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 49 focal events and 12 molecular subtypes across 513 patients, 358 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q22 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_1q32.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_2p24.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3q26.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_4q12 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7p11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q31.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q32.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q24.13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_9q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_10p15.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_11q24.1 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12p13.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12q14.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_13q34 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_15q26.3 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q25.1 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.
amp_19p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xp11.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xp11.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.32 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p32.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1q43 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q37.3 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p21.31 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3q13.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_3q29 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_4q34.3 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5p15.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q34 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6p25.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_6q22.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q26 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7p22.3 cnv correlated to 'CN_CNMF'.
del_8q24.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q26.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p15.5 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p15.1 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_12q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q14.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q34 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q24.3 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19q13.42 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_22q13.31 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xq21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 49 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, 358 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
del 1p36 32	206 (40%)	307	0.00062 (0.0018)	0.00019 (0.000614)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.00067 (0.00189)	0.00045 (0.00135)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	1e-05 (4.49e-05)
del 1p32 3	196 (38%)	317	0.0283 (0.0509)	0.00019 (0.000614)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.00164 (0.00417)	0.00061 (0.00178)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	1e-05 (4.49e-05)
del 19q13 42	278 (54%)	235	0.0347 (0.0603)	0.021 (0.039)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.0064 (0.0138)	0.021 (0.039)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	1e-05 (4.49e-05)
del 22q13 31	77 (15%)	436	0.253 (0.323)	0.0425 (0.0721)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.00089 (0.00243)	0.0429 (0.0725)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.05 (0.0821)	1e-05 (4.49e-05)	4e-05 (0.000154)	7e-05 (0.000251)
amp 4q12	30 (6%)	483	1 (1.00)	0.042 (0.0718)	8e-05 (0.000282)	1e-05 (4.49e-05)	0.00015 (0.000504)	0.336 (0.415)	5e-05 (0.000187)	1e-05 (4.49e-05)	0.00303 (0.00721)	0.00012 (0.000418)	0.00251 (0.00615)	0.00066 (0.00188)
amp 7p11 2	127 (25%)	386	0.864 (0.932)	0.782 (0.851)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.0015 (0.00387)	0.00326 (0.00764)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.00015 (0.000504)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	1e-05 (4.49e-05)
del 2q37 3	77 (15%)	436	0.367 (0.444)	0.0134 (0.0265)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.00109 (0.00289)	0.0149 (0.0288)	0.00019 (0.000614)	1e-05 (4.49e-05)	0.0264 (0.0477)	0.141 (0.197)	0.0151 (0.029)	1e-05 (4.49e-05)
del 10q26 3	151 (29%)	362	0.0821 (0.126)	0.707 (0.778)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.00156 (0.00401)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	1e-05 (4.49e-05)
del 11p15 1	72 (14%)	441	1 (1.00)	0.0301 (0.0535)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.00143 (0.00372)	0.613 (0.694)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	3e-05 (0.000119)	7e-05 (0.000251)	0.00081 (0.00225)	1e-05 (4.49e-05)
amp 3q26 33	21 (4%)	492	1 (1.00)	0.581 (0.664)	1e-05 (4.49e-05)	0.00895 (0.0186)	0.0238 (0.0433)	0.287 (0.361)	0.00067 (0.00189)	0.00124 (0.00325)	0.00049 (0.00146)	0.0189 (0.0358)	0.00101 (0.00271)	0.00369 (0.00843)
amp 10p15 3	71 (14%)	442	0.525 (0.608)	0.0847 (0.129)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.00824 (0.0174)	0.00135 (0.00353)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.00033 (0.00104)	0.076 (0.118)	0.00237 (0.00588)	1e-05 (4.49e-05)
amp 12p13 32	72 (14%)	441	0.863 (0.932)	0.0967 (0.144)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.00499 (0.011)	0.143 (0.2)	0.00012 (0.000418)	1e-05 (4.49e-05)	0.0111 (0.0223)	0.00709 (0.0151)	0.00144 (0.00373)	1e-05 (4.49e-05)
amp 12q14 1	37 (7%)	476			1e-05 (4.49e-05)	2e-05 (8.4e-05)	0.0145 (0.0285)	0.346 (0.424)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.00366 (0.00841)	1e-05 (4.49e-05)	2e-05 (8.4e-05)	6e-05 (0.000222)
del 3p21 31	49 (10%)	464	1 (1.00)	0.00663 (0.0142)	0.00093 (0.00251)	0.00353 (0.00814)	7e-05 (0.000251)	0.0437 (0.0734)	0.0585 (0.0945)	0.00093 (0.00251)	0.00161 (0.00412)	0.00242 (0.00598)	0.393 (0.472)	0.00975 (0.0199)
del 6q26	82 (16%)	431	0.0471 (0.0782)	0.58 (0.664)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.111 (0.161)	0.00914 (0.0189)	0.00041 (0.00126)	0.00014 (0.000476)	3e-05 (0.000119)	0.161 (0.217)	0.00333 (0.00771)	0.00031 (0.00098)
del 9p21 3	176 (34%)	337	0.334 (0.414)	0.0645 (0.102)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	2e-05 (8.4e-05)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.359 (0.437)	1e-05 (4.49e-05)	0.00084 (0.00232)	1e-05 (4.49e-05)
del 11p15 5	104 (20%)	409	0.646 (0.725)	0.00043 (0.0013)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.0562 (0.0912)	0.898 (0.962)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	2e-05 (8.4e-05)	0.00476 (0.0106)	0.00675 (0.0144)	1e-05 (4.49e-05)
del 13q14 2	144 (28%)	369	0.182 (0.243)	7e-05 (0.000251)	1e-05 (4.49e-05)	0.00019 (0.000614)	0.0294 (0.0526)	0.785 (0.853)	0.00013 (0.000447)	1e-05 (4.49e-05)	0.0358 (0.0617)	0.00393 (0.00885)	0.216 (0.283)	0.0113 (0.0226)
del 14q24 3	122 (24%)	391	0.303 (0.38)	0.0966 (0.144)	1e-05 (4.49e-05)	0.059 (0.0951)	0.00073 (0.00204)	0.0218 (0.04)	0.00052 (0.00154)	0.00058 (0.0017)	0.0004 (0.00124)	0.00416 (0.00934)	0.0062 (0.0135)	0.00174 (0.00441)
del xq21 1	78 (15%)	435	0.839 (0.908)	0.265 (0.337)	0.0117 (0.0234)	3e-05 (0.000119)	0.00108 (0.00287)	0.015 (0.029)	0.0121 (0.0241)	3e-05 (0.000119)	0.00049 (0.00146)	0.36 (0.438)	0.00016 (0.000532)	8e-05 (0.000282)
amp 7q31 2	173 (34%)	340	1 (1.00)	0.938 (0.999)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.102 (0.151)	0.154 (0.212)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.0108 (0.0219)	1e-05 (4.49e-05)	0.00066 (0.00188)	1e-05 (4.49e-05)
amp 7q32 3	181 (35%)	332	1 (1.00)	1 (1.00)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.147 (0.204)	0.138 (0.194)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.0335 (0.0587)	1e-05 (4.49e-05)	0.00092 (0.0025)	1e-05 (4.49e-05)
amp 8q24 13	99 (19%)	414	0.369 (0.446)	0.236 (0.307)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.25 (0.322)	0.328 (0.408)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.00835 (0.0175)	0.00043 (0.0013)	0.0147 (0.0288)	1e-05 (4.49e-05)
amp 19p13 3	129 (25%)	384	0.0737 (0.114)	0.149 (0.207)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.249 (0.322)	0.00494 (0.0109)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.00054 (0.00159)	0.154 (0.212)	2e-05 (8.4e-05)	1e-05 (4.49e-05)
del 6q22 31	78 (15%)	435	0.617 (0.695)	0.583 (0.664)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.0612 (0.0975)	0.0148 (0.0288)	0.0037 (0.00843)	0.00115 (0.00303)	0.00072 (0.00203)	0.123 (0.176)	0.00276 (0.00665)	0.00325 (0.00764)
del 8q24 3	29 (6%)	484			1e-05 (4.49e-05)	0.00014 (0.000476)	0.339 (0.417)	0.119 (0.172)	0.0059 (0.0129)	0.00637 (0.0138)	0.0433 (0.073)	0.00333 (0.00771)	0.0334 (0.0586)	0.029 (0.0519)
del 13q34	110 (21%)	403	0.506 (0.588)	0.152 (0.21)	1e-05 (4.49e-05)	0.026 (0.0472)	0.0216 (0.0397)	0.383 (0.461)	0.0137 (0.0269)	0.00105 (0.00281)	0.0467 (0.0778)	0.00276 (0.00665)	0.704 (0.778)	0.0298 (0.0532)
amp 1q32 1	43 (8%)	470			1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.292 (0.367)	0.445 (0.527)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.136 (0.193)	2e-05 (8.4e-05)	0.00328 (0.00765)	3e-05 (0.000119)
amp xp11 22	63 (12%)	450	0.655 (0.731)	1 (1.00)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.145 (0.202)	0.104 (0.153)	5e-05 (0.000187)	1e-05 (4.49e-05)	0.00065 (0.00187)	0.352 (0.43)	0.00013 (0.000447)	0.00027 (0.000858)
del 5p15 33	50 (10%)	463	1 (1.00)	0.0665 (0.105)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.777 (0.848)	0.654 (0.731)	0.00087 (0.00239)	5e-05 (0.000187)	0.00451 (0.01)	0.206 (0.271)	0.00373 (0.00847)	3e-05 (0.000119)
del 5q34	64 (12%)	449	0.445 (0.527)	0.236 (0.307)	1e-05 (4.49e-05)	1e-05 (4.49e-05)	0.0595 (0.0953)	0.0773 (0.119)	7e-05 (0.000251)	1e-05 (4.49e-05)	5e-05 (0.000187)	0.134 (0.191)	0.00817 (0.0173)	1e-05 (4.49e-05)
del 9p23	150 (29%)	363	0.445 (0.527)	0.658 (0.733)	1e-05 (4.49e-05)	4e-05 (0.000154)	0.00597 (0.013)	4e-05 (0.000154)	0.0207 (0.0386)	0.00016 (0.000532)	0.924 (0.988)	0.113 (0.164)	0.345 (0.424)	0.0322 (0.0567)
amp 2p24 3	24 (5%)	489	0.618 (0.695)	0.584 (0.664)	0.00279 (0.00669)	0.252 (0.323)	0.0891 (0.134)	0.0888 (0.134)	0.0312 (0.0553)	0.00253 (0.00617)	0.743 (0.815)	0.0354 (0.0613)	0.00041 (0.00126)	0.0314 (0.0554)
amp xp11 22	48 (9%)	465	0.651 (0.729)	1 (1.00)	2e-05 (8.4e-05)	1e-05 (4.49e-05)	0.45 (0.531)	0.166 (0.222)	0.0028 (0.00669)	3e-05 (0.000119)	0.0604 (0.0966)	0.6 (0.681)	0.0149 (0.0289)	0.00195 (0.0049)
del 1q43	36 (7%)	477			0.0198 (0.037)	0.00206 (0.00515)	0.159 (0.216)	0.192 (0.255)	0.0152 (0.0291)	0.0158 (0.0302)	0.126 (0.179)	0.19 (0.252)	0.0195 (0.0367)	0.0485 (0.0801)
del 3q13 31	39 (8%)	474	0.175 (0.234)	0.882 (0.947)	0.00185 (0.00467)	0.00932 (0.0192)	0.00967 (0.0198)	0.0192 (0.0363)	0.251 (0.322)	0.0133 (0.0263)	0.155 (0.213)	0.00044 (0.00133)	0.194 (0.257)	0.124 (0.177)
del 4q34 3	137 (27%)	376	1 (1.00)	0.356 (0.434)	0.0986 (0.146)	1e-05 (4.49e-05)	0.0421 (0.0718)	0.376 (0.453)	0.0705 (0.11)	8e-05 (0.000282)	0.0279 (0.0504)	0.0455 (0.0761)	0.685 (0.76)	4e-05 (0.000154)
del 12p13 1	38 (7%)	475			0.0109 (0.0221)	3e-05 (0.000119)	0.231 (0.301)	0.581 (0.664)	0.00221 (0.00551)	0.00693 (0.0148)	0.0221 (0.0404)	0.0449 (0.0752)	0.0947 (0.142)	0.0967 (0.144)
del 12q12	72 (14%)	441	1 (1.00)	0.151 (0.209)	2e-05 (8.4e-05)	1e-05 (4.49e-05)	0.428 (0.51)	0.983 (1.00)	0.00312 (0.0074)	1e-05 (4.49e-05)	0.00567 (0.0124)	0.496 (0.58)	0.4 (0.478)	0.00036 (0.00112)
amp 15q26 3	19 (4%)	494	1 (1.00)	0.0422 (0.0718)	0.00075 (0.00209)	0.00024 (0.000771)	0.165 (0.222)	0.195 (0.258)	0.0359 (0.0617)	0.0618 (0.0981)	0.48 (0.562)	0.284 (0.358)	0.0846 (0.129)	0.0359 (0.0617)
del 3q29	47 (9%)	466	0.174 (0.233)	0.883 (0.947)	0.00035 (0.00109)	2e-05 (8.4e-05)	0.439 (0.522)	0.604 (0.684)	0.00934 (0.0192)	6e-05 (0.000222)	0.138 (0.194)	0.00439 (0.00981)	0.135 (0.191)	0.0684 (0.108)
amp 9q34 3	46 (9%)	467	0.506 (0.588)	0.882 (0.947)	0.0216 (0.0397)	0.0105 (0.0215)	0.0182 (0.0346)	1 (1.00)	0.111 (0.162)	0.00019 (0.000614)	0.208 (0.274)	0.0862 (0.131)	0.926 (0.988)	0.156 (0.214)
amp 1q22	42 (8%)	471			0.00026 (0.000831)	0.104 (0.153)	0.0841 (0.129)	0.708 (0.778)	0.00257 (0.00624)	0.0574 (0.0929)	0.364 (0.441)	0.0899 (0.135)	0.00248 (0.0061)	0.75 (0.821)
amp 11q24 1	87 (17%)	426	0.0711 (0.111)	0.122 (0.176)	0.222 (0.291)	0.00883 (0.0184)	0.243 (0.315)	0.0473 (0.0784)	0.0526 (0.0856)	0.157 (0.214)	0.681 (0.757)	0.113 (0.164)	0.499 (0.582)	0.00858 (0.018)
amp 13q34	22 (4%)	491			0.00314 (0.00741)	0.00378 (0.00855)	0.136 (0.193)	0.769 (0.841)	0.0505 (0.0827)	0.0216 (0.0397)	0.109 (0.16)	0.691 (0.766)	0.281 (0.356)	0.11 (0.16)
amp 17q25 1	44 (9%)	469			0.0393 (0.0674)	0.58 (0.664)	0.0619 (0.0981)	0.0486 (0.0801)	0.0336 (0.0587)	0.0518 (0.0846)	0.165 (0.222)	0.565 (0.651)	0.081 (0.125)	0.34 (0.418)
del 6p25 3	50 (10%)	463			4e-05 (0.000154)	0.013 (0.0258)	0.266 (0.338)	0.329 (0.408)	0.162 (0.219)	0.0707 (0.11)	0.458 (0.539)	0.253 (0.323)	0.283 (0.358)	0.0866 (0.131)
del 7p22 3	23 (4%)	490			0.0197 (0.037)	0.0691 (0.108)	0.313 (0.392)	0.158 (0.216)	0.535 (0.617)	0.707 (0.778)	0.521 (0.604)	0.0977 (0.145)	0.529 (0.612)	0.396 (0.474)
del 18q23	78 (15%)	435	0.323 (0.403)	0.328 (0.408)	0.115 (0.167)	0.0593 (0.0952)	0.982 (1.00)	0.265 (0.337)	0.458 (0.539)	0.227 (0.297)	0.138 (0.194)	0.617 (0.695)	0.461 (0.541)	0.792 (0.86)

