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

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 72 focal events and 12 molecular subtypes across 616 patients, 433 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q31.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
amp_2q33.1 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_5p12 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_6p21.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_7p21.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_8p11.23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
amp_8p11.21 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_10q22.3 cnv correlated to 'CN_CNMF'.
amp_11p15.5 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_13q12.13 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_13q12.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_13q22.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_16p11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_17q12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_17q24.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_19q12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_20p12.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_20p11.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_20q11.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_20q12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_20q13.12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_1p36.11 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_1p33 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_1p13.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_2p12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_2q22.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
del_3p26.3 cnv correlated to 'CN_CNMF'.
del_4p16.1 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_4q22.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_4q35.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_5q12.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_5q21.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_5q22.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_5q23.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_6q26 cnv correlated to 'RPPA_CNMF'.
del_8p23.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_8p22 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_8q11.1 cnv correlated to 'CN_CNMF'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_10p15.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_10q21.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_10q25.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_11q22.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_12p13.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12q21.33 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_14q11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q31.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_15q15.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_15q21.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_15q22.33 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_16p13.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', and 'CN_CNMF'.
del_16q23.1 cnv correlated to 'MRNA_CHIERARCHICAL'.
del_17p12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17q24.3 cnv correlated to 'CN_CNMF'.
del_18p11.31 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q12.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q21.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q22.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
del_20p12.1 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_21q11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_21q21.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_22q13.32 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 72 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 433 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
del 14q11 2	212 (34%)	404	4e-05 (0.000179)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.0649 (0.126)	0.0136 (0.0331)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.00035 (0.0012)	1e-05 (5.17e-05)	0.0244 (0.0553)	0.0464 (0.094)
del 14q31 1	220 (36%)	396	0.00035 (0.0012)	5e-05 (0.000216)	1e-05 (5.17e-05)	2e-05 (9.34e-05)	0.0385 (0.0808)	0.0381 (0.0806)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.0262 (0.0586)	1e-05 (5.17e-05)	0.246 (0.37)	0.0234 (0.0534)
amp 13q12 13	402 (65%)	214	3e-05 (0.000136)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.0363 (0.0773)	0.0896 (0.164)	2e-05 (9.34e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	8e-05 (0.000332)	0.127 (0.216)
amp 20q11 21	469 (76%)	147	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.0338 (0.0728)	0.746 (0.823)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.00123 (0.00381)	0.147 (0.246)
amp 20q12	471 (76%)	145	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.0452 (0.0922)	0.721 (0.805)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.00014 (0.000547)	0.164 (0.267)
amp 20q13 12	473 (77%)	143	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.0249 (0.0561)	0.649 (0.742)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.00016 (0.000606)	0.163 (0.267)
del 17p12	370 (60%)	246	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.141 (0.236)	0.809 (0.862)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.00018 (0.000673)	1e-05 (5.17e-05)	0.0335 (0.0725)	0.0426 (0.0875)
del 18p11 31	370 (60%)	246	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.41 (0.542)	0.756 (0.829)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	2e-05 (9.34e-05)	0.00056 (0.00183)
del 18q12 2	416 (68%)	200	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.101 (0.179)	0.279 (0.411)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.00021 (0.000769)	0.00011 (0.000438)
del 18q21 2	432 (70%)	184	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.0729 (0.139)	0.375 (0.511)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.00019 (0.000705)	9e-05 (0.000372)
del 18q22 1	427 (69%)	189	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.0951 (0.173)	0.347 (0.481)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.00087 (0.00273)	0.00216 (0.00641)
amp 7p21 3	363 (59%)	253	0.00115 (0.00357)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.00011 (0.000438)	0.161 (0.265)	0.0428 (0.0875)	2e-05 (9.34e-05)	1e-05 (5.17e-05)	0.00085 (0.00269)	1e-05 (5.17e-05)	0.0733 (0.14)	0.256 (0.382)
amp 13q12 2	396 (64%)	220	2e-05 (9.34e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.0708 (0.136)	0.183 (0.293)	2e-05 (9.34e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.00022 (0.000802)	0.0787 (0.148)
amp 13q22 1	397 (64%)	219	2e-05 (9.34e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.248 (0.372)	0.284 (0.416)	3e-05 (0.000136)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.00704 (0.0189)	0.373 (0.511)
amp 16p11 2	173 (28%)	443	0.0423 (0.0872)	0.00023 (0.000831)	1e-05 (5.17e-05)	0.0167 (0.0395)	0.0156 (0.0374)	0.328 (0.464)	3e-05 (0.000136)	2e-05 (9.34e-05)	0.766 (0.836)	0.00389 (0.0109)	0.0201 (0.0466)	0.197 (0.312)
amp 20p11 21	363 (59%)	253	0.00015 (0.000576)	2e-05 (9.34e-05)	1e-05 (5.17e-05)	0.00085 (0.00269)	0.0147 (0.0355)	0.078 (0.147)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.0323 (0.0706)	1e-05 (5.17e-05)	0.094 (0.171)	0.529 (0.654)
del 21q21 1	210 (34%)	406	0.00695 (0.0187)	0.00055 (0.00181)	1e-05 (5.17e-05)	0.00334 (0.00952)	0.633 (0.733)	0.399 (0.534)	0.0001 (0.000406)	0.00066 (0.00213)	0.0172 (0.0406)	0.00868 (0.0226)	0.0765 (0.145)	0.018 (0.042)
amp 17q12	160 (26%)	456	0.0397 (0.0828)	0.0066 (0.0179)	1e-05 (5.17e-05)	0.00855 (0.0224)	0.412 (0.543)	0.0494 (0.0985)	5e-05 (0.000216)	1e-05 (5.17e-05)	0.699 (0.783)	0.0144 (0.0348)	0.072 (0.138)	0.73 (0.811)
del 1p36 11	244 (40%)	372	5e-05 (0.000216)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.00011 (0.000438)	0.0191 (0.0444)	0.219 (0.337)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.378 (0.514)	3e-05 (0.000136)	0.141 (0.236)	0.855 (0.899)
del 15q11 2	249 (40%)	367	0.00042 (0.0014)	0.00014 (0.000547)	1e-05 (5.17e-05)	0.00015 (0.000576)	0.166 (0.27)	0.909 (0.937)	0.00011 (0.000438)	1e-05 (5.17e-05)	0.00166 (0.00503)	0.00084 (0.00268)	0.101 (0.179)	0.104 (0.185)
del 15q15 2	251 (41%)	365	1e-05 (5.17e-05)	5e-05 (0.000216)	1e-05 (5.17e-05)	0.00018 (0.000673)	0.0623 (0.122)	0.577 (0.691)	0.00018 (0.000673)	1e-05 (5.17e-05)	0.00362 (0.0103)	8e-05 (0.000332)	0.0519 (0.103)	0.482 (0.614)
del 15q21 1	248 (40%)	368	0.00031 (0.00108)	0.00049 (0.00162)	1e-05 (5.17e-05)	0.00026 (0.000932)	0.124 (0.213)	0.731 (0.812)	0.0002 (0.000738)	1e-05 (5.17e-05)	0.0111 (0.0276)	0.00187 (0.00563)	0.0801 (0.15)	0.495 (0.625)
del 15q22 33	238 (39%)	378	8e-05 (0.000332)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	3e-05 (0.000136)	0.619 (0.723)	0.476 (0.609)	2e-05 (9.34e-05)	1e-05 (5.17e-05)	0.00253 (0.00734)	8e-05 (0.000332)	0.0834 (0.155)	0.208 (0.323)
del 21q11 2	214 (35%)	402	0.00796 (0.0211)	0.00039 (0.00131)	1e-05 (5.17e-05)	0.00737 (0.0197)	0.336 (0.472)	0.524 (0.652)	0.00013 (0.000513)	0.00033 (0.00115)	0.0179 (0.042)	0.0254 (0.057)	0.177 (0.286)	0.116 (0.201)
del 22q13 32	228 (37%)	388	0.00236 (0.00689)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.0309 (0.0677)	0.105 (0.185)	0.246 (0.37)	0.0266 (0.0593)	1e-05 (5.17e-05)	0.0271 (0.0601)	0.00045 (0.00149)	0.353 (0.487)	0.22 (0.338)
amp 2q33 1	140 (23%)	476	0.0797 (0.15)	0.00131 (0.00403)	1e-05 (5.17e-05)	0.00389 (0.0109)	0.285 (0.416)	0.28 (0.412)	1e-05 (5.17e-05)	8e-05 (0.000332)	0.0414 (0.0857)	0.00424 (0.0118)	0.758 (0.83)	0.923 (0.949)
amp 8q24 21	368 (60%)	248	0.203 (0.317)	0.0214 (0.0494)	1e-05 (5.17e-05)	2e-05 (9.34e-05)	0.353 (0.487)	0.0918 (0.167)	4e-05 (0.000179)	0.00133 (0.00407)	0.106 (0.187)	0.0103 (0.0259)	0.0224 (0.0515)	1 (1.00)
amp 11p15 5	138 (22%)	478	0.00061 (0.00198)	0.0009 (0.00282)	1e-05 (5.17e-05)	0.00224 (0.00661)	0.286 (0.417)	0.673 (0.762)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.953 (0.972)	1e-05 (5.17e-05)	0.585 (0.695)	0.694 (0.779)
amp 17q24 1	144 (23%)	472	0.0306 (0.0672)	0.0123 (0.0302)	1e-05 (5.17e-05)	0.00032 (0.00111)	0.506 (0.633)	0.107 (0.188)	2e-05 (9.34e-05)	1e-05 (5.17e-05)	0.45 (0.581)	0.00577 (0.0158)	0.195 (0.308)	0.45 (0.581)
amp 19q12	139 (23%)	477	0.0158 (0.0379)	0.00253 (0.00734)	1e-05 (5.17e-05)	0.536 (0.658)	0.016 (0.0382)	0.389 (0.523)	0.0404 (0.0838)	0.00933 (0.024)	0.0995 (0.178)	0.0247 (0.0557)	0.154 (0.254)	0.77 (0.839)
amp 20p12 1	278 (45%)	338	0.0166 (0.0395)	0.00262 (0.00755)	1e-05 (5.17e-05)	0.516 (0.643)	0.00201 (0.00601)	0.434 (0.564)	0.166 (0.27)	0.00023 (0.000831)	0.21 (0.325)	1e-05 (5.17e-05)	0.0385 (0.0808)	0.689 (0.775)
del 1p33	176 (29%)	440	0.0385 (0.0808)	0.00229 (0.00673)	1e-05 (5.17e-05)	0.00738 (0.0197)	0.303 (0.437)	0.665 (0.755)	5e-05 (0.000216)	0.00041 (0.00137)	0.0517 (0.103)	0.0268 (0.0595)	0.342 (0.476)	0.749 (0.823)
del 1p13 2	176 (29%)	440	0.38 (0.514)	0.0338 (0.0728)	1e-05 (5.17e-05)	0.0112 (0.0279)	0.592 (0.7)	0.859 (0.902)	0.00021 (0.000769)	0.00028 (0.001)	0.0339 (0.0728)	0.00665 (0.018)	0.537 (0.658)	0.985 (0.996)
del 4q22 1	225 (37%)	391	0.00589 (0.0161)	0.00444 (0.0123)	1e-05 (5.17e-05)	0.0102 (0.0258)	0.545 (0.662)	0.184 (0.293)	0.00487 (0.0134)	1e-05 (5.17e-05)	0.201 (0.315)	0.00039 (0.00131)	0.152 (0.253)	0.285 (0.417)
del 4q35 1	233 (38%)	383	0.00884 (0.0229)	0.00854 (0.0224)	1e-05 (5.17e-05)	0.0105 (0.0264)	0.726 (0.809)	0.257 (0.383)	0.00453 (0.0125)	2e-05 (9.34e-05)	0.0363 (0.0773)	0.1 (0.179)	0.558 (0.675)	0.858 (0.902)
del 5q12 1	159 (26%)	457	0.00031 (0.00108)	2e-05 (9.34e-05)	1e-05 (5.17e-05)	0.00262 (0.00755)	0.116 (0.201)	0.334 (0.47)	0.0307 (0.0673)	1e-05 (5.17e-05)	0.224 (0.342)	0.00016 (0.000606)	0.885 (0.921)	0.54 (0.658)
del 5q23 3	161 (26%)	455	0.00677 (0.0183)	5e-05 (0.000216)	1e-05 (5.17e-05)	0.00303 (0.00867)	0.354 (0.488)	0.641 (0.738)	0.0104 (0.0261)	0.00015 (0.000576)	0.263 (0.39)	6e-05 (0.000257)	0.606 (0.714)	0.96 (0.977)
del 8p23 2	290 (47%)	326	7e-05 (0.000298)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.498 (0.627)	0.891 (0.926)	5e-05 (0.000216)	1e-05 (5.17e-05)	0.0568 (0.112)	0.00092 (0.00287)	0.167 (0.27)	0.439 (0.569)
del 8p22	304 (49%)	312	0.00029 (0.00103)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	2e-05 (9.34e-05)	1 (1.00)	0.899 (0.932)	0.00013 (0.000513)	1e-05 (5.17e-05)	0.0985 (0.177)	0.0001 (0.000406)	0.186 (0.295)	0.378 (0.514)
del 12p13 1	92 (15%)	524	0.00342 (0.00972)	0.00031 (0.00108)	1e-05 (5.17e-05)	0.0528 (0.105)	0.972 (0.986)	0.788 (0.846)	0.0463 (0.0939)	0.00079 (0.00254)	0.0389 (0.0812)	0.156 (0.258)	0.777 (0.842)	0.0437 (0.0893)
del 20p12 1	136 (22%)	480	0.057 (0.112)	0.00231 (0.00677)	1e-05 (5.17e-05)	1e-05 (5.17e-05)	0.181 (0.29)	0.772 (0.84)	0.00015 (0.000576)	1e-05 (5.17e-05)	0.00378 (0.0107)	0.00036 (0.00123)	0.113 (0.197)	0.0989 (0.178)
del 2p12	21 (3%)	595	1 (1.00)	0.781 (0.845)	0.00219 (0.00648)	0.0101 (0.0258)	0.206 (0.32)	0.00179 (0.00541)	0.00937 (0.024)	0.013 (0.0317)	0.00036 (0.00123)	0.0843 (0.156)	1 (1.00)	0.258 (0.383)
del 4p16 1	203 (33%)	413	0.0741 (0.141)	0.00205 (0.00611)	1e-05 (5.17e-05)	0.00508 (0.0139)	0.663 (0.755)	0.498 (0.627)	0.00865 (0.0226)	1e-05 (5.17e-05)	0.423 (0.552)	0.0113 (0.0279)	0.459 (0.591)	0.93 (0.955)
del 5q21 2	187 (30%)	429	0.0289 (0.0637)	0.00082 (0.00262)	1e-05 (5.17e-05)	0.0134 (0.0326)	0.111 (0.194)	0.423 (0.552)	0.255 (0.381)	0.00161 (0.00492)	0.319 (0.454)	0.00087 (0.00273)	0.567 (0.683)	0.987 (0.997)
del 5q22 2	189 (31%)	427	0.00025 (9e-04)	3e-05 (0.000136)	1e-05 (5.17e-05)	0.0415 (0.0859)	0.159 (0.262)	0.395 (0.53)	0.0707 (0.136)	0.0001 (0.000406)	0.246 (0.371)	0.00045 (0.00149)	0.579 (0.691)	0.973 (0.986)
del 10q21 1	139 (23%)	477	0.0117 (0.0288)	0.0381 (0.0806)	1e-05 (5.17e-05)	0.018 (0.042)	0.217 (0.334)	0.808 (0.862)	0.0001 (0.000406)	0.00038 (0.00129)	0.626 (0.727)	0.0807 (0.151)	0.42 (0.552)	0.537 (0.658)
amp 5p12	118 (19%)	498	0.14 (0.236)	0.0281 (0.0622)	1e-05 (5.17e-05)	0.834 (0.885)	0.0101 (0.0257)	0.915 (0.942)	0.00406 (0.0114)	0.00751 (0.02)	0.23 (0.351)	0.703 (0.787)	0.345 (0.48)	0.49 (0.621)
amp 6p21 1	154 (25%)	462	0.0241 (0.0547)	2e-05 (9.34e-05)	1e-05 (5.17e-05)	0.131 (0.224)	0.153 (0.254)	0.294 (0.426)	0.381 (0.515)	0.00029 (0.00103)	0.181 (0.29)	0.025 (0.0561)	0.369 (0.505)	0.098 (0.177)
amp 8p11 23	211 (34%)	405	0.398 (0.533)	0.0866 (0.159)	1e-05 (5.17e-05)	0.0159 (0.0379)	0.219 (0.337)	0.612 (0.719)	0.0235 (0.0536)	0.00892 (0.0231)	0.0225 (0.0516)	0.119 (0.205)	0.555 (0.672)	0.799 (0.854)
amp 8p11 21	256 (42%)	360	0.166 (0.27)	0.0112 (0.0279)	1e-05 (5.17e-05)	0.0167 (0.0395)	0.668 (0.758)	0.312 (0.447)	0.0475 (0.0959)	0.0483 (0.097)	0.124 (0.212)	0.24 (0.364)	0.611 (0.718)	0.614 (0.719)
del 9p21 3	88 (14%)	528	0.506 (0.633)	0.236 (0.359)	0.00016 (0.000606)	0.0346 (0.0742)	0.872 (0.911)	0.298 (0.431)	0.0387 (0.081)	0.0424 (0.0873)	0.184 (0.293)	0.0327 (0.0712)	0.642 (0.739)	0.531 (0.656)
del 10p15 3	115 (19%)	501	0.0769 (0.145)	0.31 (0.446)	1e-05 (5.17e-05)	0.0363 (0.0773)	0.584 (0.695)	0.749 (0.823)	0.00962 (0.0246)	2e-05 (9.34e-05)	0.554 (0.672)	0.194 (0.307)	0.0484 (0.097)	0.0625 (0.122)
del 10q23 31	161 (26%)	455	0.0531 (0.105)	0.588 (0.698)	1e-05 (5.17e-05)	0.0153 (0.0368)	0.785 (0.846)	0.845 (0.894)	0.00477 (0.0132)	6e-05 (0.000257)	0.277 (0.409)	0.0113 (0.0279)	0.177 (0.286)	0.203 (0.317)
del 10q25 2	157 (25%)	459	0.199 (0.314)	0.229 (0.35)	1e-05 (5.17e-05)	0.0186 (0.0432)	0.209 (0.324)	0.932 (0.956)	0.00269 (0.00772)	1e-05 (5.17e-05)	0.327 (0.464)	0.0206 (0.0475)	0.478 (0.61)	0.362 (0.497)
del 12q21 33	90 (15%)	526	0.0242 (0.0548)	0.0115 (0.0282)	1e-05 (5.17e-05)	0.2 (0.314)	0.203 (0.317)	0.0862 (0.159)	0.0636 (0.123)	0.00037 (0.00126)	0.288 (0.418)	0.664 (0.755)	0.665 (0.755)	0.268 (0.396)
del 16p13 3	69 (11%)	547	0.049 (0.0981)	0.0364 (0.0773)	0.00812 (0.0215)	0.727 (0.809)	0.819 (0.871)	0.791 (0.849)	0.272 (0.402)	0.0764 (0.145)	0.526 (0.652)	0.112 (0.196)	0.564 (0.681)	0.962 (0.977)
amp 1q31 1	145 (24%)	471	0.781 (0.845)	0.337 (0.472)	2e-05 (9.34e-05)	0.764 (0.835)	0.104 (0.183)	0.161 (0.265)	0.578 (0.691)	0.427 (0.557)	0.0703 (0.136)	0.331 (0.467)	0.0104 (0.0261)	0.318 (0.453)
del 2q22 1	35 (6%)	581	0.785 (0.846)	0.649 (0.742)	0.0331 (0.0719)	0.498 (0.627)	0.337 (0.472)	0.298 (0.431)	0.169 (0.274)	0.103 (0.182)	0.046 (0.0936)	0.136 (0.23)	0.892 (0.927)	0.52 (0.647)
del 11q22 3	111 (18%)	505	0.31 (0.445)	0.0808 (0.151)	0.00908 (0.0234)	0.405 (0.538)	0.54 (0.658)	0.948 (0.968)	0.685 (0.771)	0.0476 (0.0959)	0.133 (0.226)	0.0826 (0.153)	0.476 (0.609)	0.62 (0.723)
del 19p13 3	97 (16%)	519	0.127 (0.217)	0.206 (0.32)	0.00019 (0.000705)	0.407 (0.541)	0.775 (0.841)	0.854 (0.899)	0.149 (0.248)	0.115 (0.2)	0.896 (0.93)	0.00066 (0.00213)	0.578 (0.691)	0.401 (0.535)
amp 10q22 3	40 (6%)	576	1 (1.00)	0.416 (0.547)	0.00834 (0.022)	0.366 (0.502)	0.0598 (0.117)	0.411 (0.542)	0.647 (0.742)	0.49 (0.621)	0.872 (0.911)	0.937 (0.96)	0.409 (0.541)	0.375 (0.511)
del 3p26 3	93 (15%)	523	0.581 (0.693)	0.634 (0.733)	0.00057 (0.00186)	0.337 (0.472)	0.627 (0.727)	0.124 (0.212)	0.485 (0.616)	0.533 (0.658)	0.946 (0.967)	0.736 (0.817)	0.712 (0.795)	0.471 (0.605)
del 6q26	92 (15%)	524	0.748 (0.823)	0.68 (0.768)	0.257 (0.383)	0.538 (0.658)	0.00188 (0.00564)	0.132 (0.224)	0.0594 (0.116)	0.0856 (0.158)	0.323 (0.459)	0.796 (0.852)	0.149 (0.248)	0.665 (0.755)
del 8q11 1	47 (8%)	569	0.526 (0.652)	0.315 (0.45)	0.00164 (0.00499)	0.334 (0.47)	0.247 (0.371)	0.339 (0.473)	0.284 (0.416)	0.224 (0.342)	0.604 (0.713)	0.745 (0.823)	1 (1.00)	0.648 (0.742)
del 16q23 1	84 (14%)	532	0.0715 (0.137)	0.00131 (0.00403)	0.267 (0.396)	0.481 (0.613)	0.421 (0.552)	0.904 (0.935)	0.621 (0.723)	0.574 (0.688)	0.54 (0.658)	0.0981 (0.177)	0.684 (0.771)	0.403 (0.537)
del 17q24 3	95 (15%)	521	0.905 (0.935)	0.643 (0.739)	1e-05 (5.17e-05)	0.54 (0.658)	0.455 (0.587)	0.438 (0.569)	0.75 (0.824)	0.119 (0.205)	0.154 (0.254)	0.85 (0.897)	0.907 (0.936)	0.46 (0.591)
amp 12p13 33	153 (25%)	463	0.178 (0.287)	0.589 (0.698)	0.301 (0.434)	0.0955 (0.173)	0.962 (0.977)	0.611 (0.718)	0.5 (0.627)	0.0839 (0.155)	0.868 (0.909)	0.109 (0.191)	0.188 (0.299)	0.238 (0.361)
amp 15q26 1	42 (7%)	574	0.745 (0.823)	0.38 (0.514)	0.0558 (0.11)	0.64 (0.738)	0.0991 (0.178)	0.809 (0.862)	0.572 (0.687)	0.829 (0.881)	0.359 (0.493)	0.941 (0.963)	0.959 (0.977)	0.795 (0.852)
del 3p14 2	119 (19%)	497	0.742 (0.822)	0.698 (0.783)	0.117 (0.202)	1 (1.00)	0.349 (0.484)	0.62 (0.723)	0.448 (0.581)	0.845 (0.894)	0.882 (0.919)	0.539 (0.658)	0.134 (0.226)	0.422 (0.552)
del 3q26 31	65 (11%)	551	0.556 (0.672)	0.613 (0.719)	0.0821 (0.153)	0.51 (0.637)	0.787 (0.846)	0.873 (0.911)	0.785 (0.846)	0.199 (0.314)	0.388 (0.523)	0.288 (0.418)	0.0868 (0.159)	0.6 (0.709)
del 6p25 3	80 (13%)	536	0.774 (0.841)	0.339 (0.473)	0.159 (0.262)	0.759 (0.83)	0.624 (0.725)	0.495 (0.625)	0.386 (0.52)	0.401 (0.535)	0.232 (0.352)	0.413 (0.545)	0.314 (0.449)	0.38 (0.514)
del 7q31 1	17 (3%)	599	0.33 (0.467)	0.848 (0.895)	0.567 (0.683)	1 (1.00)	0.48 (0.613)	0.866 (0.908)	0.53 (0.655)	0.991 (1.00)	0.502 (0.629)	0.678 (0.766)	0.634 (0.733)	0.835 (0.886)

