get High-res Image Gene #6: 'amp_7q11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q11.23' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0013

Table S33. Gene #7: 'amp_8q11.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
AMP PEAK 7(8Q11.23) MUTATED	35	44	43
AMP PEAK 7(8Q11.23) WILD-TYPE	13	0	15

Figure S33. Get High-res Image Gene #7: 'amp_8q11.23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q11.23' versus 'METHLYATION_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.029

Table S34. Gene #7: 'amp_8q11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	49	45
AMP PEAK 7(8Q11.23) MUTATED	52	38	32
AMP PEAK 7(8Q11.23) WILD-TYPE	4	11	13

Figure S34. Get High-res Image Gene #7: 'amp_8q11.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q11.23' versus 'RPPA_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0041

Table S35. Gene #7: 'amp_8q11.23' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
AMP PEAK 7(8Q11.23) MUTATED	44	6	6	25	14
AMP PEAK 7(8Q11.23) WILD-TYPE	1	2	4	12	4

Figure S35. Get High-res Image Gene #7: 'amp_8q11.23' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_8q11.23' versus 'RPPA_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.0014

Table S36. Gene #7: 'amp_8q11.23' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
AMP PEAK 7(8Q11.23) MUTATED	49	15	31
AMP PEAK 7(8Q11.23) WILD-TYPE	2	10	11

Figure S36. Get High-res Image Gene #7: 'amp_8q11.23' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_8q11.23' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00039

Table S37. Gene #7: 'amp_8q11.23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
AMP PEAK 7(8Q11.23) MUTATED	67	31	24
AMP PEAK 7(8Q11.23) WILD-TYPE	3	9	16

Figure S37. Get High-res Image Gene #7: 'amp_8q11.23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8q11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00034

Table S38. Gene #7: 'amp_8q11.23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
AMP PEAK 7(8Q11.23) MUTATED	40	27	8	18	6	19	4
AMP PEAK 7(8Q11.23) WILD-TYPE	3	0	4	6	2	4	9

Figure S38. Get High-res Image Gene #7: 'amp_8q11.23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q11.23' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00091

Table S39. Gene #7: 'amp_8q11.23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	57	41
AMP PEAK 7(8Q11.23) MUTATED	49	49	24
AMP PEAK 7(8Q11.23) WILD-TYPE	3	8	17

Figure S39. Get High-res Image Gene #7: 'amp_8q11.23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q11.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00039

Table S40. Gene #7: 'amp_8q11.23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
AMP PEAK 7(8Q11.23) MUTATED	67	30	25
AMP PEAK 7(8Q11.23) WILD-TYPE	3	8	17

Figure S40. Get High-res Image Gene #7: 'amp_8q11.23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q11.23' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00039

Table S41. Gene #7: 'amp_8q11.23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
AMP PEAK 7(8Q11.23) MUTATED	66	28	28
AMP PEAK 7(8Q11.23) WILD-TYPE	3	8	17

Figure S41. Get High-res Image Gene #7: 'amp_8q11.23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8q11.23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00039

Table S42. Gene #7: 'amp_8q11.23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
AMP PEAK 7(8Q11.23) MUTATED	34	33	30	25
AMP PEAK 7(8Q11.23) WILD-TYPE	3	0	8	17

Figure S42. Get High-res Image Gene #7: 'amp_8q11.23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q23.3' versus 'METHLYATION_CNMF'

P value = 0.00365 (Fisher's exact test), Q value = 0.015

Table S43. Gene #8: 'amp_8q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	49	45
AMP PEAK 8(8Q23.3) MUTATED	48	35	25
AMP PEAK 8(8Q23.3) WILD-TYPE	8	14	20

Figure S43. Get High-res Image Gene #8: 'amp_8q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q23.3' versus 'RPPA_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.056

Table S44. Gene #8: 'amp_8q23.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
AMP PEAK 8(8Q23.3) MUTATED	38	7	6	20	12
AMP PEAK 8(8Q23.3) WILD-TYPE	7	1	4	17	6

Figure S44. Get High-res Image Gene #8: 'amp_8q23.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_8q23.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.031

Table S45. Gene #8: 'amp_8q23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
AMP PEAK 8(8Q23.3) MUTATED	43	14	26
AMP PEAK 8(8Q23.3) WILD-TYPE	8	11	16

Figure S45. Get High-res Image Gene #8: 'amp_8q23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_8q23.3' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0026

Table S46. Gene #8: 'amp_8q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
AMP PEAK 8(8Q23.3) MUTATED	60	28	20
AMP PEAK 8(8Q23.3) WILD-TYPE	10	12	20

Figure S46. Get High-res Image Gene #8: 'amp_8q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00076 (Fisher's exact test), Q value = 0.005

Table S47. Gene #8: 'amp_8q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
AMP PEAK 8(8Q23.3) MUTATED	38	22	9	15	5	16	3
AMP PEAK 8(8Q23.3) WILD-TYPE	5	5	3	9	3	7	10

Figure S47. Get High-res Image Gene #8: 'amp_8q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q23.3' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00078

Table S48. Gene #8: 'amp_8q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	57	41
AMP PEAK 8(8Q23.3) MUTATED	47	41	20
AMP PEAK 8(8Q23.3) WILD-TYPE	5	16	21

Figure S48. Get High-res Image Gene #8: 'amp_8q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.0012

Table S49. Gene #8: 'amp_8q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
AMP PEAK 8(8Q23.3) MUTATED	60	28	20
AMP PEAK 8(8Q23.3) WILD-TYPE	10	10	22

Figure S49. Get High-res Image Gene #8: 'amp_8q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.0041

Table S50. Gene #8: 'amp_8q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
AMP PEAK 8(8Q23.3) MUTATED	60	23	25
AMP PEAK 8(8Q23.3) WILD-TYPE	9	13	20

Figure S50. Get High-res Image Gene #8: 'amp_8q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00164 (Fisher's exact test), Q value = 0.0084

Table S51. Gene #8: 'amp_8q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
AMP PEAK 8(8Q23.3) MUTATED	33	27	26	22
AMP PEAK 8(8Q23.3) WILD-TYPE	4	6	12	20

Figure S51. Get High-res Image Gene #8: 'amp_8q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p13.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.0378 (Fisher's exact test), Q value = 0.077

Table S52. Gene #9: 'amp_12p13.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
AMP PEAK 9(12P13.33) MUTATED	46	25	42
AMP PEAK 9(12P13.33) WILD-TYPE	5	0	0

Figure S52. Get High-res Image Gene #9: 'amp_12p13.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0232 (Fisher's exact test), Q value = 0.053

Table S53. Gene #10: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
AMP PEAK 10(12P12.1) MUTATED	34	33	38	42
AMP PEAK 10(12P12.1) WILD-TYPE	3	0	0	0

Figure S53. Get High-res Image Gene #10: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p11.21' versus 'METHLYATION_CNMF'

P value = 0.0381 (Fisher's exact test), Q value = 0.077

Table S54. Gene #11: 'amp_12p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	49	45
AMP PEAK 11(12P11.21) MUTATED	51	49	44
AMP PEAK 11(12P11.21) WILD-TYPE	5	0	1

Figure S54. Get High-res Image Gene #11: 'amp_12p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12p11.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.0352 (Fisher's exact test), Q value = 0.073

Table S55. Gene #11: 'amp_12p11.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
AMP PEAK 11(12P11.21) MUTATED	46	25	42
AMP PEAK 11(12P11.21) WILD-TYPE	5	0	0

Figure S55. Get High-res Image Gene #11: 'amp_12p11.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_12p11.21' versus 'MRNASEQ_CNMF'

P value = 0.0365 (Fisher's exact test), Q value = 0.075

Table S56. Gene #11: 'amp_12p11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
AMP PEAK 11(12P11.21) MUTATED	64	40	40
AMP PEAK 11(12P11.21) WILD-TYPE	6	0	0

Figure S56. Get High-res Image Gene #11: 'amp_12p11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0377 (Fisher's exact test), Q value = 0.077

Table S57. Gene #11: 'amp_12p11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
AMP PEAK 11(12P11.21) MUTATED	64	38	42
AMP PEAK 11(12P11.21) WILD-TYPE	6	0	0

Figure S57. Get High-res Image Gene #11: 'amp_12p11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_12p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0392 (Fisher's exact test), Q value = 0.078

Table S58. Gene #11: 'amp_12p11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
AMP PEAK 11(12P11.21) MUTATED	63	36	45
AMP PEAK 11(12P11.21) WILD-TYPE	6	0	0

Figure S58. Get High-res Image Gene #11: 'amp_12p11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_12p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0243 (Fisher's exact test), Q value = 0.055

