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 69 focal events and 12 molecular subtypes across 450 patients, 366 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_2q33.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_5p13.2 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_5q22.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
amp_6p21.1 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_7p21.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8p11.23 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
amp_8p11.21 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_8q12.1 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_11p15.5 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_12p13.33 cnv correlated to 'CN_CNMF'.
amp_13q12.13 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_13q22.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_16p11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_16q12.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17p11.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'METHLYATION_CNMF'.
amp_17q12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_17q24.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
amp_19p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19q13.11 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20p12.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_20p11.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_20q11.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20q12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20q13.12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.11 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_1p33 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_1p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_1q43 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_3p26.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_3p14.2 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
del_4p16.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_4q22.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_4q35.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_5q12.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_5q21.1 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_5q22.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_6p25.3 cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q26 cnv correlated to 'RPPA_CNMF'.
del_8p23.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p22 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8q11.1 cnv correlated to 'CN_CNMF'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_10p15.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q21.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_10q25.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_12p13.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q31.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_15q15.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_15q21.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_15q22.33 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_16q23.1 cnv correlated to 'MRNA_CHIERARCHICAL' and 'MRNASEQ_CHIERARCHICAL'.
del_17p12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17q24.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_18p11.31 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q12.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q21.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_20p12.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_21q11.2 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_22q13.32 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 69 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, 366 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
amp 20q11 21	323 (72%)	127	1e-05 (6.13e-05)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.00948 (0.0278)	4e-05 (0.000211)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.823 (0.905)	0.00166 (0.00592)	1 (1.00)	0.00405 (0.0134)
amp 20q12	324 (72%)	126	1e-05 (6.13e-05)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.0187 (0.0489)	9e-05 (0.000421)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.775 (0.88)	0.00129 (0.00471)	1 (1.00)	0.00559 (0.0176)
amp 20q13 12	326 (72%)	124	1e-05 (6.13e-05)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.0112 (0.0322)	6e-05 (0.000297)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.791 (0.889)	0.00268 (0.00925)	1 (1.00)	0.00589 (0.0184)
amp 17q12	114 (25%)	336	0.025 (0.0622)	0.0142 (0.039)	1e-05 (6.13e-05)	5e-05 (0.000254)	0.669 (0.802)	0.0188 (0.0491)	5e-05 (0.000254)	0.00108 (0.00405)	0.0365 (0.0866)	0.0139 (0.0383)	0.532 (0.688)	0.559 (0.704)
del 8p22	203 (45%)	247	0.00436 (0.0142)	0.00017 (0.000753)	1e-05 (6.13e-05)	3e-05 (0.000167)	0.42 (0.583)	0.0174 (0.0463)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.453 (0.611)	0.0145 (0.0396)	0.762 (0.87)	0.0477 (0.108)
del 14q31 1	150 (33%)	300	1e-05 (6.13e-05)	0.00012 (0.000552)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.019 (0.0492)	0.218 (0.369)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.279 (0.432)	0.0219 (0.0553)	0.27 (0.428)	0.014 (0.0386)
del 17p12	254 (56%)	196	1e-05 (6.13e-05)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.0517 (0.116)	0.00076 (0.00294)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.669 (0.802)	0.0217 (0.0552)	0.608 (0.749)	0.00131 (0.00474)
del 18p11 31	246 (55%)	204	1e-05 (6.13e-05)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.223 (0.372)	0.0045 (0.0144)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.838 (0.917)	0.0111 (0.0321)	0.162 (0.289)	0.0036 (0.0122)
del 18q12 2	274 (61%)	176	1e-05 (6.13e-05)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.361 (0.525)	0.00444 (0.0142)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.914 (0.962)	0.02 (0.0511)	0.151 (0.274)	0.00523 (0.0167)
del 18q21 2	287 (64%)	163	1e-05 (6.13e-05)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.177 (0.308)	0.00707 (0.0217)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.377 (0.543)	0.0345 (0.0824)	0.0939 (0.189)	0.00818 (0.0245)
del 20p12 1	86 (19%)	364	0.048 (0.109)	0.0285 (0.0698)	2e-05 (0.000117)	8e-05 (0.000385)	0.0835 (0.172)	0.0166 (0.0444)	1e-05 (6.13e-05)	3e-05 (0.000167)	0.105 (0.207)	0.0104 (0.0302)	0.802 (0.891)	0.0477 (0.108)
amp 7p21 2	255 (57%)	195	0.00989 (0.0289)	3e-05 (0.000167)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.0804 (0.168)	0.0005 (0.002)	4e-05 (0.000211)	1e-05 (6.13e-05)	0.544 (0.696)	0.455 (0.611)	0.843 (0.921)	0.0342 (0.0819)
amp 8q12 1	236 (52%)	214	0.488 (0.646)	0.00581 (0.0182)	1e-05 (6.13e-05)	0.00387 (0.013)	0.268 (0.428)	0.0192 (0.0493)	8e-05 (0.000385)	4e-05 (0.000211)	0.384 (0.551)	0.0378 (0.0888)	0.272 (0.43)	0.0134 (0.0374)
amp 20p11 21	252 (56%)	198	0.00211 (0.00737)	3e-05 (0.000167)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.00639 (0.0197)	0.07 (0.149)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.166 (0.293)	0.0375 (0.0888)	0.921 (0.964)	0.0504 (0.113)
del 1p36 11	168 (37%)	282	7e-05 (0.000341)	0.00785 (0.0236)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.0947 (0.19)	0.028 (0.0689)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.664 (0.799)	0.0203 (0.0517)	0.92 (0.964)	0.257 (0.416)
amp 8q24 21	260 (58%)	190	0.561 (0.705)	0.0294 (0.0713)	1e-05 (6.13e-05)	0.00014 (0.00063)	0.184 (0.318)	0.0919 (0.187)	0.00021 (0.000915)	5e-05 (0.000254)	0.713 (0.833)	0.0378 (0.0888)	0.264 (0.424)	0.0152 (0.0412)
amp 11p15 5	94 (21%)	356	5e-05 (0.000254)	0.0059 (0.0184)	3e-05 (0.000167)	7e-05 (0.000341)	0.129 (0.243)	0.19 (0.326)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.107 (0.21)	1e-05 (6.13e-05)	0.942 (0.977)	0.276 (0.43)
amp 13q12 13	275 (61%)	175	1e-05 (6.13e-05)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.0789 (0.165)	0.0897 (0.184)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.573 (0.717)	0.81 (0.896)	0.395 (0.561)	0.0161 (0.0435)
amp 16p11 2	126 (28%)	324	0.00041 (0.00166)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.00945 (0.0278)	0.106 (0.208)	0.0276 (0.0683)	0.00116 (0.00433)	1e-05 (6.13e-05)	0.893 (0.948)	0.143 (0.261)	0.959 (0.985)	0.0625 (0.136)
amp 16q12 1	111 (25%)	339	4e-05 (0.000211)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.0298 (0.0719)	0.05 (0.113)	0.0789 (0.165)	0.00102 (0.00384)	1e-05 (6.13e-05)	0.975 (0.994)	0.083 (0.172)	0.556 (0.704)	0.0229 (0.0573)
amp 17q24 1	106 (24%)	344	0.0177 (0.0466)	0.00749 (0.0227)	1e-05 (6.13e-05)	2e-05 (0.000117)	0.327 (0.492)	0.0541 (0.12)	2e-05 (0.000117)	1e-05 (6.13e-05)	0.0122 (0.0345)	0.0546 (0.121)	0.209 (0.355)	0.535 (0.689)
del 4p16 2	139 (31%)	311	0.00073 (0.00286)	0.00159 (0.0057)	1e-05 (6.13e-05)	0.00413 (0.0136)	0.796 (0.889)	0.00437 (0.0142)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.356 (0.522)	0.446 (0.608)	0.145 (0.263)	0.236 (0.388)
del 5q12 1	106 (24%)	344	0.0012 (0.00444)	0.0031 (0.0107)	1e-05 (6.13e-05)	0.0138 (0.0382)	0.0254 (0.0633)	0.194 (0.332)	5e-05 (0.000254)	7e-05 (0.000341)	0.705 (0.826)	0.566 (0.71)	1 (1.00)	0.14 (0.257)
del 8p23 3	189 (42%)	261	0.0122 (0.0345)	0.00016 (0.000716)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.402 (0.566)	0.0549 (0.121)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.22 (0.37)	0.0527 (0.118)	0.892 (0.948)	0.0436 (0.101)
del 12p13 2	60 (13%)	390	0.0104 (0.0302)	0.00321 (0.0109)	1e-05 (6.13e-05)	0.00444 (0.0142)	0.773 (0.88)	0.839 (0.918)	0.00039 (0.00159)	1e-05 (6.13e-05)	0.794 (0.889)	0.356 (0.522)	0.225 (0.375)	0.00195 (0.0069)
del 15q15 2	172 (38%)	278	0.00143 (0.00515)	0.00062 (0.00244)	1e-05 (6.13e-05)	6e-05 (0.000297)	0.012 (0.0342)	0.156 (0.279)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.923 (0.964)	0.559 (0.704)	0.155 (0.279)	0.169 (0.297)
del 15q21 1	169 (38%)	281	0.0192 (0.0493)	0.0147 (0.04)	1e-05 (6.13e-05)	0.00014 (0.00063)	0.0477 (0.108)	0.144 (0.262)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.884 (0.946)	0.677 (0.808)	0.134 (0.25)	0.13 (0.245)
del 22q13 32	160 (36%)	290	0.00054 (0.00215)	0.00026 (0.0011)	1e-05 (6.13e-05)	0.00557 (0.0176)	0.143 (0.261)	0.0116 (0.0331)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.421 (0.583)	0.792 (0.889)	0.731 (0.845)	0.546 (0.696)
amp 13q22 1	277 (62%)	173	9e-05 (0.000421)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.125 (0.239)	0.132 (0.247)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.452 (0.611)	0.996 (1.00)	0.397 (0.563)	0.0765 (0.161)
amp 19q13 11	95 (21%)	355	0.182 (0.316)	0.0311 (0.075)	0.00013 (0.000595)	0.221 (0.371)	0.0168 (0.0447)	0.778 (0.881)	0.373 (0.541)	0.00019 (0.000832)	0.46 (0.616)	0.557 (0.704)	0.0177 (0.0466)	0.00196 (0.00691)
amp 20p12 1	208 (46%)	242	0.0464 (0.106)	0.00087 (0.00332)	1e-05 (6.13e-05)	0.0806 (0.168)	0.0379 (0.0888)	0.475 (0.632)	0.0221 (0.0555)	1e-05 (6.13e-05)	0.261 (0.421)	0.339 (0.506)	0.276 (0.43)	0.527 (0.684)
del 1q43	54 (12%)	396	0.0608 (0.133)	0.502 (0.659)	2e-05 (0.000117)	0.00254 (0.0088)	0.487 (0.645)	0.392 (0.558)	9e-05 (0.000421)	0.00025 (0.00107)	0.142 (0.26)	0.00062 (0.00244)	0.0275 (0.0682)	0.961 (0.986)
del 4q22 1	151 (34%)	299	0.00037 (0.00152)	0.004 (0.0133)	1e-05 (6.13e-05)	0.00079 (0.00303)	0.691 (0.818)	0.416 (0.58)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.391 (0.558)	0.171 (0.3)	0.318 (0.482)	0.204 (0.348)
del 4q35 1	159 (35%)	291	0.00093 (0.00353)	0.00767 (0.0232)	1e-05 (6.13e-05)	3e-05 (0.000167)	0.889 (0.948)	0.285 (0.44)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.367 (0.533)	0.417 (0.58)	0.547 (0.696)	0.914 (0.962)
del 5q21 1	127 (28%)	323	0.277 (0.43)	0.0439 (0.101)	1e-05 (6.13e-05)	0.00443 (0.0142)	0.0475 (0.108)	0.325 (0.49)	0.00703 (0.0216)	0.00029 (0.00121)	0.944 (0.977)	0.892 (0.948)	0.868 (0.932)	0.495 (0.651)
del 5q22 2	130 (29%)	320	0.0136 (0.038)	0.00916 (0.0272)	1e-05 (6.13e-05)	0.0289 (0.0704)	0.0639 (0.138)	0.144 (0.262)	0.00027 (0.00113)	6e-05 (0.000297)	0.913 (0.962)	0.273 (0.43)	0.616 (0.757)	0.455 (0.611)
del 10q21 1	98 (22%)	352	0.00312 (0.0107)	0.0279 (0.0688)	1e-05 (6.13e-05)	4e-05 (0.000211)	0.591 (0.732)	0.14 (0.258)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.752 (0.862)	0.493 (0.649)	0.755 (0.864)	0.728 (0.844)
del 15q11 2	177 (39%)	273	0.00039 (0.00159)	0.00078 (0.003)	1e-05 (6.13e-05)	0.00012 (0.000552)	0.116 (0.223)	0.353 (0.521)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.981 (0.999)	0.777 (0.881)	0.257 (0.416)	0.274 (0.43)
del 15q22 33	161 (36%)	289	0.00035 (0.00145)	0.00042 (0.00169)	1e-05 (6.13e-05)	0.0001 (0.000465)	0.27 (0.429)	0.219 (0.369)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.789 (0.889)	0.851 (0.921)	0.104 (0.206)	0.0778 (0.163)
amp 6p21 1	96 (21%)	354	0.262 (0.422)	5e-05 (0.000254)	1e-05 (6.13e-05)	0.00923 (0.0273)	0.392 (0.558)	0.222 (0.372)	0.0189 (0.0492)	9e-05 (0.000421)	0.706 (0.826)	0.775 (0.88)	0.309 (0.469)	0.4 (0.564)
del 1p33	123 (27%)	327	0.0159 (0.0429)	0.559 (0.704)	1e-05 (6.13e-05)	6e-05 (0.000297)	0.358 (0.524)	0.244 (0.399)	0.00027 (0.00113)	2e-05 (0.000117)	0.718 (0.837)	0.152 (0.274)	1 (1.00)	0.351 (0.518)
del 10p15 3	80 (18%)	370	0.116 (0.223)	0.106 (0.208)	2e-05 (0.000117)	4e-05 (0.000211)	0.736 (0.85)	0.233 (0.385)	0.00031 (0.00129)	0.00014 (0.00063)	0.455 (0.611)	0.178 (0.31)	0.52 (0.678)	0.0218 (0.0552)
del 10q25 2	109 (24%)	341	0.125 (0.239)	0.018 (0.0473)	1e-05 (6.13e-05)	2e-05 (0.000117)	0.116 (0.223)	0.149 (0.271)	1e-05 (6.13e-05)	1e-05 (6.13e-05)	0.963 (0.987)	0.489 (0.646)	0.531 (0.687)	0.741 (0.853)
del 21q11 2	141 (31%)	309	0.0163 (0.0438)	0.0698 (0.149)	1e-05 (6.13e-05)	0.00608 (0.0189)	0.865 (0.931)	0.3 (0.458)	4e-05 (0.000211)	0.0004 (0.00162)	0.937 (0.976)	0.126 (0.239)	0.672 (0.804)	0.346 (0.514)
amp 2q33 1	92 (20%)	358	0.168 (0.296)	0.112 (0.218)	0.00076 (0.00294)	0.00865 (0.0259)	0.235 (0.388)	0.375 (0.541)	0.00017 (0.000753)	0.00209 (0.00733)	0.295 (0.451)	0.106 (0.208)	0.951 (0.98)	0.675 (0.806)
amp 5p13 2	88 (20%)	362	0.381 (0.547)	0.189 (0.325)	0.00023 (0.000992)	0.861 (0.929)	0.011 (0.032)	0.82 (0.903)	0.013 (0.0366)	0.00229 (0.00797)	0.729 (0.844)	0.664 (0.799)	0.757 (0.866)	0.586 (0.73)
amp 8p11 21	188 (42%)	262	0.446 (0.608)	0.0189 (0.0492)	1e-05 (6.13e-05)	0.0899 (0.184)	0.551 (0.701)	0.19 (0.326)	0.0388 (0.0904)	0.00169 (0.00601)	0.72 (0.839)	0.322 (0.487)	0.541 (0.695)	0.103 (0.204)
amp 19p13 2	75 (17%)	375	0.0675 (0.145)	0.0551 (0.121)	4e-05 (0.000211)	0.0137 (0.038)	0.37 (0.537)	0.169 (0.297)	0.462 (0.617)	0.00025 (0.00107)	0.351 (0.518)	0.438 (0.601)	0.102 (0.203)	0.0223 (0.0561)
del 1p13 1	119 (26%)	331	0.0876 (0.18)	0.544 (0.696)	1e-05 (6.13e-05)	0.00131 (0.00474)	0.291 (0.447)	0.29 (0.446)	0.00022 (0.000954)	9e-05 (0.000421)	0.8 (0.89)	0.167 (0.295)	0.954 (0.983)	0.644 (0.784)
del 10q23 31	109 (24%)	341	0.0992 (0.198)	0.0645 (0.139)	1e-05 (6.13e-05)	0.00019 (0.000832)	0.973 (0.994)	0.134 (0.25)	0.00123 (0.00451)	3e-05 (0.000167)	0.579 (0.723)	0.137 (0.254)	0.348 (0.517)	0.4 (0.564)
del 19p13 3	63 (14%)	387	0.13 (0.245)	0.124 (0.237)	0.00076 (0.00294)	0.459 (0.615)	0.59 (0.732)	0.651 (0.79)	0.004 (0.0133)	0.00102 (0.00384)	0.652 (0.791)	0.0087 (0.0259)	0.484 (0.643)	0.285 (0.44)
amp 17p11 2	44 (10%)	406	0.266 (0.424)	0.00422 (0.0138)	0.0121 (0.0344)	0.0294 (0.0713)	0.875 (0.938)	0.272 (0.43)	0.0759 (0.16)	0.225 (0.375)	0.543 (0.696)	0.803 (0.891)	0.174 (0.305)	0.0655 (0.141)
del 3p26 2	72 (16%)	378	0.219 (0.369)	0.236 (0.388)	0.0012 (0.00444)	0.0734 (0.156)	0.946 (0.978)	0.636 (0.777)	0.00718 (0.0219)	0.00327 (0.0111)	0.741 (0.853)	0.789 (0.889)	0.534 (0.689)	0.411 (0.576)
del 9p21 3	62 (14%)	388	0.453 (0.611)	0.0902 (0.184)	0.00399 (0.0133)	0.115 (0.222)	0.658 (0.796)	0.277 (0.43)	0.0192 (0.0493)	0.00123 (0.00451)	0.623 (0.763)	0.257 (0.416)	0.203 (0.346)	0.583 (0.727)
amp 5q22 3	46 (10%)	404	0.925 (0.965)	1 (1.00)	0.00724 (0.022)	0.335 (0.502)	0.339 (0.506)	0.392 (0.558)	0.179 (0.311)	0.0358 (0.0851)	0.95 (0.98)	0.701 (0.825)	0.356 (0.522)	0.329 (0.494)
amp 8p11 23	158 (35%)	292	0.303 (0.461)	0.108 (0.212)	1e-05 (6.13e-05)	0.0809 (0.168)	0.295 (0.451)	0.276 (0.43)	0.112 (0.218)	0.038 (0.089)	0.36 (0.525)	0.264 (0.424)	0.503 (0.66)	0.126 (0.239)
del 16q23 1	61 (14%)	389	0.269 (0.428)	0.00543 (0.0172)	0.417 (0.58)	0.704 (0.826)	0.902 (0.954)	0.554 (0.703)	0.277 (0.43)	0.0126 (0.0354)	0.526 (0.684)	0.465 (0.62)	0.722 (0.839)	0.477 (0.634)
del 17q24 3	69 (15%)	381	0.0968 (0.194)	0.516 (0.675)	0.00407 (0.0134)	0.226 (0.376)	0.414 (0.578)	0.422 (0.584)	0.044 (0.101)	0.138 (0.256)	0.723 (0.839)	0.97 (0.993)	0.81 (0.896)	0.432 (0.594)
amp 12p13 33	111 (25%)	339	0.657 (0.796)	0.792 (0.889)	0.0319 (0.0766)	0.0613 (0.134)	0.807 (0.895)	0.576 (0.72)	0.751 (0.862)	0.848 (0.921)	0.511 (0.669)	0.795 (0.889)	0.63 (0.771)	0.851 (0.921)
del 3p14 2	88 (20%)	362	0.555 (0.704)	0.837 (0.917)	0.156 (0.279)	0.255 (0.414)	0.437 (0.6)	0.622 (0.763)	0.126 (0.239)	0.0411 (0.0957)	0.651 (0.79)	0.698 (0.824)	0.129 (0.243)	0.702 (0.825)
del 6p25 3	56 (12%)	394	0.853 (0.922)	0.739 (0.852)	0.109 (0.212)	0.399 (0.564)	0.431 (0.593)	0.445 (0.608)	0.527 (0.684)	0.895 (0.948)	0.67 (0.802)	0.941 (0.977)	0.0549 (0.121)	0.0435 (0.101)
del 6q26	62 (14%)	388	0.587 (0.73)	0.401 (0.565)	0.919 (0.964)	0.815 (0.9)	0.0286 (0.0698)	0.767 (0.874)	0.381 (0.547)	0.686 (0.815)	0.697 (0.824)	0.939 (0.977)	0.44 (0.603)	0.0578 (0.127)
del 8q11 1	30 (7%)	420	0.261 (0.421)	0.0975 (0.195)	0.0164 (0.0439)	0.906 (0.957)	0.158 (0.281)	0.679 (0.809)	0.375 (0.541)	0.0752 (0.159)	0.2 (0.342)	0.296 (0.451)	0.662 (0.799)	0.893 (0.948)
del 2p21	17 (4%)	433	0.595 (0.737)	0.865 (0.931)	0.895 (0.948)	0.848 (0.921)	0.526 (0.684)	0.782 (0.884)	0.35 (0.518)	0.282 (0.437)	0.0914 (0.186)	0.346 (0.514)
del 2q22 1	24 (5%)	426	0.973 (0.994)	0.537 (0.69)	0.412 (0.577)	0.68 (0.809)	1 (1.00)	0.421 (0.583)	0.228 (0.378)	0.324 (0.489)	0.25 (0.407)	0.164 (0.291)	1 (1.00)	0.848 (0.921)
del 3q26 31	46 (10%)	404	0.64 (0.781)	0.537 (0.69)	0.214 (0.363)	0.447 (0.608)	0.452 (0.611)	0.932 (0.972)	0.0931 (0.189)	0.139 (0.256)	0.156 (0.279)	0.816 (0.9)	0.0926 (0.188)	0.701 (0.825)
del 7q31 1	13 (3%)	437	1 (1.00)	0.599 (0.74)	0.0505 (0.113)	0.159 (0.282)	0.427 (0.589)	0.848 (0.921)	0.36 (0.525)	0.603 (0.744)	0.795 (0.889)	0.829 (0.911)
del 13q14 13	19 (4%)	431	0.273 (0.43)	0.864 (0.931)	0.244 (0.399)	0.243 (0.398)	0.885 (0.946)	0.797 (0.889)	0.922 (0.964)	0.882 (0.944)	0.688 (0.816)	0.944 (0.977)	0.45 (0.611)	0.311 (0.471)
del 16p13 3	56 (12%)	394	0.231 (0.383)	0.0631 (0.137)	0.0937 (0.189)	0.133 (0.248)	0.956 (0.983)	0.798 (0.889)	0.0617 (0.134)	0.0687 (0.147)	0.851 (0.921)	0.701 (0.825)	0.615 (0.757)	1 (1.00)

