Correlation between copy number variation genes and molecular subtypes

Colon Adenocarcinoma (Primary solid tumor)

23 May 2013 | analyses__2013_05_23

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1NK3C1Z

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.

Summary

Testing the association between copy number variation of 68 peak regions and 12 molecular subtypes across 413 patients, 193 significant findings detected with Q value < 0.25.

Amp Peak 1(2q33.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 2(5p13.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 4(6p21.1) cnvs correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.
Amp Peak 5(8p11.23) cnvs correlated to 'CN_CNMF'.
Amp Peak 6(8p11.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 7(8q12.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 8(8q24.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 9(11p15.5) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 11(13q12.13) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 12(13q22.1) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 13(16p11.2) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 14(16q12.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 15(17q12) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Amp Peak 16(17q24.1) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Amp Peak 17(19p13.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 19(20p12.3) cnvs correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.
Amp Peak 20(20p11.23) cnvs correlated to 'CN_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 21(20p11.21) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 22(20q11.21) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 23(20q12) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 24(20q13.32) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 1(1p36.11) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 2(1p33) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 3(1p13.1) cnvs correlated to 'CN_CNMF'.
Del Peak 4(1q43) cnvs correlated to 'CN_CNMF'.
Del Peak 9(4p16.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 10(4q22.1) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 11(4q35.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 12(5q11.2) cnvs correlated to 'CN_CNMF'.
Del Peak 13(5q21.3) cnvs correlated to 'CN_CNMF'.
Del Peak 14(5q23.1) cnvs correlated to 'CN_CNMF'.
Del Peak 15(6p25.3) cnvs correlated to 'CN_CNMF'.
Del Peak 18(8p23.3) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 19(8p22) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 20(8p11.22) cnvs correlated to 'CN_CNMF'.
Del Peak 21(8p11.21) cnvs correlated to 'CN_CNMF'.
Del Peak 22(9p21.3) cnvs correlated to 'CN_CNMF'.
Del Peak 23(10p15.3) cnvs correlated to 'CN_CNMF'.
Del Peak 24(10q21.1) cnvs correlated to 'CN_CNMF'.
Del Peak 25(10q23.31) cnvs correlated to 'CN_CNMF'.
Del Peak 26(10q25.2) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
Del Peak 27(12p13.2) cnvs correlated to 'CN_CNMF'.
Del Peak 28(13q14.13) cnvs correlated to 'CN_CNMF'.
Del Peak 29(14q32.11) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 30(15q11.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 31(15q21.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 32(15q22.33) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 35(17p12) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 37(18p11.31) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 38(18q12.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 39(18q21.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 40(18q22.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 42(20p12.1) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 43(21q11.2) cnvs correlated to 'CN_CNMF'.
Del Peak 44(22q13.32) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MIRSEQ_MATURE_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 68 regions and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 193 significant findings detected.