Table S59. Gene #11: 'amp_12p11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
AMP PEAK 11(12P11.21) MUTATED	33	31	38	42
AMP PEAK 11(12P11.21) WILD-TYPE	4	2	0	0

Figure S59. Get High-res Image Gene #11: 'amp_12p11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_16q21' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0016

Table S60. Gene #13: 'amp_16q21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
AMP PEAK 13(16Q21) MUTATED	2	2	17
AMP PEAK 13(16Q21) WILD-TYPE	46	42	41

Figure S60. Get High-res Image Gene #13: 'amp_16q21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_16q21' versus 'RPPA_CNMF'

P value = 0.00306 (Fisher's exact test), Q value = 0.013

Table S61. Gene #13: 'amp_16q21' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
AMP PEAK 13(16Q21) MUTATED	1	0	2	11	2
AMP PEAK 13(16Q21) WILD-TYPE	44	8	8	26	16

Figure S61. Get High-res Image Gene #13: 'amp_16q21' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_16q21' versus 'RPPA_CHIERARCHICAL'

P value = 0.00141 (Fisher's exact test), Q value = 0.0076

Table S62. Gene #13: 'amp_16q21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
AMP PEAK 13(16Q21) MUTATED	1	7	8
AMP PEAK 13(16Q21) WILD-TYPE	50	18	34

Figure S62. Get High-res Image Gene #13: 'amp_16q21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_16q21' versus 'MRNASEQ_CNMF'

P value = 0.00295 (Fisher's exact test), Q value = 0.013

Table S63. Gene #13: 'amp_16q21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
AMP PEAK 13(16Q21) MUTATED	4	5	12
AMP PEAK 13(16Q21) WILD-TYPE	66	35	28

Figure S63. Get High-res Image Gene #13: 'amp_16q21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_16q21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00758 (Fisher's exact test), Q value = 0.024

Table S64. Gene #13: 'amp_16q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
AMP PEAK 13(16Q21) MUTATED	1	3	3	8	0	3	3
AMP PEAK 13(16Q21) WILD-TYPE	42	24	9	16	8	20	10

Figure S64. Get High-res Image Gene #13: 'amp_16q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_16q21' versus 'MIRSEQ_CNMF'

P value = 0.00116 (Fisher's exact test), Q value = 0.0068

Table S65. Gene #13: 'amp_16q21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	57	41
AMP PEAK 13(16Q21) MUTATED	1	9	11
AMP PEAK 13(16Q21) WILD-TYPE	51	48	30

Figure S65. Get High-res Image Gene #13: 'amp_16q21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_16q21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0083 (Fisher's exact test), Q value = 0.025

Table S66. Gene #13: 'amp_16q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
AMP PEAK 13(16Q21) MUTATED	4	6	11
AMP PEAK 13(16Q21) WILD-TYPE	66	32	31

Figure S66. Get High-res Image Gene #13: 'amp_16q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_16q21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0025 (Fisher's exact test), Q value = 0.012

Table S67. Gene #13: 'amp_16q21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
AMP PEAK 13(16Q21) MUTATED	4	4	13
AMP PEAK 13(16Q21) WILD-TYPE	65	32	32

Figure S67. Get High-res Image Gene #13: 'amp_16q21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_16q21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00884 (Fisher's exact test), Q value = 0.026

Table S68. Gene #13: 'amp_16q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
AMP PEAK 13(16Q21) MUTATED	1	3	5	12
AMP PEAK 13(16Q21) WILD-TYPE	36	30	33	30

Figure S68. Get High-res Image Gene #13: 'amp_16q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q11.21' versus 'CN_CNMF'

P value = 0.00497 (Fisher's exact test), Q value = 0.018

Table S69. Gene #14: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
AMP PEAK 14(20Q11.21) MUTATED	11	11	29
AMP PEAK 14(20Q11.21) WILD-TYPE	37	33	29

Figure S69. Get High-res Image Gene #14: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q11.21' versus 'METHLYATION_CNMF'

P value = 0.00288 (Fisher's exact test), Q value = 0.013

Table S70. Gene #14: 'amp_20q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	49	45
AMP PEAK 14(20Q11.21) MUTATED	10	19	22
AMP PEAK 14(20Q11.21) WILD-TYPE	46	30	23

Figure S70. Get High-res Image Gene #14: 'amp_20q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'RPPA_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.047

Table S71. Gene #14: 'amp_20q11.21' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
AMP PEAK 14(20Q11.21) MUTATED	10	1	6	15	10
AMP PEAK 14(20Q11.21) WILD-TYPE	35	7	4	22	8

Figure S71. Get High-res Image Gene #14: 'amp_20q11.21' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_20q11.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.0145 (Fisher's exact test), Q value = 0.037

Table S72. Gene #14: 'amp_20q11.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
AMP PEAK 14(20Q11.21) MUTATED	11	13	18
AMP PEAK 14(20Q11.21) WILD-TYPE	40	12	24

Figure S72. Get High-res Image Gene #14: 'amp_20q11.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNASEQ_CNMF'

P value = 0.00288 (Fisher's exact test), Q value = 0.013

Table S73. Gene #14: 'amp_20q11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
AMP PEAK 14(20Q11.21) MUTATED	16	13	22
AMP PEAK 14(20Q11.21) WILD-TYPE	54	27	18

Figure S73. Get High-res Image Gene #14: 'amp_20q11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.034 (Fisher's exact test), Q value = 0.071

Table S74. Gene #14: 'amp_20q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
AMP PEAK 14(20Q11.21) MUTATED	11	5	3	14	2	9	7
AMP PEAK 14(20Q11.21) WILD-TYPE	32	22	9	10	6	14	6

Figure S74. Get High-res Image Gene #14: 'amp_20q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.042

Table S75. Gene #14: 'amp_20q11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	57	41
AMP PEAK 14(20Q11.21) MUTATED	12	18	21
AMP PEAK 14(20Q11.21) WILD-TYPE	40	39	20

Figure S75. Get High-res Image Gene #14: 'amp_20q11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_20q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00696 (Fisher's exact test), Q value = 0.023

Table S76. Gene #14: 'amp_20q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
AMP PEAK 14(20Q11.21) MUTATED	16	13	22
AMP PEAK 14(20Q11.21) WILD-TYPE	54	25	20

Figure S76. Get High-res Image Gene #14: 'amp_20q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00969 (Fisher's exact test), Q value = 0.028

Table S77. Gene #14: 'amp_20q11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
AMP PEAK 14(20Q11.21) MUTATED	16	12	23
AMP PEAK 14(20Q11.21) WILD-TYPE	53	24	22

Figure S77. Get High-res Image Gene #14: 'amp_20q11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00799 (Fisher's exact test), Q value = 0.025

Table S78. Gene #14: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
AMP PEAK 14(20Q11.21) MUTATED	6	10	13	22
AMP PEAK 14(20Q11.21) WILD-TYPE	31	23	25	20

Figure S78. Get High-res Image Gene #14: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_22q11.21' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 7e-04

Table S79. Gene #15: 'amp_22q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
AMP PEAK 15(22Q11.21) MUTATED	13	30	14
AMP PEAK 15(22Q11.21) WILD-TYPE	35	14	44

Figure S79. Get High-res Image Gene #15: 'amp_22q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_22q11.21' versus 'METHLYATION_CNMF'

P value = 0.00665 (Fisher's exact test), Q value = 0.022

Table S80. Gene #15: 'amp_22q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	49	45
AMP PEAK 15(22Q11.21) MUTATED	30	12	15
AMP PEAK 15(22Q11.21) WILD-TYPE	26	37	30

Figure S80. Get High-res Image Gene #15: 'amp_22q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_22q11.21' versus 'RPPA_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.032

Table S81. Gene #15: 'amp_22q11.21' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
AMP PEAK 15(22Q11.21) MUTATED	24	2	4	8	3
AMP PEAK 15(22Q11.21) WILD-TYPE	21	6	6	29	15

Figure S81. Get High-res Image Gene #15: 'amp_22q11.21' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_22q11.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.00528 (Fisher's exact test), Q value = 0.018

Table S82. Gene #15: 'amp_22q11.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
AMP PEAK 15(22Q11.21) MUTATED	26	5	10
AMP PEAK 15(22Q11.21) WILD-TYPE	25	20	32

Figure S82. Get High-res Image Gene #15: 'amp_22q11.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_22q11.21' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0016

Table S83. Gene #15: 'amp_22q11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
AMP PEAK 15(22Q11.21) MUTATED	39	10	8
AMP PEAK 15(22Q11.21) WILD-TYPE	31	30	32

Figure S83. Get High-res Image Gene #15: 'amp_22q11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_22q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00034

