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

Esophageal Carcinoma (Primary solid tumor)

28 January 2016 | analyses__2016_01_28

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 (2016): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1VX0FVQ

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 82 focal events and 10 molecular subtypes across 184 patients, 345 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p34.2 cnv correlated to 'RPPA_CNMF' and 'MIRSEQ_CNMF'.
amp_1q23.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_1q42.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
amp_2q14.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_2q31.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_3q26.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_4q13.3 cnv correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.
amp_5p15.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6p21.1 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6q23.3 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7p11.2 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
amp_7q21.2 cnv correlated to 'CN_CNMF'.
amp_8p23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8p11.21 cnv correlated to 'MIRSEQ_CNMF'.
amp_8q24.21 cnv correlated to 'RPPA_CNMF'.
amp_9p13.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
amp_9q34.3 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.
amp_11p13 cnv correlated to 'CN_CNMF'.
amp_11q13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12p12.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_13q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_14q21.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_15q26.1 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_18p11.32 cnv correlated to 'MRNASEQ_CNMF'.
amp_18q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19q12 cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CNMF'.
amp_xq28 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
del_2q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q33.3 cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p26.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p14.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3q26.31 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_4p15.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_4q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_6p25.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
del_6q16.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_7q31.1 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
del_7q36.3 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
del_8p23.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_8p12 cnv correlated to 'CN_CNMF'.
del_9p23 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_10p15.3 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_10p11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q21.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_10q23.31 cnv correlated to 'CN_CNMF'.
del_11p15.4 cnv correlated to 'CN_CNMF'.
del_11q25 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_12q23.1 cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q12.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q21.31 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_14q23.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q11.2 cnv correlated to 'CN_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18p11.23 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q12.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q21.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q22.3 cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_20p12.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_21q21.1 cnv correlated to 'CN_CNMF'.
del_21q22.12 cnv correlated to 'METHLYATION_CNMF'.
del_22q11.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp21.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp11.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xq21.33 cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 82 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, 345 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 3q26 31	16 (9%)	168	0.00024 (0.00212)	0.0127 (0.0483)	0.0113 (0.0446)	0.00962 (0.0396)	0.0151 (0.054)	0.00013 (0.00125)	0.0272 (0.0781)	0.00032 (0.00255)	0.00147 (0.0088)	0.00013 (0.00125)
del 10p11 21	52 (28%)	132	1e-05 (2e-04)	0.00022 (0.00196)	0.00594 (0.0272)	0.0311 (0.0844)	0.00043 (0.00333)	1e-05 (2e-04)	9e-05 (0.000946)	3e-05 (0.000397)	0.00093 (0.0061)	3e-05 (0.000397)
del 22q11 1	79 (43%)	105	1e-05 (2e-04)	2e-05 (0.000283)	0.00043 (0.00333)	0.0044 (0.022)	1e-05 (2e-04)	1e-05 (2e-04)	0.00111 (0.00695)	1e-05 (2e-04)	1e-05 (2e-04)	2e-05 (0.000283)
amp 3q26 2	128 (70%)	56	1e-05 (2e-04)	1e-05 (2e-04)	0.0862 (0.172)	0.00061 (0.00451)	2e-05 (0.000283)	1e-05 (2e-04)	0.00484 (0.0233)	2e-05 (0.000283)	1e-05 (2e-04)	5e-05 (0.000594)
del 2q22 1	59 (32%)	125	4e-05 (0.000505)	2e-05 (0.000283)	0.135 (0.236)	0.00259 (0.0144)	1e-05 (2e-04)	1e-05 (2e-04)	2e-05 (0.000283)	1e-05 (2e-04)	4e-05 (0.000505)	2e-05 (0.000283)
del 13q12 11	76 (41%)	108	0.00013 (0.00125)	0.00084 (0.00565)	0.206 (0.319)	0.0381 (0.0971)	0.0172 (0.0583)	0.00381 (0.0196)	0.0117 (0.0454)	0.00972 (0.0399)	0.0217 (0.068)	0.0117 (0.0454)
del 16q23 1	84 (46%)	100	1e-05 (2e-04)	1e-05 (2e-04)	0.0706 (0.152)	0.0395 (0.0998)	1e-05 (2e-04)	1e-05 (2e-04)	7e-05 (0.000786)	1e-05 (2e-04)	1e-05 (2e-04)	1e-05 (2e-04)
amp 8p23 1	52 (28%)	132	0.00029 (0.0024)	0.00856 (0.0367)	0.79 (0.845)	0.176 (0.288)	0.0294 (0.0818)	8e-05 (0.000863)	0.00644 (0.029)	0.0141 (0.0513)	0.00092 (0.00608)	0.0021 (0.0124)
amp 11q13 3	104 (57%)	80	2e-05 (0.000283)	0.0158 (0.055)	0.00612 (0.0278)	0.0132 (0.0493)	0.0154 (0.0545)	0.00096 (0.00625)	0.109 (0.204)	0.00134 (0.0082)	0.211 (0.323)	0.00324 (0.017)
amp 17q12	75 (41%)	109	0.0247 (0.0743)	0.0013 (0.00808)	0.355 (0.466)	0.539 (0.642)	0.0223 (0.0694)	0.00296 (0.0161)	0.014 (0.0511)	0.0201 (0.0656)	0.0213 (0.0676)	0.00146 (0.0088)
del 3p26 2	111 (60%)	73	1e-05 (2e-04)	3e-05 (0.000397)	0.112 (0.209)	0.051 (0.12)	0.00044 (0.00337)	5e-05 (0.000594)	0.0205 (0.0661)	0.00018 (0.00168)	0.0163 (0.0563)	0.00032 (0.00255)
del 3p14 3	126 (68%)	58	1e-05 (2e-04)	1e-05 (2e-04)	0.0531 (0.123)	0.0606 (0.136)	0.00028 (0.00234)	1e-05 (2e-04)	0.00348 (0.0181)	2e-05 (0.000283)	2e-05 (0.000283)	1e-05 (2e-04)
del 3p14 2	125 (68%)	59	1e-05 (2e-04)	1e-05 (2e-04)	0.21 (0.323)	0.103 (0.196)	0.00075 (0.00526)	1e-05 (2e-04)	0.0109 (0.0432)	1e-05 (2e-04)	0.00012 (0.0012)	2e-05 (0.000283)
del 4q34 3	99 (54%)	85	5e-05 (0.000594)	0.00245 (0.0139)	0.265 (0.383)	0.887 (0.908)	0.0333 (0.0889)	0.00105 (0.00667)	0.0327 (0.0877)	0.00323 (0.017)	0.00534 (0.025)	0.00061 (0.00451)
del 16p13 3	65 (35%)	119	2e-05 (0.000283)	0.0003 (0.00244)	0.379 (0.491)	0.296 (0.412)	1e-05 (2e-04)	8e-05 (0.000863)	0.00028 (0.00234)	1e-05 (2e-04)	7e-05 (0.000786)	2e-05 (0.000283)
del 17p12	86 (47%)	98	1e-05 (2e-04)	1e-05 (2e-04)	0.0978 (0.189)	0.253 (0.37)	0.00012 (0.0012)	2e-05 (0.000283)	0.00038 (0.003)	4e-05 (0.000505)	0.0127 (0.0483)	1e-05 (2e-04)
del 18q21 2	119 (65%)	65	5e-05 (0.000594)	0.00945 (0.0393)	0.355 (0.466)	0.65 (0.739)	0.00077 (0.00535)	0.00957 (0.0396)	6e-05 (0.000693)	0.00203 (0.0121)	0.0217 (0.068)	0.00147 (0.0088)
amp 5p15 33	98 (53%)	86	1e-05 (2e-04)	8e-05 (0.000863)	0.444 (0.554)	0.283 (0.4)	0.0313 (0.0847)	0.00079 (0.00544)	0.0813 (0.165)	0.00417 (0.0212)	0.00446 (0.022)	0.00133 (0.0082)
amp 6q23 3	42 (23%)	142	0.17 (0.28)	0.0487 (0.117)	0.005 (0.0237)	0.00566 (0.0261)	0.179 (0.29)	0.0717 (0.154)	0.0133 (0.0494)	0.0309 (0.0843)	0.00477 (0.0233)	0.018 (0.0606)
amp 13q22 1	65 (35%)	119	0.00104 (0.00666)	0.0375 (0.0961)	0.983 (0.989)	0.19 (0.301)	0.203 (0.315)	0.00106 (0.00669)	0.0172 (0.0583)	0.00238 (0.0136)	0.0122 (0.0469)	0.00026 (0.00227)
amp 15q26 1	58 (32%)	126	0.0006 (0.00451)	0.276 (0.394)	0.265 (0.383)	0.0446 (0.11)	0.0107 (0.0426)	0.0152 (0.054)	0.125 (0.226)	0.0433 (0.108)	0.0252 (0.0747)	0.0157 (0.0547)
amp 18q11 2	59 (32%)	125	0.0335 (0.0892)	0.0398 (0.1)	0.0804 (0.165)	0.141 (0.246)	0.145 (0.25)	0.00491 (0.0235)	0.00305 (0.0162)	0.00909 (0.0384)	0.0281 (0.0799)	0.00053 (0.00402)
del 1p36 11	75 (41%)	109	6e-05 (0.000693)	1e-05 (2e-04)	0.968 (0.978)	0.926 (0.941)	2e-05 (0.000283)	0.0235 (0.0726)	0.186 (0.296)	0.0237 (0.0727)	0.0388 (0.0984)	0.0337 (0.0894)
del 4q22 1	105 (57%)	79	3e-05 (0.000397)	0.0125 (0.048)	0.665 (0.75)	0.955 (0.966)	0.00484 (0.0233)	0.0119 (0.0461)	0.0376 (0.0962)	0.0744 (0.158)	0.00856 (0.0367)	0.00981 (0.0399)
del 13q14 2	74 (40%)	110	0.00081 (0.00549)	0.00917 (0.0384)	0.339 (0.452)	0.131 (0.232)	0.0172 (0.0583)	0.0213 (0.0676)	0.129 (0.23)	0.0247 (0.0743)	0.0145 (0.0525)	0.0155 (0.0545)
del 14q23 3	51 (28%)	133	1e-05 (2e-04)	0.0251 (0.0747)	0.0511 (0.12)	0.0249 (0.0744)	0.00435 (0.0219)	0.0438 (0.108)	0.108 (0.203)	0.0131 (0.0493)	0.0748 (0.158)	0.00458 (0.0225)
amp 6p21 1	69 (38%)	115	0.15 (0.254)	0.0372 (0.0957)	0.181 (0.292)	0.204 (0.316)	0.0977 (0.189)	0.0309 (0.0843)	0.00274 (0.0152)	0.00211 (0.0124)	0.00287 (0.0157)	0.00249 (0.014)
del 8p23 2	92 (50%)	92	0.00062 (0.00454)	0.0232 (0.0719)	0.639 (0.731)	0.00304 (0.0162)	0.0619 (0.138)	0.0232 (0.0719)	0.00841 (0.0365)	0.0557 (0.127)	0.0201 (0.0656)	0.0641 (0.142)
del 18q12 2	111 (60%)	73	0.00019 (0.00175)	0.045 (0.11)	0.512 (0.618)	0.584 (0.68)	0.0188 (0.0619)	0.0728 (0.155)	0.00917 (0.0384)	0.00065 (0.00472)	0.0675 (0.148)	0.00017 (0.00162)
amp 14q21 1	61 (33%)	123	0.005 (0.0237)	0.129 (0.23)	0.0733 (0.156)	0.229 (0.344)	0.183 (0.293)	0.00281 (0.0155)	0.1 (0.192)	0.00407 (0.0209)	0.00703 (0.0312)	0.0147 (0.053)
amp xq28	69 (38%)	115	0.0182 (0.0609)	0.44 (0.551)	0.27 (0.389)	0.539 (0.642)	0.0478 (0.116)	0.0269 (0.0781)	0.411 (0.524)	0.00235 (0.0136)	0.287 (0.402)	0.0003 (0.00244)
del 10p15 3	54 (29%)	130	0.00071 (0.00511)	0.199 (0.311)	0.0303 (0.0838)	0.169 (0.279)	0.0774 (0.162)	0.0252 (0.0747)	0.0359 (0.0934)	0.0113 (0.0446)	0.13 (0.231)	0.0798 (0.165)
del 19p13 3	94 (51%)	90	0.00075 (0.00526)	0.00647 (0.029)	0.275 (0.394)	0.987 (0.992)	0.0185 (0.0613)	0.349 (0.462)	0.149 (0.253)	0.0134 (0.0497)	0.069 (0.149)	0.00613 (0.0278)
del 20p12 1	33 (18%)	151	0.037 (0.0955)	0.507 (0.614)	0.0795 (0.164)	0.873 (0.898)	0.0217 (0.068)	0.00704 (0.0312)	0.276 (0.394)	0.0496 (0.118)	0.682 (0.764)	0.0287 (0.0808)
del xp11 3	75 (41%)	109	0.0008 (0.00547)	0.0792 (0.164)	0.412 (0.524)	0.862 (0.891)	0.0449 (0.11)	0.0156 (0.0547)	0.106 (0.199)	0.0254 (0.0747)	0.0557 (0.127)	0.00726 (0.032)
amp 1q23 3	93 (51%)	91	0.00018 (0.00168)	2e-05 (0.000283)	0.832 (0.867)	0.646 (0.737)	0.0114 (0.0446)	0.807 (0.855)	0.371 (0.483)	0.843 (0.876)	0.0204 (0.0659)	0.938 (0.952)
del 2q33 3	36 (20%)	148	0.155 (0.26)	0.156 (0.26)	0.122 (0.222)	0.193 (0.305)	0.0499 (0.119)	0.027 (0.0781)	0.0327 (0.0877)	0.0706 (0.152)	0.154 (0.259)	0.0314 (0.0848)
del 5q12 1	112 (61%)	72	0.00027 (0.00231)	0.00011 (0.00113)	0.811 (0.856)	0.637 (0.731)	0.0128 (0.0483)	0.498 (0.603)	0.0947 (0.184)	0.0238 (0.0727)	0.373 (0.484)	0.208 (0.321)
del 18p11 23	60 (33%)	124	0.0002 (0.00182)	0.085 (0.17)	0.399 (0.511)	0.766 (0.826)	0.0786 (0.164)	0.0294 (0.0818)	0.0272 (0.0781)	0.137 (0.239)	0.0688 (0.149)	0.0409 (0.102)
del 18q22 3	112 (61%)	72	0.00424 (0.0215)	0.082 (0.166)	0.875 (0.899)	0.866 (0.894)	0.0845 (0.169)	0.134 (0.235)	0.0269 (0.0781)	0.00803 (0.035)	0.0721 (0.154)	0.0273 (0.0781)
amp 1q42 3	96 (52%)	88	1e-05 (2e-04)	1e-05 (2e-04)	0.898 (0.918)	0.413 (0.525)	0.0308 (0.0843)	0.737 (0.807)	0.454 (0.565)	0.281 (0.399)	0.181 (0.292)	0.675 (0.759)
amp 2q31 1	60 (33%)	124	0.00554 (0.0257)	9e-05 (0.000946)	0.694 (0.774)	0.233 (0.348)	0.189 (0.3)	0.0368 (0.0952)	0.972 (0.98)	0.269 (0.388)	0.168 (0.278)	0.547 (0.651)
amp 9q34 3	64 (35%)	120	0.00101 (0.00652)	0.584 (0.68)	0.212 (0.324)	0.0244 (0.0738)	0.0292 (0.0817)	0.711 (0.788)	0.0814 (0.165)	0.11 (0.206)	0.0552 (0.126)	0.331 (0.446)
amp 12p12 1	79 (43%)	105	0.00088 (0.00587)	0.142 (0.246)	0.246 (0.363)	0.56 (0.662)	0.0173 (0.0585)	0.0291 (0.0817)	0.232 (0.347)	0.0839 (0.168)	0.0867 (0.172)	0.12 (0.22)
del 1p13 2	64 (35%)	120	0.00022 (0.00196)	0.00027 (0.00231)	0.486 (0.594)	0.568 (0.666)	0.0001 (0.00104)	0.595 (0.69)	0.83 (0.866)	0.104 (0.198)	0.0751 (0.158)	0.527 (0.633)
del 9p23	108 (59%)	76	0.0168 (0.058)	0.216 (0.328)	0.367 (0.479)	0.712 (0.788)	0.0304 (0.0839)	0.0238 (0.0727)	0.275 (0.394)	0.726 (0.798)	0.981 (0.988)	0.668 (0.752)
del 9p21 3	141 (77%)	43	1e-05 (2e-04)	0.0346 (0.0905)	0.827 (0.864)	0.21 (0.323)	0.159 (0.265)	0.0208 (0.0666)	0.529 (0.633)	0.103 (0.196)	0.218 (0.331)	0.0989 (0.19)
del 11q25	81 (44%)	103	2e-05 (0.000283)	0.0453 (0.11)	0.489 (0.594)	0.262 (0.38)	0.287 (0.402)	0.0493 (0.118)	0.166 (0.275)	0.0816 (0.165)	0.0827 (0.167)	0.0654 (0.144)
del 15q11 2	63 (34%)	121	0.039 (0.0988)	0.12 (0.22)	0.817 (0.858)	0.417 (0.528)	0.059 (0.133)	0.242 (0.36)	0.594 (0.69)	0.0204 (0.0659)	0.748 (0.815)	0.0184 (0.0613)
del xp21 1	70 (38%)	114	0.00075 (0.00526)	0.0916 (0.179)	0.0836 (0.168)	0.529 (0.633)	0.0104 (0.0419)	0.146 (0.25)	0.319 (0.435)	0.13 (0.231)	0.144 (0.249)	0.0264 (0.0769)
amp 1p34 2	40 (22%)	144	0.15 (0.254)	0.824 (0.862)	0.00905 (0.0384)	0.256 (0.373)	0.113 (0.21)	0.683 (0.764)	0.0135 (0.0498)	0.32 (0.435)	0.764 (0.826)	0.713 (0.788)
amp 2q14 2	60 (33%)	124	0.0493 (0.118)	0.00547 (0.0255)	0.314 (0.43)	0.306 (0.422)	0.244 (0.362)	0.0534 (0.124)	0.582 (0.68)	0.21 (0.323)	0.394 (0.507)	0.198 (0.31)
amp 4q13 3	36 (20%)	148	0.0341 (0.0899)	0.487 (0.594)	0.233 (0.347)	0.0339 (0.0897)	0.142 (0.247)	0.178 (0.289)	0.438 (0.55)	0.0685 (0.149)	0.239 (0.356)	0.0914 (0.179)
amp 7p11 2	125 (68%)	59	0.0923 (0.18)	0.0308 (0.0843)	0.998 (1.00)	0.75 (0.815)	0.0187 (0.0618)	0.115 (0.213)	0.442 (0.553)	0.325 (0.439)	0.815 (0.858)	0.17 (0.28)
amp 9p13 3	40 (22%)	144	0.00345 (0.018)	0.105 (0.199)	0.871 (0.897)	0.784 (0.841)	0.0242 (0.0734)	0.682 (0.764)	0.108 (0.203)	0.132 (0.232)	0.213 (0.325)	0.609 (0.702)
amp 19q12	55 (30%)	129	0.0602 (0.136)	0.0764 (0.161)	0.523 (0.629)	0.231 (0.346)	0.048 (0.116)	0.164 (0.274)	0.0406 (0.102)	0.323 (0.438)	0.178 (0.289)	0.107 (0.202)
del 4p15 2	106 (58%)	78	0.028 (0.0796)	0.00859 (0.0367)	0.284 (0.401)	0.941 (0.954)	0.0682 (0.149)	0.475 (0.586)	0.428 (0.541)	0.749 (0.815)	0.0513 (0.121)	0.478 (0.59)
del 6p25 3	74 (40%)	110	0.00982 (0.0399)	0.0663 (0.145)	0.806 (0.855)	0.434 (0.548)	0.0813 (0.165)	0.335 (0.448)	0.147 (0.252)	0.0211 (0.0673)	0.253 (0.371)	0.0792 (0.164)
del 6q16 3	55 (30%)	129	0.0346 (0.0905)	0.121 (0.22)	0.397 (0.509)	0.556 (0.659)	0.0441 (0.109)	0.603 (0.696)	0.341 (0.453)	0.51 (0.616)	0.257 (0.374)	0.557 (0.659)
del 7q31 1	56 (30%)	128	0.121 (0.221)	0.00238 (0.0136)	0.202 (0.314)	0.762 (0.825)	0.0254 (0.0747)	0.459 (0.571)	0.704 (0.783)	0.0961 (0.186)	0.111 (0.207)	0.0548 (0.126)
del 7q36 3	67 (36%)	117	0.438 (0.55)	0.0283 (0.0801)	0.786 (0.841)	0.717 (0.791)	0.00299 (0.0161)	0.226 (0.341)	0.306 (0.422)	0.149 (0.254)	0.353 (0.465)	0.467 (0.579)
del 10q21 1	46 (25%)	138	0.00446 (0.022)	0.036 (0.0934)	0.408 (0.521)	0.35 (0.462)	0.091 (0.179)	0.0655 (0.144)	0.382 (0.494)	0.057 (0.129)	0.181 (0.292)	0.0502 (0.119)
del 13q21 31	69 (38%)	115	0.00504 (0.0238)	0.154 (0.26)	0.663 (0.75)	0.648 (0.737)	0.0482 (0.116)	0.115 (0.212)	0.442 (0.553)	0.134 (0.235)	0.0727 (0.155)	0.0908 (0.179)
amp 7q21 2	114 (62%)	70	0.0143 (0.0518)	0.334 (0.448)	0.53 (0.633)	0.917 (0.935)	0.48 (0.59)	0.817 (0.858)	0.338 (0.451)	0.606 (0.699)	0.846 (0.878)	0.28 (0.398)
amp 8p11 21	86 (47%)	98	0.742 (0.813)	0.48 (0.59)	0.763 (0.825)	0.751 (0.815)	0.0896 (0.178)	0.0796 (0.164)	0.0417 (0.104)	0.919 (0.935)	0.806 (0.855)	0.621 (0.713)
amp 8q24 21	145 (79%)	39	0.117 (0.216)	0.0816 (0.165)	0.0171 (0.0583)	0.0624 (0.138)	0.373 (0.484)	0.113 (0.209)	0.785 (0.841)	0.0991 (0.19)	0.189 (0.3)	0.32 (0.435)
amp 11p13	50 (27%)	134	0.00243 (0.0138)	0.179 (0.29)	0.663 (0.75)	0.429 (0.542)	0.556 (0.659)	1 (1.00)	0.707 (0.786)	0.712 (0.788)	0.59 (0.686)	0.849 (0.88)
amp 18p11 32	69 (38%)	115	0.0618 (0.138)	0.275 (0.394)	0.746 (0.815)	0.468 (0.579)	0.0439 (0.108)	0.175 (0.285)	0.0605 (0.136)	0.562 (0.663)	0.259 (0.376)	0.293 (0.409)
del 8p12	75 (41%)	109	0.00767 (0.0336)	0.285 (0.401)	0.811 (0.856)	0.485 (0.593)	0.997 (1.00)	0.134 (0.236)	0.835 (0.869)	0.802 (0.853)	0.561 (0.662)	0.597 (0.692)
del 10q23 31	65 (35%)	119	0.0344 (0.0904)	0.0765 (0.161)	0.454 (0.565)	0.0903 (0.178)	0.363 (0.473)	0.287 (0.402)	0.863 (0.891)	0.278 (0.396)	0.483 (0.593)	0.248 (0.365)
del 11p15 4	79 (43%)	105	0.0102 (0.0413)	0.182 (0.292)	0.681 (0.764)	0.484 (0.593)	0.219 (0.331)	0.361 (0.473)	0.517 (0.622)	0.185 (0.295)	0.718 (0.791)	0.246 (0.363)
del 12q23 1	52 (28%)	132	0.276 (0.394)	0.335 (0.448)	0.314 (0.43)	0.414 (0.525)	0.277 (0.395)	0.101 (0.193)	0.335 (0.448)	0.194 (0.306)	0.145 (0.25)	0.0133 (0.0494)
del 21q21 1	107 (58%)	77	0.0263 (0.0769)	0.0536 (0.124)	0.393 (0.507)	0.129 (0.23)	0.252 (0.37)	0.127 (0.228)	0.349 (0.462)	0.174 (0.284)	0.218 (0.331)	0.062 (0.138)
del 21q22 12	108 (59%)	76	0.0518 (0.121)	0.0152 (0.054)	0.487 (0.594)	0.254 (0.371)	0.121 (0.22)	0.167 (0.277)	0.0913 (0.179)	0.328 (0.443)	0.198 (0.31)	0.173 (0.284)
del xq21 33	41 (22%)	143	0.694 (0.774)	0.247 (0.364)	0.307 (0.422)	0.887 (0.908)	0.0549 (0.126)	0.35 (0.462)	0.318 (0.435)	0.0203 (0.0659)	0.566 (0.664)	0.338 (0.451)
amp 11p13	52 (28%)	132	0.0525 (0.123)	0.126 (0.228)	0.887 (0.908)	0.647 (0.737)	0.306 (0.422)	0.331 (0.446)	0.202 (0.314)	0.127 (0.228)	0.395 (0.508)	0.212 (0.324)
amp 12q15	51 (28%)	133	0.131 (0.232)	0.684 (0.765)	0.4 (0.512)	0.809 (0.856)	0.321 (0.436)	0.917 (0.935)	0.564 (0.663)	0.598 (0.692)	0.225 (0.339)	0.468 (0.579)
del 1q44	17 (9%)	167	0.943 (0.955)	0.767 (0.827)	0.053 (0.123)	0.307 (0.422)	0.797 (0.849)	0.612 (0.704)	0.489 (0.594)	0.644 (0.736)	0.795 (0.848)	0.219 (0.331)
del 3q11 1	33 (18%)	151	0.819 (0.858)	0.816 (0.858)	0.569 (0.666)	0.859 (0.889)	0.0807 (0.165)	0.821 (0.86)	0.159 (0.265)	0.793 (0.846)	0.359 (0.47)	0.564 (0.663)
del 6q26	50 (27%)	134	0.148 (0.253)	0.191 (0.303)	0.153 (0.258)	0.294 (0.41)	0.0574 (0.13)	0.198 (0.31)	0.64 (0.731)	0.73 (0.801)	0.665 (0.75)	0.298 (0.414)
del 17q25 3	41 (22%)	143	0.284 (0.401)	0.149 (0.253)	0.918 (0.935)	0.662 (0.75)	0.348 (0.461)	1 (1.00)	0.299 (0.415)	0.539 (0.642)	0.129 (0.23)	0.307 (0.422)
del xq11 2	43 (23%)	141	0.435 (0.548)	0.389 (0.502)	0.782 (0.841)	0.75 (0.815)	0.778 (0.837)	0.72 (0.793)	0.492 (0.596)	0.152 (0.256)	0.198 (0.31)	0.762 (0.825)