		Molecular subtypes	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	Chi-square test
Amp Peak 22(20q11 21)	0 (0%)	117	3.87e-10 (2.87e-07)	7.28e-12 (5.59e-09)	1.54e-43 (1.25e-40)	6.22e-10 (4.61e-07)	0.0201 (1.00)	0.000108 (0.0708)	1.47e-14 (1.16e-11)	3.85e-12 (2.97e-09)	0.443 (1.00)	1 (1.00)	1.45e-10 (1.08e-07)	7.33e-19 (5.86e-16)
Amp Peak 23(20q12)	0 (0%)	116	4.29e-11 (3.24e-08)	4.99e-12 (3.84e-09)	6.28e-43 (5.1e-40)	4.37e-09 (3.19e-06)	0.00771 (1.00)	2.18e-05 (0.0147)	5.48e-14 (4.31e-11)	1.34e-11 (1.03e-08)	0.406 (1.00)	0.948 (1.00)	1.88e-11 (1.43e-08)	1.03e-18 (8.19e-16)
Amp Peak 24(20q13 32)	0 (0%)	113	7.91e-10 (5.83e-07)	2.34e-12 (1.81e-09)	3.18e-43 (2.58e-40)	4.37e-09 (3.19e-06)	0.00832 (1.00)	1.3e-05 (0.00891)	5.48e-14 (4.31e-11)	1.34e-11 (1.03e-08)	0.414 (1.00)	0.96 (1.00)	6.8e-11 (5.12e-08)	6.03e-18 (4.8e-15)
Del Peak 35(17p12)	0 (0%)	184	2.47e-08 (1.78e-05)	4.97e-07 (0.000353)	2.81e-35 (2.27e-32)	2.58e-10 (1.92e-07)	0.0465 (1.00)	7.42e-05 (0.0489)	1.06e-10 (7.92e-08)	3.2e-08 (2.3e-05)	0.363 (1.00)	0.729 (1.00)	1.4e-09 (1.02e-06)	2.43e-10 (1.81e-07)
Del Peak 39(18q21 2)	0 (0%)	153	3.37e-11 (2.55e-08)	1.46e-10 (1.09e-07)	1.51e-45 (1.23e-42)	5.83e-13 (4.54e-10)	0.0109 (1.00)	0.000225 (0.144)	8.74e-13 (6.8e-10)	7.14e-07 (0.000503)	0.0517 (1.00)	0.901 (1.00)	6.95e-10 (5.13e-07)	6.62e-11 (5e-08)
Del Peak 40(18q22 1)	0 (0%)	153	8.76e-11 (6.58e-08)	8.34e-10 (6.13e-07)	1.58e-47 (1.29e-44)	3.42e-13 (2.67e-10)	0.0178 (1.00)	0.000224 (0.143)	4.05e-12 (3.13e-09)	2.76e-07 (0.000197)	0.0746 (1.00)	0.912 (1.00)	2.4e-10 (1.79e-07)	6.72e-11 (5.07e-08)
Amp Peak 11(13q12 13)	0 (0%)	163	1.58e-06 (0.0011)	2.07e-06 (0.00144)	5.04e-36 (4.07e-33)	0.000318 (0.2)	0.0709 (1.00)	0.0124 (1.00)	1.27e-06 (0.000888)	0.000196 (0.125)	0.459 (1.00)	0.798 (1.00)	2.46e-05 (0.0166)	1.2e-08 (8.69e-06)
Del Peak 37(18p11 31)	0 (0%)	193	6.87e-12 (5.28e-09)	7.49e-10 (5.53e-07)	1.93e-42 (1.56e-39)	1.57e-14 (1.23e-11)	0.0023 (1.00)	0.00104 (0.617)	3.11e-17 (2.47e-14)	8.19e-10 (6.03e-07)	0.48 (1.00)	0.841 (1.00)	1.44e-11 (1.1e-08)	3.44e-12 (2.66e-09)
Del Peak 38(18q12 2)	0 (0%)	166	1.09e-11 (8.36e-09)	2.66e-10 (1.98e-07)	1.87e-45 (1.52e-42)	9.4e-17 (7.45e-14)	0.0214 (1.00)	0.000421 (0.262)	7.66e-16 (6.05e-13)	1.07e-08 (7.79e-06)	0.449 (1.00)	0.865 (1.00)	8.5e-11 (6.39e-08)	4.43e-13 (3.45e-10)