Table S84. Gene #15: 'amp_22q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
AMP PEAK 15(22Q11.21) MUTATED	16	23	4	5	1	5	3
AMP PEAK 15(22Q11.21) WILD-TYPE	27	4	8	19	7	18	10

Figure S84. Get High-res Image Gene #15: 'amp_22q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_22q11.21' versus 'MIRSEQ_CNMF'

P value = 0.0132 (Fisher's exact test), Q value = 0.035

Table S85. Gene #15: 'amp_22q11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	57	41
AMP PEAK 15(22Q11.21) MUTATED	24	25	8
AMP PEAK 15(22Q11.21) WILD-TYPE	28	32	33

Figure S85. Get High-res Image Gene #15: 'amp_22q11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_22q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.0015

Table S86. Gene #15: 'amp_22q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
AMP PEAK 15(22Q11.21) MUTATED	39	9	9
AMP PEAK 15(22Q11.21) WILD-TYPE	31	29	33

Figure S86. Get High-res Image Gene #15: 'amp_22q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_22q11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0024

Table S87. Gene #15: 'amp_22q11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
AMP PEAK 15(22Q11.21) MUTATED	38	10	9
AMP PEAK 15(22Q11.21) WILD-TYPE	31	26	36

Figure S87. Get High-res Image Gene #15: 'amp_22q11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_22q11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00039

Table S88. Gene #15: 'amp_22q11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
AMP PEAK 15(22Q11.21) MUTATED	15	24	10	8
AMP PEAK 15(22Q11.21) WILD-TYPE	22	9	28	34

Figure S88. Get High-res Image Gene #15: 'amp_22q11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.31' versus 'MRNASEQ_CNMF'

P value = 0.00232 (Fisher's exact test), Q value = 0.011

Table S89. Gene #16: 'del_1p36.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
DEL PEAK 1(1P36.31) MUTATED	15	3	16
DEL PEAK 1(1P36.31) WILD-TYPE	55	37	24

Figure S89. Get High-res Image Gene #16: 'del_1p36.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.31' versus 'MIRSEQ_CNMF'

P value = 0.00441 (Fisher's exact test), Q value = 0.017

Table S90. Gene #16: 'del_1p36.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	57	41
DEL PEAK 1(1P36.31) MUTATED	12	6	16
DEL PEAK 1(1P36.31) WILD-TYPE	40	51	25

Figure S90. Get High-res Image Gene #16: 'del_1p36.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p36.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00462 (Fisher's exact test), Q value = 0.017

Table S91. Gene #16: 'del_1p36.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 1(1P36.31) MUTATED	15	3	16
DEL PEAK 1(1P36.31) WILD-TYPE	55	35	26

Figure S91. Get High-res Image Gene #16: 'del_1p36.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0017 (Fisher's exact test), Q value = 0.0085

Table S92. Gene #16: 'del_1p36.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 1(1P36.31) MUTATED	15	2	17
DEL PEAK 1(1P36.31) WILD-TYPE	54	34	28

Figure S92. Get High-res Image Gene #16: 'del_1p36.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p36.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0139 (Fisher's exact test), Q value = 0.036

Table S93. Gene #16: 'del_1p36.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
DEL PEAK 1(1P36.31) MUTATED	8	7	3	16
DEL PEAK 1(1P36.31) WILD-TYPE	29	26	35	26

Figure S93. Get High-res Image Gene #16: 'del_1p36.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p31.1' versus 'CN_CNMF'

P value = 0.00702 (Fisher's exact test), Q value = 0.023

Table S94. Gene #17: 'del_1p31.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
DEL PEAK 2(1P31.1) MUTATED	5	15	7
DEL PEAK 2(1P31.1) WILD-TYPE	43	29	51

Figure S94. Get High-res Image Gene #17: 'del_1p31.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p31.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0493 (Fisher's exact test), Q value = 0.094

Table S95. Gene #17: 'del_1p31.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
DEL PEAK 2(1P31.1) MUTATED	13	5	3
DEL PEAK 2(1P31.1) WILD-TYPE	38	20	39

Figure S95. Get High-res Image Gene #17: 'del_1p31.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_1p31.1' versus 'MIRSEQ_CNMF'

P value = 0.00819 (Fisher's exact test), Q value = 0.025

Table S96. Gene #17: 'del_1p31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	57	41
DEL PEAK 2(1P31.1) MUTATED	15	4	8
DEL PEAK 2(1P31.1) WILD-TYPE	37	53	33

Figure S96. Get High-res Image Gene #17: 'del_1p31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1q42.12' versus 'CN_CNMF'

P value = 0.0401 (Fisher's exact test), Q value = 0.08

Table S97. Gene #18: 'del_1q42.12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
DEL PEAK 3(1Q42.12) MUTATED	0	5	4
DEL PEAK 3(1Q42.12) WILD-TYPE	48	39	54

Figure S97. Get High-res Image Gene #18: 'del_1q42.12' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q42.12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0084 (Fisher's exact test), Q value = 0.025

Table S98. Gene #18: 'del_1q42.12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
DEL PEAK 3(1Q42.12) MUTATED	0	6	2	1
DEL PEAK 3(1Q42.12) WILD-TYPE	37	27	36	41

Figure S98. Get High-res Image Gene #18: 'del_1q42.12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 0.041 (Fisher's exact test), Q value = 0.081

Table S99. Gene #19: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	49	45
DEL PEAK 4(2Q37.3) MUTATED	2	9	4
DEL PEAK 4(2Q37.3) WILD-TYPE	54	40	41

Figure S99. Get High-res Image Gene #19: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p26.2' versus 'METHLYATION_CNMF'

P value = 0.0209 (Fisher's exact test), Q value = 0.05

Table S100. Gene #20: 'del_3p26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	49	45
DEL PEAK 5(3P26.2) MUTATED	16	19	6
DEL PEAK 5(3P26.2) WILD-TYPE	40	30	39

Figure S100. Get High-res Image Gene #20: 'del_3p26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p26.2' versus 'MRNASEQ_CNMF'

P value = 0.00138 (Fisher's exact test), Q value = 0.0075

Table S101. Gene #20: 'del_3p26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
DEL PEAK 5(3P26.2) MUTATED	22	16	3
DEL PEAK 5(3P26.2) WILD-TYPE	48	24	37

Figure S101. Get High-res Image Gene #20: 'del_3p26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00396 (Fisher's exact test), Q value = 0.015

Table S102. Gene #20: 'del_3p26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 5(3P26.2) MUTATED	17	5	2	2	2	12	1
DEL PEAK 5(3P26.2) WILD-TYPE	26	22	10	22	6	11	12

Figure S102. Get High-res Image Gene #20: 'del_3p26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_CNMF'

P value = 0.00661 (Fisher's exact test), Q value = 0.022

Table S103. Gene #20: 'del_3p26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	57	41
DEL PEAK 5(3P26.2) MUTATED	16	21	4
DEL PEAK 5(3P26.2) WILD-TYPE	36	36	37

Figure S103. Get High-res Image Gene #20: 'del_3p26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00364 (Fisher's exact test), Q value = 0.015

Table S104. Gene #20: 'del_3p26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 5(3P26.2) MUTATED	22	15	4
DEL PEAK 5(3P26.2) WILD-TYPE	48	23	38

Figure S104. Get High-res Image Gene #20: 'del_3p26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00166 (Fisher's exact test), Q value = 0.0084

Table S105. Gene #20: 'del_3p26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 5(3P26.2) MUTATED	22	15	4
DEL PEAK 5(3P26.2) WILD-TYPE	47	21	41

Figure S105. Get High-res Image Gene #20: 'del_3p26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.0042

Table S106. Gene #20: 'del_3p26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
DEL PEAK 5(3P26.2) MUTATED	15	7	16	3
DEL PEAK 5(3P26.2) WILD-TYPE	22	26	22	39

Figure S106. Get High-res Image Gene #20: 'del_3p26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.2' versus 'CN_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.048

Table S107. Gene #21: 'del_4q22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
DEL PEAK 6(4Q22.2) MUTATED	29	38	43
DEL PEAK 6(4Q22.2) WILD-TYPE	19	6	15

Figure S107. Get High-res Image Gene #21: 'del_4q22.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q22.2' versus 'METHLYATION_CNMF'

P value = 0.0326 (Fisher's exact test), Q value = 0.068

Table S108. Gene #21: 'del_4q22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	49	45
DEL PEAK 6(4Q22.2) MUTATED	40	42	28
DEL PEAK 6(4Q22.2) WILD-TYPE	16	7	17

Figure S108. Get High-res Image Gene #21: 'del_4q22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q22.2' versus 'MRNASEQ_CNMF'