'amp_1q22' versus 'CN_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.00083

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
AMP PEAK 1(1Q22) MUTATED	15	20	7
AMP PEAK 1(1Q22) WILD-TYPE	212	91	168

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

'amp_1q22' versus 'MRNASEQ_CNMF'

P value = 0.00257 (Fisher's exact test), Q value = 0.0062

Table S2. Gene #1: 'amp_1q22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
AMP PEAK 1(1Q22) MUTATED	8	20	3	9	2
AMP PEAK 1(1Q22) WILD-TYPE	122	95	102	124	28

Figure S2. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00248 (Fisher's exact test), Q value = 0.0061

Table S3. Gene #1: 'amp_1q22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
AMP PEAK 1(1Q22) MUTATED	11	16	1	14
AMP PEAK 1(1Q22) WILD-TYPE	116	103	104	140

Figure S3. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1q32.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S4. Gene #2: 'amp_1q32.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
AMP PEAK 2(1Q32.1) MUTATED	12	26	5
AMP PEAK 2(1Q32.1) WILD-TYPE	215	85	170

Figure S4. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q32.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S5. Gene #2: 'amp_1q32.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
AMP PEAK 2(1Q32.1) MUTATED	8	27	6	2
AMP PEAK 2(1Q32.1) WILD-TYPE	201	107	151	11

Figure S5. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q32.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S6. Gene #2: 'amp_1q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
AMP PEAK 2(1Q32.1) MUTATED	2	26	1	12	2
AMP PEAK 2(1Q32.1) WILD-TYPE	128	89	104	121	28

Figure S6. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q32.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S7. Gene #2: 'amp_1q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 2(1Q32.1) MUTATED	3	20	3	6	2	4	5
AMP PEAK 2(1Q32.1) WILD-TYPE	132	51	33	62	88	37	67

Figure S7. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q32.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8.4e-05

Table S8. Gene #2: 'amp_1q32.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 2(1Q32.1) MUTATED	8	13	22
AMP PEAK 2(1Q32.1) WILD-TYPE	214	171	81

Figure S8. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q32.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00328 (Fisher's exact test), Q value = 0.0077

Table S9. Gene #2: 'amp_1q32.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
AMP PEAK 2(1Q32.1) MUTATED	9	18	2	14
AMP PEAK 2(1Q32.1) WILD-TYPE	118	101	103	140

Figure S9. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1q32.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S10. Gene #2: 'amp_1q32.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
AMP PEAK 2(1Q32.1) MUTATED	5	3	10	1	18	6
AMP PEAK 2(1Q32.1) WILD-TYPE	94	74	108	55	45	86

Figure S10. Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_2p24.3' versus 'CN_CNMF'

P value = 0.00279 (Fisher's exact test), Q value = 0.0067

Table S11. Gene #3: 'amp_2p24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
AMP PEAK 3(2P24.3) MUTATED	9	12	3
AMP PEAK 3(2P24.3) WILD-TYPE	218	99	172

Figure S11. Get High-res Image Gene #3: 'amp_2p24.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2p24.3' versus 'MRNASEQ_CNMF'

P value = 0.0312 (Fisher's exact test), Q value = 0.055

Table S12. Gene #3: 'amp_2p24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
AMP PEAK 3(2P24.3) MUTATED	4	12	2	6	0
AMP PEAK 3(2P24.3) WILD-TYPE	126	103	103	127	30

Figure S12. Get High-res Image Gene #3: 'amp_2p24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2p24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00253 (Fisher's exact test), Q value = 0.0062

Table S13. Gene #3: 'amp_2p24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 3(2P24.3) MUTATED	3	7	1	6	2	5	0
AMP PEAK 3(2P24.3) WILD-TYPE	132	64	35	62	88	36	72

Figure S13. Get High-res Image Gene #3: 'amp_2p24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_2p24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0354 (Fisher's exact test), Q value = 0.061

Table S14. Gene #3: 'amp_2p24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 3(2P24.3) MUTATED	9	5	10
AMP PEAK 3(2P24.3) WILD-TYPE	213	179	93

Figure S14. Get High-res Image Gene #3: 'amp_2p24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_2p24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0013

Table S15. Gene #3: 'amp_2p24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
AMP PEAK 3(2P24.3) MUTATED	3	15	1	5
AMP PEAK 3(2P24.3) WILD-TYPE	124	104	104	149

Figure S15. Get High-res Image Gene #3: 'amp_2p24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_2p24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0314 (Fisher's exact test), Q value = 0.055

Table S16. Gene #3: 'amp_2p24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
AMP PEAK 3(2P24.3) MUTATED	4	7	2	1	7	3
AMP PEAK 3(2P24.3) WILD-TYPE	95	70	116	55	56	89

Figure S16. Get High-res Image Gene #3: 'amp_2p24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S17. Gene #4: 'amp_3q26.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
AMP PEAK 4(3Q26.33) MUTATED	2	19	0
AMP PEAK 4(3Q26.33) WILD-TYPE	225	92	175

Figure S17. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.33' versus 'METHLYATION_CNMF'

P value = 0.00895 (Fisher's exact test), Q value = 0.019

Table S18. Gene #4: 'amp_3q26.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
AMP PEAK 4(3Q26.33) MUTATED	7	10	2	2
AMP PEAK 4(3Q26.33) WILD-TYPE	202	124	155	11

Figure S18. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.33' versus 'RPPA_CNMF'

P value = 0.0238 (Fisher's exact test), Q value = 0.043

Table S19. Gene #4: 'amp_3q26.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	95	125	115
AMP PEAK 4(3Q26.33) MUTATED	2	8	3	1
AMP PEAK 4(3Q26.33) WILD-TYPE	89	87	122	114

Figure S19. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_3q26.33' versus 'MRNASEQ_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0019

Table S20. Gene #4: 'amp_3q26.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
AMP PEAK 4(3Q26.33) MUTATED	5	13	2	1	0
AMP PEAK 4(3Q26.33) WILD-TYPE	125	102	103	132	30

Figure S20. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00124 (Fisher's exact test), Q value = 0.0033

Table S21. Gene #4: 'amp_3q26.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 4(3Q26.33) MUTATED	4	9	1	2	0	4	1
AMP PEAK 4(3Q26.33) WILD-TYPE	131	62	35	66	90	37	71

Figure S21. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MIRSEQ_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0015

Table S22. Gene #4: 'amp_3q26.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
AMP PEAK 4(3Q26.33) MUTATED	11	8	1	1
AMP PEAK 4(3Q26.33) WILD-TYPE	129	99	81	179

Figure S22. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.036

Table S23. Gene #4: 'amp_3q26.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 4(3Q26.33) MUTATED	9	3	9
AMP PEAK 4(3Q26.33) WILD-TYPE	213	181	94

Figure S23. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00101 (Fisher's exact test), Q value = 0.0027

Table S24. Gene #4: 'amp_3q26.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
AMP PEAK 4(3Q26.33) MUTATED	4	13	1	3
AMP PEAK 4(3Q26.33) WILD-TYPE	123	106	104	151

Figure S24. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00369 (Fisher's exact test), Q value = 0.0084

Table S25. Gene #4: 'amp_3q26.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
AMP PEAK 4(3Q26.33) MUTATED	6	3	1	0	8	3
AMP PEAK 4(3Q26.33) WILD-TYPE	93	74	117	56	55	89

Figure S25. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.042 (Fisher's exact test), Q value = 0.072

Table S26. Gene #5: 'amp_4q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
AMP PEAK 5(4Q12) MUTATED	0	3	0	0
AMP PEAK 5(4Q12) WILD-TYPE	7	4	7	6

Figure S26. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_4q12' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00028

Table S27. Gene #5: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
AMP PEAK 5(4Q12) MUTATED	13	15	2
AMP PEAK 5(4Q12) WILD-TYPE	214	96	173

Figure S27. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_4q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S28. Gene #5: 'amp_4q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
AMP PEAK 5(4Q12) MUTATED	13	10	1	6
AMP PEAK 5(4Q12) WILD-TYPE	196	124	156	7

Figure S28. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_4q12' versus 'RPPA_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 5e-04

Table S29. Gene #5: 'amp_4q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	95	125	115
AMP PEAK 5(4Q12) MUTATED	3	14	1	7
AMP PEAK 5(4Q12) WILD-TYPE	88	81	124	108

Figure S29. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_4q12' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00019

Table S30. Gene #5: 'amp_4q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
AMP PEAK 5(4Q12) MUTATED	5	18	0	6	1
AMP PEAK 5(4Q12) WILD-TYPE	125	97	105	127	29

Figure S30. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_4q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S31. Gene #5: 'amp_4q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 5(4Q12) MUTATED	5	8	0	2	0	11	4
AMP PEAK 5(4Q12) WILD-TYPE	130	63	36	66	90	30	68

Figure S31. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_4q12' versus 'MIRSEQ_CNMF'

P value = 0.00303 (Fisher's exact test), Q value = 0.0072

Table S32. Gene #5: 'amp_4q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
AMP PEAK 5(4Q12) MUTATED	6	15	2	7
AMP PEAK 5(4Q12) WILD-TYPE	134	92	80	173

Figure S32. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_4q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00042

Table S33. Gene #5: 'amp_4q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 5(4Q12) MUTATED	7	7	16
AMP PEAK 5(4Q12) WILD-TYPE	215	177	87

Figure S33. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_4q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00251 (Fisher's exact test), Q value = 0.0061

Table S34. Gene #5: 'amp_4q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
AMP PEAK 5(4Q12) MUTATED	5	16	2	7
AMP PEAK 5(4Q12) WILD-TYPE	122	103	103	147

Figure S34. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_4q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.0019

Table S35. Gene #5: 'amp_4q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
AMP PEAK 5(4Q12) MUTATED	3	12	5	0	7	3
AMP PEAK 5(4Q12) WILD-TYPE	96	65	113	56	56	89

Figure S35. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S36. Gene #6: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
AMP PEAK 6(7P11.2) MUTATED	46	72	9
AMP PEAK 6(7P11.2) WILD-TYPE	181	39	166

Figure S36. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S37. Gene #6: 'amp_7p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
AMP PEAK 6(7P11.2) MUTATED	39	72	14	2
AMP PEAK 6(7P11.2) WILD-TYPE	170	62	143	11

Figure S37. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'RPPA_CNMF'

P value = 0.0015 (Fisher's exact test), Q value = 0.0039

Table S38. Gene #6: 'amp_7p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	95	125	115
AMP PEAK 6(7P11.2) MUTATED	23	36	20	22
AMP PEAK 6(7P11.2) WILD-TYPE	68	59	105	93

Figure S38. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_7p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00326 (Fisher's exact test), Q value = 0.0076

Table S39. Gene #6: 'amp_7p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	158	185
AMP PEAK 6(7P11.2) MUTATED	12	31	58
AMP PEAK 6(7P11.2) WILD-TYPE	71	127	127

Figure S39. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S40. Gene #6: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
AMP PEAK 6(7P11.2) MUTATED	22	66	9	25	5
AMP PEAK 6(7P11.2) WILD-TYPE	108	49	96	108	25

Figure S40. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S41. Gene #6: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 6(7P11.2) MUTATED	19	57	3	26	7	9	6
AMP PEAK 6(7P11.2) WILD-TYPE	116	14	33	42	83	32	66

Figure S41. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 5e-04

Table S42. Gene #6: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
AMP PEAK 6(7P11.2) MUTATED	45	37	11	32
AMP PEAK 6(7P11.2) WILD-TYPE	95	70	71	148

Figure S42. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S43. Gene #6: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 6(7P11.2) MUTATED	36	28	61
AMP PEAK 6(7P11.2) WILD-TYPE	186	156	42

Figure S43. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S44. Gene #6: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
AMP PEAK 6(7P11.2) MUTATED	33	50	9	32
AMP PEAK 6(7P11.2) WILD-TYPE	94	69	96	122

Figure S44. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S45. Gene #6: 'amp_7p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
AMP PEAK 6(7P11.2) MUTATED	15	12	20	7	53	17
AMP PEAK 6(7P11.2) WILD-TYPE	84	65	98	49	10	75

Figure S45. Get High-res Image Gene #6: 'amp_7p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S46. Gene #7: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
AMP PEAK 7(7Q31.2) MUTATED	69	79	25
AMP PEAK 7(7Q31.2) WILD-TYPE	158	32	150

Figure S46. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q31.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S47. Gene #7: 'amp_7q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
AMP PEAK 7(7Q31.2) MUTATED	74	68	28	3
AMP PEAK 7(7Q31.2) WILD-TYPE	135	66	129	10

Figure S47. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S48. Gene #7: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
AMP PEAK 7(7Q31.2) MUTATED	47	64	15	39	8
AMP PEAK 7(7Q31.2) WILD-TYPE	83	51	90	94	22

Figure S48. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S49. Gene #7: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 7(7Q31.2) MUTATED	44	53	6	32	14	9	15
AMP PEAK 7(7Q31.2) WILD-TYPE	91	18	30	36	76	32	57

Figure S49. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.022

Table S50. Gene #7: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
AMP PEAK 7(7Q31.2) MUTATED	56	44	19	52
AMP PEAK 7(7Q31.2) WILD-TYPE	84	63	63	128

Figure S50. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S51. Gene #7: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 7(7Q31.2) MUTATED	64	48	59
AMP PEAK 7(7Q31.2) WILD-TYPE	158	136	44

Figure S51. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0019

Table S52. Gene #7: 'amp_7q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
AMP PEAK 7(7Q31.2) MUTATED	43	55	21	51
AMP PEAK 7(7Q31.2) WILD-TYPE	84	64	84	103