'amp_2q33.1' versus 'CN_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0029

Table S1. Gene #1: 'amp_2q33.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
AMP PEAK 1(2Q33.1) MUTATED	27	50	15
AMP PEAK 1(2Q33.1) WILD-TYPE	175	120	63

Figure S1. Get High-res Image Gene #1: 'amp_2q33.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2q33.1' versus 'METHLYATION_CNMF'

P value = 0.00865 (Fisher's exact test), Q value = 0.026

Table S2. Gene #1: 'amp_2q33.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
AMP PEAK 1(2Q33.1) MUTATED	38	15	13
AMP PEAK 1(2Q33.1) WILD-TYPE	82	82	63

Figure S2. Get High-res Image Gene #1: 'amp_2q33.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2q33.1' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00075

Table S3. Gene #1: 'amp_2q33.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
AMP PEAK 1(2Q33.1) MUTATED	41	12	19	20
AMP PEAK 1(2Q33.1) WILD-TYPE	80	95	71	110

Figure S3. Get High-res Image Gene #1: 'amp_2q33.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2q33.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00209 (Fisher's exact test), Q value = 0.0073

Table S4. Gene #1: 'amp_2q33.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
AMP PEAK 1(2Q33.1) MUTATED	19	33	12	26	2
AMP PEAK 1(2Q33.1) WILD-TYPE	60	75	84	103	34

Figure S4. Get High-res Image Gene #1: 'amp_2q33.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5p13.2' versus 'CN_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00099

Table S5. Gene #2: 'amp_5p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
AMP PEAK 2(5P13.2) MUTATED	23	48	17
AMP PEAK 2(5P13.2) WILD-TYPE	179	122	61

Figure S5. Get High-res Image Gene #2: 'amp_5p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p13.2' versus 'RPPA_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.032

Table S6. Gene #2: 'amp_5p13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	144	125
AMP PEAK 2(5P13.2) MUTATED	26	22	19
AMP PEAK 2(5P13.2) WILD-TYPE	59	122	106

Figure S6. Get High-res Image Gene #2: 'amp_5p13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_5p13.2' versus 'MRNASEQ_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.037

Table S7. Gene #2: 'amp_5p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
AMP PEAK 2(5P13.2) MUTATED	29	10	19	30
AMP PEAK 2(5P13.2) WILD-TYPE	92	97	71	100

Figure S7. Get High-res Image Gene #2: 'amp_5p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00229 (Fisher's exact test), Q value = 0.008

Table S8. Gene #2: 'amp_5p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
AMP PEAK 2(5P13.2) MUTATED	25	16	10	32	5
AMP PEAK 2(5P13.2) WILD-TYPE	54	92	86	97	31

Figure S8. Get High-res Image Gene #2: 'amp_5p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5q22.3' versus 'CN_CNMF'

P value = 0.00724 (Fisher's exact test), Q value = 0.022

Table S9. Gene #3: 'amp_5q22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
AMP PEAK 3(5Q22.3) MUTATED	12	27	7
AMP PEAK 3(5Q22.3) WILD-TYPE	190	143	71

Figure S9. Get High-res Image Gene #3: 'amp_5q22.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0358 (Fisher's exact test), Q value = 0.085

Table S10. Gene #3: 'amp_5q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
AMP PEAK 3(5Q22.3) MUTATED	13	13	3	14	3
AMP PEAK 3(5Q22.3) WILD-TYPE	66	95	93	115	33

Figure S10. Get High-res Image Gene #3: 'amp_5q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00025

Table S11. Gene #4: 'amp_6p21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 4(6P21.1) MUTATED	3	10	16
AMP PEAK 4(6P21.1) WILD-TYPE	39	62	16

Figure S11. Get High-res Image Gene #4: 'amp_6p21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_6p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S12. Gene #4: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
AMP PEAK 4(6P21.1) MUTATED	17	62	17
AMP PEAK 4(6P21.1) WILD-TYPE	185	108	61

Figure S12. Get High-res Image Gene #4: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p21.1' versus 'METHLYATION_CNMF'

P value = 0.00923 (Fisher's exact test), Q value = 0.027

Table S13. Gene #4: 'amp_6p21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
AMP PEAK 4(6P21.1) MUTATED	38	16	12
AMP PEAK 4(6P21.1) WILD-TYPE	82	81	64

Figure S13. Get High-res Image Gene #4: 'amp_6p21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CNMF'

P value = 0.0189 (Fisher's exact test), Q value = 0.049

Table S14. Gene #4: 'amp_6p21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
AMP PEAK 4(6P21.1) MUTATED	30	12	24	30
AMP PEAK 4(6P21.1) WILD-TYPE	91	95	66	100

Figure S14. Get High-res Image Gene #4: 'amp_6p21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00042

Table S15. Gene #4: 'amp_6p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
AMP PEAK 4(6P21.1) MUTATED	26	25	9	34	2
AMP PEAK 4(6P21.1) WILD-TYPE	53	83	87	95	34

Figure S15. Get High-res Image Gene #4: 'amp_6p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7p21.2' versus 'MRNA_CNMF'

P value = 0.00989 (Fisher's exact test), Q value = 0.029

Table S16. Gene #5: 'amp_7p21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 5(7P21.2) MUTATED	11	39	11	9
AMP PEAK 5(7P21.2) WILD-TYPE	24	22	18	12

Figure S16. Get High-res Image Gene #5: 'amp_7p21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_7p21.2' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S17. Gene #5: 'amp_7p21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 5(7P21.2) MUTATED	10	34	26
AMP PEAK 5(7P21.2) WILD-TYPE	32	38	6

Figure S17. Get High-res Image Gene #5: 'amp_7p21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7p21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S18. Gene #5: 'amp_7p21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
AMP PEAK 5(7P21.2) MUTATED	70	129	56
AMP PEAK 5(7P21.2) WILD-TYPE	132	41	22

Figure S18. Get High-res Image Gene #5: 'amp_7p21.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7p21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S19. Gene #5: 'amp_7p21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
AMP PEAK 5(7P21.2) MUTATED	94	46	38
AMP PEAK 5(7P21.2) WILD-TYPE	26	51	38

Figure S19. Get High-res Image Gene #5: 'amp_7p21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7p21.2' versus 'RPPA_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.002

Table S20. Gene #5: 'amp_7p21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	51	33	35	39	42	86	22	20	26
AMP PEAK 5(7P21.2) MUTATED	38	11	24	17	27	38	10	11	18
AMP PEAK 5(7P21.2) WILD-TYPE	13	22	11	22	15	48	12	9	8

Figure S20. Get High-res Image Gene #5: 'amp_7p21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_7p21.2' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00021

Table S21. Gene #5: 'amp_7p21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
AMP PEAK 5(7P21.2) MUTATED	89	46	51	68
AMP PEAK 5(7P21.2) WILD-TYPE	32	61	39	62

Figure S21. Get High-res Image Gene #5: 'amp_7p21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7p21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S22. Gene #5: 'amp_7p21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
AMP PEAK 5(7P21.2) MUTATED	60	75	34	76	9
AMP PEAK 5(7P21.2) WILD-TYPE	19	33	62	53	27

Figure S22. Get High-res Image Gene #5: 'amp_7p21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7p21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0342 (Fisher's exact test), Q value = 0.082

Table S23. Gene #5: 'amp_7p21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	12	22	17	24	10
AMP PEAK 5(7P21.2) MUTATED	12	15	11	12	7
AMP PEAK 5(7P21.2) WILD-TYPE	0	7	6	12	3

Figure S23. Get High-res Image Gene #5: 'amp_7p21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S24. Gene #6: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
AMP PEAK 6(8P11.23) MUTATED	44	56	58
AMP PEAK 6(8P11.23) WILD-TYPE	158	114	20

Figure S24. Get High-res Image Gene #6: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.038 (Fisher's exact test), Q value = 0.089

Table S25. Gene #6: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
AMP PEAK 6(8P11.23) MUTATED	33	45	31	41	6
AMP PEAK 6(8P11.23) WILD-TYPE	46	63	65	88	30

Figure S25. Get High-res Image Gene #6: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.049

Table S26. Gene #7: 'amp_8p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 7(8P11.21) MUTATED	10	26	18
AMP PEAK 7(8P11.21) WILD-TYPE	32	46	14

Figure S26. Get High-res Image Gene #7: 'amp_8p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S27. Gene #7: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
AMP PEAK 7(8P11.21) MUTATED	50	72	66
AMP PEAK 7(8P11.21) WILD-TYPE	152	98	12

Figure S27. Get High-res Image Gene #7: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CNMF'

P value = 0.0388 (Fisher's exact test), Q value = 0.09

Table S28. Gene #7: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
AMP PEAK 7(8P11.21) MUTATED	56	36	46	48
AMP PEAK 7(8P11.21) WILD-TYPE	65	71	44	82