P value = 0.00907 (Fisher's exact test), Q value = 0.027

Table S109. Gene #21: 'del_4q22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
DEL PEAK 6(4Q22.2) MUTATED	52	35	23
DEL PEAK 6(4Q22.2) WILD-TYPE	18	5	17

Figure S109. Get High-res Image Gene #21: 'del_4q22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0015 (Fisher's exact test), Q value = 0.0078

Table S110. Gene #21: 'del_4q22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 6(4Q22.2) MUTATED	27	25	10	14	7	21	6
DEL PEAK 6(4Q22.2) WILD-TYPE	16	2	2	10	1	2	7

Figure S110. Get High-res Image Gene #21: 'del_4q22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.2' versus 'MIRSEQ_CNMF'

P value = 0.00287 (Fisher's exact test), Q value = 0.013

Table S111. Gene #21: 'del_4q22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	57	41
DEL PEAK 6(4Q22.2) MUTATED	36	50	24
DEL PEAK 6(4Q22.2) WILD-TYPE	16	7	17

Figure S111. Get High-res Image Gene #21: 'del_4q22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00469 (Fisher's exact test), Q value = 0.017

Table S112. Gene #21: 'del_4q22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 6(4Q22.2) MUTATED	52	34	24
DEL PEAK 6(4Q22.2) WILD-TYPE	18	4	18

Figure S112. Get High-res Image Gene #21: 'del_4q22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0305 (Fisher's exact test), Q value = 0.065

Table S113. Gene #21: 'del_4q22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 6(4Q22.2) MUTATED	52	31	27
DEL PEAK 6(4Q22.2) WILD-TYPE	17	5	18

Figure S113. Get High-res Image Gene #21: 'del_4q22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00995 (Fisher's exact test), Q value = 0.029

Table S114. Gene #21: 'del_4q22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
DEL PEAK 6(4Q22.2) MUTATED	24	28	33	25
DEL PEAK 6(4Q22.2) WILD-TYPE	13	5	5	17

Figure S114. Get High-res Image Gene #21: 'del_4q22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5p14.3' versus 'RPPA_CNMF'

P value = 0.0208 (Fisher's exact test), Q value = 0.05

Table S115. Gene #23: 'del_5p14.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
DEL PEAK 8(5P14.3) MUTATED	30	7	4	28	7
DEL PEAK 8(5P14.3) WILD-TYPE	15	1	6	9	11

Figure S115. Get High-res Image Gene #23: 'del_5p14.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_5q12.1' versus 'RPPA_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.032

Table S116. Gene #24: 'del_5q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
DEL PEAK 9(5Q12.1) MUTATED	33	7	4	28	7
DEL PEAK 9(5Q12.1) WILD-TYPE	12	1	6	9	11

Figure S116. Get High-res Image Gene #24: 'del_5q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_5q12.1' versus 'MRNASEQ_CNMF'

P value = 0.032 (Fisher's exact test), Q value = 0.068

Table S117. Gene #24: 'del_5q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
DEL PEAK 9(5Q12.1) MUTATED	56	23	26
DEL PEAK 9(5Q12.1) WILD-TYPE	14	17	14

Figure S117. Get High-res Image Gene #24: 'del_5q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00755 (Fisher's exact test), Q value = 0.024

Table S118. Gene #24: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 9(5Q12.1) MUTATED	30	26	9	15	4	12	9
DEL PEAK 9(5Q12.1) WILD-TYPE	13	1	3	9	4	11	4

Figure S118. Get High-res Image Gene #24: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.023 (Fisher's exact test), Q value = 0.053

Table S119. Gene #24: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 9(5Q12.1) MUTATED	56	21	28
DEL PEAK 9(5Q12.1) WILD-TYPE	14	17	14

Figure S119. Get High-res Image Gene #24: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0289 (Fisher's exact test), Q value = 0.063

Table S120. Gene #24: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 9(5Q12.1) MUTATED	55	20	30
DEL PEAK 9(5Q12.1) WILD-TYPE	14	16	15

Figure S120. Get High-res Image Gene #24: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0126 (Fisher's exact test), Q value = 0.033

Table S121. Gene #24: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
DEL PEAK 9(5Q12.1) MUTATED	27	29	20	29
DEL PEAK 9(5Q12.1) WILD-TYPE	10	4	18	13

Figure S121. Get High-res Image Gene #24: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p22.3' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00091

Table S122. Gene #25: 'del_6p22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
DEL PEAK 10(6P22.3) MUTATED	2	3	19
DEL PEAK 10(6P22.3) WILD-TYPE	46	41	39

Figure S122. Get High-res Image Gene #25: 'del_6p22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p22.3' versus 'METHLYATION_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.039

Table S123. Gene #25: 'del_6p22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	49	45
DEL PEAK 10(6P22.3) MUTATED	3	11	10
DEL PEAK 10(6P22.3) WILD-TYPE	53	38	35

Figure S123. Get High-res Image Gene #25: 'del_6p22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p22.3' versus 'RPPA_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0019

Table S124. Gene #25: 'del_6p22.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
DEL PEAK 10(6P22.3) MUTATED	2	0	0	11	8
DEL PEAK 10(6P22.3) WILD-TYPE	43	8	10	26	10

Figure S124. Get High-res Image Gene #25: 'del_6p22.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_6p22.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0043

Table S125. Gene #25: 'del_6p22.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
DEL PEAK 10(6P22.3) MUTATED	2	6	13
DEL PEAK 10(6P22.3) WILD-TYPE	49	19	29

Figure S125. Get High-res Image Gene #25: 'del_6p22.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_6p22.3' versus 'MRNASEQ_CNMF'

P value = 0.00408 (Fisher's exact test), Q value = 0.016

Table S126. Gene #25: 'del_6p22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
DEL PEAK 10(6P22.3) MUTATED	4	10	10
DEL PEAK 10(6P22.3) WILD-TYPE	66	30	30

Figure S126. Get High-res Image Gene #25: 'del_6p22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6p22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0118 (Fisher's exact test), Q value = 0.032

Table S127. Gene #25: 'del_6p22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 10(6P22.3) MUTATED	2	2	3	4	1	7	5
DEL PEAK 10(6P22.3) WILD-TYPE	41	25	9	20	7	16	8

Figure S127. Get High-res Image Gene #25: 'del_6p22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6p22.3' versus 'MIRSEQ_CNMF'

P value = 0.00519 (Fisher's exact test), Q value = 0.018

Table S128. Gene #25: 'del_6p22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	57	41
DEL PEAK 10(6P22.3) MUTATED	2	12	10
DEL PEAK 10(6P22.3) WILD-TYPE	50	45	31

Figure S128. Get High-res Image Gene #25: 'del_6p22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6p22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00351 (Fisher's exact test), Q value = 0.014

Table S129. Gene #25: 'del_6p22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 10(6P22.3) MUTATED	4	9	11
DEL PEAK 10(6P22.3) WILD-TYPE	66	29	31

Figure S129. Get High-res Image Gene #25: 'del_6p22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6p22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00384 (Fisher's exact test), Q value = 0.015

Table S130. Gene #25: 'del_6p22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 10(6P22.3) MUTATED	4	10	10
DEL PEAK 10(6P22.3) WILD-TYPE	65	26	35

Figure S130. Get High-res Image Gene #25: 'del_6p22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00757 (Fisher's exact test), Q value = 0.024

Table S131. Gene #25: 'del_6p22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
DEL PEAK 10(6P22.3) MUTATED	1	3	10	10
DEL PEAK 10(6P22.3) WILD-TYPE	36	30	28	32

Figure S131. Get High-res Image Gene #25: 'del_6p22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

P value = 0.0328 (Fisher's exact test), Q value = 0.069

Table S132. Gene #26: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
DEL PEAK 11(6Q26) MUTATED	6	4	16
DEL PEAK 11(6Q26) WILD-TYPE	42	40	42

Figure S132. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.005

Table S133. Gene #26: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	49	45
DEL PEAK 11(6Q26) MUTATED	2	14	10
DEL PEAK 11(6Q26) WILD-TYPE	54	35	35

Figure S133. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q26' versus 'RPPA_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.054

Table S134. Gene #26: 'del_6q26' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
DEL PEAK 11(6Q26) MUTATED	4	0	2	10	7
DEL PEAK 11(6Q26) WILD-TYPE	41	8	8	27	11

Figure S134. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_6q26' versus 'RPPA_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.037

Table S135. Gene #26: 'del_6q26' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
DEL PEAK 11(6Q26) MUTATED	4	7	12
DEL PEAK 11(6Q26) WILD-TYPE	47	18	30

Figure S135. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 0.00612 (Fisher's exact test), Q value = 0.021

Table S136. Gene #26: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
DEL PEAK 11(6Q26) MUTATED	5	11	10
DEL PEAK 11(6Q26) WILD-TYPE	65	29	30