Figure S52. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S53. Gene #7: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
AMP PEAK 7(7Q31.2) MUTATED	27	18	32	9	49	35
AMP PEAK 7(7Q31.2) WILD-TYPE	72	59	86	47	14	57

Figure S53. Get High-res Image Gene #7: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q32.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S54. Gene #8: 'amp_7q32.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
AMP PEAK 8(7Q32.3) MUTATED	75	80	26
AMP PEAK 8(7Q32.3) WILD-TYPE	152	31	149

Figure S54. Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q32.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S55. Gene #8: 'amp_7q32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
AMP PEAK 8(7Q32.3) MUTATED	80	69	29	3
AMP PEAK 8(7Q32.3) WILD-TYPE	129	65	128	10

Figure S55. Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7q32.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S56. Gene #8: 'amp_7q32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
AMP PEAK 8(7Q32.3) MUTATED	51	64	16	42	8
AMP PEAK 8(7Q32.3) WILD-TYPE	79	51	89	91	22

Figure S56. Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q32.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S57. Gene #8: 'amp_7q32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 8(7Q32.3) MUTATED	47	53	6	36	15	9	15
AMP PEAK 8(7Q32.3) WILD-TYPE	88	18	30	32	75	32	57

Figure S57. Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q32.3' versus 'MIRSEQ_CNMF'

P value = 0.0335 (Fisher's exact test), Q value = 0.059

Table S58. Gene #8: 'amp_7q32.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
AMP PEAK 8(7Q32.3) MUTATED	58	44	21	56
AMP PEAK 8(7Q32.3) WILD-TYPE	82	63	61	124

Figure S58. Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7q32.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S59. Gene #8: 'amp_7q32.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 8(7Q32.3) MUTATED	67	52	60
AMP PEAK 8(7Q32.3) WILD-TYPE	155	132	43

Figure S59. Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7q32.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.0025

Table S60. Gene #8: 'amp_7q32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
AMP PEAK 8(7Q32.3) MUTATED	45	57	23	53
AMP PEAK 8(7Q32.3) WILD-TYPE	82	62	82	101

Figure S60. Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7q32.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S61. Gene #8: 'amp_7q32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
AMP PEAK 8(7Q32.3) MUTATED	31	19	34	10	49	35
AMP PEAK 8(7Q32.3) WILD-TYPE	68	58	84	46	14	57

Figure S61. Get High-res Image Gene #8: 'amp_7q32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S62. Gene #9: 'amp_8q24.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
AMP PEAK 9(8Q24.13) MUTATED	65	26	8
AMP PEAK 9(8Q24.13) WILD-TYPE	162	85	167

Figure S62. Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S63. Gene #9: 'amp_8q24.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
AMP PEAK 9(8Q24.13) MUTATED	79	8	10	2
AMP PEAK 9(8Q24.13) WILD-TYPE	130	126	147	11

Figure S63. Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S64. Gene #9: 'amp_8q24.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
AMP PEAK 9(8Q24.13) MUTATED	46	14	5	26	8
AMP PEAK 9(8Q24.13) WILD-TYPE	84	101	100	107	22

Figure S64. Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S65. Gene #9: 'amp_8q24.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 9(8Q24.13) MUTATED	52	3	2	20	5	8	9
AMP PEAK 9(8Q24.13) WILD-TYPE	83	68	34	48	85	33	63

Figure S65. Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.13' versus 'MIRSEQ_CNMF'

P value = 0.00835 (Fisher's exact test), Q value = 0.018

Table S66. Gene #9: 'amp_8q24.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
AMP PEAK 9(8Q24.13) MUTATED	35	20	6	36
AMP PEAK 9(8Q24.13) WILD-TYPE	105	87	76	144

Figure S66. Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.0013

Table S67. Gene #9: 'amp_8q24.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 9(8Q24.13) MUTATED	58	30	9
AMP PEAK 9(8Q24.13) WILD-TYPE	164	154	94

Figure S67. Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.029

Table S68. Gene #9: 'amp_8q24.13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
AMP PEAK 9(8Q24.13) MUTATED	37	21	15	24
AMP PEAK 9(8Q24.13) WILD-TYPE	90	98	90	130

Figure S68. Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S69. Gene #9: 'amp_8q24.13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
AMP PEAK 9(8Q24.13) MUTATED	34	15	14	2	3	29
AMP PEAK 9(8Q24.13) WILD-TYPE	65	62	104	54	60	63

Figure S69. Get High-res Image Gene #9: 'amp_8q24.13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9q34.3' versus 'CN_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 0.04

Table S70. Gene #10: 'amp_9q34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
AMP PEAK 10(9Q34.3) MUTATED	23	15	8
AMP PEAK 10(9Q34.3) WILD-TYPE	204	96	167

Figure S70. Get High-res Image Gene #10: 'amp_9q34.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_9q34.3' versus 'METHLYATION_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.021

Table S71. Gene #10: 'amp_9q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
AMP PEAK 10(9Q34.3) MUTATED	24	10	8	4
AMP PEAK 10(9Q34.3) WILD-TYPE	185	124	149	9

Figure S71. Get High-res Image Gene #10: 'amp_9q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_9q34.3' versus 'RPPA_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.035

Table S72. Gene #10: 'amp_9q34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	95	125	115
AMP PEAK 10(9Q34.3) MUTATED	9	15	6	6
AMP PEAK 10(9Q34.3) WILD-TYPE	82	80	119	109

Figure S72. Get High-res Image Gene #10: 'amp_9q34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_9q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00061

Table S73. Gene #10: 'amp_9q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 10(9Q34.3) MUTATED	8	6	3	9	4	13	3
AMP PEAK 10(9Q34.3) WILD-TYPE	127	65	33	59	86	28	69

Figure S73. Get High-res Image Gene #10: 'amp_9q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S74. Gene #11: 'amp_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
AMP PEAK 11(10P15.3) MUTATED	60	11	0
AMP PEAK 11(10P15.3) WILD-TYPE	167	100	175

Figure S74. Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10p15.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S75. Gene #11: 'amp_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
AMP PEAK 11(10P15.3) MUTATED	59	6	0	6
AMP PEAK 11(10P15.3) WILD-TYPE	150	128	157	7

Figure S75. Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_10p15.3' versus 'RPPA_CNMF'

P value = 0.00824 (Fisher's exact test), Q value = 0.017

Table S76. Gene #11: 'amp_10p15.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	95	125	115
AMP PEAK 11(10P15.3) MUTATED	18	15	19	6
AMP PEAK 11(10P15.3) WILD-TYPE	73	80	106	109

Figure S76. Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_10p15.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00135 (Fisher's exact test), Q value = 0.0035

Table S77. Gene #11: 'amp_10p15.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	158	185
AMP PEAK 11(10P15.3) MUTATED	17	10	31
AMP PEAK 11(10P15.3) WILD-TYPE	66	148	154

Figure S77. Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_10p15.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S78. Gene #11: 'amp_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
AMP PEAK 11(10P15.3) MUTATED	37	15	0	16	3
AMP PEAK 11(10P15.3) WILD-TYPE	93	100	105	117	27

Figure S78. Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S79. Gene #11: 'amp_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 11(10P15.3) MUTATED	40	1	0	14	0	12	4
AMP PEAK 11(10P15.3) WILD-TYPE	95	70	36	54	90	29	68

Figure S79. Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10p15.3' versus 'MIRSEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.001

Table S80. Gene #11: 'amp_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
AMP PEAK 11(10P15.3) MUTATED	20	27	4	19
AMP PEAK 11(10P15.3) WILD-TYPE	120	80	78	161

Figure S80. Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_10p15.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00237 (Fisher's exact test), Q value = 0.0059

Table S81. Gene #11: 'amp_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
AMP PEAK 11(10P15.3) MUTATED	24	24	6	16
AMP PEAK 11(10P15.3) WILD-TYPE	103	95	99	138

Figure S81. Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_10p15.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S82. Gene #11: 'amp_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
AMP PEAK 11(10P15.3) MUTATED	28	16	9	0	1	16
AMP PEAK 11(10P15.3) WILD-TYPE	71	61	109	56	62	76

Figure S82. Get High-res Image Gene #11: 'amp_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q24.1' versus 'METHLYATION_CNMF'

P value = 0.00883 (Fisher's exact test), Q value = 0.018

Table S83. Gene #12: 'amp_11q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
AMP PEAK 12(11Q24.1) MUTATED	47	12	26	2
AMP PEAK 12(11Q24.1) WILD-TYPE	162	122	131	11

Figure S83. Get High-res Image Gene #12: 'amp_11q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q24.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0473 (Fisher's exact test), Q value = 0.078

Table S84. Gene #12: 'amp_11q24.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	158	185
AMP PEAK 12(11Q24.1) MUTATED	14	19	41
AMP PEAK 12(11Q24.1) WILD-TYPE	69	139	144

Figure S84. Get High-res Image Gene #12: 'amp_11q24.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_11q24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00858 (Fisher's exact test), Q value = 0.018

Table S85. Gene #12: 'amp_11q24.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
AMP PEAK 12(11Q24.1) MUTATED	22	14	18	10	2	21
AMP PEAK 12(11Q24.1) WILD-TYPE	77	63	100	46	61	71

Figure S85. Get High-res Image Gene #12: 'amp_11q24.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S86. Gene #13: 'amp_12p13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
AMP PEAK 13(12P13.32) MUTATED	45	24	3
AMP PEAK 13(12P13.32) WILD-TYPE	182	87	172

Figure S86. Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p13.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S87. Gene #13: 'amp_12p13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
AMP PEAK 13(12P13.32) MUTATED	55	10	5	2
AMP PEAK 13(12P13.32) WILD-TYPE	154	124	152	11

Figure S87. Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12p13.32' versus 'RPPA_CNMF'

P value = 0.00499 (Fisher's exact test), Q value = 0.011

Table S88. Gene #13: 'amp_12p13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	95	125	115
AMP PEAK 13(12P13.32) MUTATED	13	24	12	11
AMP PEAK 13(12P13.32) WILD-TYPE	78	71	113	104

Figure S88. Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_12p13.32' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00042

Table S89. Gene #13: 'amp_12p13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
AMP PEAK 13(12P13.32) MUTATED	29	22	4	13	4
AMP PEAK 13(12P13.32) WILD-TYPE	101	93	101	120	26

Figure S89. Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12p13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S90. Gene #13: 'amp_12p13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 13(12P13.32) MUTATED	32	8	1	14	4	12	1
AMP PEAK 13(12P13.32) WILD-TYPE	103	63	35	54	86	29	71

Figure S90. Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12p13.32' versus 'MIRSEQ_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.022

Table S91. Gene #13: 'amp_12p13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
AMP PEAK 13(12P13.32) MUTATED	17	26	11	18
AMP PEAK 13(12P13.32) WILD-TYPE	123	81	71	162

Figure S91. Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12p13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00709 (Fisher's exact test), Q value = 0.015

Table S92. Gene #13: 'amp_12p13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 13(12P13.32) MUTATED	36	15	21
AMP PEAK 13(12P13.32) WILD-TYPE	186	169	82

Figure S92. Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00144 (Fisher's exact test), Q value = 0.0037

Table S93. Gene #13: 'amp_12p13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
AMP PEAK 13(12P13.32) MUTATED	23	27	9	13
AMP PEAK 13(12P13.32) WILD-TYPE	104	92	96	141

Figure S93. Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12p13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S94. Gene #13: 'amp_12p13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
AMP PEAK 13(12P13.32) MUTATED	19	22	4	4	7	16
AMP PEAK 13(12P13.32) WILD-TYPE	80	55	114	52	56	76

Figure S94. Get High-res Image Gene #13: 'amp_12p13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S95. Gene #14: 'amp_12q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
AMP PEAK 14(12Q14.1) MUTATED	8	28	1
AMP PEAK 14(12Q14.1) WILD-TYPE	219	83	174

Figure S95. Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q14.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.4e-05

Table S96. Gene #14: 'amp_12q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
AMP PEAK 14(12Q14.1) MUTATED	8	20	4	5
AMP PEAK 14(12Q14.1) WILD-TYPE	201	114	153	8

Figure S96. Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q14.1' versus 'RPPA_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.028

Table S97. Gene #14: 'amp_12q14.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	95	125	115
AMP PEAK 14(12Q14.1) MUTATED	3	13	6	4
AMP PEAK 14(12Q14.1) WILD-TYPE	88	82	119	111

Figure S97. Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S98. Gene #14: 'amp_12q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
AMP PEAK 14(12Q14.1) MUTATED	3	27	3	3	1
AMP PEAK 14(12Q14.1) WILD-TYPE	127	88	102	130	29

Figure S98. Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S99. Gene #14: 'amp_12q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 14(12Q14.1) MUTATED	3	18	1	4	3	8	0
AMP PEAK 14(12Q14.1) WILD-TYPE	132	53	35	64	87	33	72

Figure S99. Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'MIRSEQ_CNMF'

P value = 0.00366 (Fisher's exact test), Q value = 0.0084

Table S100. Gene #14: 'amp_12q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
AMP PEAK 14(12Q14.1) MUTATED	13	15	3	6
AMP PEAK 14(12Q14.1) WILD-TYPE	127	92	79	174

Figure S100. Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S101. Gene #14: 'amp_12q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 14(12Q14.1) MUTATED	10	5	22
AMP PEAK 14(12Q14.1) WILD-TYPE	212	179	81

Figure S101. Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.4e-05

Table S102. Gene #14: 'amp_12q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
AMP PEAK 14(12Q14.1) MUTATED	9	21	1	6
AMP PEAK 14(12Q14.1) WILD-TYPE	118	98	104	148

Figure S102. Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00022

Table S103. Gene #14: 'amp_12q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
AMP PEAK 14(12Q14.1) MUTATED	6	6	2	2	15	6
AMP PEAK 14(12Q14.1) WILD-TYPE	93	71	116	54	48	86

Figure S103. Get High-res Image Gene #14: 'amp_12q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q34' versus 'CN_CNMF'

P value = 0.00314 (Fisher's exact test), Q value = 0.0074

Table S104. Gene #15: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
AMP PEAK 15(13Q34) MUTATED	15	6	1
AMP PEAK 15(13Q34) WILD-TYPE	212	105	174

Figure S104. Get High-res Image Gene #15: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q34' versus 'METHLYATION_CNMF'

P value = 0.00378 (Fisher's exact test), Q value = 0.0085

Table S105. Gene #15: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
AMP PEAK 15(13Q34) MUTATED	14	5	1	2
AMP PEAK 15(13Q34) WILD-TYPE	195	129	156	11

Figure S105. Get High-res Image Gene #15: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0216 (Fisher's exact test), Q value = 0.04

Table S106. Gene #15: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 15(13Q34) MUTATED	8	3	0	4	0	5	2
AMP PEAK 15(13Q34) WILD-TYPE	127	68	36	64	90	36	70

