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

Brain Lower Grade Glioma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1ZC81NH

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 50 focal events and 12 molecular subtypes across 512 patients, 201 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q22 cnv correlated to 'CN_CNMF'.
amp_1q32.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3q26.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_4q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7p11.2 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_7q31.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q32.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q24.13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_10p15.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12p13.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12q14.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_15q26.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_19p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xp11.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xp11.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.32 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p32.3 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q37.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p21.31 cnv correlated to 'CN_CNMF'.
del_3q29 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_4q34.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_5p15.33 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_5q34 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_6p25.3 cnv correlated to 'CN_CNMF'.
del_6q22.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q24.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8q24.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_9p23 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', '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 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_12q12 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_13q14.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_13q14.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_13q34 cnv correlated to 'CN_CNMF'.
del_14q24.3 cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_15q21.3 cnv correlated to 'MRNASEQ_CNMF'.
del_19q13.42 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_22q13.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 50 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 201 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
del 1p36 32	206 (40%)	306	0.00056 (0.216)	0.00018 (0.0743)	1e-05 (0.0058)	1e-05 (0.0058)	0.00074 (0.277)	0.846 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	1e-05 (0.0058)	1e-05 (0.0058)	1e-05 (0.0058)	1e-05 (0.0058)
del 1p32 3	196 (38%)	316	0.0284 (1.00)	0.00019 (0.0783)	1e-05 (0.0058)	1e-05 (0.0058)	0.00056 (0.216)	0.615 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	1e-05 (0.0058)	1e-05 (0.0058)	1e-05 (0.0058)	1e-05 (0.0058)
del 10q26 3	151 (29%)	361	0.0836 (1.00)	0.706 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	1e-05 (0.0058)	0.00028 (0.113)	1e-05 (0.0058)	1e-05 (0.0058)	1e-05 (0.0058)	1e-05 (0.0058)	1e-05 (0.0058)	1e-05 (0.0058)
amp 7p11 2	127 (25%)	385	0.765 (1.00)	0.406 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	5e-05 (0.0215)	0.0127 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	0.00037 (0.147)	1e-05 (0.0058)	1e-05 (0.0058)	1e-05 (0.0058)
del 9p21 3	176 (34%)	336	0.335 (1.00)	0.0642 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	4e-05 (0.0174)	2e-05 (0.00894)	1e-05 (0.0058)	1e-05 (0.0058)	0.315 (1.00)	1e-05 (0.0058)	0.00056 (0.216)	1e-05 (0.0058)
del 19q13 42	278 (54%)	234	0.0363 (1.00)	0.0208 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	0.00207 (0.72)	0.575 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	1e-05 (0.0058)	1e-05 (0.0058)	1e-05 (0.0058)	1e-05 (0.0058)
amp 7q31 2	173 (34%)	339	1 (1.00)	0.812 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	0.00447 (1.00)	0.185 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	0.0295 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	1e-05 (0.0058)
amp 7q32 3	181 (35%)	331	0.694 (1.00)	1 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	0.00619 (1.00)	0.167 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	0.0818 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	1e-05 (0.0058)
amp 12q14 1	37 (7%)	475			1e-05 (0.0058)	1e-05 (0.0058)	0.0156 (1.00)	0.733 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	0.00269 (0.912)	1e-05 (0.0058)	1e-05 (0.0058)	1e-05 (0.0058)
amp xp11 22	62 (12%)	450	0.652 (1.00)	1 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	0.0268 (1.00)	0.388 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	0.00034 (0.136)	0.00405 (1.00)	0.00013 (0.0546)	2e-05 (0.00894)
del 22q13 31	77 (15%)	435	0.248 (1.00)	0.0428 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	0.00019 (0.0783)	0.0123 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	0.0611 (1.00)	0.00016 (0.0664)	0.00153 (0.545)	2e-05 (0.00894)
amp 1q32 1	43 (8%)	469			1e-05 (0.0058)	1e-05 (0.0058)	0.162 (1.00)	0.355 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	0.55 (1.00)	1e-05 (0.0058)	0.00102 (0.374)	1e-05 (0.0058)
amp 4q12	30 (6%)	482	1 (1.00)	0.0426 (1.00)	6e-05 (0.0258)	6e-05 (0.0258)	0.00869 (1.00)	0.28 (1.00)	2e-05 (0.00894)	2e-05 (0.00894)	0.00431 (1.00)	0.00275 (0.929)	3e-05 (0.0131)	0.00064 (0.243)
amp 8q24 13	100 (20%)	412	0.369 (1.00)	0.237 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	0.0417 (1.00)	0.487 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	0.0585 (1.00)	0.00101 (0.372)	1e-05 (0.0058)	0.00011 (0.0464)
amp 10p15 3	70 (14%)	442	0.526 (1.00)	0.0853 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	0.0293 (1.00)	0.134 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	0.00082 (0.307)	0.01 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)
amp 12p13 32	71 (14%)	441	0.864 (1.00)	0.0978 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	0.118 (1.00)	0.191 (1.00)	0.00016 (0.0664)	2e-05 (0.00894)	0.00478 (1.00)	0.00119 (0.431)	0.00048 (0.188)	0.00014 (0.0585)
amp 19p13 3	128 (25%)	384	0.0758 (1.00)	0.15 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	0.884 (1.00)	0.574 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	0.00456 (1.00)	0.00308 (1.00)	1e-05 (0.0058)	6e-05 (0.0258)