'amp_1p34.2' versus 'RPPA_CNMF'

P value = 0.00905 (Fisher's exact test), Q value = 0.038

Table S1. Gene #1: 'amp_1p34.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	28	30	34	8
AMP PEAK 1(1P34.2) MUTATED	6	7	10	1	3
AMP PEAK 1(1P34.2) WILD-TYPE	20	21	20	33	5

Figure S1. Get High-res Image Gene #1: 'amp_1p34.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_1p34.2' versus 'MIRSEQ_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.05

Table S2. Gene #1: 'amp_1p34.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
AMP PEAK 1(1P34.2) MUTATED	17	4	5	2	9	3
AMP PEAK 1(1P34.2) WILD-TYPE	53	11	5	16	19	39

Figure S2. Get High-res Image Gene #1: 'amp_1p34.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q23.3' versus 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0017

Table S3. Gene #2: 'amp_1q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
AMP PEAK 2(1Q23.3) MUTATED	41	6	46
AMP PEAK 2(1Q23.3) WILD-TYPE	33	27	31

Figure S3. Get High-res Image Gene #2: 'amp_1q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q23.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S4. Gene #2: 'amp_1q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
AMP PEAK 2(1Q23.3) MUTATED	25	17	0	31	13	3	4
AMP PEAK 2(1Q23.3) WILD-TYPE	11	25	2	10	24	14	5

Figure S4. Get High-res Image Gene #2: 'amp_1q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q23.3' versus 'MRNASEQ_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.045

Table S5. Gene #2: 'amp_1q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
AMP PEAK 2(1Q23.3) MUTATED	37	8	15	22	2	9
AMP PEAK 2(1Q23.3) WILD-TYPE	36	6	27	7	7	7

Figure S5. Get High-res Image Gene #2: 'amp_1q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0204 (Fisher's exact test), Q value = 0.066

Table S6. Gene #2: 'amp_1q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	67	35	12
AMP PEAK 2(1Q23.3) MUTATED	35	40	10	5
AMP PEAK 2(1Q23.3) WILD-TYPE	29	27	25	7

Figure S6. Get High-res Image Gene #2: 'amp_1q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_1q42.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S7. Gene #3: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
AMP PEAK 3(1Q42.3) MUTATED	42	5	49
AMP PEAK 3(1Q42.3) WILD-TYPE	32	28	28

Figure S7. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q42.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S8. Gene #3: 'amp_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
AMP PEAK 3(1Q42.3) MUTATED	27	14	0	31	16	3	5
AMP PEAK 3(1Q42.3) WILD-TYPE	9	28	2	10	21	14	4

Figure S8. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q42.3' versus 'MRNASEQ_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.084

Table S9. Gene #3: 'amp_1q42.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
AMP PEAK 3(1Q42.3) MUTATED	35	9	17	22	3	10
AMP PEAK 3(1Q42.3) WILD-TYPE	38	5	25	7	6	6

Figure S9. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_2q14.2' versus 'CN_CNMF'

P value = 0.0493 (Fisher's exact test), Q value = 0.12

Table S10. Gene #4: 'amp_2q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
AMP PEAK 4(2Q14.2) MUTATED	22	6	32
AMP PEAK 4(2Q14.2) WILD-TYPE	52	27	45

Figure S10. Get High-res Image Gene #4: 'amp_2q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2q14.2' versus 'METHLYATION_CNMF'

P value = 0.00547 (Fisher's exact test), Q value = 0.025

Table S11. Gene #4: 'amp_2q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
AMP PEAK 4(2Q14.2) MUTATED	11	9	2	21	7	5	5
AMP PEAK 4(2Q14.2) WILD-TYPE	25	33	0	20	30	12	4

Figure S11. Get High-res Image Gene #4: 'amp_2q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_2q31.1' versus 'CN_CNMF'

P value = 0.00554 (Fisher's exact test), Q value = 0.026

Table S12. Gene #5: 'amp_2q31.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
AMP PEAK 5(2Q31.1) MUTATED	23	4	33
AMP PEAK 5(2Q31.1) WILD-TYPE	51	29	44

Figure S12. Get High-res Image Gene #5: 'amp_2q31.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2q31.1' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00095

Table S13. Gene #5: 'amp_2q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
AMP PEAK 5(2Q31.1) MUTATED	16	7	2	22	8	1	4
AMP PEAK 5(2Q31.1) WILD-TYPE	20	35	0	19	29	16	5

Figure S13. Get High-res Image Gene #5: 'amp_2q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_2q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0368 (Fisher's exact test), Q value = 0.095

Table S14. Gene #5: 'amp_2q31.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
AMP PEAK 5(2Q31.1) MUTATED	15	10	35
AMP PEAK 5(2Q31.1) WILD-TYPE	52	10	61

Figure S14. Get High-res Image Gene #5: 'amp_2q31.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S15. Gene #6: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
AMP PEAK 6(3Q26.2) MUTATED	43	9	76
AMP PEAK 6(3Q26.2) WILD-TYPE	31	24	1

Figure S15. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S16. Gene #6: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
AMP PEAK 6(3Q26.2) MUTATED	19	26	1	40	31	5	6
AMP PEAK 6(3Q26.2) WILD-TYPE	17	16	1	1	6	12	3

Figure S16. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.0045

Table S17. Gene #6: 'amp_3q26.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	23	21	22	26	34
AMP PEAK 6(3Q26.2) MUTATED	12	12	14	25	29
AMP PEAK 6(3Q26.2) WILD-TYPE	11	9	8	1	5

Figure S17. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_3q26.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S18. Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
AMP PEAK 6(3Q26.2) MUTATED	39	13	33	28	5	9
AMP PEAK 6(3Q26.2) WILD-TYPE	34	1	9	1	4	7

Figure S18. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S19. Gene #6: 'amp_3q26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
AMP PEAK 6(3Q26.2) MUTATED	38	7	82
AMP PEAK 6(3Q26.2) WILD-TYPE	29	13	14