'amp_1q31.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S1. Gene #1: 'amp_1q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
AMP PEAK 1(1Q31.1) MUTATED	27	69	41	8
AMP PEAK 1(1Q31.1) WILD-TYPE	188	178	91	14

Figure S1. Get High-res Image Gene #1: 'amp_1q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q31.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.026

Table S2. Gene #1: 'amp_1q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	40	38	22
AMP PEAK 1(1Q31.1) MUTATED	3	15	12	3
AMP PEAK 1(1Q31.1) WILD-TYPE	32	25	26	19

Figure S2. Get High-res Image Gene #1: 'amp_1q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_2q33.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00131 (Fisher's exact test), Q value = 0.004

Table S3. Gene #2: 'amp_2q33.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
AMP PEAK 2(2Q33.1) MUTATED	5	27	8
AMP PEAK 2(2Q33.1) WILD-TYPE	45	62	69

Figure S3. Get High-res Image Gene #2: 'amp_2q33.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_2q33.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S4. Gene #2: 'amp_2q33.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
AMP PEAK 2(2Q33.1) MUTATED	23	70	33	14
AMP PEAK 2(2Q33.1) WILD-TYPE	192	177	99	8

Figure S4. Get High-res Image Gene #2: 'amp_2q33.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2q33.1' versus 'METHLYATION_CNMF'

P value = 0.00389 (Fisher's exact test), Q value = 0.011

Table S5. Gene #2: 'amp_2q33.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
AMP PEAK 2(2Q33.1) MUTATED	22	46	30
AMP PEAK 2(2Q33.1) WILD-TYPE	95	83	114

Figure S5. Get High-res Image Gene #2: 'amp_2q33.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2q33.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S6. Gene #2: 'amp_2q33.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
AMP PEAK 2(2Q33.1) MUTATED	56	15	32	36
AMP PEAK 2(2Q33.1) WILD-TYPE	100	113	99	162

Figure S6. Get High-res Image Gene #2: 'amp_2q33.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2q33.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00033

Table S7. Gene #2: 'amp_2q33.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
AMP PEAK 2(2Q33.1) MUTATED	27	17	7	13	32	33	10
AMP PEAK 2(2Q33.1) WILD-TYPE	53	69	57	44	58	105	88

Figure S7. Get High-res Image Gene #2: 'amp_2q33.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_2q33.1' versus 'MIRSEQ_CNMF'

P value = 0.0414 (Fisher's exact test), Q value = 0.086

Table S8. Gene #2: 'amp_2q33.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
AMP PEAK 2(2Q33.1) MUTATED	40	27	18	33
AMP PEAK 2(2Q33.1) WILD-TYPE	113	68	68	172

Figure S8. Get High-res Image Gene #2: 'amp_2q33.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_2q33.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00424 (Fisher's exact test), Q value = 0.012

Table S9. Gene #2: 'amp_2q33.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
AMP PEAK 2(2Q33.1) MUTATED	9	19	5	25	4	15	14	6	21
AMP PEAK 2(2Q33.1) WILD-TYPE	40	55	24	61	73	39	43	26	60

Figure S9. Get High-res Image Gene #2: 'amp_2q33.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5p12' versus 'MRNA_CHIERARCHICAL'

P value = 0.0281 (Fisher's exact test), Q value = 0.062

Table S10. Gene #3: 'amp_5p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
AMP PEAK 3(5P12) MUTATED	8	27	11
AMP PEAK 3(5P12) WILD-TYPE	42	62	66

Figure S10. Get High-res Image Gene #3: 'amp_5p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_5p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S11. Gene #3: 'amp_5p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
AMP PEAK 3(5P12) MUTATED	17	66	28	7
AMP PEAK 3(5P12) WILD-TYPE	198	181	104	15

Figure S11. Get High-res Image Gene #3: 'amp_5p12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p12' versus 'RPPA_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.026

Table S12. Gene #3: 'amp_5p12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	108	197	177
AMP PEAK 3(5P12) MUTATED	31	32	26
AMP PEAK 3(5P12) WILD-TYPE	77	165	151

Figure S12. Get High-res Image Gene #3: 'amp_5p12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_5p12' versus 'MRNASEQ_CNMF'

P value = 0.00406 (Fisher's exact test), Q value = 0.011

Table S13. Gene #3: 'amp_5p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
AMP PEAK 3(5P12) MUTATED	40	12	27	39
AMP PEAK 3(5P12) WILD-TYPE	116	116	104	159

Figure S13. Get High-res Image Gene #3: 'amp_5p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00751 (Fisher's exact test), Q value = 0.02

Table S14. Gene #3: 'amp_5p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
AMP PEAK 3(5P12) MUTATED	17	10	6	10	25	36	14
AMP PEAK 3(5P12) WILD-TYPE	63	76	58	47	65	102	84

Figure S14. Get High-res Image Gene #3: 'amp_5p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MRNA_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.055

Table S15. Gene #4: 'amp_6p21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
AMP PEAK 4(6P21.1) MUTATED	9	16	22	4
AMP PEAK 4(6P21.1) WILD-TYPE	36	47	43	39

Figure S15. Get High-res Image Gene #4: 'amp_6p21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_6p21.1' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S16. Gene #4: 'amp_6p21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
AMP PEAK 4(6P21.1) MUTATED	4	35	12
AMP PEAK 4(6P21.1) WILD-TYPE	46	54	65

Figure S16. Get High-res Image Gene #4: 'amp_6p21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_6p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S17. Gene #4: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
AMP PEAK 4(6P21.1) MUTATED	10	93	41	10
AMP PEAK 4(6P21.1) WILD-TYPE	205	154	91	12

Figure S17. Get High-res Image Gene #4: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.001

Table S18. Gene #4: 'amp_6p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
AMP PEAK 4(6P21.1) MUTATED	19	20	7	20	31	44	13
AMP PEAK 4(6P21.1) WILD-TYPE	61	66	57	37	59	94	85

Figure S18. Get High-res Image Gene #4: 'amp_6p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S19. Gene #4: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
AMP PEAK 4(6P21.1) MUTATED	13	19	6	28	9	12	20	7	28
AMP PEAK 4(6P21.1) WILD-TYPE	36	55	23	58	68	42	37	25	53

Figure S19. Get High-res Image Gene #4: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7p21.3' versus 'MRNA_CNMF'

P value = 0.00115 (Fisher's exact test), Q value = 0.0036

Table S20. Gene #5: 'amp_7p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
AMP PEAK 5(7P21.3) MUTATED	16	42	37	15
AMP PEAK 5(7P21.3) WILD-TYPE	29	21	28	28

Figure S20. Get High-res Image Gene #5: 'amp_7p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_7p21.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S21. Gene #5: 'amp_7p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
AMP PEAK 5(7P21.3) MUTATED	13	64	33
AMP PEAK 5(7P21.3) WILD-TYPE	37	25	44

Figure S21. Get High-res Image Gene #5: 'amp_7p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S22. Gene #5: 'amp_7p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
AMP PEAK 5(7P21.3) MUTATED	60	190	92	21
AMP PEAK 5(7P21.3) WILD-TYPE	155	57	40	1

Figure S22. Get High-res Image Gene #5: 'amp_7p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7p21.3' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00044

Table S23. Gene #5: 'amp_7p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
AMP PEAK 5(7P21.3) MUTATED	67	101	79
AMP PEAK 5(7P21.3) WILD-TYPE	50	28	65

Figure S23. Get High-res Image Gene #5: 'amp_7p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0428 (Fisher's exact test), Q value = 0.088

Table S24. Gene #5: 'amp_7p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	228	168	86
AMP PEAK 5(7P21.3) MUTATED	139	85	56
AMP PEAK 5(7P21.3) WILD-TYPE	89	83	30

Figure S24. Get High-res Image Gene #5: 'amp_7p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_7p21.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S25. Gene #5: 'amp_7p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
AMP PEAK 5(7P21.3) MUTATED	118	61	78	104
AMP PEAK 5(7P21.3) WILD-TYPE	38	67	53	94

Figure S25. Get High-res Image Gene #5: 'amp_7p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S26. Gene #5: 'amp_7p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
AMP PEAK 5(7P21.3) MUTATED	53	54	14	42	73	91	34
AMP PEAK 5(7P21.3) WILD-TYPE	27	32	50	15	17	47	64

Figure S26. Get High-res Image Gene #5: 'amp_7p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7p21.3' versus 'MIRSEQ_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.0027

Table S27. Gene #5: 'amp_7p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
AMP PEAK 5(7P21.3) MUTATED	96	62	62	101
AMP PEAK 5(7P21.3) WILD-TYPE	57	33	24	104

Figure S27. Get High-res Image Gene #5: 'amp_7p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S28. Gene #5: 'amp_7p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
AMP PEAK 5(7P21.3) MUTATED	32	49	16	60	22	27	41	16	58
AMP PEAK 5(7P21.3) WILD-TYPE	17	25	13	26	55	27	16	16	23

Figure S28. Get High-res Image Gene #5: 'amp_7p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S29. Gene #6: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
AMP PEAK 6(8P11.23) MUTATED	44	88	69	10
AMP PEAK 6(8P11.23) WILD-TYPE	171	159	63	12

Figure S29. Get High-res Image Gene #6: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.23' versus 'METHLYATION_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.038

Table S30. Gene #6: 'amp_8p11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
AMP PEAK 6(8P11.23) MUTATED	38	62	48
AMP PEAK 6(8P11.23) WILD-TYPE	79	67	96

Figure S30. Get High-res Image Gene #6: 'amp_8p11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8p11.23' versus 'MRNASEQ_CNMF'

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

Table S31. Gene #6: 'amp_8p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
AMP PEAK 6(8P11.23) MUTATED	66	41	48	54
AMP PEAK 6(8P11.23) WILD-TYPE	90	87	83	144

Figure S31. Get High-res Image Gene #6: 'amp_8p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00892 (Fisher's exact test), Q value = 0.023

Table S32. Gene #6: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
AMP PEAK 6(8P11.23) MUTATED	36	28	22	21	39	43	20
AMP PEAK 6(8P11.23) WILD-TYPE	44	58	42	36	51	95	78

Figure S32. Get High-res Image Gene #6: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.23' versus 'MIRSEQ_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.052

Table S33. Gene #6: 'amp_8p11.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
AMP PEAK 6(8P11.23) MUTATED	61	32	37	56
AMP PEAK 6(8P11.23) WILD-TYPE	92	63	49	149

Figure S33. Get High-res Image Gene #6: 'amp_8p11.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8p11.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.028

Table S34. Gene #7: 'amp_8p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
AMP PEAK 7(8P11.21) MUTATED	13	43	23
AMP PEAK 7(8P11.21) WILD-TYPE	37	46	54

Figure S34. Get High-res Image Gene #7: 'amp_8p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S35. Gene #7: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
AMP PEAK 7(8P11.21) MUTATED	47	103	96	10
AMP PEAK 7(8P11.21) WILD-TYPE	168	144	36	12

Figure S35. Get High-res Image Gene #7: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'METHLYATION_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.04

Table S36. Gene #7: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
AMP PEAK 7(8P11.21) MUTATED	48	71	56
AMP PEAK 7(8P11.21) WILD-TYPE	69	58	88

Figure S36. Get High-res Image Gene #7: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CNMF'

P value = 0.0475 (Fisher's exact test), Q value = 0.096

Table S37. Gene #7: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
AMP PEAK 7(8P11.21) MUTATED	75	46	61	72
AMP PEAK 7(8P11.21) WILD-TYPE	81	82	70	126

Figure S37. Get High-res Image Gene #7: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0483 (Fisher's exact test), Q value = 0.097

Table S38. Gene #7: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
AMP PEAK 7(8P11.21) MUTATED	37	35	23	25	48	57	29
AMP PEAK 7(8P11.21) WILD-TYPE	43	51	41	32	42	81	69

Figure S38. Get High-res Image Gene #7: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.0214 (Fisher's exact test), Q value = 0.049

Table S39. Gene #8: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
AMP PEAK 8(8Q24.21) MUTATED	23	60	39
AMP PEAK 8(8Q24.21) WILD-TYPE	27	29	38

Figure S39. Get High-res Image Gene #8: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S40. Gene #8: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
AMP PEAK 8(8Q24.21) MUTATED	64	158	128	18
AMP PEAK 8(8Q24.21) WILD-TYPE	151	89	4	4

Figure S40. Get High-res Image Gene #8: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S41. Gene #8: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
AMP PEAK 8(8Q24.21) MUTATED	67	103	75
AMP PEAK 8(8Q24.21) WILD-TYPE	50	26	69