Figure S28. Get High-res Image Gene #7: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00169 (Fisher's exact test), Q value = 0.006

Table S29. Gene #7: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
AMP PEAK 7(8P11.21) MUTATED	44	49	32	54	7
AMP PEAK 7(8P11.21) WILD-TYPE	35	59	64	75	29

Figure S29. Get High-res Image Gene #7: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q12.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00581 (Fisher's exact test), Q value = 0.018

Table S30. Gene #8: 'amp_8q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 8(8Q12.1) MUTATED	13	34	22
AMP PEAK 8(8Q12.1) WILD-TYPE	29	38	10

Figure S30. Get High-res Image Gene #8: 'amp_8q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S31. Gene #8: 'amp_8q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
AMP PEAK 8(8Q12.1) MUTATED	63	98	75
AMP PEAK 8(8Q12.1) WILD-TYPE	139	72	3

Figure S31. Get High-res Image Gene #8: 'amp_8q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q12.1' versus 'METHLYATION_CNMF'

P value = 0.00387 (Fisher's exact test), Q value = 0.013

Table S32. Gene #8: 'amp_8q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
AMP PEAK 8(8Q12.1) MUTATED	81	44	41
AMP PEAK 8(8Q12.1) WILD-TYPE	39	53	35

Figure S32. Get High-res Image Gene #8: 'amp_8q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q12.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0192 (Fisher's exact test), Q value = 0.049

Table S33. Gene #8: 'amp_8q12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	51	33	35	39	42	86	22	20	26
AMP PEAK 8(8Q12.1) MUTATED	35	13	15	19	20	41	7	9	19
AMP PEAK 8(8Q12.1) WILD-TYPE	16	20	20	20	22	45	15	11	7

Figure S33. Get High-res Image Gene #8: 'amp_8q12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8q12.1' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00039

Table S34. Gene #8: 'amp_8q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
AMP PEAK 8(8Q12.1) MUTATED	78	40	55	61
AMP PEAK 8(8Q12.1) WILD-TYPE	43	67	35	69

Figure S34. Get High-res Image Gene #8: 'amp_8q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00021

Table S35. Gene #8: 'amp_8q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
AMP PEAK 8(8Q12.1) MUTATED	51	65	39	71	8
AMP PEAK 8(8Q12.1) WILD-TYPE	28	43	57	58	28

Figure S35. Get High-res Image Gene #8: 'amp_8q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0378 (Fisher's exact test), Q value = 0.089

Table S36. Gene #8: 'amp_8q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	50	77	135
AMP PEAK 8(8Q12.1) MUTATED	66	30	50	63
AMP PEAK 8(8Q12.1) WILD-TYPE	69	20	27	72

Figure S36. Get High-res Image Gene #8: 'amp_8q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.037

Table S37. Gene #8: 'amp_8q12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	12	22	17	24	10
AMP PEAK 8(8Q12.1) MUTATED	10	18	9	9	6
AMP PEAK 8(8Q12.1) WILD-TYPE	2	4	8	15	4

Figure S37. Get High-res Image Gene #8: 'amp_8q12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.0294 (Fisher's exact test), Q value = 0.071

Table S38. Gene #9: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 9(8Q24.21) MUTATED	17	38	23
AMP PEAK 9(8Q24.21) WILD-TYPE	25	34	9

Figure S38. Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S39. Gene #9: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
AMP PEAK 9(8Q24.21) MUTATED	72	111	77
AMP PEAK 9(8Q24.21) WILD-TYPE	130	59	1

Figure S39. Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00063

Table S40. Gene #9: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
AMP PEAK 9(8Q24.21) MUTATED	90	46	44
AMP PEAK 9(8Q24.21) WILD-TYPE	30	51	32

Figure S40. Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00092

Table S41. Gene #9: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
AMP PEAK 9(8Q24.21) MUTATED	84	46	59	69
AMP PEAK 9(8Q24.21) WILD-TYPE	37	61	31	61

Figure S41. Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00025

Table S42. Gene #9: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
AMP PEAK 9(8Q24.21) MUTATED	56	69	44	78	11
AMP PEAK 9(8Q24.21) WILD-TYPE	23	39	52	51	25

Figure S42. Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0378 (Fisher's exact test), Q value = 0.089

Table S43. Gene #9: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	50	77	135
AMP PEAK 9(8Q24.21) MUTATED	73	33	54	71
AMP PEAK 9(8Q24.21) WILD-TYPE	62	17	23	64

Figure S43. Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0152 (Fisher's exact test), Q value = 0.041

Table S44. Gene #9: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	12	22	17	24	10
AMP PEAK 9(8Q24.21) MUTATED	10	19	11	10	6
AMP PEAK 9(8Q24.21) WILD-TYPE	2	3	6	14	4

Figure S44. Get High-res Image Gene #9: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11p15.5' versus 'MRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00025

Table S45. Gene #10: 'amp_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 10(11P15.5) MUTATED	2	18	3	12
AMP PEAK 10(11P15.5) WILD-TYPE	33	43	26	9

Figure S45. Get High-res Image Gene #10: 'amp_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11p15.5' versus 'MRNA_CHIERARCHICAL'

P value = 0.0059 (Fisher's exact test), Q value = 0.018

Table S46. Gene #10: 'amp_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 10(11P15.5) MUTATED	3	21	11
AMP PEAK 10(11P15.5) WILD-TYPE	39	51	21

Figure S46. Get High-res Image Gene #10: 'amp_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11p15.5' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S47. Gene #10: 'amp_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
AMP PEAK 10(11P15.5) MUTATED	23	50	21
AMP PEAK 10(11P15.5) WILD-TYPE	179	120	57

Figure S47. Get High-res Image Gene #10: 'amp_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11p15.5' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00034

Table S48. Gene #10: 'amp_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
AMP PEAK 10(11P15.5) MUTATED	35	6	15
AMP PEAK 10(11P15.5) WILD-TYPE	85	91	61

Figure S48. Get High-res Image Gene #10: 'amp_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11p15.5' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S49. Gene #10: 'amp_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
AMP PEAK 10(11P15.5) MUTATED	40	6	17	30
AMP PEAK 10(11P15.5) WILD-TYPE	81	101	73	100

Figure S49. Get High-res Image Gene #10: 'amp_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S50. Gene #10: 'amp_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
AMP PEAK 10(11P15.5) MUTATED	21	27	3	41	1
AMP PEAK 10(11P15.5) WILD-TYPE	58	81	93	88	35

Figure S50. Get High-res Image Gene #10: 'amp_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	50	77	135
AMP PEAK 10(11P15.5) MUTATED	8	12	46	18
AMP PEAK 10(11P15.5) WILD-TYPE	127	38	31	117

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

'amp_12p13.33' versus 'CN_CNMF'

P value = 0.0319 (Fisher's exact test), Q value = 0.077

Table S52. Gene #11: 'amp_12p13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
AMP PEAK 11(12P13.33) MUTATED	55	31	25
AMP PEAK 11(12P13.33) WILD-TYPE	147	139	53

Figure S52. Get High-res Image Gene #11: 'amp_12p13.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q12.13' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S53. Gene #12: 'amp_13q12.13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 12(13Q12.13) MUTATED	15	51	10	16
AMP PEAK 12(13Q12.13) WILD-TYPE	20	10	19	5

Figure S53. Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_13q12.13' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S54. Gene #12: 'amp_13q12.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 12(13Q12.13) MUTATED	13	49	30
AMP PEAK 12(13Q12.13) WILD-TYPE	29	23	2

Figure S54. Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_13q12.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S55. Gene #12: 'amp_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
AMP PEAK 12(13Q12.13) MUTATED	66	159	50
AMP PEAK 12(13Q12.13) WILD-TYPE	136	11	28

Figure S55. Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q12.13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S56. Gene #12: 'amp_13q12.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
AMP PEAK 12(13Q12.13) MUTATED	101	43	36
AMP PEAK 12(13Q12.13) WILD-TYPE	19	54	40

Figure S56. Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q12.13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S57. Gene #12: 'amp_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
AMP PEAK 12(13Q12.13) MUTATED	92	37	55	89
AMP PEAK 12(13Q12.13) WILD-TYPE	29	70	35	41

Figure S57. Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q12.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S58. Gene #12: 'amp_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
AMP PEAK 12(13Q12.13) MUTATED	68	76	26	95	8
AMP PEAK 12(13Q12.13) WILD-TYPE	11	32	70	34	28

Figure S58. Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q12.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0161 (Fisher's exact test), Q value = 0.044

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	12	22	17	24	10
AMP PEAK 12(13Q12.13) MUTATED	10	19	13	11	5
AMP PEAK 12(13Q12.13) WILD-TYPE	2	3	4	13	5

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

'amp_13q22.1' versus 'MRNA_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00042

Table S60. Gene #13: 'amp_13q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 13(13Q22.1) MUTATED	15	49	12	15
AMP PEAK 13(13Q22.1) WILD-TYPE	20	12	17	6

Figure S60. Get High-res Image Gene #13: 'amp_13q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_13q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S61. Gene #13: 'amp_13q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 13(13Q22.1) MUTATED	13	48	30
AMP PEAK 13(13Q22.1) WILD-TYPE	29	24	2

Figure S61. Get High-res Image Gene #13: 'amp_13q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_13q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S62. Gene #13: 'amp_13q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
AMP PEAK 13(13Q22.1) MUTATED	71	155	51
AMP PEAK 13(13Q22.1) WILD-TYPE	131	15	27

Figure S62. Get High-res Image Gene #13: 'amp_13q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S63. Gene #13: 'amp_13q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
AMP PEAK 13(13Q22.1) MUTATED	99	47	36
AMP PEAK 13(13Q22.1) WILD-TYPE	21	50	40

Figure S63. Get High-res Image Gene #13: 'amp_13q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S64. Gene #13: 'amp_13q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
AMP PEAK 13(13Q22.1) MUTATED	92	40	56	87
AMP PEAK 13(13Q22.1) WILD-TYPE	29	67	34	43

Figure S64. Get High-res Image Gene #13: 'amp_13q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S65. Gene #13: 'amp_13q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
AMP PEAK 13(13Q22.1) MUTATED	67	76	30	93	9
AMP PEAK 13(13Q22.1) WILD-TYPE	12	32	66	36	27

Figure S65. Get High-res Image Gene #13: 'amp_13q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'MRNA_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0017

Table S66. Gene #14: 'amp_16p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 14(16P11.2) MUTATED	6	24	3	12
AMP PEAK 14(16P11.2) WILD-TYPE	29	37	26	9

Figure S66. Get High-res Image Gene #14: 'amp_16p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_16p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S67. Gene #14: 'amp_16p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 14(16P11.2) MUTATED	6	16	23
AMP PEAK 14(16P11.2) WILD-TYPE	36	56	9

Figure S67. Get High-res Image Gene #14: 'amp_16p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_16p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S68. Gene #14: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
AMP PEAK 14(16P11.2) MUTATED	20	89	17
AMP PEAK 14(16P11.2) WILD-TYPE	182	81	61

Figure S68. Get High-res Image Gene #14: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_16p11.2' versus 'METHLYATION_CNMF'

P value = 0.00945 (Fisher's exact test), Q value = 0.028

Table S69. Gene #14: 'amp_16p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
AMP PEAK 14(16P11.2) MUTATED	43	17	20
AMP PEAK 14(16P11.2) WILD-TYPE	77	80	56

Figure S69. Get High-res Image Gene #14: 'amp_16p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_16p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0276 (Fisher's exact test), Q value = 0.068

Table S70. Gene #14: 'amp_16p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	51	33	35	39	42	86	22	20	26
AMP PEAK 14(16P11.2) MUTATED	20	3	14	12	12	22	2	6	6
AMP PEAK 14(16P11.2) WILD-TYPE	31	30	21	27	30	64	20	14	20

Figure S70. Get High-res Image Gene #14: 'amp_16p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_16p11.2' versus 'MRNASEQ_CNMF'

P value = 0.00116 (Fisher's exact test), Q value = 0.0043

Table S71. Gene #14: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
AMP PEAK 14(16P11.2) MUTATED	43	16	23	44
AMP PEAK 14(16P11.2) WILD-TYPE	78	91	67	86

Figure S71. Get High-res Image Gene #14: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_16p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S72. Gene #14: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
AMP PEAK 14(16P11.2) MUTATED	30	30	12	53	1
AMP PEAK 14(16P11.2) WILD-TYPE	49	78	84	76	35

Figure S72. Get High-res Image Gene #14: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_16q12.1' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00021

Table S73. Gene #15: 'amp_16q12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 15(16Q12.1) MUTATED	4	22	2	12
AMP PEAK 15(16Q12.1) WILD-TYPE	31	39	27	9

Figure S73. Get High-res Image Gene #15: 'amp_16q12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_16q12.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S74. Gene #15: 'amp_16q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 15(16Q12.1) MUTATED	3	17	20
AMP PEAK 15(16Q12.1) WILD-TYPE	39	55	12

Figure S74. Get High-res Image Gene #15: 'amp_16q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_16q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S75. Gene #15: 'amp_16q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
AMP PEAK 15(16Q12.1) MUTATED	16	82	13
AMP PEAK 15(16Q12.1) WILD-TYPE	186	88	65

Figure S75. Get High-res Image Gene #15: 'amp_16q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_16q12.1' versus 'METHLYATION_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.072

Table S76. Gene #15: 'amp_16q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
AMP PEAK 15(16Q12.1) MUTATED	37	15	18
AMP PEAK 15(16Q12.1) WILD-TYPE	83	82	58

Figure S76. Get High-res Image Gene #15: 'amp_16q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_16q12.1' versus 'MRNASEQ_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.0038

Table S77. Gene #15: 'amp_16q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
AMP PEAK 15(16Q12.1) MUTATED	39	13	20	39
AMP PEAK 15(16Q12.1) WILD-TYPE	82	94	70	91

Figure S77. Get High-res Image Gene #15: 'amp_16q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_16q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S78. Gene #15: 'amp_16q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
AMP PEAK 15(16Q12.1) MUTATED	29	25	10	47	0
AMP PEAK 15(16Q12.1) WILD-TYPE	50	83	86	82	36

Figure S78. Get High-res Image Gene #15: 'amp_16q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_16q12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0229 (Fisher's exact test), Q value = 0.057

Table S79. Gene #15: 'amp_16q12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	12	22	17	24	10
AMP PEAK 15(16Q12.1) MUTATED	7	10	4	3	2
AMP PEAK 15(16Q12.1) WILD-TYPE	5	12	13	21	8

Figure S79. Get High-res Image Gene #15: 'amp_16q12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00422 (Fisher's exact test), Q value = 0.014

Table S80. Gene #16: 'amp_17p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 16(17P11.2) MUTATED	2	3	8
AMP PEAK 16(17P11.2) WILD-TYPE	40	69	24

Figure S80. Get High-res Image Gene #16: 'amp_17p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17p11.2' versus 'CN_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.034

Table S81. Gene #16: 'amp_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
AMP PEAK 16(17P11.2) MUTATED	13	26	5
AMP PEAK 16(17P11.2) WILD-TYPE	189	144	73

Figure S81. Get High-res Image Gene #16: 'amp_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17p11.2' versus 'METHLYATION_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 0.071

Table S82. Gene #16: 'amp_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
AMP PEAK 16(17P11.2) MUTATED	20	8	4
AMP PEAK 16(17P11.2) WILD-TYPE	100	89	72

Figure S82. Get High-res Image Gene #16: 'amp_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q12' versus 'MRNA_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.062

Table S83. Gene #17: 'amp_17q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 17(17Q12) MUTATED	4	21	4	7
AMP PEAK 17(17Q12) WILD-TYPE	31	40	25	14

Figure S83. Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.0142 (Fisher's exact test), Q value = 0.039

Table S84. Gene #17: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 17(17Q12) MUTATED	6	16	14
AMP PEAK 17(17Q12) WILD-TYPE	36	56	18

Figure S84. Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S85. Gene #17: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
AMP PEAK 17(17Q12) MUTATED	25	63	26
AMP PEAK 17(17Q12) WILD-TYPE	177	107	52