Figure S19. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_CNMF'

P value = 0.00484 (Fisher's exact test), Q value = 0.023

Table S20. Gene #6: 'amp_3q26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
AMP PEAK 6(3Q26.2) MUTATED	37	13	8	15	19	35
AMP PEAK 6(3Q26.2) WILD-TYPE	33	2	2	3	9	7

Figure S20. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S21. Gene #6: 'amp_3q26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
AMP PEAK 6(3Q26.2) MUTATED	33	13	56	25
AMP PEAK 6(3Q26.2) WILD-TYPE	29	13	6	8

Figure S21. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S22. Gene #6: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	67	35	12
AMP PEAK 6(3Q26.2) MUTATED	34	62	23	7
AMP PEAK 6(3Q26.2) WILD-TYPE	30	5	12	5

Figure S22. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00059

Table S23. Gene #6: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
AMP PEAK 6(3Q26.2) MUTATED	31	15	80
AMP PEAK 6(3Q26.2) WILD-TYPE	24	14	14

Figure S23. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q13.3' versus 'CN_CNMF'

P value = 0.0341 (Fisher's exact test), Q value = 0.09

Table S24. Gene #7: 'amp_4q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
AMP PEAK 7(4Q13.3) MUTATED	9	5	22
AMP PEAK 7(4Q13.3) WILD-TYPE	65	28	55

Figure S24. Get High-res Image Gene #7: 'amp_4q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4q13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0339 (Fisher's exact test), Q value = 0.09

Table S25. Gene #7: 'amp_4q13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	23	21	22	26	34
AMP PEAK 7(4Q13.3) MUTATED	2	7	9	6	4
AMP PEAK 7(4Q13.3) WILD-TYPE	21	14	13	20	30

Figure S25. Get High-res Image Gene #7: 'amp_4q13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S26. Gene #8: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
AMP PEAK 8(5P15.33) MUTATED	36	7	55
AMP PEAK 8(5P15.33) WILD-TYPE	38	26	22

Figure S26. Get High-res Image Gene #8: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00086

Table S27. Gene #8: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
AMP PEAK 8(5P15.33) MUTATED	15	16	0	34	22	6	5
AMP PEAK 8(5P15.33) WILD-TYPE	21	26	2	7	15	11	4

Figure S27. Get High-res Image Gene #8: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.085

Table S28. Gene #8: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
AMP PEAK 8(5P15.33) MUTATED	30	7	26	22	4	9
AMP PEAK 8(5P15.33) WILD-TYPE	43	7	16	7	5	7

Figure S28. Get High-res Image Gene #8: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.0054

Table S29. Gene #8: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
AMP PEAK 8(5P15.33) MUTATED	30	5	63
AMP PEAK 8(5P15.33) WILD-TYPE	37	15	33

Figure S29. Get High-res Image Gene #8: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00417 (Fisher's exact test), Q value = 0.021

Table S30. Gene #8: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
AMP PEAK 8(5P15.33) MUTATED	24	11	40	23
AMP PEAK 8(5P15.33) WILD-TYPE	38	15	22	10

Figure S30. Get High-res Image Gene #8: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00446 (Fisher's exact test), Q value = 0.022

Table S31. Gene #8: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	67	35	12
AMP PEAK 8(5P15.33) MUTATED	25	47	19	7
AMP PEAK 8(5P15.33) WILD-TYPE	39	20	16	5

Figure S31. Get High-res Image Gene #8: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00133 (Fisher's exact test), Q value = 0.0082

Table S32. Gene #8: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
AMP PEAK 8(5P15.33) MUTATED	20	15	63
AMP PEAK 8(5P15.33) WILD-TYPE	35	14	31

Figure S32. Get High-res Image Gene #8: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6p21.1' versus 'METHLYATION_CNMF'

P value = 0.0372 (Fisher's exact test), Q value = 0.096

Table S33. Gene #9: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
AMP PEAK 9(6P21.1) MUTATED	21	18	0	13	9	4	4
AMP PEAK 9(6P21.1) WILD-TYPE	15	24	2	28	28	13	5

Figure S33. Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0309 (Fisher's exact test), Q value = 0.084

Table S34. Gene #9: 'amp_6p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
AMP PEAK 9(6P21.1) MUTATED	30	11	28
AMP PEAK 9(6P21.1) WILD-TYPE	37	9	68

Figure S34. Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_CNMF'

P value = 0.00274 (Fisher's exact test), Q value = 0.015

Table S35. Gene #9: 'amp_6p21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
AMP PEAK 9(6P21.1) MUTATED	36	4	7	5	6	10
AMP PEAK 9(6P21.1) WILD-TYPE	34	11	3	13	22	32

Figure S35. Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6p21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00211 (Fisher's exact test), Q value = 0.012

Table S36. Gene #9: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
AMP PEAK 9(6P21.1) MUTATED	35	7	16	10
AMP PEAK 9(6P21.1) WILD-TYPE	27	19	46	23

Figure S36. Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00287 (Fisher's exact test), Q value = 0.016

Table S37. Gene #9: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	67	35	12
AMP PEAK 9(6P21.1) MUTATED	36	19	9	4
AMP PEAK 9(6P21.1) WILD-TYPE	28	48	26	8

Figure S37. Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00249 (Fisher's exact test), Q value = 0.014

Table S38. Gene #9: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
AMP PEAK 9(6P21.1) MUTATED	31	11	26
AMP PEAK 9(6P21.1) WILD-TYPE	24	18	68

Figure S38. Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q23.3' versus 'METHLYATION_CNMF'

P value = 0.0487 (Fisher's exact test), Q value = 0.12

Table S39. Gene #10: 'amp_6q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
AMP PEAK 10(6Q23.3) MUTATED	12	13	0	4	9	1	3
AMP PEAK 10(6Q23.3) WILD-TYPE	24	29	2	37	28	16	6

Figure S39. Get High-res Image Gene #10: 'amp_6q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q23.3' versus 'RPPA_CNMF'

P value = 0.005 (Fisher's exact test), Q value = 0.024

Table S40. Gene #10: 'amp_6q23.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	28	30	34	8
AMP PEAK 10(6Q23.3) MUTATED	9	10	3	2	2
AMP PEAK 10(6Q23.3) WILD-TYPE	17	18	27	32	6

Figure S40. Get High-res Image Gene #10: 'amp_6q23.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_6q23.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00566 (Fisher's exact test), Q value = 0.026

Table S41. Gene #10: 'amp_6q23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	23	21	22	26	34
AMP PEAK 10(6Q23.3) MUTATED	5	10	5	1	5
AMP PEAK 10(6Q23.3) WILD-TYPE	18	11	17	25	29

Figure S41. Get High-res Image Gene #10: 'amp_6q23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_6q23.3' versus 'MIRSEQ_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.049

Table S42. Gene #10: 'amp_6q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
AMP PEAK 10(6Q23.3) MUTATED	25	3	3	1	3	6
AMP PEAK 10(6Q23.3) WILD-TYPE	45	12	7	17	25	36

Figure S42. Get High-res Image Gene #10: 'amp_6q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0309 (Fisher's exact test), Q value = 0.084

Table S43. Gene #10: 'amp_6q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
AMP PEAK 10(6Q23.3) MUTATED	22	4	9	6
AMP PEAK 10(6Q23.3) WILD-TYPE	40	22	53	27

Figure S43. Get High-res Image Gene #10: 'amp_6q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00477 (Fisher's exact test), Q value = 0.023

Table S44. Gene #10: 'amp_6q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	67	35	12
AMP PEAK 10(6Q23.3) MUTATED	23	11	3	4
AMP PEAK 10(6Q23.3) WILD-TYPE	41	56	32	8

Figure S44. Get High-res Image Gene #10: 'amp_6q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.018 (Fisher's exact test), Q value = 0.061

Table S45. Gene #10: 'amp_6q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
AMP PEAK 10(6Q23.3) MUTATED	20	6	15
AMP PEAK 10(6Q23.3) WILD-TYPE	35	23	79

Figure S45. Get High-res Image Gene #10: 'amp_6q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p11.2' versus 'METHLYATION_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.084

Table S46. Gene #11: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
AMP PEAK 11(7P11.2) MUTATED	25	34	1	32	20	8	5
AMP PEAK 11(7P11.2) WILD-TYPE	11	8	1	9	17	9	4

Figure S46. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 0.0187 (Fisher's exact test), Q value = 0.062

Table S47. Gene #11: 'amp_7p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
AMP PEAK 11(7P11.2) MUTATED	55	12	26	18	2	12
AMP PEAK 11(7P11.2) WILD-TYPE	18	2	16	11	7	4

Figure S47. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7q21.2' versus 'CN_CNMF'

P value = 0.0143 (Fisher's exact test), Q value = 0.052

Table S48. Gene #12: 'amp_7q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
AMP PEAK 12(7Q21.2) MUTATED	49	13	52
AMP PEAK 12(7Q21.2) WILD-TYPE	25	20	25

Figure S48. Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p23.1' versus 'CN_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0024

Table S49. Gene #13: 'amp_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
AMP PEAK 13(8P23.1) MUTATED	28	14	10
AMP PEAK 13(8P23.1) WILD-TYPE	46	19	67

Figure S49. Get High-res Image Gene #13: 'amp_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p23.1' versus 'METHLYATION_CNMF'

P value = 0.00856 (Fisher's exact test), Q value = 0.037

Table S50. Gene #13: 'amp_8p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
AMP PEAK 13(8P23.1) MUTATED	14	17	1	10	3	6	1
AMP PEAK 13(8P23.1) WILD-TYPE	22	25	1	31	34	11	8

Figure S50. Get High-res Image Gene #13: 'amp_8p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8p23.1' versus 'MRNASEQ_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 0.082

Table S51. Gene #13: 'amp_8p23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
AMP PEAK 13(8P23.1) MUTATED	30	4	5	7	2	4
AMP PEAK 13(8P23.1) WILD-TYPE	43	10	37	22	7	12

Figure S51. Get High-res Image Gene #13: 'amp_8p23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8p23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00086

Table S52. Gene #13: 'amp_8p23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
AMP PEAK 13(8P23.1) MUTATED	32	2	18
AMP PEAK 13(8P23.1) WILD-TYPE	35	18	78

Figure S52. Get High-res Image Gene #13: 'amp_8p23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8p23.1' versus 'MIRSEQ_CNMF'

P value = 0.00644 (Fisher's exact test), Q value = 0.029

Table S53. Gene #13: 'amp_8p23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
AMP PEAK 13(8P23.1) MUTATED	28	2	3	4	10	4
AMP PEAK 13(8P23.1) WILD-TYPE	42	13	7	14	18	38

Figure S53. Get High-res Image Gene #13: 'amp_8p23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8p23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0141 (Fisher's exact test), Q value = 0.051

Table S54. Gene #13: 'amp_8p23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
AMP PEAK 13(8P23.1) MUTATED	25	9	10	7
AMP PEAK 13(8P23.1) WILD-TYPE	37	17	52	26

Figure S54. Get High-res Image Gene #13: 'amp_8p23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8p23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.0061

Table S55. Gene #13: 'amp_8p23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	67	35	12
AMP PEAK 13(8P23.1) MUTATED	26	8	12	2
AMP PEAK 13(8P23.1) WILD-TYPE	38	59	23	10

Figure S55. Get High-res Image Gene #13: 'amp_8p23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8p23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0021 (Fisher's exact test), Q value = 0.012

Table S56. Gene #13: 'amp_8p23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
AMP PEAK 13(8P23.1) MUTATED	22	11	15
AMP PEAK 13(8P23.1) WILD-TYPE	33	18	79

Figure S56. Get High-res Image Gene #13: 'amp_8p23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_CNMF'

P value = 0.0417 (Fisher's exact test), Q value = 0.1

Table S57. Gene #14: 'amp_8p11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
AMP PEAK 14(8P11.21) MUTATED	35	5	8	11	13	13
AMP PEAK 14(8P11.21) WILD-TYPE	35	10	2	7	15	29

Figure S57. Get High-res Image Gene #14: 'amp_8p11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'RPPA_CNMF'

P value = 0.0171 (Fisher's exact test), Q value = 0.058

Table S58. Gene #15: 'amp_8q24.21' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	28	30	34	8
AMP PEAK 15(8Q24.21) MUTATED	21	22	21	33	5
AMP PEAK 15(8Q24.21) WILD-TYPE	5	6	9	1	3

Figure S58. Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_9p13.3' versus 'CN_CNMF'

P value = 0.00345 (Fisher's exact test), Q value = 0.018

Table S59. Gene #16: 'amp_9p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
AMP PEAK 16(9P13.3) MUTATED	22	1	17
AMP PEAK 16(9P13.3) WILD-TYPE	52	32	60

Figure S59. Get High-res Image Gene #16: 'amp_9p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p13.3' versus 'MRNASEQ_CNMF'

P value = 0.0242 (Fisher's exact test), Q value = 0.073

Table S60. Gene #16: 'amp_9p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
AMP PEAK 16(9P13.3) MUTATED	16	3	4	13	1	3
AMP PEAK 16(9P13.3) WILD-TYPE	57	11	38	16	8	13

Figure S60. Get High-res Image Gene #16: 'amp_9p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_9q34.3' versus 'CN_CNMF'

P value = 0.00101 (Fisher's exact test), Q value = 0.0065

Table S61. Gene #17: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
AMP PEAK 17(9Q34.3) MUTATED	28	3	33
AMP PEAK 17(9Q34.3) WILD-TYPE	46	30	44

Figure S61. Get High-res Image Gene #17: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9q34.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0244 (Fisher's exact test), Q value = 0.074

Table S62. Gene #17: 'amp_9q34.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	23	21	22	26	34
AMP PEAK 17(9Q34.3) MUTATED	8	7	6	17	9
AMP PEAK 17(9Q34.3) WILD-TYPE	15	14	16	9	25

Figure S62. Get High-res Image Gene #17: 'amp_9q34.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_9q34.3' versus 'MRNASEQ_CNMF'

P value = 0.0292 (Fisher's exact test), Q value = 0.082

Table S63. Gene #17: 'amp_9q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
AMP PEAK 17(9Q34.3) MUTATED	23	3	16	17	1	3
AMP PEAK 17(9Q34.3) WILD-TYPE	50	11	26	12	8	13

Figure S63. Get High-res Image Gene #17: 'amp_9q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_11p13' versus 'CN_CNMF'

P value = 0.00243 (Fisher's exact test), Q value = 0.014

Table S64. Gene #19: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
AMP PEAK 19(11P13) MUTATED	20	2	28
AMP PEAK 19(11P13) WILD-TYPE	54	31	49

Figure S64. Get High-res Image Gene #19: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S65. Gene #20: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
AMP PEAK 20(11Q13.3) MUTATED	32	12	60
AMP PEAK 20(11Q13.3) WILD-TYPE	42	21	17

Figure S65. Get High-res Image Gene #20: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.055

Table S66. Gene #20: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
AMP PEAK 20(11Q13.3) MUTATED	17	18	0	29	27	8	5
AMP PEAK 20(11Q13.3) WILD-TYPE	19	24	2	12	10	9	4

Figure S66. Get High-res Image Gene #20: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'RPPA_CNMF'

P value = 0.00612 (Fisher's exact test), Q value = 0.028

Table S67. Gene #20: 'amp_11q13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	28	30	34	8
AMP PEAK 20(11Q13.3) MUTATED	9	23	17	23	4
AMP PEAK 20(11Q13.3) WILD-TYPE	17	5	13	11	4

Figure S67. Get High-res Image Gene #20: 'amp_11q13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_11q13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0132 (Fisher's exact test), Q value = 0.049

Table S68. Gene #20: 'amp_11q13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	23	21	22	26	34
AMP PEAK 20(11Q13.3) MUTATED	7	17	13	17	22
AMP PEAK 20(11Q13.3) WILD-TYPE	16	4	9	9	12

Figure S68. Get High-res Image Gene #20: 'amp_11q13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.055

Table S69. Gene #20: 'amp_11q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
AMP PEAK 20(11Q13.3) MUTATED	31	9	28	20	3	12
AMP PEAK 20(11Q13.3) WILD-TYPE	42	5	14	9	6	4

Figure S69. Get High-res Image Gene #20: 'amp_11q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00096 (Fisher's exact test), Q value = 0.0062

Table S70. Gene #20: 'amp_11q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
AMP PEAK 20(11Q13.3) MUTATED	27	10	66
AMP PEAK 20(11Q13.3) WILD-TYPE	40	10	30