Figure S136. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00149 (Fisher's exact test), Q value = 0.0078

Table S137. Gene #26: 'del_6q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 11(6Q26) MUTATED	1	4	3	3	3	6	6
DEL PEAK 11(6Q26) WILD-TYPE	42	23	9	21	5	17	7

Figure S137. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 0.0139 (Fisher's exact test), Q value = 0.036

Table S138. Gene #26: 'del_6q26' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	57	41
DEL PEAK 11(6Q26) MUTATED	3	13	10
DEL PEAK 11(6Q26) WILD-TYPE	49	44	31

Figure S138. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00519 (Fisher's exact test), Q value = 0.018

Table S139. Gene #26: 'del_6q26' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 11(6Q26) MUTATED	5	11	10
DEL PEAK 11(6Q26) WILD-TYPE	65	27	32

Figure S139. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00502 (Fisher's exact test), Q value = 0.018

Table S140. Gene #26: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 11(6Q26) MUTATED	5	11	10
DEL PEAK 11(6Q26) WILD-TYPE	64	25	35

Figure S140. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0156 (Fisher's exact test), Q value = 0.039

Table S141. Gene #26: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
DEL PEAK 11(6Q26) MUTATED	2	3	11	10
DEL PEAK 11(6Q26) WILD-TYPE	35	30	27	32

Figure S141. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q11.22' versus 'METHLYATION_CNMF'

P value = 0.00755 (Fisher's exact test), Q value = 0.024

Table S142. Gene #27: 'del_7q11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	49	45
DEL PEAK 12(7Q11.22) MUTATED	0	0	4
DEL PEAK 12(7Q11.22) WILD-TYPE	56	49	41

Figure S142. Get High-res Image Gene #27: 'del_7q11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q11.22' versus 'RPPA_CHIERARCHICAL'

P value = 0.0286 (Fisher's exact test), Q value = 0.063

Table S143. Gene #27: 'del_7q11.22' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
DEL PEAK 12(7Q11.22) MUTATED	0	0	4
DEL PEAK 12(7Q11.22) WILD-TYPE	51	25	38

Figure S143. Get High-res Image Gene #27: 'del_7q11.22' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_7q11.22' versus 'MRNASEQ_CNMF'

P value = 0.00948 (Fisher's exact test), Q value = 0.028

Table S144. Gene #27: 'del_7q11.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
DEL PEAK 12(7Q11.22) MUTATED	0	0	4
DEL PEAK 12(7Q11.22) WILD-TYPE	70	40	36

Figure S144. Get High-res Image Gene #27: 'del_7q11.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_7q11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0303 (Fisher's exact test), Q value = 0.065

Table S145. Gene #27: 'del_7q11.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 12(7Q11.22) MUTATED	0	0	1	1	0	0	2
DEL PEAK 12(7Q11.22) WILD-TYPE	43	27	11	23	8	23	11

Figure S145. Get High-res Image Gene #27: 'del_7q11.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_7q11.22' versus 'MIRSEQ_CNMF'

P value = 0.0048 (Fisher's exact test), Q value = 0.018

Table S146. Gene #27: 'del_7q11.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	57	41
DEL PEAK 12(7Q11.22) MUTATED	0	0	4
DEL PEAK 12(7Q11.22) WILD-TYPE	52	57	37

Figure S146. Get High-res Image Gene #27: 'del_7q11.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_7q11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00936 (Fisher's exact test), Q value = 0.027

Table S147. Gene #27: 'del_7q11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 12(7Q11.22) MUTATED	0	0	4
DEL PEAK 12(7Q11.22) WILD-TYPE	70	38	38

Figure S147. Get High-res Image Gene #27: 'del_7q11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_7q11.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.029

Table S148. Gene #27: 'del_7q11.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 12(7Q11.22) MUTATED	0	0	4
DEL PEAK 12(7Q11.22) WILD-TYPE	69	36	41

Figure S148. Get High-res Image Gene #27: 'del_7q11.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_7q11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.037

Table S149. Gene #27: 'del_7q11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
DEL PEAK 12(7Q11.22) MUTATED	0	0	0	4
DEL PEAK 12(7Q11.22) WILD-TYPE	37	33	38	38

Figure S149. Get High-res Image Gene #27: 'del_7q11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q36.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0292 (Fisher's exact test), Q value = 0.063

Table S150. Gene #28: 'del_7q36.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
DEL PEAK 13(7Q36.1) MUTATED	4	0	8
DEL PEAK 13(7Q36.1) WILD-TYPE	47	25	34

Figure S150. Get High-res Image Gene #28: 'del_7q36.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_7q36.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.029

Table S151. Gene #28: 'del_7q36.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 13(7Q36.1) MUTATED	0	6	3	2	0	2	2
DEL PEAK 13(7Q36.1) WILD-TYPE	43	21	9	22	8	21	11

Figure S151. Get High-res Image Gene #28: 'del_7q36.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_7q36.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0292 (Fisher's exact test), Q value = 0.063

Table S152. Gene #28: 'del_7q36.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
DEL PEAK 13(7Q36.1) MUTATED	0	6	3	6
DEL PEAK 13(7Q36.1) WILD-TYPE	37	27	35	36

Figure S152. Get High-res Image Gene #28: 'del_7q36.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 0.0372 (Fisher's exact test), Q value = 0.076

Table S153. Gene #30: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
DEL PEAK 15(9P23) MUTATED	16	17	33
DEL PEAK 15(9P23) WILD-TYPE	32	27	25

Figure S153. Get High-res Image Gene #30: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q33.3' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0024

Table S154. Gene #31: 'del_9q33.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
DEL PEAK 16(9Q33.3) MUTATED	12	13	35
DEL PEAK 16(9Q33.3) WILD-TYPE	36	31	23

Figure S154. Get High-res Image Gene #31: 'del_9q33.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q33.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0151 (Fisher's exact test), Q value = 0.038

Table S155. Gene #31: 'del_9q33.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 16(9Q33.3) MUTATED	14	8	9	12	1	13	3
DEL PEAK 16(9Q33.3) WILD-TYPE	29	19	3	12	7	10	10

Figure S155. Get High-res Image Gene #31: 'del_9q33.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9q34.2' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0028

Table S156. Gene #32: 'del_9q34.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
DEL PEAK 17(9Q34.2) MUTATED	12	13	35
DEL PEAK 17(9Q34.2) WILD-TYPE	36	31	23

Figure S156. Get High-res Image Gene #32: 'del_9q34.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q34.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00394 (Fisher's exact test), Q value = 0.015

Table S157. Gene #32: 'del_9q34.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 17(9Q34.2) MUTATED	14	8	9	12	1	14	2
DEL PEAK 17(9Q34.2) WILD-TYPE	29	19	3	12	7	9	11

Figure S157. Get High-res Image Gene #32: 'del_9q34.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9q34.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0276 (Fisher's exact test), Q value = 0.061

Table S158. Gene #32: 'del_9q34.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 17(9Q34.2) MUTATED	22	22	16
DEL PEAK 17(9Q34.2) WILD-TYPE	48	16	26

Figure S158. Get High-res Image Gene #32: 'del_9q34.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.0075

Table S159. Gene #33: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
DEL PEAK 18(10P15.3) MUTATED	20	21	43
DEL PEAK 18(10P15.3) WILD-TYPE	28	23	15

Figure S159. Get High-res Image Gene #33: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.003

Table S160. Gene #33: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	49	45
DEL PEAK 18(10P15.3) MUTATED	21	37	26
DEL PEAK 18(10P15.3) WILD-TYPE	35	12	19

Figure S160. Get High-res Image Gene #33: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p15.3' versus 'RPPA_CNMF'

P value = 0.00391 (Fisher's exact test), Q value = 0.015

Table S161. Gene #33: 'del_10p15.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
DEL PEAK 18(10P15.3) MUTATED	17	3	5	25	15
DEL PEAK 18(10P15.3) WILD-TYPE	28	5	5	12	3

Figure S161. Get High-res Image Gene #33: 'del_10p15.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_10p15.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00306 (Fisher's exact test), Q value = 0.013

Table S162. Gene #33: 'del_10p15.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
DEL PEAK 18(10P15.3) MUTATED	19	16	30
DEL PEAK 18(10P15.3) WILD-TYPE	32	9	12

Figure S162. Get High-res Image Gene #33: 'del_10p15.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0015

Table S163. Gene #33: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
DEL PEAK 18(10P15.3) MUTATED	28	32	24
DEL PEAK 18(10P15.3) WILD-TYPE	42	8	16

Figure S163. Get High-res Image Gene #33: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0012 (Fisher's exact test), Q value = 0.0069