Figure S106. Get High-res Image Gene #15: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0422 (Fisher's exact test), Q value = 0.072

Table S107. Gene #16: 'amp_15q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
AMP PEAK 16(15Q26.3) MUTATED	0	3	0	0
AMP PEAK 16(15Q26.3) WILD-TYPE	7	4	7	6

Figure S107. Get High-res Image Gene #16: 'amp_15q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_15q26.3' versus 'CN_CNMF'

P value = 0.00075 (Fisher's exact test), Q value = 0.0021

Table S108. Gene #16: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
AMP PEAK 16(15Q26.3) MUTATED	12	7	0
AMP PEAK 16(15Q26.3) WILD-TYPE	215	104	175

Figure S108. Get High-res Image Gene #16: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_15q26.3' versus 'METHLYATION_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00077

Table S109. Gene #16: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
AMP PEAK 16(15Q26.3) MUTATED	11	5	0	3
AMP PEAK 16(15Q26.3) WILD-TYPE	198	129	157	10

Figure S109. Get High-res Image Gene #16: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CNMF'

P value = 0.0359 (Fisher's exact test), Q value = 0.062

Table S110. Gene #16: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
AMP PEAK 16(15Q26.3) MUTATED	5	8	0	4	2
AMP PEAK 16(15Q26.3) WILD-TYPE	125	107	105	129	28

Figure S110. Get High-res Image Gene #16: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_15q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0359 (Fisher's exact test), Q value = 0.062

Table S111. Gene #16: 'amp_15q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
AMP PEAK 16(15Q26.3) MUTATED	3	8	2	0	3	3
AMP PEAK 16(15Q26.3) WILD-TYPE	96	69	116	56	60	89

Figure S111. Get High-res Image Gene #16: 'amp_15q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q25.1' versus 'CN_CNMF'

P value = 0.0393 (Fisher's exact test), Q value = 0.067

Table S112. Gene #17: 'amp_17q25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
AMP PEAK 17(17Q25.1) MUTATED	18	16	10
AMP PEAK 17(17Q25.1) WILD-TYPE	209	95	165

Figure S112. Get High-res Image Gene #17: 'amp_17q25.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q25.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0486 (Fisher's exact test), Q value = 0.08

Table S113. Gene #17: 'amp_17q25.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	158	185
AMP PEAK 17(17Q25.1) MUTATED	11	7	12
AMP PEAK 17(17Q25.1) WILD-TYPE	72	151	173

Figure S113. Get High-res Image Gene #17: 'amp_17q25.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q25.1' versus 'MRNASEQ_CNMF'

P value = 0.0336 (Fisher's exact test), Q value = 0.059

Table S114. Gene #17: 'amp_17q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
AMP PEAK 17(17Q25.1) MUTATED	10	18	7	9	0
AMP PEAK 17(17Q25.1) WILD-TYPE	120	97	98	124	30

Figure S114. Get High-res Image Gene #17: 'amp_17q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S115. Gene #18: 'amp_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
AMP PEAK 18(19P13.3) MUTATED	24	29	76
AMP PEAK 18(19P13.3) WILD-TYPE	203	82	99

Figure S115. Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S116. Gene #18: 'amp_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
AMP PEAK 18(19P13.3) MUTATED	19	30	80	0
AMP PEAK 18(19P13.3) WILD-TYPE	190	104	77	13

Figure S116. Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00494 (Fisher's exact test), Q value = 0.011

Table S117. Gene #18: 'amp_19p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	158	185
AMP PEAK 18(19P13.3) MUTATED	12	34	59
AMP PEAK 18(19P13.3) WILD-TYPE	71	124	126

Figure S117. Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_19p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S118. Gene #18: 'amp_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
AMP PEAK 18(19P13.3) MUTATED	10	30	53	34	2
AMP PEAK 18(19P13.3) WILD-TYPE	120	85	52	99	28

Figure S118. Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S119. Gene #18: 'amp_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 18(19P13.3) MUTATED	8	25	18	10	40	6	22
AMP PEAK 18(19P13.3) WILD-TYPE	127	46	18	58	50	35	50

Figure S119. Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.3' versus 'MIRSEQ_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.0016

Table S120. Gene #18: 'amp_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
AMP PEAK 18(19P13.3) MUTATED	26	23	36	44
AMP PEAK 18(19P13.3) WILD-TYPE	114	84	46	136

Figure S120. Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.4e-05

Table S121. Gene #18: 'amp_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
AMP PEAK 18(19P13.3) MUTATED	19	27	46	37
AMP PEAK 18(19P13.3) WILD-TYPE	108	92	59	117

Figure S121. Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S122. Gene #18: 'amp_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
AMP PEAK 18(19P13.3) MUTATED	12	15	30	27	23	22
AMP PEAK 18(19P13.3) WILD-TYPE	87	62	88	29	40	70

Figure S122. Get High-res Image Gene #18: 'amp_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xp11.22' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.4e-05

Table S123. Gene #19: 'amp_xp11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
AMP PEAK 19(XP11.22) MUTATED	33	13	2
AMP PEAK 19(XP11.22) WILD-TYPE	194	98	173

Figure S123. Get High-res Image Gene #19: 'amp_xp11.22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xp11.22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S124. Gene #19: 'amp_xp11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
AMP PEAK 19(XP11.22) MUTATED	38	6	1	3
AMP PEAK 19(XP11.22) WILD-TYPE	171	128	156	10

Figure S124. Get High-res Image Gene #19: 'amp_xp11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xp11.22' versus 'MRNASEQ_CNMF'

P value = 0.0028 (Fisher's exact test), Q value = 0.0067

Table S125. Gene #19: 'amp_xp11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
AMP PEAK 19(XP11.22) MUTATED	18	13	1	13	3
AMP PEAK 19(XP11.22) WILD-TYPE	112	102	104	120	27

Figure S125. Get High-res Image Gene #19: 'amp_xp11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xp11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S126. Gene #19: 'amp_xp11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 19(XP11.22) MUTATED	22	3	0	9	1	8	5
AMP PEAK 19(XP11.22) WILD-TYPE	113	68	36	59	89	33	67

Figure S126. Get High-res Image Gene #19: 'amp_xp11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.029

Table S127. Gene #19: 'amp_xp11.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
AMP PEAK 19(XP11.22) MUTATED	17	15	3	12
AMP PEAK 19(XP11.22) WILD-TYPE	110	104	102	142

Figure S127. Get High-res Image Gene #19: 'amp_xp11.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_xp11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00195 (Fisher's exact test), Q value = 0.0049

Table S128. Gene #19: 'amp_xp11.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
AMP PEAK 19(XP11.22) MUTATED	16	12	8	0	3	8
AMP PEAK 19(XP11.22) WILD-TYPE	83	65	110	56	60	84

Figure S128. Get High-res Image Gene #19: 'amp_xp11.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xp11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S129. Gene #20: 'amp_xp11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
AMP PEAK 20(XP11.22) MUTATED	47	14	2
AMP PEAK 20(XP11.22) WILD-TYPE	180	97	173

Figure S129. Get High-res Image Gene #20: 'amp_xp11.22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xp11.22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S130. Gene #20: 'amp_xp11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
AMP PEAK 20(XP11.22) MUTATED	49	9	1	4
AMP PEAK 20(XP11.22) WILD-TYPE	160	125	156	9

Figure S130. Get High-res Image Gene #20: 'amp_xp11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xp11.22' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00019

Table S131. Gene #20: 'amp_xp11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
AMP PEAK 20(XP11.22) MUTATED	24	19	1	15	4
AMP PEAK 20(XP11.22) WILD-TYPE	106	96	104	118	26

Figure S131. Get High-res Image Gene #20: 'amp_xp11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xp11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S132. Gene #20: 'amp_xp11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
AMP PEAK 20(XP11.22) MUTATED	30	5	0	12	1	11	4
AMP PEAK 20(XP11.22) WILD-TYPE	105	66	36	56	89	30	68

Figure S132. Get High-res Image Gene #20: 'amp_xp11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.22' versus 'MIRSEQ_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.0019

Table S133. Gene #20: 'amp_xp11.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
AMP PEAK 20(XP11.22) MUTATED	22	19	1	20
AMP PEAK 20(XP11.22) WILD-TYPE	118	88	81	160

Figure S133. Get High-res Image Gene #20: 'amp_xp11.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_xp11.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00045

Table S134. Gene #20: 'amp_xp11.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
AMP PEAK 20(XP11.22) MUTATED	26	18	3	15
AMP PEAK 20(XP11.22) WILD-TYPE	101	101	102	139

Figure S134. Get High-res Image Gene #20: 'amp_xp11.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_xp11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.00086

Table S135. Gene #20: 'amp_xp11.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
AMP PEAK 20(XP11.22) MUTATED	22	13	11	0	4	12
AMP PEAK 20(XP11.22) WILD-TYPE	77	64	107	56	59	80

Figure S135. Get High-res Image Gene #20: 'amp_xp11.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.32' versus 'MRNA_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.0018

Table S136. Gene #21: 'del_1p36.32' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S136. Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.32' versus 'MRNA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00061

Table S137. Gene #21: 'del_1p36.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S137. Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S138. Gene #21: 'del_1p36.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
DEL PEAK 1(1P36.32) MUTATED	13	24	169
DEL PEAK 1(1P36.32) WILD-TYPE	214	87	6

Figure S138. Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S139. Gene #21: 'del_1p36.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
DEL PEAK 1(1P36.32) MUTATED	11	38	157	0
DEL PEAK 1(1P36.32) WILD-TYPE	198	96	0	13

Figure S139. Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.32' versus 'RPPA_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0019

Table S140. Gene #21: 'del_1p36.32' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	95	125	115
DEL PEAK 1(1P36.32) MUTATED	25	37	52	64
DEL PEAK 1(1P36.32) WILD-TYPE	66	58	73	51

Figure S140. Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p36.32' versus 'RPPA_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0013

Table S141. Gene #21: 'del_1p36.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	158	185
DEL PEAK 1(1P36.32) MUTATED	26	85	67
DEL PEAK 1(1P36.32) WILD-TYPE	57	73	118

Figure S141. Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1p36.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S142. Gene #21: 'del_1p36.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
DEL PEAK 1(1P36.32) MUTATED	5	22	104	62	13
DEL PEAK 1(1P36.32) WILD-TYPE	125	93	1	71	17

Figure S142. Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S143. Gene #21: 'del_1p36.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 1(1P36.32) MUTATED	7	19	36	5	88	1	50
DEL PEAK 1(1P36.32) WILD-TYPE	128	52	0	63	2	40	22

Figure S143. Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S144. Gene #21: 'del_1p36.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
DEL PEAK 1(1P36.32) MUTATED	35	12	69	90
DEL PEAK 1(1P36.32) WILD-TYPE	105	95	13	90

Figure S144. Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S145. Gene #21: 'del_1p36.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 1(1P36.32) MUTATED	84	101	21
DEL PEAK 1(1P36.32) WILD-TYPE	138	83	82

Figure S145. Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S146. Gene #21: 'del_1p36.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
DEL PEAK 1(1P36.32) MUTATED	23	23	84	76
DEL PEAK 1(1P36.32) WILD-TYPE	104	96	21	78

Figure S146. Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S147. Gene #21: 'del_1p36.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
DEL PEAK 1(1P36.32) MUTATED	7	26	63	55	16	39
DEL PEAK 1(1P36.32) WILD-TYPE	92	51	55	1	47	53

Figure S147. Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p32.3' versus 'MRNA_CNMF'

P value = 0.0283 (Fisher's exact test), Q value = 0.051

Table S148. Gene #22: 'del_1p32.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	10	8
DEL PEAK 2(1P32.3) MUTATED	1	7	2
DEL PEAK 2(1P32.3) WILD-TYPE	8	3	6

Figure S148. Get High-res Image Gene #22: 'del_1p32.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p32.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00061

Table S149. Gene #22: 'del_1p32.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S149. Get High-res Image Gene #22: 'del_1p32.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p32.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S150. Gene #22: 'del_1p32.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
DEL PEAK 2(1P32.3) MUTATED	10	20	166
DEL PEAK 2(1P32.3) WILD-TYPE	217	91	9

Figure S150. Get High-res Image Gene #22: 'del_1p32.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p32.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S151. Gene #22: 'del_1p32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
DEL PEAK 2(1P32.3) MUTATED	5	34	157	0
DEL PEAK 2(1P32.3) WILD-TYPE	204	100	0	13

Figure S151. Get High-res Image Gene #22: 'del_1p32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p32.3' versus 'RPPA_CNMF'

P value = 0.00164 (Fisher's exact test), Q value = 0.0042

Table S152. Gene #22: 'del_1p32.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	95	125	115
DEL PEAK 2(1P32.3) MUTATED	26	31	51	61
DEL PEAK 2(1P32.3) WILD-TYPE	65	64	74	54

Figure S152. Get High-res Image Gene #22: 'del_1p32.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p32.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.0018

Table S153. Gene #22: 'del_1p32.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	158	185
DEL PEAK 2(1P32.3) MUTATED	24	81	64
DEL PEAK 2(1P32.3) WILD-TYPE	59	77	121

Figure S153. Get High-res Image Gene #22: 'del_1p32.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1p32.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S154. Gene #22: 'del_1p32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
DEL PEAK 2(1P32.3) MUTATED	4	17	104	59	12
DEL PEAK 2(1P32.3) WILD-TYPE	126	98	1	74	18

Figure S154. Get High-res Image Gene #22: 'del_1p32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p32.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S155. Gene #22: 'del_1p32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 2(1P32.3) MUTATED	5	16	36	2	88	0	49
DEL PEAK 2(1P32.3) WILD-TYPE	130	55	0	66	2	41	23

Figure S155. Get High-res Image Gene #22: 'del_1p32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p32.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S156. Gene #22: 'del_1p32.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
DEL PEAK 2(1P32.3) MUTATED	35	9	68	84
DEL PEAK 2(1P32.3) WILD-TYPE	105	98	14	96

Figure S156. Get High-res Image Gene #22: 'del_1p32.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p32.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S157. Gene #22: 'del_1p32.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 2(1P32.3) MUTATED	82	96	18
DEL PEAK 2(1P32.3) WILD-TYPE	140	88	85

Figure S157. Get High-res Image Gene #22: 'del_1p32.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p32.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S158. Gene #22: 'del_1p32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
DEL PEAK 2(1P32.3) MUTATED	20	22	83	71
DEL PEAK 2(1P32.3) WILD-TYPE	107	97	22	83

Figure S158. Get High-res Image Gene #22: 'del_1p32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p32.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S159. Gene #22: 'del_1p32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
DEL PEAK 2(1P32.3) MUTATED	7	25	61	55	12	36
DEL PEAK 2(1P32.3) WILD-TYPE	92	52	57	1	51	56

Figure S159. Get High-res Image Gene #22: 'del_1p32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1q43' versus 'CN_CNMF'

