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

Thyroid Adenocarcinoma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1PN94MZ

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 98 focal events and 10 molecular subtypes across 501 patients, 156 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q31.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
amp_1q43 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_4q22.1 cnv correlated to 'CN_CNMF'.
amp_4q28.2 cnv correlated to 'CN_CNMF'.
amp_5p14.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_5q21.1 cnv correlated to 'CN_CNMF'.
amp_5q21.1 cnv correlated to 'CN_CNMF'.
amp_5q33.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_5q35.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_7q11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_7q21.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_7q31.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_7q34 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_12p11.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_12q21.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_12q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_13q14.2 cnv correlated to 'CN_CNMF'.
amp_14q12 cnv correlated to 'CN_CNMF'.
amp_14q32.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_18q12.1 cnv correlated to 'CN_CNMF'.
amp_19p13.3 cnv correlated to 'CN_CNMF'.
amp_20p13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_20q13.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_20q13.2 cnv correlated to 'CN_CNMF'.
amp_20q13.2 cnv correlated to 'CN_CNMF'.
amp_xp22.12 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_xp11.4 cnv correlated to 'CN_CNMF'.
amp_xp11.22 cnv correlated to 'CN_CNMF'.
amp_xp11.22 cnv correlated to 'CN_CNMF'.
amp_xp11.21 cnv correlated to 'CN_CNMF'.
amp_xq21.2 cnv correlated to 'CN_CNMF'.
amp_xq23 cnv correlated to 'CN_CNMF'.
amp_xq24 cnv correlated to 'CN_CNMF'.
amp_xq24 cnv correlated to 'CN_CNMF'.
amp_xq28 cnv correlated to 'CN_CNMF'.
del_2p23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_2q37.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q22.31 cnv correlated to 'CN_CNMF'.
del_8p23.2 cnv correlated to 'CN_CNMF'.
del_8p22 cnv correlated to 'CN_CNMF'.
del_8p12 cnv correlated to 'CN_CNMF'.
del_8q24.22 cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
del_9p21.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9q22.33 cnv correlated to 'CN_CNMF'.
del_10p12.31 cnv correlated to 'CN_CNMF'.
del_10q23.31 cnv correlated to 'CN_CNMF'.
del_11p15.1 cnv correlated to 'CN_CNMF'.
del_15q25.3 cnv correlated to 'MIRSEQ_CHIERARCHICAL'.
del_19p13.2 cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_21q21.1 cnv correlated to 'CN_CNMF'.
del_22q12.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_22q13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_22q13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_22q13.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 98 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 156 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
del 22q13 1	89 (18%)	412	1e-05 (0.0093)	1e-05 (0.0093)	0.118 (1.00)	0.504 (1.00)	1e-05 (0.0093)	1e-05 (0.0093)	0.00031 (0.241)	1e-05 (0.0093)	0.00022 (0.174)	0.00019 (0.151)
del 22q13 2	89 (18%)	412	1e-05 (0.0093)	1e-05 (0.0093)	0.118 (1.00)	0.503 (1.00)	1e-05 (0.0093)	1e-05 (0.0093)	0.00029 (0.226)	3e-05 (0.0254)	0.00013 (0.105)	0.0003 (0.234)
del 22q13 32	90 (18%)	411	1e-05 (0.0093)	1e-05 (0.0093)	0.118 (1.00)	0.502 (1.00)	1e-05 (0.0093)	1e-05 (0.0093)	0.00016 (0.129)	4e-05 (0.0335)	0.0002 (0.159)	0.00019 (0.151)
del 2p23 1	12 (2%)	489	1e-05 (0.0093)	1e-05 (0.0093)	0.773 (1.00)	0.09 (1.00)	1e-05 (0.0093)	1e-05 (0.0093)	1e-05 (0.0093)	1e-05 (0.0093)	0.254 (1.00)	0.00017 (0.136)
del 2q37 3	13 (3%)	488	1e-05 (0.0093)	1e-05 (0.0093)	0.634 (1.00)	0.0964 (1.00)	4e-05 (0.0335)	4e-05 (0.0335)	1e-05 (0.0093)	1e-05 (0.0093)	0.084 (1.00)	0.00031 (0.241)
amp 5q33 1	21 (4%)	480	1e-05 (0.0093)	9e-05 (0.0734)	1 (1.00)	0.0644 (1.00)	0.00014 (0.113)	7e-05 (0.0577)	0.0003 (0.234)	2e-05 (0.0172)	0.69 (1.00)	0.0029 (1.00)
amp 7q31 1	22 (4%)	479	1e-05 (0.0093)	1e-05 (0.0093)	0.556 (1.00)	0.00995 (1.00)	0.0001 (0.0814)	2e-05 (0.0172)	7e-05 (0.0577)	1e-05 (0.0093)	0.735 (1.00)	0.00036 (0.278)
amp 12p11 1	16 (3%)	485	1e-05 (0.0093)	2e-05 (0.0172)	0.659 (1.00)	0.282 (1.00)	4e-05 (0.0335)	1e-05 (0.0093)	8e-05 (0.0656)	1e-05 (0.0093)	0.605 (1.00)	0.00245 (1.00)
amp 12q21 31	17 (3%)	484	1e-05 (0.0093)	2e-05 (0.0172)	0.866 (1.00)	0.0383 (1.00)	1e-05 (0.0093)	1e-05 (0.0093)	3e-05 (0.0254)	1e-05 (0.0093)	0.148 (1.00)	0.00162 (1.00)
amp 12q23 1	17 (3%)	484	1e-05 (0.0093)	4e-05 (0.0335)	1 (1.00)	0.273 (1.00)	0.00011 (0.0893)	4e-05 (0.0335)	0.00016 (0.129)	1e-05 (0.0093)	0.25 (1.00)	0.00918 (1.00)
del 2q22 1	10 (2%)	491	1e-05 (0.0093)	1e-05 (0.0093)	0.774 (1.00)	0.0926 (1.00)	8e-05 (0.0656)	3e-05 (0.0254)	1e-05 (0.0093)	1e-05 (0.0093)	0.235 (1.00)	0.00038 (0.291)
del 22q12 3	90 (18%)	411	1e-05 (0.0093)	1e-05 (0.0093)	0.118 (1.00)	0.501 (1.00)	1e-05 (0.0093)	1e-05 (0.0093)	0.00053 (0.397)	3e-05 (0.0254)	0.00021 (0.166)	0.00039 (0.298)
amp 7q34	22 (4%)	479	1e-05 (0.0093)	7e-05 (0.0577)	0.39 (1.00)	0.00383 (1.00)	0.00043 (0.326)	0.00025 (0.196)	2e-05 (0.0172)	1e-05 (0.0093)	0.536 (1.00)	0.0108 (1.00)
amp 20p13	14 (3%)	487	1e-05 (0.0093)	3e-05 (0.0254)	0.633 (1.00)	0.0156 (1.00)	0.00032 (0.248)	6e-05 (0.0496)	0.00045 (0.341)	2e-05 (0.0172)	0.412 (1.00)	0.0221 (1.00)
amp 5q35 2	20 (4%)	481	1e-05 (0.0093)	0.00013 (0.105)	0.691 (1.00)	0.0345 (1.00)	0.00063 (0.466)	6e-05 (0.0496)	0.00087 (0.633)	3e-05 (0.0254)	0.865 (1.00)	0.00933 (1.00)
amp 7q11 21	20 (4%)	481	1e-05 (0.0093)	5e-05 (0.0415)	0.537 (1.00)	0.0158 (1.00)	0.00059 (0.438)	0.00027 (0.211)	0.00312 (1.00)	0.00023 (0.181)	0.429 (1.00)	0.0223 (1.00)
amp 14q32 31	13 (3%)	488	1e-05 (0.0093)	0.00013 (0.105)	1 (1.00)	0.16 (1.00)	0.00058 (0.432)	0.00017 (0.136)	0.00034 (0.263)	8e-05 (0.0656)	1 (1.00)	0.00075 (0.551)