amp 19p13 2	122 (24%)	390	0.0747 (1.00)	0.151 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	0.275 (1.00)	0.203 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	0.00974 (1.00)	0.00507 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)
del 5q34	64 (12%)	448	0.447 (1.00)	0.235 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	0.162 (1.00)	1 (1.00)	0.00024 (0.0977)	6e-05 (0.0258)	3e-05 (0.0131)	0.0107 (1.00)	0.00063 (0.24)	0.00228 (0.787)
del 6q24 3	82 (16%)	430	0.166 (1.00)	0.279 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	0.0997 (1.00)	0.619 (1.00)	0.00146 (0.521)	0.00013 (0.0546)	0.0002 (0.0816)	0.00239 (0.817)	0.00019 (0.0783)	0.00029 (0.117)
del 11p15 5	103 (20%)	409	0.643 (1.00)	0.00051 (0.199)	1e-05 (0.0058)	1e-05 (0.0058)	0.148 (1.00)	0.632 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	0.0011 (0.401)	0.00052 (0.202)	0.0124 (1.00)	0.00249 (0.849)
del 2q37 3	77 (15%)	435	0.371 (1.00)	0.0128 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	0.00466 (1.00)	0.02 (1.00)	0.00019 (0.0783)	0.00012 (0.0505)	0.0408 (1.00)	0.00872 (1.00)	0.0206 (1.00)	1e-05 (0.0058)
del 13q14 2	141 (28%)	371	0.181 (1.00)	4e-05 (0.0174)	1e-05 (0.0058)	0.0006 (0.229)	0.0336 (1.00)	0.608 (1.00)	0.00024 (0.0977)	6e-05 (0.0258)	0.0209 (1.00)	0.0246 (1.00)	0.0581 (1.00)	0.0286 (1.00)
del 13q14 2	143 (28%)	369	0.181 (1.00)	6e-05 (0.0258)	1e-05 (0.0058)	0.0004 (0.158)	0.0325 (1.00)	0.713 (1.00)	0.00015 (0.0624)	3e-05 (0.0131)	0.0199 (1.00)	0.0144 (1.00)	0.0435 (1.00)	0.0169 (1.00)
amp 3q26 33	21 (4%)	491	1 (1.00)	0.583 (1.00)	1e-05 (0.0058)	0.0003 (0.121)	0.145 (1.00)	0.849 (1.00)	0.0007 (0.265)	0.00033 (0.132)	0.00099 (0.365)	0.00202 (0.705)	0.00032 (0.128)	0.011 (1.00)
amp xp11 22	47 (9%)	465	0.65 (1.00)	1 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	0.318 (1.00)	0.732 (1.00)	0.0018 (0.632)	7e-05 (0.0297)	0.0449 (1.00)	0.133 (1.00)	0.0513 (1.00)	0.00026 (0.105)
del 6q22 31	78 (15%)	434	0.614 (1.00)	0.582 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	0.114 (1.00)	0.507 (1.00)	0.00464 (1.00)	0.00046 (0.181)	0.00141 (0.508)	0.00226 (0.782)	0.00948 (1.00)	0.00048 (0.188)
del 8q24 3	28 (5%)	484			1e-05 (0.0058)	2e-05 (0.00894)	0.926 (1.00)	0.46 (1.00)	0.00112 (0.407)	0.00052 (0.202)	0.0102 (1.00)	0.0265 (1.00)	0.101 (1.00)	0.00123 (0.444)
del 14q24 3	121 (24%)	391	0.303 (1.00)	0.0983 (1.00)	0.00237 (0.813)	0.0361 (1.00)	0.00158 (0.559)	0.036 (1.00)	0.00053 (0.205)	9e-05 (0.0381)	0.00014 (0.0585)	0.0119 (1.00)	0.00283 (0.954)	0.0021 (0.729)
amp 15q26 3	19 (4%)	493	1 (1.00)	0.0439 (1.00)	4e-05 (0.0174)	0.00045 (0.177)	0.223 (1.00)	0.606 (1.00)	0.0425 (1.00)	0.00958 (1.00)	0.206 (1.00)	0.149 (1.00)	0.0238 (1.00)	0.376 (1.00)
del 3q29	47 (9%)	465	0.175 (1.00)	0.883 (1.00)	1e-05 (0.0058)	0.00044 (0.174)	0.408 (1.00)	0.921 (1.00)	0.00408 (1.00)	0.00104 (0.381)	0.274 (1.00)	0.014 (1.00)	0.00778 (1.00)	0.00531 (1.00)
del 4q34 3	137 (27%)	375	1 (1.00)	0.354 (1.00)	0.00057 (0.218)	1e-05 (0.0058)	0.164 (1.00)	0.226 (1.00)	0.0603 (1.00)	0.0751 (1.00)	0.0131 (1.00)	0.00439 (1.00)	0.289 (1.00)	0.00073 (0.275)
del 5p15 33	50 (10%)	462	1 (1.00)	0.0677 (1.00)	1e-05 (0.0058)	2e-05 (0.00894)	0.865 (1.00)	0.579 (1.00)	0.00503 (1.00)	0.00083 (0.31)	0.003 (1.00)	0.234 (1.00)	0.0193 (1.00)	0.0579 (1.00)
del 9p23	150 (29%)	362	0.449 (1.00)	0.657 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	0.0389 (1.00)	0.00263 (0.894)	0.0123 (1.00)	0.0197 (1.00)	0.934 (1.00)	0.0369 (1.00)	0.338 (1.00)	0.0273 (1.00)
del 12q12	68 (13%)	444	1 (1.00)	0.581 (1.00)	1e-05 (0.0058)	1e-05 (0.0058)	0.647 (1.00)	0.149 (1.00)	0.0116 (1.00)	0.00787 (1.00)	0.00837 (1.00)	0.797 (1.00)	0.141 (1.00)	0.476 (1.00)
amp 1q22	42 (8%)	470			0.00035 (0.139)	0.00144 (0.516)	0.249 (1.00)	0.884 (1.00)	0.00143 (0.513)	0.0146 (1.00)	0.825 (1.00)	0.281 (1.00)	0.0592 (1.00)	0.366 (1.00)
del 3p21 31	48 (9%)	464	1 (1.00)	0.0067 (1.00)	1e-05 (0.0058)	0.00357 (1.00)	0.0023 (0.791)	0.26 (1.00)	0.0209 (1.00)	0.00442 (1.00)	0.00774 (1.00)	0.0042 (1.00)	0.0215 (1.00)	0.00177 (0.623)
del 6p25 3	50 (10%)	462			2e-05 (0.00894)	0.117 (1.00)	0.236 (1.00)	0.926 (1.00)	0.072 (1.00)	0.113 (1.00)	0.465 (1.00)	0.177 (1.00)	0.0927 (1.00)	0.0101 (1.00)
del 13q34	109 (21%)	403	0.507 (1.00)	0.15 (1.00)	1e-05 (0.0058)	0.0691 (1.00)	0.083 (1.00)	0.757 (1.00)	0.00818 (1.00)	0.00154 (0.547)	0.0715 (1.00)	0.091 (1.00)	0.0188 (1.00)	0.0774 (1.00)
del 15q21 3	66 (13%)	446	0.841 (1.00)	0.493 (1.00)	0.956 (1.00)	0.0123 (1.00)	0.0178 (1.00)	0.005 (1.00)	4e-05 (0.0174)	0.00092 (0.342)	0.542 (1.00)	0.785 (1.00)	0.0146 (1.00)	0.303 (1.00)
amp 2p24 3	24 (5%)	488	0.615 (1.00)	0.584 (1.00)	0.00073 (0.275)	0.0401 (1.00)	0.489 (1.00)	1 (1.00)	0.0239 (1.00)	0.0135 (1.00)	0.495 (1.00)	0.0407 (1.00)	0.158 (1.00)	0.0861 (1.00)
amp 9q34 3	45 (9%)	467	0.51 (1.00)	0.884 (1.00)	0.0599 (1.00)	0.0928 (1.00)	0.209 (1.00)	0.761 (1.00)	0.0583 (1.00)	0.0138 (1.00)	0.212 (1.00)	0.181 (1.00)	0.271 (1.00)	0.0777 (1.00)
amp 11q24 1	86 (17%)	426	0.0696 (1.00)	0.119 (1.00)	0.324 (1.00)	0.0168 (1.00)	0.0543 (1.00)	0.0293 (1.00)	0.0708 (1.00)	0.0661 (1.00)	0.261 (1.00)	0.00807 (1.00)	0.0774 (1.00)	0.0163 (1.00)
amp 13q34	22 (4%)	490			0.00097 (0.359)	0.00094 (0.349)	0.186 (1.00)	0.716 (1.00)	0.0436 (1.00)	0.0091 (1.00)	0.324 (1.00)	0.036 (1.00)	0.244 (1.00)	0.138 (1.00)
amp 17q25 1	44 (9%)	468			0.0548 (1.00)	0.257 (1.00)	0.332 (1.00)	0.438 (1.00)	0.0595 (1.00)	0.0716 (1.00)	0.176 (1.00)	0.675 (1.00)	0.674 (1.00)	0.183 (1.00)
del 1q43	31 (6%)	481			0.0019 (0.665)	0.00717 (1.00)	0.101 (1.00)	0.538 (1.00)	0.0273 (1.00)	0.0142 (1.00)	0.188 (1.00)	0.586 (1.00)	0.0438 (1.00)	0.11 (1.00)
del 7p22 3	21 (4%)	491			0.0175 (1.00)	0.006 (1.00)	0.253 (1.00)	0.352 (1.00)	0.352 (1.00)	0.382 (1.00)	0.796 (1.00)	0.102 (1.00)	0.605 (1.00)	0.051 (1.00)
del 12p13 1	39 (8%)	473			0.00111 (0.404)	0.00398 (1.00)	0.193 (1.00)	0.955 (1.00)	0.00958 (1.00)	0.0212 (1.00)	0.018 (1.00)	0.109 (1.00)	0.0148 (1.00)	0.0841 (1.00)
del 18q23	78 (15%)	434	0.32 (1.00)	0.329 (1.00)	0.703 (1.00)	0.0057 (1.00)	0.459 (1.00)	0.0751 (1.00)	0.41 (1.00)	0.0811 (1.00)	0.264 (1.00)	0.391 (1.00)	0.607 (1.00)	0.545 (1.00)
del xq21 1	78 (15%)	434	0.839 (1.00)	0.268 (1.00)	0.228 (1.00)	0.0136 (1.00)	0.0523 (1.00)	0.152 (1.00)	0.00828 (1.00)	0.00069 (0.262)	0.00587 (1.00)	0.00618 (1.00)	0.00173 (0.611)	0.00696 (1.00)