P value = 0.0198 (Fisher's exact test), Q value = 0.037

Table S160. Gene #23: 'del_1q43' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
DEL PEAK 3(1Q43) MUTATED	20	11	5
DEL PEAK 3(1Q43) WILD-TYPE	207	100	170

Figure S160. Get High-res Image Gene #23: 'del_1q43' versus Molecular Subtype #3: 'CN_CNMF'

'del_1q43' versus 'METHLYATION_CNMF'

P value = 0.00206 (Fisher's exact test), Q value = 0.0052

Table S161. Gene #23: 'del_1q43' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
DEL PEAK 3(1Q43) MUTATED	20	10	3	3
DEL PEAK 3(1Q43) WILD-TYPE	189	124	154	10

Figure S161. Get High-res Image Gene #23: 'del_1q43' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1q43' versus 'MRNASEQ_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.029

Table S162. Gene #23: 'del_1q43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
DEL PEAK 3(1Q43) MUTATED	14	11	1	9	1
DEL PEAK 3(1Q43) WILD-TYPE	116	104	104	124	29

Figure S162. Get High-res Image Gene #23: 'del_1q43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1q43' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0158 (Fisher's exact test), Q value = 0.03

Table S163. Gene #23: 'del_1q43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 3(1Q43) MUTATED	16	5	1	2	1	5	6
DEL PEAK 3(1Q43) WILD-TYPE	119	66	35	66	89	36	66

Figure S163. Get High-res Image Gene #23: 'del_1q43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1q43' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0195 (Fisher's exact test), Q value = 0.037

Table S164. Gene #23: 'del_1q43' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
DEL PEAK 3(1Q43) MUTATED	16	9	3	7
DEL PEAK 3(1Q43) WILD-TYPE	111	110	102	147

Figure S164. Get High-res Image Gene #23: 'del_1q43' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1q43' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0485 (Fisher's exact test), Q value = 0.08

Table S165. Gene #23: 'del_1q43' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
DEL PEAK 3(1Q43) MUTATED	9	10	8	1	5	2
DEL PEAK 3(1Q43) WILD-TYPE	90	67	110	55	58	90

Figure S165. Get High-res Image Gene #23: 'del_1q43' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q37.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.027

Table S166. Gene #24: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
DEL PEAK 4(2Q37.3) MUTATED	0	4	0	2
DEL PEAK 4(2Q37.3) WILD-TYPE	7	3	7	4

Figure S166. Get High-res Image Gene #24: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S167. Gene #24: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
DEL PEAK 4(2Q37.3) MUTATED	48	24	5
DEL PEAK 4(2Q37.3) WILD-TYPE	179	87	170

Figure S167. Get High-res Image Gene #24: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S168. Gene #24: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
DEL PEAK 4(2Q37.3) MUTATED	59	7	6	5
DEL PEAK 4(2Q37.3) WILD-TYPE	150	127	151	8

Figure S168. Get High-res Image Gene #24: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q37.3' versus 'RPPA_CNMF'

P value = 0.00109 (Fisher's exact test), Q value = 0.0029

Table S169. Gene #24: 'del_2q37.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	95	125	115
DEL PEAK 4(2Q37.3) MUTATED	10	26	19	9
DEL PEAK 4(2Q37.3) WILD-TYPE	81	69	106	106

Figure S169. Get High-res Image Gene #24: 'del_2q37.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_2q37.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0149 (Fisher's exact test), Q value = 0.029

Table S170. Gene #24: 'del_2q37.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	158	185
DEL PEAK 4(2Q37.3) MUTATED	11	15	38
DEL PEAK 4(2Q37.3) WILD-TYPE	72	143	147

Figure S170. Get High-res Image Gene #24: 'del_2q37.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00061

Table S171. Gene #24: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
DEL PEAK 4(2Q37.3) MUTATED	32	23	6	13	3
DEL PEAK 4(2Q37.3) WILD-TYPE	98	92	99	120	27

Figure S171. Get High-res Image Gene #24: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S172. Gene #24: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 4(2Q37.3) MUTATED	31	2	1	16	5	21	1
DEL PEAK 4(2Q37.3) WILD-TYPE	104	69	35	52	85	20	71

Figure S172. Get High-res Image Gene #24: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 0.0264 (Fisher's exact test), Q value = 0.048

Table S173. Gene #24: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
DEL PEAK 4(2Q37.3) MUTATED	27	22	8	19
DEL PEAK 4(2Q37.3) WILD-TYPE	113	85	74	161

Figure S173. Get High-res Image Gene #24: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q37.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0151 (Fisher's exact test), Q value = 0.029

Table S174. Gene #24: 'del_2q37.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
DEL PEAK 4(2Q37.3) MUTATED	27	22	9	17
DEL PEAK 4(2Q37.3) WILD-TYPE	100	97	96	137

Figure S174. Get High-res Image Gene #24: 'del_2q37.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_2q37.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S175. Gene #24: 'del_2q37.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
DEL PEAK 4(2Q37.3) MUTATED	22	23	10	4	1	15
DEL PEAK 4(2Q37.3) WILD-TYPE	77	54	108	52	62	77

Figure S175. Get High-res Image Gene #24: 'del_2q37.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p21.31' versus 'MRNA_CHIERARCHICAL'

P value = 0.00663 (Fisher's exact test), Q value = 0.014

Table S176. Gene #25: 'del_3p21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
DEL PEAK 5(3P21.31) MUTATED	0	4	0	0
DEL PEAK 5(3P21.31) WILD-TYPE	7	3	7	6

Figure S176. Get High-res Image Gene #25: 'del_3p21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p21.31' versus 'CN_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.0025

Table S177. Gene #25: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
DEL PEAK 5(3P21.31) MUTATED	23	19	7
DEL PEAK 5(3P21.31) WILD-TYPE	204	92	168

Figure S177. Get High-res Image Gene #25: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p21.31' versus 'METHLYATION_CNMF'

P value = 0.00353 (Fisher's exact test), Q value = 0.0081

Table S178. Gene #25: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
DEL PEAK 5(3P21.31) MUTATED	28	12	6	3
DEL PEAK 5(3P21.31) WILD-TYPE	181	122	151	10

Figure S178. Get High-res Image Gene #25: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p21.31' versus 'RPPA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00025

Table S179. Gene #25: 'del_3p21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	95	125	115
DEL PEAK 5(3P21.31) MUTATED	5	22	10	5
DEL PEAK 5(3P21.31) WILD-TYPE	86	73	115	110

Figure S179. Get High-res Image Gene #25: 'del_3p21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p21.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0437 (Fisher's exact test), Q value = 0.073

Table S180. Gene #25: 'del_3p21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	158	185
DEL PEAK 5(3P21.31) MUTATED	5	11	26
DEL PEAK 5(3P21.31) WILD-TYPE	78	147	159

Figure S180. Get High-res Image Gene #25: 'del_3p21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00093 (Fisher's exact test), Q value = 0.0025

Table S181. Gene #25: 'del_3p21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 5(3P21.31) MUTATED	15	7	2	7	3	12	3
DEL PEAK 5(3P21.31) WILD-TYPE	120	64	34	61	87	29	69

Figure S181. Get High-res Image Gene #25: 'del_3p21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.0041

Table S182. Gene #25: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
DEL PEAK 5(3P21.31) MUTATED	13	20	8	8
DEL PEAK 5(3P21.31) WILD-TYPE	127	87	74	172

Figure S182. Get High-res Image Gene #25: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00242 (Fisher's exact test), Q value = 0.006

Table S183. Gene #25: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 5(3P21.31) MUTATED	24	8	17
DEL PEAK 5(3P21.31) WILD-TYPE	198	176	86

Figure S183. Get High-res Image Gene #25: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00975 (Fisher's exact test), Q value = 0.02

Table S184. Gene #25: 'del_3p21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
DEL PEAK 5(3P21.31) MUTATED	12	15	5	2	5	9
DEL PEAK 5(3P21.31) WILD-TYPE	87	62	113	54	58	83

Figure S184. Get High-res Image Gene #25: 'del_3p21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q13.31' versus 'CN_CNMF'

P value = 0.00185 (Fisher's exact test), Q value = 0.0047

Table S185. Gene #26: 'del_3q13.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
DEL PEAK 6(3Q13.31) MUTATED	25	10	4
DEL PEAK 6(3Q13.31) WILD-TYPE	202	101	171

Figure S185. Get High-res Image Gene #26: 'del_3q13.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q13.31' versus 'METHLYATION_CNMF'

P value = 0.00932 (Fisher's exact test), Q value = 0.019

Table S186. Gene #26: 'del_3q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
DEL PEAK 6(3Q13.31) MUTATED	24	10	4	1
DEL PEAK 6(3Q13.31) WILD-TYPE	185	124	153	12

Figure S186. Get High-res Image Gene #26: 'del_3q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3q13.31' versus 'RPPA_CNMF'

P value = 0.00967 (Fisher's exact test), Q value = 0.02

Table S187. Gene #26: 'del_3q13.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	95	125	115
DEL PEAK 6(3Q13.31) MUTATED	2	11	17	7
DEL PEAK 6(3Q13.31) WILD-TYPE	89	84	108	108

Figure S187. Get High-res Image Gene #26: 'del_3q13.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3q13.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0192 (Fisher's exact test), Q value = 0.036

Table S188. Gene #26: 'del_3q13.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	158	185
DEL PEAK 6(3Q13.31) MUTATED	3	10	24
DEL PEAK 6(3Q13.31) WILD-TYPE	80	148	161

Figure S188. Get High-res Image Gene #26: 'del_3q13.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0133 (Fisher's exact test), Q value = 0.026

Table S189. Gene #26: 'del_3q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 6(3Q13.31) MUTATED	14	4	1	7	2	8	3
DEL PEAK 6(3Q13.31) WILD-TYPE	121	67	35	61	88	33	69

Figure S189. Get High-res Image Gene #26: 'del_3q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.0013

Table S190. Gene #26: 'del_3q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 6(3Q13.31) MUTATED	16	6	17
DEL PEAK 6(3Q13.31) WILD-TYPE	206	178	86

Figure S190. Get High-res Image Gene #26: 'del_3q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3q29' versus 'CN_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0011

Table S191. Gene #27: 'del_3q29' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
DEL PEAK 7(3Q29) MUTATED	27	15	5
DEL PEAK 7(3Q29) WILD-TYPE	200	96	170

Figure S191. Get High-res Image Gene #27: 'del_3q29' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q29' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.4e-05

Table S192. Gene #27: 'del_3q29' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
DEL PEAK 7(3Q29) MUTATED	28	9	4	6
DEL PEAK 7(3Q29) WILD-TYPE	181	125	153	7

Figure S192. Get High-res Image Gene #27: 'del_3q29' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3q29' versus 'MRNASEQ_CNMF'

P value = 0.00934 (Fisher's exact test), Q value = 0.019

Table S193. Gene #27: 'del_3q29' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
DEL PEAK 7(3Q29) MUTATED	16	16	2	11	2
DEL PEAK 7(3Q29) WILD-TYPE	114	99	103	122	28

Figure S193. Get High-res Image Gene #27: 'del_3q29' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3q29' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00022

Table S194. Gene #27: 'del_3q29' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 7(3Q29) MUTATED	16	5	1	6	2	13	4
DEL PEAK 7(3Q29) WILD-TYPE	119	66	35	62	88	28	68

Figure S194. Get High-res Image Gene #27: 'del_3q29' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3q29' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00439 (Fisher's exact test), Q value = 0.0098

Table S195. Gene #27: 'del_3q29' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 7(3Q29) MUTATED	19	10	18
DEL PEAK 7(3Q29) WILD-TYPE	203	174	85

Figure S195. Get High-res Image Gene #27: 'del_3q29' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S196. Gene #28: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
DEL PEAK 8(4Q34.3) MUTATED	68	14	50	5
DEL PEAK 8(4Q34.3) WILD-TYPE	141	120	107	8

Figure S196. Get High-res Image Gene #28: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q34.3' versus 'RPPA_CNMF'

P value = 0.0421 (Fisher's exact test), Q value = 0.072

Table S197. Gene #28: 'del_4q34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	95	125	115
DEL PEAK 8(4Q34.3) MUTATED	16	34	34	28
DEL PEAK 8(4Q34.3) WILD-TYPE	75	61	91	87

Figure S197. Get High-res Image Gene #28: 'del_4q34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00028

Table S198. Gene #28: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 8(4Q34.3) MUTATED	36	5	17	18	25	16	20
DEL PEAK 8(4Q34.3) WILD-TYPE	99	66	19	50	65	25	52

Figure S198. Get High-res Image Gene #28: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CNMF'

P value = 0.0279 (Fisher's exact test), Q value = 0.05

Table S199. Gene #28: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
DEL PEAK 8(4Q34.3) MUTATED	26	30	30	50
DEL PEAK 8(4Q34.3) WILD-TYPE	114	77	52	130

Figure S199. Get High-res Image Gene #28: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0455 (Fisher's exact test), Q value = 0.076

Table S200. Gene #28: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 8(4Q34.3) MUTATED	62	56	18
DEL PEAK 8(4Q34.3) WILD-TYPE	160	128	85

Figure S200. Get High-res Image Gene #28: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00015

Table S201. Gene #28: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
DEL PEAK 8(4Q34.3) MUTATED	22	30	31	18	4	31
DEL PEAK 8(4Q34.3) WILD-TYPE	77	47	87	38	59	61

Figure S201. Get High-res Image Gene #28: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S202. Gene #29: 'del_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
DEL PEAK 9(5P15.33) MUTATED	27	20	3
DEL PEAK 9(5P15.33) WILD-TYPE	200	91	172

Figure S202. Get High-res Image Gene #29: 'del_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_5p15.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S203. Gene #29: 'del_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
DEL PEAK 9(5P15.33) MUTATED	34	10	3	3
DEL PEAK 9(5P15.33) WILD-TYPE	175	124	154	10

Figure S203. Get High-res Image Gene #29: 'del_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5p15.33' versus 'MRNASEQ_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0024

Table S204. Gene #29: 'del_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
DEL PEAK 9(5P15.33) MUTATED	14	18	1	13	4
DEL PEAK 9(5P15.33) WILD-TYPE	116	97	104	120	26

Figure S204. Get High-res Image Gene #29: 'del_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00019

Table S205. Gene #29: 'del_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 9(5P15.33) MUTATED	17	4	0	9	2	12	6
DEL PEAK 9(5P15.33) WILD-TYPE	118	67	36	59	88	29	66

Figure S205. Get High-res Image Gene #29: 'del_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5p15.33' versus 'MIRSEQ_CNMF'

P value = 0.00451 (Fisher's exact test), Q value = 0.01

Table S206. Gene #29: 'del_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
DEL PEAK 9(5P15.33) MUTATED	10	20	3	17
DEL PEAK 9(5P15.33) WILD-TYPE	130	87	79	163