Figure S41. Get High-res Image Gene #8: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00018

Table S42. Gene #8: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
AMP PEAK 8(8Q24.21) MUTATED	111	57	85	112
AMP PEAK 8(8Q24.21) WILD-TYPE	45	71	46	86

Figure S42. Get High-res Image Gene #8: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00133 (Fisher's exact test), Q value = 0.0041

Table S43. Gene #8: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
AMP PEAK 8(8Q24.21) MUTATED	54	44	30	37	66	86	48
AMP PEAK 8(8Q24.21) WILD-TYPE	26	42	34	20	24	52	50

Figure S43. Get High-res Image Gene #8: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.026

Table S44. Gene #8: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
AMP PEAK 8(8Q24.21) MUTATED	25	47	21	64	34	32	33	18	50
AMP PEAK 8(8Q24.21) WILD-TYPE	24	27	8	22	43	22	24	14	31

Figure S44. Get High-res Image Gene #8: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0224 (Fisher's exact test), Q value = 0.051

Table S45. Gene #8: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	40	38	22
AMP PEAK 8(8Q24.21) MUTATED	20	33	30	12
AMP PEAK 8(8Q24.21) WILD-TYPE	15	7	8	10

Figure S45. Get High-res Image Gene #8: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_10q22.3' versus 'CN_CNMF'

P value = 0.00834 (Fisher's exact test), Q value = 0.022

Table S46. Gene #9: 'amp_10q22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
AMP PEAK 9(10Q22.3) MUTATED	6	17	14	3
AMP PEAK 9(10Q22.3) WILD-TYPE	209	230	118	19

Figure S46. Get High-res Image Gene #9: 'amp_10q22.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11p15.5' versus 'MRNA_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.002

Table S47. Gene #10: 'amp_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
AMP PEAK 10(11P15.5) MUTATED	4	19	24	5
AMP PEAK 10(11P15.5) WILD-TYPE	41	44	41	38

Figure S47. Get High-res Image Gene #10: 'amp_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11p15.5' versus 'MRNA_CHIERARCHICAL'

P value = 9e-04 (Fisher's exact test), Q value = 0.0028

Table S48. Gene #10: 'amp_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
AMP PEAK 10(11P15.5) MUTATED	3	25	24
AMP PEAK 10(11P15.5) WILD-TYPE	47	64	53

Figure S48. Get High-res Image Gene #10: 'amp_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S49. Gene #10: 'amp_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
AMP PEAK 10(11P15.5) MUTATED	22	72	35	9
AMP PEAK 10(11P15.5) WILD-TYPE	193	175	97	13

Figure S49. Get High-res Image Gene #10: 'amp_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11p15.5' versus 'METHLYATION_CNMF'

P value = 0.00224 (Fisher's exact test), Q value = 0.0066

Table S50. Gene #10: 'amp_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
AMP PEAK 10(11P15.5) MUTATED	25	38	18
AMP PEAK 10(11P15.5) WILD-TYPE	92	91	126

Figure S50. Get High-res Image Gene #10: 'amp_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11p15.5' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S51. Gene #10: 'amp_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
AMP PEAK 10(11P15.5) MUTATED	54	11	24	47
AMP PEAK 10(11P15.5) WILD-TYPE	102	117	107	151

Figure S51. Get High-res Image Gene #10: 'amp_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S52. Gene #10: 'amp_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
AMP PEAK 10(11P15.5) MUTATED	30	15	2	10	21	43	15
AMP PEAK 10(11P15.5) WILD-TYPE	50	71	62	47	69	95	83

Figure S52. Get High-res Image Gene #10: 'amp_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S53. Gene #10: 'amp_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
AMP PEAK 10(11P15.5) MUTATED	5	14	1	26	4	40	14	2	17
AMP PEAK 10(11P15.5) WILD-TYPE	44	60	28	60	73	14	43	30	64

Figure S53. Get High-res Image Gene #10: 'amp_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_13q12.13' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00014

Table S54. Gene #12: 'amp_13q12.13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
AMP PEAK 12(13Q12.13) MUTATED	21	49	53	18
AMP PEAK 12(13Q12.13) WILD-TYPE	24	14	12	25

Figure S54. Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_13q12.13' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S55. Gene #12: 'amp_13q12.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
AMP PEAK 12(13Q12.13) MUTATED	16	75	50
AMP PEAK 12(13Q12.13) WILD-TYPE	34	14	27

Figure S55. Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_13q12.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S56. Gene #12: 'amp_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
AMP PEAK 12(13Q12.13) MUTATED	71	236	82	13
AMP PEAK 12(13Q12.13) WILD-TYPE	144	11	50	9

Figure S56. Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q12.13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S57. Gene #12: 'amp_13q12.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
AMP PEAK 12(13Q12.13) MUTATED	68	114	77
AMP PEAK 12(13Q12.13) WILD-TYPE	49	15	67

Figure S57. Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q12.13' versus 'RPPA_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.077

Table S58. Gene #12: 'amp_13q12.13' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	108	197	177
AMP PEAK 12(13Q12.13) MUTATED	74	136	101
AMP PEAK 12(13Q12.13) WILD-TYPE	34	61	76

Figure S58. Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_13q12.13' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S59. Gene #12: 'amp_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
AMP PEAK 12(13Q12.13) MUTATED	125	64	80	130
AMP PEAK 12(13Q12.13) WILD-TYPE	31	64	51	68

Figure S59. Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q12.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S60. Gene #12: 'amp_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
AMP PEAK 12(13Q12.13) MUTATED	60	55	14	45	75	110	40
AMP PEAK 12(13Q12.13) WILD-TYPE	20	31	50	12	15	28	58

Figure S60. Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q12.13' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S61. Gene #12: 'amp_13q12.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
AMP PEAK 12(13Q12.13) MUTATED	99	64	74	116
AMP PEAK 12(13Q12.13) WILD-TYPE	54	31	12	89

Figure S61. Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q12.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S62. Gene #12: 'amp_13q12.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
AMP PEAK 12(13Q12.13) MUTATED	31	48	18	64	28	32	47	20	65
AMP PEAK 12(13Q12.13) WILD-TYPE	18	26	11	22	49	22	10	12	16

Figure S62. Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_13q12.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00033

Table S63. Gene #12: 'amp_13q12.13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	40	38	22
AMP PEAK 12(13Q12.13) MUTATED	23	33	36	10
AMP PEAK 12(13Q12.13) WILD-TYPE	12	7	2	12

Figure S63. Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_13q12.2' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S64. Gene #13: 'amp_13q12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
AMP PEAK 13(13Q12.2) MUTATED	20	48	51	19
AMP PEAK 13(13Q12.2) WILD-TYPE	25	15	14	24

Figure S64. Get High-res Image Gene #13: 'amp_13q12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_13q12.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S65. Gene #13: 'amp_13q12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
AMP PEAK 13(13Q12.2) MUTATED	16	74	48
AMP PEAK 13(13Q12.2) WILD-TYPE	34	15	29

Figure S65. Get High-res Image Gene #13: 'amp_13q12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_13q12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S66. Gene #13: 'amp_13q12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
AMP PEAK 13(13Q12.2) MUTATED	68	234	81	13
AMP PEAK 13(13Q12.2) WILD-TYPE	147	13	51	9

Figure S66. Get High-res Image Gene #13: 'amp_13q12.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q12.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S67. Gene #13: 'amp_13q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
AMP PEAK 13(13Q12.2) MUTATED	68	114	74
AMP PEAK 13(13Q12.2) WILD-TYPE	49	15	70

Figure S67. Get High-res Image Gene #13: 'amp_13q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q12.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S68. Gene #13: 'amp_13q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
AMP PEAK 13(13Q12.2) MUTATED	124	63	79	127
AMP PEAK 13(13Q12.2) WILD-TYPE	32	65	52	71

Figure S68. Get High-res Image Gene #13: 'amp_13q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S69. Gene #13: 'amp_13q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
AMP PEAK 13(13Q12.2) MUTATED	59	54	13	45	75	109	38
AMP PEAK 13(13Q12.2) WILD-TYPE	21	32	51	12	15	29	60

Figure S69. Get High-res Image Gene #13: 'amp_13q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q12.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S70. Gene #13: 'amp_13q12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
AMP PEAK 13(13Q12.2) MUTATED	96	64	75	112
AMP PEAK 13(13Q12.2) WILD-TYPE	57	31	11	93

Figure S70. Get High-res Image Gene #13: 'amp_13q12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S71. Gene #13: 'amp_13q12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
AMP PEAK 13(13Q12.2) MUTATED	31	48	18	60	27	31	47	20	65
AMP PEAK 13(13Q12.2) WILD-TYPE	18	26	11	26	50	23	10	12	16

Figure S71. Get High-res Image Gene #13: 'amp_13q12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_13q12.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 8e-04

Table S72. Gene #13: 'amp_13q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	40	38	22
AMP PEAK 13(13Q12.2) MUTATED	22	33	35	10
AMP PEAK 13(13Q12.2) WILD-TYPE	13	7	3	12

Figure S72. Get High-res Image Gene #13: 'amp_13q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_13q22.1' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S73. Gene #14: 'amp_13q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
AMP PEAK 14(13Q22.1) MUTATED	19	49	50	19
AMP PEAK 14(13Q22.1) WILD-TYPE	26	14	15	24

Figure S73. Get High-res Image Gene #14: 'amp_13q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_13q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S74. Gene #14: 'amp_13q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
AMP PEAK 14(13Q22.1) MUTATED	14	73	50
AMP PEAK 14(13Q22.1) WILD-TYPE	36	16	27

Figure S74. Get High-res Image Gene #14: 'amp_13q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_13q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S75. Gene #14: 'amp_13q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
AMP PEAK 14(13Q22.1) MUTATED	73	231	80	13
AMP PEAK 14(13Q22.1) WILD-TYPE	142	16	52	9

Figure S75. Get High-res Image Gene #14: 'amp_13q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S76. Gene #14: 'amp_13q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
AMP PEAK 14(13Q22.1) MUTATED	69	109	79
AMP PEAK 14(13Q22.1) WILD-TYPE	48	20	65

Figure S76. Get High-res Image Gene #14: 'amp_13q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00014

Table S77. Gene #14: 'amp_13q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
AMP PEAK 14(13Q22.1) MUTATED	122	63	81	128
AMP PEAK 14(13Q22.1) WILD-TYPE	34	65	50	70

Figure S77. Get High-res Image Gene #14: 'amp_13q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S78. Gene #14: 'amp_13q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
AMP PEAK 14(13Q22.1) MUTATED	59	52	18	44	73	111	37
AMP PEAK 14(13Q22.1) WILD-TYPE	21	34	46	13	17	27	61

Figure S78. Get High-res Image Gene #14: 'amp_13q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S79. Gene #14: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
AMP PEAK 14(13Q22.1) MUTATED	97	65	76	113
AMP PEAK 14(13Q22.1) WILD-TYPE	56	30	10	92

Figure S79. Get High-res Image Gene #14: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S80. Gene #14: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
AMP PEAK 14(13Q22.1) MUTATED	31	49	18	59	28	35	48	20	63
AMP PEAK 14(13Q22.1) WILD-TYPE	18	25	11	27	49	19	9	12	18

Figure S80. Get High-res Image Gene #14: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00704 (Fisher's exact test), Q value = 0.019

Table S81. Gene #14: 'amp_13q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	40	38	22
AMP PEAK 14(13Q22.1) MUTATED	25	32	34	11
AMP PEAK 14(13Q22.1) WILD-TYPE	10	8	4	11

Figure S81. Get High-res Image Gene #14: 'amp_13q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_16p11.2' versus 'MRNA_CNMF'

P value = 0.0423 (Fisher's exact test), Q value = 0.087

Table S82. Gene #16: 'amp_16p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
AMP PEAK 16(16P11.2) MUTATED	10	24	23	7
AMP PEAK 16(16P11.2) WILD-TYPE	35	39	42	36

Figure S82. Get High-res Image Gene #16: 'amp_16p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_16p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.00083

Table S83. Gene #16: 'amp_16p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
AMP PEAK 16(16P11.2) MUTATED	8	40	16
AMP PEAK 16(16P11.2) WILD-TYPE	42	49	61

Figure S83. Get High-res Image Gene #16: 'amp_16p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_16p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S84. Gene #16: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
AMP PEAK 16(16P11.2) MUTATED	9	116	38	10
AMP PEAK 16(16P11.2) WILD-TYPE	206	131	94	12

Figure S84. Get High-res Image Gene #16: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_16p11.2' versus 'METHLYATION_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.04

Table S85. Gene #16: 'amp_16p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
AMP PEAK 16(16P11.2) MUTATED	33	46	29
AMP PEAK 16(16P11.2) WILD-TYPE	84	83	115

Figure S85. Get High-res Image Gene #16: 'amp_16p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_16p11.2' versus 'RPPA_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.037

Table S86. Gene #16: 'amp_16p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	108	197	177
AMP PEAK 16(16P11.2) MUTATED	41	48	41
AMP PEAK 16(16P11.2) WILD-TYPE	67	149	136

Figure S86. Get High-res Image Gene #16: 'amp_16p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_16p11.2' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00014

Table S87. Gene #16: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
AMP PEAK 16(16P11.2) MUTATED	60	18	32	62
AMP PEAK 16(16P11.2) WILD-TYPE	96	110	99	136

Figure S87. Get High-res Image Gene #16: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_16p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S88. Gene #16: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
AMP PEAK 16(16P11.2) MUTATED	20	24	6	15	35	54	18
AMP PEAK 16(16P11.2) WILD-TYPE	60	62	58	42	55	84	80

Figure S88. Get High-res Image Gene #16: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00389 (Fisher's exact test), Q value = 0.011

Table S89. Gene #16: 'amp_16p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
AMP PEAK 16(16P11.2) MUTATED	14	23	5	27	9	13	19	12	33
AMP PEAK 16(16P11.2) WILD-TYPE	35	51	24	59	68	41	38	20	48

Figure S89. Get High-res Image Gene #16: 'amp_16p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.047

Table S90. Gene #16: 'amp_16p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	40	38	22
AMP PEAK 16(16P11.2) MUTATED	15	17	11	2
AMP PEAK 16(16P11.2) WILD-TYPE	20	23	27	20

Figure S90. Get High-res Image Gene #16: 'amp_16p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q12' versus 'MRNA_CNMF'

P value = 0.0397 (Fisher's exact test), Q value = 0.083

Table S91. Gene #17: 'amp_17q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
AMP PEAK 17(17Q12) MUTATED	8	24	18	7
AMP PEAK 17(17Q12) WILD-TYPE	37	39	47	36

Figure S91. Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.0066 (Fisher's exact test), Q value = 0.018

Table S92. Gene #17: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
AMP PEAK 17(17Q12) MUTATED	6	32	19
AMP PEAK 17(17Q12) WILD-TYPE	44	57	58

Figure S92. Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S93. Gene #17: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
AMP PEAK 17(17Q12) MUTATED	20	84	49	7
AMP PEAK 17(17Q12) WILD-TYPE	195	163	83	15

Figure S93. Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 0.00855 (Fisher's exact test), Q value = 0.022

Table S94. Gene #17: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
AMP PEAK 17(17Q12) MUTATED	28	46	28
AMP PEAK 17(17Q12) WILD-TYPE	89	83	116

Figure S94. Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.0494 (Fisher's exact test), Q value = 0.099

Table S95. Gene #17: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	228	168	86
AMP PEAK 17(17Q12) MUTATED	59	32	28
AMP PEAK 17(17Q12) WILD-TYPE	169	136	58

Figure S95. Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00022

Table S96. Gene #17: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
AMP PEAK 17(17Q12) MUTATED	63	22	24	50
AMP PEAK 17(17Q12) WILD-TYPE	93	106	107	148

Figure S96. Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S97. Gene #17: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
AMP PEAK 17(17Q12) MUTATED	30	20	5	13	28	50	13
AMP PEAK 17(17Q12) WILD-TYPE	50	66	59	44	62	88	85

Figure S97. Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.035

Table S98. Gene #17: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
AMP PEAK 17(17Q12) MUTATED	15	17	5	32	8	16	15	8	22
AMP PEAK 17(17Q12) WILD-TYPE	34	57	24	54	69	38	42	24	59

Figure S98. Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q24.1' versus 'MRNA_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 0.067

Table S99. Gene #18: 'amp_17q24.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
AMP PEAK 18(17Q24.1) MUTATED	5	20	19	7
AMP PEAK 18(17Q24.1) WILD-TYPE	40	43	46	36

Figure S99. Get High-res Image Gene #18: 'amp_17q24.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q24.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0123 (Fisher's exact test), Q value = 0.03

Table S100. Gene #18: 'amp_17q24.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
AMP PEAK 18(17Q24.1) MUTATED	5	28	18
AMP PEAK 18(17Q24.1) WILD-TYPE	45	61	59

Figure S100. Get High-res Image Gene #18: 'amp_17q24.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S101. Gene #18: 'amp_17q24.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
AMP PEAK 18(17Q24.1) MUTATED	19	81	42	2
AMP PEAK 18(17Q24.1) WILD-TYPE	196	166	90	20

Figure S101. Get High-res Image Gene #18: 'amp_17q24.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q24.1' versus 'METHLYATION_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0011

Table S102. Gene #18: 'amp_17q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
AMP PEAK 18(17Q24.1) MUTATED	21	47	25
AMP PEAK 18(17Q24.1) WILD-TYPE	96	82	119

Figure S102. Get High-res Image Gene #18: 'amp_17q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q24.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S103. Gene #18: 'amp_17q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
AMP PEAK 18(17Q24.1) MUTATED	59	21	19	44
AMP PEAK 18(17Q24.1) WILD-TYPE	97	107	112	154

Figure S103. Get High-res Image Gene #18: 'amp_17q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S104. Gene #18: 'amp_17q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
AMP PEAK 18(17Q24.1) MUTATED	29	20	4	11	24	43	12
AMP PEAK 18(17Q24.1) WILD-TYPE	51	66	60	46	66	95	86

Figure S104. Get High-res Image Gene #18: 'amp_17q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00577 (Fisher's exact test), Q value = 0.016

Table S105. Gene #18: 'amp_17q24.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
AMP PEAK 18(17Q24.1) MUTATED	14	13	3	29	7	14	14	6	22
AMP PEAK 18(17Q24.1) WILD-TYPE	35	61	26	57	70	40	43	26	59

Figure S105. Get High-res Image Gene #18: 'amp_17q24.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MRNA_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.038

Table S106. Gene #19: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
AMP PEAK 19(19Q12) MUTATED	6	22	9	8
AMP PEAK 19(19Q12) WILD-TYPE	39	41	56	35