Table S164. Gene #33: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 18(10P15.3) MUTATED	16	12	8	14	5	21	8
DEL PEAK 18(10P15.3) WILD-TYPE	27	15	4	10	3	2	5

Figure S164. Get High-res Image Gene #33: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_CNMF'

P value = 0.0204 (Fisher's exact test), Q value = 0.049

Table S165. Gene #33: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	57	41
DEL PEAK 18(10P15.3) MUTATED	21	37	26
DEL PEAK 18(10P15.3) WILD-TYPE	31	20	15

Figure S165. Get High-res Image Gene #33: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10p15.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00067 (Fisher's exact test), Q value = 0.0046

Table S166. Gene #33: 'del_10p15.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 18(10P15.3) MUTATED	28	29	27
DEL PEAK 18(10P15.3) WILD-TYPE	42	9	15

Figure S166. Get High-res Image Gene #33: 'del_10p15.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0028

Table S167. Gene #33: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 18(10P15.3) MUTATED	28	29	27
DEL PEAK 18(10P15.3) WILD-TYPE	41	7	18

Figure S167. Get High-res Image Gene #33: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10p15.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.003

Table S168. Gene #33: 'del_10p15.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
DEL PEAK 18(10P15.3) MUTATED	12	16	30	26
DEL PEAK 18(10P15.3) WILD-TYPE	25	17	8	16

Figure S168. Get High-res Image Gene #33: 'del_10p15.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.1' versus 'CN_CNMF'

P value = 0.00509 (Fisher's exact test), Q value = 0.018

Table S169. Gene #34: 'del_10q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
DEL PEAK 19(10Q23.1) MUTATED	19	15	37
DEL PEAK 19(10Q23.1) WILD-TYPE	29	29	21

Figure S169. Get High-res Image Gene #34: 'del_10q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00039

Table S170. Gene #34: 'del_10q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	49	45
DEL PEAK 19(10Q23.1) MUTATED	15	37	19
DEL PEAK 19(10Q23.1) WILD-TYPE	41	12	26

Figure S170. Get High-res Image Gene #34: 'del_10q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.1' versus 'RPPA_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 0.054

Table S171. Gene #34: 'del_10q23.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
DEL PEAK 19(10Q23.1) MUTATED	15	2	4	21	13
DEL PEAK 19(10Q23.1) WILD-TYPE	30	6	6	16	5

Figure S171. Get High-res Image Gene #34: 'del_10q23.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_10q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.036

Table S172. Gene #34: 'del_10q23.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
DEL PEAK 19(10Q23.1) MUTATED	16	14	25
DEL PEAK 19(10Q23.1) WILD-TYPE	35	11	17

Figure S172. Get High-res Image Gene #34: 'del_10q23.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10q23.1' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00054

Table S173. Gene #34: 'del_10q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
DEL PEAK 19(10Q23.1) MUTATED	22	31	18
DEL PEAK 19(10Q23.1) WILD-TYPE	48	9	22

Figure S173. Get High-res Image Gene #34: 'del_10q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.0025

Table S174. Gene #34: 'del_10q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 19(10Q23.1) MUTATED	14	8	9	12	5	19	4
DEL PEAK 19(10Q23.1) WILD-TYPE	29	19	3	12	3	4	9

Figure S174. Get High-res Image Gene #34: 'del_10q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.1' versus 'MIRSEQ_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.044

Table S175. Gene #34: 'del_10q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	57	41
DEL PEAK 19(10Q23.1) MUTATED	17	34	20
DEL PEAK 19(10Q23.1) WILD-TYPE	35	23	21

Figure S175. Get High-res Image Gene #34: 'del_10q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00054

Table S176. Gene #34: 'del_10q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 19(10Q23.1) MUTATED	22	29	20
DEL PEAK 19(10Q23.1) WILD-TYPE	48	9	22

Figure S176. Get High-res Image Gene #34: 'del_10q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.001

Table S177. Gene #34: 'del_10q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 19(10Q23.1) MUTATED	22	27	22
DEL PEAK 19(10Q23.1) WILD-TYPE	47	9	23

Figure S177. Get High-res Image Gene #34: 'del_10q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.0014

Table S178. Gene #34: 'del_10q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
DEL PEAK 19(10Q23.1) MUTATED	10	12	29	20
DEL PEAK 19(10Q23.1) WILD-TYPE	27	21	9	22

Figure S178. Get High-res Image Gene #34: 'del_10q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q26.3' versus 'CN_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0031

Table S179. Gene #35: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
DEL PEAK 20(10Q26.3) MUTATED	18	17	41
DEL PEAK 20(10Q26.3) WILD-TYPE	30	27	17

Figure S179. Get High-res Image Gene #35: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q26.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00034

Table S180. Gene #35: 'del_10q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	49	45
DEL PEAK 20(10Q26.3) MUTATED	16	38	22
DEL PEAK 20(10Q26.3) WILD-TYPE	40	11	23

Figure S180. Get High-res Image Gene #35: 'del_10q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q26.3' versus 'RPPA_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.032

Table S181. Gene #35: 'del_10q26.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
DEL PEAK 20(10Q26.3) MUTATED	15	2	5	23	13
DEL PEAK 20(10Q26.3) WILD-TYPE	30	6	5	14	5

Figure S181. Get High-res Image Gene #35: 'del_10q26.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_10q26.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00291 (Fisher's exact test), Q value = 0.013

Table S182. Gene #35: 'del_10q26.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
DEL PEAK 20(10Q26.3) MUTATED	16	15	27
DEL PEAK 20(10Q26.3) WILD-TYPE	35	10	15

Figure S182. Get High-res Image Gene #35: 'del_10q26.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00039

Table S183. Gene #35: 'del_10q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
DEL PEAK 20(10Q26.3) MUTATED	24	33	19
DEL PEAK 20(10Q26.3) WILD-TYPE	46	7	21

Figure S183. Get High-res Image Gene #35: 'del_10q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.0013

Table S184. Gene #35: 'del_10q26.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 20(10Q26.3) MUTATED	16	8	10	13	6	19	4
DEL PEAK 20(10Q26.3) WILD-TYPE	27	19	2	11	2	4	9

Figure S184. Get High-res Image Gene #35: 'del_10q26.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 0.051

Table S185. Gene #35: 'del_10q26.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	57	41
DEL PEAK 20(10Q26.3) MUTATED	19	36	21
DEL PEAK 20(10Q26.3) WILD-TYPE	33	21	20

Figure S185. Get High-res Image Gene #35: 'del_10q26.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00091

Table S186. Gene #35: 'del_10q26.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 20(10Q26.3) MUTATED	24	30	22
DEL PEAK 20(10Q26.3) WILD-TYPE	46	8	20

Figure S186. Get High-res Image Gene #35: 'del_10q26.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00039

Table S187. Gene #35: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 20(10Q26.3) MUTATED	24	29	23
DEL PEAK 20(10Q26.3) WILD-TYPE	45	7	22

Figure S187. Get High-res Image Gene #35: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00091

Table S188. Gene #35: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
DEL PEAK 20(10Q26.3) MUTATED	12	12	31	21
DEL PEAK 20(10Q26.3) WILD-TYPE	25	21	7	21

Figure S188. Get High-res Image Gene #35: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 0.0256 (Fisher's exact test), Q value = 0.058

Table S189. Gene #36: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
DEL PEAK 21(11P15.5) MUTATED	24	34	36
DEL PEAK 21(11P15.5) WILD-TYPE	24	10	22

Figure S189. Get High-res Image Gene #36: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 0.00281 (Fisher's exact test), Q value = 0.013

Table S190. Gene #36: 'del_11p15.5' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
DEL PEAK 21(11P15.5) MUTATED	51	27	16
DEL PEAK 21(11P15.5) WILD-TYPE	19	13	24

Figure S190. Get High-res Image Gene #36: 'del_11p15.5' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00418 (Fisher's exact test), Q value = 0.016

Table S191. Gene #36: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 21(11P15.5) MUTATED	31	20	8	12	4	17	2
DEL PEAK 21(11P15.5) WILD-TYPE	12	7	4	12	4	6	11

Figure S191. Get High-res Image Gene #36: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 0.00524 (Fisher's exact test), Q value = 0.018

Table S192. Gene #36: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	57	41
DEL PEAK 21(11P15.5) MUTATED	36	41	17
DEL PEAK 21(11P15.5) WILD-TYPE	16	16	24

Figure S192. Get High-res Image Gene #36: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00241 (Fisher's exact test), Q value = 0.011

Table S193. Gene #36: 'del_11p15.5' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 21(11P15.5) MUTATED	51	26	17
DEL PEAK 21(11P15.5) WILD-TYPE	19	12	25