'amp_1q22' versus 'CN_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.14

Table S1. Gene #1: 'amp_1q22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
AMP PEAK 1(1Q22) MUTATED	18	17	7
AMP PEAK 1(1Q22) WILD-TYPE	150	101	219

Figure S1. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q32.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S2. Gene #2: 'amp_1q32.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
AMP PEAK 2(1Q32.1) MUTATED	10	27	6
AMP PEAK 2(1Q32.1) WILD-TYPE	158	91	220

Figure S2. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q32.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S3. Gene #2: 'amp_1q32.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
AMP PEAK 2(1Q32.1) MUTATED	12	22	3	6
AMP PEAK 2(1Q32.1) WILD-TYPE	211	50	54	149

Figure S3. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q32.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S4. Gene #2: 'amp_1q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
AMP PEAK 2(1Q32.1) MUTATED	2	26	1	12	2
AMP PEAK 2(1Q32.1) WILD-TYPE	133	86	107	115	26

Figure S4. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q32.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S5. Gene #2: 'amp_1q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
AMP PEAK 2(1Q32.1) MUTATED	3	24	5	11
AMP PEAK 2(1Q32.1) WILD-TYPE	132	89	120	126

Figure S5. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q32.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S6. Gene #2: 'amp_1q32.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	107	137	100
AMP PEAK 2(1Q32.1) MUTATED	6	4	9	23
AMP PEAK 2(1Q32.1) WILD-TYPE	149	103	128	77

Figure S6. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q32.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S7. Gene #2: 'amp_1q32.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
AMP PEAK 2(1Q32.1) MUTATED	6	5	8	23
AMP PEAK 2(1Q32.1) WILD-TYPE	142	136	104	75

Figure S7. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S8. Gene #4: 'amp_3q26.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
AMP PEAK 4(3Q26.33) MUTATED	5	14	2
AMP PEAK 4(3Q26.33) WILD-TYPE	163	104	224

Figure S8. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.33' versus 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.12

Table S9. Gene #4: 'amp_3q26.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
AMP PEAK 4(3Q26.33) MUTATED	9	10	0	2
AMP PEAK 4(3Q26.33) WILD-TYPE	214	62	57	153

Figure S9. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.13

Table S10. Gene #4: 'amp_3q26.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
AMP PEAK 4(3Q26.33) MUTATED	4	13	1	3
AMP PEAK 4(3Q26.33) WILD-TYPE	131	100	124	134

Figure S10. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.13

Table S11. Gene #4: 'amp_3q26.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
AMP PEAK 4(3Q26.33) MUTATED	6	11	0	1	1	2	0
AMP PEAK 4(3Q26.33) WILD-TYPE	107	83	69	145	33	16	25

Figure S11. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_4q12' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.026

Table S12. Gene #5: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
AMP PEAK 5(4Q12) MUTATED	19	8	3
AMP PEAK 5(4Q12) WILD-TYPE	149	110	223

Figure S12. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_4q12' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.026

Table S13. Gene #5: 'amp_4q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
AMP PEAK 5(4Q12) MUTATED	19	9	1	1
AMP PEAK 5(4Q12) WILD-TYPE	204	63	56	154

Figure S13. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_4q12' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S14. Gene #5: 'amp_4q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
AMP PEAK 5(4Q12) MUTATED	5	18	0	6	1
AMP PEAK 5(4Q12) WILD-TYPE	130	94	108	121	27

Figure S14. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_4q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S15. Gene #5: 'amp_4q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
AMP PEAK 5(4Q12) MUTATED	5	19	0	6
AMP PEAK 5(4Q12) WILD-TYPE	130	94	125	131

Figure S15. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_4q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.013

Table S16. Gene #5: 'amp_4q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
AMP PEAK 5(4Q12) MUTATED	4	8	1	6	0	7	3
AMP PEAK 5(4Q12) WILD-TYPE	109	86	68	140	34	11	22

Figure S16. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_4q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00064 (Fisher's exact test), Q value = 0.24

Table S17. Gene #5: 'amp_4q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
AMP PEAK 5(4Q12) MUTATED	8	2	5	14
AMP PEAK 5(4Q12) WILD-TYPE	140	139	107	84

Figure S17. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S18. Gene #6: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
AMP PEAK 6(7P11.2) MUTATED	22	97	8
AMP PEAK 6(7P11.2) WILD-TYPE	146	21	218

Figure S18. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S19. Gene #6: 'amp_7p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
AMP PEAK 6(7P11.2) MUTATED	38	59	14	14
AMP PEAK 6(7P11.2) WILD-TYPE	185	13	43	141

Figure S19. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'RPPA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.022

Table S20. Gene #6: 'amp_7p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
AMP PEAK 6(7P11.2) MUTATED	13	31	12	12
AMP PEAK 6(7P11.2) WILD-TYPE	39	31	56	62

Figure S20. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S21. Gene #6: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
AMP PEAK 6(7P11.2) MUTATED	22	66	9	23	5
AMP PEAK 6(7P11.2) WILD-TYPE	113	46	99	104	23

Figure S21. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S22. Gene #6: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
AMP PEAK 6(7P11.2) MUTATED	19	65	10	31
AMP PEAK 6(7P11.2) WILD-TYPE	116	48	115	106

Figure S22. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.15

Table S23. Gene #6: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	136	104	187	72
AMP PEAK 6(7P11.2) MUTATED	45	36	32	12
AMP PEAK 6(7P11.2) WILD-TYPE	91	68	155	60

Figure S23. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S24. Gene #6: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	107	137	100
AMP PEAK 6(7P11.2) MUTATED	30	15	18	62
AMP PEAK 6(7P11.2) WILD-TYPE	125	92	119	38

Figure S24. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S25. Gene #6: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
AMP PEAK 6(7P11.2) MUTATED	21	54	5	27	8	6	4
AMP PEAK 6(7P11.2) WILD-TYPE	92	40	64	119	26	12	21

Figure S25. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S26. Gene #6: 'amp_7p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
AMP PEAK 6(7P11.2) MUTATED	27	22	14	62
AMP PEAK 6(7P11.2) WILD-TYPE	121	119	98	36

Figure S26. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S27. Gene #7: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
AMP PEAK 7(7Q31.2) MUTATED	49	103	21
AMP PEAK 7(7Q31.2) WILD-TYPE	119	15	205

Figure S27. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q31.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S28. Gene #7: 'amp_7q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
AMP PEAK 7(7Q31.2) MUTATED	75	55	13	28
AMP PEAK 7(7Q31.2) WILD-TYPE	148	17	44	127

Figure S28. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S29. Gene #7: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
AMP PEAK 7(7Q31.2) MUTATED	48	63	15	37	8
AMP PEAK 7(7Q31.2) WILD-TYPE	87	49	93	90	20

Figure S29. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S30. Gene #7: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
AMP PEAK 7(7Q31.2) MUTATED	44	61	20	46
AMP PEAK 7(7Q31.2) WILD-TYPE	91	52	105	91

Figure S30. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S31. Gene #7: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	107	137	100
AMP PEAK 7(7Q31.2) MUTATED	53	28	30	60
AMP PEAK 7(7Q31.2) WILD-TYPE	102	79	107	40

Figure S31. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S32. Gene #7: 'amp_7q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
AMP PEAK 7(7Q31.2) MUTATED	40	52	10	43	15	6	5
AMP PEAK 7(7Q31.2) WILD-TYPE	73	42	59	103	19	12	20

Figure S32. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S33. Gene #7: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
AMP PEAK 7(7Q31.2) MUTATED	48	37	26	60
AMP PEAK 7(7Q31.2) WILD-TYPE	100	104	86	38

Figure S33. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q32.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S34. Gene #8: 'amp_7q32.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
AMP PEAK 8(7Q32.3) MUTATED	51	107	23
AMP PEAK 8(7Q32.3) WILD-TYPE	117	11	203

Figure S34. Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q32.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S35. Gene #8: 'amp_7q32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
AMP PEAK 8(7Q32.3) MUTATED	80	56	14	29
AMP PEAK 8(7Q32.3) WILD-TYPE	143	16	43	126

Figure S35. Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7q32.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S36. Gene #8: 'amp_7q32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
AMP PEAK 8(7Q32.3) MUTATED	52	63	16	40	8
AMP PEAK 8(7Q32.3) WILD-TYPE	83	49	92	87	20

Figure S36. Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q32.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S37. Gene #8: 'amp_7q32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
AMP PEAK 8(7Q32.3) MUTATED	47	61	21	50
AMP PEAK 8(7Q32.3) WILD-TYPE	88	52	104	87

Figure S37. Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q32.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S38. Gene #8: 'amp_7q32.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	107	137	100
AMP PEAK 8(7Q32.3) MUTATED	55	30	33	61
AMP PEAK 8(7Q32.3) WILD-TYPE	100	77	104	39