amp 20q13 11	14 (3%)	487	1e-05 (0.0093)	5e-05 (0.0415)	0.601 (1.00)	0.0455 (1.00)	0.00039 (0.298)	0.00011 (0.0893)	0.00055 (0.412)	5e-05 (0.0415)	0.803 (1.00)	0.0215 (1.00)
del 19p13 2	7 (1%)	494	0.00019 (0.151)	0.00045 (0.341)	0.856 (1.00)	0.302 (1.00)	0.00161 (1.00)	0.00115 (0.83)	0.00016 (0.129)	3e-05 (0.0254)	0.0539 (1.00)	7e-05 (0.0577)
amp 1q43	29 (6%)	472	1e-05 (0.0093)	0.00641 (1.00)	0.00152 (1.00)	0.0379 (1.00)	0.00025 (0.196)	1e-05 (0.0093)	0.0194 (1.00)	0.0111 (1.00)	0.00171 (1.00)	0.00251 (1.00)
amp 5p14 3	23 (5%)	478	1e-05 (0.0093)	0.00927 (1.00)	0.366 (1.00)	0.204 (1.00)	0.00884 (1.00)	4e-05 (0.0335)	0.00144 (1.00)	0.00016 (0.129)	0.302 (1.00)	0.00194 (1.00)
amp 7q21 11	21 (4%)	480	1e-05 (0.0093)	0.00025 (0.196)	0.806 (1.00)	0.0539 (1.00)	0.00205 (1.00)	0.00069 (0.509)	0.00123 (0.882)	0.00012 (0.0971)	0.452 (1.00)	0.00267 (1.00)
amp 1q31 2	29 (6%)	472	1e-05 (0.0093)	0.0263 (1.00)	0.0015 (1.00)	0.022 (1.00)	0.00037 (0.285)	1e-05 (0.0093)	0.123 (1.00)	0.0828 (1.00)	0.0136 (1.00)	0.031 (1.00)
amp xp22 12	10 (2%)	491	1e-05 (0.0093)	0.00027 (0.211)	0.746 (1.00)	0.298 (1.00)	0.00675 (1.00)	0.00756 (1.00)	0.0356 (1.00)	0.00621 (1.00)	0.642 (1.00)	0.0323 (1.00)
del 8q24 22	7 (1%)	494	0.0005 (0.376)	0.00035 (0.271)	0.84 (1.00)	0.171 (1.00)	0.00174 (1.00)	0.00098 (0.71)	0.00023 (0.181)	3e-05 (0.0254)	0.00426 (1.00)	0.00037 (0.285)
del 9p21 3	20 (4%)	481	1e-05 (0.0093)	0.00811 (1.00)	0.243 (1.00)	0.649 (1.00)	0.0254 (1.00)	0.0246 (1.00)	0.00039 (0.298)	0.00061 (0.452)	0.243 (1.00)	0.00021 (0.166)
amp 4q22 1	7 (1%)	494	0.00029 (0.226)	0.0113 (1.00)	1 (1.00)	0.535 (1.00)	0.0289 (1.00)	0.133 (1.00)	0.307 (1.00)	0.137 (1.00)	0.8 (1.00)	0.394 (1.00)
amp 4q28 2	6 (1%)	495	9e-05 (0.0734)	0.029 (1.00)			0.073 (1.00)	0.0268 (1.00)	0.0836 (1.00)	0.0184 (1.00)	0.784 (1.00)	0.114 (1.00)
amp 5q21 1	23 (5%)	478	1e-05 (0.0093)	0.00153 (1.00)	0.849 (1.00)	0.0803 (1.00)	0.00653 (1.00)	0.0124 (1.00)	0.00879 (1.00)	0.0056 (1.00)	0.875 (1.00)	0.106 (1.00)
amp 5q21 1	20 (4%)	481	1e-05 (0.0093)	0.00101 (0.731)	1 (1.00)	0.082 (1.00)	0.00274 (1.00)	0.00067 (0.495)	0.00078 (0.572)	0.00045 (0.341)	0.674 (1.00)	0.0645 (1.00)
amp 13q14 2	6 (1%)	495	0.00011 (0.0893)	0.0927 (1.00)	0.384 (1.00)	0.213 (1.00)	0.121 (1.00)	0.268 (1.00)	0.527 (1.00)	0.349 (1.00)	0.746 (1.00)	0.637 (1.00)
amp 14q12	13 (3%)	488	1e-05 (0.0093)	0.00224 (1.00)	1 (1.00)	0.159 (1.00)	0.00371 (1.00)	0.00326 (1.00)	0.0171 (1.00)	0.00334 (1.00)	0.41 (1.00)	0.0208 (1.00)
amp 18q12 1	7 (1%)	494	2e-05 (0.0172)	0.0302 (1.00)			0.0585 (1.00)	0.119 (1.00)	0.101 (1.00)	0.0298 (1.00)	0.27 (1.00)	0.183 (1.00)
amp 19p13 3	8 (2%)	493	2e-05 (0.0172)	0.00452 (1.00)			0.0126 (1.00)	0.00528 (1.00)	0.00176 (1.00)	0.00036 (0.278)	0.452 (1.00)	0.318 (1.00)
amp 20q13 2	14 (3%)	487	1e-05 (0.0093)	0.00055 (0.412)	0.54 (1.00)	0.028 (1.00)	0.00303 (1.00)	0.00106 (0.766)	0.00052 (0.391)	0.00122 (0.876)	0.673 (1.00)	0.0439 (1.00)
amp 20q13 2	13 (3%)	488	1e-05 (0.0093)	0.00171 (1.00)	0.794 (1.00)	0.0925 (1.00)	0.00842 (1.00)	0.00233 (1.00)	0.0102 (1.00)	0.00145 (1.00)	0.785 (1.00)	0.106 (1.00)
amp xp11 4	9 (2%)	492	1e-05 (0.0093)	0.0114 (1.00)	0.838 (1.00)	0.505 (1.00)	0.0976 (1.00)	0.14 (1.00)	0.0879 (1.00)	0.134 (1.00)	0.8 (1.00)	0.184 (1.00)
amp xp11 22	8 (2%)	493	1e-05 (0.0093)	0.012 (1.00)	1 (1.00)	0.279 (1.00)	0.115 (1.00)	0.058 (1.00)	0.177 (1.00)	0.0722 (1.00)	1 (1.00)	0.184 (1.00)
amp xp11 22	8 (2%)	493	1e-05 (0.0093)	0.00082 (0.599)	0.837 (1.00)	0.503 (1.00)	0.0113 (1.00)	0.00528 (1.00)	0.0134 (1.00)	0.00207 (1.00)	0.801 (1.00)	0.0102 (1.00)
amp xp11 21	9 (2%)	492	1e-05 (0.0093)	0.00721 (1.00)	0.537 (1.00)	0.682 (1.00)	0.0298 (1.00)	0.0106 (1.00)	0.0184 (1.00)	0.00401 (1.00)	0.824 (1.00)	0.0179 (1.00)
amp xq21 2	9 (2%)	492	1e-05 (0.0093)	0.0543 (1.00)	0.837 (1.00)	0.499 (1.00)	0.0884 (1.00)	0.073 (1.00)	0.207 (1.00)	0.0719 (1.00)	1 (1.00)	0.205 (1.00)
amp xq23	9 (2%)	492	3e-05 (0.0254)	0.0538 (1.00)	1 (1.00)	0.827 (1.00)	0.0893 (1.00)	0.0485 (1.00)	0.206 (1.00)	0.133 (1.00)	1 (1.00)	0.396 (1.00)
amp xq24	9 (2%)	492	2e-05 (0.0172)	0.0551 (1.00)	0.536 (1.00)	0.683 (1.00)	0.0888 (1.00)	0.0729 (1.00)	0.205 (1.00)	0.0717 (1.00)	1 (1.00)	0.208 (1.00)
amp xq24	9 (2%)	492	2e-05 (0.0172)	0.0555 (1.00)	0.745 (1.00)	0.605 (1.00)	0.203 (1.00)	0.0726 (1.00)	0.205 (1.00)	0.0709 (1.00)	1 (1.00)	0.207 (1.00)
amp xq28	10 (2%)	491	4e-05 (0.0335)	0.13 (1.00)	0.536 (1.00)	0.263 (1.00)	0.273 (1.00)	0.221 (1.00)	0.439 (1.00)	0.228 (1.00)	0.914 (1.00)	0.399 (1.00)
del 6q22 31	7 (1%)	494	2e-05 (0.0172)	0.00219 (1.00)	0.0127 (1.00)	0.575 (1.00)	0.0282 (1.00)	0.0187 (1.00)	0.00482 (1.00)	0.00068 (0.502)	1 (1.00)	0.01 (1.00)
del 8p23 2	4 (1%)	497	0.00016 (0.129)	0.0182 (1.00)			0.036 (1.00)	0.0464 (1.00)	0.00799 (1.00)	0.00439 (1.00)	0.111 (1.00)	0.0191 (1.00)
del 8p22	4 (1%)	497	0.00022 (0.174)	0.0185 (1.00)			0.0359 (1.00)	0.047 (1.00)	0.00875 (1.00)	0.00422 (1.00)	0.11 (1.00)	0.0184 (1.00)
del 8p12	4 (1%)	497	0.00019 (0.151)	0.0185 (1.00)			0.036 (1.00)	0.0467 (1.00)	0.00797 (1.00)	0.0039 (1.00)	0.112 (1.00)	0.0186 (1.00)
del 9q22 33	27 (5%)	474	1e-05 (0.0093)	0.0936 (1.00)	0.171 (1.00)	0.115 (1.00)	0.156 (1.00)	0.0287 (1.00)	0.00437 (1.00)	0.00354 (1.00)	0.202 (1.00)	0.00217 (1.00)
del 10p12 31	7 (1%)	494	2e-05 (0.0172)	0.0112 (1.00)	0.495 (1.00)	0.265 (1.00)	0.0201 (1.00)	0.0153 (1.00)	0.00491 (1.00)	0.00084 (0.613)	0.8 (1.00)	0.0103 (1.00)
del 10q23 31	12 (2%)	489	6e-05 (0.0496)	0.00419 (1.00)	0.0504 (1.00)	0.148 (1.00)	0.00059 (0.438)	0.00412 (1.00)	0.00368 (1.00)	0.00056 (0.418)	0.263 (1.00)	0.00805 (1.00)
del 11p15 1	7 (1%)	494	1e-05 (0.0093)	0.0113 (1.00)	0.494 (1.00)	0.958 (1.00)	0.00705 (1.00)	0.0179 (1.00)	0.00484 (1.00)	0.00052 (0.391)	0.801 (1.00)	0.0101 (1.00)
del 15q25 3	9 (2%)	492	0.00069 (0.509)	0.00148 (1.00)	0.243 (1.00)	0.0618 (1.00)	0.00476 (1.00)	0.00164 (1.00)	0.00041 (0.312)	0.0001 (0.0814)	0.452 (1.00)	0.0113 (1.00)
del 21q21 1	9 (2%)	492	8e-05 (0.0656)	0.306 (1.00)	0.147 (1.00)	0.323 (1.00)	0.795 (1.00)	0.802 (1.00)	0.0639 (1.00)	0.0229 (1.00)	0.264 (1.00)	0.0227 (1.00)
amp 1p36 32	5 (1%)	496	0.00133 (0.952)	0.841 (1.00)			0.446 (1.00)	0.0384 (1.00)	0.631 (1.00)	0.542 (1.00)	0.275 (1.00)	0.834 (1.00)