Figure S70. Get High-res Image Gene #20: 'amp_11q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00134 (Fisher's exact test), Q value = 0.0082

Table S71. Gene #20: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
AMP PEAK 20(11Q13.3) MUTATED	29	8	43	23
AMP PEAK 20(11Q13.3) WILD-TYPE	33	18	19	10

Figure S71. Get High-res Image Gene #20: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00324 (Fisher's exact test), Q value = 0.017

Table S72. Gene #20: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
AMP PEAK 20(11Q13.3) MUTATED	25	12	65
AMP PEAK 20(11Q13.3) WILD-TYPE	30	17	29

Figure S72. Get High-res Image Gene #20: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p12.1' versus 'CN_CNMF'

P value = 0.00088 (Fisher's exact test), Q value = 0.0059

Table S73. Gene #21: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
AMP PEAK 21(12P12.1) MUTATED	30	6	43
AMP PEAK 21(12P12.1) WILD-TYPE	44	27	34

Figure S73. Get High-res Image Gene #21: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 0.059

Table S74. Gene #21: 'amp_12p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
AMP PEAK 21(12P12.1) MUTATED	22	8	18	17	3	11
AMP PEAK 21(12P12.1) WILD-TYPE	51	6	24	12	6	5

Figure S74. Get High-res Image Gene #21: 'amp_12p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0291 (Fisher's exact test), Q value = 0.082

Table S75. Gene #21: 'amp_12p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
AMP PEAK 21(12P12.1) MUTATED	21	8	50
AMP PEAK 21(12P12.1) WILD-TYPE	46	12	46

Figure S75. Get High-res Image Gene #21: 'amp_12p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'CN_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.0067

Table S76. Gene #23: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
AMP PEAK 23(13Q22.1) MUTATED	38	7	20
AMP PEAK 23(13Q22.1) WILD-TYPE	36	26	57

Figure S76. Get High-res Image Gene #23: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q22.1' versus 'METHLYATION_CNMF'

P value = 0.0375 (Fisher's exact test), Q value = 0.096

Table S77. Gene #23: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
AMP PEAK 23(13Q22.1) MUTATED	19	19	0	13	8	3	3
AMP PEAK 23(13Q22.1) WILD-TYPE	17	23	2	28	29	14	6

Figure S77. Get High-res Image Gene #23: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00106 (Fisher's exact test), Q value = 0.0067

Table S78. Gene #23: 'amp_13q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
AMP PEAK 23(13Q22.1) MUTATED	30	12	23
AMP PEAK 23(13Q22.1) WILD-TYPE	37	8	73

Figure S78. Get High-res Image Gene #23: 'amp_13q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_CNMF'

P value = 0.0172 (Fisher's exact test), Q value = 0.058

Table S79. Gene #23: 'amp_13q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
AMP PEAK 23(13Q22.1) MUTATED	35	6	2	6	6	9
AMP PEAK 23(13Q22.1) WILD-TYPE	35	9	8	12	22	33

Figure S79. Get High-res Image Gene #23: 'amp_13q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_13q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00238 (Fisher's exact test), Q value = 0.014

Table S80. Gene #23: 'amp_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
AMP PEAK 23(13Q22.1) MUTATED	31	12	14	7
AMP PEAK 23(13Q22.1) WILD-TYPE	31	14	48	26

Figure S80. Get High-res Image Gene #23: 'amp_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.047

Table S81. Gene #23: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	67	35	12
AMP PEAK 23(13Q22.1) MUTATED	33	19	8	4
AMP PEAK 23(13Q22.1) WILD-TYPE	31	48	27	8

Figure S81. Get High-res Image Gene #23: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.0023

Table S82. Gene #23: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
AMP PEAK 23(13Q22.1) MUTATED	28	15	21
AMP PEAK 23(13Q22.1) WILD-TYPE	27	14	73

Figure S82. Get High-res Image Gene #23: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_14q21.1' versus 'CN_CNMF'

P value = 0.005 (Fisher's exact test), Q value = 0.024

Table S83. Gene #24: 'amp_14q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
AMP PEAK 24(14Q21.1) MUTATED	17	8	36
AMP PEAK 24(14Q21.1) WILD-TYPE	57	25	41

Figure S83. Get High-res Image Gene #24: 'amp_14q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_14q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00281 (Fisher's exact test), Q value = 0.015

Table S84. Gene #24: 'amp_14q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
AMP PEAK 24(14Q21.1) MUTATED	17	2	42
AMP PEAK 24(14Q21.1) WILD-TYPE	50	18	54

Figure S84. Get High-res Image Gene #24: 'amp_14q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_14q21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00407 (Fisher's exact test), Q value = 0.021

Table S85. Gene #24: 'amp_14q21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
AMP PEAK 24(14Q21.1) MUTATED	14	5	31	10
AMP PEAK 24(14Q21.1) WILD-TYPE	48	21	31	23

Figure S85. Get High-res Image Gene #24: 'amp_14q21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_14q21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00703 (Fisher's exact test), Q value = 0.031

Table S86. Gene #24: 'amp_14q21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	67	35	12
AMP PEAK 24(14Q21.1) MUTATED	14	30	9	7
AMP PEAK 24(14Q21.1) WILD-TYPE	50	37	26	5

Figure S86. Get High-res Image Gene #24: 'amp_14q21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_14q21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0147 (Fisher's exact test), Q value = 0.053

Table S87. Gene #24: 'amp_14q21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
AMP PEAK 24(14Q21.1) MUTATED	13	6	41
AMP PEAK 24(14Q21.1) WILD-TYPE	42	23	53

Figure S87. Get High-res Image Gene #24: 'amp_14q21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_15q26.1' versus 'CN_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0045

Table S88. Gene #25: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
AMP PEAK 25(15Q26.1) MUTATED	35	5	18
AMP PEAK 25(15Q26.1) WILD-TYPE	39	28	59

Figure S88. Get High-res Image Gene #25: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_15q26.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0446 (Fisher's exact test), Q value = 0.11

Table S89. Gene #25: 'amp_15q26.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	23	21	22	26	34
AMP PEAK 25(15Q26.1) MUTATED	11	10	4	5	8
AMP PEAK 25(15Q26.1) WILD-TYPE	12	11	18	21	26

Figure S89. Get High-res Image Gene #25: 'amp_15q26.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_15q26.1' versus 'MRNASEQ_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.043

Table S90. Gene #25: 'amp_15q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
AMP PEAK 25(15Q26.1) MUTATED	30	2	10	5	1	9
AMP PEAK 25(15Q26.1) WILD-TYPE	43	12	32	24	8	7

Figure S90. Get High-res Image Gene #25: 'amp_15q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_15q26.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0152 (Fisher's exact test), Q value = 0.054

Table S91. Gene #25: 'amp_15q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
AMP PEAK 25(15Q26.1) MUTATED	27	9	21
AMP PEAK 25(15Q26.1) WILD-TYPE	40	11	75

Figure S91. Get High-res Image Gene #25: 'amp_15q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0433 (Fisher's exact test), Q value = 0.11

Table S92. Gene #25: 'amp_15q26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
AMP PEAK 25(15Q26.1) MUTATED	28	8	14	8
AMP PEAK 25(15Q26.1) WILD-TYPE	34	18	48	25

Figure S92. Get High-res Image Gene #25: 'amp_15q26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_15q26.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0252 (Fisher's exact test), Q value = 0.075

Table S93. Gene #25: 'amp_15q26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	67	35	12
AMP PEAK 25(15Q26.1) MUTATED	29	17	7	5
AMP PEAK 25(15Q26.1) WILD-TYPE	35	50	28	7

Figure S93. Get High-res Image Gene #25: 'amp_15q26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_15q26.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0157 (Fisher's exact test), Q value = 0.055

Table S94. Gene #25: 'amp_15q26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
AMP PEAK 25(15Q26.1) MUTATED	25	11	22
AMP PEAK 25(15Q26.1) WILD-TYPE	30	18	72

Figure S94. Get High-res Image Gene #25: 'amp_15q26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.074

Table S95. Gene #26: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
AMP PEAK 26(17Q12) MUTATED	39	10	26
AMP PEAK 26(17Q12) WILD-TYPE	35	23	51

Figure S95. Get High-res Image Gene #26: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 0.0013 (Fisher's exact test), Q value = 0.0081

Table S96. Gene #26: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
AMP PEAK 26(17Q12) MUTATED	19	24	1	19	7	4	1
AMP PEAK 26(17Q12) WILD-TYPE	17	18	1	22	30	13	8

Figure S96. Get High-res Image Gene #26: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 0.0223 (Fisher's exact test), Q value = 0.069

Table S97. Gene #26: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
AMP PEAK 26(17Q12) MUTATED	38	7	10	14	2	4
AMP PEAK 26(17Q12) WILD-TYPE	35	7	32	15	7	12

Figure S97. Get High-res Image Gene #26: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00296 (Fisher's exact test), Q value = 0.016

Table S98. Gene #26: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
AMP PEAK 26(17Q12) MUTATED	38	8	29
AMP PEAK 26(17Q12) WILD-TYPE	29	12	67

Figure S98. Get High-res Image Gene #26: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.051

Table S99. Gene #26: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
AMP PEAK 26(17Q12) MUTATED	37	6	6	8	6	11
AMP PEAK 26(17Q12) WILD-TYPE	33	9	4	10	22	31

Figure S99. Get High-res Image Gene #26: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0201 (Fisher's exact test), Q value = 0.066

Table S100. Gene #26: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
AMP PEAK 26(17Q12) MUTATED	32	14	18	10
AMP PEAK 26(17Q12) WILD-TYPE	30	12	44	23

Figure S100. Get High-res Image Gene #26: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0213 (Fisher's exact test), Q value = 0.068

Table S101. Gene #26: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	67	35	12
AMP PEAK 26(17Q12) MUTATED	35	21	10	5
AMP PEAK 26(17Q12) WILD-TYPE	29	46	25	7

Figure S101. Get High-res Image Gene #26: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00146 (Fisher's exact test), Q value = 0.0088

Table S102. Gene #26: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
AMP PEAK 26(17Q12) MUTATED	28	17	26
AMP PEAK 26(17Q12) WILD-TYPE	27	12	68

Figure S102. Get High-res Image Gene #26: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18p11.32' versus 'MRNASEQ_CNMF'

P value = 0.0439 (Fisher's exact test), Q value = 0.11

Table S103. Gene #27: 'amp_18p11.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
AMP PEAK 27(18P11.32) MUTATED	21	8	17	16	1	6
AMP PEAK 27(18P11.32) WILD-TYPE	52	6	25	13	8	10

Figure S103. Get High-res Image Gene #27: 'amp_18p11.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'CN_CNMF'

P value = 0.0335 (Fisher's exact test), Q value = 0.089

Table S104. Gene #28: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
AMP PEAK 28(18Q11.2) MUTATED	32	8	19
AMP PEAK 28(18Q11.2) WILD-TYPE	42	25	58

Figure S104. Get High-res Image Gene #28: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 0.0398 (Fisher's exact test), Q value = 0.1

Table S105. Gene #28: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
AMP PEAK 28(18Q11.2) MUTATED	16	19	0	12	6	5	1
AMP PEAK 28(18Q11.2) WILD-TYPE	20	23	2	29	31	12	8

Figure S105. Get High-res Image Gene #28: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00491 (Fisher's exact test), Q value = 0.024

Table S106. Gene #28: 'amp_18q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
AMP PEAK 28(18Q11.2) MUTATED	28	10	21
AMP PEAK 28(18Q11.2) WILD-TYPE	39	10	75

Figure S106. Get High-res Image Gene #28: 'amp_18q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00305 (Fisher's exact test), Q value = 0.016

Table S107. Gene #28: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
AMP PEAK 28(18Q11.2) MUTATED	34	3	5	4	6	7
AMP PEAK 28(18Q11.2) WILD-TYPE	36	12	5	14	22	35

Figure S107. Get High-res Image Gene #28: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00909 (Fisher's exact test), Q value = 0.038

Table S108. Gene #28: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
AMP PEAK 28(18Q11.2) MUTATED	28	11	14	6
AMP PEAK 28(18Q11.2) WILD-TYPE	34	15	48	27

Figure S108. Get High-res Image Gene #28: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0281 (Fisher's exact test), Q value = 0.08

Table S109. Gene #28: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	67	35	12
AMP PEAK 28(18Q11.2) MUTATED	29	15	9	5
AMP PEAK 28(18Q11.2) WILD-TYPE	35	52	26	7

Figure S109. Get High-res Image Gene #28: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.004

Table S110. Gene #28: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
AMP PEAK 28(18Q11.2) MUTATED	24	15	19
AMP PEAK 28(18Q11.2) WILD-TYPE	31	14	75

Figure S110. Get High-res Image Gene #28: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 0.048 (Fisher's exact test), Q value = 0.12

Table S111. Gene #29: 'amp_19q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
AMP PEAK 29(19Q12) MUTATED	24	8	6	9	2	6
AMP PEAK 29(19Q12) WILD-TYPE	49	6	36	20	7	10

Figure S111. Get High-res Image Gene #29: 'amp_19q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 0.0406 (Fisher's exact test), Q value = 0.1

Table S112. Gene #29: 'amp_19q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
AMP PEAK 29(19Q12) MUTATED	27	4	5	7	6	6
AMP PEAK 29(19Q12) WILD-TYPE	43	11	5	11	22	36

Figure S112. Get High-res Image Gene #29: 'amp_19q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_xq28' versus 'CN_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.061

Table S113. Gene #30: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
AMP PEAK 30(XQ28) MUTATED	21	10	38
AMP PEAK 30(XQ28) WILD-TYPE	53	23	39

Figure S113. Get High-res Image Gene #30: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq28' versus 'MRNASEQ_CNMF'

P value = 0.0478 (Fisher's exact test), Q value = 0.12

Table S114. Gene #30: 'amp_xq28' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
AMP PEAK 30(XQ28) MUTATED	22	6	17	18	2	4
AMP PEAK 30(XQ28) WILD-TYPE	51	8	25	11	7	12

Figure S114. Get High-res Image Gene #30: 'amp_xq28' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_xq28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0269 (Fisher's exact test), Q value = 0.078

Table S115. Gene #30: 'amp_xq28' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
AMP PEAK 30(XQ28) MUTATED	18	6	45
AMP PEAK 30(XQ28) WILD-TYPE	49	14	51

Figure S115. Get High-res Image Gene #30: 'amp_xq28' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00235 (Fisher's exact test), Q value = 0.014

Table S116. Gene #30: 'amp_xq28' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
AMP PEAK 30(XQ28) MUTATED	22	2	29	15
AMP PEAK 30(XQ28) WILD-TYPE	40	24	33	18

Figure S116. Get High-res Image Gene #30: 'amp_xq28' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0024

Table S117. Gene #30: 'amp_xq28' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
AMP PEAK 30(XQ28) MUTATED	22	2	43
AMP PEAK 30(XQ28) WILD-TYPE	33	27	51

Figure S117. Get High-res Image Gene #30: 'amp_xq28' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.11' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00069

Table S118. Gene #31: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 1(1P36.11) MUTATED	43	5	27
DEL PEAK 1(1P36.11) WILD-TYPE	31	28	50

Figure S118. Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S119. Gene #31: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
DEL PEAK 1(1P36.11) MUTATED	18	24	0	24	5	3	1
DEL PEAK 1(1P36.11) WILD-TYPE	18	18	2	17	32	14	8

Figure S119. Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S120. Gene #31: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 1(1P36.11) MUTATED	41	5	8	18	0	3
DEL PEAK 1(1P36.11) WILD-TYPE	32	9	34	11	9	13

Figure S120. Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0235 (Fisher's exact test), Q value = 0.073

Table S121. Gene #31: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
DEL PEAK 1(1P36.11) MUTATED	36	8	31
DEL PEAK 1(1P36.11) WILD-TYPE	31	12	65

Figure S121. Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0237 (Fisher's exact test), Q value = 0.073

Table S122. Gene #31: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 1(1P36.11) MUTATED	33	11	24	7
DEL PEAK 1(1P36.11) WILD-TYPE	29	15	38	26

Figure S122. Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0388 (Fisher's exact test), Q value = 0.098

Table S123. Gene #31: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	67	35	12
DEL PEAK 1(1P36.11) MUTATED	35	26	10	3
DEL PEAK 1(1P36.11) WILD-TYPE	29	41	25	9

Figure S123. Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0337 (Fisher's exact test), Q value = 0.089

Table S124. Gene #31: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
DEL PEAK 1(1P36.11) MUTATED	30	13	31
DEL PEAK 1(1P36.11) WILD-TYPE	25	16	63