Figure S106. Get High-res Image Gene #19: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00253 (Fisher's exact test), Q value = 0.0073

Table S107. Gene #19: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
AMP PEAK 19(19Q12) MUTATED	4	28	13
AMP PEAK 19(19Q12) WILD-TYPE	46	61	64

Figure S107. Get High-res Image Gene #19: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S108. Gene #19: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
AMP PEAK 19(19Q12) MUTATED	21	81	29	8
AMP PEAK 19(19Q12) WILD-TYPE	194	166	103	14

Figure S108. Get High-res Image Gene #19: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q12' versus 'RPPA_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.038

Table S109. Gene #19: 'amp_19q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	108	197	177
AMP PEAK 19(19Q12) MUTATED	32	48	28
AMP PEAK 19(19Q12) WILD-TYPE	76	149	149

Figure S109. Get High-res Image Gene #19: 'amp_19q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 0.0404 (Fisher's exact test), Q value = 0.084

Table S110. Gene #19: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
AMP PEAK 19(19Q12) MUTATED	48	27	27	36
AMP PEAK 19(19Q12) WILD-TYPE	108	101	104	162

Figure S110. Get High-res Image Gene #19: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00933 (Fisher's exact test), Q value = 0.024

Table S111. Gene #19: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
AMP PEAK 19(19Q12) MUTATED	17	24	6	16	27	34	14
AMP PEAK 19(19Q12) WILD-TYPE	63	62	58	41	63	104	84

Figure S111. Get High-res Image Gene #19: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0247 (Fisher's exact test), Q value = 0.056

Table S112. Gene #19: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
AMP PEAK 19(19Q12) MUTATED	15	17	6	17	7	11	11	13	20
AMP PEAK 19(19Q12) WILD-TYPE	34	57	23	69	70	43	46	19	61

Figure S112. Get High-res Image Gene #19: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20p12.1' versus 'MRNA_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.04

Table S113. Gene #20: 'amp_20p12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
AMP PEAK 20(20P12.1) MUTATED	14	32	39	17
AMP PEAK 20(20P12.1) WILD-TYPE	31	31	26	26

Figure S113. Get High-res Image Gene #20: 'amp_20p12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20p12.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00262 (Fisher's exact test), Q value = 0.0075

Table S114. Gene #20: 'amp_20p12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
AMP PEAK 20(20P12.1) MUTATED	13	47	42
AMP PEAK 20(20P12.1) WILD-TYPE	37	42	35

Figure S114. Get High-res Image Gene #20: 'amp_20p12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S115. Gene #20: 'amp_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
AMP PEAK 20(20P12.1) MUTATED	70	125	62	21
AMP PEAK 20(20P12.1) WILD-TYPE	145	122	70	1

Figure S115. Get High-res Image Gene #20: 'amp_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p12.1' versus 'RPPA_CNMF'

P value = 0.00201 (Fisher's exact test), Q value = 0.006

Table S116. Gene #20: 'amp_20p12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	108	197	177
AMP PEAK 20(20P12.1) MUTATED	62	82	64
AMP PEAK 20(20P12.1) WILD-TYPE	46	115	113

Figure S116. Get High-res Image Gene #20: 'amp_20p12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.00083

Table S117. Gene #20: 'amp_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
AMP PEAK 20(20P12.1) MUTATED	39	38	15	33	40	76	35
AMP PEAK 20(20P12.1) WILD-TYPE	41	48	49	24	50	62	63

Figure S117. Get High-res Image Gene #20: 'amp_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S118. Gene #20: 'amp_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
AMP PEAK 20(20P12.1) MUTATED	20	32	13	39	15	28	30	14	52
AMP PEAK 20(20P12.1) WILD-TYPE	29	42	16	47	62	26	27	18	29

Figure S118. Get High-res Image Gene #20: 'amp_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20p12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0385 (Fisher's exact test), Q value = 0.081

Table S119. Gene #20: 'amp_20p12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	40	38	22
AMP PEAK 20(20P12.1) MUTATED	18	24	17	5
AMP PEAK 20(20P12.1) WILD-TYPE	17	16	21	17

Figure S119. Get High-res Image Gene #20: 'amp_20p12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20p11.21' versus 'MRNA_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00058

Table S120. Gene #21: 'amp_20p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
AMP PEAK 21(20P11.21) MUTATED	16	44	46	19
AMP PEAK 21(20P11.21) WILD-TYPE	29	19	19	24

Figure S120. Get High-res Image Gene #21: 'amp_20p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20p11.21' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S121. Gene #21: 'amp_20p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
AMP PEAK 21(20P11.21) MUTATED	14	62	49
AMP PEAK 21(20P11.21) WILD-TYPE	36	27	28

Figure S121. Get High-res Image Gene #21: 'amp_20p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S122. Gene #21: 'amp_20p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
AMP PEAK 21(20P11.21) MUTATED	74	185	82	22
AMP PEAK 21(20P11.21) WILD-TYPE	141	62	50	0

Figure S122. Get High-res Image Gene #21: 'amp_20p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p11.21' versus 'METHLYATION_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.0027

Table S123. Gene #21: 'amp_20p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
AMP PEAK 21(20P11.21) MUTATED	64	94	75
AMP PEAK 21(20P11.21) WILD-TYPE	53	35	69

Figure S123. Get High-res Image Gene #21: 'amp_20p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20p11.21' versus 'RPPA_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.036

Table S124. Gene #21: 'amp_20p11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	108	197	177
AMP PEAK 21(20P11.21) MUTATED	73	115	89
AMP PEAK 21(20P11.21) WILD-TYPE	35	82	88

Figure S124. Get High-res Image Gene #21: 'amp_20p11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20p11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S125. Gene #21: 'amp_20p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
AMP PEAK 21(20P11.21) MUTATED	121	56	70	113
AMP PEAK 21(20P11.21) WILD-TYPE	35	72	61	85

Figure S125. Get High-res Image Gene #21: 'amp_20p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S126. Gene #21: 'amp_20p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
AMP PEAK 21(20P11.21) MUTATED	56	51	17	40	61	99	36
AMP PEAK 21(20P11.21) WILD-TYPE	24	35	47	17	29	39	62

Figure S126. Get High-res Image Gene #21: 'amp_20p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20p11.21' versus 'MIRSEQ_CNMF'

P value = 0.0323 (Fisher's exact test), Q value = 0.071

Table S127. Gene #21: 'amp_20p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
AMP PEAK 21(20P11.21) MUTATED	93	61	57	104
AMP PEAK 21(20P11.21) WILD-TYPE	60	34	29	101

Figure S127. Get High-res Image Gene #21: 'amp_20p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S128. Gene #21: 'amp_20p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
AMP PEAK 21(20P11.21) MUTATED	28	41	19	58	18	38	38	15	60
AMP PEAK 21(20P11.21) WILD-TYPE	21	33	10	28	59	16	19	17	21

Figure S128. Get High-res Image Gene #21: 'amp_20p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S129. Gene #22: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
AMP PEAK 22(20Q11.21) MUTATED	19	61	59	25
AMP PEAK 22(20Q11.21) WILD-TYPE	26	2	6	18

Figure S129. Get High-res Image Gene #22: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q11.21' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S130. Gene #22: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
AMP PEAK 22(20Q11.21) MUTATED	15	86	63
AMP PEAK 22(20Q11.21) WILD-TYPE	35	3	14

Figure S130. Get High-res Image Gene #22: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S131. Gene #22: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
AMP PEAK 22(20Q11.21) MUTATED	92	245	110	22
AMP PEAK 22(20Q11.21) WILD-TYPE	123	2	22	0

Figure S131. Get High-res Image Gene #22: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S132. Gene #22: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
AMP PEAK 22(20Q11.21) MUTATED	83	128	88
AMP PEAK 22(20Q11.21) WILD-TYPE	34	1	56

Figure S132. Get High-res Image Gene #22: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'RPPA_CNMF'

P value = 0.0338 (Fisher's exact test), Q value = 0.073

Table S133. Gene #22: 'amp_20q11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	108	197	177
AMP PEAK 22(20Q11.21) MUTATED	86	157	122
AMP PEAK 22(20Q11.21) WILD-TYPE	22	40	55

Figure S133. Get High-res Image Gene #22: 'amp_20q11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S134. Gene #22: 'amp_20q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
AMP PEAK 22(20Q11.21) MUTATED	152	74	93	147
AMP PEAK 22(20Q11.21) WILD-TYPE	4	54	38	51

Figure S134. Get High-res Image Gene #22: 'amp_20q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S135. Gene #22: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
AMP PEAK 22(20Q11.21) MUTATED	74	63	17	50	84	132	46
AMP PEAK 22(20Q11.21) WILD-TYPE	6	23	47	7	6	6	52

Figure S135. Get High-res Image Gene #22: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S136. Gene #22: 'amp_20q11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
AMP PEAK 22(20Q11.21) MUTATED	111	78	83	137
AMP PEAK 22(20Q11.21) WILD-TYPE	42	17	3	68

Figure S136. Get High-res Image Gene #22: 'amp_20q11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S137. Gene #22: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
AMP PEAK 22(20Q11.21) MUTATED	36	56	20	74	28	48	51	20	76
AMP PEAK 22(20Q11.21) WILD-TYPE	13	18	9	12	49	6	6	12	5

Figure S137. Get High-res Image Gene #22: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00123 (Fisher's exact test), Q value = 0.0038

Table S138. Gene #22: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	40	38	22
AMP PEAK 22(20Q11.21) MUTATED	28	37	35	12
AMP PEAK 22(20Q11.21) WILD-TYPE	7	3	3	10

Figure S138. Get High-res Image Gene #22: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S139. Gene #23: 'amp_20q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
AMP PEAK 23(20Q12) MUTATED	18	61	59	24
AMP PEAK 23(20Q12) WILD-TYPE	27	2	6	19

Figure S139. Get High-res Image Gene #23: 'amp_20q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S140. Gene #23: 'amp_20q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
AMP PEAK 23(20Q12) MUTATED	14	86	62
AMP PEAK 23(20Q12) WILD-TYPE	36	3	15

Figure S140. Get High-res Image Gene #23: 'amp_20q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S141. Gene #23: 'amp_20q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
AMP PEAK 23(20Q12) MUTATED	91	245	113	22
AMP PEAK 23(20Q12) WILD-TYPE	124	2	19	0

Figure S141. Get High-res Image Gene #23: 'amp_20q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S142. Gene #23: 'amp_20q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
AMP PEAK 23(20Q12) MUTATED	84	128	91
AMP PEAK 23(20Q12) WILD-TYPE	33	1	53

Figure S142. Get High-res Image Gene #23: 'amp_20q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q12' versus 'RPPA_CNMF'

P value = 0.0452 (Fisher's exact test), Q value = 0.092

Table S143. Gene #23: 'amp_20q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	108	197	177
AMP PEAK 23(20Q12) MUTATED	85	158	123
AMP PEAK 23(20Q12) WILD-TYPE	23	39	54

Figure S143. Get High-res Image Gene #23: 'amp_20q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S144. Gene #23: 'amp_20q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
AMP PEAK 23(20Q12) MUTATED	152	75	95	146
AMP PEAK 23(20Q12) WILD-TYPE	4	53	36	52

Figure S144. Get High-res Image Gene #23: 'amp_20q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S145. Gene #23: 'amp_20q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
AMP PEAK 23(20Q12) MUTATED	74	64	19	50	85	132	44
AMP PEAK 23(20Q12) WILD-TYPE	6	22	45	7	5	6	54

Figure S145. Get High-res Image Gene #23: 'amp_20q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S146. Gene #23: 'amp_20q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
AMP PEAK 23(20Q12) MUTATED	113	79	83	136
AMP PEAK 23(20Q12) WILD-TYPE	40	16	3	69

Figure S146. Get High-res Image Gene #23: 'amp_20q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S147. Gene #23: 'amp_20q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
AMP PEAK 23(20Q12) MUTATED	36	57	20	75	28	48	51	20	76
AMP PEAK 23(20Q12) WILD-TYPE	13	17	9	11	49	6	6	12	5

Figure S147. Get High-res Image Gene #23: 'amp_20q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00055

Table S148. Gene #23: 'amp_20q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	40	38	22
AMP PEAK 23(20Q12) MUTATED	29	38	36	12
AMP PEAK 23(20Q12) WILD-TYPE	6	2	2	10

Figure S148. Get High-res Image Gene #23: 'amp_20q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S149. Gene #24: 'amp_20q13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
AMP PEAK 24(20Q13.12) MUTATED	19	61	59	25
AMP PEAK 24(20Q13.12) WILD-TYPE	26	2	6	18

Figure S149. Get High-res Image Gene #24: 'amp_20q13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q13.12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S150. Gene #24: 'amp_20q13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
AMP PEAK 24(20Q13.12) MUTATED	15	86	63
AMP PEAK 24(20Q13.12) WILD-TYPE	35	3	14

Figure S150. Get High-res Image Gene #24: 'amp_20q13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q13.12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S151. Gene #24: 'amp_20q13.12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
AMP PEAK 24(20Q13.12) MUTATED	93	245	113	22
AMP PEAK 24(20Q13.12) WILD-TYPE	122	2	19	0

Figure S151. Get High-res Image Gene #24: 'amp_20q13.12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S152. Gene #24: 'amp_20q13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
AMP PEAK 24(20Q13.12) MUTATED	84	128	91
AMP PEAK 24(20Q13.12) WILD-TYPE	33	1	53

Figure S152. Get High-res Image Gene #24: 'amp_20q13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.12' versus 'RPPA_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 0.056

Table S153. Gene #24: 'amp_20q13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	108	197	177
AMP PEAK 24(20Q13.12) MUTATED	85	160	123
AMP PEAK 24(20Q13.12) WILD-TYPE	23	37	54

Figure S153. Get High-res Image Gene #24: 'amp_20q13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q13.12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S154. Gene #24: 'amp_20q13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
AMP PEAK 24(20Q13.12) MUTATED	152	75	95	148
AMP PEAK 24(20Q13.12) WILD-TYPE	4	53	36	50

Figure S154. Get High-res Image Gene #24: 'amp_20q13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q13.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S155. Gene #24: 'amp_20q13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
AMP PEAK 24(20Q13.12) MUTATED	74	64	19	50	85	132	46
AMP PEAK 24(20Q13.12) WILD-TYPE	6	22	45	7	5	6	52

Figure S155. Get High-res Image Gene #24: 'amp_20q13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S156. Gene #24: 'amp_20q13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
AMP PEAK 24(20Q13.12) MUTATED	114	79	83	138
AMP PEAK 24(20Q13.12) WILD-TYPE	39	16	3	67

Figure S156. Get High-res Image Gene #24: 'amp_20q13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q13.12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S157. Gene #24: 'amp_20q13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
AMP PEAK 24(20Q13.12) MUTATED	36	57	21	75	30	48	51	20	76
AMP PEAK 24(20Q13.12) WILD-TYPE	13	17	8	11	47	6	6	12	5

Figure S157. Get High-res Image Gene #24: 'amp_20q13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00061

Table S158. Gene #24: 'amp_20q13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	40	38	22
AMP PEAK 24(20Q13.12) MUTATED	29	38	36	12
AMP PEAK 24(20Q13.12) WILD-TYPE	6	2	2	10

Figure S158. Get High-res Image Gene #24: 'amp_20q13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00022

Table S159. Gene #25: 'del_1p36.11' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
DEL PEAK 1(1P36.11) MUTATED	14	37	34	8
DEL PEAK 1(1P36.11) WILD-TYPE	31	26	31	35

Figure S159. Get High-res Image Gene #25: 'del_1p36.11' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.11' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S160. Gene #25: 'del_1p36.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 1(1P36.11) MUTATED	12	54	27
DEL PEAK 1(1P36.11) WILD-TYPE	38	35	50

Figure S160. Get High-res Image Gene #25: 'del_1p36.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S161. Gene #25: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 1(1P36.11) MUTATED	34	131	63	16
DEL PEAK 1(1P36.11) WILD-TYPE	181	116	69	6

Figure S161. Get High-res Image Gene #25: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00044

Table S162. Gene #25: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 1(1P36.11) MUTATED	42	68	40
DEL PEAK 1(1P36.11) WILD-TYPE	75	61	104

Figure S162. Get High-res Image Gene #25: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.11' versus 'RPPA_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.044

Table S163. Gene #25: 'del_1p36.11' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	108	197	177
DEL PEAK 1(1P36.11) MUTATED	42	89	55
DEL PEAK 1(1P36.11) WILD-TYPE	66	108	122

Figure S163. Get High-res Image Gene #25: 'del_1p36.11' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S164. Gene #25: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 1(1P36.11) MUTATED	81	28	54	80
DEL PEAK 1(1P36.11) WILD-TYPE	75	100	77	118

Figure S164. Get High-res Image Gene #25: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S165. Gene #25: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 1(1P36.11) MUTATED	36	30	6	22	48	72	29
DEL PEAK 1(1P36.11) WILD-TYPE	44	56	58	35	42	66	69

Figure S165. Get High-res Image Gene #25: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00014

Table S166. Gene #25: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 1(1P36.11) MUTATED	20	28	8	38	12	32	23	12	41
DEL PEAK 1(1P36.11) WILD-TYPE	29	46	21	48	65	22	34	20	40

Figure S166. Get High-res Image Gene #25: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p33' versus 'MRNA_CNMF'

P value = 0.0385 (Fisher's exact test), Q value = 0.081

Table S167. Gene #26: 'del_1p33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
DEL PEAK 2(1P33) MUTATED	12	21	22	5
DEL PEAK 2(1P33) WILD-TYPE	33	42	43	38

Figure S167. Get High-res Image Gene #26: 'del_1p33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p33' versus 'MRNA_CHIERARCHICAL'

P value = 0.00229 (Fisher's exact test), Q value = 0.0067

Table S168. Gene #26: 'del_1p33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 2(1P33) MUTATED	10	36	14
DEL PEAK 2(1P33) WILD-TYPE	40	53	63

Figure S168. Get High-res Image Gene #26: 'del_1p33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S169. Gene #26: 'del_1p33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 2(1P33) MUTATED	21	103	38	14
DEL PEAK 2(1P33) WILD-TYPE	194	144	94	8

Figure S169. Get High-res Image Gene #26: 'del_1p33' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p33' versus 'METHLYATION_CNMF'

P value = 0.00738 (Fisher's exact test), Q value = 0.02

Table S170. Gene #26: 'del_1p33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 2(1P33) MUTATED	36	49	30
DEL PEAK 2(1P33) WILD-TYPE	81	80	114

Figure S170. Get High-res Image Gene #26: 'del_1p33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p33' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00022