Figure S206. Get High-res Image Gene #29: 'del_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00373 (Fisher's exact test), Q value = 0.0085

Table S207. Gene #29: 'del_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
DEL PEAK 9(5P15.33) MUTATED	14	20	3	13
DEL PEAK 9(5P15.33) WILD-TYPE	113	99	102	141

Figure S207. Get High-res Image Gene #29: 'del_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S208. Gene #29: 'del_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
DEL PEAK 9(5P15.33) MUTATED	7	20	9	0	4	10
DEL PEAK 9(5P15.33) WILD-TYPE	92	57	109	56	59	82

Figure S208. Get High-res Image Gene #29: 'del_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S209. Gene #30: 'del_5q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
DEL PEAK 10(5Q34) MUTATED	41	19	4
DEL PEAK 10(5Q34) WILD-TYPE	186	92	171

Figure S209. Get High-res Image Gene #30: 'del_5q34' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q34' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S210. Gene #30: 'del_5q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
DEL PEAK 10(5Q34) MUTATED	41	11	3	9
DEL PEAK 10(5Q34) WILD-TYPE	168	123	154	4

Figure S210. Get High-res Image Gene #30: 'del_5q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q34' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00025

Table S211. Gene #30: 'del_5q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
DEL PEAK 10(5Q34) MUTATED	19	24	2	14	5
DEL PEAK 10(5Q34) WILD-TYPE	111	91	103	119	25

Figure S211. Get High-res Image Gene #30: 'del_5q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S212. Gene #30: 'del_5q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 10(5Q34) MUTATED	20	3	0	11	3	22	5
DEL PEAK 10(5Q34) WILD-TYPE	115	68	36	57	87	19	67

Figure S212. Get High-res Image Gene #30: 'del_5q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q34' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00019

Table S213. Gene #30: 'del_5q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
DEL PEAK 10(5Q34) MUTATED	14	29	4	17
DEL PEAK 10(5Q34) WILD-TYPE	126	78	78	163

Figure S213. Get High-res Image Gene #30: 'del_5q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q34' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00817 (Fisher's exact test), Q value = 0.017

Table S214. Gene #30: 'del_5q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
DEL PEAK 10(5Q34) MUTATED	20	23	6	15
DEL PEAK 10(5Q34) WILD-TYPE	107	96	99	139

Figure S214. Get High-res Image Gene #30: 'del_5q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q34' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S215. Gene #30: 'del_5q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
DEL PEAK 10(5Q34) MUTATED	14	23	10	0	3	14
DEL PEAK 10(5Q34) WILD-TYPE	85	54	108	56	60	78

Figure S215. Get High-res Image Gene #30: 'del_5q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00015

Table S216. Gene #31: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
DEL PEAK 11(6P25.3) MUTATED	21	23	6
DEL PEAK 11(6P25.3) WILD-TYPE	206	88	169

Figure S216. Get High-res Image Gene #31: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.026

Table S217. Gene #31: 'del_6p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
DEL PEAK 11(6P25.3) MUTATED	24	14	8	4
DEL PEAK 11(6P25.3) WILD-TYPE	185	120	149	9

Figure S217. Get High-res Image Gene #31: 'del_6p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q22.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S218. Gene #32: 'del_6q22.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
DEL PEAK 12(6Q22.31) MUTATED	31	41	6
DEL PEAK 12(6Q22.31) WILD-TYPE	196	70	169

Figure S218. Get High-res Image Gene #32: 'del_6q22.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q22.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S219. Gene #32: 'del_6q22.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
DEL PEAK 12(6Q22.31) MUTATED	44	23	7	4
DEL PEAK 12(6Q22.31) WILD-TYPE	165	111	150	9

Figure S219. Get High-res Image Gene #32: 'del_6q22.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q22.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0148 (Fisher's exact test), Q value = 0.029

Table S220. Gene #32: 'del_6q22.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	158	185
DEL PEAK 12(6Q22.31) MUTATED	10	17	40
DEL PEAK 12(6Q22.31) WILD-TYPE	73	141	145

Figure S220. Get High-res Image Gene #32: 'del_6q22.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_6q22.31' versus 'MRNASEQ_CNMF'

P value = 0.0037 (Fisher's exact test), Q value = 0.0084

Table S221. Gene #32: 'del_6q22.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
DEL PEAK 12(6Q22.31) MUTATED	25	26	6	17	4
DEL PEAK 12(6Q22.31) WILD-TYPE	105	89	99	116	26

Figure S221. Get High-res Image Gene #32: 'del_6q22.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q22.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00115 (Fisher's exact test), Q value = 0.003

Table S222. Gene #32: 'del_6q22.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 12(6Q22.31) MUTATED	27	16	1	12	6	10	6
DEL PEAK 12(6Q22.31) WILD-TYPE	108	55	35	56	84	31	66

Figure S222. Get High-res Image Gene #32: 'del_6q22.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q22.31' versus 'MIRSEQ_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.002

Table S223. Gene #32: 'del_6q22.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
DEL PEAK 12(6Q22.31) MUTATED	35	17	6	19
DEL PEAK 12(6Q22.31) WILD-TYPE	105	90	76	161

Figure S223. Get High-res Image Gene #32: 'del_6q22.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q22.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00276 (Fisher's exact test), Q value = 0.0067

Table S224. Gene #32: 'del_6q22.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
DEL PEAK 12(6Q22.31) MUTATED	29	21	7	18
DEL PEAK 12(6Q22.31) WILD-TYPE	98	98	98	136

Figure S224. Get High-res Image Gene #32: 'del_6q22.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6q22.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00325 (Fisher's exact test), Q value = 0.0076

Table S225. Gene #32: 'del_6q22.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
DEL PEAK 12(6Q22.31) MUTATED	24	9	13	5	16	8
DEL PEAK 12(6Q22.31) WILD-TYPE	75	68	105	51	47	84

Figure S225. Get High-res Image Gene #32: 'del_6q22.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q26' versus 'MRNA_CNMF'

P value = 0.0471 (Fisher's exact test), Q value = 0.078

Table S226. Gene #33: 'del_6q26' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	10	8
DEL PEAK 13(6Q26) MUTATED	3	0	0
DEL PEAK 13(6Q26) WILD-TYPE	6	10	8

Figure S226. Get High-res Image Gene #33: 'del_6q26' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S227. Gene #33: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
DEL PEAK 13(6Q26) MUTATED	33	42	7
DEL PEAK 13(6Q26) WILD-TYPE	194	69	168

Figure S227. Get High-res Image Gene #33: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S228. Gene #33: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
DEL PEAK 13(6Q26) MUTATED	47	25	7	3
DEL PEAK 13(6Q26) WILD-TYPE	162	109	150	10

Figure S228. Get High-res Image Gene #33: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q26' versus 'RPPA_CHIERARCHICAL'

P value = 0.00914 (Fisher's exact test), Q value = 0.019

Table S229. Gene #33: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	158	185
DEL PEAK 13(6Q26) MUTATED	12	16	41
DEL PEAK 13(6Q26) WILD-TYPE	71	142	144

Figure S229. Get High-res Image Gene #33: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0013

Table S230. Gene #33: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
DEL PEAK 13(6Q26) MUTATED	31	25	6	16	4
DEL PEAK 13(6Q26) WILD-TYPE	99	90	99	117	26

Figure S230. Get High-res Image Gene #33: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00048

Table S231. Gene #33: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 13(6Q26) MUTATED	33	17	1	12	6	7	6
DEL PEAK 13(6Q26) WILD-TYPE	102	54	35	56	84	34	66

Figure S231. Get High-res Image Gene #33: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S232. Gene #33: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
DEL PEAK 13(6Q26) MUTATED	40	16	5	20
DEL PEAK 13(6Q26) WILD-TYPE	100	91	77	160

Figure S232. Get High-res Image Gene #33: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00333 (Fisher's exact test), Q value = 0.0077

Table S233. Gene #33: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
DEL PEAK 13(6Q26) MUTATED	29	22	7	20
DEL PEAK 13(6Q26) WILD-TYPE	98	97	98	134

Figure S233. Get High-res Image Gene #33: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.00098

Table S234. Gene #33: 'del_6q26' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
DEL PEAK 13(6Q26) MUTATED	27	7	13	5	17	9
DEL PEAK 13(6Q26) WILD-TYPE	72	70	105	51	46	83

Figure S234. Get High-res Image Gene #33: 'del_6q26' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7p22.3' versus 'CN_CNMF'

P value = 0.0197 (Fisher's exact test), Q value = 0.037

Table S235. Gene #34: 'del_7p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
DEL PEAK 14(7P22.3) MUTATED	17	2	4
DEL PEAK 14(7P22.3) WILD-TYPE	210	109	171

Figure S235. Get High-res Image Gene #34: 'del_7p22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_8q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S236. Gene #35: 'del_8q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
DEL PEAK 15(8Q24.3) MUTATED	16	13	0
DEL PEAK 15(8Q24.3) WILD-TYPE	211	98	175

Figure S236. Get High-res Image Gene #35: 'del_8q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_8q24.3' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00048

Table S237. Gene #35: 'del_8q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
DEL PEAK 15(8Q24.3) MUTATED	17	11	0	1
DEL PEAK 15(8Q24.3) WILD-TYPE	192	123	157	12

Figure S237. Get High-res Image Gene #35: 'del_8q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8q24.3' versus 'MRNASEQ_CNMF'

P value = 0.0059 (Fisher's exact test), Q value = 0.013

Table S238. Gene #35: 'del_8q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
DEL PEAK 15(8Q24.3) MUTATED	10	11	0	6	2
DEL PEAK 15(8Q24.3) WILD-TYPE	120	104	105	127	28

Figure S238. Get High-res Image Gene #35: 'del_8q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00637 (Fisher's exact test), Q value = 0.014

Table S239. Gene #35: 'del_8q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 15(8Q24.3) MUTATED	10	9	0	4	0	3	3
DEL PEAK 15(8Q24.3) WILD-TYPE	125	62	36	64	90	38	69

Figure S239. Get High-res Image Gene #35: 'del_8q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8q24.3' versus 'MIRSEQ_CNMF'

P value = 0.0433 (Fisher's exact test), Q value = 0.073

Table S240. Gene #35: 'del_8q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
DEL PEAK 15(8Q24.3) MUTATED	12	9	1	7
DEL PEAK 15(8Q24.3) WILD-TYPE	128	98	81	173

Figure S240. Get High-res Image Gene #35: 'del_8q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00333 (Fisher's exact test), Q value = 0.0077

Table S241. Gene #35: 'del_8q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 15(8Q24.3) MUTATED	11	5	13
DEL PEAK 15(8Q24.3) WILD-TYPE	211	179	90

Figure S241. Get High-res Image Gene #35: 'del_8q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0334 (Fisher's exact test), Q value = 0.059

Table S242. Gene #35: 'del_8q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
DEL PEAK 15(8Q24.3) MUTATED	10	11	2	5
DEL PEAK 15(8Q24.3) WILD-TYPE	117	108	103	149

Figure S242. Get High-res Image Gene #35: 'del_8q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.029 (Fisher's exact test), Q value = 0.052

Table S243. Gene #35: 'del_8q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
DEL PEAK 15(8Q24.3) MUTATED	7	5	3	0	8	5
DEL PEAK 15(8Q24.3) WILD-TYPE	92	72	115	56	55	87

Figure S243. Get High-res Image Gene #35: 'del_8q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S244. Gene #36: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
DEL PEAK 16(9P23) MUTATED	65	58	27
DEL PEAK 16(9P23) WILD-TYPE	162	53	148

Figure S244. Get High-res Image Gene #36: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00015

Table S245. Gene #36: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
DEL PEAK 16(9P23) MUTATED	72	42	27	9
DEL PEAK 16(9P23) WILD-TYPE	137	92	130	4

Figure S245. Get High-res Image Gene #36: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p23' versus 'RPPA_CNMF'

P value = 0.00597 (Fisher's exact test), Q value = 0.013

Table S246. Gene #36: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	95	125	115
DEL PEAK 16(9P23) MUTATED	21	42	38	28
DEL PEAK 16(9P23) WILD-TYPE	70	53	87	87

Figure S246. Get High-res Image Gene #36: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p23' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00015

Table S247. Gene #36: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	158	185
DEL PEAK 16(9P23) MUTATED	15	37	77
DEL PEAK 16(9P23) WILD-TYPE	68	121	108

Figure S247. Get High-res Image Gene #36: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.039

Table S248. Gene #36: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
DEL PEAK 16(9P23) MUTATED	34	44	20	44	8
DEL PEAK 16(9P23) WILD-TYPE	96	71	85	89	22

Figure S248. Get High-res Image Gene #36: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00053

Table S249. Gene #36: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 16(9P23) MUTATED	39	27	10	31	15	16	12
DEL PEAK 16(9P23) WILD-TYPE	96	44	26	37	75	25	60

Figure S249. Get High-res Image Gene #36: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0322 (Fisher's exact test), Q value = 0.057

Table S250. Gene #36: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
DEL PEAK 16(9P23) MUTATED	30	21	34	8	27	28
DEL PEAK 16(9P23) WILD-TYPE	69	56	84	48	36	64

Figure S250. Get High-res Image Gene #36: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S251. Gene #37: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
DEL PEAK 17(9P21.3) MUTATED	75	74	27
DEL PEAK 17(9P21.3) WILD-TYPE	152	37	148

Figure S251. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S252. Gene #37: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
DEL PEAK 17(9P21.3) MUTATED	75	65	26	10
DEL PEAK 17(9P21.3) WILD-TYPE	134	69	131	3

Figure S252. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.4e-05

Table S253. Gene #37: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	95	125	115
DEL PEAK 17(9P21.3) MUTATED	22	52	46	29
DEL PEAK 17(9P21.3) WILD-TYPE	69	43	79	86

Figure S253. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S254. Gene #37: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	158	185
DEL PEAK 17(9P21.3) MUTATED	14	38	97
DEL PEAK 17(9P21.3) WILD-TYPE	69	120	88

Figure S254. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S255. Gene #37: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
DEL PEAK 17(9P21.3) MUTATED	38	67	18	45	8
DEL PEAK 17(9P21.3) WILD-TYPE	92	48	87	88	22

Figure S255. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S256. Gene #37: '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	135	71	36	68	90	41	72
DEL PEAK 17(9P21.3) MUTATED	44	47	10	31	13	18	13
DEL PEAK 17(9P21.3) WILD-TYPE	91	24	26	37	77	23	59

Figure S256. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S257. Gene #37: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 17(9P21.3) MUTATED	59	56	60
DEL PEAK 17(9P21.3) WILD-TYPE	163	128	43