Figure S124. Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p13.2' versus 'CN_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.002

Table S125. Gene #32: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 2(1P13.2) MUTATED	30	2	32
DEL PEAK 2(1P13.2) WILD-TYPE	44	31	45

Figure S125. Get High-res Image Gene #32: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p13.2' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0023

Table S126. Gene #32: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
DEL PEAK 2(1P13.2) MUTATED	13	18	0	23	8	0	2
DEL PEAK 2(1P13.2) WILD-TYPE	23	24	2	18	29	17	7

Figure S126. Get High-res Image Gene #32: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p13.2' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.001

Table S127. Gene #32: 'del_1p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 2(1P13.2) MUTATED	30	1	11	19	1	2
DEL PEAK 2(1P13.2) WILD-TYPE	43	13	31	10	8	14

Figure S127. Get High-res Image Gene #32: 'del_1p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q22.1' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 5e-04

Table S128. Gene #34: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 4(2Q22.1) MUTATED	12	8	39
DEL PEAK 4(2Q22.1) WILD-TYPE	62	25	38

Figure S128. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S129. Gene #34: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
DEL PEAK 4(2Q22.1) MUTATED	5	6	0	24	18	4	2
DEL PEAK 4(2Q22.1) WILD-TYPE	31	36	2	17	19	13	7

Figure S129. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00259 (Fisher's exact test), Q value = 0.014

Table S130. Gene #34: 'del_2q22.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	23	21	22	26	34
DEL PEAK 4(2Q22.1) MUTATED	3	7	4	10	20
DEL PEAK 4(2Q22.1) WILD-TYPE	20	14	18	16	14

Figure S130. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S131. Gene #34: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 4(2Q22.1) MUTATED	10	6	18	19	1	4
DEL PEAK 4(2Q22.1) WILD-TYPE	63	8	24	10	8	12

Figure S131. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S132. Gene #34: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
DEL PEAK 4(2Q22.1) MUTATED	6	6	46
DEL PEAK 4(2Q22.1) WILD-TYPE	61	14	50

Figure S132. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S133. Gene #34: 'del_2q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
DEL PEAK 4(2Q22.1) MUTATED	10	4	4	9	8	24
DEL PEAK 4(2Q22.1) WILD-TYPE	60	11	6	9	20	18

Figure S133. Get High-res Image Gene #34: '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 = 2e-04

Table S134. Gene #34: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 4(2Q22.1) MUTATED	10	3	26	20
DEL PEAK 4(2Q22.1) WILD-TYPE	52	23	36	13

Figure S134. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 5e-04

Table S135. Gene #34: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	67	35	12
DEL PEAK 4(2Q22.1) MUTATED	10	37	8	4
DEL PEAK 4(2Q22.1) WILD-TYPE	54	30	27	8

Figure S135. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_2q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S136. Gene #34: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
DEL PEAK 4(2Q22.1) MUTATED	9	4	46
DEL PEAK 4(2Q22.1) WILD-TYPE	46	25	48

Figure S136. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q33.3' versus 'MRNASEQ_CNMF'

P value = 0.0499 (Fisher's exact test), Q value = 0.12

Table S137. Gene #35: 'del_2q33.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 5(2Q33.3) MUTATED	8	5	8	10	1	4
DEL PEAK 5(2Q33.3) WILD-TYPE	65	9	34	19	8	12

Figure S137. Get High-res Image Gene #35: 'del_2q33.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q33.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.027 (Fisher's exact test), Q value = 0.078

Table S138. Gene #35: 'del_2q33.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
DEL PEAK 5(2Q33.3) MUTATED	7	3	26
DEL PEAK 5(2Q33.3) WILD-TYPE	60	17	70

Figure S138. Get High-res Image Gene #35: 'del_2q33.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q33.3' versus 'MIRSEQ_CNMF'

P value = 0.0327 (Fisher's exact test), Q value = 0.088

Table S139. Gene #35: 'del_2q33.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
DEL PEAK 5(2Q33.3) MUTATED	6	3	1	6	8	11
DEL PEAK 5(2Q33.3) WILD-TYPE	64	12	9	12	20	31

Figure S139. Get High-res Image Gene #35: 'del_2q33.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q33.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0314 (Fisher's exact test), Q value = 0.085

Table S140. Gene #35: 'del_2q33.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
DEL PEAK 5(2Q33.3) MUTATED	6	3	25
DEL PEAK 5(2Q33.3) WILD-TYPE	49	26	69

Figure S140. Get High-res Image Gene #35: 'del_2q33.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S141. Gene #36: 'del_3p26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 6(3P26.2) MUTATED	35	12	64
DEL PEAK 6(3P26.2) WILD-TYPE	39	21	13

Figure S141. Get High-res Image Gene #36: 'del_3p26.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p26.2' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4e-04

Table S142. Gene #36: 'del_3p26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
DEL PEAK 6(3P26.2) MUTATED	20	16	0	35	27	7	6
DEL PEAK 6(3P26.2) WILD-TYPE	16	26	2	6	10	10	3

Figure S142. Get High-res Image Gene #36: 'del_3p26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p26.2' versus 'MRNASEQ_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0034

Table S143. Gene #36: 'del_3p26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 6(3P26.2) MUTATED	34	10	29	26	4	7
DEL PEAK 6(3P26.2) WILD-TYPE	39	4	13	3	5	9

Figure S143. Get High-res Image Gene #36: 'del_3p26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00059

Table S144. Gene #36: 'del_3p26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
DEL PEAK 6(3P26.2) MUTATED	27	11	72
DEL PEAK 6(3P26.2) WILD-TYPE	40	9	24

Figure S144. Get High-res Image Gene #36: 'del_3p26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_CNMF'

P value = 0.0205 (Fisher's exact test), Q value = 0.066

Table S145. Gene #36: 'del_3p26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
DEL PEAK 6(3P26.2) MUTATED	34	11	5	13	15	33
DEL PEAK 6(3P26.2) WILD-TYPE	36	4	5	5	13	9

Figure S145. Get High-res Image Gene #36: 'del_3p26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.0017

Table S146. Gene #36: 'del_3p26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 6(3P26.2) MUTATED	29	10	48	24
DEL PEAK 6(3P26.2) WILD-TYPE	33	16	14	9

Figure S146. Get High-res Image Gene #36: 'del_3p26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.056

Table S147. Gene #36: 'del_3p26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	67	35	12
DEL PEAK 6(3P26.2) MUTATED	32	51	20	7
DEL PEAK 6(3P26.2) WILD-TYPE	32	16	15	5

Figure S147. Get High-res Image Gene #36: 'del_3p26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.0025

Table S148. Gene #36: 'del_3p26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
DEL PEAK 6(3P26.2) MUTATED	27	12	71
DEL PEAK 6(3P26.2) WILD-TYPE	28	17	23

Figure S148. Get High-res Image Gene #36: 'del_3p26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S149. Gene #37: 'del_3p14.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 7(3P14.3) MUTATED	41	13	72
DEL PEAK 7(3P14.3) WILD-TYPE	33	20	5

Figure S149. Get High-res Image Gene #37: 'del_3p14.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S150. Gene #37: 'del_3p14.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
DEL PEAK 7(3P14.3) MUTATED	20	21	0	39	32	8	6
DEL PEAK 7(3P14.3) WILD-TYPE	16	21	2	2	5	9	3

Figure S150. Get High-res Image Gene #37: 'del_3p14.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p14.3' versus 'MRNASEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0023

Table S151. Gene #37: 'del_3p14.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 7(3P14.3) MUTATED	40	11	34	27	5	8
DEL PEAK 7(3P14.3) WILD-TYPE	33	3	8	2	4	8

Figure S151. Get High-res Image Gene #37: 'del_3p14.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p14.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S152. Gene #37: 'del_3p14.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
DEL PEAK 7(3P14.3) MUTATED	32	11	82
DEL PEAK 7(3P14.3) WILD-TYPE	35	9	14

Figure S152. Get High-res Image Gene #37: 'del_3p14.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.3' versus 'MIRSEQ_CNMF'

P value = 0.00348 (Fisher's exact test), Q value = 0.018

Table S153. Gene #37: 'del_3p14.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
DEL PEAK 7(3P14.3) MUTATED	37	10	8	13	21	37
DEL PEAK 7(3P14.3) WILD-TYPE	33	5	2	5	7	5

Figure S153. Get High-res Image Gene #37: 'del_3p14.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p14.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S154. Gene #37: 'del_3p14.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 7(3P14.3) MUTATED	32	12	54	28
DEL PEAK 7(3P14.3) WILD-TYPE	30	14	8	5

Figure S154. Get High-res Image Gene #37: 'del_3p14.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S155. Gene #37: 'del_3p14.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	67	35	12
DEL PEAK 7(3P14.3) MUTATED	32	60	24	8
DEL PEAK 7(3P14.3) WILD-TYPE	32	7	11	4

Figure S155. Get High-res Image Gene #37: 'del_3p14.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p14.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S156. Gene #37: 'del_3p14.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
DEL PEAK 7(3P14.3) MUTATED	28	15	81
DEL PEAK 7(3P14.3) WILD-TYPE	27	14	13

Figure S156. Get High-res Image Gene #37: 'del_3p14.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S157. Gene #38: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 8(3P14.2) MUTATED	42	12	71
DEL PEAK 8(3P14.2) WILD-TYPE	32	21	6

Figure S157. Get High-res Image Gene #38: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S158. Gene #38: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
DEL PEAK 8(3P14.2) MUTATED	20	22	0	38	32	7	6
DEL PEAK 8(3P14.2) WILD-TYPE	16	20	2	3	5	10	3

Figure S158. Get High-res Image Gene #38: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p14.2' versus 'MRNASEQ_CNMF'

P value = 0.00075 (Fisher's exact test), Q value = 0.0053

Table S159. Gene #38: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 8(3P14.2) MUTATED	41	11	34	26	4	8
DEL PEAK 8(3P14.2) WILD-TYPE	32	3	8	3	5	8

Figure S159. Get High-res Image Gene #38: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S160. Gene #38: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
DEL PEAK 8(3P14.2) MUTATED	31	12	81
DEL PEAK 8(3P14.2) WILD-TYPE	36	8	15

Figure S160. Get High-res Image Gene #38: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.043

Table S161. Gene #38: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
DEL PEAK 8(3P14.2) MUTATED	37	11	8	13	20	36
DEL PEAK 8(3P14.2) WILD-TYPE	33	4	2	5	8	6

Figure S161. Get High-res Image Gene #38: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S162. Gene #38: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 8(3P14.2) MUTATED	33	11	53	28
DEL PEAK 8(3P14.2) WILD-TYPE	29	15	9	5

Figure S162. Get High-res Image Gene #38: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0012

Table S163. Gene #38: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	67	35	12
DEL PEAK 8(3P14.2) MUTATED	34	59	23	7
DEL PEAK 8(3P14.2) WILD-TYPE	30	8	12	5

Figure S163. Get High-res Image Gene #38: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S164. Gene #38: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
DEL PEAK 8(3P14.2) MUTATED	29	14	80
DEL PEAK 8(3P14.2) WILD-TYPE	26	15	14

Figure S164. Get High-res Image Gene #38: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q26.31' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0021

Table S165. Gene #40: 'del_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 10(3Q26.31) MUTATED	14	1	1
DEL PEAK 10(3Q26.31) WILD-TYPE	60	32	76

Figure S165. Get High-res Image Gene #40: 'del_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q26.31' versus 'METHLYATION_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.048

Table S166. Gene #40: 'del_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
DEL PEAK 10(3Q26.31) MUTATED	7	7	0	0	1	1	0
DEL PEAK 10(3Q26.31) WILD-TYPE	29	35	2	41	36	16	9

Figure S166. Get High-res Image Gene #40: 'del_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q26.31' versus 'RPPA_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.045

Table S167. Gene #40: 'del_3q26.31' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	28	30	34	8
DEL PEAK 10(3Q26.31) MUTATED	6	3	1	0	0
DEL PEAK 10(3Q26.31) WILD-TYPE	20	25	29	34	8

Figure S167. Get High-res Image Gene #40: 'del_3q26.31' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_3q26.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00962 (Fisher's exact test), Q value = 0.04

Table S168. Gene #40: 'del_3q26.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	23	21	22	26	34
DEL PEAK 10(3Q26.31) MUTATED	4	3	3	0	0
DEL PEAK 10(3Q26.31) WILD-TYPE	19	18	19	26	34

Figure S168. Get High-res Image Gene #40: 'del_3q26.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_3q26.31' versus 'MRNASEQ_CNMF'

P value = 0.0151 (Fisher's exact test), Q value = 0.054

Table S169. Gene #40: 'del_3q26.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 10(3Q26.31) MUTATED	13	0	1	0	1	1
DEL PEAK 10(3Q26.31) WILD-TYPE	60	14	41	29	8	15

Figure S169. Get High-res Image Gene #40: 'del_3q26.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3q26.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.0013

Table S170. Gene #40: 'del_3q26.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
DEL PEAK 10(3Q26.31) MUTATED	12	3	1
DEL PEAK 10(3Q26.31) WILD-TYPE	55	17	95

Figure S170. Get High-res Image Gene #40: 'del_3q26.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3q26.31' versus 'MIRSEQ_CNMF'

P value = 0.0272 (Fisher's exact test), Q value = 0.078

Table S171. Gene #40: 'del_3q26.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
DEL PEAK 10(3Q26.31) MUTATED	13	1	0	0	1	1
DEL PEAK 10(3Q26.31) WILD-TYPE	57	14	10	18	27	41

Figure S171. Get High-res Image Gene #40: 'del_3q26.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3q26.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.0025

Table S172. Gene #40: 'del_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 10(3Q26.31) MUTATED	11	4	0	1
DEL PEAK 10(3Q26.31) WILD-TYPE	51	22	62	32

Figure S172. Get High-res Image Gene #40: 'del_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3q26.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00147 (Fisher's exact test), Q value = 0.0088

Table S173. Gene #40: 'del_3q26.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	67	35	12
DEL PEAK 10(3Q26.31) MUTATED	13	1	2	0
DEL PEAK 10(3Q26.31) WILD-TYPE	51	66	33	12

Figure S173. Get High-res Image Gene #40: 'del_3q26.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3q26.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.0013

Table S174. Gene #40: 'del_3q26.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
DEL PEAK 10(3Q26.31) MUTATED	10	5	1
DEL PEAK 10(3Q26.31) WILD-TYPE	45	24	93

Figure S174. Get High-res Image Gene #40: 'del_3q26.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p15.2' versus 'CN_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.08

Table S175. Gene #41: 'del_4p15.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 11(4P15.2) MUTATED	46	12	48
DEL PEAK 11(4P15.2) WILD-TYPE	28	21	29

Figure S175. Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_4p15.2' versus 'METHLYATION_CNMF'

P value = 0.00859 (Fisher's exact test), Q value = 0.037

Table S176. Gene #41: 'del_4p15.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
DEL PEAK 11(4P15.2) MUTATED	21	26	0	31	20	6	2
DEL PEAK 11(4P15.2) WILD-TYPE	15	16	2	10	17	11	7

Figure S176. Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q22.1' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4e-04

Table S177. Gene #42: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 12(4Q22.1) MUTATED	55	9	41
DEL PEAK 12(4Q22.1) WILD-TYPE	19	24	36

Figure S177. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.048

Table S178. Gene #42: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
DEL PEAK 12(4Q22.1) MUTATED	26	28	0	25	17	7	2
DEL PEAK 12(4Q22.1) WILD-TYPE	10	14	2	16	20	10	7

Figure S178. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00484 (Fisher's exact test), Q value = 0.023

Table S179. Gene #42: 'del_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 12(4Q22.1) MUTATED	51	7	23	18	2	4
DEL PEAK 12(4Q22.1) WILD-TYPE	22	7	19	11	7	12

Figure S179. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0119 (Fisher's exact test), Q value = 0.046

Table S180. Gene #42: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
DEL PEAK 12(4Q22.1) MUTATED	48	10	47
DEL PEAK 12(4Q22.1) WILD-TYPE	19	10	49

Figure S180. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_CNMF'

P value = 0.0376 (Fisher's exact test), Q value = 0.096

Table S181. Gene #42: 'del_4q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
DEL PEAK 12(4Q22.1) MUTATED	49	6	6	12	11	21
DEL PEAK 12(4Q22.1) WILD-TYPE	21	9	4	6	17	21

Figure S181. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00856 (Fisher's exact test), Q value = 0.037