Figure S38. Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7q32.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S39. Gene #8: 'amp_7q32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
AMP PEAK 8(7Q32.3) MUTATED	44	52	11	46	15	6	5
AMP PEAK 8(7Q32.3) WILD-TYPE	69	42	58	100	19	12	20

Figure S39. Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7q32.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S40. Gene #8: 'amp_7q32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
AMP PEAK 8(7Q32.3) MUTATED	53	38	28	60
AMP PEAK 8(7Q32.3) WILD-TYPE	95	103	84	38

Figure S40. Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S41. Gene #9: 'amp_8q24.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
AMP PEAK 9(8Q24.13) MUTATED	74	15	11
AMP PEAK 9(8Q24.13) WILD-TYPE	94	103	215

Figure S41. Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S42. Gene #9: 'amp_8q24.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
AMP PEAK 9(8Q24.13) MUTATED	82	3	5	10
AMP PEAK 9(8Q24.13) WILD-TYPE	141	69	52	145

Figure S42. Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S43. Gene #9: 'amp_8q24.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
AMP PEAK 9(8Q24.13) MUTATED	51	12	5	25	6
AMP PEAK 9(8Q24.13) WILD-TYPE	84	100	103	102	22

Figure S43. Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S44. Gene #9: 'amp_8q24.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
AMP PEAK 9(8Q24.13) MUTATED	52	12	7	28
AMP PEAK 9(8Q24.13) WILD-TYPE	83	101	118	109

Figure S44. Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S45. Gene #9: 'amp_8q24.13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
AMP PEAK 9(8Q24.13) MUTATED	42	8	4	26	5	4	6
AMP PEAK 9(8Q24.13) WILD-TYPE	71	86	65	120	29	14	19

Figure S45. Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.046

Table S46. Gene #9: 'amp_8q24.13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
AMP PEAK 9(8Q24.13) MUTATED	47	23	14	11
AMP PEAK 9(8Q24.13) WILD-TYPE	101	118	98	87

Figure S46. Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S47. Gene #11: 'amp_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
AMP PEAK 11(10P15.3) MUTATED	59	6	5
AMP PEAK 11(10P15.3) WILD-TYPE	109	112	221

Figure S47. Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10p15.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S48. Gene #11: 'amp_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
AMP PEAK 11(10P15.3) MUTATED	64	2	4	0
AMP PEAK 11(10P15.3) WILD-TYPE	159	70	53	155

Figure S48. Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_10p15.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S49. Gene #11: 'amp_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
AMP PEAK 11(10P15.3) MUTATED	41	13	0	15	1
AMP PEAK 11(10P15.3) WILD-TYPE	94	99	108	112	27

Figure S49. Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S50. Gene #11: 'amp_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
AMP PEAK 11(10P15.3) MUTATED	40	13	0	17
AMP PEAK 11(10P15.3) WILD-TYPE	95	100	125	120

Figure S50. Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10p15.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S51. Gene #11: 'amp_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
AMP PEAK 11(10P15.3) MUTATED	27	8	1	15	6	7	3
AMP PEAK 11(10P15.3) WILD-TYPE	86	86	68	131	28	11	22

Figure S51. Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_10p15.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S52. Gene #11: 'amp_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
AMP PEAK 11(10P15.3) MUTATED	39	11	10	7
AMP PEAK 11(10P15.3) WILD-TYPE	109	130	102	91

Figure S52. Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S53. Gene #13: 'amp_12p13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
AMP PEAK 13(12P13.32) MUTATED	52	15	4
AMP PEAK 13(12P13.32) WILD-TYPE	116	103	222

Figure S53. Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p13.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S54. Gene #13: 'amp_12p13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
AMP PEAK 13(12P13.32) MUTATED	54	9	3	5
AMP PEAK 13(12P13.32) WILD-TYPE	169	63	54	150

Figure S54. Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12p13.32' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.066

Table S55. Gene #13: 'amp_12p13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
AMP PEAK 13(12P13.32) MUTATED	30	21	4	12	4
AMP PEAK 13(12P13.32) WILD-TYPE	105	91	104	115	24

Figure S55. Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12p13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S56. Gene #13: 'amp_12p13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
AMP PEAK 13(12P13.32) MUTATED	32	20	5	14
AMP PEAK 13(12P13.32) WILD-TYPE	103	93	120	123

Figure S56. Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12p13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.19

Table S57. Gene #13: 'amp_12p13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
AMP PEAK 13(12P13.32) MUTATED	25	12	6	10	7	7	3
AMP PEAK 13(12P13.32) WILD-TYPE	88	82	63	136	27	11	22

Figure S57. Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12p13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.059

Table S58. Gene #13: 'amp_12p13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
AMP PEAK 13(12P13.32) MUTATED	33	15	5	17
AMP PEAK 13(12P13.32) WILD-TYPE	115	126	107	81

Figure S58. Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S59. Gene #14: 'amp_12q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
AMP PEAK 14(12Q14.1) MUTATED	13	22	2
AMP PEAK 14(12Q14.1) WILD-TYPE	155	96	224

Figure S59. Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q14.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S60. Gene #14: 'amp_12q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
AMP PEAK 14(12Q14.1) MUTATED	14	18	1	4
AMP PEAK 14(12Q14.1) WILD-TYPE	209	54	56	151

Figure S60. Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S61. Gene #14: 'amp_12q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
AMP PEAK 14(12Q14.1) MUTATED	3	27	3	3	1
AMP PEAK 14(12Q14.1) WILD-TYPE	132	85	105	124	27

Figure S61. Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S62. Gene #14: 'amp_12q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
AMP PEAK 14(12Q14.1) MUTATED	3	26	4	4
AMP PEAK 14(12Q14.1) WILD-TYPE	132	87	121	133

Figure S62. Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S63. Gene #14: 'amp_12q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	107	137	100
AMP PEAK 14(12Q14.1) MUTATED	8	4	2	23
AMP PEAK 14(12Q14.1) WILD-TYPE	147	103	135	77

Figure S63. Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S64. Gene #14: 'amp_12q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
AMP PEAK 14(12Q14.1) MUTATED	3	20	1	2	5	4	2
AMP PEAK 14(12Q14.1) WILD-TYPE	110	74	68	144	29	14	23

Figure S64. Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S65. Gene #14: 'amp_12q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
AMP PEAK 14(12Q14.1) MUTATED	8	5	3	21
AMP PEAK 14(12Q14.1) WILD-TYPE	140	136	109	77

Figure S65. Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_15q26.3' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.017

Table S66. Gene #16: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
AMP PEAK 16(15Q26.3) MUTATED	13	6	0
AMP PEAK 16(15Q26.3) WILD-TYPE	155	112	226

Figure S66. Get High-res Image Gene #16: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_15q26.3' versus 'METHLYATION_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.18

Table S67. Gene #16: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
AMP PEAK 16(15Q26.3) MUTATED	15	4	0	0
AMP PEAK 16(15Q26.3) WILD-TYPE	208	68	57	155

Figure S67. Get High-res Image Gene #16: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S68. Gene #18: 'amp_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
AMP PEAK 18(19P13.3) MUTATED	11	39	78
AMP PEAK 18(19P13.3) WILD-TYPE	157	79	148

Figure S68. Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S69. Gene #18: 'amp_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
AMP PEAK 18(19P13.3) MUTATED	18	26	5	75
AMP PEAK 18(19P13.3) WILD-TYPE	205	46	52	80

Figure S69. Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S70. Gene #18: 'amp_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
AMP PEAK 18(19P13.3) MUTATED	10	30	56	30	2
AMP PEAK 18(19P13.3) WILD-TYPE	125	82	52	97	26

Figure S70. Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S71. Gene #18: 'amp_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
AMP PEAK 18(19P13.3) MUTATED	8	31	58	31
AMP PEAK 18(19P13.3) WILD-TYPE	127	82	67	106

Figure S71. Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S72. Gene #18: 'amp_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
AMP PEAK 18(19P13.3) MUTATED	8	27	36	37	10	3	5
AMP PEAK 18(19P13.3) WILD-TYPE	105	67	33	109	24	15	20

Figure S72. Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.026

Table S73. Gene #18: 'amp_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
AMP PEAK 18(19P13.3) MUTATED	19	51	27	29
AMP PEAK 18(19P13.3) WILD-TYPE	129	90	85	69

Figure S73. Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S74. Gene #19: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
AMP PEAK 19(19P13.2) MUTATED	7	42	73
AMP PEAK 19(19P13.2) WILD-TYPE	161	76	153