Figure S257. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.0023

Table S258. Gene #37: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
DEL PEAK 17(9P21.3) MUTATED	49	55	23	47
DEL PEAK 17(9P21.3) WILD-TYPE	78	64	82	107

Figure S258. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S259. Gene #37: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
DEL PEAK 17(9P21.3) MUTATED	32	26	36	8	45	27
DEL PEAK 17(9P21.3) WILD-TYPE	67	51	82	48	18	65

Figure S259. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S260. Gene #38: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
DEL PEAK 18(10Q26.3) MUTATED	68	73	10
DEL PEAK 18(10Q26.3) WILD-TYPE	159	38	165

Figure S260. Get High-res Image Gene #38: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q26.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S261. Gene #38: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
DEL PEAK 18(10Q26.3) MUTATED	55	77	8	11
DEL PEAK 18(10Q26.3) WILD-TYPE	154	57	149	2

Figure S261. Get High-res Image Gene #38: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q26.3' versus 'RPPA_CNMF'

P value = 0.00156 (Fisher's exact test), Q value = 0.004

Table S262. Gene #38: 'del_10q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	95	125	115
DEL PEAK 18(10Q26.3) MUTATED	20	41	33	23
DEL PEAK 18(10Q26.3) WILD-TYPE	71	54	92	92

Figure S262. Get High-res Image Gene #38: 'del_10q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_10q26.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S263. Gene #38: 'del_10q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	158	185
DEL PEAK 18(10Q26.3) MUTATED	10	31	76
DEL PEAK 18(10Q26.3) WILD-TYPE	73	127	109

Figure S263. Get High-res Image Gene #38: 'del_10q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S264. Gene #38: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
DEL PEAK 18(10Q26.3) MUTATED	32	81	4	27	7
DEL PEAK 18(10Q26.3) WILD-TYPE	98	34	101	106	23

Figure S264. Get High-res Image Gene #38: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S265. Gene #38: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 18(10Q26.3) MUTATED	34	60	3	24	5	22	3
DEL PEAK 18(10Q26.3) WILD-TYPE	101	11	33	44	85	19	69

Figure S265. Get High-res Image Gene #38: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S266. Gene #38: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
DEL PEAK 18(10Q26.3) MUTATED	55	46	11	39
DEL PEAK 18(10Q26.3) WILD-TYPE	85	61	71	141

Figure S266. Get High-res Image Gene #38: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S267. Gene #38: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 18(10Q26.3) MUTATED	49	28	74
DEL PEAK 18(10Q26.3) WILD-TYPE	173	156	29

Figure S267. Get High-res Image Gene #38: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S268. Gene #38: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
DEL PEAK 18(10Q26.3) MUTATED	57	51	12	31
DEL PEAK 18(10Q26.3) WILD-TYPE	70	68	93	123

Figure S268. Get High-res Image Gene #38: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S269. Gene #38: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
DEL PEAK 18(10Q26.3) MUTATED	28	23	20	3	55	22
DEL PEAK 18(10Q26.3) WILD-TYPE	71	54	98	53	8	70

Figure S269. Get High-res Image Gene #38: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'MRNA_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.0013

Table S270. Gene #39: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
DEL PEAK 19(11P15.5) MUTATED	1	6	0	0
DEL PEAK 19(11P15.5) WILD-TYPE	6	1	7	6

Figure S270. Get High-res Image Gene #39: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S271. Gene #39: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
DEL PEAK 19(11P15.5) MUTATED	75	27	2
DEL PEAK 19(11P15.5) WILD-TYPE	152	84	173

Figure S271. Get High-res Image Gene #39: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S272. Gene #39: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
DEL PEAK 19(11P15.5) MUTATED	73	22	0	9
DEL PEAK 19(11P15.5) WILD-TYPE	136	112	157	4

Figure S272. Get High-res Image Gene #39: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S273. Gene #39: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
DEL PEAK 19(11P15.5) MUTATED	36	36	0	24	8
DEL PEAK 19(11P15.5) WILD-TYPE	94	79	105	109	22

Figure S273. Get High-res Image Gene #39: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S274. Gene #39: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 19(11P15.5) MUTATED	38	9	0	18	0	29	10
DEL PEAK 19(11P15.5) WILD-TYPE	97	62	36	50	90	12	62

Figure S274. Get High-res Image Gene #39: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.4e-05

Table S275. Gene #39: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
DEL PEAK 19(11P15.5) MUTATED	23	41	7	33
DEL PEAK 19(11P15.5) WILD-TYPE	117	66	75	147

Figure S275. Get High-res Image Gene #39: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00476 (Fisher's exact test), Q value = 0.011

Table S276. Gene #39: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 19(11P15.5) MUTATED	42	29	33
DEL PEAK 19(11P15.5) WILD-TYPE	180	155	70

Figure S276. Get High-res Image Gene #39: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00675 (Fisher's exact test), Q value = 0.014

Table S277. Gene #39: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
DEL PEAK 19(11P15.5) MUTATED	33	31	11	28
DEL PEAK 19(11P15.5) WILD-TYPE	94	88	94	126

Figure S277. Get High-res Image Gene #39: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S278. Gene #39: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
DEL PEAK 19(11P15.5) MUTATED	21	33	19	0	8	22
DEL PEAK 19(11P15.5) WILD-TYPE	78	44	99	56	55	70

Figure S278. Get High-res Image Gene #39: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0301 (Fisher's exact test), Q value = 0.054

Table S279. Gene #40: 'del_11p15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
DEL PEAK 20(11P15.1) MUTATED	1	4	0	0
DEL PEAK 20(11P15.1) WILD-TYPE	6	3	7	6

Figure S279. Get High-res Image Gene #40: 'del_11p15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11p15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S280. Gene #40: 'del_11p15.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
DEL PEAK 20(11P15.1) MUTATED	47	23	2
DEL PEAK 20(11P15.1) WILD-TYPE	180	88	173

Figure S280. Get High-res Image Gene #40: 'del_11p15.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S281. Gene #40: 'del_11p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
DEL PEAK 20(11P15.1) MUTATED	42	20	1	9
DEL PEAK 20(11P15.1) WILD-TYPE	167	114	156	4

Figure S281. Get High-res Image Gene #40: 'del_11p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11p15.1' versus 'RPPA_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.0037

Table S282. Gene #40: 'del_11p15.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	95	125	115
DEL PEAK 20(11P15.1) MUTATED	16	21	7	13
DEL PEAK 20(11P15.1) WILD-TYPE	75	74	118	102

Figure S282. Get High-res Image Gene #40: 'del_11p15.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_11p15.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S283. Gene #40: 'del_11p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
DEL PEAK 20(11P15.1) MUTATED	16	35	1	13	7
DEL PEAK 20(11P15.1) WILD-TYPE	114	80	104	120	23

Figure S283. Get High-res Image Gene #40: 'del_11p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11p15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S284. Gene #40: 'del_11p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 20(11P15.1) MUTATED	20	9	0	6	1	29	7
DEL PEAK 20(11P15.1) WILD-TYPE	115	62	36	62	89	12	65

Figure S284. Get High-res Image Gene #40: 'del_11p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.1' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S285. Gene #40: 'del_11p15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
DEL PEAK 20(11P15.1) MUTATED	16	32	5	19
DEL PEAK 20(11P15.1) WILD-TYPE	124	75	77	161

Figure S285. Get High-res Image Gene #40: 'del_11p15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11p15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00025

Table S286. Gene #40: 'del_11p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 20(11P15.1) MUTATED	27	16	29
DEL PEAK 20(11P15.1) WILD-TYPE	195	168	74

Figure S286. Get High-res Image Gene #40: 'del_11p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0022

Table S287. Gene #40: 'del_11p15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
DEL PEAK 20(11P15.1) MUTATED	22	27	6	16
DEL PEAK 20(11P15.1) WILD-TYPE	105	92	99	138

Figure S287. Get High-res Image Gene #40: 'del_11p15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11p15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S288. Gene #40: 'del_11p15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
DEL PEAK 20(11P15.1) MUTATED	13	29	11	0	9	9
DEL PEAK 20(11P15.1) WILD-TYPE	86	48	107	56	54	83

Figure S288. Get High-res Image Gene #40: 'del_11p15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12p13.1' versus 'CN_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.022

Table S289. Gene #41: 'del_12p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
DEL PEAK 21(12P13.1) MUTATED	23	10	5
DEL PEAK 21(12P13.1) WILD-TYPE	204	101	170

Figure S289. Get High-res Image Gene #41: 'del_12p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S290. Gene #41: 'del_12p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
DEL PEAK 21(12P13.1) MUTATED	21	6	5	6
DEL PEAK 21(12P13.1) WILD-TYPE	188	128	152	7

Figure S290. Get High-res Image Gene #41: 'del_12p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12p13.1' versus 'MRNASEQ_CNMF'

P value = 0.00221 (Fisher's exact test), Q value = 0.0055

Table S291. Gene #41: 'del_12p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
DEL PEAK 21(12P13.1) MUTATED	15	13	1	9	0
DEL PEAK 21(12P13.1) WILD-TYPE	115	102	104	124	30

Figure S291. Get High-res Image Gene #41: 'del_12p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00693 (Fisher's exact test), Q value = 0.015

Table S292. Gene #41: '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	135	71	36	68	90	41	72
DEL PEAK 21(12P13.1) MUTATED	15	4	1	3	3	9	3
DEL PEAK 21(12P13.1) WILD-TYPE	120	67	35	65	87	32	69

Figure S292. Get High-res Image Gene #41: 'del_12p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.04

Table S293. Gene #41: 'del_12p13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
DEL PEAK 21(12P13.1) MUTATED	7	16	5	10
DEL PEAK 21(12P13.1) WILD-TYPE	133	91	77	170

Figure S293. Get High-res Image Gene #41: 'del_12p13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_12p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0449 (Fisher's exact test), Q value = 0.075

Table S294. Gene #41: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 21(12P13.1) MUTATED	13	11	14
DEL PEAK 21(12P13.1) WILD-TYPE	209	173	89

Figure S294. Get High-res Image Gene #41: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q12' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.4e-05

Table S295. Gene #42: 'del_12q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
DEL PEAK 22(12Q12) MUTATED	50	12	10
DEL PEAK 22(12Q12) WILD-TYPE	177	99	165

Figure S295. Get High-res Image Gene #42: 'del_12q12' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S296. Gene #42: 'del_12q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
DEL PEAK 22(12Q12) MUTATED	45	12	8	7
DEL PEAK 22(12Q12) WILD-TYPE	164	122	149	6

Figure S296. Get High-res Image Gene #42: 'del_12q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12q12' versus 'MRNASEQ_CNMF'

P value = 0.00312 (Fisher's exact test), Q value = 0.0074

Table S297. Gene #42: 'del_12q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
DEL PEAK 22(12Q12) MUTATED	23	22	4	18	5
DEL PEAK 22(12Q12) WILD-TYPE	107	93	101	115	25

Figure S297. Get High-res Image Gene #42: 'del_12q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S298. Gene #42: 'del_12q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 22(12Q12) MUTATED	25	4	3	11	4	18	7
DEL PEAK 22(12Q12) WILD-TYPE	110	67	33	57	86	23	65

Figure S298. Get High-res Image Gene #42: 'del_12q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q12' versus 'MIRSEQ_CNMF'

P value = 0.00567 (Fisher's exact test), Q value = 0.012

Table S299. Gene #42: 'del_12q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
DEL PEAK 22(12Q12) MUTATED	14	27	9	22
DEL PEAK 22(12Q12) WILD-TYPE	126	80	73	158

Figure S299. Get High-res Image Gene #42: 'del_12q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_12q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.0011

Table S300. Gene #42: 'del_12q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
DEL PEAK 22(12Q12) MUTATED	16	22	13	4	2	15
DEL PEAK 22(12Q12) WILD-TYPE	83	55	105	52	61	77

Figure S300. Get High-res Image Gene #42: 'del_12q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00025

Table S301. Gene #43: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
DEL PEAK 23(13Q14.2) MUTATED	2	7	0	0
DEL PEAK 23(13Q14.2) WILD-TYPE	5	0	7	6

Figure S301. Get High-res Image Gene #43: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S302. Gene #43: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
DEL PEAK 23(13Q14.2) MUTATED	59	57	28
DEL PEAK 23(13Q14.2) WILD-TYPE	168	54	147

Figure S302. Get High-res Image Gene #43: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00061

Table S303. Gene #43: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
DEL PEAK 23(13Q14.2) MUTATED	70	39	27	8
DEL PEAK 23(13Q14.2) WILD-TYPE	139	95	130	5

Figure S303. Get High-res Image Gene #43: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'RPPA_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 0.053

Table S304. Gene #43: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	95	125	115
DEL PEAK 23(13Q14.2) MUTATED	20	38	30	32
DEL PEAK 23(13Q14.2) WILD-TYPE	71	57	95	83

Figure S304. Get High-res Image Gene #43: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00045

Table S305. Gene #43: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
DEL PEAK 23(13Q14.2) MUTATED	39	49	16	32	8
DEL PEAK 23(13Q14.2) WILD-TYPE	91	66	89	101	22

Figure S305. Get High-res Image Gene #43: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S306. Gene #43: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 23(13Q14.2) MUTATED	44	22	2	17	18	25	16
DEL PEAK 23(13Q14.2) WILD-TYPE	91	49	34	51	72	16	56

Figure S306. Get High-res Image Gene #43: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 0.0358 (Fisher's exact test), Q value = 0.062

Table S307. Gene #43: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
DEL PEAK 23(13Q14.2) MUTATED	40	41	22	40
DEL PEAK 23(13Q14.2) WILD-TYPE	100	66	60	140

Figure S307. Get High-res Image Gene #43: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00393 (Fisher's exact test), Q value = 0.0089

Table S308. Gene #43: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 23(13Q14.2) MUTATED	67	37	39
DEL PEAK 23(13Q14.2) WILD-TYPE	155	147	64

Figure S308. Get High-res Image Gene #43: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.023

Table S309. Gene #43: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
DEL PEAK 23(13Q14.2) MUTATED	24	31	25	10	21	32
DEL PEAK 23(13Q14.2) WILD-TYPE	75	46	93	46	42	60

Figure S309. Get High-res Image Gene #43: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S310. Gene #44: 'del_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
DEL PEAK 24(13Q34) MUTATED	34	50	26
DEL PEAK 24(13Q34) WILD-TYPE	193	61	149

Figure S310. Get High-res Image Gene #44: 'del_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q34' versus 'METHLYATION_CNMF'

P value = 0.026 (Fisher's exact test), Q value = 0.047

Table S311. Gene #44: 'del_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
DEL PEAK 24(13Q34) MUTATED	44	35	25	6
DEL PEAK 24(13Q34) WILD-TYPE	165	99	132	7

Figure S311. Get High-res Image Gene #44: 'del_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q34' versus 'RPPA_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 0.04