amp 1p32 3	5 (1%)	496	0.141 (1.00)	0.549 (1.00)			0.549 (1.00)	0.696 (1.00)	0.283 (1.00)	0.156 (1.00)	0.554 (1.00)	0.198 (1.00)
amp 1p31 1	5 (1%)	496	0.096 (1.00)	0.553 (1.00)			0.55 (1.00)	0.963 (1.00)	0.867 (1.00)	0.641 (1.00)	0.845 (1.00)	0.684 (1.00)
amp 2p16 1	3 (1%)	498	0.0518 (1.00)	1 (1.00)			1 (1.00)	0.876 (1.00)	1 (1.00)	1 (1.00)	0.309 (1.00)	1 (1.00)
amp 2q37 2	3 (1%)	498	0.205 (1.00)	0.549 (1.00)			0.494 (1.00)	0.591 (1.00)	0.201 (1.00)	0.265 (1.00)
amp 3p22 3	4 (1%)	497	0.0104 (1.00)	0.184 (1.00)	1 (1.00)	0.884 (1.00)	0.243 (1.00)	0.317 (1.00)	0.113 (1.00)	0.0661 (1.00)	1 (1.00)	0.0671 (1.00)
amp 3p14 1	5 (1%)	496	0.0163 (1.00)	0.427 (1.00)	0.782 (1.00)	0.439 (1.00)	0.695 (1.00)	0.438 (1.00)	0.867 (1.00)	0.64 (1.00)	1 (1.00)	0.64 (1.00)
amp 4p16 1	7 (1%)	494	0.00041 (0.312)	0.0106 (1.00)	0.279 (1.00)	0.422 (1.00)	0.0288 (1.00)	0.0103 (1.00)	0.0333 (1.00)	0.00629 (1.00)	0.713 (1.00)	0.0468 (1.00)
amp 4q31 21	10 (2%)	491	0.00263 (1.00)	0.113 (1.00)	1 (1.00)	0.576 (1.00)	0.275 (1.00)	0.202 (1.00)	0.525 (1.00)	0.658 (1.00)	1 (1.00)	0.404 (1.00)
amp 4q32 3	7 (1%)	494	0.00045 (0.341)	0.0114 (1.00)	0.324 (1.00)	0.0631 (1.00)	0.0285 (1.00)	0.0184 (1.00)	0.0332 (1.00)	0.0064 (1.00)	0.9 (1.00)	0.185 (1.00)
amp 6p22 3	3 (1%)	498	0.0504 (1.00)	0.0499 (1.00)			0.136 (1.00)	0.51 (1.00)	0.302 (1.00)	0.187 (1.00)	0.778 (1.00)	0.191 (1.00)
amp 6p22 2	4 (1%)	497	0.112 (1.00)	0.0448 (1.00)	0.84 (1.00)	0.307 (1.00)	0.0969 (1.00)	0.244 (1.00)	0.114 (1.00)	0.0656 (1.00)	1 (1.00)	0.0681 (1.00)
amp 6p21 31	3 (1%)	498	0.0499 (1.00)	0.549 (1.00)			0.747 (1.00)	0.401 (1.00)	0.203 (1.00)	0.265 (1.00)	0.11 (1.00)	0.274 (1.00)
amp 6p21 2	4 (1%)	497	0.113 (1.00)	0.792 (1.00)	0.635 (1.00)	0.342 (1.00)	0.668 (1.00)	0.747 (1.00)	0.112 (1.00)	0.568 (1.00)	0.776 (1.00)	0.192 (1.00)
amp 6p12 2	3 (1%)	498	0.0497 (1.00)	0.55 (1.00)			0.747 (1.00)	0.719 (1.00)	0.205 (1.00)	0.265 (1.00)	0.11 (1.00)	0.273 (1.00)
amp 6q12	3 (1%)	498	0.372 (1.00)	0.124 (1.00)			0.136 (1.00)	0.674 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
amp 6q27	4 (1%)	497	0.114 (1.00)	0.183 (1.00)	0.39 (1.00)	0.0131 (1.00)	0.46 (1.00)	0.394 (1.00)	0.113 (1.00)	0.0661 (1.00)	0.693 (1.00)	0.0665 (1.00)
amp 9q22 31	6 (1%)	495	0.0248 (1.00)	0.863 (1.00)	0.493 (1.00)	0.851 (1.00)	0.943 (1.00)	0.353 (1.00)	0.781 (1.00)	1 (1.00)	0.0641 (1.00)	0.382 (1.00)
amp 9q31 1	6 (1%)	495	0.0243 (1.00)	0.418 (1.00)	0.278 (1.00)	0.82 (1.00)	0.628 (1.00)	0.434 (1.00)	1 (1.00)	0.887 (1.00)	0.336 (1.00)	0.773 (1.00)
amp 9q34 3	7 (1%)	494	0.0619 (1.00)	0.294 (1.00)	0.855 (1.00)	0.827 (1.00)	0.628 (1.00)	0.346 (1.00)	0.799 (1.00)	0.628 (1.00)	0.104 (1.00)	0.773 (1.00)
amp 10q24 2	3 (1%)	498	0.0505 (1.00)	0.0487 (1.00)			0.0987 (1.00)	0.151 (1.00)	0.0272 (1.00)	0.0167 (1.00)
amp 10q25 1	4 (1%)	497	0.0103 (1.00)	0.792 (1.00)			0.899 (1.00)	0.878 (1.00)	0.692 (1.00)	0.568 (1.00)	1 (1.00)	1 (1.00)
amp 11p13	8 (2%)	493	0.00259 (1.00)	0.116 (1.00)	1 (1.00)	0.112 (1.00)	0.0936 (1.00)	0.14 (1.00)	0.161 (1.00)	0.0822 (1.00)	0.529 (1.00)	0.456 (1.00)
amp 13q34	7 (1%)	494	0.00055 (0.412)	0.048 (1.00)	0.147 (1.00)	0.0348 (1.00)	0.0516 (1.00)	0.17 (1.00)	0.308 (1.00)	0.137 (1.00)	1 (1.00)	1 (1.00)
amp 18q22 1	7 (1%)	494	0.00035 (0.271)	0.241 (1.00)	0.496 (1.00)	0.0882 (1.00)	0.152 (1.00)	0.271 (1.00)	0.271 (1.00)	0.184 (1.00)	0.802 (1.00)	0.633 (1.00)
amp 18q22 3	8 (2%)	493	0.00057 (0.425)	0.0254 (1.00)			0.0353 (1.00)	0.119 (1.00)	0.0214 (1.00)	0.00689 (1.00)	0.157 (1.00)	0.398 (1.00)
amp 21q21 3	6 (1%)	495	0.00119 (0.857)	0.0706 (1.00)			0.631 (1.00)	0.84 (1.00)	0.525 (1.00)	0.346 (1.00)	0.746 (1.00)	0.638 (1.00)
amp 22q11 21	7 (1%)	494	0.00288 (1.00)	0.00394 (1.00)			0.0082 (1.00)	0.0358 (1.00)	0.0332 (1.00)	0.0302 (1.00)	0.0274 (1.00)	0.0102 (1.00)
amp xq22 3	15 (3%)	486	0.00043 (0.326)	0.716 (1.00)	0.837 (1.00)	0.5 (1.00)	0.743 (1.00)	0.894 (1.00)	0.949 (1.00)	0.638 (1.00)	0.493 (1.00)	1 (1.00)
del 1q24 2	3 (1%)	498	0.0014 (1.00)	0.0493 (1.00)			0.0984 (1.00)	0.153 (1.00)	0.0281 (1.00)	0.0168 (1.00)	1 (1.00)	0.193 (1.00)
del 1q42 13	5 (1%)	496	0.0163 (1.00)	0.168 (1.00)	0.459 (1.00)	0.935 (1.00)	0.048 (1.00)	0.156 (1.00)	0.0412 (1.00)	0.31 (1.00)	0.845 (1.00)	0.196 (1.00)
del 4q34 3	5 (1%)	496	0.0161 (1.00)	0.169 (1.00)	1 (1.00)	0.504 (1.00)	0.387 (1.00)	0.574 (1.00)	0.238 (1.00)	0.0713 (1.00)	1 (1.00)	0.076 (1.00)
del 5p15 2	4 (1%)	497	0.114 (1.00)	0.365 (1.00)			0.38 (1.00)	0.273 (1.00)	0.556 (1.00)	0.683 (1.00)	0.398 (1.00)	0.567 (1.00)
del 7q34	4 (1%)	497	1 (1.00)	0.792 (1.00)			0.747 (1.00)	0.674 (1.00)	0.688 (1.00)	1 (1.00)	0.335 (1.00)	1 (1.00)
del 10q21 2	12 (2%)	489	0.00079 (0.578)	0.0637 (1.00)	0.155 (1.00)	0.677 (1.00)	0.0187 (1.00)	0.0658 (1.00)	0.135 (1.00)	0.173 (1.00)	0.58 (1.00)	0.0474 (1.00)
del 13q12 13	18 (4%)	483	0.00038 (0.291)	0.00092 (0.668)	0.184 (1.00)	0.0843 (1.00)	0.018 (1.00)	0.0357 (1.00)	0.0753 (1.00)	0.0214 (1.00)	0.428 (1.00)	0.0331 (1.00)
del 13q22 1	19 (4%)	482	0.00203 (1.00)	0.0375 (1.00)	0.0547 (1.00)	0.186 (1.00)	0.0012 (0.863)	0.00076 (0.558)	0.00297 (1.00)	0.00085 (0.62)	0.013 (1.00)	0.00327 (1.00)
del 16q23 3	6 (1%)	495	0.0246 (1.00)	0.148 (1.00)	0.445 (1.00)	0.445 (1.00)	0.138 (1.00)	0.149 (1.00)	0.226 (1.00)	0.205 (1.00)	0.0691 (1.00)	0.0616 (1.00)
del 17p13 1	8 (2%)	493	0.0146 (1.00)	0.416 (1.00)	1 (1.00)	0.388 (1.00)	0.636 (1.00)	0.597 (1.00)	0.0925 (1.00)	0.161 (1.00)	0.128 (1.00)	0.205 (1.00)
del 18q12 3	4 (1%)	497	0.00179 (1.00)	0.185 (1.00)	1 (1.00)	0.386 (1.00)	0.245 (1.00)	0.316 (1.00)	0.0733 (1.00)	0.0916 (1.00)	0.533 (1.00)	0.274 (1.00)
del 19p13 12	8 (2%)	493	0.00266 (1.00)	0.00458 (1.00)	0.131 (1.00)	0.0978 (1.00)	0.0116 (1.00)	0.00557 (1.00)	0.00116 (0.836)	0.00038 (0.291)	0.0948 (1.00)	0.00087 (0.633)
del xq23	4 (1%)	497	0.0106 (1.00)	0.0449 (1.00)	0.278 (1.00)	0.198 (1.00)	0.0976 (1.00)	0.247 (1.00)	0.0737 (1.00)	0.0911 (1.00)	0.217 (1.00)	0.0947 (1.00)
del xq22 3	4 (1%)	497	0.0106 (1.00)	0.044 (1.00)	0.278 (1.00)	0.198 (1.00)	0.0984 (1.00)	0.248 (1.00)	0.0743 (1.00)	0.0912 (1.00)	0.22 (1.00)	0.0964 (1.00)