Figure S193. Get High-res Image Gene #36: 'del_11p15.5' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00624 (Fisher's exact test), Q value = 0.021

Table S194. Gene #36: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 21(11P15.5) MUTATED	51	23	20
DEL PEAK 21(11P15.5) WILD-TYPE	18	13	25

Figure S194. Get High-res Image Gene #36: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00709 (Fisher's exact test), Q value = 0.023

Table S195. Gene #36: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
DEL PEAK 21(11P15.5) MUTATED	27	24	26	17
DEL PEAK 21(11P15.5) WILD-TYPE	10	9	12	25

Figure S195. Get High-res Image Gene #36: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p12' versus 'MRNASEQ_CNMF'

P value = 0.0016 (Fisher's exact test), Q value = 0.0083

Table S196. Gene #37: 'del_11p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
DEL PEAK 22(11P12) MUTATED	52	30	17
DEL PEAK 22(11P12) WILD-TYPE	18	10	23

Figure S196. Get High-res Image Gene #37: 'del_11p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00508 (Fisher's exact test), Q value = 0.018

Table S197. Gene #37: 'del_11p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 22(11P12) MUTATED	31	21	8	12	5	19	3
DEL PEAK 22(11P12) WILD-TYPE	12	6	4	12	3	4	10

Figure S197. Get High-res Image Gene #37: 'del_11p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p12' versus 'MIRSEQ_CNMF'

P value = 0.00209 (Fisher's exact test), Q value = 0.01

Table S198. Gene #37: 'del_11p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	57	41
DEL PEAK 22(11P12) MUTATED	37	44	18
DEL PEAK 22(11P12) WILD-TYPE	15	13	23

Figure S198. Get High-res Image Gene #37: 'del_11p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00137 (Fisher's exact test), Q value = 0.0075

Table S199. Gene #37: 'del_11p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 22(11P12) MUTATED	52	29	18
DEL PEAK 22(11P12) WILD-TYPE	18	9	24

Figure S199. Get High-res Image Gene #37: 'del_11p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00652 (Fisher's exact test), Q value = 0.022

Table S200. Gene #37: 'del_11p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 22(11P12) MUTATED	51	27	21
DEL PEAK 22(11P12) WILD-TYPE	18	9	24

Figure S200. Get High-res Image Gene #37: 'del_11p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00422 (Fisher's exact test), Q value = 0.016

Table S201. Gene #37: 'del_11p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
DEL PEAK 22(11P12) MUTATED	28	24	29	18
DEL PEAK 22(11P12) WILD-TYPE	9	9	9	24

Figure S201. Get High-res Image Gene #37: 'del_11p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q12.3' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00078

Table S202. Gene #38: 'del_11q12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
DEL PEAK 23(11Q12.3) MUTATED	30	43	41
DEL PEAK 23(11Q12.3) WILD-TYPE	18	1	17

Figure S202. Get High-res Image Gene #38: 'del_11q12.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q12.3' versus 'RPPA_CNMF'

P value = 0.0322 (Fisher's exact test), Q value = 0.068

Table S203. Gene #38: 'del_11q12.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
DEL PEAK 23(11Q12.3) MUTATED	39	7	5	23	13
DEL PEAK 23(11Q12.3) WILD-TYPE	6	1	5	14	5

Figure S203. Get High-res Image Gene #38: 'del_11q12.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_11q12.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0222 (Fisher's exact test), Q value = 0.052

Table S204. Gene #38: 'del_11q12.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
DEL PEAK 23(11Q12.3) MUTATED	44	16	27
DEL PEAK 23(11Q12.3) WILD-TYPE	7	9	15

Figure S204. Get High-res Image Gene #38: 'del_11q12.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_11q12.3' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.0011

Table S205. Gene #38: 'del_11q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
DEL PEAK 23(11Q12.3) MUTATED	62	32	20
DEL PEAK 23(11Q12.3) WILD-TYPE	8	8	20

Figure S205. Get High-res Image Gene #38: 'del_11q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q12.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00039

Table S206. Gene #38: 'del_11q12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 23(11Q12.3) MUTATED	35	27	9	14	6	20	3
DEL PEAK 23(11Q12.3) WILD-TYPE	8	0	3	10	2	3	10

Figure S206. Get High-res Image Gene #38: 'del_11q12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q12.3' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00078

Table S207. Gene #38: 'del_11q12.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	57	41
DEL PEAK 23(11Q12.3) MUTATED	44	50	20
DEL PEAK 23(11Q12.3) WILD-TYPE	8	7	21

Figure S207. Get High-res Image Gene #38: 'del_11q12.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11q12.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00034

Table S208. Gene #38: 'del_11q12.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 23(11Q12.3) MUTATED	62	32	20
DEL PEAK 23(11Q12.3) WILD-TYPE	8	6	22

Figure S208. Get High-res Image Gene #38: 'del_11q12.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11q12.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00091

Table S209. Gene #38: 'del_11q12.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 23(11Q12.3) MUTATED	61	30	23
DEL PEAK 23(11Q12.3) WILD-TYPE	8	6	22

Figure S209. Get High-res Image Gene #38: 'del_11q12.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q12.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00039

Table S210. Gene #38: 'del_11q12.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
DEL PEAK 23(11Q12.3) MUTATED	30	32	31	21
DEL PEAK 23(11Q12.3) WILD-TYPE	7	1	7	21

Figure S210. Get High-res Image Gene #38: 'del_11q12.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q24.2' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00091

Table S211. Gene #39: 'del_11q24.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
DEL PEAK 24(11Q24.2) MUTATED	33	44	45
DEL PEAK 24(11Q24.2) WILD-TYPE	15	0	13

Figure S211. Get High-res Image Gene #39: 'del_11q24.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q24.2' versus 'MRNASEQ_CNMF'

P value = 0.00882 (Fisher's exact test), Q value = 0.026

Table S212. Gene #39: 'del_11q24.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
DEL PEAK 24(11Q24.2) MUTATED	62	34	26
DEL PEAK 24(11Q24.2) WILD-TYPE	8	6	14

Figure S212. Get High-res Image Gene #39: 'del_11q24.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q24.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00059 (Fisher's exact test), Q value = 0.0042

Table S213. Gene #39: 'del_11q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 24(11Q24.2) MUTATED	35	27	10	18	7	20	5
DEL PEAK 24(11Q24.2) WILD-TYPE	8	0	2	6	1	3	8

Figure S213. Get High-res Image Gene #39: 'del_11q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q24.2' versus 'MIRSEQ_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.033

Table S214. Gene #39: 'del_11q24.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	57	41
DEL PEAK 24(11Q24.2) MUTATED	44	51	27
DEL PEAK 24(11Q24.2) WILD-TYPE	8	6	14

Figure S214. Get High-res Image Gene #39: 'del_11q24.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11q24.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0067 (Fisher's exact test), Q value = 0.022

Table S215. Gene #39: 'del_11q24.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 24(11Q24.2) MUTATED	62	33	27
DEL PEAK 24(11Q24.2) WILD-TYPE	8	5	15

Figure S215. Get High-res Image Gene #39: 'del_11q24.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11q24.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 0.038

Table S216. Gene #39: 'del_11q24.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 24(11Q24.2) MUTATED	61	31	30
DEL PEAK 24(11Q24.2) WILD-TYPE	8	5	15

Figure S216. Get High-res Image Gene #39: 'del_11q24.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q24.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00081 (Fisher's exact test), Q value = 0.0051

Table S217. Gene #39: 'del_11q24.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
DEL PEAK 24(11Q24.2) MUTATED	29	33	32	28
DEL PEAK 24(11Q24.2) WILD-TYPE	8	0	6	14

Figure S217. Get High-res Image Gene #39: 'del_11q24.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q34' versus 'CN_CNMF'

P value = 0.0444 (Fisher's exact test), Q value = 0.086

Table S218. Gene #40: 'del_13q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
DEL PEAK 25(13Q34) MUTATED	33	39	41
DEL PEAK 25(13Q34) WILD-TYPE	15	5	17

Figure S218. Get High-res Image Gene #40: 'del_13q34' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00207 (Fisher's exact test), Q value = 0.01

Table S219. Gene #40: 'del_13q34' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 25(13Q34) MUTATED	30	27	11	15	6	17	7
DEL PEAK 25(13Q34) WILD-TYPE	13	0	1	9	2	6	6

Figure S219. Get High-res Image Gene #40: 'del_13q34' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q34' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00207 (Fisher's exact test), Q value = 0.01

Table S220. Gene #40: 'del_13q34' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
DEL PEAK 25(13Q34) MUTATED	25	32	29	27
DEL PEAK 25(13Q34) WILD-TYPE	12	1	9	15