Figure S74. Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S75. Gene #19: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
AMP PEAK 19(19P13.2) MUTATED	12	29	5	72
AMP PEAK 19(19P13.2) WILD-TYPE	211	43	52	83

Figure S75. Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S76. Gene #19: 'amp_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
AMP PEAK 19(19P13.2) MUTATED	6	34	54	25	3
AMP PEAK 19(19P13.2) WILD-TYPE	129	78	54	102	25

Figure S76. Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S77. Gene #19: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
AMP PEAK 19(19P13.2) MUTATED	6	33	57	26
AMP PEAK 19(19P13.2) WILD-TYPE	129	80	68	111

Figure S77. Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S78. Gene #19: 'amp_19p13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
AMP PEAK 19(19P13.2) MUTATED	7	31	36	32	8	2	4
AMP PEAK 19(19P13.2) WILD-TYPE	106	63	33	114	26	16	21

Figure S78. Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S79. Gene #19: 'amp_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
AMP PEAK 19(19P13.2) MUTATED	17	48	24	31
AMP PEAK 19(19P13.2) WILD-TYPE	131	93	88	67

Figure S79. Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xp11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S80. Gene #20: 'amp_xp11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
AMP PEAK 20(XP11.22) MUTATED	37	5	5
AMP PEAK 20(XP11.22) WILD-TYPE	131	113	221

Figure S80. Get High-res Image Gene #20: 'amp_xp11.22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xp11.22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S81. Gene #20: 'amp_xp11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
AMP PEAK 20(XP11.22) MUTATED	40	4	2	1
AMP PEAK 20(XP11.22) WILD-TYPE	183	68	55	154

Figure S81. Get High-res Image Gene #20: 'amp_xp11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xp11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.03

Table S82. Gene #20: 'amp_xp11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
AMP PEAK 20(XP11.22) MUTATED	22	11	1	13
AMP PEAK 20(XP11.22) WILD-TYPE	113	102	124	124

Figure S82. Get High-res Image Gene #20: 'amp_xp11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.11

Table S83. Gene #20: 'amp_xp11.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
AMP PEAK 20(XP11.22) MUTATED	24	3	10	8
AMP PEAK 20(XP11.22) WILD-TYPE	124	138	102	90

Figure S83. Get High-res Image Gene #20: 'amp_xp11.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xp11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S84. Gene #21: 'amp_xp11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
AMP PEAK 21(XP11.22) MUTATED	52	6	4
AMP PEAK 21(XP11.22) WILD-TYPE	116	112	222

Figure S84. Get High-res Image Gene #21: 'amp_xp11.22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xp11.22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S85. Gene #21: 'amp_xp11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
AMP PEAK 21(XP11.22) MUTATED	53	3	5	1
AMP PEAK 21(XP11.22) WILD-TYPE	170	69	52	154

Figure S85. Get High-res Image Gene #21: 'amp_xp11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xp11.22' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S86. Gene #21: 'amp_xp11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
AMP PEAK 21(XP11.22) MUTATED	27	17	1	14	3
AMP PEAK 21(XP11.22) WILD-TYPE	108	95	107	113	25

Figure S86. Get High-res Image Gene #21: 'amp_xp11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xp11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S87. Gene #21: 'amp_xp11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
AMP PEAK 21(XP11.22) MUTATED	30	16	1	15
AMP PEAK 21(XP11.22) WILD-TYPE	105	97	124	122

Figure S87. Get High-res Image Gene #21: 'amp_xp11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.22' versus 'MIRSEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.14

Table S88. Gene #21: 'amp_xp11.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	136	104	187	72
AMP PEAK 21(XP11.22) MUTATED	20	17	21	0
AMP PEAK 21(XP11.22) WILD-TYPE	116	87	166	72

Figure S88. Get High-res Image Gene #21: 'amp_xp11.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_xp11.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.055

Table S89. Gene #21: 'amp_xp11.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
AMP PEAK 21(XP11.22) MUTATED	24	15	0	13	3	1	2
AMP PEAK 21(XP11.22) WILD-TYPE	89	79	69	133	31	17	23

Figure S89. Get High-res Image Gene #21: 'amp_xp11.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_xp11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S90. Gene #21: 'amp_xp11.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
AMP PEAK 21(XP11.22) MUTATED	31	4	12	11
AMP PEAK 21(XP11.22) WILD-TYPE	117	137	100	87

Figure S90. Get High-res Image Gene #21: 'amp_xp11.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.32' versus 'MRNA_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.22

Table S91. Gene #22: 'del_1p36.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	10	8
DEL PEAK 1(1P36.32) MUTATED	0	8	2
DEL PEAK 1(1P36.32) WILD-TYPE	9	2	6

Figure S91. Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.32' versus 'MRNA_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.074

Table S92. Gene #22: 'del_1p36.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
DEL PEAK 1(1P36.32) MUTATED	0	1	7	2
DEL PEAK 1(1P36.32) WILD-TYPE	7	6	0	4

Figure S92. Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S93. Gene #22: 'del_1p36.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
DEL PEAK 1(1P36.32) MUTATED	11	32	163
DEL PEAK 1(1P36.32) WILD-TYPE	157	86	63

Figure S93. Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S94. Gene #22: 'del_1p36.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
DEL PEAK 1(1P36.32) MUTATED	11	16	20	155
DEL PEAK 1(1P36.32) WILD-TYPE	212	56	37	0

Figure S94. Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S95. Gene #22: 'del_1p36.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
DEL PEAK 1(1P36.32) MUTATED	5	22	107	58	14
DEL PEAK 1(1P36.32) WILD-TYPE	130	90	1	69	14

Figure S95. Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S96. Gene #22: 'del_1p36.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
DEL PEAK 1(1P36.32) MUTATED	7	21	123	55
DEL PEAK 1(1P36.32) WILD-TYPE	128	92	2	82

Figure S96. Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S97. Gene #22: 'del_1p36.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	136	104	187	72
DEL PEAK 1(1P36.32) MUTATED	35	13	97	59
DEL PEAK 1(1P36.32) WILD-TYPE	101	91	90	13

Figure S97. Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S98. Gene #22: 'del_1p36.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	107	137	100
DEL PEAK 1(1P36.32) MUTATED	34	83	66	21
DEL PEAK 1(1P36.32) WILD-TYPE	121	24	71	79

Figure S98. Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S99. Gene #22: 'del_1p36.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
DEL PEAK 1(1P36.32) MUTATED	4	30	65	76	14	1	14
DEL PEAK 1(1P36.32) WILD-TYPE	109	64	4	70	20	17	11

Figure S99. Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S100. Gene #22: 'del_1p36.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
DEL PEAK 1(1P36.32) MUTATED	22	102	58	22
DEL PEAK 1(1P36.32) WILD-TYPE	126	39	54	76

Figure S100. Get High-res Image Gene #22: 'del_1p36.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p32.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.078

Table S101. Gene #23: 'del_1p32.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
DEL PEAK 2(1P32.3) MUTATED	0	1	7	2
DEL PEAK 2(1P32.3) WILD-TYPE	7	6	0	4

Figure S101. Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p32.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S102. Gene #23: 'del_1p32.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
DEL PEAK 2(1P32.3) MUTATED	7	27	162
DEL PEAK 2(1P32.3) WILD-TYPE	161	91	64

Figure S102. Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p32.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S103. Gene #23: 'del_1p32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
DEL PEAK 2(1P32.3) MUTATED	5	13	20	155
DEL PEAK 2(1P32.3) WILD-TYPE	218	59	37	0

Figure S103. Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p32.3' versus 'RPPA_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.22

Table S104. Gene #23: 'del_1p32.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
DEL PEAK 2(1P32.3) MUTATED	8	16	28	35
DEL PEAK 2(1P32.3) WILD-TYPE	44	46	40	39

Figure S104. Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p32.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S105. Gene #23: 'del_1p32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
DEL PEAK 2(1P32.3) MUTATED	4	17	107	55	13
DEL PEAK 2(1P32.3) WILD-TYPE	131	95	1	72	15

Figure S105. Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p32.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S106. Gene #23: 'del_1p32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
DEL PEAK 2(1P32.3) MUTATED	5	17	123	51
DEL PEAK 2(1P32.3) WILD-TYPE	130	96	2	86

Figure S106. Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p32.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S107. Gene #23: 'del_1p32.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	136	104	187	72
DEL PEAK 2(1P32.3) MUTATED	34	10	92	58
DEL PEAK 2(1P32.3) WILD-TYPE	102	94	95	14