Table S312. Gene #44: 'del_13q34' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	95	125	115
DEL PEAK 24(13Q34) MUTATED	14	30	20	25
DEL PEAK 24(13Q34) WILD-TYPE	77	65	105	90

Figure S312. Get High-res Image Gene #44: 'del_13q34' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q34' versus 'MRNASEQ_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.027

Table S313. Gene #44: 'del_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
DEL PEAK 24(13Q34) MUTATED	28	38	16	23	5
DEL PEAK 24(13Q34) WILD-TYPE	102	77	89	110	25

Figure S313. Get High-res Image Gene #44: 'del_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00105 (Fisher's exact test), Q value = 0.0028

Table S314. Gene #44: 'del_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 24(13Q34) MUTATED	31	20	2	9	17	18	13
DEL PEAK 24(13Q34) WILD-TYPE	104	51	34	59	73	23	59

Figure S314. Get High-res Image Gene #44: 'del_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q34' versus 'MIRSEQ_CNMF'

P value = 0.0467 (Fisher's exact test), Q value = 0.078

Table S315. Gene #44: 'del_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
DEL PEAK 24(13Q34) MUTATED	28	33	18	30
DEL PEAK 24(13Q34) WILD-TYPE	112	74	64	150

Figure S315. Get High-res Image Gene #44: 'del_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00276 (Fisher's exact test), Q value = 0.0067

Table S316. Gene #44: 'del_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 24(13Q34) MUTATED	49	27	33
DEL PEAK 24(13Q34) WILD-TYPE	173	157	70

Figure S316. Get High-res Image Gene #44: 'del_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q34' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0298 (Fisher's exact test), Q value = 0.053

Table S317. Gene #44: 'del_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
DEL PEAK 24(13Q34) MUTATED	15	20	19	9	19	27
DEL PEAK 24(13Q34) WILD-TYPE	84	57	99	47	44	65

Figure S317. Get High-res Image Gene #44: 'del_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S318. Gene #45: 'del_14q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
DEL PEAK 25(14Q24.3) MUTATED	36	53	33
DEL PEAK 25(14Q24.3) WILD-TYPE	191	58	142

Figure S318. Get High-res Image Gene #45: 'del_14q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q24.3' versus 'RPPA_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.002

Table S319. Gene #45: 'del_14q24.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	95	125	115
DEL PEAK 25(14Q24.3) MUTATED	11	36	31	26
DEL PEAK 25(14Q24.3) WILD-TYPE	80	59	94	89

Figure S319. Get High-res Image Gene #45: 'del_14q24.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_14q24.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.04

Table S320. Gene #45: 'del_14q24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	158	185
DEL PEAK 25(14Q24.3) MUTATED	14	33	57
DEL PEAK 25(14Q24.3) WILD-TYPE	69	125	128

Figure S320. Get High-res Image Gene #45: 'del_14q24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_14q24.3' versus 'MRNASEQ_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0015

Table S321. Gene #45: 'del_14q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
DEL PEAK 25(14Q24.3) MUTATED	24	45	23	22	8
DEL PEAK 25(14Q24.3) WILD-TYPE	106	70	82	111	22

Figure S321. Get High-res Image Gene #45: 'del_14q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.0017

Table S322. Gene #45: 'del_14q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 25(14Q24.3) MUTATED	33	27	8	12	17	17	8
DEL PEAK 25(14Q24.3) WILD-TYPE	102	44	28	56	73	24	64

Figure S322. Get High-res Image Gene #45: 'del_14q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q24.3' versus 'MIRSEQ_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0012

Table S323. Gene #45: 'del_14q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
DEL PEAK 25(14Q24.3) MUTATED	52	20	17	32
DEL PEAK 25(14Q24.3) WILD-TYPE	88	87	65	148

Figure S323. Get High-res Image Gene #45: 'del_14q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_14q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00416 (Fisher's exact test), Q value = 0.0093

Table S324. Gene #45: 'del_14q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 25(14Q24.3) MUTATED	55	31	35
DEL PEAK 25(14Q24.3) WILD-TYPE	167	153	68

Figure S324. Get High-res Image Gene #45: 'del_14q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0062 (Fisher's exact test), Q value = 0.013

Table S325. Gene #45: 'del_14q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
DEL PEAK 25(14Q24.3) MUTATED	37	37	24	23
DEL PEAK 25(14Q24.3) WILD-TYPE	90	82	81	131

Figure S325. Get High-res Image Gene #45: 'del_14q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_14q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00174 (Fisher's exact test), Q value = 0.0044

Table S326. Gene #45: 'del_14q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
DEL PEAK 25(14Q24.3) MUTATED	27	25	18	13	24	14
DEL PEAK 25(14Q24.3) WILD-TYPE	72	52	100	43	39	78

Figure S326. Get High-res Image Gene #45: 'del_14q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.42' versus 'MRNA_CNMF'

P value = 0.0347 (Fisher's exact test), Q value = 0.06

Table S327. Gene #47: 'del_19q13.42' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	10	8
DEL PEAK 27(19Q13.42) MUTATED	7	10	4
DEL PEAK 27(19Q13.42) WILD-TYPE	2	0	4

Figure S327. Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19q13.42' versus 'MRNA_CHIERARCHICAL'

P value = 0.021 (Fisher's exact test), Q value = 0.039

Table S328. Gene #47: 'del_19q13.42' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
DEL PEAK 27(19Q13.42) MUTATED	4	7	7	3
DEL PEAK 27(19Q13.42) WILD-TYPE	3	0	0	3

Figure S328. Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19q13.42' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S329. Gene #47: 'del_19q13.42' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
DEL PEAK 27(19Q13.42) MUTATED	63	44	171
DEL PEAK 27(19Q13.42) WILD-TYPE	164	67	4

Figure S329. Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.42' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S330. Gene #47: 'del_19q13.42' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
DEL PEAK 27(19Q13.42) MUTATED	78	35	157	8
DEL PEAK 27(19Q13.42) WILD-TYPE	131	99	0	5

Figure S330. Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.42' versus 'RPPA_CNMF'

P value = 0.0064 (Fisher's exact test), Q value = 0.014

Table S331. Gene #47: 'del_19q13.42' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	95	125	115
DEL PEAK 27(19Q13.42) MUTATED	36	56	72	72
DEL PEAK 27(19Q13.42) WILD-TYPE	55	39	53	43

Figure S331. Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19q13.42' versus 'RPPA_CHIERARCHICAL'

P value = 0.021 (Fisher's exact test), Q value = 0.039

Table S332. Gene #47: 'del_19q13.42' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	158	185
DEL PEAK 27(19Q13.42) MUTATED	36	98	102
DEL PEAK 27(19Q13.42) WILD-TYPE	47	60	83

Figure S332. Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_19q13.42' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S333. Gene #47: 'del_19q13.42' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
DEL PEAK 27(19Q13.42) MUTATED	46	37	105	77	13
DEL PEAK 27(19Q13.42) WILD-TYPE	84	78	0	56	17

Figure S333. Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19q13.42' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S334. Gene #47: 'del_19q13.42' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 27(19Q13.42) MUTATED	46	9	36	21	89	23	54
DEL PEAK 27(19Q13.42) WILD-TYPE	89	62	0	47	1	18	18

Figure S334. Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.42' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S335. Gene #47: 'del_19q13.42' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
DEL PEAK 27(19Q13.42) MUTATED	59	38	77	104
DEL PEAK 27(19Q13.42) WILD-TYPE	81	69	5	76

Figure S335. Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19q13.42' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S336. Gene #47: 'del_19q13.42' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 27(19Q13.42) MUTATED	137	119	22
DEL PEAK 27(19Q13.42) WILD-TYPE	85	65	81

Figure S336. Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.42' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S337. Gene #47: 'del_19q13.42' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
DEL PEAK 27(19Q13.42) MUTATED	49	45	95	88
DEL PEAK 27(19Q13.42) WILD-TYPE	78	74	10	66

Figure S337. Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19q13.42' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S338. Gene #47: 'del_19q13.42' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
DEL PEAK 27(19Q13.42) MUTATED	39	51	74	56	4	53
DEL PEAK 27(19Q13.42) WILD-TYPE	60	26	44	0	59	39

Figure S338. Get High-res Image Gene #47: 'del_19q13.42' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.31' versus 'MRNA_CHIERARCHICAL'

P value = 0.0425 (Fisher's exact test), Q value = 0.072

Table S339. Gene #48: 'del_22q13.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	7	7	6
DEL PEAK 28(22Q13.31) MUTATED	2	4	0	0
DEL PEAK 28(22Q13.31) WILD-TYPE	5	3	7	6

Figure S339. Get High-res Image Gene #48: 'del_22q13.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_22q13.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S340. Gene #48: 'del_22q13.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
DEL PEAK 28(22Q13.31) MUTATED	36	37	4
DEL PEAK 28(22Q13.31) WILD-TYPE	191	74	171

Figure S340. Get High-res Image Gene #48: 'del_22q13.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S341. Gene #48: 'del_22q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
DEL PEAK 28(22Q13.31) MUTATED	36	34	4	3
DEL PEAK 28(22Q13.31) WILD-TYPE	173	100	153	10

Figure S341. Get High-res Image Gene #48: 'del_22q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q13.31' versus 'RPPA_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.0024

Table S342. Gene #48: 'del_22q13.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	95	125	115
DEL PEAK 28(22Q13.31) MUTATED	10	27	13	12
DEL PEAK 28(22Q13.31) WILD-TYPE	81	68	112	103

Figure S342. Get High-res Image Gene #48: 'del_22q13.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_22q13.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0429 (Fisher's exact test), Q value = 0.073

Table S343. Gene #48: 'del_22q13.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	158	185
DEL PEAK 28(22Q13.31) MUTATED	10	16	36
DEL PEAK 28(22Q13.31) WILD-TYPE	73	142	149

Figure S343. Get High-res Image Gene #48: 'del_22q13.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_22q13.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S344. Gene #48: 'del_22q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
DEL PEAK 28(22Q13.31) MUTATED	14	40	2	15	6
DEL PEAK 28(22Q13.31) WILD-TYPE	116	75	103	118	24

Figure S344. Get High-res Image Gene #48: 'del_22q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S345. Gene #48: 'del_22q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 28(22Q13.31) MUTATED	17	26	2	14	2	14	2
DEL PEAK 28(22Q13.31) WILD-TYPE	118	45	34	54	88	27	70

Figure S345. Get High-res Image Gene #48: 'del_22q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_CNMF'

P value = 0.05 (Fisher's exact test), Q value = 0.082

Table S346. Gene #48: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
DEL PEAK 28(22Q13.31) MUTATED	26	22	7	22
DEL PEAK 28(22Q13.31) WILD-TYPE	114	85	75	158

Figure S346. Get High-res Image Gene #48: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_22q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S347. Gene #48: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 28(22Q13.31) MUTATED	27	18	32
DEL PEAK 28(22Q13.31) WILD-TYPE	195	166	71

Figure S347. Get High-res Image Gene #48: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00015

Table S348. Gene #48: 'del_22q13.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
DEL PEAK 28(22Q13.31) MUTATED	23	32	6	15
DEL PEAK 28(22Q13.31) WILD-TYPE	104	87	99	139

Figure S348. Get High-res Image Gene #48: 'del_22q13.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_22q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00025

Table S349. Gene #48: 'del_22q13.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
DEL PEAK 28(22Q13.31) MUTATED	10	20	14	3	20	9
DEL PEAK 28(22Q13.31) WILD-TYPE	89	57	104	53	43	83

Figure S349. Get High-res Image Gene #48: 'del_22q13.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xq21.1' versus 'CN_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.023

Table S350. Gene #49: 'del_xq21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	227	111	175
DEL PEAK 29(XQ21.1) MUTATED	23	23	32
DEL PEAK 29(XQ21.1) WILD-TYPE	204	88	143

Figure S350. Get High-res Image Gene #49: 'del_xq21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_xq21.1' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S351. Gene #49: 'del_xq21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	209	134	157	13
DEL PEAK 29(XQ21.1) MUTATED	30	10	30	8
DEL PEAK 29(XQ21.1) WILD-TYPE	179	124	127	5

Figure S351. Get High-res Image Gene #49: 'del_xq21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xq21.1' versus 'RPPA_CNMF'

P value = 0.00108 (Fisher's exact test), Q value = 0.0029

Table S352. Gene #49: 'del_xq21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	95	125	115
DEL PEAK 29(XQ21.1) MUTATED	6	26	20	14
DEL PEAK 29(XQ21.1) WILD-TYPE	85	69	105	101

Figure S352. Get High-res Image Gene #49: 'del_xq21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_xq21.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 0.029

Table S353. Gene #49: 'del_xq21.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	158	185
DEL PEAK 29(XQ21.1) MUTATED	6	22	38
DEL PEAK 29(XQ21.1) WILD-TYPE	77	136	147

Figure S353. Get High-res Image Gene #49: 'del_xq21.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_xq21.1' versus 'MRNASEQ_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.024

Table S354. Gene #49: 'del_xq21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	130	115	105	133	30
DEL PEAK 29(XQ21.1) MUTATED	14	24	23	16	1
DEL PEAK 29(XQ21.1) WILD-TYPE	116	91	82	117	29

Figure S354. Get High-res Image Gene #49: 'del_xq21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_xq21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S355. Gene #49: 'del_xq21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	135	71	36	68	90	41	72
DEL PEAK 29(XQ21.1) MUTATED	13	8	9	8	20	16	4
DEL PEAK 29(XQ21.1) WILD-TYPE	122	63	27	60	70	25	68

Figure S355. Get High-res Image Gene #49: 'del_xq21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_xq21.1' versus 'MIRSEQ_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0015

Table S356. Gene #49: 'del_xq21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	107	82	180
DEL PEAK 29(XQ21.1) MUTATED	14	18	25	21
DEL PEAK 29(XQ21.1) WILD-TYPE	126	89	57	159

Figure S356. Get High-res Image Gene #49: 'del_xq21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_xq21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00053

Table S357. Gene #49: 'del_xq21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	127	119	105	154
DEL PEAK 29(XQ21.1) MUTATED	20	15	30	12
DEL PEAK 29(XQ21.1) WILD-TYPE	107	104	75	142

Figure S357. Get High-res Image Gene #49: 'del_xq21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_xq21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00028

Table S358. Gene #49: 'del_xq21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	77	118	56	63	92
DEL PEAK 29(XQ21.1) MUTATED	12	18	6	13	6	22
DEL PEAK 29(XQ21.1) WILD-TYPE	87	59	112	43	57	70

Figure S358. Get High-res Image Gene #49: 'del_xq21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_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/LGG-TP/22533658/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LGG-TP/22553887/LGG-TP.transferedmergedcluster.txt
Number of patients = 513
Number of significantly focal cnvs = 49
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)

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