Table S171. Gene #26: 'del_1p33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 2(1P33) MUTATED	64	21	39	51
DEL PEAK 2(1P33) WILD-TYPE	92	107	92	147

Figure S171. Get High-res Image Gene #26: 'del_1p33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0014

Table S172. Gene #26: 'del_1p33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 2(1P33) MUTATED	29	21	7	18	34	47	19
DEL PEAK 2(1P33) WILD-TYPE	51	65	57	39	56	91	79

Figure S172. Get High-res Image Gene #26: 'del_1p33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 0.059

Table S173. Gene #26: 'del_1p33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 2(1P33) MUTATED	15	20	5	25	11	24	18	9	25
DEL PEAK 2(1P33) WILD-TYPE	34	54	24	61	66	30	39	23	56

Figure S173. Get High-res Image Gene #26: 'del_1p33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p13.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0338 (Fisher's exact test), Q value = 0.073

Table S174. Gene #27: 'del_1p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 3(1P13.2) MUTATED	10	32	15
DEL PEAK 3(1P13.2) WILD-TYPE	40	57	62

Figure S174. Get High-res Image Gene #27: 'del_1p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S175. Gene #27: 'del_1p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 3(1P13.2) MUTATED	25	103	35	13
DEL PEAK 3(1P13.2) WILD-TYPE	190	144	97	9

Figure S175. Get High-res Image Gene #27: 'del_1p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p13.2' versus 'METHLYATION_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.028

Table S176. Gene #27: 'del_1p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 3(1P13.2) MUTATED	33	51	33
DEL PEAK 3(1P13.2) WILD-TYPE	84	78	111

Figure S176. Get High-res Image Gene #27: 'del_1p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p13.2' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00077

Table S177. Gene #27: 'del_1p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 3(1P13.2) MUTATED	59	20	43	53
DEL PEAK 3(1P13.2) WILD-TYPE	97	108	88	145

Figure S177. Get High-res Image Gene #27: 'del_1p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.001

Table S178. Gene #27: 'del_1p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 3(1P13.2) MUTATED	30	20	8	15	37	46	19
DEL PEAK 3(1P13.2) WILD-TYPE	50	66	56	42	53	92	79

Figure S178. Get High-res Image Gene #27: 'del_1p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.2' versus 'MIRSEQ_CNMF'

P value = 0.0339 (Fisher's exact test), Q value = 0.073

Table S179. Gene #27: 'del_1p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
DEL PEAK 3(1P13.2) MUTATED	39	35	29	46
DEL PEAK 3(1P13.2) WILD-TYPE	114	60	57	159

Figure S179. Get High-res Image Gene #27: 'del_1p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00665 (Fisher's exact test), Q value = 0.018

Table S180. Gene #27: 'del_1p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 3(1P13.2) MUTATED	15	18	6	26	8	22	19	9	26
DEL PEAK 3(1P13.2) WILD-TYPE	34	56	23	60	69	32	38	23	55

Figure S180. Get High-res Image Gene #27: 'del_1p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2p12' versus 'CN_CNMF'

P value = 0.00219 (Fisher's exact test), Q value = 0.0065

Table S181. Gene #28: 'del_2p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 4(2P12) MUTATED	1	10	10	0
DEL PEAK 4(2P12) WILD-TYPE	214	237	122	22

Figure S181. Get High-res Image Gene #28: 'del_2p12' versus Molecular Subtype #3: 'CN_CNMF'

'del_2p12' versus 'METHLYATION_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.026

Table S182. Gene #28: 'del_2p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 4(2P12) MUTATED	0	6	1
DEL PEAK 4(2P12) WILD-TYPE	117	123	143

Figure S182. Get High-res Image Gene #28: 'del_2p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2p12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00179 (Fisher's exact test), Q value = 0.0054

Table S183. Gene #28: 'del_2p12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	228	168	86
DEL PEAK 4(2P12) MUTATED	6	2	9
DEL PEAK 4(2P12) WILD-TYPE	222	166	77

Figure S183. Get High-res Image Gene #28: 'del_2p12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_2p12' versus 'MRNASEQ_CNMF'

P value = 0.00937 (Fisher's exact test), Q value = 0.024

Table S184. Gene #28: 'del_2p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 4(2P12) MUTATED	4	1	2	14
DEL PEAK 4(2P12) WILD-TYPE	152	127	129	184

Figure S184. Get High-res Image Gene #28: 'del_2p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.013 (Fisher's exact test), Q value = 0.032

Table S185. Gene #28: 'del_2p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 4(2P12) MUTATED	0	1	0	2	2	8	8
DEL PEAK 4(2P12) WILD-TYPE	80	85	64	55	88	130	90

Figure S185. Get High-res Image Gene #28: 'del_2p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2p12' versus 'MIRSEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0012

Table S186. Gene #28: 'del_2p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
DEL PEAK 4(2P12) MUTATED	1	0	8	11
DEL PEAK 4(2P12) WILD-TYPE	152	95	78	194

Figure S186. Get High-res Image Gene #28: 'del_2p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'CN_CNMF'

P value = 0.0331 (Fisher's exact test), Q value = 0.072

Table S187. Gene #29: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 5(2Q22.1) MUTATED	5	19	9	2
DEL PEAK 5(2Q22.1) WILD-TYPE	210	228	123	20

Figure S187. Get High-res Image Gene #29: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q22.1' versus 'MIRSEQ_CNMF'

P value = 0.046 (Fisher's exact test), Q value = 0.094

Table S188. Gene #29: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
DEL PEAK 5(2Q22.1) MUTATED	4	3	9	14
DEL PEAK 5(2Q22.1) WILD-TYPE	149	92	77	191

Figure S188. Get High-res Image Gene #29: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p26.3' versus 'CN_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0019

Table S189. Gene #30: 'del_3p26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 6(3P26.3) MUTATED	18	51	18	6
DEL PEAK 6(3P26.3) WILD-TYPE	197	196	114	16

Figure S189. Get High-res Image Gene #30: 'del_3p26.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00205 (Fisher's exact test), Q value = 0.0061

Table S190. Gene #33: 'del_4p16.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 9(4P16.1) MUTATED	11	43	21
DEL PEAK 9(4P16.1) WILD-TYPE	39	46	56

Figure S190. Get High-res Image Gene #33: 'del_4p16.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4p16.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S191. Gene #33: 'del_4p16.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 9(4P16.1) MUTATED	23	111	52	17
DEL PEAK 9(4P16.1) WILD-TYPE	192	136	80	5

Figure S191. Get High-res Image Gene #33: 'del_4p16.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.1' versus 'METHLYATION_CNMF'

P value = 0.00508 (Fisher's exact test), Q value = 0.014

Table S192. Gene #33: 'del_4p16.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 9(4P16.1) MUTATED	36	55	35
DEL PEAK 9(4P16.1) WILD-TYPE	81	74	109

Figure S192. Get High-res Image Gene #33: 'del_4p16.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p16.1' versus 'MRNASEQ_CNMF'

P value = 0.00865 (Fisher's exact test), Q value = 0.023

Table S193. Gene #33: 'del_4p16.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 9(4P16.1) MUTATED	60	27	48	67
DEL PEAK 9(4P16.1) WILD-TYPE	96	101	83	131

Figure S193. Get High-res Image Gene #33: 'del_4p16.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p16.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S194. Gene #33: 'del_4p16.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 9(4P16.1) MUTATED	29	25	5	19	41	58	25
DEL PEAK 9(4P16.1) WILD-TYPE	51	61	59	38	49	80	73

Figure S194. Get High-res Image Gene #33: 'del_4p16.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.028

Table S195. Gene #33: 'del_4p16.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 9(4P16.1) MUTATED	17	18	9	33	14	14	21	12	37
DEL PEAK 9(4P16.1) WILD-TYPE	32	56	20	53	63	40	36	20	44

Figure S195. Get High-res Image Gene #33: 'del_4p16.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MRNA_CNMF'

P value = 0.00589 (Fisher's exact test), Q value = 0.016

Table S196. Gene #34: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
DEL PEAK 10(4Q22.1) MUTATED	14	27	30	7
DEL PEAK 10(4Q22.1) WILD-TYPE	31	36	35	36

Figure S196. Get High-res Image Gene #34: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00444 (Fisher's exact test), Q value = 0.012

Table S197. Gene #34: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 10(4Q22.1) MUTATED	11	43	24
DEL PEAK 10(4Q22.1) WILD-TYPE	39	46	53

Figure S197. Get High-res Image Gene #34: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S198. Gene #34: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 10(4Q22.1) MUTATED	28	126	55	16
DEL PEAK 10(4Q22.1) WILD-TYPE	187	121	77	6

Figure S198. Get High-res Image Gene #34: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.026

Table S199. Gene #34: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 10(4Q22.1) MUTATED	47	59	41
DEL PEAK 10(4Q22.1) WILD-TYPE	70	70	103

Figure S199. Get High-res Image Gene #34: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00487 (Fisher's exact test), Q value = 0.013

Table S200. Gene #34: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 10(4Q22.1) MUTATED	69	31	49	75
DEL PEAK 10(4Q22.1) WILD-TYPE	87	97	82	123

Figure S200. Get High-res Image Gene #34: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S201. Gene #34: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 10(4Q22.1) MUTATED	36	25	8	27	40	61	27
DEL PEAK 10(4Q22.1) WILD-TYPE	44	61	56	30	50	77	71

Figure S201. Get High-res Image Gene #34: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0013

Table S202. Gene #34: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 10(4Q22.1) MUTATED	18	18	9	39	15	19	25	10	42
DEL PEAK 10(4Q22.1) WILD-TYPE	31	56	20	47	62	35	32	22	39

Figure S202. Get High-res Image Gene #34: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MRNA_CNMF'

P value = 0.00884 (Fisher's exact test), Q value = 0.023

Table S203. Gene #35: 'del_4q35.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
DEL PEAK 11(4Q35.1) MUTATED	13	29	29	8
DEL PEAK 11(4Q35.1) WILD-TYPE	32	34	36	35

Figure S203. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q35.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00854 (Fisher's exact test), Q value = 0.022

Table S204. Gene #35: 'del_4q35.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 11(4Q35.1) MUTATED	12	43	24
DEL PEAK 11(4Q35.1) WILD-TYPE	38	46	53

Figure S204. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q35.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S205. Gene #35: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 11(4Q35.1) MUTATED	26	129	61	17
DEL PEAK 11(4Q35.1) WILD-TYPE	189	118	71	5

Figure S205. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q35.1' versus 'METHLYATION_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.026

Table S206. Gene #35: 'del_4q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 11(4Q35.1) MUTATED	48	60	42
DEL PEAK 11(4Q35.1) WILD-TYPE	69	69	102

Figure S206. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q35.1' versus 'MRNASEQ_CNMF'

P value = 0.00453 (Fisher's exact test), Q value = 0.013

Table S207. Gene #35: 'del_4q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 11(4Q35.1) MUTATED	69	32	55	76
DEL PEAK 11(4Q35.1) WILD-TYPE	87	96	76	122

Figure S207. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S208. Gene #35: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 11(4Q35.1) MUTATED	38	26	8	26	44	61	29
DEL PEAK 11(4Q35.1) WILD-TYPE	42	60	56	31	46	77	69

Figure S208. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MIRSEQ_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.077

Table S209. Gene #35: 'del_4q35.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
DEL PEAK 11(4Q35.1) MUTATED	55	34	44	68
DEL PEAK 11(4Q35.1) WILD-TYPE	98	61	42	137

Figure S209. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q12.1' versus 'MRNA_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0011

Table S210. Gene #36: 'del_5q12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
DEL PEAK 12(5Q12.1) MUTATED	10	21	19	1
DEL PEAK 12(5Q12.1) WILD-TYPE	35	42	46	42

Figure S210. Get High-res Image Gene #36: 'del_5q12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q12.1' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S211. Gene #36: 'del_5q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 12(5Q12.1) MUTATED	9	36	6
DEL PEAK 12(5Q12.1) WILD-TYPE	41	53	71

Figure S211. Get High-res Image Gene #36: 'del_5q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S212. Gene #36: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 12(5Q12.1) MUTATED	11	74	61	13
DEL PEAK 12(5Q12.1) WILD-TYPE	204	173	71	9

Figure S212. Get High-res Image Gene #36: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 0.00262 (Fisher's exact test), Q value = 0.0075

Table S213. Gene #36: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 12(5Q12.1) MUTATED	30	50	29
DEL PEAK 12(5Q12.1) WILD-TYPE	87	79	115

Figure S213. Get High-res Image Gene #36: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q12.1' versus 'MRNASEQ_CNMF'

P value = 0.0307 (Fisher's exact test), Q value = 0.067

Table S214. Gene #36: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 12(5Q12.1) MUTATED	49	22	39	49
DEL PEAK 12(5Q12.1) WILD-TYPE	107	106	92	149

Figure S214. Get High-res Image Gene #36: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S215. Gene #36: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 12(5Q12.1) MUTATED	25	19	4	21	32	43	15
DEL PEAK 12(5Q12.1) WILD-TYPE	55	67	60	36	58	95	83

Figure S215. Get High-res Image Gene #36: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00061

Table S216. Gene #36: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 12(5Q12.1) MUTATED	12	17	12	31	8	5	16	9	27
DEL PEAK 12(5Q12.1) WILD-TYPE	37	57	17	55	69	49	41	23	54

Figure S216. Get High-res Image Gene #36: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q21.2' versus 'MRNA_CNMF'

P value = 0.0289 (Fisher's exact test), Q value = 0.064

Table S217. Gene #37: 'del_5q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
DEL PEAK 13(5Q21.2) MUTATED	10	23	23	6
DEL PEAK 13(5Q21.2) WILD-TYPE	35	40	42	37

Figure S217. Get High-res Image Gene #37: 'del_5q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q21.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00082 (Fisher's exact test), Q value = 0.0026

Table S218. Gene #37: 'del_5q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 13(5Q21.2) MUTATED	10	38	14
DEL PEAK 13(5Q21.2) WILD-TYPE	40	51	63

Figure S218. Get High-res Image Gene #37: 'del_5q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S219. Gene #37: 'del_5q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 13(5Q21.2) MUTATED	17	84	72	14
DEL PEAK 13(5Q21.2) WILD-TYPE	198	163	60	8

Figure S219. Get High-res Image Gene #37: 'del_5q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q21.2' versus 'METHLYATION_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.033

Table S220. Gene #37: 'del_5q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 13(5Q21.2) MUTATED	34	54	37
DEL PEAK 13(5Q21.2) WILD-TYPE	83	75	107

Figure S220. Get High-res Image Gene #37: 'del_5q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00161 (Fisher's exact test), Q value = 0.0049

Table S221. Gene #37: 'del_5q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 13(5Q21.2) MUTATED	28	24	8	20	34	51	21
DEL PEAK 13(5Q21.2) WILD-TYPE	52	62	56	37	56	87	77

Figure S221. Get High-res Image Gene #37: 'del_5q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00087 (Fisher's exact test), Q value = 0.0027

Table S222. Gene #37: 'del_5q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 13(5Q21.2) MUTATED	15	18	13	34	10	11	21	13	29
DEL PEAK 13(5Q21.2) WILD-TYPE	34	56	16	52	67	43	36	19	52

Figure S222. Get High-res Image Gene #37: 'del_5q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q22.2' versus 'MRNA_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 9e-04

Table S223. Gene #38: 'del_5q22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
DEL PEAK 14(5Q22.2) MUTATED	9	24	25	3
DEL PEAK 14(5Q22.2) WILD-TYPE	36	39	40	40

Figure S223. Get High-res Image Gene #38: 'del_5q22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q22.2' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00014

Table S224. Gene #38: 'del_5q22.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 14(5Q22.2) MUTATED	9	40	12
DEL PEAK 14(5Q22.2) WILD-TYPE	41	49	65

Figure S224. Get High-res Image Gene #38: 'del_5q22.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S225. Gene #38: 'del_5q22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 14(5Q22.2) MUTATED	22	85	68	14
DEL PEAK 14(5Q22.2) WILD-TYPE	193	162	64	8

Figure S225. Get High-res Image Gene #38: 'del_5q22.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q22.2' versus 'METHLYATION_CNMF'

P value = 0.0415 (Fisher's exact test), Q value = 0.086

Table S226. Gene #38: 'del_5q22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 14(5Q22.2) MUTATED	36	53	39
DEL PEAK 14(5Q22.2) WILD-TYPE	81	76	105

Figure S226. Get High-res Image Gene #38: 'del_5q22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00041

Table S227. Gene #38: 'del_5q22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 14(5Q22.2) MUTATED	32	25	8	22	30	53	18
DEL PEAK 14(5Q22.2) WILD-TYPE	48	61	56	35	60	85	80

Figure S227. Get High-res Image Gene #38: 'del_5q22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0015

Table S228. Gene #38: 'del_5q22.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 14(5Q22.2) MUTATED	16	16	13	37	10	13	21	13	28
DEL PEAK 14(5Q22.2) WILD-TYPE	33	58	16	49	67	41	36	19	53

Figure S228. Get High-res Image Gene #38: 'del_5q22.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q23.3' versus 'MRNA_CNMF'

P value = 0.00677 (Fisher's exact test), Q value = 0.018

Table S229. Gene #39: 'del_5q23.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
DEL PEAK 15(5Q23.3) MUTATED	9	21	19	3
DEL PEAK 15(5Q23.3) WILD-TYPE	36	42	46	40

Figure S229. Get High-res Image Gene #39: 'del_5q23.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q23.3' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00022

Table S230. Gene #39: 'del_5q23.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 15(5Q23.3) MUTATED	9	35	8
DEL PEAK 15(5Q23.3) WILD-TYPE	41	54	69

Figure S230. Get High-res Image Gene #39: 'del_5q23.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S231. Gene #39: 'del_5q23.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 15(5Q23.3) MUTATED	10	72	67	12
DEL PEAK 15(5Q23.3) WILD-TYPE	205	175	65	10

Figure S231. Get High-res Image Gene #39: 'del_5q23.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q23.3' versus 'METHLYATION_CNMF'

P value = 0.00303 (Fisher's exact test), Q value = 0.0087

Table S232. Gene #39: 'del_5q23.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 15(5Q23.3) MUTATED	33	49	28
DEL PEAK 15(5Q23.3) WILD-TYPE	84	80	116

Figure S232. Get High-res Image Gene #39: 'del_5q23.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q23.3' versus 'MRNASEQ_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.026

Table S233. Gene #39: 'del_5q23.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 15(5Q23.3) MUTATED	54	22	35	50
DEL PEAK 15(5Q23.3) WILD-TYPE	102	106	96	148

Figure S233. Get High-res Image Gene #39: 'del_5q23.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00058