Figure S107. Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p32.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S108. Gene #23: 'del_1p32.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	107	137	100
DEL PEAK 2(1P32.3) MUTATED	33	82	62	17
DEL PEAK 2(1P32.3) WILD-TYPE	122	25	75	83

Figure S108. Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p32.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S109. Gene #23: 'del_1p32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
DEL PEAK 2(1P32.3) MUTATED	5	24	64	72	13	1	15
DEL PEAK 2(1P32.3) WILD-TYPE	108	70	5	74	21	17	10

Figure S109. Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p32.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S110. Gene #23: 'del_1p32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
DEL PEAK 2(1P32.3) MUTATED	20	100	56	18
DEL PEAK 2(1P32.3) WILD-TYPE	128	41	56	80

Figure S110. Get High-res Image Gene #23: 'del_1p32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S111. Gene #25: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
DEL PEAK 4(2Q37.3) MUTATED	51	18	8
DEL PEAK 4(2Q37.3) WILD-TYPE	117	100	218

Figure S111. Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S112. Gene #25: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
DEL PEAK 4(2Q37.3) MUTATED	64	4	3	6
DEL PEAK 4(2Q37.3) WILD-TYPE	159	68	54	149

Figure S112. Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.078

Table S113. Gene #25: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
DEL PEAK 4(2Q37.3) MUTATED	33	22	6	13	3
DEL PEAK 4(2Q37.3) WILD-TYPE	102	90	102	114	25

Figure S113. Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.051

Table S114. Gene #25: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
DEL PEAK 4(2Q37.3) MUTATED	31	23	6	17
DEL PEAK 4(2Q37.3) WILD-TYPE	104	90	119	120

Figure S114. Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S115. Gene #25: 'del_2q37.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
DEL PEAK 4(2Q37.3) MUTATED	41	14	10	10
DEL PEAK 4(2Q37.3) WILD-TYPE	107	127	102	88

Figure S115. Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p21.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S116. Gene #26: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
DEL PEAK 5(3P21.31) MUTATED	32	11	5
DEL PEAK 5(3P21.31) WILD-TYPE	136	107	221

Figure S116. Get High-res Image Gene #26: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q29' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S117. Gene #27: 'del_3q29' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
DEL PEAK 6(3Q29) MUTATED	34	9	4
DEL PEAK 6(3Q29) WILD-TYPE	134	109	222

Figure S117. Get High-res Image Gene #27: 'del_3q29' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q29' versus 'METHLYATION_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.17

Table S118. Gene #27: 'del_3q29' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
DEL PEAK 6(3Q29) MUTATED	32	7	4	4
DEL PEAK 6(3Q29) WILD-TYPE	191	65	53	151

Figure S118. Get High-res Image Gene #27: 'del_3q29' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q34.3' versus 'CN_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.22

Table S119. Gene #28: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
DEL PEAK 7(4Q34.3) MUTATED	62	20	55
DEL PEAK 7(4Q34.3) WILD-TYPE	106	98	171

Figure S119. Get High-res Image Gene #28: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S120. Gene #28: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
DEL PEAK 7(4Q34.3) MUTATED	77	5	5	50
DEL PEAK 7(4Q34.3) WILD-TYPE	146	67	52	105

Figure S120. Get High-res Image Gene #28: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S121. Gene #29: 'del_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
DEL PEAK 8(5P15.33) MUTATED	37	8	5
DEL PEAK 8(5P15.33) WILD-TYPE	131	110	221

Figure S121. Get High-res Image Gene #29: 'del_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_5p15.33' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S122. Gene #29: 'del_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
DEL PEAK 8(5P15.33) MUTATED	37	7	3	3
DEL PEAK 8(5P15.33) WILD-TYPE	186	65	54	152

Figure S122. Get High-res Image Gene #29: 'del_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S123. Gene #30: 'del_5q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
DEL PEAK 9(5Q34) MUTATED	53	4	7
DEL PEAK 9(5Q34) WILD-TYPE	115	114	219

Figure S123. Get High-res Image Gene #30: 'del_5q34' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q34' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S124. Gene #30: 'del_5q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
DEL PEAK 9(5Q34) MUTATED	52	5	4	3
DEL PEAK 9(5Q34) WILD-TYPE	171	67	53	152

Figure S124. Get High-res Image Gene #30: 'del_5q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q34' versus 'MRNASEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.098

Table S125. Gene #30: 'del_5q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
DEL PEAK 9(5Q34) MUTATED	19	24	3	12	5
DEL PEAK 9(5Q34) WILD-TYPE	116	88	105	115	23

Figure S125. Get High-res Image Gene #30: 'del_5q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.026

Table S126. Gene #30: 'del_5q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
DEL PEAK 9(5Q34) MUTATED	20	25	3	15
DEL PEAK 9(5Q34) WILD-TYPE	115	88	122	122

Figure S126. Get High-res Image Gene #30: 'del_5q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q34' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.013

Table S127. Gene #30: 'del_5q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	136	104	187	72
DEL PEAK 9(5Q34) MUTATED	14	28	18	2
DEL PEAK 9(5Q34) WILD-TYPE	122	76	169	70

Figure S127. Get High-res Image Gene #30: 'del_5q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q34' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.24

Table S128. Gene #30: 'del_5q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
DEL PEAK 9(5Q34) MUTATED	16	13	3	14	5	9	2
DEL PEAK 9(5Q34) WILD-TYPE	97	81	66	132	29	9	23

Figure S128. Get High-res Image Gene #30: 'del_5q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6p25.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S129. Gene #31: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
DEL PEAK 10(6P25.3) MUTATED	24	19	7
DEL PEAK 10(6P25.3) WILD-TYPE	144	99	219

Figure S129. Get High-res Image Gene #31: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q22.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S130. Gene #32: 'del_6q22.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
DEL PEAK 11(6Q22.31) MUTATED	38	28	12
DEL PEAK 11(6Q22.31) WILD-TYPE	130	90	214

Figure S130. Get High-res Image Gene #32: 'del_6q22.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q22.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S131. Gene #32: 'del_6q22.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
DEL PEAK 11(6Q22.31) MUTATED	49	13	9	7
DEL PEAK 11(6Q22.31) WILD-TYPE	174	59	48	148

Figure S131. Get High-res Image Gene #32: 'del_6q22.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q22.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.18

Table S132. Gene #32: 'del_6q22.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
DEL PEAK 11(6Q22.31) MUTATED	27	25	7	18
DEL PEAK 11(6Q22.31) WILD-TYPE	108	88	118	119

Figure S132. Get High-res Image Gene #32: 'del_6q22.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q22.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00048 (Fisher's exact test), Q value = 0.19

Table S133. Gene #32: 'del_6q22.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
DEL PEAK 11(6Q22.31) MUTATED	31	10	12	22
DEL PEAK 11(6Q22.31) WILD-TYPE	117	131	100	76

Figure S133. Get High-res Image Gene #32: 'del_6q22.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S134. Gene #33: 'del_6q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
DEL PEAK 12(6Q24.3) MUTATED	41	28	13
DEL PEAK 12(6Q24.3) WILD-TYPE	127	90	213

Figure S134. Get High-res Image Gene #33: 'del_6q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q24.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S135. Gene #33: 'del_6q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
DEL PEAK 12(6Q24.3) MUTATED	53	13	9	7
DEL PEAK 12(6Q24.3) WILD-TYPE	170	59	48	148

Figure S135. Get High-res Image Gene #33: 'del_6q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.055

Table S136. Gene #33: 'del_6q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
DEL PEAK 12(6Q24.3) MUTATED	31	25	7	18
DEL PEAK 12(6Q24.3) WILD-TYPE	104	88	118	119

Figure S136. Get High-res Image Gene #33: 'del_6q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q24.3' versus 'MIRSEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.082

Table S137. Gene #33: 'del_6q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	136	104	187	72
DEL PEAK 12(6Q24.3) MUTATED	34	21	20	4
DEL PEAK 12(6Q24.3) WILD-TYPE	102	83	167	68

Figure S137. Get High-res Image Gene #33: 'del_6q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.078

Table S138. Gene #33: 'del_6q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
DEL PEAK 12(6Q24.3) MUTATED	26	22	3	16	5	6	1
DEL PEAK 12(6Q24.3) WILD-TYPE	87	72	66	130	29	12	24