Table S182. Gene #42: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	67	35	12
DEL PEAK 12(4Q22.1) MUTATED	44	35	14	10
DEL PEAK 12(4Q22.1) WILD-TYPE	20	32	21	2

Figure S182. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00981 (Fisher's exact test), Q value = 0.04

Table S183. Gene #42: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
DEL PEAK 12(4Q22.1) MUTATED	40	18	45
DEL PEAK 12(4Q22.1) WILD-TYPE	15	11	49

Figure S183. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00059

Table S184. Gene #43: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 13(4Q34.3) MUTATED	53	9	37
DEL PEAK 13(4Q34.3) WILD-TYPE	21	24	40

Figure S184. Get High-res Image Gene #43: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 0.00245 (Fisher's exact test), Q value = 0.014

Table S185. Gene #43: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
DEL PEAK 13(4Q34.3) MUTATED	24	29	0	22	18	5	1
DEL PEAK 13(4Q34.3) WILD-TYPE	12	13	2	19	19	12	8

Figure S185. Get High-res Image Gene #43: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 0.0333 (Fisher's exact test), Q value = 0.089

Table S186. Gene #43: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 13(4Q34.3) MUTATED	48	7	20	17	2	5
DEL PEAK 13(4Q34.3) WILD-TYPE	25	7	22	12	7	11

Figure S186. Get High-res Image Gene #43: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00105 (Fisher's exact test), Q value = 0.0067

Table S187. Gene #43: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
DEL PEAK 13(4Q34.3) MUTATED	48	9	42
DEL PEAK 13(4Q34.3) WILD-TYPE	19	11	54

Figure S187. Get High-res Image Gene #43: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CNMF'

P value = 0.0327 (Fisher's exact test), Q value = 0.088

Table S188. Gene #43: 'del_4q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
DEL PEAK 13(4Q34.3) MUTATED	48	6	4	10	10	21
DEL PEAK 13(4Q34.3) WILD-TYPE	22	9	6	8	18	21

Figure S188. Get High-res Image Gene #43: 'del_4q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00323 (Fisher's exact test), Q value = 0.017

Table S189. Gene #43: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 13(4Q34.3) MUTATED	44	14	30	11
DEL PEAK 13(4Q34.3) WILD-TYPE	18	12	32	22

Figure S189. Get High-res Image Gene #43: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00534 (Fisher's exact test), Q value = 0.025

Table S190. Gene #43: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	67	35	12
DEL PEAK 13(4Q34.3) MUTATED	42	32	13	10
DEL PEAK 13(4Q34.3) WILD-TYPE	22	35	22	2

Figure S190. Get High-res Image Gene #43: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.0045

Table S191. Gene #43: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
DEL PEAK 13(4Q34.3) MUTATED	41	16	40
DEL PEAK 13(4Q34.3) WILD-TYPE	14	13	54

Figure S191. Get High-res Image Gene #43: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0023

Table S192. Gene #44: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 14(5Q12.1) MUTATED	53	10	49
DEL PEAK 14(5Q12.1) WILD-TYPE	21	23	28

Figure S192. Get High-res Image Gene #44: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0011

Table S193. Gene #44: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
DEL PEAK 14(5Q12.1) MUTATED	28	27	0	32	16	6	3
DEL PEAK 14(5Q12.1) WILD-TYPE	8	15	2	9	21	11	6

Figure S193. Get High-res Image Gene #44: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q12.1' versus 'MRNASEQ_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.048

Table S194. Gene #44: 'del_5q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 14(5Q12.1) MUTATED	48	12	17	21	4	10
DEL PEAK 14(5Q12.1) WILD-TYPE	25	2	25	8	5	6

Figure S194. Get High-res Image Gene #44: 'del_5q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0238 (Fisher's exact test), Q value = 0.073

Table S195. Gene #44: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 14(5Q12.1) MUTATED	46	12	32	21
DEL PEAK 14(5Q12.1) WILD-TYPE	16	14	30	12

Figure S195. Get High-res Image Gene #44: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

P value = 0.00982 (Fisher's exact test), Q value = 0.04

Table S196. Gene #45: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 15(6P25.3) MUTATED	36	6	32
DEL PEAK 15(6P25.3) WILD-TYPE	38	27	45

Figure S196. Get High-res Image Gene #45: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0211 (Fisher's exact test), Q value = 0.067

Table S197. Gene #45: 'del_6p25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 15(6P25.3) MUTATED	31	10	26	6
DEL PEAK 15(6P25.3) WILD-TYPE	31	16	36	27

Figure S197. Get High-res Image Gene #45: 'del_6p25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q16.3' versus 'CN_CNMF'

P value = 0.0346 (Fisher's exact test), Q value = 0.09

Table S198. Gene #46: 'del_6q16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 16(6Q16.3) MUTATED	20	5	30
DEL PEAK 16(6Q16.3) WILD-TYPE	54	28	47

Figure S198. Get High-res Image Gene #46: 'del_6q16.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q16.3' versus 'MRNASEQ_CNMF'

P value = 0.0441 (Fisher's exact test), Q value = 0.11

Table S199. Gene #46: 'del_6q16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 16(6Q16.3) MUTATED	21	3	11	16	2	2
DEL PEAK 16(6Q16.3) WILD-TYPE	52	11	31	13	7	14

Figure S199. Get High-res Image Gene #46: 'del_6q16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_7q31.1' versus 'METHLYATION_CNMF'

P value = 0.00238 (Fisher's exact test), Q value = 0.014

Table S200. Gene #48: 'del_7q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
DEL PEAK 18(7Q31.1) MUTATED	16	14	0	4	17	4	1
DEL PEAK 18(7Q31.1) WILD-TYPE	20	28	2	37	20	13	8

Figure S200. Get High-res Image Gene #48: 'del_7q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q31.1' versus 'MRNASEQ_CNMF'

P value = 0.0254 (Fisher's exact test), Q value = 0.075

Table S201. Gene #48: 'del_7q31.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 18(7Q31.1) MUTATED	29	4	16	3	1	3
DEL PEAK 18(7Q31.1) WILD-TYPE	44	10	26	26	8	13

Figure S201. Get High-res Image Gene #48: 'del_7q31.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_7q36.3' versus 'METHLYATION_CNMF'

P value = 0.0283 (Fisher's exact test), Q value = 0.08

Table S202. Gene #49: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
DEL PEAK 19(7Q36.3) MUTATED	17	14	0	11	19	6	0
DEL PEAK 19(7Q36.3) WILD-TYPE	19	28	2	30	18	11	9

Figure S202. Get High-res Image Gene #49: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q36.3' versus 'MRNASEQ_CNMF'

P value = 0.00299 (Fisher's exact test), Q value = 0.016

Table S203. Gene #49: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 19(7Q36.3) MUTATED	29	6	22	4	0	6
DEL PEAK 19(7Q36.3) WILD-TYPE	44	8	20	25	9	10

Figure S203. Get High-res Image Gene #49: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'CN_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.0045

Table S204. Gene #50: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 20(8P23.2) MUTATED	35	8	49
DEL PEAK 20(8P23.2) WILD-TYPE	39	25	28

Figure S204. Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 0.0232 (Fisher's exact test), Q value = 0.072

Table S205. Gene #50: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
DEL PEAK 20(8P23.2) MUTATED	15	18	2	23	26	5	3
DEL PEAK 20(8P23.2) WILD-TYPE	21	24	0	18	11	12	6

Figure S205. Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00304 (Fisher's exact test), Q value = 0.016

Table S206. Gene #50: 'del_8p23.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	23	21	22	26	34
DEL PEAK 20(8P23.2) MUTATED	5	8	14	14	24
DEL PEAK 20(8P23.2) WILD-TYPE	18	13	8	12	10

Figure S206. Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0232 (Fisher's exact test), Q value = 0.072

Table S207. Gene #50: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
DEL PEAK 20(8P23.2) MUTATED	27	7	57
DEL PEAK 20(8P23.2) WILD-TYPE	40	13	39

Figure S207. Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 0.00841 (Fisher's exact test), Q value = 0.036

Table S208. Gene #50: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
DEL PEAK 20(8P23.2) MUTATED	25	12	7	9	13	26
DEL PEAK 20(8P23.2) WILD-TYPE	45	3	3	9	15	16

Figure S208. Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.066

Table S209. Gene #50: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	67	35	12
DEL PEAK 20(8P23.2) MUTATED	25	43	14	6
DEL PEAK 20(8P23.2) WILD-TYPE	39	24	21	6

Figure S209. Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8p12' versus 'CN_CNMF'

P value = 0.00767 (Fisher's exact test), Q value = 0.034

Table S210. Gene #51: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 21(8P12) MUTATED	31	6	38
DEL PEAK 21(8P12) WILD-TYPE	43	27	39

Figure S210. Get High-res Image Gene #51: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'CN_CNMF'

P value = 0.0168 (Fisher's exact test), Q value = 0.058

Table S211. Gene #52: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 22(9P23) MUTATED	51	13	44
DEL PEAK 22(9P23) WILD-TYPE	23	20	33

Figure S211. Get High-res Image Gene #52: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 0.0304 (Fisher's exact test), Q value = 0.084

Table S212. Gene #52: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 22(9P23) MUTATED	47	12	25	14	4	5
DEL PEAK 22(9P23) WILD-TYPE	26	2	17	15	5	11

Figure S212. Get High-res Image Gene #52: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0238 (Fisher's exact test), Q value = 0.073

Table S213. Gene #52: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
DEL PEAK 22(9P23) MUTATED	46	7	54
DEL PEAK 22(9P23) WILD-TYPE	21	13	42

Figure S213. Get High-res Image Gene #52: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S214. Gene #53: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 23(9P21.3) MUTATED	55	16	70
DEL PEAK 23(9P21.3) WILD-TYPE	19	17	7

Figure S214. Get High-res Image Gene #53: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 0.0346 (Fisher's exact test), Q value = 0.09

Table S215. Gene #53: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
DEL PEAK 23(9P21.3) MUTATED	27	28	0	37	30	12	7
DEL PEAK 23(9P21.3) WILD-TYPE	9	14	2	4	7	5	2

Figure S215. Get High-res Image Gene #53: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0208 (Fisher's exact test), Q value = 0.067

Table S216. Gene #53: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
DEL PEAK 23(9P21.3) MUTATED	49	11	80
DEL PEAK 23(9P21.3) WILD-TYPE	18	9	16

Figure S216. Get High-res Image Gene #53: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0051

Table S217. Gene #54: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 24(10P15.3) MUTATED	18	3	33
DEL PEAK 24(10P15.3) WILD-TYPE	56	30	44

Figure S217. Get High-res Image Gene #54: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'RPPA_CNMF'

P value = 0.0303 (Fisher's exact test), Q value = 0.084

Table S218. Gene #54: 'del_10p15.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	28	30	34	8
DEL PEAK 24(10P15.3) MUTATED	4	7	16	13	2
DEL PEAK 24(10P15.3) WILD-TYPE	22	21	14	21	6

Figure S218. Get High-res Image Gene #54: 'del_10p15.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0252 (Fisher's exact test), Q value = 0.075

Table S219. Gene #54: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
DEL PEAK 24(10P15.3) MUTATED	12	6	36
DEL PEAK 24(10P15.3) WILD-TYPE	55	14	60

Figure S219. Get High-res Image Gene #54: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_CNMF'

P value = 0.0359 (Fisher's exact test), Q value = 0.093

Table S220. Gene #54: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
DEL PEAK 24(10P15.3) MUTATED	13	8	2	7	12	12
DEL PEAK 24(10P15.3) WILD-TYPE	57	7	8	11	16	30

Figure S220. Get High-res Image Gene #54: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10p15.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.045

Table S221. Gene #54: 'del_10p15.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 24(10P15.3) MUTATED	12	7	28	7
DEL PEAK 24(10P15.3) WILD-TYPE	50	19	34	26

Figure S221. Get High-res Image Gene #54: 'del_10p15.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S222. Gene #55: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 25(10P11.21) MUTATED	9	5	38
DEL PEAK 25(10P11.21) WILD-TYPE	65	28	39

Figure S222. Get High-res Image Gene #55: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p11.21' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.002

Table S223. Gene #55: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
DEL PEAK 25(10P11.21) MUTATED	3	6	0	19	17	4	3
DEL PEAK 25(10P11.21) WILD-TYPE	33	36	2	22	20	13	6

Figure S223. Get High-res Image Gene #55: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p11.21' versus 'RPPA_CNMF'

P value = 0.00594 (Fisher's exact test), Q value = 0.027

Table S224. Gene #55: 'del_10p11.21' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	28	30	34	8
DEL PEAK 25(10P11.21) MUTATED	2	8	12	17	3
DEL PEAK 25(10P11.21) WILD-TYPE	24	20	18	17	5

Figure S224. Get High-res Image Gene #55: 'del_10p11.21' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_10p11.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.0311 (Fisher's exact test), Q value = 0.084

Table S225. Gene #55: 'del_10p11.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	23	21	22	26	34
DEL PEAK 25(10P11.21) MUTATED	2	7	7	13	13
DEL PEAK 25(10P11.21) WILD-TYPE	21	14	15	13	21

Figure S225. Get High-res Image Gene #55: 'del_10p11.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10p11.21' versus 'MRNASEQ_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.0033

Table S226. Gene #55: 'del_10p11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 25(10P11.21) MUTATED	8	3	18	13	3	6
DEL PEAK 25(10P11.21) WILD-TYPE	65	11	24	16	6	10

Figure S226. Get High-res Image Gene #55: 'del_10p11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S227. Gene #55: 'del_10p11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
DEL PEAK 25(10P11.21) MUTATED	7	3	41
DEL PEAK 25(10P11.21) WILD-TYPE	60	17	55

Figure S227. Get High-res Image Gene #55: 'del_10p11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10p11.21' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00095

Table S228. Gene #55: 'del_10p11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
DEL PEAK 25(10P11.21) MUTATED	7	9	3	4	12	16
DEL PEAK 25(10P11.21) WILD-TYPE	63	6	7	14	16	26

Figure S228. Get High-res Image Gene #55: 'del_10p11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 4e-04

Table S229. Gene #55: 'del_10p11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 25(10P11.21) MUTATED	7	3	27	14
DEL PEAK 25(10P11.21) WILD-TYPE	55	23	35	19

Figure S229. Get High-res Image Gene #55: 'del_10p11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.0061

Table S230. Gene #55: 'del_10p11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	67	35	12
DEL PEAK 25(10P11.21) MUTATED	8	29	10	4
DEL PEAK 25(10P11.21) WILD-TYPE	56	38	25	8

Figure S230. Get High-res Image Gene #55: 'del_10p11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 4e-04

Table S231. Gene #55: 'del_10p11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
DEL PEAK 25(10P11.21) MUTATED	6	4	41
DEL PEAK 25(10P11.21) WILD-TYPE	49	25	53

Figure S231. Get High-res Image Gene #55: 'del_10p11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q21.1' versus 'CN_CNMF'

P value = 0.00446 (Fisher's exact test), Q value = 0.022

Table S232. Gene #56: 'del_10q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 26(10Q21.1) MUTATED	12	5	29
DEL PEAK 26(10Q21.1) WILD-TYPE	62	28	48

Figure S232. Get High-res Image Gene #56: 'del_10q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q21.1' versus 'METHLYATION_CNMF'

P value = 0.036 (Fisher's exact test), Q value = 0.093

Table S233. Gene #56: 'del_10q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
DEL PEAK 26(10Q21.1) MUTATED	7	6	0	19	9	3	2
DEL PEAK 26(10Q21.1) WILD-TYPE	29	36	2	22	28	14	7

Figure S233. Get High-res Image Gene #56: 'del_10q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'CN_CNMF'

P value = 0.0344 (Fisher's exact test), Q value = 0.09

Table S234. Gene #57: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 27(10Q23.31) MUTATED	23	7	35
DEL PEAK 27(10Q23.31) WILD-TYPE	51	26	42

Figure S234. Get High-res Image Gene #57: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.4' versus 'CN_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.041

Table S235. Gene #58: 'del_11p15.4' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 28(11P15.4) MUTATED	32	7	40
DEL PEAK 28(11P15.4) WILD-TYPE	42	26	37

Figure S235. Get High-res Image Gene #58: 'del_11p15.4' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q25' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S236. Gene #59: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 29(11Q25) MUTATED	26	6	49
DEL PEAK 29(11Q25) WILD-TYPE	48	27	28

Figure S236. Get High-res Image Gene #59: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q25' versus 'METHLYATION_CNMF'