Amp Peak 12(13q22 1)	0 (0%)	159	0.000586 (0.356)	4.41e-05 (0.0294)	7.2e-33 (5.81e-30)	0.0002 (0.128)	0.152 (1.00)	0.0444 (1.00)	1.15e-06 (0.000804)	7.67e-05 (0.0505)	0.272 (1.00)	0.977 (1.00)	3.61e-05 (0.0241)	6.29e-07 (0.000444)
Del Peak 19(8p22)	0 (0%)	228	0.00264 (1.00)	0.000174 (0.112)	2.41e-30 (1.94e-27)	7.14e-08 (5.11e-05)	0.0649 (1.00)	0.00013 (0.0841)	2.16e-05 (0.0147)	0.000656 (0.397)	0.115 (1.00)	0.832 (1.00)	1.99e-05 (0.0136)	1.73e-05 (0.0118)
Amp Peak 21(20p11 21)	0 (0%)	183	0.00304 (1.00)	1.6e-05 (0.011)	4e-23 (3.22e-20)	0.000479 (0.295)	0.0624 (1.00)	0.0394 (1.00)	2.41e-07 (0.000172)	1.39e-06 (0.000968)	0.174 (1.00)	0.509 (1.00)	6.09e-07 (0.000431)	1.56e-08 (1.13e-05)
Del Peak 29(14q32 11)	0 (0%)	280	1.58e-06 (0.0011)	3.23e-05 (0.0217)	1.61e-20 (1.29e-17)	0.000457 (0.282)	0.00347 (1.00)	0.0236 (1.00)	7.3e-05 (0.0483)	0.00084 (0.503)	0.319 (1.00)	0.0612 (1.00)	2.46e-05 (0.0166)	3.39e-05 (0.0227)
Del Peak 32(15q22 33)	0 (0%)	268	0.000273 (0.172)	0.000835 (0.5)	2.48e-21 (1.99e-18)	0.000336 (0.211)	0.141 (1.00)	0.0512 (1.00)	3.07e-08 (2.2e-05)	7.55e-06 (0.00521)	0.949 (1.00)	0.365 (1.00)	0.000461 (0.284)	1.77e-05 (0.012)
Amp Peak 9(11p15 5)	0 (0%)	327	6.09e-06 (0.00421)	0.000343 (0.215)	1.54e-09 (1.13e-06)	4.01e-05 (0.0267)	0.00156 (0.9)	0.00358 (1.00)	0.00193 (1.00)	0.00845 (1.00)	0.117 (1.00)	0.201 (1.00)	0.00207 (1.00)	7.43e-07 (0.000522)
Amp Peak 14(16q12 1)	0 (0%)	311	0.000126 (0.082)	2.53e-05 (0.0171)	1.67e-20 (1.34e-17)	0.0156 (1.00)	0.619 (1.00)	0.081 (1.00)	0.000642 (0.389)	0.00254 (1.00)	0.902 (1.00)	0.93 (1.00)	0.000237 (0.15)	5.23e-07 (0.000371)
Del Peak 1(1p36 11)	0 (0%)	263	0.00015 (0.0967)	0.00247 (1.00)	6.32e-17 (5.01e-14)	0.000328 (0.207)	0.0155 (1.00)	0.0238 (1.00)	0.000347 (0.217)	0.0012 (0.703)	0.409 (1.00)	0.0624 (1.00)	0.00621 (1.00)	1.25e-05 (0.00862)
Del Peak 18(8p23 3)	0 (0%)	242	0.0114 (1.00)	6.76e-05 (0.0448)	6.84e-26 (5.51e-23)	7.25e-07 (0.00051)	0.0514 (1.00)	0.00096 (0.571)	0.000672 (0.406)	0.00231 (1.00)	0.154 (1.00)	0.848 (1.00)	1.49e-05 (0.0103)	0.000112 (0.0733)
Del Peak 10(4q22 1)	0 (0%)	287	0.000383 (0.239)	0.00214 (1.00)	8.5e-12 (6.52e-09)	0.000546 (0.332)	0.516 (1.00)	0.391 (1.00)	9.23e-05 (0.0607)	2.81e-05 (0.0189)	0.21 (1.00)	0.518 (1.00)	0.00448 (1.00)	0.00334 (1.00)
Del Peak 30(15q11 2)	0 (0%)	253	0.000468 (0.288)	0.00159 (0.915)	1.2e-21 (9.61e-19)	0.0101 (1.00)	0.0746 (1.00)	0.07 (1.00)	2.09e-06 (0.00145)	0.000117 (0.0762)	0.877 (1.00)	0.893 (1.00)	0.000524 (0.32)	8.5e-06 (0.00585)