Table S234. Gene #39: 'del_5q23.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 15(5Q23.3) MUTATED	28	16	6	22	28	43	18
DEL PEAK 15(5Q23.3) WILD-TYPE	52	70	58	35	62	95	80

Figure S234. Get High-res Image Gene #39: 'del_5q23.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00026

Table S235. Gene #39: 'del_5q23.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 15(5Q23.3) MUTATED	13	16	11	36	8	6	18	10	23
DEL PEAK 15(5Q23.3) WILD-TYPE	36	58	18	50	69	48	39	22	58

Figure S235. Get High-res Image Gene #39: 'del_5q23.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'RPPA_CNMF'

P value = 0.00188 (Fisher's exact test), Q value = 0.0056

Table S236. Gene #41: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	108	197	177
DEL PEAK 17(6Q26) MUTATED	27	26	17
DEL PEAK 17(6Q26) WILD-TYPE	81	171	160

Figure S236. Get High-res Image Gene #41: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_8p23.2' versus 'MRNA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 3e-04

Table S237. Gene #43: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
DEL PEAK 19(8P23.2) MUTATED	17	42	37	11
DEL PEAK 19(8P23.2) WILD-TYPE	28	21	28	32

Figure S237. Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p23.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S238. Gene #43: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 19(8P23.2) MUTATED	14	59	34
DEL PEAK 19(8P23.2) WILD-TYPE	36	30	43

Figure S238. Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S239. Gene #43: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 19(8P23.2) MUTATED	23	152	105	10
DEL PEAK 19(8P23.2) WILD-TYPE	192	95	27	12

Figure S239. Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S240. Gene #43: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 19(8P23.2) MUTATED	48	83	51
DEL PEAK 19(8P23.2) WILD-TYPE	69	46	93

Figure S240. Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00022

Table S241. Gene #43: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 19(8P23.2) MUTATED	87	37	66	99
DEL PEAK 19(8P23.2) WILD-TYPE	69	91	65	99

Figure S241. Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S242. Gene #43: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 19(8P23.2) MUTATED	38	33	10	31	59	83	35
DEL PEAK 19(8P23.2) WILD-TYPE	42	53	54	26	31	55	63

Figure S242. Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00092 (Fisher's exact test), Q value = 0.0029

Table S243. Gene #43: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 19(8P23.2) MUTATED	20	33	11	52	21	27	32	13	46
DEL PEAK 19(8P23.2) WILD-TYPE	29	41	18	34	56	27	25	19	35

Figure S243. Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p22' versus 'MRNA_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.001

Table S244. Gene #44: 'del_8p22' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
DEL PEAK 20(8P22) MUTATED	16	40	40	13
DEL PEAK 20(8P22) WILD-TYPE	29	23	25	30

Figure S244. Get High-res Image Gene #44: 'del_8p22' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p22' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S245. Gene #44: 'del_8p22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 20(8P22) MUTATED	13	59	37
DEL PEAK 20(8P22) WILD-TYPE	37	30	40

Figure S245. Get High-res Image Gene #44: 'del_8p22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S246. Gene #44: 'del_8p22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 20(8P22) MUTATED	25	157	111	11
DEL PEAK 20(8P22) WILD-TYPE	190	90	21	11

Figure S246. Get High-res Image Gene #44: 'del_8p22' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p22' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S247. Gene #44: 'del_8p22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 20(8P22) MUTATED	51	87	56
DEL PEAK 20(8P22) WILD-TYPE	66	42	88

Figure S247. Get High-res Image Gene #44: 'del_8p22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p22' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00051

Table S248. Gene #44: 'del_8p22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 20(8P22) MUTATED	92	42	69	100
DEL PEAK 20(8P22) WILD-TYPE	64	86	62	98

Figure S248. Get High-res Image Gene #44: 'del_8p22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S249. Gene #44: 'del_8p22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 20(8P22) MUTATED	39	39	10	32	62	85	36
DEL PEAK 20(8P22) WILD-TYPE	41	47	54	25	28	53	62

Figure S249. Get High-res Image Gene #44: 'del_8p22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00041

Table S250. Gene #44: 'del_8p22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 20(8P22) MUTATED	20	36	15	55	20	28	33	13	48
DEL PEAK 20(8P22) WILD-TYPE	29	38	14	31	57	26	24	19	33

Figure S250. Get High-res Image Gene #44: 'del_8p22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8q11.1' versus 'CN_CNMF'

P value = 0.00164 (Fisher's exact test), Q value = 0.005

Table S251. Gene #45: 'del_8q11.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 21(8Q11.1) MUTATED	8	30	6	3
DEL PEAK 21(8Q11.1) WILD-TYPE	207	217	126	19

Figure S251. Get High-res Image Gene #45: 'del_8q11.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00061

Table S252. Gene #46: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 22(9P21.3) MUTATED	14	49	21	4
DEL PEAK 22(9P21.3) WILD-TYPE	201	198	111	18

Figure S252. Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 0.0346 (Fisher's exact test), Q value = 0.074

Table S253. Gene #46: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 22(9P21.3) MUTATED	18	27	14
DEL PEAK 22(9P21.3) WILD-TYPE	99	102	130

Figure S253. Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 0.0387 (Fisher's exact test), Q value = 0.081

Table S254. Gene #46: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 22(9P21.3) MUTATED	32	14	21	21
DEL PEAK 22(9P21.3) WILD-TYPE	124	114	110	177

Figure S254. Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0424 (Fisher's exact test), Q value = 0.087

Table S255. Gene #46: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 22(9P21.3) MUTATED	11	12	4	14	16	23	8
DEL PEAK 22(9P21.3) WILD-TYPE	69	74	60	43	74	115	90

Figure S255. Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0327 (Fisher's exact test), Q value = 0.071

Table S256. Gene #46: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 22(9P21.3) MUTATED	8	10	3	18	2	9	11	4	13
DEL PEAK 22(9P21.3) WILD-TYPE	41	64	26	68	75	45	46	28	68

Figure S256. Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S257. Gene #47: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 23(10P15.3) MUTATED	14	52	40	9
DEL PEAK 23(10P15.3) WILD-TYPE	201	195	92	13

Figure S257. Get High-res Image Gene #47: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.077

Table S258. Gene #47: 'del_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 23(10P15.3) MUTATED	23	34	20
DEL PEAK 23(10P15.3) WILD-TYPE	94	95	124

Figure S258. Get High-res Image Gene #47: 'del_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 0.00962 (Fisher's exact test), Q value = 0.025

Table S259. Gene #47: 'del_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 23(10P15.3) MUTATED	41	14	25	34
DEL PEAK 23(10P15.3) WILD-TYPE	115	114	106	164

Figure S259. Get High-res Image Gene #47: 'del_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S260. Gene #47: 'del_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 23(10P15.3) MUTATED	14	12	3	11	33	29	12
DEL PEAK 23(10P15.3) WILD-TYPE	66	74	61	46	57	109	86

Figure S260. Get High-res Image Gene #47: 'del_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0484 (Fisher's exact test), Q value = 0.097

Table S261. Gene #47: 'del_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	40	38	22
DEL PEAK 23(10P15.3) MUTATED	8	14	9	1
DEL PEAK 23(10P15.3) WILD-TYPE	27	26	29	21

Figure S261. Get High-res Image Gene #47: 'del_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q21.1' versus 'MRNA_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.029

Table S262. Gene #48: 'del_10q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
DEL PEAK 24(10Q21.1) MUTATED	6	14	23	5
DEL PEAK 24(10Q21.1) WILD-TYPE	39	49	42	38

Figure S262. Get High-res Image Gene #48: 'del_10q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q21.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0381 (Fisher's exact test), Q value = 0.081

Table S263. Gene #48: 'del_10q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 24(10Q21.1) MUTATED	6	27	15
DEL PEAK 24(10Q21.1) WILD-TYPE	44	62	62

Figure S263. Get High-res Image Gene #48: 'del_10q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S264. Gene #48: 'del_10q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 24(10Q21.1) MUTATED	15	70	45	9
DEL PEAK 24(10Q21.1) WILD-TYPE	200	177	87	13

Figure S264. Get High-res Image Gene #48: 'del_10q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q21.1' versus 'METHLYATION_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.042

Table S265. Gene #48: 'del_10q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 24(10Q21.1) MUTATED	21	41	28
DEL PEAK 24(10Q21.1) WILD-TYPE	96	88	116

Figure S265. Get High-res Image Gene #48: 'del_10q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q21.1' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00041

Table S266. Gene #48: 'del_10q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 24(10Q21.1) MUTATED	54	16	25	43
DEL PEAK 24(10Q21.1) WILD-TYPE	102	112	106	155

Figure S266. Get High-res Image Gene #48: 'del_10q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.0013

Table S267. Gene #48: 'del_10q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 24(10Q21.1) MUTATED	20	18	3	13	30	38	16
DEL PEAK 24(10Q21.1) WILD-TYPE	60	68	61	44	60	100	82

Figure S267. Get High-res Image Gene #48: 'del_10q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S268. Gene #49: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 25(10Q23.31) MUTATED	20	74	57	10
DEL PEAK 25(10Q23.31) WILD-TYPE	195	173	75	12

Figure S268. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.037

Table S269. Gene #49: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 25(10Q23.31) MUTATED	25	48	36
DEL PEAK 25(10Q23.31) WILD-TYPE	92	81	108

Figure S269. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 0.00477 (Fisher's exact test), Q value = 0.013

Table S270. Gene #49: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 25(10Q23.31) MUTATED	57	25	33	44
DEL PEAK 25(10Q23.31) WILD-TYPE	99	103	98	154

Figure S270. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00026

Table S271. Gene #49: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 25(10Q23.31) MUTATED	27	21	4	13	38	33	23
DEL PEAK 25(10Q23.31) WILD-TYPE	53	65	60	44	52	105	75

Figure S271. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.028

Table S272. Gene #49: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 25(10Q23.31) MUTATED	11	24	6	33	9	12	15	6	24
DEL PEAK 25(10Q23.31) WILD-TYPE	38	50	23	53	68	42	42	26	57

Figure S272. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S273. Gene #50: 'del_10q25.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 26(10Q25.2) MUTATED	20	73	52	12
DEL PEAK 26(10Q25.2) WILD-TYPE	195	174	80	10

Figure S273. Get High-res Image Gene #50: 'del_10q25.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q25.2' versus 'METHLYATION_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.043

Table S274. Gene #50: 'del_10q25.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 26(10Q25.2) MUTATED	23	45	34
DEL PEAK 26(10Q25.2) WILD-TYPE	94	84	110

Figure S274. Get High-res Image Gene #50: 'del_10q25.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q25.2' versus 'MRNASEQ_CNMF'

P value = 0.00269 (Fisher's exact test), Q value = 0.0077

Table S275. Gene #50: 'del_10q25.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 26(10Q25.2) MUTATED	53	19	33	50
DEL PEAK 26(10Q25.2) WILD-TYPE	103	109	98	148

Figure S275. Get High-res Image Gene #50: 'del_10q25.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S276. Gene #50: 'del_10q25.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 26(10Q25.2) MUTATED	26	15	2	11	39	35	27
DEL PEAK 26(10Q25.2) WILD-TYPE	54	71	62	46	51	103	71

Figure S276. Get High-res Image Gene #50: 'del_10q25.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q25.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0206 (Fisher's exact test), Q value = 0.048

Table S277. Gene #50: 'del_10q25.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 26(10Q25.2) MUTATED	9	21	6	32	10	10	14	8	26
DEL PEAK 26(10Q25.2) WILD-TYPE	40	53	23	54	67	44	43	24	55

Figure S277. Get High-res Image Gene #50: 'del_10q25.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11q22.3' versus 'CN_CNMF'

P value = 0.00908 (Fisher's exact test), Q value = 0.023

Table S278. Gene #51: 'del_11q22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 27(11Q22.3) MUTATED	25	58	24	4
DEL PEAK 27(11Q22.3) WILD-TYPE	190	189	108	18

Figure S278. Get High-res Image Gene #51: 'del_11q22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0476 (Fisher's exact test), Q value = 0.096

Table S279. Gene #51: 'del_11q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 27(11Q22.3) MUTATED	15	17	3	13	13	29	20
DEL PEAK 27(11Q22.3) WILD-TYPE	65	69	61	44	77	109	78

Figure S279. Get High-res Image Gene #51: 'del_11q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MRNA_CNMF'

P value = 0.00342 (Fisher's exact test), Q value = 0.0097

Table S280. Gene #52: 'del_12p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
DEL PEAK 28(12P13.1) MUTATED	2	14	11	1
DEL PEAK 28(12P13.1) WILD-TYPE	43	49	54	42

Figure S280. Get High-res Image Gene #52: 'del_12p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12p13.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.0011

Table S281. Gene #52: 'del_12p13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 28(12P13.1) MUTATED	0	19	9
DEL PEAK 28(12P13.1) WILD-TYPE	50	70	68

Figure S281. Get High-res Image Gene #52: 'del_12p13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S282. Gene #52: 'del_12p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 28(12P13.1) MUTATED	6	62	21	3
DEL PEAK 28(12P13.1) WILD-TYPE	209	185	111	19

Figure S282. Get High-res Image Gene #52: 'del_12p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_12p13.1' versus 'MRNASEQ_CNMF'

P value = 0.0463 (Fisher's exact test), Q value = 0.094

Table S283. Gene #52: 'del_12p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 28(12P13.1) MUTATED	34	13	18	27
DEL PEAK 28(12P13.1) WILD-TYPE	122	115	113	171

Figure S283. Get High-res Image Gene #52: 'del_12p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.0025

Table S284. Gene #52: 'del_12p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 28(12P13.1) MUTATED	18	12	1	12	16	25	8
DEL PEAK 28(12P13.1) WILD-TYPE	62	74	63	45	74	113	90

Figure S284. Get High-res Image Gene #52: 'del_12p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_CNMF'

P value = 0.0389 (Fisher's exact test), Q value = 0.081

Table S285. Gene #52: 'del_12p13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
DEL PEAK 28(12P13.1) MUTATED	18	21	18	25
DEL PEAK 28(12P13.1) WILD-TYPE	135	74	68	180

Figure S285. Get High-res Image Gene #52: 'del_12p13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_12p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0437 (Fisher's exact test), Q value = 0.089

Table S286. Gene #52: 'del_12p13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	16	34	22
DEL PEAK 28(12P13.1) MUTATED	8	5	3	7
DEL PEAK 28(12P13.1) WILD-TYPE	55	11	31	15

Figure S286. Get High-res Image Gene #52: 'del_12p13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q21.33' versus 'MRNA_CNMF'

P value = 0.0242 (Fisher's exact test), Q value = 0.055

Table S287. Gene #53: 'del_12q21.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
DEL PEAK 29(12Q21.33) MUTATED	4	15	12	2
DEL PEAK 29(12Q21.33) WILD-TYPE	41	48	53	41

Figure S287. Get High-res Image Gene #53: 'del_12q21.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12q21.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.0115 (Fisher's exact test), Q value = 0.028

Table S288. Gene #53: 'del_12q21.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 29(12Q21.33) MUTATED	3	21	9
DEL PEAK 29(12Q21.33) WILD-TYPE	47	68	68

Figure S288. Get High-res Image Gene #53: 'del_12q21.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12q21.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S289. Gene #53: 'del_12q21.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 29(12Q21.33) MUTATED	6	61	18	5
DEL PEAK 29(12Q21.33) WILD-TYPE	209	186	114	17

Figure S289. Get High-res Image Gene #53: 'del_12q21.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q21.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.0013

Table S290. Gene #53: 'del_12q21.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 29(12Q21.33) MUTATED	16	4	3	10	21	26	10
DEL PEAK 29(12Q21.33) WILD-TYPE	64	82	61	47	69	112	88

Figure S290. Get High-res Image Gene #53: 'del_12q21.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q11.2' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00018

Table S291. Gene #54: 'del_14q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
DEL PEAK 30(14Q11.2) MUTATED	8	32	32	7
DEL PEAK 30(14Q11.2) WILD-TYPE	37	31	33	36

Figure S291. Get High-res Image Gene #54: 'del_14q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S292. Gene #54: 'del_14q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 30(14Q11.2) MUTATED	5	47	27
DEL PEAK 30(14Q11.2) WILD-TYPE	45	42	50

Figure S292. Get High-res Image Gene #54: 'del_14q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S293. Gene #54: 'del_14q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 30(14Q11.2) MUTATED	21	158	25	8
DEL PEAK 30(14Q11.2) WILD-TYPE	194	89	107	14

Figure S293. Get High-res Image Gene #54: 'del_14q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S294. Gene #54: 'del_14q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 30(14Q11.2) MUTATED	35	65	32
DEL PEAK 30(14Q11.2) WILD-TYPE	82	64	112

Figure S294. Get High-res Image Gene #54: 'del_14q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.033

Table S295. Gene #54: 'del_14q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	228	168	86
DEL PEAK 30(14Q11.2) MUTATED	72	54	42
DEL PEAK 30(14Q11.2) WILD-TYPE	156	114	44

Figure S295. Get High-res Image Gene #54: 'del_14q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_14q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S296. Gene #54: 'del_14q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 30(14Q11.2) MUTATED	83	25	30	73
DEL PEAK 30(14Q11.2) WILD-TYPE	73	103	101	125

Figure S296. Get High-res Image Gene #54: 'del_14q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S297. Gene #54: 'del_14q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 30(14Q11.2) MUTATED	37	25	3	23	38	67	18
DEL PEAK 30(14Q11.2) WILD-TYPE	43	61	61	34	52	71	80

Figure S297. Get High-res Image Gene #54: 'del_14q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0012

Table S298. Gene #54: 'del_14q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
DEL PEAK 30(14Q11.2) MUTATED	43	34	46	59
DEL PEAK 30(14Q11.2) WILD-TYPE	110	61	40	146

Figure S298. Get High-res Image Gene #54: 'del_14q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_14q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S299. Gene #54: 'del_14q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 30(14Q11.2) MUTATED	14	20	9	28	9	29	29	10	34
DEL PEAK 30(14Q11.2) WILD-TYPE	35	54	20	58	68	25	28	22	47

Figure S299. Get High-res Image Gene #54: 'del_14q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 0.055

Table S300. Gene #54: 'del_14q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	40	38	22
DEL PEAK 30(14Q11.2) MUTATED	15	14	23	5
DEL PEAK 30(14Q11.2) WILD-TYPE	20	26	15	17

Figure S300. Get High-res Image Gene #54: 'del_14q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_14q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0464 (Fisher's exact test), Q value = 0.094

Table S301. Gene #54: 'del_14q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	16	34	22
DEL PEAK 30(14Q11.2) MUTATED	20	6	17	14
DEL PEAK 30(14Q11.2) WILD-TYPE	43	10	17	8