P value = 0.0453 (Fisher's exact test), Q value = 0.11

Table S237. Gene #59: 'del_11q25' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
DEL PEAK 29(11Q25) MUTATED	14	14	0	24	21	4	4
DEL PEAK 29(11Q25) WILD-TYPE	22	28	2	17	16	13	5

Figure S237. Get High-res Image Gene #59: 'del_11q25' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q25' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0493 (Fisher's exact test), Q value = 0.12

Table S238. Gene #59: 'del_11q25' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
DEL PEAK 29(11Q25) MUTATED	22	8	50
DEL PEAK 29(11Q25) WILD-TYPE	45	12	46

Figure S238. Get High-res Image Gene #59: 'del_11q25' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0133 (Fisher's exact test), Q value = 0.049

Table S239. Gene #60: 'del_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
DEL PEAK 30(12Q23.1) MUTATED	15	15	21
DEL PEAK 30(12Q23.1) WILD-TYPE	40	14	73

Figure S239. Get High-res Image Gene #60: 'del_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q12.11' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0013

Table S240. Gene #61: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 31(13Q12.11) MUTATED	27	5	44
DEL PEAK 31(13Q12.11) WILD-TYPE	47	28	33

Figure S240. Get High-res Image Gene #61: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q12.11' versus 'METHLYATION_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.0056

Table S241. Gene #61: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
DEL PEAK 31(13Q12.11) MUTATED	13	11	1	18	26	3	4
DEL PEAK 31(13Q12.11) WILD-TYPE	23	31	1	23	11	14	5

Figure S241. Get High-res Image Gene #61: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q12.11' versus 'RPPA_CHIERARCHICAL'

P value = 0.0381 (Fisher's exact test), Q value = 0.097

Table S242. Gene #61: 'del_13q12.11' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	23	21	22	26	34
DEL PEAK 31(13Q12.11) MUTATED	7	5	9	17	16
DEL PEAK 31(13Q12.11) WILD-TYPE	16	16	13	9	18

Figure S242. Get High-res Image Gene #61: 'del_13q12.11' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_13q12.11' versus 'MRNASEQ_CNMF'

P value = 0.0172 (Fisher's exact test), Q value = 0.058

Table S243. Gene #61: 'del_13q12.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 31(13Q12.11) MUTATED	20	9	24	11	4	7
DEL PEAK 31(13Q12.11) WILD-TYPE	53	5	18	18	5	9

Figure S243. Get High-res Image Gene #61: 'del_13q12.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q12.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00381 (Fisher's exact test), Q value = 0.02

Table S244. Gene #61: 'del_13q12.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
DEL PEAK 31(13Q12.11) MUTATED	23	3	49
DEL PEAK 31(13Q12.11) WILD-TYPE	44	17	47

Figure S244. Get High-res Image Gene #61: 'del_13q12.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q12.11' versus 'MIRSEQ_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.045

Table S245. Gene #61: 'del_13q12.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
DEL PEAK 31(13Q12.11) MUTATED	19	8	7	7	11	24
DEL PEAK 31(13Q12.11) WILD-TYPE	51	7	3	11	17	18

Figure S245. Get High-res Image Gene #61: 'del_13q12.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_13q12.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00972 (Fisher's exact test), Q value = 0.04

Table S246. Gene #61: 'del_13q12.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 31(13Q12.11) MUTATED	19	7	30	20
DEL PEAK 31(13Q12.11) WILD-TYPE	43	19	32	13

Figure S246. Get High-res Image Gene #61: 'del_13q12.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q12.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.068

Table S247. Gene #61: 'del_13q12.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	67	35	12
DEL PEAK 31(13Q12.11) MUTATED	19	37	12	5
DEL PEAK 31(13Q12.11) WILD-TYPE	45	30	23	7

Figure S247. Get High-res Image Gene #61: 'del_13q12.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_13q12.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0117 (Fisher's exact test), Q value = 0.045

Table S248. Gene #61: 'del_13q12.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
DEL PEAK 31(13Q12.11) MUTATED	18	7	48
DEL PEAK 31(13Q12.11) WILD-TYPE	37	22	46

Figure S248. Get High-res Image Gene #61: 'del_13q12.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0055

Table S249. Gene #62: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 32(13Q14.2) MUTATED	24	7	43
DEL PEAK 32(13Q14.2) WILD-TYPE	50	26	34

Figure S249. Get High-res Image Gene #62: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 0.00917 (Fisher's exact test), Q value = 0.038

Table S250. Gene #62: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
DEL PEAK 32(13Q14.2) MUTATED	14	11	0	19	23	3	4
DEL PEAK 32(13Q14.2) WILD-TYPE	22	31	2	22	14	14	5

Figure S250. Get High-res Image Gene #62: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 0.0172 (Fisher's exact test), Q value = 0.058

Table S251. Gene #62: 'del_13q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 32(13Q14.2) MUTATED	20	10	22	11	4	7
DEL PEAK 32(13Q14.2) WILD-TYPE	53	4	20	18	5	9

Figure S251. Get High-res Image Gene #62: 'del_13q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0213 (Fisher's exact test), Q value = 0.068

Table S252. Gene #62: 'del_13q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
DEL PEAK 32(13Q14.2) MUTATED	21	5	48
DEL PEAK 32(13Q14.2) WILD-TYPE	46	15	48

Figure S252. Get High-res Image Gene #62: 'del_13q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0247 (Fisher's exact test), Q value = 0.074

Table S253. Gene #62: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 32(13Q14.2) MUTATED	21	5	31	16
DEL PEAK 32(13Q14.2) WILD-TYPE	41	21	31	17

Figure S253. Get High-res Image Gene #62: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.053

Table S254. Gene #62: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	67	35	12
DEL PEAK 32(13Q14.2) MUTATED	20	37	10	4
DEL PEAK 32(13Q14.2) WILD-TYPE	44	30	25	8

Figure S254. Get High-res Image Gene #62: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0155 (Fisher's exact test), Q value = 0.055

Table S255. Gene #62: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
DEL PEAK 32(13Q14.2) MUTATED	19	6	46
DEL PEAK 32(13Q14.2) WILD-TYPE	36	23	48

Figure S255. Get High-res Image Gene #62: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q21.31' versus 'CN_CNMF'

P value = 0.00504 (Fisher's exact test), Q value = 0.024

Table S256. Gene #63: 'del_13q21.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 33(13Q21.31) MUTATED	25	6	38
DEL PEAK 33(13Q21.31) WILD-TYPE	49	27	39

Figure S256. Get High-res Image Gene #63: 'del_13q21.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q21.31' versus 'MRNASEQ_CNMF'

P value = 0.0482 (Fisher's exact test), Q value = 0.12

Table S257. Gene #63: 'del_13q21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 33(13Q21.31) MUTATED	20	10	18	10	4	7
DEL PEAK 33(13Q21.31) WILD-TYPE	53	4	24	19	5	9

Figure S257. Get High-res Image Gene #63: 'del_13q21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S258. Gene #64: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 34(14Q23.3) MUTATED	35	0	16
DEL PEAK 34(14Q23.3) WILD-TYPE	39	33	61

Figure S258. Get High-res Image Gene #64: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q23.3' versus 'METHLYATION_CNMF'

P value = 0.0251 (Fisher's exact test), Q value = 0.075

Table S259. Gene #64: 'del_14q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
DEL PEAK 34(14Q23.3) MUTATED	16	15	0	7	9	1	3
DEL PEAK 34(14Q23.3) WILD-TYPE	20	27	2	34	28	16	6

Figure S259. Get High-res Image Gene #64: 'del_14q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q23.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0249 (Fisher's exact test), Q value = 0.074

Table S260. Gene #64: 'del_14q23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	23	21	22	26	34
DEL PEAK 34(14Q23.3) MUTATED	6	11	7	6	4
DEL PEAK 34(14Q23.3) WILD-TYPE	17	10	15	20	30

Figure S260. Get High-res Image Gene #64: 'del_14q23.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_14q23.3' versus 'MRNASEQ_CNMF'

P value = 0.00435 (Fisher's exact test), Q value = 0.022

Table S261. Gene #64: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 34(14Q23.3) MUTATED	29	7	8	5	0	2
DEL PEAK 34(14Q23.3) WILD-TYPE	44	7	34	24	9	14

Figure S261. Get High-res Image Gene #64: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0438 (Fisher's exact test), Q value = 0.11

Table S262. Gene #64: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
DEL PEAK 34(14Q23.3) MUTATED	26	5	20
DEL PEAK 34(14Q23.3) WILD-TYPE	41	15	76

Figure S262. Get High-res Image Gene #64: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 0.049

Table S263. Gene #64: 'del_14q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 34(14Q23.3) MUTATED	27	5	13	6
DEL PEAK 34(14Q23.3) WILD-TYPE	35	21	49	27

Figure S263. Get High-res Image Gene #64: 'del_14q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00458 (Fisher's exact test), Q value = 0.022

Table S264. Gene #64: 'del_14q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
DEL PEAK 34(14Q23.3) MUTATED	25	7	19
DEL PEAK 34(14Q23.3) WILD-TYPE	30	22	75

Figure S264. Get High-res Image Gene #64: 'del_14q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q11.2' versus 'CN_CNMF'

P value = 0.039 (Fisher's exact test), Q value = 0.099

Table S265. Gene #65: 'del_15q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 35(15Q11.2) MUTATED	32	6	25
DEL PEAK 35(15Q11.2) WILD-TYPE	42	27	52

Figure S265. Get High-res Image Gene #65: 'del_15q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0204 (Fisher's exact test), Q value = 0.066

Table S266. Gene #65: 'del_15q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 35(15Q11.2) MUTATED	19	16	20	8
DEL PEAK 35(15Q11.2) WILD-TYPE	43	10	42	25

Figure S266. Get High-res Image Gene #65: 'del_15q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0184 (Fisher's exact test), Q value = 0.061

Table S267. Gene #65: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
DEL PEAK 35(15Q11.2) MUTATED	18	17	28
DEL PEAK 35(15Q11.2) WILD-TYPE	37	12	66

Figure S267. Get High-res Image Gene #65: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16p13.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S268. Gene #66: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 36(16P13.3) MUTATED	41	7	17
DEL PEAK 36(16P13.3) WILD-TYPE	33	26	60

Figure S268. Get High-res Image Gene #66: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16p13.3' versus 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0024

Table S269. Gene #66: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
DEL PEAK 36(16P13.3) MUTATED	23	20	0	9	8	3	2
DEL PEAK 36(16P13.3) WILD-TYPE	13	22	2	32	29	14	7

Figure S269. Get High-res Image Gene #66: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S270. Gene #66: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 36(16P13.3) MUTATED	37	9	3	9	2	5
DEL PEAK 36(16P13.3) WILD-TYPE	36	5	39	20	7	11

Figure S270. Get High-res Image Gene #66: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00086

Table S271. Gene #66: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
DEL PEAK 36(16P13.3) MUTATED	34	11	20
DEL PEAK 36(16P13.3) WILD-TYPE	33	9	76

Figure S271. Get High-res Image Gene #66: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0023

Table S272. Gene #66: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
DEL PEAK 36(16P13.3) MUTATED	37	5	5	6	5	6
DEL PEAK 36(16P13.3) WILD-TYPE	33	10	5	12	23	36

Figure S272. Get High-res Image Gene #66: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S273. Gene #66: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 36(16P13.3) MUTATED	37	9	14	4
DEL PEAK 36(16P13.3) WILD-TYPE	25	17	48	29

Figure S273. Get High-res Image Gene #66: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00079

Table S274. Gene #66: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	67	35	12
DEL PEAK 36(16P13.3) MUTATED	36	13	9	5
DEL PEAK 36(16P13.3) WILD-TYPE	28	54	26	7

Figure S274. Get High-res Image Gene #66: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S275. Gene #66: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
DEL PEAK 36(16P13.3) MUTATED	32	13	18
DEL PEAK 36(16P13.3) WILD-TYPE	23	16	76

Figure S275. Get High-res Image Gene #66: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S276. Gene #67: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 37(16Q23.1) MUTATED	56	10	18
DEL PEAK 37(16Q23.1) WILD-TYPE	18	23	59

Figure S276. Get High-res Image Gene #67: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S277. Gene #67: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
DEL PEAK 37(16Q23.1) MUTATED	24	32	0	10	8	6	4
DEL PEAK 37(16Q23.1) WILD-TYPE	12	10	2	31	29	11	5

Figure S277. Get High-res Image Gene #67: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0395 (Fisher's exact test), Q value = 0.1

Table S278. Gene #67: 'del_16q23.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	23	21	22	26	34
DEL PEAK 37(16Q23.1) MUTATED	11	13	11	7	9
DEL PEAK 37(16Q23.1) WILD-TYPE	12	8	11	19	25

Figure S278. Get High-res Image Gene #67: 'del_16q23.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S279. Gene #67: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 37(16Q23.1) MUTATED	50	9	9	6	3	7
DEL PEAK 37(16Q23.1) WILD-TYPE	23	5	33	23	6	9

Figure S279. Get High-res Image Gene #67: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S280. Gene #67: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
DEL PEAK 37(16Q23.1) MUTATED	49	12	23
DEL PEAK 37(16Q23.1) WILD-TYPE	18	8	73

Figure S280. Get High-res Image Gene #67: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00079

Table S281. Gene #67: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
DEL PEAK 37(16Q23.1) MUTATED	48	6	4	7	9	9
DEL PEAK 37(16Q23.1) WILD-TYPE	22	9	6	11	19	33

Figure S281. Get High-res Image Gene #67: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S282. Gene #67: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 37(16Q23.1) MUTATED	46	16	14	7
DEL PEAK 37(16Q23.1) WILD-TYPE	16	10	48	26

Figure S282. Get High-res Image Gene #67: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S283. Gene #67: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	67	35	12
DEL PEAK 37(16Q23.1) MUTATED	47	18	11	5
DEL PEAK 37(16Q23.1) WILD-TYPE	17	49	24	7

Figure S283. Get High-res Image Gene #67: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S284. Gene #67: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
DEL PEAK 37(16Q23.1) MUTATED	41	19	21
DEL PEAK 37(16Q23.1) WILD-TYPE	14	10	73

Figure S284. Get High-res Image Gene #67: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S285. Gene #68: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 38(17P12) MUTATED	53	9	24
DEL PEAK 38(17P12) WILD-TYPE	21	24	53

Figure S285. Get High-res Image Gene #68: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S286. Gene #68: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
DEL PEAK 38(17P12) MUTATED	25	30	0	17	8	5	1
DEL PEAK 38(17P12) WILD-TYPE	11	12	2	24	29	12	8

Figure S286. Get High-res Image Gene #68: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0012

Table S287. Gene #68: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 38(17P12) MUTATED	50	6	13	10	3	4
DEL PEAK 38(17P12) WILD-TYPE	23	8	29	19	6	12

Figure S287. Get High-res Image Gene #68: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S288. Gene #68: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
DEL PEAK 38(17P12) MUTATED	46	11	29
DEL PEAK 38(17P12) WILD-TYPE	21	9	67

Figure S288. Get High-res Image Gene #68: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_CNMF'

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

Table S289. Gene #68: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
DEL PEAK 38(17P12) MUTATED	47	5	6	6	7	15
DEL PEAK 38(17P12) WILD-TYPE	23	10	4	12	21	27

Figure S289. Get High-res Image Gene #68: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 5e-04

Table S290. Gene #68: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 38(17P12) MUTATED	41	17	19	9
DEL PEAK 38(17P12) WILD-TYPE	21	9	43	24

Figure S290. Get High-res Image Gene #68: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.048

Table S291. Gene #68: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	67	35	12
DEL PEAK 38(17P12) MUTATED	41	25	14	5
DEL PEAK 38(17P12) WILD-TYPE	23	42	21	7

Figure S291. Get High-res Image Gene #68: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S292. Gene #68: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
DEL PEAK 38(17P12) MUTATED	36	21	28
DEL PEAK 38(17P12) WILD-TYPE	19	8	66

Figure S292. Get High-res Image Gene #68: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18p11.23' versus 'CN_CNMF'

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

Table S293. Gene #70: 'del_18p11.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 40(18P11.23) MUTATED	36	4	20
DEL PEAK 40(18P11.23) WILD-TYPE	38	29	57

Figure S293. Get High-res Image Gene #70: 'del_18p11.23' versus Molecular Subtype #1: 'CN_CNMF'

'del_18p11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0294 (Fisher's exact test), Q value = 0.082