Figure S85. Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00025

Table S86. Gene #17: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
AMP PEAK 17(17Q12) MUTATED	48	18	11
AMP PEAK 17(17Q12) WILD-TYPE	72	79	65

Figure S86. Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.0188 (Fisher's exact test), Q value = 0.049

Table S87. Gene #17: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	51	33	35	39	42	86	22	20	26
AMP PEAK 17(17Q12) MUTATED	17	5	6	8	13	19	0	5	10
AMP PEAK 17(17Q12) WILD-TYPE	34	28	29	31	29	67	22	15	16

Figure S87. Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00025

Table S88. Gene #17: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
AMP PEAK 17(17Q12) MUTATED	50	15	16	32
AMP PEAK 17(17Q12) WILD-TYPE	71	92	74	98

Figure S88. Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00108 (Fisher's exact test), Q value = 0.004

Table S89. Gene #17: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
AMP PEAK 17(17Q12) MUTATED	21	38	12	37	5
AMP PEAK 17(17Q12) WILD-TYPE	58	70	84	92	31

Figure S89. Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 0.0365 (Fisher's exact test), Q value = 0.087

Table S90. Gene #17: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	65	172
AMP PEAK 17(17Q12) MUTATED	48	9	44
AMP PEAK 17(17Q12) WILD-TYPE	112	56	128

Figure S90. Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0139 (Fisher's exact test), Q value = 0.038

Table S91. Gene #17: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	50	77	135
AMP PEAK 17(17Q12) MUTATED	30	12	31	28
AMP PEAK 17(17Q12) WILD-TYPE	105	38	46	107

Figure S91. Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q24.1' versus 'MRNA_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.047

Table S92. Gene #18: 'amp_17q24.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 18(17Q24.1) MUTATED	2	19	5	6
AMP PEAK 18(17Q24.1) WILD-TYPE	33	42	24	15

Figure S92. Get High-res Image Gene #18: 'amp_17q24.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q24.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00749 (Fisher's exact test), Q value = 0.023

Table S93. Gene #18: 'amp_17q24.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 18(17Q24.1) MUTATED	4	15	13
AMP PEAK 18(17Q24.1) WILD-TYPE	38	57	19

Figure S93. Get High-res Image Gene #18: 'amp_17q24.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S94. Gene #18: 'amp_17q24.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
AMP PEAK 18(17Q24.1) MUTATED	20	59	27
AMP PEAK 18(17Q24.1) WILD-TYPE	182	111	51

Figure S94. Get High-res Image Gene #18: 'amp_17q24.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q24.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S95. Gene #18: 'amp_17q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
AMP PEAK 18(17Q24.1) MUTATED	47	18	8
AMP PEAK 18(17Q24.1) WILD-TYPE	73	79	68

Figure S95. Get High-res Image Gene #18: 'amp_17q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q24.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S96. Gene #18: 'amp_17q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
AMP PEAK 18(17Q24.1) MUTATED	49	15	14	28
AMP PEAK 18(17Q24.1) WILD-TYPE	72	92	76	102

Figure S96. Get High-res Image Gene #18: 'amp_17q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S97. Gene #18: 'amp_17q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
AMP PEAK 18(17Q24.1) MUTATED	21	39	8	34	4
AMP PEAK 18(17Q24.1) WILD-TYPE	58	69	88	95	32

Figure S97. Get High-res Image Gene #18: 'amp_17q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q24.1' versus 'MIRSEQ_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.035

Table S98. Gene #18: 'amp_17q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	65	172
AMP PEAK 18(17Q24.1) MUTATED	46	7	39
AMP PEAK 18(17Q24.1) WILD-TYPE	114	58	133

Figure S98. Get High-res Image Gene #18: 'amp_17q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19p13.2' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00021

Table S99. Gene #19: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
AMP PEAK 19(19P13.2) MUTATED	17	44	14
AMP PEAK 19(19P13.2) WILD-TYPE	185	126	64

Figure S99. Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.2' versus 'METHLYATION_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.038

Table S100. Gene #19: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
AMP PEAK 19(19P13.2) MUTATED	33	15	9
AMP PEAK 19(19P13.2) WILD-TYPE	87	82	67

Figure S100. Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.0011

Table S101. Gene #19: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
AMP PEAK 19(19P13.2) MUTATED	25	18	9	22	1
AMP PEAK 19(19P13.2) WILD-TYPE	54	90	87	107	35

Figure S101. Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0223 (Fisher's exact test), Q value = 0.056

Table S102. Gene #19: 'amp_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	12	22	17	24	10
AMP PEAK 19(19P13.2) MUTATED	3	8	1	1	1
AMP PEAK 19(19P13.2) WILD-TYPE	9	14	16	23	9

Figure S102. Get High-res Image Gene #19: 'amp_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q13.11' versus 'MRNA_CHIERARCHICAL'

P value = 0.0311 (Fisher's exact test), Q value = 0.075

Table S103. Gene #20: 'amp_19q13.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 20(19Q13.11) MUTATED	2	16	7
AMP PEAK 20(19Q13.11) WILD-TYPE	40	56	25

Figure S103. Get High-res Image Gene #20: 'amp_19q13.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q13.11' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00059

Table S104. Gene #20: 'amp_19q13.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
AMP PEAK 20(19Q13.11) MUTATED	27	54	14
AMP PEAK 20(19Q13.11) WILD-TYPE	175	116	64

Figure S104. Get High-res Image Gene #20: 'amp_19q13.11' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q13.11' versus 'RPPA_CNMF'

P value = 0.0168 (Fisher's exact test), Q value = 0.045

Table S105. Gene #20: 'amp_19q13.11' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	144	125
AMP PEAK 20(19Q13.11) MUTATED	25	33	17
AMP PEAK 20(19Q13.11) WILD-TYPE	60	111	108

Figure S105. Get High-res Image Gene #20: 'amp_19q13.11' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19q13.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00083

Table S106. Gene #20: 'amp_19q13.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
AMP PEAK 20(19Q13.11) MUTATED	28	24	13	29	1
AMP PEAK 20(19Q13.11) WILD-TYPE	51	84	83	100	35

Figure S106. Get High-res Image Gene #20: 'amp_19q13.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q13.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.047

Table S107. Gene #20: 'amp_19q13.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	32	24
AMP PEAK 20(19Q13.11) MUTATED	5	11	1
AMP PEAK 20(19Q13.11) WILD-TYPE	24	21	23

Figure S107. Get High-res Image Gene #20: 'amp_19q13.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19q13.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00196 (Fisher's exact test), Q value = 0.0069

Table S108. Gene #20: 'amp_19q13.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	12	22	17	24	10
AMP PEAK 20(19Q13.11) MUTATED	4	10	1	1	1
AMP PEAK 20(19Q13.11) WILD-TYPE	8	12	16	23	9

Figure S108. Get High-res Image Gene #20: 'amp_19q13.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20p12.1' versus 'MRNA_CNMF'

P value = 0.0464 (Fisher's exact test), Q value = 0.11

Table S109. Gene #21: 'amp_20p12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 21(20P12.1) MUTATED	12	33	13	15
AMP PEAK 21(20P12.1) WILD-TYPE	23	28	16	6

Figure S109. Get High-res Image Gene #21: 'amp_20p12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20p12.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00087 (Fisher's exact test), Q value = 0.0033

Table S110. Gene #21: 'amp_20p12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 21(20P12.1) MUTATED	11	44	18
AMP PEAK 21(20P12.1) WILD-TYPE	31	28	14

Figure S110. Get High-res Image Gene #21: 'amp_20p12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S111. Gene #21: 'amp_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
AMP PEAK 21(20P12.1) MUTATED	65	104	39
AMP PEAK 21(20P12.1) WILD-TYPE	137	66	39

Figure S111. Get High-res Image Gene #21: 'amp_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p12.1' versus 'RPPA_CNMF'

P value = 0.0379 (Fisher's exact test), Q value = 0.089

Table S112. Gene #21: 'amp_20p12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	144	125
AMP PEAK 21(20P12.1) MUTATED	45	63	44
AMP PEAK 21(20P12.1) WILD-TYPE	40	81	81

Figure S112. Get High-res Image Gene #21: 'amp_20p12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20p12.1' versus 'MRNASEQ_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.056

Table S113. Gene #21: 'amp_20p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
AMP PEAK 21(20P12.1) MUTATED	62	38	37	69
AMP PEAK 21(20P12.1) WILD-TYPE	59	69	53	61

Figure S113. Get High-res Image Gene #21: 'amp_20p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S114. Gene #21: 'amp_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
AMP PEAK 21(20P12.1) MUTATED	39	55	29	77	6
AMP PEAK 21(20P12.1) WILD-TYPE	40	53	67	52	30

Figure S114. Get High-res Image Gene #21: 'amp_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20p11.21' versus 'MRNA_CNMF'

P value = 0.00211 (Fisher's exact test), Q value = 0.0074

Table S115. Gene #22: 'amp_20p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 22(20P11.21) MUTATED	12	41	13	16
AMP PEAK 22(20P11.21) WILD-TYPE	23	20	16	5

Figure S115. Get High-res Image Gene #22: 'amp_20p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20p11.21' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S116. Gene #22: 'amp_20p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 22(20P11.21) MUTATED	11	48	23
AMP PEAK 22(20P11.21) WILD-TYPE	31	24	9

Figure S116. Get High-res Image Gene #22: 'amp_20p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S117. Gene #22: 'amp_20p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
AMP PEAK 22(20P11.21) MUTATED	69	138	45
AMP PEAK 22(20P11.21) WILD-TYPE	133	32	33

Figure S117. Get High-res Image Gene #22: 'amp_20p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S118. Gene #22: 'amp_20p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
AMP PEAK 22(20P11.21) MUTATED	89	44	33
AMP PEAK 22(20P11.21) WILD-TYPE	31	53	43

Figure S118. Get High-res Image Gene #22: 'amp_20p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20p11.21' versus 'RPPA_CNMF'

P value = 0.00639 (Fisher's exact test), Q value = 0.02

Table S119. Gene #22: 'amp_20p11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	144	125
AMP PEAK 22(20P11.21) MUTATED	56	81	55
AMP PEAK 22(20P11.21) WILD-TYPE	29	63	70

Figure S119. Get High-res Image Gene #22: 'amp_20p11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20p11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S120. Gene #22: 'amp_20p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
AMP PEAK 22(20P11.21) MUTATED	91	38	47	74
AMP PEAK 22(20P11.21) WILD-TYPE	30	69	43	56

Figure S120. Get High-res Image Gene #22: 'amp_20p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S121. Gene #22: 'amp_20p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
AMP PEAK 22(20P11.21) MUTATED	51	75	31	87	6
AMP PEAK 22(20P11.21) WILD-TYPE	28	33	65	42	30

Figure S121. Get High-res Image Gene #22: 'amp_20p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0375 (Fisher's exact test), Q value = 0.089

Table S122. Gene #22: 'amp_20p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	50	77	135
AMP PEAK 22(20P11.21) MUTATED	74	25	54	69
AMP PEAK 22(20P11.21) WILD-TYPE	61	25	23	66

Figure S122. Get High-res Image Gene #22: 'amp_20p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S123. Gene #23: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 23(20Q11.21) MUTATED	13	58	16	18
AMP PEAK 23(20Q11.21) WILD-TYPE	22	3	13	3

Figure S123. Get High-res Image Gene #23: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q11.21' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S124. Gene #23: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 23(20Q11.21) MUTATED	12	62	31
AMP PEAK 23(20Q11.21) WILD-TYPE	30	10	1

Figure S124. Get High-res Image Gene #23: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S125. Gene #23: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
AMP PEAK 23(20Q11.21) MUTATED	89	170	64
AMP PEAK 23(20Q11.21) WILD-TYPE	113	0	14

Figure S125. Get High-res Image Gene #23: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S126. Gene #23: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
AMP PEAK 23(20Q11.21) MUTATED	117	50	45
AMP PEAK 23(20Q11.21) WILD-TYPE	3	47	31

Figure S126. Get High-res Image Gene #23: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'RPPA_CNMF'

P value = 0.00948 (Fisher's exact test), Q value = 0.028

Table S127. Gene #23: 'amp_20q11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	144	125
AMP PEAK 23(20Q11.21) MUTATED	67	107	76
AMP PEAK 23(20Q11.21) WILD-TYPE	18	37	49

Figure S127. Get High-res Image Gene #23: 'amp_20q11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q11.21' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00021

Table S128. Gene #23: 'amp_20q11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	51	33	35	39	42	86	22	20	26
AMP PEAK 23(20Q11.21) MUTATED	46	20	29	25	31	49	11	16	23
AMP PEAK 23(20Q11.21) WILD-TYPE	5	13	6	14	11	37	11	4	3

Figure S128. Get High-res Image Gene #23: 'amp_20q11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S129. Gene #23: 'amp_20q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
AMP PEAK 23(20Q11.21) MUTATED	117	46	64	94
AMP PEAK 23(20Q11.21) WILD-TYPE	4	61	26	36

Figure S129. Get High-res Image Gene #23: 'amp_20q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S130. Gene #23: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
AMP PEAK 23(20Q11.21) MUTATED	73	96	34	111	7
AMP PEAK 23(20Q11.21) WILD-TYPE	6	12	62	18	29

Figure S130. Get High-res Image Gene #23: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00166 (Fisher's exact test), Q value = 0.0059

Table S131. Gene #23: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	50	77	135
AMP PEAK 23(20Q11.21) MUTATED	92	36	68	88
AMP PEAK 23(20Q11.21) WILD-TYPE	43	14	9	47

Figure S131. Get High-res Image Gene #23: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00405 (Fisher's exact test), Q value = 0.013

Table S132. Gene #23: 'amp_20q11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	12	22	17	24	10
AMP PEAK 23(20Q11.21) MUTATED	12	19	14	12	9
AMP PEAK 23(20Q11.21) WILD-TYPE	0	3	3	12	1

Figure S132. Get High-res Image Gene #23: 'amp_20q11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S133. Gene #24: 'amp_20q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 24(20Q12) MUTATED	12	58	15	18
AMP PEAK 24(20Q12) WILD-TYPE	23	3	14	3

Figure S133. Get High-res Image Gene #24: 'amp_20q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S134. Gene #24: 'amp_20q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 24(20Q12) MUTATED	11	61	31
AMP PEAK 24(20Q12) WILD-TYPE	31	11	1

Figure S134. Get High-res Image Gene #24: 'amp_20q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S135. Gene #24: 'amp_20q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
AMP PEAK 24(20Q12) MUTATED	88	170	66
AMP PEAK 24(20Q12) WILD-TYPE	114	0	12

Figure S135. Get High-res Image Gene #24: 'amp_20q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S136. Gene #24: 'amp_20q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
AMP PEAK 24(20Q12) MUTATED	117	52	46
AMP PEAK 24(20Q12) WILD-TYPE	3	45	30

Figure S136. Get High-res Image Gene #24: 'amp_20q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q12' versus 'RPPA_CNMF'

P value = 0.0187 (Fisher's exact test), Q value = 0.049

Table S137. Gene #24: 'amp_20q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	144	125
AMP PEAK 24(20Q12) MUTATED	66	108	77
AMP PEAK 24(20Q12) WILD-TYPE	19	36	48

Figure S137. Get High-res Image Gene #24: 'amp_20q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q12' versus 'RPPA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00042

Table S138. Gene #24: 'amp_20q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	51	33	35	39	42	86	22	20	26
AMP PEAK 24(20Q12) MUTATED	46	19	29	27	31	49	11	16	23
AMP PEAK 24(20Q12) WILD-TYPE	5	14	6	12	11	37	11	4	3

Figure S138. Get High-res Image Gene #24: 'amp_20q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S139. Gene #24: 'amp_20q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
AMP PEAK 24(20Q12) MUTATED	117	47	66	92
AMP PEAK 24(20Q12) WILD-TYPE	4	60	24	38

Figure S139. Get High-res Image Gene #24: 'amp_20q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S140. Gene #24: 'amp_20q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
AMP PEAK 24(20Q12) MUTATED	74	96	36	110	6
AMP PEAK 24(20Q12) WILD-TYPE	5	12	60	19	30