Del Peak 31(15q21 1)	0 (0%)	262	0.0261 (1.00)	0.0142 (1.00)	8.15e-18 (6.48e-15)	0.00624 (1.00)	0.0441 (1.00)	0.0657 (1.00)	2.03e-07 (0.000145)	2.05e-05 (0.0139)	0.979 (1.00)	0.621 (1.00)	0.00116 (0.68)	0.000165 (0.106)
Amp Peak 13(16p11 2)	0 (0%)	297	0.00114 (0.669)	0.000129 (0.0838)	8.55e-19 (6.83e-16)	0.00705 (1.00)	0.373 (1.00)	0.033 (1.00)	0.000429 (0.266)	0.00838 (1.00)	0.771 (1.00)	0.809 (1.00)	0.00105 (0.619)	2.15e-06 (0.00149)
Amp Peak 20(20p11 23)	0 (0%)	208	0.0773 (1.00)	0.000507 (0.311)	1.26e-16 (9.98e-14)	0.109 (1.00)	0.0479 (1.00)	0.183 (1.00)	0.000513 (0.314)	0.00104 (0.616)	0.455 (1.00)	0.212 (1.00)	0.00011 (0.072)	0.000249 (0.157)
Del Peak 9(4p16 2)	0 (0%)	292	0.000733 (0.441)	0.00397 (1.00)	1.16e-12 (8.97e-10)	0.00374 (1.00)	0.442 (1.00)	0.0866 (1.00)	0.000237 (0.15)	0.000107 (0.0699)	0.376 (1.00)	0.206 (1.00)	0.0159 (1.00)	0.000752 (0.451)
Del Peak 11(4q35 1)	0 (0%)	276	0.00098 (0.582)	0.00363 (1.00)	1.05e-13 (8.2e-11)	1.63e-05 (0.0112)	0.173 (1.00)	0.146 (1.00)	0.000239 (0.151)	0.000527 (0.321)	0.416 (1.00)	0.235 (1.00)	0.000452 (0.28)	0.0177 (1.00)
Del Peak 44(22q13 32)	0 (0%)	275	0.000892 (0.533)	0.000232 (0.148)	9.76e-13 (7.59e-10)	0.00123 (0.719)	0.306 (1.00)	0.218 (1.00)	0.00222 (1.00)	0.00106 (0.628)	0.394 (1.00)	0.069 (1.00)	8.8e-05 (0.0579)	0.00049 (0.301)
Amp Peak 4(6p21 1)	0 (0%)	324	0.196 (1.00)	0.000191 (0.123)	3.37e-09 (2.46e-06)	0.0569 (1.00)	0.83 (1.00)	0.178 (1.00)	0.00644 (1.00)	0.033 (1.00)	0.776 (1.00)	0.258 (1.00)	0.0199 (1.00)	0.00186 (1.00)
Amp Peak 15(17q12)	0 (0%)	312	0.0538 (1.00)	0.075 (1.00)	7.53e-07 (0.000529)	0.00527 (1.00)	0.582 (1.00)	0.00276 (1.00)	4.59e-05 (0.0305)	0.0142 (1.00)	0.0121 (1.00)	0.986 (1.00)	0.031 (1.00)	0.0185 (1.00)
Amp Peak 16(17q24 1)	0 (0%)	321	0.0504 (1.00)	0.0263 (1.00)	1.61e-08 (1.16e-05)	0.00368 (1.00)	0.304 (1.00)	0.00527 (1.00)	6.04e-06 (0.00418)	0.00312 (1.00)	0.00254 (1.00)	0.781 (1.00)	0.0234 (1.00)	0.000747 (0.449)
Amp Peak 19(20p12 3)	0 (0%)	229	0.00898 (1.00)	0.000356 (0.223)	1.86e-12 (1.44e-09)	0.465 (1.00)	0.0113 (1.00)	0.478 (1.00)	0.0305 (1.00)	0.00972 (1.00)	0.597 (1.00)	0.195 (1.00)	0.00438 (1.00)	0.00141 (0.82)
Del Peak 2(1p33)	0 (0%)	306	0.0223 (1.00)	0.376 (1.00)	1.09e-11 (8.32e-09)	0.00167 (0.96)	0.556 (1.00)	0.395 (1.00)	0.0051 (1.00)	0.0141 (1.00)	0.893 (1.00)	0.0519 (1.00)	0.0406 (1.00)	3.25e-05 (0.0217)