Figure S220. Get High-res Image Gene #40: 'del_13q34' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.0075

Table S221. Gene #41: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
DEL PEAK 26(16Q23.1) MUTATED	14	29	23
DEL PEAK 26(16Q23.1) WILD-TYPE	34	15	35

Figure S221. Get High-res Image Gene #41: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_18p11.32' versus 'MRNASEQ_CNMF'

P value = 0.0486 (Fisher's exact test), Q value = 0.094

Table S222. Gene #42: 'del_18p11.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
DEL PEAK 27(18P11.32) MUTATED	55	36	27
DEL PEAK 27(18P11.32) WILD-TYPE	15	4	13

Figure S222. Get High-res Image Gene #42: 'del_18p11.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18p11.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.046

Table S223. Gene #42: 'del_18p11.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 27(18P11.32) MUTATED	55	35	28
DEL PEAK 27(18P11.32) WILD-TYPE	15	3	14

Figure S223. Get High-res Image Gene #42: 'del_18p11.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0412 (Fisher's exact test), Q value = 0.081

Table S224. Gene #43: 'del_18q22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 28(18Q22.2) MUTATED	58	36	31
DEL PEAK 28(18Q22.2) WILD-TYPE	12	2	11

Figure S224. Get High-res Image Gene #43: 'del_18q22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0257 (Fisher's exact test), Q value = 0.058

Table S225. Gene #43: 'del_18q22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
DEL PEAK 28(18Q22.2) MUTATED	27	31	35	32
DEL PEAK 28(18Q22.2) WILD-TYPE	10	2	3	10

Figure S225. Get High-res Image Gene #43: 'del_18q22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.41' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00034

Table S226. Gene #44: 'del_19q13.41' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
DEL PEAK 29(19Q13.41) MUTATED	14	7	37
DEL PEAK 29(19Q13.41) WILD-TYPE	34	37	21

Figure S226. Get High-res Image Gene #44: 'del_19q13.41' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.41' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00034

Table S227. Gene #44: 'del_19q13.41' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	49	45
DEL PEAK 29(19Q13.41) MUTATED	2	37	19
DEL PEAK 29(19Q13.41) WILD-TYPE	54	12	26

Figure S227. Get High-res Image Gene #44: 'del_19q13.41' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.41' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00034

Table S228. Gene #44: 'del_19q13.41' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	8	10	37	18
DEL PEAK 29(19Q13.41) MUTATED	1	2	4	25	15
DEL PEAK 29(19Q13.41) WILD-TYPE	44	6	6	12	3

Figure S228. Get High-res Image Gene #44: 'del_19q13.41' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_19q13.41' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00034

Table S229. Gene #44: 'del_19q13.41' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	25	42
DEL PEAK 29(19Q13.41) MUTATED	1	15	31
DEL PEAK 29(19Q13.41) WILD-TYPE	50	10	11

Figure S229. Get High-res Image Gene #44: 'del_19q13.41' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_19q13.41' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00034

Table S230. Gene #44: 'del_19q13.41' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
DEL PEAK 29(19Q13.41) MUTATED	1	33	24
DEL PEAK 29(19Q13.41) WILD-TYPE	69	7	16

Figure S230. Get High-res Image Gene #44: 'del_19q13.41' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19q13.41' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00034

Table S231. Gene #44: 'del_19q13.41' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 29(19Q13.41) MUTATED	0	1	11	14	5	20	7
DEL PEAK 29(19Q13.41) WILD-TYPE	43	26	1	10	3	3	6

Figure S231. Get High-res Image Gene #44: 'del_19q13.41' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.41' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00034

Table S232. Gene #44: 'del_19q13.41' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	57	41
DEL PEAK 29(19Q13.41) MUTATED	1	32	25
DEL PEAK 29(19Q13.41) WILD-TYPE	51	25	16

Figure S232. Get High-res Image Gene #44: 'del_19q13.41' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19q13.41' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00034

Table S233. Gene #44: 'del_19q13.41' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 29(19Q13.41) MUTATED	1	32	25
DEL PEAK 29(19Q13.41) WILD-TYPE	69	6	17

Figure S233. Get High-res Image Gene #44: 'del_19q13.41' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.41' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00034

Table S234. Gene #44: 'del_19q13.41' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 29(19Q13.41) MUTATED	1	28	29
DEL PEAK 29(19Q13.41) WILD-TYPE	68	8	16

Figure S234. Get High-res Image Gene #44: 'del_19q13.41' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19q13.41' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00034

Table S235. Gene #44: 'del_19q13.41' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
DEL PEAK 29(19Q13.41) MUTATED	0	1	31	26
DEL PEAK 29(19Q13.41) WILD-TYPE	37	32	7	16

Figure S235. Get High-res Image Gene #44: 'del_19q13.41' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_CNMF'

P value = 0.0261 (Fisher's exact test), Q value = 0.058

Table S236. Gene #45: 'del_20p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	57	41
DEL PEAK 30(20P12.1) MUTATED	5	17	7
DEL PEAK 30(20P12.1) WILD-TYPE	47	40	34

Figure S236. Get High-res Image Gene #45: 'del_20p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_20p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0124 (Fisher's exact test), Q value = 0.033

Table S237. Gene #45: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
DEL PEAK 30(20P12.1) MUTATED	2	9	12	6
DEL PEAK 30(20P12.1) WILD-TYPE	35	24	26	36

Figure S237. Get High-res Image Gene #45: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0052

Table S238. Gene #46: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	49	45
DEL PEAK 31(XP21.1) MUTATED	5	6	17
DEL PEAK 31(XP21.1) WILD-TYPE	51	43	28

Figure S238. Get High-res Image Gene #46: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp21.1' versus 'MRNASEQ_CNMF'

P value = 0.0445 (Fisher's exact test), Q value = 0.086

Table S239. Gene #46: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
DEL PEAK 31(XP21.1) MUTATED	10	5	13
DEL PEAK 31(XP21.1) WILD-TYPE	60	35	27

Figure S239. Get High-res Image Gene #46: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp21.1' versus 'MIRSEQ_CNMF'

P value = 0.0433 (Fisher's exact test), Q value = 0.085

Table S240. Gene #46: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	57	41
DEL PEAK 31(XP21.1) MUTATED	6	9	13
DEL PEAK 31(XP21.1) WILD-TYPE	46	48	28

Figure S240. Get High-res Image Gene #46: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xp21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0491 (Fisher's exact test), Q value = 0.094

Table S241. Gene #46: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	36	45
DEL PEAK 31(XP21.1) MUTATED	10	4	14
DEL PEAK 31(XP21.1) WILD-TYPE	59	32	31

Figure S241. Get High-res Image Gene #46: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xp21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00085 (Fisher's exact test), Q value = 0.0052

Table S242. Gene #46: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	33	38	42
DEL PEAK 31(XP21.1) MUTATED	1	9	4	14
DEL PEAK 31(XP21.1) WILD-TYPE	36	24	34	28

Figure S242. Get High-res Image Gene #46: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xq27.3' versus 'CN_CNMF'

P value = 0.00113 (Fisher's exact test), Q value = 0.0067

Table S243. Gene #47: 'del_xq27.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
DEL PEAK 32(XQ27.3) MUTATED	2	11	17
DEL PEAK 32(XQ27.3) WILD-TYPE	46	33	41

Figure S243. Get High-res Image Gene #47: 'del_xq27.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq27.3' versus 'METHLYATION_CNMF'

P value = 0.00147 (Fisher's exact test), Q value = 0.0078

Table S244. Gene #47: 'del_xq27.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	49	45
DEL PEAK 32(XQ27.3) MUTATED	5	8	17
DEL PEAK 32(XQ27.3) WILD-TYPE	51	41	28

Figure S244. Get High-res Image Gene #47: 'del_xq27.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq27.3' versus 'MIRSEQ_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.031

Table S245. Gene #47: 'del_xq27.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	57	41
DEL PEAK 32(XQ27.3) MUTATED	8	7	15
DEL PEAK 32(XQ27.3) WILD-TYPE	44	50	26

Figure S245. Get High-res Image Gene #47: 'del_xq27.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xq27.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0116 (Fisher's exact test), Q value = 0.032

Table S246. Gene #47: 'del_xq27.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	38	42
DEL PEAK 32(XQ27.3) MUTATED	11	4	15
DEL PEAK 32(XQ27.3) WILD-TYPE	59	34	27

Figure S246. Get High-res Image Gene #47: 'del_xq27.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/TGCT-TP/19781845/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/TGCT-TP/20140863/TGCT-TP.transferedmergedcluster.txt
Number of patients = 150
Number of significantly focal cnvs = 47
Number of molecular subtypes = 10
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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