'amp_1q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S1. Gene #4: 'amp_1q31.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 4(1Q31.2) MUTATED	19	9	1
AMP PEAK 4(1Q31.2) WILD-TYPE	37	347	88

Figure S1. Get High-res Image Gene #4: 'amp_1q31.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S2. Gene #4: 'amp_1q31.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
AMP PEAK 4(1Q31.2) MUTATED	18	3	1	2	5
AMP PEAK 4(1Q31.2) WILD-TYPE	87	131	85	94	73

Figure S2. Get High-res Image Gene #4: 'amp_1q31.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1q43' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S3. Gene #5: 'amp_1q43' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 5(1Q43) MUTATED	20	8	1
AMP PEAK 5(1Q43) WILD-TYPE	36	348	88

Figure S3. Get High-res Image Gene #5: 'amp_1q43' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q43' versus 'MRNASEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.2

Table S4. Gene #5: 'amp_1q43' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	168	155	59	117
AMP PEAK 5(1Q43) MUTATED	19	2	5	3
AMP PEAK 5(1Q43) WILD-TYPE	149	153	54	114

Figure S4. Get High-res Image Gene #5: 'amp_1q43' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q43' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S5. Gene #5: 'amp_1q43' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
AMP PEAK 5(1Q43) MUTATED	19	2	1	3	4
AMP PEAK 5(1Q43) WILD-TYPE	86	132	85	93	74

Figure S5. Get High-res Image Gene #5: 'amp_1q43' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_4q22.1' versus 'CN_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.23

Table S6. Gene #11: 'amp_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 13(4Q22.1) MUTATED	5	1	1
AMP PEAK 13(4Q22.1) WILD-TYPE	51	355	88

Figure S6. Get High-res Image Gene #11: 'amp_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4q28.2' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.073

Table S7. Gene #12: 'amp_4q28.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 14(4Q28.2) MUTATED	5	1	0
AMP PEAK 14(4Q28.2) WILD-TYPE	51	355	89

Figure S7. Get High-res Image Gene #12: 'amp_4q28.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p14.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S8. Gene #15: 'amp_5p14.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 17(5P14.3) MUTATED	23	0	0
AMP PEAK 17(5P14.3) WILD-TYPE	33	356	89

Figure S8. Get High-res Image Gene #15: 'amp_5p14.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p14.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.034

Table S9. Gene #15: 'amp_5p14.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
AMP PEAK 17(5P14.3) MUTATED	8	14	0	1	0
AMP PEAK 17(5P14.3) WILD-TYPE	97	120	86	95	78

Figure S9. Get High-res Image Gene #15: 'amp_5p14.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5p14.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.13

Table S10. Gene #15: 'amp_5p14.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
AMP PEAK 17(5P14.3) MUTATED	9	13	1
AMP PEAK 17(5P14.3) WILD-TYPE	170	115	192

Figure S10. Get High-res Image Gene #15: 'amp_5p14.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S11. Gene #16: 'amp_5q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 18(5Q21.1) MUTATED	19	3	1
AMP PEAK 18(5Q21.1) WILD-TYPE	37	353	88

Figure S11. Get High-res Image Gene #16: 'amp_5q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S12. Gene #17: 'amp_5q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 19(5Q21.1) MUTATED	18	2	0
AMP PEAK 19(5Q21.1) WILD-TYPE	38	354	89

Figure S12. Get High-res Image Gene #17: 'amp_5q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q33.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S13. Gene #18: 'amp_5q33.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 20(5Q33.1) MUTATED	18	3	0
AMP PEAK 20(5Q33.1) WILD-TYPE	38	353	89

Figure S13. Get High-res Image Gene #18: 'amp_5q33.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q33.1' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.073

Table S14. Gene #18: 'amp_5q33.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
AMP PEAK 20(5Q33.1) MUTATED	4	16	1
AMP PEAK 20(5Q33.1) WILD-TYPE	273	138	69

Figure S14. Get High-res Image Gene #18: 'amp_5q33.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5q33.1' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.11

Table S15. Gene #18: 'amp_5q33.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	168	155	59	117
AMP PEAK 20(5Q33.1) MUTATED	2	16	0	3
AMP PEAK 20(5Q33.1) WILD-TYPE	166	139	59	114

Figure S15. Get High-res Image Gene #18: 'amp_5q33.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5q33.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.058

Table S16. Gene #18: 'amp_5q33.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
AMP PEAK 20(5Q33.1) MUTATED	2	16	1	2	0
AMP PEAK 20(5Q33.1) WILD-TYPE	103	118	85	94	78

Figure S16. Get High-res Image Gene #18: 'amp_5q33.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5q33.1' versus 'MIRSEQ_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.23

Table S17. Gene #18: 'amp_5q33.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
AMP PEAK 20(5Q33.1) MUTATED	4	15	2
AMP PEAK 20(5Q33.1) WILD-TYPE	178	136	165

Figure S17. Get High-res Image Gene #18: 'amp_5q33.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5q33.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S18. Gene #18: 'amp_5q33.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
AMP PEAK 20(5Q33.1) MUTATED	4	15	2
AMP PEAK 20(5Q33.1) WILD-TYPE	175	113	191

Figure S18. Get High-res Image Gene #18: 'amp_5q33.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5q35.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S19. Gene #19: 'amp_5q35.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 21(5Q35.2) MUTATED	18	2	0
AMP PEAK 21(5Q35.2) WILD-TYPE	38	354	89

Figure S19. Get High-res Image Gene #19: 'amp_5q35.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q35.2' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.11

Table S20. Gene #19: 'amp_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
AMP PEAK 21(5Q35.2) MUTATED	4	15	1
AMP PEAK 21(5Q35.2) WILD-TYPE	273	139	69

Figure S20. Get High-res Image Gene #19: 'amp_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5q35.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.05

Table S21. Gene #19: 'amp_5q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
AMP PEAK 21(5Q35.2) MUTATED	3	15	0	2	0
AMP PEAK 21(5Q35.2) WILD-TYPE	102	119	86	94	78