Del Peak 26(10q25 2)	0 (0%)	320	0.125 (1.00)	0.00187 (1.00)	1.91e-11 (1.45e-08)	0.00765 (1.00)	0.03 (1.00)	0.319 (1.00)	0.00312 (1.00)	0.0025 (1.00)	0.921 (1.00)	0.593 (1.00)	1.81e-05 (0.0123)	0.00934 (1.00)
Del Peak 42(20p12 1)	0 (0%)	334	0.0484 (1.00)	0.203 (1.00)	1.38e-13 (1.08e-10)	0.000428 (0.266)	0.323 (1.00)	0.278 (1.00)	0.00015 (0.0967)	0.00674 (1.00)	0.0931 (1.00)	0.101 (1.00)	0.00584 (1.00)	0.00123 (0.719)
Amp Peak 1(2q33 1)	0 (0%)	334	0.166 (1.00)	0.0365 (1.00)	3.05e-05 (0.0205)	0.128 (1.00)	0.245 (1.00)	0.0652 (1.00)	0.000516 (0.315)	0.0137 (1.00)	0.277 (1.00)	0.258 (1.00)	0.339 (1.00)	0.11 (1.00)
Amp Peak 2(5p13 2)	0 (0%)	332	0.38 (1.00)	0.268 (1.00)	0.000202 (0.129)	0.392 (1.00)	0.00999 (1.00)	0.724 (1.00)	0.0864 (1.00)	0.0696 (1.00)	0.927 (1.00)	0.581 (1.00)	0.299 (1.00)	0.0475 (1.00)
Amp Peak 5(8p11 23)	0 (0%)	269	0.302 (1.00)	0.126 (1.00)	2.99e-13 (2.34e-10)	0.919 (1.00)	0.864 (1.00)	0.733 (1.00)	0.211 (1.00)	0.783 (1.00)	0.179 (1.00)	0.189 (1.00)	0.249 (1.00)	0.444 (1.00)
Amp Peak 6(8p11 21)	0 (0%)	240	0.444 (1.00)	0.0716 (1.00)	4.51e-10 (3.35e-07)	0.658 (1.00)	0.27 (1.00)	0.00672 (1.00)	0.421 (1.00)	0.606 (1.00)	0.502 (1.00)	0.218 (1.00)	0.327 (1.00)	0.327 (1.00)
Amp Peak 7(8q12 1)	0 (0%)	198	0.489 (1.00)	0.0389 (1.00)	9.31e-12 (7.13e-09)	0.016 (1.00)	0.0228 (1.00)	0.00068 (0.41)	0.0141 (1.00)	0.228 (1.00)	0.126 (1.00)	0.295 (1.00)	0.00255 (1.00)	0.0054 (1.00)
Amp Peak 8(8q24 21)	0 (0%)	174	0.563 (1.00)	0.0685 (1.00)	7.86e-14 (6.17e-11)	0.00368 (1.00)	0.103 (1.00)	0.0104 (1.00)	0.00636 (1.00)	0.445 (1.00)	0.404 (1.00)	0.215 (1.00)	0.0163 (1.00)	0.00488 (1.00)
Amp Peak 17(19p13 2)	0 (0%)	348	0.0674 (1.00)	0.0263 (1.00)	4.82e-05 (0.032)	0.198 (1.00)	0.734 (1.00)	0.341 (1.00)	0.501 (1.00)	0.539 (1.00)	0.204 (1.00)	0.385 (1.00)	0.00699 (1.00)	0.0134 (1.00)
Del Peak 3(1p13 1)	0 (0%)	310	0.0872 (1.00)	0.262 (1.00)	6.85e-10 (5.07e-07)	0.0821 (1.00)	0.56 (1.00)	0.89 (1.00)	0.0836 (1.00)	0.00481 (1.00)	0.868 (1.00)	0.379 (1.00)	0.431 (1.00)	0.00114 (0.671)
Del Peak 4(1q43)	0 (0%)	369	0.0616 (1.00)	0.461 (1.00)	6.98e-06 (0.00482)	0.0142 (1.00)	0.393 (1.00)	0.664 (1.00)	0.0312 (1.00)	0.0114 (1.00)	0.335 (1.00)	0.301 (1.00)	0.00777 (1.00)	0.00291 (1.00)
Del Peak 12(5q11 2)	0 (0%)	322	0.00115 (0.671)	0.00127 (0.736)	4.94e-09 (3.59e-06)	0.0572 (1.00)	0.048 (1.00)	0.0118 (1.00)	0.00142 (0.823)	0.00781 (1.00)	0.835 (1.00)	0.215 (1.00)	0.00263 (1.00)	0.00406 (1.00)