Figure S140. Get High-res Image Gene #24: 'amp_20q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00129 (Fisher's exact test), Q value = 0.0047

Table S141. Gene #24: 'amp_20q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	50	77	135
AMP PEAK 24(20Q12) MUTATED	92	37	68	88
AMP PEAK 24(20Q12) WILD-TYPE	43	13	9	47

Figure S141. Get High-res Image Gene #24: 'amp_20q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00559 (Fisher's exact test), Q value = 0.018

Table S142. Gene #24: 'amp_20q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	12	22	17	24	10
AMP PEAK 24(20Q12) MUTATED	12	20	14	13	9
AMP PEAK 24(20Q12) WILD-TYPE	0	2	3	11	1

Figure S142. Get High-res Image Gene #24: 'amp_20q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S143. Gene #25: 'amp_20q13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 25(20Q13.12) MUTATED	13	58	16	18
AMP PEAK 25(20Q13.12) WILD-TYPE	22	3	13	3

Figure S143. Get High-res Image Gene #25: 'amp_20q13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q13.12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S144. Gene #25: 'amp_20q13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
AMP PEAK 25(20Q13.12) MUTATED	12	62	31
AMP PEAK 25(20Q13.12) WILD-TYPE	30	10	1

Figure S144. Get High-res Image Gene #25: 'amp_20q13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q13.12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S145. Gene #25: 'amp_20q13.12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
AMP PEAK 25(20Q13.12) MUTATED	88	170	68
AMP PEAK 25(20Q13.12) WILD-TYPE	114	0	10

Figure S145. Get High-res Image Gene #25: 'amp_20q13.12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S146. Gene #25: 'amp_20q13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
AMP PEAK 25(20Q13.12) MUTATED	117	52	46
AMP PEAK 25(20Q13.12) WILD-TYPE	3	45	30

Figure S146. Get High-res Image Gene #25: 'amp_20q13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.12' versus 'RPPA_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.032

Table S147. Gene #25: 'amp_20q13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	144	125
AMP PEAK 25(20Q13.12) MUTATED	66	110	77
AMP PEAK 25(20Q13.12) WILD-TYPE	19	34	48

Figure S147. Get High-res Image Gene #25: 'amp_20q13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q13.12' versus 'RPPA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 3e-04

Table S148. Gene #25: 'amp_20q13.12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	51	33	35	39	42	86	22	20	26
AMP PEAK 25(20Q13.12) MUTATED	46	19	29	28	32	49	11	16	23
AMP PEAK 25(20Q13.12) WILD-TYPE	5	14	6	11	10	37	11	4	3

Figure S148. Get High-res Image Gene #25: 'amp_20q13.12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20q13.12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S149. Gene #25: 'amp_20q13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
AMP PEAK 25(20Q13.12) MUTATED	117	48	66	93
AMP PEAK 25(20Q13.12) WILD-TYPE	4	59	24	37

Figure S149. Get High-res Image Gene #25: 'amp_20q13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q13.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S150. Gene #25: 'amp_20q13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
AMP PEAK 25(20Q13.12) MUTATED	74	96	36	111	7
AMP PEAK 25(20Q13.12) WILD-TYPE	5	12	60	18	29

Figure S150. Get High-res Image Gene #25: 'amp_20q13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00268 (Fisher's exact test), Q value = 0.0092

Table S151. Gene #25: 'amp_20q13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	50	77	135
AMP PEAK 25(20Q13.12) MUTATED	93	37	68	90
AMP PEAK 25(20Q13.12) WILD-TYPE	42	13	9	45

Figure S151. Get High-res Image Gene #25: 'amp_20q13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00589 (Fisher's exact test), Q value = 0.018

Table S152. Gene #25: 'amp_20q13.12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	12	22	17	24	10
AMP PEAK 25(20Q13.12) MUTATED	12	20	14	13	9
AMP PEAK 25(20Q13.12) WILD-TYPE	0	2	3	11	1

Figure S152. Get High-res Image Gene #25: 'amp_20q13.12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.11' versus 'MRNA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00034

Table S153. Gene #26: 'del_1p36.11' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 1(1P36.11) MUTATED	9	36	4	10
DEL PEAK 1(1P36.11) WILD-TYPE	26	25	25	11

Figure S153. Get High-res Image Gene #26: 'del_1p36.11' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.11' versus 'MRNA_CHIERARCHICAL'

P value = 0.00785 (Fisher's exact test), Q value = 0.024

Table S154. Gene #26: 'del_1p36.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 1(1P36.11) MUTATED	9	33	17
DEL PEAK 1(1P36.11) WILD-TYPE	33	39	15

Figure S154. Get High-res Image Gene #26: 'del_1p36.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S155. Gene #26: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 1(1P36.11) MUTATED	43	101	24
DEL PEAK 1(1P36.11) WILD-TYPE	159	69	54

Figure S155. Get High-res Image Gene #26: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S156. Gene #26: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
DEL PEAK 1(1P36.11) MUTATED	64	21	22
DEL PEAK 1(1P36.11) WILD-TYPE	56	76	54

Figure S156. Get High-res Image Gene #26: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.11' versus 'RPPA_CHIERARCHICAL'

P value = 0.028 (Fisher's exact test), Q value = 0.069

Table S157. Gene #26: 'del_1p36.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	51	33	35	39	42	86	22	20	26
DEL PEAK 1(1P36.11) MUTATED	22	12	15	15	19	17	8	10	12
DEL PEAK 1(1P36.11) WILD-TYPE	29	21	20	24	23	69	14	10	14

Figure S157. Get High-res Image Gene #26: 'del_1p36.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S158. Gene #26: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 1(1P36.11) MUTATED	64	17	34	52
DEL PEAK 1(1P36.11) WILD-TYPE	57	90	56	78

Figure S158. Get High-res Image Gene #26: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S159. Gene #26: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 1(1P36.11) MUTATED	42	48	12	61	4
DEL PEAK 1(1P36.11) WILD-TYPE	37	60	84	68	32

Figure S159. Get High-res Image Gene #26: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0203 (Fisher's exact test), Q value = 0.052

Table S160. Gene #26: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	50	77	135
DEL PEAK 1(1P36.11) MUTATED	45	17	41	46
DEL PEAK 1(1P36.11) WILD-TYPE	90	33	36	89

Figure S160. Get High-res Image Gene #26: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p33' versus 'MRNA_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.043

Table S161. Gene #27: 'del_1p33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 2(1P33) MUTATED	10	23	2	5
DEL PEAK 2(1P33) WILD-TYPE	25	38	27	16

Figure S161. Get High-res Image Gene #27: 'del_1p33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S162. Gene #27: 'del_1p33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 2(1P33) MUTATED	33	80	10
DEL PEAK 2(1P33) WILD-TYPE	169	90	68

Figure S162. Get High-res Image Gene #27: 'del_1p33' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p33' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 3e-04

Table S163. Gene #27: 'del_1p33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
DEL PEAK 2(1P33) MUTATED	49	15	17
DEL PEAK 2(1P33) WILD-TYPE	71	82	59

Figure S163. Get High-res Image Gene #27: 'del_1p33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p33' versus 'MRNASEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0011

Table S164. Gene #27: 'del_1p33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 2(1P33) MUTATED	46	14	24	38
DEL PEAK 2(1P33) WILD-TYPE	75	93	66	92

Figure S164. Get High-res Image Gene #27: 'del_1p33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S165. Gene #27: 'del_1p33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 2(1P33) MUTATED	34	33	10	39	6
DEL PEAK 2(1P33) WILD-TYPE	45	75	86	90	30

Figure S165. Get High-res Image Gene #27: 'del_1p33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S166. Gene #28: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 3(1P13.1) MUTATED	36	76	7
DEL PEAK 3(1P13.1) WILD-TYPE	166	94	71

Figure S166. Get High-res Image Gene #28: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p13.1' versus 'METHLYATION_CNMF'

P value = 0.00131 (Fisher's exact test), Q value = 0.0047

Table S167. Gene #28: 'del_1p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
DEL PEAK 3(1P13.1) MUTATED	46	17	16
DEL PEAK 3(1P13.1) WILD-TYPE	74	80	60

Figure S167. Get High-res Image Gene #28: 'del_1p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p13.1' versus 'MRNASEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00095

Table S168. Gene #28: 'del_1p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 3(1P13.1) MUTATED	43	12	24	39
DEL PEAK 3(1P13.1) WILD-TYPE	78	95	66	91

Figure S168. Get High-res Image Gene #28: 'del_1p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00042

Table S169. Gene #28: 'del_1p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 3(1P13.1) MUTATED	31	31	12	40	4
DEL PEAK 3(1P13.1) WILD-TYPE	48	77	84	89	32

Figure S169. Get High-res Image Gene #28: 'del_1p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1q43' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S170. Gene #29: 'del_1q43' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 4(1Q43) MUTATED	9	35	10
DEL PEAK 4(1Q43) WILD-TYPE	193	135	68

Figure S170. Get High-res Image Gene #29: 'del_1q43' versus Molecular Subtype #3: 'CN_CNMF'

'del_1q43' versus 'METHLYATION_CNMF'

P value = 0.00254 (Fisher's exact test), Q value = 0.0088

Table S171. Gene #29: 'del_1q43' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
DEL PEAK 4(1Q43) MUTATED	25	5	9
DEL PEAK 4(1Q43) WILD-TYPE	95	92	67

Figure S171. Get High-res Image Gene #29: 'del_1q43' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1q43' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00042

Table S172. Gene #29: 'del_1q43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 4(1Q43) MUTATED	23	2	15	13
DEL PEAK 4(1Q43) WILD-TYPE	98	105	75	117

Figure S172. Get High-res Image Gene #29: 'del_1q43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1q43' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.0011

Table S173. Gene #29: 'del_1q43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 4(1Q43) MUTATED	18	17	3	14	1
DEL PEAK 4(1Q43) WILD-TYPE	61	91	93	115	35

Figure S173. Get High-res Image Gene #29: 'del_1q43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1q43' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0024

Table S174. Gene #29: 'del_1q43' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	50	77	135
DEL PEAK 4(1Q43) MUTATED	16	9	17	6
DEL PEAK 4(1Q43) WILD-TYPE	119	41	60	129

Figure S174. Get High-res Image Gene #29: 'del_1q43' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1q43' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0275 (Fisher's exact test), Q value = 0.068

Table S175. Gene #29: 'del_1q43' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	29	32	24
DEL PEAK 4(1Q43) MUTATED	9	2	6
DEL PEAK 4(1Q43) WILD-TYPE	20	30	18

Figure S175. Get High-res Image Gene #29: 'del_1q43' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p26.2' versus 'CN_CNMF'

P value = 0.0012 (Fisher's exact test), Q value = 0.0044

Table S176. Gene #32: 'del_3p26.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 7(3P26.2) MUTATED	21	41	10
DEL PEAK 7(3P26.2) WILD-TYPE	181	129	68

Figure S176. Get High-res Image Gene #32: 'del_3p26.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p26.2' versus 'MRNASEQ_CNMF'

P value = 0.00718 (Fisher's exact test), Q value = 0.022

Table S177. Gene #32: 'del_3p26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 7(3P26.2) MUTATED	23	7	14	28
DEL PEAK 7(3P26.2) WILD-TYPE	98	100	76	102

Figure S177. Get High-res Image Gene #32: 'del_3p26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00327 (Fisher's exact test), Q value = 0.011

Table S178. Gene #32: 'del_3p26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 7(3P26.2) MUTATED	18	16	7	29	2
DEL PEAK 7(3P26.2) WILD-TYPE	61	92	89	100	34

Figure S178. Get High-res Image Gene #32: 'del_3p26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0411 (Fisher's exact test), Q value = 0.096

Table S179. Gene #33: 'del_3p14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 8(3P14.2) MUTATED	19	25	9	29	6
DEL PEAK 8(3P14.2) WILD-TYPE	60	83	87	100	30

Figure S179. Get High-res Image Gene #33: 'del_3p14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.2' versus 'MRNA_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.0029

Table S180. Gene #35: 'del_4p16.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 10(4P16.2) MUTATED	7	29	3	9
DEL PEAK 10(4P16.2) WILD-TYPE	28	32	26	12

Figure S180. Get High-res Image Gene #35: 'del_4p16.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4p16.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00159 (Fisher's exact test), Q value = 0.0057

Table S181. Gene #35: 'del_4p16.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 10(4P16.2) MUTATED	7	23	18
DEL PEAK 10(4P16.2) WILD-TYPE	35	49	14

Figure S181. Get High-res Image Gene #35: 'del_4p16.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4p16.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S182. Gene #35: 'del_4p16.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 10(4P16.2) MUTATED	33	87	19
DEL PEAK 10(4P16.2) WILD-TYPE	169	83	59

Figure S182. Get High-res Image Gene #35: 'del_4p16.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.2' versus 'METHLYATION_CNMF'

P value = 0.00413 (Fisher's exact test), Q value = 0.014

Table S183. Gene #35: 'del_4p16.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
DEL PEAK 10(4P16.2) MUTATED	48	19	21
DEL PEAK 10(4P16.2) WILD-TYPE	72	78	55

Figure S183. Get High-res Image Gene #35: 'del_4p16.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p16.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00437 (Fisher's exact test), Q value = 0.014

Table S184. Gene #35: 'del_4p16.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	51	33	35	39	42	86	22	20	26
DEL PEAK 10(4P16.2) MUTATED	18	7	12	12	19	14	7	1	9
DEL PEAK 10(4P16.2) WILD-TYPE	33	26	23	27	23	72	15	19	17

Figure S184. Get High-res Image Gene #35: 'del_4p16.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4p16.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S185. Gene #35: 'del_4p16.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 10(4P16.2) MUTATED	52	13	30	43
DEL PEAK 10(4P16.2) WILD-TYPE	69	94	60	87

Figure S185. Get High-res Image Gene #35: 'del_4p16.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p16.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S186. Gene #35: 'del_4p16.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 10(4P16.2) MUTATED	36	38	8	52	4
DEL PEAK 10(4P16.2) WILD-TYPE	43	70	88	77	32

Figure S186. Get High-res Image Gene #35: 'del_4p16.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MRNA_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0015

Table S187. Gene #36: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 11(4Q22.1) MUTATED	9	27	2	11
DEL PEAK 11(4Q22.1) WILD-TYPE	26	34	27	10

Figure S187. Get High-res Image Gene #36: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.004 (Fisher's exact test), Q value = 0.013

Table S188. Gene #36: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 11(4Q22.1) MUTATED	7	25	17
DEL PEAK 11(4Q22.1) WILD-TYPE	35	47	15

Figure S188. Get High-res Image Gene #36: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S189. Gene #36: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 11(4Q22.1) MUTATED	35	96	20
DEL PEAK 11(4Q22.1) WILD-TYPE	167	74	58

Figure S189. Get High-res Image Gene #36: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.003

Table S190. Gene #36: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
DEL PEAK 11(4Q22.1) MUTATED	55	21	25
DEL PEAK 11(4Q22.1) WILD-TYPE	65	76	51

Figure S190. Get High-res Image Gene #36: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S191. Gene #36: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 11(4Q22.1) MUTATED	57	16	28	49
DEL PEAK 11(4Q22.1) WILD-TYPE	64	91	62	81

Figure S191. Get High-res Image Gene #36: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S192. Gene #36: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 11(4Q22.1) MUTATED	40	44	9	53	4
DEL PEAK 11(4Q22.1) WILD-TYPE	39	64	87	76	32

Figure S192. Get High-res Image Gene #36: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MRNA_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.0035

Table S193. Gene #37: 'del_4q35.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 12(4Q35.1) MUTATED	8	30	4	11
DEL PEAK 12(4Q35.1) WILD-TYPE	27	31	25	10

Figure S193. Get High-res Image Gene #37: 'del_4q35.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q35.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00767 (Fisher's exact test), Q value = 0.023

Table S194. Gene #37: 'del_4q35.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 12(4Q35.1) MUTATED	8	28	17
DEL PEAK 12(4Q35.1) WILD-TYPE	34	44	15

Figure S194. Get High-res Image Gene #37: 'del_4q35.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q35.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S195. Gene #37: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 12(4Q35.1) MUTATED	36	101	22
DEL PEAK 12(4Q35.1) WILD-TYPE	166	69	56