Figure S21. Get High-res Image Gene #19: 'amp_5q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5q35.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S22. Gene #19: 'amp_5q35.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
AMP PEAK 21(5Q35.2) MUTATED	4	14	2
AMP PEAK 21(5Q35.2) WILD-TYPE	175	114	191

Figure S22. Get High-res Image Gene #19: 'amp_5q35.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S23. Gene #27: 'amp_7q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 29(7Q11.21) MUTATED	18	2	0
AMP PEAK 29(7Q11.21) WILD-TYPE	38	354	89

Figure S23. Get High-res Image Gene #27: 'amp_7q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q11.21' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.041

Table S24. Gene #27: 'amp_7q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
AMP PEAK 29(7Q11.21) MUTATED	3	15	2
AMP PEAK 29(7Q11.21) WILD-TYPE	274	139	68

Figure S24. Get High-res Image Gene #27: 'amp_7q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.21

Table S25. Gene #27: 'amp_7q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
AMP PEAK 29(7Q11.21) MUTATED	2	15	1	1	1
AMP PEAK 29(7Q11.21) WILD-TYPE	103	119	85	95	77

Figure S25. Get High-res Image Gene #27: 'amp_7q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.18

Table S26. Gene #27: 'amp_7q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
AMP PEAK 29(7Q11.21) MUTATED	5	13	2
AMP PEAK 29(7Q11.21) WILD-TYPE	174	115	191

Figure S26. Get High-res Image Gene #27: 'amp_7q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q21.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S27. Gene #28: 'amp_7q21.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 30(7Q21.11) MUTATED	20	1	0
AMP PEAK 30(7Q21.11) WILD-TYPE	36	355	89

Figure S27. Get High-res Image Gene #28: 'amp_7q21.11' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q21.11' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.2

Table S28. Gene #28: 'amp_7q21.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
AMP PEAK 30(7Q21.11) MUTATED	4	15	2
AMP PEAK 30(7Q21.11) WILD-TYPE	273	139	68

Figure S28. Get High-res Image Gene #28: 'amp_7q21.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q21.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.097

Table S29. Gene #28: 'amp_7q21.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
AMP PEAK 30(7Q21.11) MUTATED	5	14	2
AMP PEAK 30(7Q21.11) WILD-TYPE	174	114	191

Figure S29. Get High-res Image Gene #28: 'amp_7q21.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S30. Gene #29: 'amp_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 31(7Q31.1) MUTATED	19	2	1
AMP PEAK 31(7Q31.1) WILD-TYPE	37	354	88

Figure S30. Get High-res Image Gene #29: 'amp_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q31.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S31. Gene #29: 'amp_7q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
AMP PEAK 31(7Q31.1) MUTATED	2	18	2
AMP PEAK 31(7Q31.1) WILD-TYPE	275	136	68

Figure S31. Get High-res Image Gene #29: 'amp_7q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q31.1' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.081

Table S32. Gene #29: 'amp_7q31.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	168	155	59	117
AMP PEAK 31(7Q31.1) MUTATED	3	17	1	1
AMP PEAK 31(7Q31.1) WILD-TYPE	165	138	58	116

Figure S32. Get High-res Image Gene #29: 'amp_7q31.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S33. Gene #29: 'amp_7q31.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
AMP PEAK 31(7Q31.1) MUTATED	2	17	1	1	1
AMP PEAK 31(7Q31.1) WILD-TYPE	103	117	85	95	77

Figure S33. Get High-res Image Gene #29: 'amp_7q31.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.1' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.058

Table S34. Gene #29: 'amp_7q31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
AMP PEAK 31(7Q31.1) MUTATED	5	16	1
AMP PEAK 31(7Q31.1) WILD-TYPE	177	135	166

Figure S34. Get High-res Image Gene #29: 'amp_7q31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S35. Gene #29: 'amp_7q31.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
AMP PEAK 31(7Q31.1) MUTATED	5	16	1
AMP PEAK 31(7Q31.1) WILD-TYPE	174	112	192

Figure S35. Get High-res Image Gene #29: 'amp_7q31.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S36. Gene #30: 'amp_7q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 32(7Q34) MUTATED	19	2	1
AMP PEAK 32(7Q34) WILD-TYPE	37	354	88

Figure S36. Get High-res Image Gene #30: 'amp_7q34' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q34' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.058

Table S37. Gene #30: 'amp_7q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
AMP PEAK 32(7Q34) MUTATED	3	16	3
AMP PEAK 32(7Q34) WILD-TYPE	274	138	67

Figure S37. Get High-res Image Gene #30: 'amp_7q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.2

Table S38. Gene #30: 'amp_7q34' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
AMP PEAK 32(7Q34) MUTATED	2	16	2	1	1
AMP PEAK 32(7Q34) WILD-TYPE	103	118	84	95	77

Figure S38. Get High-res Image Gene #30: 'amp_7q34' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q34' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S39. Gene #30: 'amp_7q34' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
AMP PEAK 32(7Q34) MUTATED	4	17	1
AMP PEAK 32(7Q34) WILD-TYPE	178	134	166

Figure S39. Get High-res Image Gene #30: 'amp_7q34' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S40. Gene #30: 'amp_7q34' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
AMP PEAK 32(7Q34) MUTATED	4	17	1
AMP PEAK 32(7Q34) WILD-TYPE	175	111	192

Figure S40. Get High-res Image Gene #30: 'amp_7q34' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_12p11.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S41. Gene #37: 'amp_12p11.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 39(12P11.1) MUTATED	15	1	0
AMP PEAK 39(12P11.1) WILD-TYPE	41	355	89

Figure S41. Get High-res Image Gene #37: 'amp_12p11.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p11.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S42. Gene #37: 'amp_12p11.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
AMP PEAK 39(12P11.1) MUTATED	2	14	0
AMP PEAK 39(12P11.1) WILD-TYPE	275	140	70

Figure S42. Get High-res Image Gene #37: 'amp_12p11.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12p11.1' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.034

Table S43. Gene #37: 'amp_12p11.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	168	155	59	117
AMP PEAK 39(12P11.1) MUTATED	1	14	0	1
AMP PEAK 39(12P11.1) WILD-TYPE	167	141	59	116

Figure S43. Get High-res Image Gene #37: 'amp_12p11.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12p11.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S44. Gene #37: 'amp_12p11.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
AMP PEAK 39(12P11.1) MUTATED	1	14	0	1	0
AMP PEAK 39(12P11.1) WILD-TYPE	104	120	86	95	78

Figure S44. Get High-res Image Gene #37: 'amp_12p11.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_12p11.1' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.066

Table S45. Gene #37: 'amp_12p11.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
AMP PEAK 39(12P11.1) MUTATED	2	13	1
AMP PEAK 39(12P11.1) WILD-TYPE	180	138	166

Figure S45. Get High-res Image Gene #37: 'amp_12p11.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_12p11.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S46. Gene #37: 'amp_12p11.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
AMP PEAK 39(12P11.1) MUTATED	2	13	1
AMP PEAK 39(12P11.1) WILD-TYPE	177	115	192

Figure S46. Get High-res Image Gene #37: 'amp_12p11.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_12q21.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S47. Gene #38: 'amp_12q21.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 40(12Q21.31) MUTATED	14	1	2
AMP PEAK 40(12Q21.31) WILD-TYPE	42	355	87

Figure S47. Get High-res Image Gene #38: 'amp_12q21.31' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q21.31' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S48. Gene #38: 'amp_12q21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
AMP PEAK 40(12Q21.31) MUTATED	2	15	0
AMP PEAK 40(12Q21.31) WILD-TYPE	275	139	70

Figure S48. Get High-res Image Gene #38: 'amp_12q21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12q21.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S49. Gene #38: 'amp_12q21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	168	155	59	117
AMP PEAK 40(12Q21.31) MUTATED	0	15	0	2
AMP PEAK 40(12Q21.31) WILD-TYPE	168	140	59	115

Figure S49. Get High-res Image Gene #38: 'amp_12q21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12q21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S50. Gene #38: 'amp_12q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
AMP PEAK 40(12Q21.31) MUTATED	0	15	1	1	0
AMP PEAK 40(12Q21.31) WILD-TYPE	105	119	85	95	78

Figure S50. Get High-res Image Gene #38: 'amp_12q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_12q21.31' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S51. Gene #38: 'amp_12q21.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
AMP PEAK 40(12Q21.31) MUTATED	1	14	2
AMP PEAK 40(12Q21.31) WILD-TYPE	181	137	165

Figure S51. Get High-res Image Gene #38: 'amp_12q21.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_12q21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S52. Gene #38: 'amp_12q21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
AMP PEAK 40(12Q21.31) MUTATED	1	14	2
AMP PEAK 40(12Q21.31) WILD-TYPE	178	114	191

Figure S52. Get High-res Image Gene #38: 'amp_12q21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_12q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S53. Gene #39: 'amp_12q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 41(12Q23.1) MUTATED	14	2	1
AMP PEAK 41(12Q23.1) WILD-TYPE	42	354	88

Figure S53. Get High-res Image Gene #39: 'amp_12q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q23.1' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.034

Table S54. Gene #39: 'amp_12q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
AMP PEAK 41(12Q23.1) MUTATED	3	14	0
AMP PEAK 41(12Q23.1) WILD-TYPE	274	140	70