Del Peak 13(5q21 3)	0 (0%)	296	0.0661 (1.00)	0.0105 (1.00)	1.14e-09 (8.38e-07)	0.0295 (1.00)	0.0651 (1.00)	0.0971 (1.00)	0.00438 (1.00)	0.0104 (1.00)	0.654 (1.00)	0.36 (1.00)	0.0481 (1.00)	0.00682 (1.00)
Del Peak 14(5q23 1)	0 (0%)	306	0.0497 (1.00)	0.0242 (1.00)	1.57e-08 (1.13e-05)	0.0692 (1.00)	0.044 (1.00)	0.15 (1.00)	0.0219 (1.00)	0.0126 (1.00)	0.622 (1.00)	0.246 (1.00)	0.00738 (1.00)	0.0108 (1.00)
Del Peak 15(6p25 3)	0 (0%)	359	0.852 (1.00)	0.756 (1.00)	0.000102 (0.0672)	0.0708 (1.00)	0.337 (1.00)	0.828 (1.00)	0.353 (1.00)	0.788 (1.00)	0.406 (1.00)	0.453 (1.00)	0.0601 (1.00)	0.0895 (1.00)
Del Peak 20(8p11 22)	0 (0%)	333	0.402 (1.00)	0.137 (1.00)	8.88e-09 (6.45e-06)	0.0397 (1.00)	0.049 (1.00)	0.00534 (1.00)	0.0993 (1.00)	0.0804 (1.00)	0.359 (1.00)	0.831 (1.00)	0.129 (1.00)	0.0521 (1.00)
Del Peak 21(8p11 21)	0 (0%)	370	0.0251 (1.00)	0.355 (1.00)	5.81e-07 (0.000411)	0.441 (1.00)	0.156 (1.00)	0.024 (1.00)	0.483 (1.00)	0.308 (1.00)	0.0997 (1.00)	0.549 (1.00)	0.0934 (1.00)	0.412 (1.00)
Del Peak 22(9p21 3)	0 (0%)	357	0.563 (1.00)	0.0923 (1.00)	4.51e-05 (0.03)	0.266 (1.00)	0.768 (1.00)	0.214 (1.00)	0.0637 (1.00)	0.127 (1.00)	0.904 (1.00)	0.663 (1.00)	0.113 (1.00)	0.385 (1.00)
Del Peak 23(10p15 3)	0 (0%)	345	0.115 (1.00)	0.102 (1.00)	2.25e-08 (1.62e-05)	0.00869 (1.00)	0.0673 (1.00)	0.104 (1.00)	0.126 (1.00)	0.034 (1.00)	0.68 (1.00)	0.566 (1.00)	0.00707 (1.00)	0.00339 (1.00)
Del Peak 24(10q21 1)	0 (0%)	331	0.00335 (1.00)	0.00888 (1.00)	2.24e-11 (1.7e-08)	0.136 (1.00)	0.277 (1.00)	0.144 (1.00)	0.191 (1.00)	0.0431 (1.00)	0.887 (1.00)	0.831 (1.00)	0.00864 (1.00)	0.0618 (1.00)
Del Peak 25(10q23 31)	0 (0%)	319	0.146 (1.00)	0.0306 (1.00)	3.46e-07 (0.000246)	0.052 (1.00)	0.123 (1.00)	0.375 (1.00)	0.0348 (1.00)	0.165 (1.00)	0.885 (1.00)	0.985 (1.00)	0.00111 (0.651)	0.0249 (1.00)
Del Peak 27(12p13 2)	0 (0%)	369	0.0356 (1.00)	0.00831 (1.00)	9.87e-08 (7.06e-05)	0.115 (1.00)	0.383 (1.00)	0.87 (1.00)	0.0262 (1.00)	0.00369 (1.00)	0.695 (1.00)	0.973 (1.00)	0.00277 (1.00)	0.112 (1.00)
Del Peak 28(13q14 13)	0 (0%)	395	0.275 (1.00)	0.876 (1.00)	0.000128 (0.0828)	0.167 (1.00)	0.212 (1.00)	0.34 (1.00)	0.228 (1.00)	0.452 (1.00)	0.614 (1.00)	0.834 (1.00)	0.27 (1.00)	0.981 (1.00)
Del Peak 43(21q11 2)	0 (0%)	288	0.0264 (1.00)	0.0387 (1.00)	3.37e-09 (2.46e-06)	0.0124 (1.00)	0.236 (1.00)	0.455 (1.00)	0.000897 (0.534)	0.0187 (1.00)	0.923 (1.00)	0.47 (1.00)	0.00256 (1.00)	0.0392 (1.00)