Figure S138. Get High-res Image Gene #33: 'del_6q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.12

Table S139. Gene #33: 'del_6q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
DEL PEAK 12(6Q24.3) MUTATED	35	11	12	21
DEL PEAK 12(6Q24.3) WILD-TYPE	113	130	100	77

Figure S139. Get High-res Image Gene #33: 'del_6q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S140. Gene #35: 'del_8q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
DEL PEAK 14(8Q24.3) MUTATED	14	13	1
DEL PEAK 14(8Q24.3) WILD-TYPE	154	105	225

Figure S140. Get High-res Image Gene #35: 'del_8q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_8q24.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S141. Gene #35: 'del_8q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
DEL PEAK 14(8Q24.3) MUTATED	16	11	1	0
DEL PEAK 14(8Q24.3) WILD-TYPE	207	61	56	155

Figure S141. Get High-res Image Gene #35: 'del_8q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.2

Table S142. Gene #35: 'del_8q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
DEL PEAK 14(8Q24.3) MUTATED	10	12	0	6
DEL PEAK 14(8Q24.3) WILD-TYPE	125	101	125	131

Figure S142. Get High-res Image Gene #35: 'del_8q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S143. Gene #36: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
DEL PEAK 15(9P23) MUTATED	65	53	32
DEL PEAK 15(9P23) WILD-TYPE	103	65	194

Figure S143. Get High-res Image Gene #36: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S144. Gene #36: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
DEL PEAK 15(9P23) MUTATED	80	32	9	27
DEL PEAK 15(9P23) WILD-TYPE	143	40	48	128

Figure S144. Get High-res Image Gene #36: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S145. Gene #37: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
DEL PEAK 16(9P21.3) MUTATED	70	74	32
DEL PEAK 16(9P21.3) WILD-TYPE	98	44	194

Figure S145. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S146. Gene #37: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
DEL PEAK 16(9P21.3) MUTATED	83	54	11	26
DEL PEAK 16(9P21.3) WILD-TYPE	140	18	46	129

Figure S146. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.017

Table S147. Gene #37: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
DEL PEAK 16(9P21.3) MUTATED	12	38	26	18
DEL PEAK 16(9P21.3) WILD-TYPE	40	24	42	56

Figure S147. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S148. Gene #37: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	131	58
DEL PEAK 16(9P21.3) MUTATED	11	65	18
DEL PEAK 16(9P21.3) WILD-TYPE	56	66	40

Figure S148. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S149. Gene #37: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
DEL PEAK 16(9P21.3) MUTATED	40	66	19	44	7
DEL PEAK 16(9P21.3) WILD-TYPE	95	46	89	83	21

Figure S149. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S150. Gene #37: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
DEL PEAK 16(9P21.3) MUTATED	44	65	23	44
DEL PEAK 16(9P21.3) WILD-TYPE	91	48	102	93

Figure S150. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S151. Gene #37: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	107	137	100
DEL PEAK 16(9P21.3) MUTATED	48	20	42	60
DEL PEAK 16(9P21.3) WILD-TYPE	107	87	95	40

Figure S151. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.22

Table S152. Gene #37: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
DEL PEAK 16(9P21.3) MUTATED	33	50	14	48	11	8	6
DEL PEAK 16(9P21.3) WILD-TYPE	80	44	55	98	23	10	19

Figure S152. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S153. Gene #37: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
DEL PEAK 16(9P21.3) MUTATED	51	28	32	59
DEL PEAK 16(9P21.3) WILD-TYPE	97	113	80	39

Figure S153. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S154. Gene #38: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
DEL PEAK 17(10Q26.3) MUTATED	56	83	12
DEL PEAK 17(10Q26.3) WILD-TYPE	112	35	214

Figure S154. Get High-res Image Gene #38: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q26.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S155. Gene #38: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
DEL PEAK 17(10Q26.3) MUTATED	65	65	12	8
DEL PEAK 17(10Q26.3) WILD-TYPE	158	7	45	147

Figure S155. Get High-res Image Gene #38: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q26.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S156. Gene #38: 'del_10q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
DEL PEAK 17(10Q26.3) MUTATED	13	35	14	11
DEL PEAK 17(10Q26.3) WILD-TYPE	39	27	54	63

Figure S156. Get High-res Image Gene #38: 'del_10q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_10q26.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.11

Table S157. Gene #38: 'del_10q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	131	58
DEL PEAK 17(10Q26.3) MUTATED	11	52	10
DEL PEAK 17(10Q26.3) WILD-TYPE	56	79	48

Figure S157. Get High-res Image Gene #38: 'del_10q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S158. Gene #38: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
DEL PEAK 17(10Q26.3) MUTATED	32	81	4	26	7
DEL PEAK 17(10Q26.3) WILD-TYPE	103	31	104	101	21

Figure S158. Get High-res Image Gene #38: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S159. Gene #38: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
DEL PEAK 17(10Q26.3) MUTATED	34	81	8	27
DEL PEAK 17(10Q26.3) WILD-TYPE	101	32	117	110

Figure S159. Get High-res Image Gene #38: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S160. Gene #38: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	136	104	187	72
DEL PEAK 17(10Q26.3) MUTATED	54	43	40	11
DEL PEAK 17(10Q26.3) WILD-TYPE	82	61	147	61

Figure S160. Get High-res Image Gene #38: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S161. Gene #38: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	107	137	100
DEL PEAK 17(10Q26.3) MUTATED	40	14	22	72
DEL PEAK 17(10Q26.3) WILD-TYPE	115	93	115	28

Figure S161. Get High-res Image Gene #38: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S162. Gene #38: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
DEL PEAK 17(10Q26.3) MUTATED	25	59	6	27	17	9	5
DEL PEAK 17(10Q26.3) WILD-TYPE	88	35	63	119	17	9	20

Figure S162. Get High-res Image Gene #38: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S163. Gene #38: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
DEL PEAK 17(10Q26.3) MUTATED	42	15	16	75
DEL PEAK 17(10Q26.3) WILD-TYPE	106	126	96	23

Figure S163. Get High-res Image Gene #38: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'MRNA_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.2

Table S164. Gene #39: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
DEL PEAK 18(11P15.5) MUTATED	1	6	0	0
DEL PEAK 18(11P15.5) WILD-TYPE	6	1	7	6

Figure S164. Get High-res Image Gene #39: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S165. Gene #39: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
DEL PEAK 18(11P15.5) MUTATED	76	17	10
DEL PEAK 18(11P15.5) WILD-TYPE	92	101	216

Figure S165. Get High-res Image Gene #39: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S166. Gene #39: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
DEL PEAK 18(11P15.5) MUTATED	85	12	6	0
DEL PEAK 18(11P15.5) WILD-TYPE	138	60	51	155

Figure S166. Get High-res Image Gene #39: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S167. Gene #39: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
DEL PEAK 18(11P15.5) MUTATED	39	35	0	22	6
DEL PEAK 18(11P15.5) WILD-TYPE	96	77	108	105	22

Figure S167. Get High-res Image Gene #39: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S168. Gene #39: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
DEL PEAK 18(11P15.5) MUTATED	38	38	0	26
DEL PEAK 18(11P15.5) WILD-TYPE	97	75	125	111

Figure S168. Get High-res Image Gene #39: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.2

Table S169. Gene #39: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	107	137	100
DEL PEAK 18(11P15.5) MUTATED	37	8	26	28
DEL PEAK 18(11P15.5) WILD-TYPE	118	99	111	72

Figure S169. Get High-res Image Gene #39: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S170. Gene #41: 'del_12q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
DEL PEAK 20(12Q12) MUTATED	51	6	11
DEL PEAK 20(12Q12) WILD-TYPE	117	112	215

Figure S170. Get High-res Image Gene #41: 'del_12q12' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S171. Gene #41: 'del_12q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
DEL PEAK 20(12Q12) MUTATED	52	3	5	8
DEL PEAK 20(12Q12) WILD-TYPE	171	69	52	147

Figure S171. Get High-res Image Gene #41: 'del_12q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.017

Table S172. Gene #42: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
DEL PEAK 21(13Q14.2) MUTATED	2	7	0	0
DEL PEAK 21(13Q14.2) WILD-TYPE	5	0	7	6

Figure S172. Get High-res Image Gene #42: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S173. Gene #42: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
DEL PEAK 21(13Q14.2) MUTATED	80	32	29
DEL PEAK 21(13Q14.2) WILD-TYPE	88	86	197