Figure S195. Get High-res Image Gene #37: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q35.1' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S196. Gene #37: 'del_4q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
DEL PEAK 12(4Q35.1) MUTATED	59	17	26
DEL PEAK 12(4Q35.1) WILD-TYPE	61	80	50

Figure S196. Get High-res Image Gene #37: 'del_4q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q35.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S197. Gene #37: 'del_4q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 12(4Q35.1) MUTATED	61	19	29	49
DEL PEAK 12(4Q35.1) WILD-TYPE	60	88	61	81

Figure S197. Get High-res Image Gene #37: 'del_4q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S198. Gene #37: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 12(4Q35.1) MUTATED	40	44	12	56	6
DEL PEAK 12(4Q35.1) WILD-TYPE	39	64	84	73	30

Figure S198. Get High-res Image Gene #37: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MRNA_CNMF'

P value = 0.0012 (Fisher's exact test), Q value = 0.0044

Table S199. Gene #38: 'del_5q12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 13(5Q12.1) MUTATED	8	20	0	6
DEL PEAK 13(5Q12.1) WILD-TYPE	27	41	29	15

Figure S199. Get High-res Image Gene #38: 'del_5q12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q12.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0031 (Fisher's exact test), Q value = 0.011

Table S200. Gene #38: 'del_5q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 13(5Q12.1) MUTATED	7	12	15
DEL PEAK 13(5Q12.1) WILD-TYPE	35	60	17

Figure S200. Get High-res Image Gene #38: 'del_5q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S201. Gene #38: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 13(5Q12.1) MUTATED	19	63	24
DEL PEAK 13(5Q12.1) WILD-TYPE	183	107	54

Figure S201. Get High-res Image Gene #38: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 0.0138 (Fisher's exact test), Q value = 0.038

Table S202. Gene #38: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
DEL PEAK 13(5Q12.1) MUTATED	39	15	18
DEL PEAK 13(5Q12.1) WILD-TYPE	81	82	58

Figure S202. Get High-res Image Gene #38: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q12.1' versus 'RPPA_CNMF'

P value = 0.0254 (Fisher's exact test), Q value = 0.063

Table S203. Gene #38: 'del_5q12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	144	125
DEL PEAK 13(5Q12.1) MUTATED	28	27	23
DEL PEAK 13(5Q12.1) WILD-TYPE	57	117	102

Figure S203. Get High-res Image Gene #38: 'del_5q12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_5q12.1' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00025

Table S204. Gene #38: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 13(5Q12.1) MUTATED	41	9	23	33
DEL PEAK 13(5Q12.1) WILD-TYPE	80	98	67	97

Figure S204. Get High-res Image Gene #38: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00034

Table S205. Gene #38: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 13(5Q12.1) MUTATED	29	29	9	35	4
DEL PEAK 13(5Q12.1) WILD-TYPE	50	79	87	94	32

Figure S205. Get High-res Image Gene #38: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q21.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0439 (Fisher's exact test), Q value = 0.1

Table S206. Gene #39: 'del_5q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 14(5Q21.1) MUTATED	9	18	15
DEL PEAK 14(5Q21.1) WILD-TYPE	33	54	17

Figure S206. Get High-res Image Gene #39: 'del_5q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S207. Gene #39: 'del_5q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 14(5Q21.1) MUTATED	30	71	26
DEL PEAK 14(5Q21.1) WILD-TYPE	172	99	52

Figure S207. Get High-res Image Gene #39: 'del_5q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q21.1' versus 'METHLYATION_CNMF'

P value = 0.00443 (Fisher's exact test), Q value = 0.014

Table S208. Gene #39: 'del_5q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
DEL PEAK 14(5Q21.1) MUTATED	45	17	23
DEL PEAK 14(5Q21.1) WILD-TYPE	75	80	53

Figure S208. Get High-res Image Gene #39: 'del_5q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q21.1' versus 'RPPA_CNMF'

P value = 0.0475 (Fisher's exact test), Q value = 0.11

Table S209. Gene #39: 'del_5q21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	144	125
DEL PEAK 14(5Q21.1) MUTATED	31	33	28
DEL PEAK 14(5Q21.1) WILD-TYPE	54	111	97

Figure S209. Get High-res Image Gene #39: 'del_5q21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_5q21.1' versus 'MRNASEQ_CNMF'

P value = 0.00703 (Fisher's exact test), Q value = 0.022

Table S210. Gene #39: 'del_5q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 14(5Q21.1) MUTATED	47	20	22	38
DEL PEAK 14(5Q21.1) WILD-TYPE	74	87	68	92

Figure S210. Get High-res Image Gene #39: 'del_5q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.0012

Table S211. Gene #39: 'del_5q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 14(5Q21.1) MUTATED	29	36	12	44	6
DEL PEAK 14(5Q21.1) WILD-TYPE	50	72	84	85	30

Figure S211. Get High-res Image Gene #39: 'del_5q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q22.2' versus 'MRNA_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.038

Table S212. Gene #40: 'del_5q22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 15(5Q22.2) MUTATED	8	23	2	6
DEL PEAK 15(5Q22.2) WILD-TYPE	27	38	27	15

Figure S212. Get High-res Image Gene #40: 'del_5q22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q22.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00916 (Fisher's exact test), Q value = 0.027

Table S213. Gene #40: 'del_5q22.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 15(5Q22.2) MUTATED	6	18	15
DEL PEAK 15(5Q22.2) WILD-TYPE	36	54	17

Figure S213. Get High-res Image Gene #40: 'del_5q22.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S214. Gene #40: 'del_5q22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 15(5Q22.2) MUTATED	30	72	28
DEL PEAK 15(5Q22.2) WILD-TYPE	172	98	50

Figure S214. Get High-res Image Gene #40: 'del_5q22.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q22.2' versus 'METHLYATION_CNMF'

P value = 0.0289 (Fisher's exact test), Q value = 0.07

Table S215. Gene #40: 'del_5q22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
DEL PEAK 15(5Q22.2) MUTATED	46	21	23
DEL PEAK 15(5Q22.2) WILD-TYPE	74	76	53

Figure S215. Get High-res Image Gene #40: 'del_5q22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q22.2' versus 'MRNASEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0011

Table S216. Gene #40: 'del_5q22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 15(5Q22.2) MUTATED	51	17	24	37
DEL PEAK 15(5Q22.2) WILD-TYPE	70	90	66	93

Figure S216. Get High-res Image Gene #40: 'del_5q22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 3e-04

Table S217. Gene #40: 'del_5q22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 15(5Q22.2) MUTATED	29	38	15	44	3
DEL PEAK 15(5Q22.2) WILD-TYPE	50	70	81	85	33

Figure S217. Get High-res Image Gene #40: 'del_5q22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6p25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0435 (Fisher's exact test), Q value = 0.1

Table S218. Gene #41: 'del_6p25.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	12	22	17	24	10
DEL PEAK 16(6P25.3) MUTATED	1	0	1	5	3
DEL PEAK 16(6P25.3) WILD-TYPE	11	22	16	19	7

Figure S218. Get High-res Image Gene #41: 'del_6p25.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q26' versus 'RPPA_CNMF'

P value = 0.0286 (Fisher's exact test), Q value = 0.07

Table S219. Gene #42: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	144	125
DEL PEAK 17(6Q26) MUTATED	16	22	9
DEL PEAK 17(6Q26) WILD-TYPE	69	122	116

Figure S219. Get High-res Image Gene #42: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_8p23.3' versus 'MRNA_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.035

Table S220. Gene #44: 'del_8p23.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 19(8P23.3) MUTATED	12	33	6	11
DEL PEAK 19(8P23.3) WILD-TYPE	23	28	23	10

Figure S220. Get High-res Image Gene #44: 'del_8p23.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p23.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00072

Table S221. Gene #44: 'del_8p23.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 19(8P23.3) MUTATED	10	29	23
DEL PEAK 19(8P23.3) WILD-TYPE	32	43	9

Figure S221. Get High-res Image Gene #44: 'del_8p23.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S222. Gene #44: 'del_8p23.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 19(8P23.3) MUTATED	35	99	55
DEL PEAK 19(8P23.3) WILD-TYPE	167	71	23

Figure S222. Get High-res Image Gene #44: 'del_8p23.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S223. Gene #44: 'del_8p23.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
DEL PEAK 19(8P23.3) MUTATED	70	28	27
DEL PEAK 19(8P23.3) WILD-TYPE	50	69	49

Figure S223. Get High-res Image Gene #44: 'del_8p23.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S224. Gene #44: 'del_8p23.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 19(8P23.3) MUTATED	65	22	43	59
DEL PEAK 19(8P23.3) WILD-TYPE	56	85	47	71

Figure S224. Get High-res Image Gene #44: 'del_8p23.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S225. Gene #44: 'del_8p23.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 19(8P23.3) MUTATED	47	50	19	67	6
DEL PEAK 19(8P23.3) WILD-TYPE	32	58	77	62	30

Figure S225. Get High-res Image Gene #44: 'del_8p23.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0436 (Fisher's exact test), Q value = 0.1

Table S226. Gene #44: 'del_8p23.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	12	22	17	24	10
DEL PEAK 19(8P23.3) MUTATED	9	12	10	6	5
DEL PEAK 19(8P23.3) WILD-TYPE	3	10	7	18	5

Figure S226. Get High-res Image Gene #44: 'del_8p23.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p22' versus 'MRNA_CNMF'

P value = 0.00436 (Fisher's exact test), Q value = 0.014

Table S227. Gene #45: 'del_8p22' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 20(8P22) MUTATED	9	35	8	11
DEL PEAK 20(8P22) WILD-TYPE	26	26	21	10

Figure S227. Get High-res Image Gene #45: 'del_8p22' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p22' versus 'MRNA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00075

Table S228. Gene #45: 'del_8p22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 20(8P22) MUTATED	8	34	21
DEL PEAK 20(8P22) WILD-TYPE	34	38	11

Figure S228. Get High-res Image Gene #45: 'del_8p22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S229. Gene #45: 'del_8p22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 20(8P22) MUTATED	36	108	59
DEL PEAK 20(8P22) WILD-TYPE	166	62	19

Figure S229. Get High-res Image Gene #45: 'del_8p22' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p22' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S230. Gene #45: 'del_8p22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
DEL PEAK 20(8P22) MUTATED	77	32	29
DEL PEAK 20(8P22) WILD-TYPE	43	65	47

Figure S230. Get High-res Image Gene #45: 'del_8p22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p22' versus 'RPPA_CHIERARCHICAL'

P value = 0.0174 (Fisher's exact test), Q value = 0.046

Table S231. Gene #45: 'del_8p22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	51	33	35	39	42	86	22	20	26
DEL PEAK 20(8P22) MUTATED	33	12	16	15	17	31	5	9	15
DEL PEAK 20(8P22) WILD-TYPE	18	21	19	24	25	55	17	11	11

Figure S231. Get High-res Image Gene #45: 'del_8p22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_8p22' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S232. Gene #45: 'del_8p22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 20(8P22) MUTATED	73	27	46	57
DEL PEAK 20(8P22) WILD-TYPE	48	80	44	73

Figure S232. Get High-res Image Gene #45: 'del_8p22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S233. Gene #45: 'del_8p22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 20(8P22) MUTATED	52	54	23	69	5
DEL PEAK 20(8P22) WILD-TYPE	27	54	73	60	31

Figure S233. Get High-res Image Gene #45: 'del_8p22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0145 (Fisher's exact test), Q value = 0.04

Table S234. Gene #45: 'del_8p22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	50	77	135
DEL PEAK 20(8P22) MUTATED	55	26	46	53
DEL PEAK 20(8P22) WILD-TYPE	80	24	31	82

Figure S234. Get High-res Image Gene #45: 'del_8p22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0477 (Fisher's exact test), Q value = 0.11

Table S235. Gene #45: 'del_8p22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	12	22	17	24	10
DEL PEAK 20(8P22) MUTATED	8	14	10	6	5
DEL PEAK 20(8P22) WILD-TYPE	4	8	7	18	5

Figure S235. Get High-res Image Gene #45: 'del_8p22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8q11.1' versus 'CN_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.044

Table S236. Gene #46: 'del_8q11.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 21(8Q11.1) MUTATED	11	18	1
DEL PEAK 21(8Q11.1) WILD-TYPE	191	152	77

Figure S236. Get High-res Image Gene #46: 'del_8q11.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 0.00399 (Fisher's exact test), Q value = 0.013

Table S237. Gene #47: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 22(9P21.3) MUTATED	16	32	14
DEL PEAK 22(9P21.3) WILD-TYPE	186	138	64

Figure S237. Get High-res Image Gene #47: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.049

Table S238. Gene #47: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 22(9P21.3) MUTATED	26	8	13	15
DEL PEAK 22(9P21.3) WILD-TYPE	95	99	77	115

Figure S238. Get High-res Image Gene #47: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00123 (Fisher's exact test), Q value = 0.0045

Table S239. Gene #47: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 22(9P21.3) MUTATED	16	19	6	21	0
DEL PEAK 22(9P21.3) WILD-TYPE	63	89	90	108	36

Figure S239. Get High-res Image Gene #47: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S240. Gene #48: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 23(10P15.3) MUTATED	16	46	18
DEL PEAK 23(10P15.3) WILD-TYPE	186	124	60

Figure S240. Get High-res Image Gene #48: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00021

Table S241. Gene #48: 'del_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
DEL PEAK 23(10P15.3) MUTATED	37	7	13
DEL PEAK 23(10P15.3) WILD-TYPE	83	90	63

Figure S241. Get High-res Image Gene #48: 'del_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0013

Table S242. Gene #48: 'del_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 23(10P15.3) MUTATED	33	7	18	21
DEL PEAK 23(10P15.3) WILD-TYPE	88	100	72	109

Figure S242. Get High-res Image Gene #48: 'del_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00063

Table S243. Gene #48: 'del_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 23(10P15.3) MUTATED	27	19	7	23	3
DEL PEAK 23(10P15.3) WILD-TYPE	52	89	89	106	33

Figure S243. Get High-res Image Gene #48: 'del_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.055

Table S244. Gene #48: 'del_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	12	22	17	24	10
DEL PEAK 23(10P15.3) MUTATED	4	8	0	3	2
DEL PEAK 23(10P15.3) WILD-TYPE	8	14	17	21	8

Figure S244. Get High-res Image Gene #48: 'del_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q21.1' versus 'MRNA_CNMF'

P value = 0.00312 (Fisher's exact test), Q value = 0.011

Table S245. Gene #49: 'del_10q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 24(10Q21.1) MUTATED	3	19	1	4
DEL PEAK 24(10Q21.1) WILD-TYPE	32	42	28	17

Figure S245. Get High-res Image Gene #49: 'del_10q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q21.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0279 (Fisher's exact test), Q value = 0.069

Table S246. Gene #49: 'del_10q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 24(10Q21.1) MUTATED	3	14	10
DEL PEAK 24(10Q21.1) WILD-TYPE	39	58	22

Figure S246. Get High-res Image Gene #49: 'del_10q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S247. Gene #49: 'del_10q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 24(10Q21.1) MUTATED	17	63	18
DEL PEAK 24(10Q21.1) WILD-TYPE	185	107	60

Figure S247. Get High-res Image Gene #49: 'del_10q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q21.1' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00021

Table S248. Gene #49: 'del_10q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
DEL PEAK 24(10Q21.1) MUTATED	44	12	14
DEL PEAK 24(10Q21.1) WILD-TYPE	76	85	62

Figure S248. Get High-res Image Gene #49: 'del_10q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q21.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S249. Gene #49: 'del_10q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 24(10Q21.1) MUTATED	45	8	19	25
DEL PEAK 24(10Q21.1) WILD-TYPE	76	99	71	105

Figure S249. Get High-res Image Gene #49: 'del_10q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S250. Gene #49: 'del_10q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 24(10Q21.1) MUTATED	28	27	9	32	1
DEL PEAK 24(10Q21.1) WILD-TYPE	51	81	87	97	35