Amp Peak 3(5q22 3)	0 (0%)	373	0.915 (1.00)	0.677 (1.00)	0.0293 (1.00)	0.876 (1.00)	0.394 (1.00)	0.494 (1.00)	0.165 (1.00)	0.112 (1.00)	0.693 (1.00)	0.839 (1.00)	0.3 (1.00)	0.28 (1.00)
Amp Peak 10(12p13 33)	0 (0%)	309	0.537 (1.00)	0.801 (1.00)	0.0612 (1.00)	0.351 (1.00)	0.429 (1.00)	0.958 (1.00)	0.334 (1.00)	0.977 (1.00)	0.304 (1.00)	0.173 (1.00)	0.908 (1.00)	0.498 (1.00)
Amp Peak 18(19q13 11)	0 (0%)	330	0.181 (1.00)	0.0232 (1.00)	0.002 (1.00)	0.433 (1.00)	0.173 (1.00)	0.688 (1.00)	0.0736 (1.00)	0.167 (1.00)	0.417 (1.00)	0.491 (1.00)	0.0253 (1.00)	0.00412 (1.00)
Del Peak 5(2q37 2)	0 (0%)	392	0.805 (1.00)	0.0652 (1.00)	0.977 (1.00)	0.65 (1.00)	0.23 (1.00)	0.208 (1.00)	1 (1.00)	0.184 (1.00)	0.447 (1.00)	0.447 (1.00)	0.58 (1.00)	0.642 (1.00)
Del Peak 6(3p26 1)	0 (0%)	353	0.399 (1.00)	0.281 (1.00)	0.00043 (0.267)	0.0737 (1.00)	0.942 (1.00)	0.861 (1.00)	0.539 (1.00)	0.0883 (1.00)	0.541 (1.00)	0.958 (1.00)	0.0103 (1.00)	0.386 (1.00)
Del Peak 7(3p14 2)	0 (0%)	338	0.554 (1.00)	0.556 (1.00)	0.205 (1.00)	0.623 (1.00)	0.566 (1.00)	0.29 (1.00)	0.632 (1.00)	0.483 (1.00)	0.203 (1.00)	0.536 (1.00)	0.0257 (1.00)	0.425 (1.00)
Del Peak 8(3q26 31)	0 (0%)	374	0.559 (1.00)	0.646 (1.00)	0.00818 (1.00)	0.41 (1.00)	0.288 (1.00)	0.369 (1.00)	0.458 (1.00)	0.0223 (1.00)	0.15 (1.00)	0.939 (1.00)	0.00263 (1.00)	0.0415 (1.00)
Del Peak 16(6q26)	0 (0%)	353	0.524 (1.00)	0.258 (1.00)	0.157 (1.00)	0.423 (1.00)	0.189 (1.00)	0.355 (1.00)	0.873 (1.00)	0.697 (1.00)	0.797 (1.00)	0.53 (1.00)	0.213 (1.00)	0.235 (1.00)
Del Peak 17(7q31 1)	0 (0%)	402	1 (1.00)	0.504 (1.00)	0.816 (1.00)	0.797 (1.00)	0.354 (1.00)	0.219 (1.00)	0.49 (1.00)	1 (1.00)	1 (1.00)	0.564 (1.00)	0.876 (1.00)	0.047 (1.00)
Del Peak 33(16p13 3)	0 (0%)	368	0.303 (1.00)	0.338 (1.00)	0.208 (1.00)	0.463 (1.00)	0.418 (1.00)	0.913 (1.00)	0.62 (1.00)	0.572 (1.00)	0.842 (1.00)	0.739 (1.00)	0.198 (1.00)	0.543 (1.00)
Del Peak 34(16q23 1)	0 (0%)	364	0.269 (1.00)	0.00608 (1.00)	0.131 (1.00)	0.406 (1.00)	0.489 (1.00)	0.821 (1.00)	0.0421 (1.00)	0.0701 (1.00)	0.977 (1.00)	0.505 (1.00)	0.538 (1.00)	0.568 (1.00)
Del Peak 36(17q24 3)	0 (0%)	354	0.0956 (1.00)	0.707 (1.00)	0.00348 (1.00)	0.00569 (1.00)	0.874 (1.00)	0.338 (1.00)	0.00329 (1.00)	0.0329 (1.00)	0.681 (1.00)	0.979 (1.00)	0.135 (1.00)	0.137 (1.00)
Del Peak 41(19p13 3)	0 (0%)	356	0.131 (1.00)	0.0385 (1.00)	0.00362 (1.00)	0.187 (1.00)	0.88 (1.00)	0.0676 (1.00)	0.0512 (1.00)	0.0244 (1.00)	0.582 (1.00)	0.0166 (1.00)	0.367 (1.00)	0.199 (1.00)