Table S294. Gene #70: 'del_18p11.23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
DEL PEAK 40(18P11.23) MUTATED	29	7	23
DEL PEAK 40(18P11.23) WILD-TYPE	38	13	73

Figure S294. Get High-res Image Gene #70: 'del_18p11.23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18p11.23' versus 'MIRSEQ_CNMF'

P value = 0.0272 (Fisher's exact test), Q value = 0.078

Table S295. Gene #70: 'del_18p11.23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
DEL PEAK 40(18P11.23) MUTATED	32	1	2	5	10	10
DEL PEAK 40(18P11.23) WILD-TYPE	38	14	8	13	18	32

Figure S295. Get High-res Image Gene #70: 'del_18p11.23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18p11.23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0409 (Fisher's exact test), Q value = 0.1

Table S296. Gene #70: 'del_18p11.23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
DEL PEAK 40(18P11.23) MUTATED	24	11	23
DEL PEAK 40(18P11.23) WILD-TYPE	31	18	71

Figure S296. Get High-res Image Gene #70: 'del_18p11.23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q12.2' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0018

Table S297. Gene #71: 'del_18q12.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 41(18Q12.2) MUTATED	57	12	42
DEL PEAK 41(18Q12.2) WILD-TYPE	17	21	35

Figure S297. Get High-res Image Gene #71: 'del_18q12.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q12.2' versus 'METHLYATION_CNMF'

P value = 0.045 (Fisher's exact test), Q value = 0.11

Table S298. Gene #71: 'del_18q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
DEL PEAK 41(18Q12.2) MUTATED	27	29	0	18	22	9	6
DEL PEAK 41(18Q12.2) WILD-TYPE	9	13	2	23	15	8	3

Figure S298. Get High-res Image Gene #71: 'del_18q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q12.2' versus 'MRNASEQ_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.062

Table S299. Gene #71: 'del_18q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 41(18Q12.2) MUTATED	53	4	25	15	6	7
DEL PEAK 41(18Q12.2) WILD-TYPE	20	10	17	14	3	9

Figure S299. Get High-res Image Gene #71: 'del_18q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q12.2' versus 'MIRSEQ_CNMF'

P value = 0.00917 (Fisher's exact test), Q value = 0.038

Table S300. Gene #71: 'del_18q12.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
DEL PEAK 41(18Q12.2) MUTATED	51	10	2	7	17	24
DEL PEAK 41(18Q12.2) WILD-TYPE	19	5	8	11	11	18

Figure S300. Get High-res Image Gene #71: 'del_18q12.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00065 (Fisher's exact test), Q value = 0.0047

Table S301. Gene #71: 'del_18q12.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 41(18Q12.2) MUTATED	38	23	38	12
DEL PEAK 41(18Q12.2) WILD-TYPE	24	3	24	21

Figure S301. Get High-res Image Gene #71: 'del_18q12.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S302. Gene #71: 'del_18q12.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
DEL PEAK 41(18Q12.2) MUTATED	33	27	49
DEL PEAK 41(18Q12.2) WILD-TYPE	22	2	45

Figure S302. Get High-res Image Gene #71: 'del_18q12.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q21.2' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00059

Table S303. Gene #72: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 42(18Q21.2) MUTATED	60	13	46
DEL PEAK 42(18Q21.2) WILD-TYPE	14	20	31

Figure S303. Get High-res Image Gene #72: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 0.00945 (Fisher's exact test), Q value = 0.039

Table S304. Gene #72: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
DEL PEAK 42(18Q21.2) MUTATED	30	31	0	20	23	9	6
DEL PEAK 42(18Q21.2) WILD-TYPE	6	11	2	21	14	8	3

Figure S304. Get High-res Image Gene #72: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.0054

Table S305. Gene #72: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 42(18Q21.2) MUTATED	59	5	27	13	6	8
DEL PEAK 42(18Q21.2) WILD-TYPE	14	9	15	16	3	8

Figure S305. Get High-res Image Gene #72: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00957 (Fisher's exact test), Q value = 0.04

Table S306. Gene #72: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
DEL PEAK 42(18Q21.2) MUTATED	51	15	52
DEL PEAK 42(18Q21.2) WILD-TYPE	16	5	44

Figure S306. Get High-res Image Gene #72: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00069

Table S307. Gene #72: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
DEL PEAK 42(18Q21.2) MUTATED	57	9	1	7	19	26
DEL PEAK 42(18Q21.2) WILD-TYPE	13	6	9	11	9	16

Figure S307. Get High-res Image Gene #72: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00203 (Fisher's exact test), Q value = 0.012

Table S308. Gene #72: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 42(18Q21.2) MUTATED	43	23	39	14
DEL PEAK 42(18Q21.2) WILD-TYPE	19	3	23	19

Figure S308. Get High-res Image Gene #72: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.068

Table S309. Gene #72: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	67	35	12
DEL PEAK 42(18Q21.2) MUTATED	48	34	25	9
DEL PEAK 42(18Q21.2) WILD-TYPE	16	33	10	3

Figure S309. Get High-res Image Gene #72: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00147 (Fisher's exact test), Q value = 0.0088

Table S310. Gene #72: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
DEL PEAK 42(18Q21.2) MUTATED	38	26	52
DEL PEAK 42(18Q21.2) WILD-TYPE	17	3	42

Figure S310. Get High-res Image Gene #72: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q22.3' versus 'CN_CNMF'

P value = 0.00424 (Fisher's exact test), Q value = 0.021

Table S311. Gene #73: 'del_18q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 43(18Q22.3) MUTATED	52	12	48
DEL PEAK 43(18Q22.3) WILD-TYPE	22	21	29

Figure S311. Get High-res Image Gene #73: 'del_18q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q22.3' versus 'MIRSEQ_CNMF'

P value = 0.0269 (Fisher's exact test), Q value = 0.078

Table S312. Gene #73: 'del_18q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
DEL PEAK 43(18Q22.3) MUTATED	49	9	3	6	19	26
DEL PEAK 43(18Q22.3) WILD-TYPE	21	6	7	12	9	16

Figure S312. Get High-res Image Gene #73: 'del_18q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00803 (Fisher's exact test), Q value = 0.035

Table S313. Gene #73: 'del_18q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 43(18Q22.3) MUTATED	35	23	38	16
DEL PEAK 43(18Q22.3) WILD-TYPE	27	3	24	17

Figure S313. Get High-res Image Gene #73: 'del_18q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0273 (Fisher's exact test), Q value = 0.078

Table S314. Gene #73: 'del_18q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
DEL PEAK 43(18Q22.3) MUTATED	32	24	53
DEL PEAK 43(18Q22.3) WILD-TYPE	23	5	41

Figure S314. Get High-res Image Gene #73: 'del_18q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 0.00075 (Fisher's exact test), Q value = 0.0053

Table S315. Gene #74: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 44(19P13.3) MUTATED	47	8	39
DEL PEAK 44(19P13.3) WILD-TYPE	27	25	38

Figure S315. Get High-res Image Gene #74: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 0.00647 (Fisher's exact test), Q value = 0.029

Table S316. Gene #74: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
DEL PEAK 44(19P13.3) MUTATED	26	21	0	23	17	3	4
DEL PEAK 44(19P13.3) WILD-TYPE	10	21	2	18	20	14	5

Figure S316. Get High-res Image Gene #74: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.061

Table S317. Gene #74: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 44(19P13.3) MUTATED	43	11	18	13	1	8
DEL PEAK 44(19P13.3) WILD-TYPE	30	3	24	16	8	8

Figure S317. Get High-res Image Gene #74: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.05

Table S318. Gene #74: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 44(19P13.3) MUTATED	41	9	26	18
DEL PEAK 44(19P13.3) WILD-TYPE	21	17	36	15

Figure S318. Get High-res Image Gene #74: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00613 (Fisher's exact test), Q value = 0.028

Table S319. Gene #74: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
DEL PEAK 44(19P13.3) MUTATED	38	11	43
DEL PEAK 44(19P13.3) WILD-TYPE	17	18	51

Figure S319. Get High-res Image Gene #74: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p12.1' versus 'CN_CNMF'

P value = 0.037 (Fisher's exact test), Q value = 0.096

Table S320. Gene #75: 'del_20p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 45(20P12.1) MUTATED	20	4	9
DEL PEAK 45(20P12.1) WILD-TYPE	54	29	68

Figure S320. Get High-res Image Gene #75: 'del_20p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_20p12.1' versus 'MRNASEQ_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.068

Table S321. Gene #75: 'del_20p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 45(20P12.1) MUTATED	18	6	3	4	1	1
DEL PEAK 45(20P12.1) WILD-TYPE	55	8	39	25	8	15

Figure S321. Get High-res Image Gene #75: 'del_20p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00704 (Fisher's exact test), Q value = 0.031

Table S322. Gene #75: 'del_20p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
DEL PEAK 45(20P12.1) MUTATED	20	2	11
DEL PEAK 45(20P12.1) WILD-TYPE	47	18	85

Figure S322. Get High-res Image Gene #75: 'del_20p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0496 (Fisher's exact test), Q value = 0.12

Table S323. Gene #75: 'del_20p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 45(20P12.1) MUTATED	15	7	5	6
DEL PEAK 45(20P12.1) WILD-TYPE	47	19	57	27

Figure S323. Get High-res Image Gene #75: 'del_20p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0287 (Fisher's exact test), Q value = 0.081

Table S324. Gene #75: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
DEL PEAK 45(20P12.1) MUTATED	13	9	11
DEL PEAK 45(20P12.1) WILD-TYPE	42	20	83

Figure S324. Get High-res Image Gene #75: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q21.1' versus 'CN_CNMF'

P value = 0.0263 (Fisher's exact test), Q value = 0.077

Table S325. Gene #76: 'del_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 46(21Q21.1) MUTATED	50	13	44
DEL PEAK 46(21Q21.1) WILD-TYPE	24	20	33

Figure S325. Get High-res Image Gene #76: 'del_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q22.12' versus 'METHLYATION_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.054

Table S326. Gene #77: 'del_21q22.12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
DEL PEAK 47(21Q22.12) MUTATED	21	32	0	24	22	7	2
DEL PEAK 47(21Q22.12) WILD-TYPE	15	10	2	17	15	10	7

Figure S326. Get High-res Image Gene #77: 'del_21q22.12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q11.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S327. Gene #78: 'del_22q11.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 48(22Q11.1) MUTATED	51	8	20
DEL PEAK 48(22Q11.1) WILD-TYPE	23	25	57

Figure S327. Get High-res Image Gene #78: 'del_22q11.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q11.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S328. Gene #78: 'del_22q11.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	36	42	2	41	37	17	9
DEL PEAK 48(22Q11.1) MUTATED	25	26	0	11	10	5	2
DEL PEAK 48(22Q11.1) WILD-TYPE	11	16	2	30	27	12	7

Figure S328. Get High-res Image Gene #78: 'del_22q11.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q11.1' versus 'RPPA_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.0033

Table S329. Gene #78: 'del_22q11.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	26	28	30	34	8
DEL PEAK 48(22Q11.1) MUTATED	19	12	10	7	1
DEL PEAK 48(22Q11.1) WILD-TYPE	7	16	20	27	7

Figure S329. Get High-res Image Gene #78: 'del_22q11.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_22q11.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0044 (Fisher's exact test), Q value = 0.022

Table S330. Gene #78: 'del_22q11.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	23	21	22	26	34
DEL PEAK 48(22Q11.1) MUTATED	14	12	9	8	6
DEL PEAK 48(22Q11.1) WILD-TYPE	9	9	13	18	28

Figure S330. Get High-res Image Gene #78: 'del_22q11.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_22q11.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S331. Gene #78: 'del_22q11.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 48(22Q11.1) MUTATED	48	8	10	8	2	3
DEL PEAK 48(22Q11.1) WILD-TYPE	25	6	32	21	7	13

Figure S331. Get High-res Image Gene #78: 'del_22q11.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q11.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S332. Gene #78: 'del_22q11.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
DEL PEAK 48(22Q11.1) MUTATED	43	10	26
DEL PEAK 48(22Q11.1) WILD-TYPE	24	10	70

Figure S332. Get High-res Image Gene #78: 'del_22q11.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q11.1' versus 'MIRSEQ_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0069

Table S333. Gene #78: 'del_22q11.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	70	15	10	18	28	42
DEL PEAK 48(22Q11.1) MUTATED	44	6	4	7	8	10
DEL PEAK 48(22Q11.1) WILD-TYPE	26	9	6	11	20	32

Figure S333. Get High-res Image Gene #78: 'del_22q11.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q11.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S334. Gene #78: 'del_22q11.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 48(22Q11.1) MUTATED	43	11	16	9
DEL PEAK 48(22Q11.1) WILD-TYPE	19	15	46	24

Figure S334. Get High-res Image Gene #78: 'del_22q11.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q11.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S335. Gene #78: 'del_22q11.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	64	67	35	12
DEL PEAK 48(22Q11.1) MUTATED	46	19	8	4
DEL PEAK 48(22Q11.1) WILD-TYPE	18	48	27	8

Figure S335. Get High-res Image Gene #78: 'del_22q11.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q11.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S336. Gene #78: 'del_22q11.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
DEL PEAK 48(22Q11.1) MUTATED	38	15	24
DEL PEAK 48(22Q11.1) WILD-TYPE	17	14	70

Figure S336. Get High-res Image Gene #78: 'del_22q11.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp21.1' versus 'CN_CNMF'

P value = 0.00075 (Fisher's exact test), Q value = 0.0053

Table S337. Gene #79: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 49(XP21.1) MUTATED	25	5	40
DEL PEAK 49(XP21.1) WILD-TYPE	49	28	37

Figure S337. Get High-res Image Gene #79: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp21.1' versus 'MRNASEQ_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.042

Table S338. Gene #79: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 49(XP21.1) MUTATED	26	7	17	17	2	1
DEL PEAK 49(XP21.1) WILD-TYPE	47	7	25	12	7	15

Figure S338. Get High-res Image Gene #79: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0264 (Fisher's exact test), Q value = 0.077

Table S339. Gene #79: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
DEL PEAK 49(XP21.1) MUTATED	21	5	42
DEL PEAK 49(XP21.1) WILD-TYPE	34	24	52

Figure S339. Get High-res Image Gene #79: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp11.3' versus 'CN_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0055

Table S340. Gene #80: 'del_xp11.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	33	77
DEL PEAK 50(XP11.3) MUTATED	25	7	43
DEL PEAK 50(XP11.3) WILD-TYPE	49	26	34

Figure S340. Get High-res Image Gene #80: 'del_xp11.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp11.3' versus 'MRNASEQ_CNMF'

P value = 0.0449 (Fisher's exact test), Q value = 0.11

Table S341. Gene #80: 'del_xp11.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	14	42	29	9	16
DEL PEAK 50(XP11.3) MUTATED	25	8	21	16	2	3
DEL PEAK 50(XP11.3) WILD-TYPE	48	6	21	13	7	13

Figure S341. Get High-res Image Gene #80: 'del_xp11.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp11.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0156 (Fisher's exact test), Q value = 0.055

Table S342. Gene #80: 'del_xp11.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	20	96
DEL PEAK 50(XP11.3) MUTATED	20	6	49
DEL PEAK 50(XP11.3) WILD-TYPE	47	14	47

Figure S342. Get High-res Image Gene #80: 'del_xp11.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp11.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0254 (Fisher's exact test), Q value = 0.075

Table S343. Gene #80: 'del_xp11.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 50(XP11.3) MUTATED	21	6	29	19
DEL PEAK 50(XP11.3) WILD-TYPE	41	20	33	14

Figure S343. Get High-res Image Gene #80: 'del_xp11.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xp11.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00726 (Fisher's exact test), Q value = 0.032

Table S344. Gene #80: 'del_xp11.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	29	94
DEL PEAK 50(XP11.3) MUTATED	19	6	48
DEL PEAK 50(XP11.3) WILD-TYPE	36	23	46

Figure S344. Get High-res Image Gene #80: 'del_xp11.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xq21.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0203 (Fisher's exact test), Q value = 0.066

Table S345. Gene #82: 'del_xq21.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	62	26	62	33
DEL PEAK 52(XQ21.33) MUTATED	20	3	8	10
DEL PEAK 52(XQ21.33) WILD-TYPE	42	23	54	23

Figure S345. Get High-res Image Gene #82: 'del_xq21.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ESCA-TP/22519066/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/ESCA-TP/22541001/ESCA-TP.transferedmergedcluster.txt
Number of patients = 184
Number of significantly focal cnvs = 82
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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