Figure S250. Get High-res Image Gene #49: 'del_10q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S251. Gene #50: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 25(10Q23.31) MUTATED	25	63	21
DEL PEAK 25(10Q23.31) WILD-TYPE	177	107	57

Figure S251. Get High-res Image Gene #50: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00083

Table S252. Gene #50: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
DEL PEAK 25(10Q23.31) MUTATED	47	15	16
DEL PEAK 25(10Q23.31) WILD-TYPE	73	82	60

Figure S252. Get High-res Image Gene #50: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 0.00123 (Fisher's exact test), Q value = 0.0045

Table S253. Gene #50: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 25(10Q23.31) MUTATED	45	18	20	25
DEL PEAK 25(10Q23.31) WILD-TYPE	76	89	70	105

Figure S253. Get High-res Image Gene #50: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S254. Gene #50: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 25(10Q23.31) MUTATED	29	32	12	33	2
DEL PEAK 25(10Q23.31) WILD-TYPE	50	76	84	96	34

Figure S254. Get High-res Image Gene #50: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q25.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.018 (Fisher's exact test), Q value = 0.047

Table S255. Gene #51: 'del_10q25.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 26(10Q25.2) MUTATED	3	18	10
DEL PEAK 26(10Q25.2) WILD-TYPE	39	54	22

Figure S255. Get High-res Image Gene #51: 'del_10q25.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S256. Gene #51: 'del_10q25.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 26(10Q25.2) MUTATED	23	68	18
DEL PEAK 26(10Q25.2) WILD-TYPE	179	102	60

Figure S256. Get High-res Image Gene #51: 'del_10q25.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q25.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S257. Gene #51: 'del_10q25.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
DEL PEAK 26(10Q25.2) MUTATED	49	13	13
DEL PEAK 26(10Q25.2) WILD-TYPE	71	84	63

Figure S257. Get High-res Image Gene #51: 'del_10q25.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q25.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S258. Gene #51: 'del_10q25.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 26(10Q25.2) MUTATED	48	10	20	30
DEL PEAK 26(10Q25.2) WILD-TYPE	73	97	70	100

Figure S258. Get High-res Image Gene #51: 'del_10q25.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S259. Gene #51: 'del_10q25.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 26(10Q25.2) MUTATED	32	29	7	39	1
DEL PEAK 26(10Q25.2) WILD-TYPE	47	79	89	90	35

Figure S259. Get High-res Image Gene #51: 'del_10q25.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.2' versus 'MRNA_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.03

Table S260. Gene #52: 'del_12p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 27(12P13.2) MUTATED	2	13	0	2
DEL PEAK 27(12P13.2) WILD-TYPE	33	48	29	19

Figure S260. Get High-res Image Gene #52: 'del_12p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12p13.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00321 (Fisher's exact test), Q value = 0.011

Table S261. Gene #52: 'del_12p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 27(12P13.2) MUTATED	0	10	7
DEL PEAK 27(12P13.2) WILD-TYPE	42	62	25

Figure S261. Get High-res Image Gene #52: 'del_12p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S262. Gene #52: 'del_12p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 27(12P13.2) MUTATED	5	44	11
DEL PEAK 27(12P13.2) WILD-TYPE	197	126	67

Figure S262. Get High-res Image Gene #52: 'del_12p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_12p13.2' versus 'METHLYATION_CNMF'

P value = 0.00444 (Fisher's exact test), Q value = 0.014

Table S263. Gene #52: 'del_12p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
DEL PEAK 27(12P13.2) MUTATED	28	10	6
DEL PEAK 27(12P13.2) WILD-TYPE	92	87	70

Figure S263. Get High-res Image Gene #52: 'del_12p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12p13.2' versus 'MRNASEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0016

Table S264. Gene #52: 'del_12p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 27(12P13.2) MUTATED	27	4	11	18
DEL PEAK 27(12P13.2) WILD-TYPE	94	103	79	112

Figure S264. Get High-res Image Gene #52: 'del_12p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S265. Gene #52: 'del_12p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 27(12P13.2) MUTATED	16	21	2	21	0
DEL PEAK 27(12P13.2) WILD-TYPE	63	87	94	108	36

Figure S265. Get High-res Image Gene #52: 'del_12p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00195 (Fisher's exact test), Q value = 0.0069

Table S266. Gene #52: 'del_12p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	12	22	17	24	10
DEL PEAK 27(12P13.2) MUTATED	4	3	0	0	3
DEL PEAK 27(12P13.2) WILD-TYPE	8	19	17	24	7

Figure S266. Get High-res Image Gene #52: 'del_12p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q31.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S267. Gene #54: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 29(14Q31.1) MUTATED	6	36	3	10
DEL PEAK 29(14Q31.1) WILD-TYPE	29	25	26	11

Figure S267. Get High-res Image Gene #54: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q31.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00055

Table S268. Gene #54: 'del_14q31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 29(14Q31.1) MUTATED	6	29	20
DEL PEAK 29(14Q31.1) WILD-TYPE	36	43	12

Figure S268. Get High-res Image Gene #54: 'del_14q31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S269. Gene #54: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 29(14Q31.1) MUTATED	28	107	15
DEL PEAK 29(14Q31.1) WILD-TYPE	174	63	63

Figure S269. Get High-res Image Gene #54: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q31.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S270. Gene #54: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
DEL PEAK 29(14Q31.1) MUTATED	57	18	18
DEL PEAK 29(14Q31.1) WILD-TYPE	63	79	58

Figure S270. Get High-res Image Gene #54: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q31.1' versus 'RPPA_CNMF'

P value = 0.019 (Fisher's exact test), Q value = 0.049

Table S271. Gene #54: 'del_14q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	144	125
DEL PEAK 29(14Q31.1) MUTATED	31	57	30
DEL PEAK 29(14Q31.1) WILD-TYPE	54	87	95

Figure S271. Get High-res Image Gene #54: 'del_14q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_14q31.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S272. Gene #54: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 29(14Q31.1) MUTATED	62	12	23	53
DEL PEAK 29(14Q31.1) WILD-TYPE	59	95	67	77

Figure S272. Get High-res Image Gene #54: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S273. Gene #54: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 29(14Q31.1) MUTATED	33	46	9	60	2
DEL PEAK 29(14Q31.1) WILD-TYPE	46	62	87	69	34

Figure S273. Get High-res Image Gene #54: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0219 (Fisher's exact test), Q value = 0.055

Table S274. Gene #54: 'del_14q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	50	77	135
DEL PEAK 29(14Q31.1) MUTATED	42	9	34	45
DEL PEAK 29(14Q31.1) WILD-TYPE	93	41	43	90

Figure S274. Get High-res Image Gene #54: 'del_14q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.039

Table S275. Gene #54: 'del_14q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	12	22	17	24	10
DEL PEAK 29(14Q31.1) MUTATED	5	8	7	4	8
DEL PEAK 29(14Q31.1) WILD-TYPE	7	14	10	20	2

Figure S275. Get High-res Image Gene #54: 'del_14q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q11.2' versus 'MRNA_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0016

Table S276. Gene #55: 'del_15q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 30(15Q11.2) MUTATED	8	35	6	11
DEL PEAK 30(15Q11.2) WILD-TYPE	27	26	23	10

Figure S276. Get High-res Image Gene #55: 'del_15q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.003

Table S277. Gene #55: 'del_15q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 30(15Q11.2) MUTATED	8	33	19
DEL PEAK 30(15Q11.2) WILD-TYPE	34	39	13

Figure S277. Get High-res Image Gene #55: 'del_15q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S278. Gene #55: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 30(15Q11.2) MUTATED	34	117	26
DEL PEAK 30(15Q11.2) WILD-TYPE	168	53	52

Figure S278. Get High-res Image Gene #55: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q11.2' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00055

Table S279. Gene #55: 'del_15q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
DEL PEAK 30(15Q11.2) MUTATED	65	28	22
DEL PEAK 30(15Q11.2) WILD-TYPE	55	69	54

Figure S279. Get High-res Image Gene #55: 'del_15q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S280. Gene #55: 'del_15q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 30(15Q11.2) MUTATED	64	18	36	58
DEL PEAK 30(15Q11.2) WILD-TYPE	57	89	54	72

Figure S280. Get High-res Image Gene #55: 'del_15q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S281. Gene #55: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 30(15Q11.2) MUTATED	44	52	11	63	6
DEL PEAK 30(15Q11.2) WILD-TYPE	35	56	85	66	30

Figure S281. Get High-res Image Gene #55: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q15.2' versus 'MRNA_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.0051

Table S282. Gene #56: 'del_15q15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 31(15Q15.2) MUTATED	8	33	6	11
DEL PEAK 31(15Q15.2) WILD-TYPE	27	28	23	10

Figure S282. Get High-res Image Gene #56: 'del_15q15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q15.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0024

Table S283. Gene #56: 'del_15q15.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 31(15Q15.2) MUTATED	7	33	18
DEL PEAK 31(15Q15.2) WILD-TYPE	35	39	14

Figure S283. Get High-res Image Gene #56: 'del_15q15.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q15.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S284. Gene #56: 'del_15q15.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 31(15Q15.2) MUTATED	35	112	25
DEL PEAK 31(15Q15.2) WILD-TYPE	167	58	53

Figure S284. Get High-res Image Gene #56: 'del_15q15.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q15.2' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 3e-04

Table S285. Gene #56: 'del_15q15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
DEL PEAK 31(15Q15.2) MUTATED	64	26	22
DEL PEAK 31(15Q15.2) WILD-TYPE	56	71	54

Figure S285. Get High-res Image Gene #56: 'del_15q15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q15.2' versus 'RPPA_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.034

Table S286. Gene #56: 'del_15q15.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	144	125
DEL PEAK 31(15Q15.2) MUTATED	42	47	38
DEL PEAK 31(15Q15.2) WILD-TYPE	43	97	87

Figure S286. Get High-res Image Gene #56: 'del_15q15.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_15q15.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S287. Gene #56: 'del_15q15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 31(15Q15.2) MUTATED	63	19	33	56
DEL PEAK 31(15Q15.2) WILD-TYPE	58	88	57	74

Figure S287. Get High-res Image Gene #56: 'del_15q15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q15.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S288. Gene #56: 'del_15q15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 31(15Q15.2) MUTATED	41	50	12	63	5
DEL PEAK 31(15Q15.2) WILD-TYPE	38	58	84	66	31

Figure S288. Get High-res Image Gene #56: 'del_15q15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q21.1' versus 'MRNA_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.049

Table S289. Gene #57: 'del_15q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 32(15Q21.1) MUTATED	11	31	6	11
DEL PEAK 32(15Q21.1) WILD-TYPE	24	30	23	10

Figure S289. Get High-res Image Gene #57: 'del_15q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q21.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0147 (Fisher's exact test), Q value = 0.04

Table S290. Gene #57: 'del_15q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 32(15Q21.1) MUTATED	10	31	18
DEL PEAK 32(15Q21.1) WILD-TYPE	32	41	14

Figure S290. Get High-res Image Gene #57: 'del_15q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S291. Gene #57: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 32(15Q21.1) MUTATED	35	109	25
DEL PEAK 32(15Q21.1) WILD-TYPE	167	61	53

Figure S291. Get High-res Image Gene #57: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q21.1' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00063

Table S292. Gene #57: 'del_15q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
DEL PEAK 32(15Q21.1) MUTATED	61	25	22
DEL PEAK 32(15Q21.1) WILD-TYPE	59	72	54

Figure S292. Get High-res Image Gene #57: 'del_15q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q21.1' versus 'RPPA_CNMF'

P value = 0.0477 (Fisher's exact test), Q value = 0.11

Table S293. Gene #57: 'del_15q21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	144	125
DEL PEAK 32(15Q21.1) MUTATED	40	48	39
DEL PEAK 32(15Q21.1) WILD-TYPE	45	96	86

Figure S293. Get High-res Image Gene #57: 'del_15q21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_15q21.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S294. Gene #57: 'del_15q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 32(15Q21.1) MUTATED	61	18	32	57
DEL PEAK 32(15Q21.1) WILD-TYPE	60	89	58	73

Figure S294. Get High-res Image Gene #57: 'del_15q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S295. Gene #57: 'del_15q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 32(15Q21.1) MUTATED	39	49	11	61	8
DEL PEAK 32(15Q21.1) WILD-TYPE	40	59	85	68	28

Figure S295. Get High-res Image Gene #57: 'del_15q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q22.33' versus 'MRNA_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0014

Table S296. Gene #58: 'del_15q22.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 33(15Q22.33) MUTATED	8	31	3	10
DEL PEAK 33(15Q22.33) WILD-TYPE	27	30	26	11

Figure S296. Get High-res Image Gene #58: 'del_15q22.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q22.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.0017

Table S297. Gene #58: 'del_15q22.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 33(15Q22.33) MUTATED	6	28	18
DEL PEAK 33(15Q22.33) WILD-TYPE	36	44	14

Figure S297. Get High-res Image Gene #58: 'del_15q22.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q22.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S298. Gene #58: 'del_15q22.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 33(15Q22.33) MUTATED	29	109	23
DEL PEAK 33(15Q22.33) WILD-TYPE	173	61	55

Figure S298. Get High-res Image Gene #58: 'del_15q22.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q22.33' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00047

Table S299. Gene #58: 'del_15q22.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
DEL PEAK 33(15Q22.33) MUTATED	62	23	23
DEL PEAK 33(15Q22.33) WILD-TYPE	58	74	53

Figure S299. Get High-res Image Gene #58: 'del_15q22.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q22.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S300. Gene #58: 'del_15q22.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 33(15Q22.33) MUTATED	61	15	32	52
DEL PEAK 33(15Q22.33) WILD-TYPE	60	92	58	78

Figure S300. Get High-res Image Gene #58: 'del_15q22.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q22.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S301. Gene #58: 'del_15q22.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 33(15Q22.33) MUTATED	41	47	11	58	3
DEL PEAK 33(15Q22.33) WILD-TYPE	38	61	85	71	33

Figure S301. Get High-res Image Gene #58: 'del_15q22.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00543 (Fisher's exact test), Q value = 0.017

Table S302. Gene #60: 'del_16q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 35(16Q23.1) MUTATED	13	6	3
DEL PEAK 35(16Q23.1) WILD-TYPE	29	66	29

Figure S302. Get High-res Image Gene #60: 'del_16q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0126 (Fisher's exact test), Q value = 0.035

Table S303. Gene #60: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 35(16Q23.1) MUTATED	9	13	15	12	12
DEL PEAK 35(16Q23.1) WILD-TYPE	70	95	81	117	24

Figure S303. Get High-res Image Gene #60: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S304. Gene #61: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 36(17P12) MUTATED	10	49	8	15
DEL PEAK 36(17P12) WILD-TYPE	25	12	21	6

Figure S304. Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S305. Gene #61: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 36(17P12) MUTATED	9	47	26
DEL PEAK 36(17P12) WILD-TYPE	33	25	6

Figure S305. Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S306. Gene #61: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 36(17P12) MUTATED	53	147	54
DEL PEAK 36(17P12) WILD-TYPE	149	23	24

Figure S306. Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S307. Gene #61: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
DEL PEAK 36(17P12) MUTATED	103	34	31
DEL PEAK 36(17P12) WILD-TYPE	17	63	45

Figure S307. Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00076 (Fisher's exact test), Q value = 0.0029

Table S308. Gene #61: 'del_17p12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	51	33	35	39	42	86	22	20	26
DEL PEAK 36(17P12) MUTATED	35	14	26	22	23	37	8	10	21
DEL PEAK 36(17P12) WILD-TYPE	16	19	9	17	19	49	14	10	5

Figure S308. Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S309. Gene #61: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 36(17P12) MUTATED	101	29	46	77
DEL PEAK 36(17P12) WILD-TYPE	20	78	44	53

Figure S309. Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S310. Gene #61: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 36(17P12) MUTATED	55	83	20	91	4
DEL PEAK 36(17P12) WILD-TYPE	24	25	76	38	32

Figure S310. Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0217 (Fisher's exact test), Q value = 0.055

Table S311. Gene #61: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	50	77	135
DEL PEAK 36(17P12) MUTATED	74	24	55	71
DEL PEAK 36(17P12) WILD-TYPE	61	26	22	64