Figure S301. Get High-res Image Gene #54: 'del_14q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q31.1' versus 'MRNA_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0012

Table S302. Gene #55: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
DEL PEAK 31(14Q31.1) MUTATED	11	32	32	8
DEL PEAK 31(14Q31.1) WILD-TYPE	34	31	33	35

Figure S302. Get High-res Image Gene #55: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q31.1' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00022

Table S303. Gene #55: 'del_14q31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 31(14Q31.1) MUTATED	8	48	27
DEL PEAK 31(14Q31.1) WILD-TYPE	42	41	50

Figure S303. Get High-res Image Gene #55: 'del_14q31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S304. Gene #55: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 31(14Q31.1) MUTATED	22	159	29	10
DEL PEAK 31(14Q31.1) WILD-TYPE	193	88	103	12

Figure S304. Get High-res Image Gene #55: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q31.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S305. Gene #55: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 31(14Q31.1) MUTATED	34	67	35
DEL PEAK 31(14Q31.1) WILD-TYPE	83	62	109

Figure S305. Get High-res Image Gene #55: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q31.1' versus 'RPPA_CNMF'

P value = 0.0385 (Fisher's exact test), Q value = 0.081

Table S306. Gene #55: 'del_14q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	108	197	177
DEL PEAK 31(14Q31.1) MUTATED	43	80	51
DEL PEAK 31(14Q31.1) WILD-TYPE	65	117	126

Figure S306. Get High-res Image Gene #55: 'del_14q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_14q31.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0381 (Fisher's exact test), Q value = 0.081

Table S307. Gene #55: 'del_14q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	228	168	86
DEL PEAK 31(14Q31.1) MUTATED	73	60	41
DEL PEAK 31(14Q31.1) WILD-TYPE	155	108	45

Figure S307. Get High-res Image Gene #55: 'del_14q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_14q31.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S308. Gene #55: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 31(14Q31.1) MUTATED	83	27	32	77
DEL PEAK 31(14Q31.1) WILD-TYPE	73	101	99	121

Figure S308. Get High-res Image Gene #55: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S309. Gene #55: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 31(14Q31.1) MUTATED	35	27	6	25	36	69	21
DEL PEAK 31(14Q31.1) WILD-TYPE	45	59	58	32	54	69	77

Figure S309. Get High-res Image Gene #55: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MIRSEQ_CNMF'

P value = 0.0262 (Fisher's exact test), Q value = 0.059

Table S310. Gene #55: 'del_14q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
DEL PEAK 31(14Q31.1) MUTATED	47	36	42	66
DEL PEAK 31(14Q31.1) WILD-TYPE	106	59	44	139

Figure S310. Get High-res Image Gene #55: 'del_14q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_14q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S311. Gene #55: 'del_14q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 31(14Q31.1) MUTATED	15	21	9	31	9	29	27	12	38
DEL PEAK 31(14Q31.1) WILD-TYPE	34	53	20	55	68	25	30	20	43

Figure S311. Get High-res Image Gene #55: 'del_14q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0234 (Fisher's exact test), Q value = 0.053

Table S312. Gene #55: 'del_14q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	16	34	22
DEL PEAK 31(14Q31.1) MUTATED	21	6	18	15
DEL PEAK 31(14Q31.1) WILD-TYPE	42	10	16	7

Figure S312. Get High-res Image Gene #55: 'del_14q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q11.2' versus 'MRNA_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0014

Table S313. Gene #56: 'del_15q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
DEL PEAK 32(15Q11.2) MUTATED	12	33	36	10
DEL PEAK 32(15Q11.2) WILD-TYPE	33	30	29	33

Figure S313. Get High-res Image Gene #56: 'del_15q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00055

Table S314. Gene #56: 'del_15q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 32(15Q11.2) MUTATED	12	52	27
DEL PEAK 32(15Q11.2) WILD-TYPE	38	37	50

Figure S314. Get High-res Image Gene #56: 'del_15q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S315. Gene #56: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 32(15Q11.2) MUTATED	23	150	61	15
DEL PEAK 32(15Q11.2) WILD-TYPE	192	97	71	7

Figure S315. Get High-res Image Gene #56: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q11.2' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00058

Table S316. Gene #56: 'del_15q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 32(15Q11.2) MUTATED	39	71	47
DEL PEAK 32(15Q11.2) WILD-TYPE	78	58	97

Figure S316. Get High-res Image Gene #56: 'del_15q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00044

Table S317. Gene #56: 'del_15q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 32(15Q11.2) MUTATED	82	33	52	81
DEL PEAK 32(15Q11.2) WILD-TYPE	74	95	79	117

Figure S317. Get High-res Image Gene #56: 'del_15q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S318. Gene #56: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 32(15Q11.2) MUTATED	38	32	3	23	52	65	35
DEL PEAK 32(15Q11.2) WILD-TYPE	42	54	61	34	38	73	63

Figure S318. Get High-res Image Gene #56: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00166 (Fisher's exact test), Q value = 0.005

Table S319. Gene #56: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
DEL PEAK 32(15Q11.2) MUTATED	52	46	47	71
DEL PEAK 32(15Q11.2) WILD-TYPE	101	49	39	134

Figure S319. Get High-res Image Gene #56: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00084 (Fisher's exact test), Q value = 0.0027

Table S320. Gene #56: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 32(15Q11.2) MUTATED	16	34	8	44	16	18	29	13	38
DEL PEAK 32(15Q11.2) WILD-TYPE	33	40	21	42	61	36	28	19	43

Figure S320. Get High-res Image Gene #56: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_15q15.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S321. Gene #57: 'del_15q15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
DEL PEAK 33(15Q15.2) MUTATED	11	34	38	9
DEL PEAK 33(15Q15.2) WILD-TYPE	34	29	27	34

Figure S321. Get High-res Image Gene #57: 'del_15q15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q15.2' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00022

Table S322. Gene #57: 'del_15q15.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 33(15Q15.2) MUTATED	11	53	28
DEL PEAK 33(15Q15.2) WILD-TYPE	39	36	49

Figure S322. Get High-res Image Gene #57: 'del_15q15.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q15.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S323. Gene #57: 'del_15q15.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 33(15Q15.2) MUTATED	25	146	64	16
DEL PEAK 33(15Q15.2) WILD-TYPE	190	101	68	6

Figure S323. Get High-res Image Gene #57: 'del_15q15.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q15.2' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00067

Table S324. Gene #57: 'del_15q15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 33(15Q15.2) MUTATED	42	71	45
DEL PEAK 33(15Q15.2) WILD-TYPE	75	58	99

Figure S324. Get High-res Image Gene #57: 'del_15q15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q15.2' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00067

Table S325. Gene #57: 'del_15q15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 33(15Q15.2) MUTATED	84	36	49	81
DEL PEAK 33(15Q15.2) WILD-TYPE	72	92	82	117

Figure S325. Get High-res Image Gene #57: 'del_15q15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q15.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S326. Gene #57: 'del_15q15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 33(15Q15.2) MUTATED	41	32	5	23	47	66	36
DEL PEAK 33(15Q15.2) WILD-TYPE	39	54	59	34	43	72	62

Figure S326. Get High-res Image Gene #57: 'del_15q15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q15.2' versus 'MIRSEQ_CNMF'

P value = 0.00362 (Fisher's exact test), Q value = 0.01

Table S327. Gene #57: 'del_15q15.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
DEL PEAK 33(15Q15.2) MUTATED	51	44	47	73
DEL PEAK 33(15Q15.2) WILD-TYPE	102	51	39	132

Figure S327. Get High-res Image Gene #57: 'del_15q15.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q15.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00033

Table S328. Gene #57: 'del_15q15.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 33(15Q15.2) MUTATED	17	30	9	43	13	19	30	14	40
DEL PEAK 33(15Q15.2) WILD-TYPE	32	44	20	43	64	35	27	18	41

Figure S328. Get High-res Image Gene #57: 'del_15q15.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_15q21.1' versus 'MRNA_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0011

Table S329. Gene #58: 'del_15q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
DEL PEAK 34(15Q21.1) MUTATED	14	33	37	9
DEL PEAK 34(15Q21.1) WILD-TYPE	31	30	28	34

Figure S329. Get High-res Image Gene #58: 'del_15q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q21.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.0016

Table S330. Gene #58: 'del_15q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 34(15Q21.1) MUTATED	14	52	27
DEL PEAK 34(15Q21.1) WILD-TYPE	36	37	50

Figure S330. Get High-res Image Gene #58: 'del_15q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S331. Gene #58: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 34(15Q21.1) MUTATED	26	142	64	16
DEL PEAK 34(15Q21.1) WILD-TYPE	189	105	68	6

Figure S331. Get High-res Image Gene #58: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q21.1' versus 'METHLYATION_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.00093

Table S332. Gene #58: 'del_15q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 34(15Q21.1) MUTATED	41	69	44
DEL PEAK 34(15Q21.1) WILD-TYPE	76	60	100

Figure S332. Get High-res Image Gene #58: 'del_15q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q21.1' versus 'MRNASEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.00074

Table S333. Gene #58: 'del_15q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 34(15Q21.1) MUTATED	82	35	48	82
DEL PEAK 34(15Q21.1) WILD-TYPE	74	93	83	116

Figure S333. Get High-res Image Gene #58: 'del_15q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S334. Gene #58: 'del_15q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 34(15Q21.1) MUTATED	39	31	5	23	46	65	38
DEL PEAK 34(15Q21.1) WILD-TYPE	41	55	59	34	44	73	60

Figure S334. Get High-res Image Gene #58: 'del_15q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q21.1' versus 'MIRSEQ_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.028

Table S335. Gene #58: 'del_15q21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
DEL PEAK 34(15Q21.1) MUTATED	51	44	45	74
DEL PEAK 34(15Q21.1) WILD-TYPE	102	51	41	131

Figure S335. Get High-res Image Gene #58: 'del_15q21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00187 (Fisher's exact test), Q value = 0.0056

Table S336. Gene #58: 'del_15q21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 34(15Q21.1) MUTATED	17	30	9	42	15	19	29	14	39
DEL PEAK 34(15Q21.1) WILD-TYPE	32	44	20	44	62	35	28	18	42

Figure S336. Get High-res Image Gene #58: 'del_15q21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_15q22.33' versus 'MRNA_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00033

Table S337. Gene #59: 'del_15q22.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
DEL PEAK 35(15Q22.33) MUTATED	12	31	35	7
DEL PEAK 35(15Q22.33) WILD-TYPE	33	32	30	36

Figure S337. Get High-res Image Gene #59: 'del_15q22.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q22.33' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S338. Gene #59: 'del_15q22.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 35(15Q22.33) MUTATED	11	52	22
DEL PEAK 35(15Q22.33) WILD-TYPE	39	37	55

Figure S338. Get High-res Image Gene #59: 'del_15q22.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q22.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S339. Gene #59: 'del_15q22.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 35(15Q22.33) MUTATED	18	140	63	17
DEL PEAK 35(15Q22.33) WILD-TYPE	197	107	69	5

Figure S339. Get High-res Image Gene #59: 'del_15q22.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q22.33' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00014

Table S340. Gene #59: 'del_15q22.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 35(15Q22.33) MUTATED	41	70	41
DEL PEAK 35(15Q22.33) WILD-TYPE	76	59	103

Figure S340. Get High-res Image Gene #59: 'del_15q22.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q22.33' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S341. Gene #59: 'del_15q22.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 35(15Q22.33) MUTATED	80	29	50	78
DEL PEAK 35(15Q22.33) WILD-TYPE	76	99	81	120

Figure S341. Get High-res Image Gene #59: 'del_15q22.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q22.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S342. Gene #59: 'del_15q22.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 35(15Q22.33) MUTATED	37	29	3	23	50	64	31
DEL PEAK 35(15Q22.33) WILD-TYPE	43	57	61	34	40	74	67

Figure S342. Get High-res Image Gene #59: 'del_15q22.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q22.33' versus 'MIRSEQ_CNMF'

P value = 0.00253 (Fisher's exact test), Q value = 0.0073

Table S343. Gene #59: 'del_15q22.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
DEL PEAK 35(15Q22.33) MUTATED	50	45	44	66
DEL PEAK 35(15Q22.33) WILD-TYPE	103	50	42	139

Figure S343. Get High-res Image Gene #59: 'del_15q22.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q22.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00033

Table S344. Gene #59: 'del_15q22.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 35(15Q22.33) MUTATED	17	31	8	37	11	18	29	14	40
DEL PEAK 35(15Q22.33) WILD-TYPE	32	43	21	49	66	36	28	18	41

Figure S344. Get High-res Image Gene #59: 'del_15q22.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MRNA_CNMF'

P value = 0.049 (Fisher's exact test), Q value = 0.098

Table S345. Gene #60: 'del_16p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
DEL PEAK 36(16P13.3) MUTATED	6	12	6	1
DEL PEAK 36(16P13.3) WILD-TYPE	39	51	59	42

Figure S345. Get High-res Image Gene #60: 'del_16p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_16p13.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0364 (Fisher's exact test), Q value = 0.077

Table S346. Gene #60: 'del_16p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 36(16P13.3) MUTATED	5	16	4
DEL PEAK 36(16P13.3) WILD-TYPE	45	73	73

Figure S346. Get High-res Image Gene #60: 'del_16p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_16p13.3' versus 'CN_CNMF'

P value = 0.00812 (Fisher's exact test), Q value = 0.021

Table S347. Gene #60: 'del_16p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 36(16P13.3) MUTATED	14	28	24	3
DEL PEAK 36(16P13.3) WILD-TYPE	201	219	108	19

Figure S347. Get High-res Image Gene #60: 'del_16p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q23.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00131 (Fisher's exact test), Q value = 0.004

Table S348. Gene #61: 'del_16q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 37(16Q23.1) MUTATED	15	10	5
DEL PEAK 37(16Q23.1) WILD-TYPE	35	79	72

Figure S348. Get High-res Image Gene #61: 'del_16q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S349. Gene #62: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
DEL PEAK 38(17P12) MUTATED	17	51	50	15
DEL PEAK 38(17P12) WILD-TYPE	28	12	15	28

Figure S349. Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S350. Gene #62: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 38(17P12) MUTATED	14	70	49
DEL PEAK 38(17P12) WILD-TYPE	36	19	28

Figure S350. Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S351. Gene #62: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 38(17P12) MUTATED	46	204	105	15
DEL PEAK 38(17P12) WILD-TYPE	169	43	27	7

Figure S351. Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S352. Gene #62: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 38(17P12) MUTATED	57	106	71
DEL PEAK 38(17P12) WILD-TYPE	60	23	73

Figure S352. Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S353. Gene #62: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 38(17P12) MUTATED	122	53	72	121
DEL PEAK 38(17P12) WILD-TYPE	34	75	59	77

Figure S353. Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S354. Gene #62: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 38(17P12) MUTATED	58	49	8	39	68	106	40
DEL PEAK 38(17P12) WILD-TYPE	22	37	56	18	22	32	58

Figure S354. Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00067

Table S355. Gene #62: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
DEL PEAK 38(17P12) MUTATED	86	57	69	111
DEL PEAK 38(17P12) WILD-TYPE	67	38	17	94

Figure S355. Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S356. Gene #62: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 38(17P12) MUTATED	26	43	18	60	20	38	41	17	60
DEL PEAK 38(17P12) WILD-TYPE	23	31	11	26	57	16	16	15	21

Figure S356. Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0335 (Fisher's exact test), Q value = 0.072

Table S357. Gene #62: 'del_17p12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	40	38	22
DEL PEAK 38(17P12) MUTATED	20	28	29	9
DEL PEAK 38(17P12) WILD-TYPE	15	12	9	13

Figure S357. Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0426 (Fisher's exact test), Q value = 0.088

Table S358. Gene #62: 'del_17p12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	16	34	22
DEL PEAK 38(17P12) MUTATED	35	12	20	19
DEL PEAK 38(17P12) WILD-TYPE	28	4	14	3

Figure S358. Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S359. Gene #63: 'del_17q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 39(17Q24.3) MUTATED	15	43	27	10
DEL PEAK 39(17Q24.3) WILD-TYPE	200	204	105	12

Figure S359. Get High-res Image Gene #63: 'del_17q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_18p11.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S360. Gene #64: 'del_18p11.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
DEL PEAK 40(18P11.31) MUTATED	11	52	50	14
DEL PEAK 40(18P11.31) WILD-TYPE	34	11	15	29

Figure S360. Get High-res Image Gene #64: 'del_18p11.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18p11.31' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S361. Gene #64: 'del_18p11.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 40(18P11.31) MUTATED	9	75	43
DEL PEAK 40(18P11.31) WILD-TYPE	41	14	34

Figure S361. Get High-res Image Gene #64: 'del_18p11.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18p11.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S362. Gene #64: 'del_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 40(18P11.31) MUTATED	45	221	87	17
DEL PEAK 40(18P11.31) WILD-TYPE	170	26	45	5

Figure S362. Get High-res Image Gene #64: 'del_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_18p11.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S363. Gene #64: 'del_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 40(18P11.31) MUTATED	62	120	59
DEL PEAK 40(18P11.31) WILD-TYPE	55	9	85

Figure S363. Get High-res Image Gene #64: 'del_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18p11.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S364. Gene #64: 'del_18p11.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 40(18P11.31) MUTATED	141	41	72	114
DEL PEAK 40(18P11.31) WILD-TYPE	15	87	59	84

Figure S364. Get High-res Image Gene #64: 'del_18p11.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18p11.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S365. Gene #64: 'del_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 40(18P11.31) MUTATED	66	46	6	40	70	106	34
DEL PEAK 40(18P11.31) WILD-TYPE	14	40	58	17	20	32	64

Figure S365. Get High-res Image Gene #64: 'del_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18p11.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S366. Gene #64: 'del_18p11.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
DEL PEAK 40(18P11.31) MUTATED	84	60	74	101
DEL PEAK 40(18P11.31) WILD-TYPE	69	35	12	104

Figure S366. Get High-res Image Gene #64: 'del_18p11.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18p11.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S367. Gene #64: 'del_18p11.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 40(18P11.31) MUTATED	26	41	17	57	15	41	42	16	64
DEL PEAK 40(18P11.31) WILD-TYPE	23	33	12	29	62	13	15	16	17

Figure S367. Get High-res Image Gene #64: 'del_18p11.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18p11.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S368. Gene #64: 'del_18p11.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	40	38	22
DEL PEAK 40(18P11.31) MUTATED	24	28	34	6
DEL PEAK 40(18P11.31) WILD-TYPE	11	12	4	16

Figure S368. Get High-res Image Gene #64: 'del_18p11.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18p11.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0018