Figure S54. Get High-res Image Gene #39: 'amp_12q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12q23.1' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.089

Table S55. Gene #39: 'amp_12q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	168	155	59	117
AMP PEAK 41(12Q23.1) MUTATED	1	14	0	2
AMP PEAK 41(12Q23.1) WILD-TYPE	167	141	59	115

Figure S55. Get High-res Image Gene #39: 'amp_12q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.034

Table S56. Gene #39: 'amp_12q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
AMP PEAK 41(12Q23.1) MUTATED	0	14	0	2	1
AMP PEAK 41(12Q23.1) WILD-TYPE	105	120	86	94	77

Figure S56. Get High-res Image Gene #39: 'amp_12q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_12q23.1' versus 'MIRSEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.13

Table S57. Gene #39: 'amp_12q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
AMP PEAK 41(12Q23.1) MUTATED	3	13	1
AMP PEAK 41(12Q23.1) WILD-TYPE	179	138	166

Figure S57. Get High-res Image Gene #39: 'amp_12q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_12q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S58. Gene #39: 'amp_12q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
AMP PEAK 41(12Q23.1) MUTATED	2	13	2
AMP PEAK 41(12Q23.1) WILD-TYPE	177	115	191

Figure S58. Get High-res Image Gene #39: 'amp_12q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_13q14.2' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.089

Table S59. Gene #40: 'amp_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 42(13Q14.2) MUTATED	5	1	0
AMP PEAK 42(13Q14.2) WILD-TYPE	51	355	89

Figure S59. Get High-res Image Gene #40: 'amp_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_14q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S60. Gene #42: 'amp_14q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 44(14Q12) MUTATED	10	2	1
AMP PEAK 44(14Q12) WILD-TYPE	46	354	88

Figure S60. Get High-res Image Gene #42: 'amp_14q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_14q32.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S61. Gene #43: 'amp_14q32.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 45(14Q32.31) MUTATED	10	2	1
AMP PEAK 45(14Q32.31) WILD-TYPE	46	354	88

Figure S61. Get High-res Image Gene #43: 'amp_14q32.31' versus Molecular Subtype #1: 'CN_CNMF'

'amp_14q32.31' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.11

Table S62. Gene #43: 'amp_14q32.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
AMP PEAK 45(14Q32.31) MUTATED	1	11	1
AMP PEAK 45(14Q32.31) WILD-TYPE	276	143	69

Figure S62. Get High-res Image Gene #43: 'amp_14q32.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_14q32.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.14

Table S63. Gene #43: 'amp_14q32.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
AMP PEAK 45(14Q32.31) MUTATED	1	11	0	0	1
AMP PEAK 45(14Q32.31) WILD-TYPE	104	123	86	96	77

Figure S63. Get High-res Image Gene #43: 'amp_14q32.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_14q32.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.066

Table S64. Gene #43: 'amp_14q32.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
AMP PEAK 45(14Q32.31) MUTATED	3	10	0
AMP PEAK 45(14Q32.31) WILD-TYPE	176	118	193

Figure S64. Get High-res Image Gene #43: 'amp_14q32.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_18q12.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S65. Gene #44: 'amp_18q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 48(18Q12.1) MUTATED	5	0	2
AMP PEAK 48(18Q12.1) WILD-TYPE	51	356	87

Figure S65. Get High-res Image Gene #44: 'amp_18q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19p13.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S66. Gene #47: 'amp_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 51(19P13.3) MUTATED	7	1	0
AMP PEAK 51(19P13.3) WILD-TYPE	49	355	89

Figure S66. Get High-res Image Gene #47: 'amp_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S67. Gene #48: 'amp_20p13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 52(20P13) MUTATED	13	0	1
AMP PEAK 52(20P13) WILD-TYPE	43	356	88

Figure S67. Get High-res Image Gene #48: 'amp_20p13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20p13' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S68. Gene #48: 'amp_20p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
AMP PEAK 52(20P13) MUTATED	1	12	1
AMP PEAK 52(20P13) WILD-TYPE	276	142	69

Figure S68. Get High-res Image Gene #48: 'amp_20p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20p13' versus 'MRNASEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.25

Table S69. Gene #48: 'amp_20p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	168	155	59	117
AMP PEAK 52(20P13) MUTATED	1	12	0	1
AMP PEAK 52(20P13) WILD-TYPE	167	143	59	116

Figure S69. Get High-res Image Gene #48: 'amp_20p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_20p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.05

Table S70. Gene #48: 'amp_20p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
AMP PEAK 52(20P13) MUTATED	1	12	0	1	0
AMP PEAK 52(20P13) WILD-TYPE	104	122	86	95	78

Figure S70. Get High-res Image Gene #48: 'amp_20p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S71. Gene #48: 'amp_20p13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
AMP PEAK 52(20P13) MUTATED	2	11	1
AMP PEAK 52(20P13) WILD-TYPE	177	117	192

Figure S71. Get High-res Image Gene #48: 'amp_20p13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S72. Gene #49: 'amp_20q13.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 53(20Q13.11) MUTATED	12	0	2
AMP PEAK 53(20Q13.11) WILD-TYPE	44	356	87

Figure S72. Get High-res Image Gene #49: 'amp_20q13.11' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.11' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.041

Table S73. Gene #49: 'amp_20q13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
AMP PEAK 53(20Q13.11) MUTATED	1	12	1
AMP PEAK 53(20Q13.11) WILD-TYPE	276	142	69

Figure S73. Get High-res Image Gene #49: 'amp_20q13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q13.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.089

Table S74. Gene #49: 'amp_20q13.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
AMP PEAK 53(20Q13.11) MUTATED	1	12	0	1	0
AMP PEAK 53(20Q13.11) WILD-TYPE	104	122	86	95	78

Figure S74. Get High-res Image Gene #49: 'amp_20q13.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.041

Table S75. Gene #49: 'amp_20q13.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
AMP PEAK 53(20Q13.11) MUTATED	2	11	1
AMP PEAK 53(20Q13.11) WILD-TYPE	177	117	192

Figure S75. Get High-res Image Gene #49: 'amp_20q13.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S76. Gene #50: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 54(20Q13.2) MUTATED	13	0	1
AMP PEAK 54(20Q13.2) WILD-TYPE	43	356	88

Figure S76. Get High-res Image Gene #50: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S77. Gene #51: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 55(20Q13.2) MUTATED	13	0	0
AMP PEAK 55(20Q13.2) WILD-TYPE	43	356	89

Figure S77. Get High-res Image Gene #51: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp22.12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S78. Gene #54: 'amp_xp22.12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 58(XP22.12) MUTATED	8	1	1
AMP PEAK 58(XP22.12) WILD-TYPE	48	355	88

Figure S78. Get High-res Image Gene #54: 'amp_xp22.12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp22.12' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.21

Table S79. Gene #54: 'amp_xp22.12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
AMP PEAK 58(XP22.12) MUTATED	0	8	2
AMP PEAK 58(XP22.12) WILD-TYPE	277	146	68

Figure S79. Get High-res Image Gene #54: 'amp_xp22.12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xp11.4' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S80. Gene #55: 'amp_xp11.4' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 59(XP11.4) MUTATED	9	0	0
AMP PEAK 59(XP11.4) WILD-TYPE	47	356	89

Figure S80. Get High-res Image Gene #55: 'amp_xp11.4' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S81. Gene #56: 'amp_xp11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 60(XP11.22) MUTATED	7	1	0
AMP PEAK 60(XP11.22) WILD-TYPE	49	355	89

Figure S81. Get High-res Image Gene #56: 'amp_xp11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S82. Gene #57: 'amp_xp11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 61(XP11.22) MUTATED	8	0	0
AMP PEAK 61(XP11.22) WILD-TYPE	48	356	89

Figure S82. Get High-res Image Gene #57: 'amp_xp11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S83. Gene #58: 'amp_xp11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 62(XP11.21) MUTATED	8	1	0
AMP PEAK 62(XP11.21) WILD-TYPE	48	355	89

Figure S83. Get High-res Image Gene #58: 'amp_xp11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S84. Gene #59: 'amp_xq21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 63(XQ21.2) MUTATED	8	1	0
AMP PEAK 63(XQ21.2) WILD-TYPE	48	355	89

Figure S84. Get High-res Image Gene #59: 'amp_xq21.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq23' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S85. Gene #61: 'amp_xq23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 65(XQ23) MUTATED	7	2	0
AMP PEAK 65(XQ23) WILD-TYPE	49	354	89

Figure S85. Get High-res Image Gene #61: 'amp_xq23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq24' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S86. Gene #62: 'amp_xq24' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 66(XQ24) MUTATED	7	2	0
AMP PEAK 66(XQ24) WILD-TYPE	49	354	89

Figure S86. Get High-res Image Gene #62: 'amp_xq24' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq24' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S87. Gene #63: 'amp_xq24' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 67(XQ24) MUTATED	7	2	0
AMP PEAK 67(XQ24) WILD-TYPE	49	354	89

Figure S87. Get High-res Image Gene #63: 'amp_xq24' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq28' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.034

Table S88. Gene #64: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
AMP PEAK 68(XQ28) MUTATED	7	3	0
AMP PEAK 68(XQ28) WILD-TYPE	49	353	89