Figure S311. Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00131 (Fisher's exact test), Q value = 0.0047

Table S312. Gene #61: 'del_17p12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	12	22	17	24	10
DEL PEAK 36(17P12) MUTATED	8	17	11	8	10
DEL PEAK 36(17P12) WILD-TYPE	4	5	6	16	0

Figure S312. Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q24.3' versus 'CN_CNMF'

P value = 0.00407 (Fisher's exact test), Q value = 0.013

Table S313. Gene #62: 'del_17q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 37(17Q24.3) MUTATED	20	38	11
DEL PEAK 37(17Q24.3) WILD-TYPE	182	132	67

Figure S313. Get High-res Image Gene #62: 'del_17q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_17q24.3' versus 'MRNASEQ_CNMF'

P value = 0.044 (Fisher's exact test), Q value = 0.1

Table S314. Gene #62: 'del_17q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 37(17Q24.3) MUTATED	26	9	12	22
DEL PEAK 37(17Q24.3) WILD-TYPE	95	98	78	108

Figure S314. Get High-res Image Gene #62: 'del_17q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18p11.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S315. Gene #63: 'del_18p11.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 38(18P11.31) MUTATED	6	50	7	15
DEL PEAK 38(18P11.31) WILD-TYPE	29	11	22	6

Figure S315. Get High-res Image Gene #63: 'del_18p11.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18p11.31' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S316. Gene #63: 'del_18p11.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 38(18P11.31) MUTATED	5	47	26
DEL PEAK 38(18P11.31) WILD-TYPE	37	25	6

Figure S316. Get High-res Image Gene #63: 'del_18p11.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18p11.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S317. Gene #63: 'del_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 38(18P11.31) MUTATED	47	154	45
DEL PEAK 38(18P11.31) WILD-TYPE	155	16	33

Figure S317. Get High-res Image Gene #63: 'del_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_18p11.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S318. Gene #63: 'del_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
DEL PEAK 38(18P11.31) MUTATED	105	27	33
DEL PEAK 38(18P11.31) WILD-TYPE	15	70	43

Figure S318. Get High-res Image Gene #63: 'del_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18p11.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0045 (Fisher's exact test), Q value = 0.014

Table S319. Gene #63: 'del_18p11.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	51	33	35	39	42	86	22	20	26
DEL PEAK 38(18P11.31) MUTATED	29	19	23	19	23	35	8	11	22
DEL PEAK 38(18P11.31) WILD-TYPE	22	14	12	20	19	51	14	9	4

Figure S319. Get High-res Image Gene #63: 'del_18p11.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_18p11.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S320. Gene #63: 'del_18p11.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 38(18P11.31) MUTATED	106	21	46	72
DEL PEAK 38(18P11.31) WILD-TYPE	15	86	44	58

Figure S320. Get High-res Image Gene #63: 'del_18p11.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18p11.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S321. Gene #63: 'del_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 38(18P11.31) MUTATED	61	81	12	89	2
DEL PEAK 38(18P11.31) WILD-TYPE	18	27	84	40	34

Figure S321. Get High-res Image Gene #63: 'del_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18p11.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0111 (Fisher's exact test), Q value = 0.032

Table S322. Gene #63: 'del_18p11.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	50	77	135
DEL PEAK 38(18P11.31) MUTATED	68	23	54	67
DEL PEAK 38(18P11.31) WILD-TYPE	67	27	23	68

Figure S322. Get High-res Image Gene #63: 'del_18p11.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18p11.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0036 (Fisher's exact test), Q value = 0.012

Table S323. Gene #63: 'del_18p11.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	12	22	17	24	10
DEL PEAK 38(18P11.31) MUTATED	10	13	10	7	9
DEL PEAK 38(18P11.31) WILD-TYPE	2	9	7	17	1

Figure S323. Get High-res Image Gene #63: 'del_18p11.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q12.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S324. Gene #64: 'del_18q12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 39(18Q12.2) MUTATED	8	53	9	16
DEL PEAK 39(18Q12.2) WILD-TYPE	27	8	20	5

Figure S324. Get High-res Image Gene #64: 'del_18q12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q12.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S325. Gene #64: 'del_18q12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 39(18Q12.2) MUTATED	7	51	28
DEL PEAK 39(18Q12.2) WILD-TYPE	35	21	4

Figure S325. Get High-res Image Gene #64: 'del_18q12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18q12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S326. Gene #64: 'del_18q12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 39(18Q12.2) MUTATED	55	159	60
DEL PEAK 39(18Q12.2) WILD-TYPE	147	11	18

Figure S326. Get High-res Image Gene #64: 'del_18q12.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q12.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S327. Gene #64: 'del_18q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
DEL PEAK 39(18Q12.2) MUTATED	112	35	36
DEL PEAK 39(18Q12.2) WILD-TYPE	8	62	40

Figure S327. Get High-res Image Gene #64: 'del_18q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q12.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00444 (Fisher's exact test), Q value = 0.014

Table S328. Gene #64: 'del_18q12.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	51	33	35	39	42	86	22	20	26
DEL PEAK 39(18Q12.2) MUTATED	36	17	25	23	26	38	9	13	21
DEL PEAK 39(18Q12.2) WILD-TYPE	15	16	10	16	16	48	13	7	5

Figure S328. Get High-res Image Gene #64: 'del_18q12.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_18q12.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S329. Gene #64: 'del_18q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 39(18Q12.2) MUTATED	108	28	55	82
DEL PEAK 39(18Q12.2) WILD-TYPE	13	79	35	48

Figure S329. Get High-res Image Gene #64: 'del_18q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S330. Gene #64: 'del_18q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 39(18Q12.2) MUTATED	67	87	19	97	3
DEL PEAK 39(18Q12.2) WILD-TYPE	12	21	77	32	33

Figure S330. Get High-res Image Gene #64: 'del_18q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.02 (Fisher's exact test), Q value = 0.051

Table S331. Gene #64: 'del_18q12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	50	77	135
DEL PEAK 39(18Q12.2) MUTATED	79	28	58	74
DEL PEAK 39(18Q12.2) WILD-TYPE	56	22	19	61

Figure S331. Get High-res Image Gene #64: 'del_18q12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00523 (Fisher's exact test), Q value = 0.017

Table S332. Gene #64: 'del_18q12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	12	22	17	24	10
DEL PEAK 39(18Q12.2) MUTATED	10	17	11	10	10
DEL PEAK 39(18Q12.2) WILD-TYPE	2	5	6	14	0

Figure S332. Get High-res Image Gene #64: 'del_18q12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q21.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S333. Gene #65: 'del_18q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 40(18Q21.2) MUTATED	8	53	10	16
DEL PEAK 40(18Q21.2) WILD-TYPE	27	8	19	5

Figure S333. Get High-res Image Gene #65: 'del_18q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q21.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S334. Gene #65: 'del_18q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 40(18Q21.2) MUTATED	7	52	28
DEL PEAK 40(18Q21.2) WILD-TYPE	35	20	4

Figure S334. Get High-res Image Gene #65: 'del_18q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S335. Gene #65: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 40(18Q21.2) MUTATED	63	161	63
DEL PEAK 40(18Q21.2) WILD-TYPE	139	9	15

Figure S335. Get High-res Image Gene #65: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S336. Gene #65: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
DEL PEAK 40(18Q21.2) MUTATED	114	45	36
DEL PEAK 40(18Q21.2) WILD-TYPE	6	52	40

Figure S336. Get High-res Image Gene #65: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q21.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00707 (Fisher's exact test), Q value = 0.022

Table S337. Gene #65: 'del_18q21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	51	33	35	39	42	86	22	20	26
DEL PEAK 40(18Q21.2) MUTATED	38	18	25	26	27	41	10	15	21
DEL PEAK 40(18Q21.2) WILD-TYPE	13	15	10	13	15	45	12	5	5

Figure S337. Get High-res Image Gene #65: 'del_18q21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S338. Gene #65: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 40(18Q21.2) MUTATED	109	37	58	82
DEL PEAK 40(18Q21.2) WILD-TYPE	12	70	32	48

Figure S338. Get High-res Image Gene #65: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S339. Gene #65: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 40(18Q21.2) MUTATED	69	89	27	97	4
DEL PEAK 40(18Q21.2) WILD-TYPE	10	19	69	32	32

Figure S339. Get High-res Image Gene #65: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0345 (Fisher's exact test), Q value = 0.082

Table S340. Gene #65: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	50	77	135
DEL PEAK 40(18Q21.2) MUTATED	86	30	59	77
DEL PEAK 40(18Q21.2) WILD-TYPE	49	20	18	58

Figure S340. Get High-res Image Gene #65: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00818 (Fisher's exact test), Q value = 0.025

Table S341. Gene #65: 'del_18q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	12	22	17	24	10
DEL PEAK 40(18Q21.2) MUTATED	10	17	14	11	10
DEL PEAK 40(18Q21.2) WILD-TYPE	2	5	3	13	0

Figure S341. Get High-res Image Gene #65: 'del_18q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0029

Table S342. Gene #66: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 41(19P13.3) MUTATED	15	33	15
DEL PEAK 41(19P13.3) WILD-TYPE	187	137	63

Figure S342. Get High-res Image Gene #66: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 0.004 (Fisher's exact test), Q value = 0.013

Table S343. Gene #66: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 41(19P13.3) MUTATED	24	5	13	21
DEL PEAK 41(19P13.3) WILD-TYPE	97	102	77	109

Figure S343. Get High-res Image Gene #66: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00102 (Fisher's exact test), Q value = 0.0038

Table S344. Gene #66: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 41(19P13.3) MUTATED	10	20	5	27	1
DEL PEAK 41(19P13.3) WILD-TYPE	69	88	91	102	35

Figure S344. Get High-res Image Gene #66: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0087 (Fisher's exact test), Q value = 0.026

Table S345. Gene #66: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	50	77	135
DEL PEAK 41(19P13.3) MUTATED	18	1	17	20
DEL PEAK 41(19P13.3) WILD-TYPE	117	49	60	115

Figure S345. Get High-res Image Gene #66: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MRNA_CNMF'

P value = 0.048 (Fisher's exact test), Q value = 0.11

Table S346. Gene #67: 'del_20p12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 42(20P12.1) MUTATED	3	17	3	2
DEL PEAK 42(20P12.1) WILD-TYPE	32	44	26	19

Figure S346. Get High-res Image Gene #67: 'del_20p12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_20p12.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0285 (Fisher's exact test), Q value = 0.07

Table S347. Gene #67: 'del_20p12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 42(20P12.1) MUTATED	3	12	10
DEL PEAK 42(20P12.1) WILD-TYPE	39	60	22

Figure S347. Get High-res Image Gene #67: 'del_20p12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_20p12.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S348. Gene #67: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 42(20P12.1) MUTATED	19	47	20
DEL PEAK 42(20P12.1) WILD-TYPE	183	123	58

Figure S348. Get High-res Image Gene #67: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_20p12.1' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00039

Table S349. Gene #67: 'del_20p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
DEL PEAK 42(20P12.1) MUTATED	39	9	12
DEL PEAK 42(20P12.1) WILD-TYPE	81	88	64

Figure S349. Get High-res Image Gene #67: 'del_20p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_20p12.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.044

Table S350. Gene #67: 'del_20p12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	51	33	35	39	42	86	22	20	26
DEL PEAK 42(20P12.1) MUTATED	12	1	11	11	6	14	2	6	8
DEL PEAK 42(20P12.1) WILD-TYPE	39	32	24	28	36	72	20	14	18

Figure S350. Get High-res Image Gene #67: 'del_20p12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_20p12.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S351. Gene #67: 'del_20p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 42(20P12.1) MUTATED	44	7	15	20
DEL PEAK 42(20P12.1) WILD-TYPE	77	100	75	110

Figure S351. Get High-res Image Gene #67: 'del_20p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S352. Gene #67: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 42(20P12.1) MUTATED	24	30	5	23	4
DEL PEAK 42(20P12.1) WILD-TYPE	55	78	91	106	32

Figure S352. Get High-res Image Gene #67: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.03

Table S353. Gene #67: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	135	50	77	135
DEL PEAK 42(20P12.1) MUTATED	26	12	22	15
DEL PEAK 42(20P12.1) WILD-TYPE	109	38	55	120

Figure S353. Get High-res Image Gene #67: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0477 (Fisher's exact test), Q value = 0.11

Table S354. Gene #67: 'del_20p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	12	22	17	24	10
DEL PEAK 42(20P12.1) MUTATED	2	5	6	1	4
DEL PEAK 42(20P12.1) WILD-TYPE	10	17	11	23	6

Figure S354. Get High-res Image Gene #67: 'del_20p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q11.2' versus 'MRNA_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.044

Table S355. Gene #68: 'del_21q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 43(21Q11.2) MUTATED	7	29	6	6
DEL PEAK 43(21Q11.2) WILD-TYPE	28	32	23	15

Figure S355. Get High-res Image Gene #68: 'del_21q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_21q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S356. Gene #68: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 43(21Q11.2) MUTATED	42	82	17
DEL PEAK 43(21Q11.2) WILD-TYPE	160	88	61

Figure S356. Get High-res Image Gene #68: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 0.00608 (Fisher's exact test), Q value = 0.019

Table S357. Gene #68: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
DEL PEAK 43(21Q11.2) MUTATED	49	21	20
DEL PEAK 43(21Q11.2) WILD-TYPE	71	76	56

Figure S357. Get High-res Image Gene #68: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00021

Table S358. Gene #68: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 43(21Q11.2) MUTATED	57	17	26	40
DEL PEAK 43(21Q11.2) WILD-TYPE	64	90	64	90

Figure S358. Get High-res Image Gene #68: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_21q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.0016

Table S359. Gene #68: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 43(21Q11.2) MUTATED	35	35	18	47	5
DEL PEAK 43(21Q11.2) WILD-TYPE	44	73	78	82	31

Figure S359. Get High-res Image Gene #68: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MRNA_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.0021

Table S360. Gene #69: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 44(22Q13.32) MUTATED	8	34	5	10
DEL PEAK 44(22Q13.32) WILD-TYPE	27	27	24	11

Figure S360. Get High-res Image Gene #69: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_22q13.32' versus 'MRNA_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.0011

Table S361. Gene #69: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	72	32
DEL PEAK 44(22Q13.32) MUTATED	6	35	16
DEL PEAK 44(22Q13.32) WILD-TYPE	36	37	16

Figure S361. Get High-res Image Gene #69: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S362. Gene #69: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	202	170	78
DEL PEAK 44(22Q13.32) MUTATED	40	98	22
DEL PEAK 44(22Q13.32) WILD-TYPE	162	72	56

Figure S362. Get High-res Image Gene #69: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 0.00557 (Fisher's exact test), Q value = 0.018

Table S363. Gene #69: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	120	97	76
DEL PEAK 44(22Q13.32) MUTATED	50	21	28
DEL PEAK 44(22Q13.32) WILD-TYPE	70	76	48

Figure S363. Get High-res Image Gene #69: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q13.32' versus 'RPPA_CHIERARCHICAL'

P value = 0.0116 (Fisher's exact test), Q value = 0.033

Table S364. Gene #69: 'del_22q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	51	33	35	39	42	86	22	20	26
DEL PEAK 44(22Q13.32) MUTATED	17	7	23	10	14	25	7	7	10
DEL PEAK 44(22Q13.32) WILD-TYPE	34	26	12	29	28	61	15	13	16

Figure S364. Get High-res Image Gene #69: 'del_22q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S365. Gene #69: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	121	107	90	130
DEL PEAK 44(22Q13.32) MUTATED	56	18	32	53
DEL PEAK 44(22Q13.32) WILD-TYPE	65	89	58	77

Figure S365. Get High-res Image Gene #69: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.1e-05

Table S366. Gene #69: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	79	108	96	129	36
DEL PEAK 44(22Q13.32) MUTATED	37	45	13	61	3
DEL PEAK 44(22Q13.32) WILD-TYPE	42	63	83	68	33

Figure S366. Get High-res Image Gene #69: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_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/COAD-TP/19780705/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/COAD-TP/20125559/COAD-TP.transferedmergedcluster.txt
Number of patients = 450
Number of significantly focal cnvs = 69
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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