Table S369. Gene #64: 'del_18p11.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	16	34	22
DEL PEAK 40(18P11.31) MUTATED	34	14	23	21
DEL PEAK 40(18P11.31) WILD-TYPE	29	2	11	1

Figure S369. Get High-res Image Gene #64: 'del_18p11.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q12.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S370. Gene #65: 'del_18q12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
DEL PEAK 41(18Q12.2) MUTATED	17	55	54	18
DEL PEAK 41(18Q12.2) WILD-TYPE	28	8	11	25

Figure S370. Get High-res Image Gene #65: 'del_18q12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q12.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S371. Gene #65: 'del_18q12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 41(18Q12.2) MUTATED	14	79	51
DEL PEAK 41(18Q12.2) WILD-TYPE	36	10	26

Figure S371. Get High-res Image Gene #65: 'del_18q12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18q12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S372. Gene #65: 'del_18q12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 41(18Q12.2) MUTATED	53	232	114	17
DEL PEAK 41(18Q12.2) WILD-TYPE	162	15	18	5

Figure S372. Get High-res Image Gene #65: 'del_18q12.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q12.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S373. Gene #65: 'del_18q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 41(18Q12.2) MUTATED	71	123	74
DEL PEAK 41(18Q12.2) WILD-TYPE	46	6	70

Figure S373. Get High-res Image Gene #65: 'del_18q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q12.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S374. Gene #65: 'del_18q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 41(18Q12.2) MUTATED	143	56	83	132
DEL PEAK 41(18Q12.2) WILD-TYPE	13	72	48	66

Figure S374. Get High-res Image Gene #65: 'del_18q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S375. Gene #65: 'del_18q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 41(18Q12.2) MUTATED	67	58	8	45	77	114	45
DEL PEAK 41(18Q12.2) WILD-TYPE	13	28	56	12	13	24	53

Figure S375. Get High-res Image Gene #65: 'del_18q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q12.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S376. Gene #65: 'del_18q12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
DEL PEAK 41(18Q12.2) MUTATED	93	67	81	121
DEL PEAK 41(18Q12.2) WILD-TYPE	60	28	5	84

Figure S376. Get High-res Image Gene #65: 'del_18q12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18q12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S377. Gene #65: 'del_18q12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 41(18Q12.2) MUTATED	31	47	18	65	21	43	50	19	68
DEL PEAK 41(18Q12.2) WILD-TYPE	18	27	11	21	56	11	7	13	13

Figure S377. Get High-res Image Gene #65: 'del_18q12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q12.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00077

Table S378. Gene #65: 'del_18q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	40	38	22
DEL PEAK 41(18Q12.2) MUTATED	26	32	36	10
DEL PEAK 41(18Q12.2) WILD-TYPE	9	8	2	12

Figure S378. Get High-res Image Gene #65: 'del_18q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00044

Table S379. Gene #65: 'del_18q12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	16	34	22
DEL PEAK 41(18Q12.2) MUTATED	40	16	26	22
DEL PEAK 41(18Q12.2) WILD-TYPE	23	0	8	0

Figure S379. Get High-res Image Gene #65: 'del_18q12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q21.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S380. Gene #66: 'del_18q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
DEL PEAK 42(18Q21.2) MUTATED	17	56	55	19
DEL PEAK 42(18Q21.2) WILD-TYPE	28	7	10	24

Figure S380. Get High-res Image Gene #66: 'del_18q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q21.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S381. Gene #66: 'del_18q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 42(18Q21.2) MUTATED	14	79	54
DEL PEAK 42(18Q21.2) WILD-TYPE	36	10	23

Figure S381. Get High-res Image Gene #66: 'del_18q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S382. Gene #66: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 42(18Q21.2) MUTATED	62	235	117	18
DEL PEAK 42(18Q21.2) WILD-TYPE	153	12	15	4

Figure S382. Get High-res Image Gene #66: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S383. Gene #66: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 42(18Q21.2) MUTATED	71	124	86
DEL PEAK 42(18Q21.2) WILD-TYPE	46	5	58

Figure S383. Get High-res Image Gene #66: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S384. Gene #66: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 42(18Q21.2) MUTATED	144	63	88	135
DEL PEAK 42(18Q21.2) WILD-TYPE	12	65	43	63

Figure S384. Get High-res Image Gene #66: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S385. Gene #66: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 42(18Q21.2) MUTATED	68	62	13	45	80	116	46
DEL PEAK 42(18Q21.2) WILD-TYPE	12	24	51	12	10	22	52

Figure S385. Get High-res Image Gene #66: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S386. Gene #66: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
DEL PEAK 42(18Q21.2) MUTATED	103	68	81	126
DEL PEAK 42(18Q21.2) WILD-TYPE	50	27	5	79

Figure S386. Get High-res Image Gene #66: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S387. Gene #66: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 42(18Q21.2) MUTATED	32	50	22	65	25	44	51	19	70
DEL PEAK 42(18Q21.2) WILD-TYPE	17	24	7	21	52	10	6	13	11

Figure S387. Get High-res Image Gene #66: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 7e-04

Table S388. Gene #66: 'del_18q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	40	38	22
DEL PEAK 42(18Q21.2) MUTATED	27	33	37	11
DEL PEAK 42(18Q21.2) WILD-TYPE	8	7	1	11

Figure S388. Get High-res Image Gene #66: 'del_18q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00037

Table S389. Gene #66: 'del_18q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	16	34	22
DEL PEAK 42(18Q21.2) MUTATED	41	16	29	22
DEL PEAK 42(18Q21.2) WILD-TYPE	22	0	5	0

Figure S389. Get High-res Image Gene #66: 'del_18q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q22.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S390. Gene #67: 'del_18q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
DEL PEAK 43(18Q22.1) MUTATED	17	56	54	20
DEL PEAK 43(18Q22.1) WILD-TYPE	28	7	11	23

Figure S390. Get High-res Image Gene #67: 'del_18q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S391. Gene #67: 'del_18q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 43(18Q22.1) MUTATED	15	79	53
DEL PEAK 43(18Q22.1) WILD-TYPE	35	10	24

Figure S391. Get High-res Image Gene #67: 'del_18q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S392. Gene #67: 'del_18q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 43(18Q22.1) MUTATED	60	235	114	18
DEL PEAK 43(18Q22.1) WILD-TYPE	155	12	18	4

Figure S392. Get High-res Image Gene #67: 'del_18q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S393. Gene #67: 'del_18q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 43(18Q22.1) MUTATED	68	124	84
DEL PEAK 43(18Q22.1) WILD-TYPE	49	5	60

Figure S393. Get High-res Image Gene #67: 'del_18q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S394. Gene #67: 'del_18q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 43(18Q22.1) MUTATED	143	62	85	135
DEL PEAK 43(18Q22.1) WILD-TYPE	13	66	46	63

Figure S394. Get High-res Image Gene #67: 'del_18q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S395. Gene #67: 'del_18q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 43(18Q22.1) MUTATED	67	61	13	43	79	115	47
DEL PEAK 43(18Q22.1) WILD-TYPE	13	25	51	14	11	23	51

Figure S395. Get High-res Image Gene #67: 'del_18q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q22.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S396. Gene #67: 'del_18q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
DEL PEAK 43(18Q22.1) MUTATED	101	66	80	126
DEL PEAK 43(18Q22.1) WILD-TYPE	52	29	6	79

Figure S396. Get High-res Image Gene #67: 'del_18q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S397. Gene #67: 'del_18q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 43(18Q22.1) MUTATED	32	49	21	63	26	43	51	19	69
DEL PEAK 43(18Q22.1) WILD-TYPE	17	25	8	23	51	11	6	13	12

Figure S397. Get High-res Image Gene #67: 'del_18q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0027

Table S398. Gene #67: 'del_18q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	40	38	22
DEL PEAK 43(18Q22.1) MUTATED	27	32	36	11
DEL PEAK 43(18Q22.1) WILD-TYPE	8	8	2	11

Figure S398. Get High-res Image Gene #67: 'del_18q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00216 (Fisher's exact test), Q value = 0.0064

Table S399. Gene #67: 'del_18q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	16	34	22
DEL PEAK 43(18Q22.1) MUTATED	41	16	29	20
DEL PEAK 43(18Q22.1) WILD-TYPE	22	0	5	2

Figure S399. Get High-res Image Gene #67: 'del_18q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 7e-04

Table S400. Gene #68: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 44(19P13.3) MUTATED	16	47	29	5
DEL PEAK 44(19P13.3) WILD-TYPE	199	200	103	17

Figure S400. Get High-res Image Gene #68: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.0021

Table S401. Gene #68: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 44(19P13.3) MUTATED	9	7	5	29	5	6	7	6	14
DEL PEAK 44(19P13.3) WILD-TYPE	40	67	24	57	72	48	50	26	67

Figure S401. Get High-res Image Gene #68: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00231 (Fisher's exact test), Q value = 0.0068

Table S402. Gene #69: 'del_20p12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 45(20P12.1) MUTATED	4	28	12
DEL PEAK 45(20P12.1) WILD-TYPE	46	61	65

Figure S402. Get High-res Image Gene #69: 'del_20p12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_20p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S403. Gene #69: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 45(20P12.1) MUTATED	16	83	37	0
DEL PEAK 45(20P12.1) WILD-TYPE	199	164	95	22

Figure S403. Get High-res Image Gene #69: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_20p12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S404. Gene #69: 'del_20p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 45(20P12.1) MUTATED	23	50	19
DEL PEAK 45(20P12.1) WILD-TYPE	94	79	125

Figure S404. Get High-res Image Gene #69: 'del_20p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_20p12.1' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00058

Table S405. Gene #69: 'del_20p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 45(20P12.1) MUTATED	55	21	26	33
DEL PEAK 45(20P12.1) WILD-TYPE	101	107	105	165

Figure S405. Get High-res Image Gene #69: 'del_20p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S406. Gene #69: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 45(20P12.1) MUTATED	25	21	0	14	29	36	10
DEL PEAK 45(20P12.1) WILD-TYPE	55	65	64	43	61	102	88

Figure S406. Get High-res Image Gene #69: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_CNMF'

P value = 0.00378 (Fisher's exact test), Q value = 0.011

Table S407. Gene #69: 'del_20p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
DEL PEAK 45(20P12.1) MUTATED	33	17	31	34
DEL PEAK 45(20P12.1) WILD-TYPE	120	78	55	171

Figure S407. Get High-res Image Gene #69: 'del_20p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_20p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.0012

Table S408. Gene #69: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 45(20P12.1) MUTATED	9	16	6	30	6	11	16	1	20
DEL PEAK 45(20P12.1) WILD-TYPE	40	58	23	56	71	43	41	31	61

Figure S408. Get High-res Image Gene #69: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MRNA_CNMF'

P value = 0.00796 (Fisher's exact test), Q value = 0.021

Table S409. Gene #70: 'del_21q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
DEL PEAK 46(21Q11.2) MUTATED	11	30	24	8
DEL PEAK 46(21Q11.2) WILD-TYPE	34	33	41	35

Figure S409. Get High-res Image Gene #70: 'del_21q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_21q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0013

Table S410. Gene #70: 'del_21q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 46(21Q11.2) MUTATED	11	44	18
DEL PEAK 46(21Q11.2) WILD-TYPE	39	45	59

Figure S410. Get High-res Image Gene #70: 'del_21q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_21q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S411. Gene #70: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 46(21Q11.2) MUTATED	37	117	46	14
DEL PEAK 46(21Q11.2) WILD-TYPE	178	130	86	8

Figure S411. Get High-res Image Gene #70: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 0.00737 (Fisher's exact test), Q value = 0.02

Table S412. Gene #70: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 46(21Q11.2) MUTATED	37	60	42
DEL PEAK 46(21Q11.2) WILD-TYPE	80	69	102

Figure S412. Get High-res Image Gene #70: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00051

Table S413. Gene #70: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 46(21Q11.2) MUTATED	77	32	40	63
DEL PEAK 46(21Q11.2) WILD-TYPE	79	96	91	135

Figure S413. Get High-res Image Gene #70: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_21q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.0011

Table S414. Gene #70: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 46(21Q11.2) MUTATED	35	27	9	23	38	55	25
DEL PEAK 46(21Q11.2) WILD-TYPE	45	59	55	34	52	83	73

Figure S414. Get High-res Image Gene #70: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.042

Table S415. Gene #70: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
DEL PEAK 46(21Q11.2) MUTATED	48	32	43	65
DEL PEAK 46(21Q11.2) WILD-TYPE	105	63	43	140

Figure S415. Get High-res Image Gene #70: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_21q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0254 (Fisher's exact test), Q value = 0.057

Table S416. Gene #70: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 46(21Q11.2) MUTATED	17	20	8	31	17	25	28	10	32
DEL PEAK 46(21Q11.2) WILD-TYPE	32	54	21	55	60	29	29	22	49

Figure S416. Get High-res Image Gene #70: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_21q21.1' versus 'MRNA_CNMF'

P value = 0.00695 (Fisher's exact test), Q value = 0.019

Table S417. Gene #71: 'del_21q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
DEL PEAK 47(21Q21.1) MUTATED	11	29	23	7
DEL PEAK 47(21Q21.1) WILD-TYPE	34	34	42	36

Figure S417. Get High-res Image Gene #71: 'del_21q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_21q21.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.0018

Table S418. Gene #71: 'del_21q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 47(21Q21.1) MUTATED	10	42	18
DEL PEAK 47(21Q21.1) WILD-TYPE	40	47	59

Figure S418. Get High-res Image Gene #71: 'del_21q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_21q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S419. Gene #71: 'del_21q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 47(21Q21.1) MUTATED	37	114	45	14
DEL PEAK 47(21Q21.1) WILD-TYPE	178	133	87	8

Figure S419. Get High-res Image Gene #71: 'del_21q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q21.1' versus 'METHLYATION_CNMF'

P value = 0.00334 (Fisher's exact test), Q value = 0.0095

Table S420. Gene #71: 'del_21q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 47(21Q21.1) MUTATED	37	61	41
DEL PEAK 47(21Q21.1) WILD-TYPE	80	68	103

Figure S420. Get High-res Image Gene #71: 'del_21q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_21q21.1' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00041

Table S421. Gene #71: 'del_21q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 47(21Q21.1) MUTATED	76	31	39	62
DEL PEAK 47(21Q21.1) WILD-TYPE	80	97	92	136

Figure S421. Get High-res Image Gene #71: 'del_21q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_21q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.0021

Table S422. Gene #71: 'del_21q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 47(21Q21.1) MUTATED	32	27	10	21	40	55	23
DEL PEAK 47(21Q21.1) WILD-TYPE	48	59	54	36	50	83	75

Figure S422. Get High-res Image Gene #71: 'del_21q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_21q21.1' versus 'MIRSEQ_CNMF'

P value = 0.0172 (Fisher's exact test), Q value = 0.041

Table S423. Gene #71: 'del_21q21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
DEL PEAK 47(21Q21.1) MUTATED	46	33	42	63
DEL PEAK 47(21Q21.1) WILD-TYPE	107	62	44	142

Figure S423. Get High-res Image Gene #71: 'del_21q21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_21q21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00868 (Fisher's exact test), Q value = 0.023

Table S424. Gene #71: 'del_21q21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 47(21Q21.1) MUTATED	17	21	7	32	15	23	28	8	33
DEL PEAK 47(21Q21.1) WILD-TYPE	32	53	22	54	62	31	29	24	48

Figure S424. Get High-res Image Gene #71: 'del_21q21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_21q21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.018 (Fisher's exact test), Q value = 0.042

Table S425. Gene #71: 'del_21q21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	16	34	22
DEL PEAK 47(21Q21.1) MUTATED	19	9	20	12
DEL PEAK 47(21Q21.1) WILD-TYPE	44	7	14	10

Figure S425. Get High-res Image Gene #71: 'del_21q21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.32' versus 'MRNA_CNMF'

P value = 0.00236 (Fisher's exact test), Q value = 0.0069

Table S426. Gene #72: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	63	65	43
DEL PEAK 48(22Q13.32) MUTATED	13	31	33	9
DEL PEAK 48(22Q13.32) WILD-TYPE	32	32	32	34

Figure S426. Get High-res Image Gene #72: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_22q13.32' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S427. Gene #72: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	77
DEL PEAK 48(22Q13.32) MUTATED	7	47	32
DEL PEAK 48(22Q13.32) WILD-TYPE	43	42	45

Figure S427. Get High-res Image Gene #72: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S428. Gene #72: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	215	247	132	22
DEL PEAK 48(22Q13.32) MUTATED	29	130	55	14
DEL PEAK 48(22Q13.32) WILD-TYPE	186	117	77	8

Figure S428. Get High-res Image Gene #72: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 0.0309 (Fisher's exact test), Q value = 0.068

Table S429. Gene #72: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	129	144
DEL PEAK 48(22Q13.32) MUTATED	44	55	40
DEL PEAK 48(22Q13.32) WILD-TYPE	73	74	104

Figure S429. Get High-res Image Gene #72: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 0.0266 (Fisher's exact test), Q value = 0.059

Table S430. Gene #72: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	128	131	198
DEL PEAK 48(22Q13.32) MUTATED	69	35	46	77
DEL PEAK 48(22Q13.32) WILD-TYPE	87	93	85	121

Figure S430. Get High-res Image Gene #72: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S431. Gene #72: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	80	86	64	57	90	138	98
DEL PEAK 48(22Q13.32) MUTATED	34	29	8	24	38	67	27
DEL PEAK 48(22Q13.32) WILD-TYPE	46	57	56	33	52	71	71

Figure S431. Get High-res Image Gene #72: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CNMF'

P value = 0.0271 (Fisher's exact test), Q value = 0.06

Table S432. Gene #72: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	95	86	205
DEL PEAK 48(22Q13.32) MUTATED	47	37	43	72
DEL PEAK 48(22Q13.32) WILD-TYPE	106	58	43	133

Figure S432. Get High-res Image Gene #72: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_22q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0015

Table S433. Gene #72: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	49	74	29	86	77	54	57	32	81
DEL PEAK 48(22Q13.32) MUTATED	16	26	3	34	17	23	29	12	39
DEL PEAK 48(22Q13.32) WILD-TYPE	33	48	26	52	60	31	28	20	42

Figure S433. Get High-res Image Gene #72: 'del_22q13.32' versus Molecular Subtype #10: '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/COADREAD-TP/22524544/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/COADREAD-TP/22555066/COADREAD-TP.transferedmergedcluster.txt
Number of patients = 616
Number of significantly focal cnvs = 72
Number of molecular subtypes = 12
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

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

Q value calculation

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

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)

Made with Nozzle