Figure S88. Get High-res Image Gene #64: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

'del_2p23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S89. Gene #67: 'del_2p23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
DEL PEAK 3(2P23.1) MUTATED	9	1	2
DEL PEAK 3(2P23.1) WILD-TYPE	47	355	87

Figure S89. Get High-res Image Gene #67: 'del_2p23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2p23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S90. Gene #67: 'del_2p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
DEL PEAK 3(2P23.1) MUTATED	0	11	1
DEL PEAK 3(2P23.1) WILD-TYPE	277	143	69

Figure S90. Get High-res Image Gene #67: 'del_2p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2p23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S91. Gene #67: 'del_2p23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	168	155	59	117
DEL PEAK 3(2P23.1) MUTATED	0	12	0	0
DEL PEAK 3(2P23.1) WILD-TYPE	168	143	59	117

Figure S91. Get High-res Image Gene #67: 'del_2p23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2p23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S92. Gene #67: 'del_2p23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
DEL PEAK 3(2P23.1) MUTATED	0	11	1	0	0
DEL PEAK 3(2P23.1) WILD-TYPE	105	123	85	96	78

Figure S92. Get High-res Image Gene #67: 'del_2p23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2p23.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S93. Gene #67: 'del_2p23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
DEL PEAK 3(2P23.1) MUTATED	0	12	0
DEL PEAK 3(2P23.1) WILD-TYPE	182	139	167

Figure S93. Get High-res Image Gene #67: 'del_2p23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2p23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S94. Gene #67: 'del_2p23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
DEL PEAK 3(2P23.1) MUTATED	0	11	1
DEL PEAK 3(2P23.1) WILD-TYPE	179	117	192

Figure S94. Get High-res Image Gene #67: 'del_2p23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2p23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.14

Table S95. Gene #67: 'del_2p23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	126	179
DEL PEAK 3(2P23.1) MUTATED	1	8	0
DEL PEAK 3(2P23.1) WILD-TYPE	164	118	179

Figure S95. Get High-res Image Gene #67: 'del_2p23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S96. Gene #68: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
DEL PEAK 4(2Q22.1) MUTATED	10	0	0
DEL PEAK 4(2Q22.1) WILD-TYPE	46	356	89

Figure S96. Get High-res Image Gene #68: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S97. Gene #68: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
DEL PEAK 4(2Q22.1) MUTATED	0	10	0
DEL PEAK 4(2Q22.1) WILD-TYPE	277	144	70

Figure S97. Get High-res Image Gene #68: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.066

Table S98. Gene #68: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	168	155	59	117
DEL PEAK 4(2Q22.1) MUTATED	0	10	0	0
DEL PEAK 4(2Q22.1) WILD-TYPE	168	145	59	117

Figure S98. Get High-res Image Gene #68: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S99. Gene #68: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
DEL PEAK 4(2Q22.1) MUTATED	0	10	0	0	0
DEL PEAK 4(2Q22.1) WILD-TYPE	105	124	86	96	78

Figure S99. Get High-res Image Gene #68: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S100. Gene #68: 'del_2q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
DEL PEAK 4(2Q22.1) MUTATED	0	10	0
DEL PEAK 4(2Q22.1) WILD-TYPE	182	141	167

Figure S100. Get High-res Image Gene #68: 'del_2q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S101. Gene #68: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
DEL PEAK 4(2Q22.1) MUTATED	0	10	0
DEL PEAK 4(2Q22.1) WILD-TYPE	179	118	193

Figure S101. Get High-res Image Gene #68: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S102. Gene #69: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
DEL PEAK 5(2Q37.3) MUTATED	11	2	0
DEL PEAK 5(2Q37.3) WILD-TYPE	45	354	89

Figure S102. Get High-res Image Gene #69: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S103. Gene #69: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
DEL PEAK 5(2Q37.3) MUTATED	0	12	1
DEL PEAK 5(2Q37.3) WILD-TYPE	277	142	69

Figure S103. Get High-res Image Gene #69: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.034

Table S104. Gene #69: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	168	155	59	117
DEL PEAK 5(2Q37.3) MUTATED	0	12	0	1
DEL PEAK 5(2Q37.3) WILD-TYPE	168	143	59	116

Figure S104. Get High-res Image Gene #69: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.034

Table S105. Gene #69: 'del_2q37.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
DEL PEAK 5(2Q37.3) MUTATED	0	12	1	0	0
DEL PEAK 5(2Q37.3) WILD-TYPE	105	122	85	96	78

Figure S105. Get High-res Image Gene #69: 'del_2q37.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S106. Gene #69: 'del_2q37.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
DEL PEAK 5(2Q37.3) MUTATED	1	12	0
DEL PEAK 5(2Q37.3) WILD-TYPE	181	139	167

Figure S106. Get High-res Image Gene #69: 'del_2q37.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S107. Gene #69: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
DEL PEAK 5(2Q37.3) MUTATED	0	12	1
DEL PEAK 5(2Q37.3) WILD-TYPE	179	116	192

Figure S107. Get High-res Image Gene #69: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.24

Table S108. Gene #69: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	126	179
DEL PEAK 5(2Q37.3) MUTATED	1	9	1
DEL PEAK 5(2Q37.3) WILD-TYPE	164	117	178

Figure S108. Get High-res Image Gene #69: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q22.31' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S109. Gene #72: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
DEL PEAK 11(6Q22.31) MUTATED	6	1	0
DEL PEAK 11(6Q22.31) WILD-TYPE	50	355	89

Figure S109. Get High-res Image Gene #72: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.2' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.13

Table S110. Gene #74: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
DEL PEAK 14(8P23.2) MUTATED	4	0	0
DEL PEAK 14(8P23.2) WILD-TYPE	52	356	89

Figure S110. Get High-res Image Gene #74: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p22' versus 'CN_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.17

Table S111. Gene #75: 'del_8p22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
DEL PEAK 15(8P22) MUTATED	4	0	0
DEL PEAK 15(8P22) WILD-TYPE	52	356	89

Figure S111. Get High-res Image Gene #75: 'del_8p22' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p12' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.15

Table S112. Gene #76: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
DEL PEAK 16(8P12) MUTATED	4	0	0
DEL PEAK 16(8P12) WILD-TYPE	52	356	89

Figure S112. Get High-res Image Gene #76: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_8q24.22' versus 'MIRSEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.18

Table S113. Gene #77: 'del_8q24.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
DEL PEAK 17(8Q24.22) MUTATED	0	7	0
DEL PEAK 17(8Q24.22) WILD-TYPE	182	144	167

Figure S113. Get High-res Image Gene #77: 'del_8q24.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8q24.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S114. Gene #77: 'del_8q24.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
DEL PEAK 17(8Q24.22) MUTATED	0	7	0
DEL PEAK 17(8Q24.22) WILD-TYPE	179	121	193

Figure S114. Get High-res Image Gene #77: 'del_8q24.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S115. Gene #78: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
DEL PEAK 18(9P21.3) MUTATED	16	2	2
DEL PEAK 18(9P21.3) WILD-TYPE	40	354	87

Figure S115. Get High-res Image Gene #78: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.17

Table S116. Gene #78: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	126	179
DEL PEAK 18(9P21.3) MUTATED	8	10	0
DEL PEAK 18(9P21.3) WILD-TYPE	157	116	179

Figure S116. Get High-res Image Gene #78: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q22.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S117. Gene #79: 'del_9q22.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
DEL PEAK 19(9Q22.33) MUTATED	21	2	4
DEL PEAK 19(9Q22.33) WILD-TYPE	35	354	85

Figure S117. Get High-res Image Gene #79: 'del_9q22.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p12.31' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S118. Gene #80: 'del_10p12.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
DEL PEAK 20(10P12.31) MUTATED	6	0	1
DEL PEAK 20(10P12.31) WILD-TYPE	50	356	88

Figure S118. Get High-res Image Gene #80: 'del_10p12.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.05

Table S119. Gene #82: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
DEL PEAK 22(10Q23.31) MUTATED	7	3	2
DEL PEAK 22(10Q23.31) WILD-TYPE	49	353	87

Figure S119. Get High-res Image Gene #82: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S120. Gene #83: 'del_11p15.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
DEL PEAK 23(11P15.1) MUTATED	6	0	1
DEL PEAK 23(11P15.1) WILD-TYPE	50	356	88

Figure S120. Get High-res Image Gene #83: 'del_11p15.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.081

Table S121. Gene #86: 'del_15q25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
DEL PEAK 27(15Q25.3) MUTATED	0	8	1
DEL PEAK 27(15Q25.3) WILD-TYPE	179	120	192

Figure S121. Get High-res Image Gene #86: 'del_15q25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.2' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.15

Table S122. Gene #90: 'del_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
DEL PEAK 32(19P13.2) MUTATED	5	1	1
DEL PEAK 32(19P13.2) WILD-TYPE	51	355	88

Figure S122. Get High-res Image Gene #90: 'del_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.2' versus 'MIRSEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.13

Table S123. Gene #90: 'del_19p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
DEL PEAK 32(19P13.2) MUTATED	0	7	0
DEL PEAK 32(19P13.2) WILD-TYPE	182	144	167