Figure S173. Get High-res Image Gene #42: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.23

Table S174. Gene #42: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
DEL PEAK 21(13Q14.2) MUTATED	79	23	12	27
DEL PEAK 21(13Q14.2) WILD-TYPE	144	49	45	128

Figure S174. Get High-res Image Gene #42: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.098

Table S175. Gene #42: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
DEL PEAK 21(13Q14.2) MUTATED	40	47	16	31	7
DEL PEAK 21(13Q14.2) WILD-TYPE	95	65	92	96	21

Figure S175. Get High-res Image Gene #42: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.026

Table S176. Gene #42: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
DEL PEAK 21(13Q14.2) MUTATED	43	47	19	32
DEL PEAK 21(13Q14.2) WILD-TYPE	92	66	106	105

Figure S176. Get High-res Image Gene #42: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.026

Table S177. Gene #43: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
DEL PEAK 22(13Q14.2) MUTATED	2	7	0	0
DEL PEAK 22(13Q14.2) WILD-TYPE	5	0	7	6

Figure S177. Get High-res Image Gene #43: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S178. Gene #43: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
DEL PEAK 22(13Q14.2) MUTATED	81	33	29
DEL PEAK 22(13Q14.2) WILD-TYPE	87	85	197

Figure S178. Get High-res Image Gene #43: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.16

Table S179. Gene #43: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
DEL PEAK 22(13Q14.2) MUTATED	80	24	12	27
DEL PEAK 22(13Q14.2) WILD-TYPE	143	48	45	128

Figure S179. Get High-res Image Gene #43: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.062

Table S180. Gene #43: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
DEL PEAK 22(13Q14.2) MUTATED	41	48	16	31	7
DEL PEAK 22(13Q14.2) WILD-TYPE	94	64	92	96	21

Figure S180. Get High-res Image Gene #43: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.013

Table S181. Gene #43: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
DEL PEAK 22(13Q14.2) MUTATED	44	48	19	32
DEL PEAK 22(13Q14.2) WILD-TYPE	91	65	106	105

Figure S181. Get High-res Image Gene #43: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S182. Gene #44: 'del_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
DEL PEAK 23(13Q34) MUTATED	57	27	25
DEL PEAK 23(13Q34) WILD-TYPE	111	91	201

Figure S182. Get High-res Image Gene #44: 'del_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q24.3' versus 'MRNASEQ_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.21

Table S183. Gene #45: 'del_14q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
DEL PEAK 24(14Q24.3) MUTATED	25	44	23	21	7
DEL PEAK 24(14Q24.3) WILD-TYPE	110	68	85	106	21

Figure S183. Get High-res Image Gene #45: 'del_14q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.038

Table S184. Gene #45: 'del_14q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
DEL PEAK 24(14Q24.3) MUTATED	32	44	24	20
DEL PEAK 24(14Q24.3) WILD-TYPE	103	69	101	117

Figure S184. Get High-res Image Gene #45: 'del_14q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q24.3' versus 'MIRSEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.059

Table S185. Gene #45: 'del_14q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	136	104	187	72
DEL PEAK 24(14Q24.3) MUTATED	51	20	30	15
DEL PEAK 24(14Q24.3) WILD-TYPE	85	84	157	57

Figure S185. Get High-res Image Gene #45: 'del_14q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q21.3' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.017

Table S186. Gene #46: 'del_15q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
DEL PEAK 25(15Q21.3) MUTATED	6	23	23	10	4
DEL PEAK 25(15Q21.3) WILD-TYPE	129	89	85	117	24

Figure S186. Get High-res Image Gene #46: 'del_15q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19q13.42' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S187. Gene #48: 'del_19q13.42' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
DEL PEAK 27(19Q13.42) MUTATED	58	36	184
DEL PEAK 27(19Q13.42) WILD-TYPE	110	82	42

Figure S187. Get High-res Image Gene #48: 'del_19q13.42' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.42' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S188. Gene #48: 'del_19q13.42' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
DEL PEAK 27(19Q13.42) MUTATED	88	11	21	155
DEL PEAK 27(19Q13.42) WILD-TYPE	135	61	36	0

Figure S188. Get High-res Image Gene #48: 'del_19q13.42' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.42' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S189. Gene #48: 'del_19q13.42' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
DEL PEAK 27(19Q13.42) MUTATED	49	35	108	73	12
DEL PEAK 27(19Q13.42) WILD-TYPE	86	77	0	54	16

Figure S189. Get High-res Image Gene #48: 'del_19q13.42' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19q13.42' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S190. Gene #48: 'del_19q13.42' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
DEL PEAK 27(19Q13.42) MUTATED	46	33	124	74
DEL PEAK 27(19Q13.42) WILD-TYPE	89	80	1	63

Figure S190. Get High-res Image Gene #48: 'del_19q13.42' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.42' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S191. Gene #48: 'del_19q13.42' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	136	104	187	72
DEL PEAK 27(19Q13.42) MUTATED	56	38	112	65
DEL PEAK 27(19Q13.42) WILD-TYPE	80	66	75	7

Figure S191. Get High-res Image Gene #48: 'del_19q13.42' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19q13.42' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S192. Gene #48: 'del_19q13.42' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	107	137	100
DEL PEAK 27(19Q13.42) MUTATED	78	93	78	22
DEL PEAK 27(19Q13.42) WILD-TYPE	77	14	59	78

Figure S192. Get High-res Image Gene #48: 'del_19q13.42' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.42' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S193. Gene #48: 'del_19q13.42' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	113	94	69	146	34	18	25
DEL PEAK 27(19Q13.42) MUTATED	46	32	67	87	19	6	14
DEL PEAK 27(19Q13.42) WILD-TYPE	67	62	2	59	15	12	11

Figure S193. Get High-res Image Gene #48: 'del_19q13.42' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19q13.42' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S194. Gene #48: 'del_19q13.42' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
DEL PEAK 27(19Q13.42) MUTATED	73	110	71	17
DEL PEAK 27(19Q13.42) WILD-TYPE	75	31	41	81

Figure S194. Get High-res Image Gene #48: 'del_19q13.42' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S195. Gene #49: 'del_22q13.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	168	118	226
DEL PEAK 28(22Q13.31) MUTATED	39	34	4
DEL PEAK 28(22Q13.31) WILD-TYPE	129	84	222

Figure S195. Get High-res Image Gene #49: 'del_22q13.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S196. Gene #49: 'del_22q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	223	72	57	155
DEL PEAK 28(22Q13.31) MUTATED	39	25	8	4
DEL PEAK 28(22Q13.31) WILD-TYPE	184	47	49	151

Figure S196. Get High-res Image Gene #49: 'del_22q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q13.31' versus 'RPPA_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.078

Table S197. Gene #49: 'del_22q13.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
DEL PEAK 28(22Q13.31) MUTATED	4	21	8	6
DEL PEAK 28(22Q13.31) WILD-TYPE	48	41	60	68

Figure S197. Get High-res Image Gene #49: 'del_22q13.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_22q13.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S198. Gene #49: 'del_22q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	135	112	108	127	28
DEL PEAK 28(22Q13.31) MUTATED	15	40	2	14	5
DEL PEAK 28(22Q13.31) WILD-TYPE	120	72	106	113	23

Figure S198. Get High-res Image Gene #49: 'del_22q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S199. Gene #49: 'del_22q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	113	125	137
DEL PEAK 28(22Q13.31) MUTATED	17	39	4	16
DEL PEAK 28(22Q13.31) WILD-TYPE	118	74	121	121

Figure S199. Get High-res Image Gene #49: 'del_22q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.066

Table S200. Gene #49: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	155	107	137	100
DEL PEAK 28(22Q13.31) MUTATED	22	7	16	29
DEL PEAK 28(22Q13.31) WILD-TYPE	133	100	121	71

Figure S200. Get High-res Image Gene #49: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0089

Table S201. Gene #49: 'del_22q13.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	141	112	98
DEL PEAK 28(22Q13.31) MUTATED	23	9	11	31
DEL PEAK 28(22Q13.31) WILD-TYPE	125	132	101	67

Figure S201. Get High-res Image Gene #49: 'del_22q13.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = LGG-TP.transferedmergedcluster.txt
Number of patients = 512
Number of significantly focal cnvs = 50
Number of molecular subtypes = 12
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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