Figure S123. Get High-res Image Gene #90: 'del_19p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S124. Gene #90: 'del_19p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
DEL PEAK 32(19P13.2) MUTATED	0	7	0
DEL PEAK 32(19P13.2) WILD-TYPE	179	121	193

Figure S124. Get High-res Image Gene #90: 'del_19p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.058

Table S125. Gene #90: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	126	179
DEL PEAK 32(19P13.2) MUTATED	0	7	0
DEL PEAK 32(19P13.2) WILD-TYPE	165	119	179

Figure S125. Get High-res Image Gene #90: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q21.1' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.066

Table S126. Gene #92: 'del_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
DEL PEAK 36(21Q21.1) MUTATED	6	2	1
DEL PEAK 36(21Q21.1) WILD-TYPE	50	354	88

Figure S126. Get High-res Image Gene #92: 'del_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q12.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S127. Gene #93: 'del_22q12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
DEL PEAK 37(22Q12.3) MUTATED	13	0	77
DEL PEAK 37(22Q12.3) WILD-TYPE	43	356	12

Figure S127. Get High-res Image Gene #93: 'del_22q12.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q12.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S128. Gene #93: 'del_22q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
DEL PEAK 37(22Q12.3) MUTATED	37	47	6
DEL PEAK 37(22Q12.3) WILD-TYPE	240	107	64

Figure S128. Get High-res Image Gene #93: 'del_22q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q12.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S129. Gene #93: 'del_22q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	168	155	59	117
DEL PEAK 37(22Q12.3) MUTATED	8	47	8	27
DEL PEAK 37(22Q12.3) WILD-TYPE	160	108	51	90

Figure S129. Get High-res Image Gene #93: 'del_22q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q12.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S130. Gene #93: 'del_22q12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
DEL PEAK 37(22Q12.3) MUTATED	9	42	13	24	2
DEL PEAK 37(22Q12.3) WILD-TYPE	96	92	73	72	76

Figure S130. Get High-res Image Gene #93: 'del_22q12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q12.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S131. Gene #93: 'del_22q12.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
DEL PEAK 37(22Q12.3) MUTATED	22	40	28
DEL PEAK 37(22Q12.3) WILD-TYPE	157	88	165

Figure S131. Get High-res Image Gene #93: 'del_22q12.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q12.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.17

Table S132. Gene #93: 'del_22q12.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	164	146
DEL PEAK 37(22Q12.3) MUTATED	17	24	41
DEL PEAK 37(22Q12.3) WILD-TYPE	143	140	105

Figure S132. Get High-res Image Gene #93: 'del_22q12.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S133. Gene #94: 'del_22q13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
DEL PEAK 38(22Q13.1) MUTATED	13	0	76
DEL PEAK 38(22Q13.1) WILD-TYPE	43	356	13

Figure S133. Get High-res Image Gene #94: 'del_22q13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S134. Gene #94: 'del_22q13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
DEL PEAK 38(22Q13.1) MUTATED	36	47	6
DEL PEAK 38(22Q13.1) WILD-TYPE	241	107	64

Figure S134. Get High-res Image Gene #94: 'del_22q13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S135. Gene #94: 'del_22q13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	168	155	59	117
DEL PEAK 38(22Q13.1) MUTATED	8	47	8	26
DEL PEAK 38(22Q13.1) WILD-TYPE	160	108	51	91

Figure S135. Get High-res Image Gene #94: 'del_22q13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S136. Gene #94: 'del_22q13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
DEL PEAK 38(22Q13.1) MUTATED	9	42	13	23	2
DEL PEAK 38(22Q13.1) WILD-TYPE	96	92	73	73	76

Figure S136. Get High-res Image Gene #94: 'del_22q13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.1' versus 'MIRSEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.24

Table S137. Gene #94: 'del_22q13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
DEL PEAK 38(22Q13.1) MUTATED	23	43	23
DEL PEAK 38(22Q13.1) WILD-TYPE	159	108	144

Figure S137. Get High-res Image Gene #94: 'del_22q13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S138. Gene #94: 'del_22q13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
DEL PEAK 38(22Q13.1) MUTATED	21	40	28
DEL PEAK 38(22Q13.1) WILD-TYPE	158	88	165

Figure S138. Get High-res Image Gene #94: 'del_22q13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.17

Table S139. Gene #94: 'del_22q13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	164	146
DEL PEAK 38(22Q13.1) MUTATED	17	23	41
DEL PEAK 38(22Q13.1) WILD-TYPE	143	141	105

Figure S139. Get High-res Image Gene #94: 'del_22q13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.15

Table S140. Gene #94: 'del_22q13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	126	179
DEL PEAK 38(22Q13.1) MUTATED	22	37	22
DEL PEAK 38(22Q13.1) WILD-TYPE	143	89	157

Figure S140. Get High-res Image Gene #94: 'del_22q13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S141. Gene #95: 'del_22q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
DEL PEAK 39(22Q13.2) MUTATED	13	0	76
DEL PEAK 39(22Q13.2) WILD-TYPE	43	356	13

Figure S141. Get High-res Image Gene #95: 'del_22q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S142. Gene #95: 'del_22q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
DEL PEAK 39(22Q13.2) MUTATED	36	47	6
DEL PEAK 39(22Q13.2) WILD-TYPE	241	107	64

Figure S142. Get High-res Image Gene #95: 'del_22q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S143. Gene #95: 'del_22q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	168	155	59	117
DEL PEAK 39(22Q13.2) MUTATED	8	47	8	26
DEL PEAK 39(22Q13.2) WILD-TYPE	160	108	51	91

Figure S143. Get High-res Image Gene #95: 'del_22q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S144. Gene #95: 'del_22q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
DEL PEAK 39(22Q13.2) MUTATED	9	42	13	23	2
DEL PEAK 39(22Q13.2) WILD-TYPE	96	92	73	73	76

Figure S144. Get High-res Image Gene #95: 'del_22q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.2' versus 'MIRSEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.23

Table S145. Gene #95: 'del_22q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
DEL PEAK 39(22Q13.2) MUTATED	23	43	23
DEL PEAK 39(22Q13.2) WILD-TYPE	159	108	144

Figure S145. Get High-res Image Gene #95: 'del_22q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S146. Gene #95: 'del_22q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
DEL PEAK 39(22Q13.2) MUTATED	21	40	28
DEL PEAK 39(22Q13.2) WILD-TYPE	158	88	165

Figure S146. Get High-res Image Gene #95: 'del_22q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.11

Table S147. Gene #95: 'del_22q13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	164	146
DEL PEAK 39(22Q13.2) MUTATED	17	23	41
DEL PEAK 39(22Q13.2) WILD-TYPE	143	141	105

Figure S147. Get High-res Image Gene #95: 'del_22q13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.23

Table S148. Gene #95: 'del_22q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	126	179
DEL PEAK 39(22Q13.2) MUTATED	22	37	22
DEL PEAK 39(22Q13.2) WILD-TYPE	143	89	157

Figure S148. Get High-res Image Gene #95: 'del_22q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S149. Gene #96: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	356	89
DEL PEAK 40(22Q13.32) MUTATED	13	1	76
DEL PEAK 40(22Q13.32) WILD-TYPE	43	355	13

Figure S149. Get High-res Image Gene #96: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S150. Gene #96: 'del_22q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	277	154	70
DEL PEAK 40(22Q13.32) MUTATED	36	48	6
DEL PEAK 40(22Q13.32) WILD-TYPE	241	106	64

Figure S150. Get High-res Image Gene #96: 'del_22q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S151. Gene #96: 'del_22q13.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	168	155	59	117
DEL PEAK 40(22Q13.32) MUTATED	8	48	8	26
DEL PEAK 40(22Q13.32) WILD-TYPE	160	107	51	91

Figure S151. Get High-res Image Gene #96: 'del_22q13.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S152. Gene #96: 'del_22q13.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	105	134	86	96	78
DEL PEAK 40(22Q13.32) MUTATED	9	43	13	23	2
DEL PEAK 40(22Q13.32) WILD-TYPE	96	91	73	73	76

Figure S152. Get High-res Image Gene #96: 'del_22q13.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.13

Table S153. Gene #96: 'del_22q13.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	151	167
DEL PEAK 40(22Q13.32) MUTATED	23	44	23
DEL PEAK 40(22Q13.32) WILD-TYPE	159	107	144

Figure S153. Get High-res Image Gene #96: 'del_22q13.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.034

Table S154. Gene #96: 'del_22q13.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	128	193
DEL PEAK 40(22Q13.32) MUTATED	21	41	28
DEL PEAK 40(22Q13.32) WILD-TYPE	158	87	165

Figure S154. Get High-res Image Gene #96: 'del_22q13.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.16

Table S155. Gene #96: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	164	146
DEL PEAK 40(22Q13.32) MUTATED	17	24	41
DEL PEAK 40(22Q13.32) WILD-TYPE	143	140	105

Figure S155. Get High-res Image Gene #96: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.15

Table S156. Gene #96: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	126	179
DEL PEAK 40(22Q13.32) MUTATED	22	38	22
DEL PEAK 40(22Q13.32) WILD-TYPE	143	88	157

Figure S156. Get High-res Image Gene #96: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = THCA-TP.transferedmergedcluster.txt
Number of patients = 501
Number of significantly focal cnvs = 98
Number of molecular subtypes = 10
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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