'Amp Peak 1(2q33.1)' versus 'CN_CNMF'

P value = 3.05e-05 (Fisher's exact test), Q value = 0.021

Table S1. Gene #1: 'Amp Peak 1(2q33.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 1(2Q33.1) CNV	49	18	8	4
AMP PEAK 1(2Q33.1) WILD-TYPE	121	169	24	20

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(2q33.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 2(5p13.2)' versus 'CN_CNMF'

P value = 0.000202 (Fisher's exact test), Q value = 0.13

Table S2. Gene #2: 'Amp Peak 2(5p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 2(5P13.2) CNV	46	20	10	5
AMP PEAK 2(5P13.2) WILD-TYPE	124	167	22	19

Figure S2. Get High-res Image Gene #2: 'Amp Peak 2(5p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 4(6p21.1)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000191 (Fisher's exact test), Q value = 0.12

Table S3. Gene #4: 'Amp Peak 4(6p21.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
AMP PEAK 4(6P21.1) CNV	8	3	19
AMP PEAK 4(6P21.1) WILD-TYPE	48	40	28

Figure S3. Get High-res Image Gene #4: 'Amp Peak 4(6p21.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 4(6p21.1)' versus 'CN_CNMF'

P value = 3.37e-09 (Fisher's exact test), Q value = 2.5e-06

Table S4. Gene #4: 'Amp Peak 4(6p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 4(6P21.1) CNV	61	16	8	4
AMP PEAK 4(6P21.1) WILD-TYPE	109	171	24	20

Figure S4. Get High-res Image Gene #4: 'Amp Peak 4(6p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 5(8p11.23)' versus 'CN_CNMF'

P value = 2.99e-13 (Fisher's exact test), Q value = 2.3e-10

Table S5. Gene #5: 'Amp Peak 5(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 5(8P11.23) CNV	56	47	17	24
AMP PEAK 5(8P11.23) WILD-TYPE	114	140	15	0

Figure S5. Get High-res Image Gene #5: 'Amp Peak 5(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 6(8p11.21)' versus 'CN_CNMF'

P value = 4.51e-10 (Fisher's exact test), Q value = 3.3e-07

Table S6. Gene #6: 'Amp Peak 6(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 6(8P11.21) CNV	75	55	21	22
AMP PEAK 6(8P11.21) WILD-TYPE	95	132	11	2

Figure S6. Get High-res Image Gene #6: 'Amp Peak 6(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 7(8q12.1)' versus 'CN_CNMF'

P value = 9.31e-12 (Fisher's exact test), Q value = 7.1e-09

Table S7. Gene #7: 'Amp Peak 7(8q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 7(8Q12.1) CNV	106	64	23	22
AMP PEAK 7(8Q12.1) WILD-TYPE	64	123	9	2

Figure S7. Get High-res Image Gene #7: 'Amp Peak 7(8q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 8(8q24.21)' versus 'CN_CNMF'

P value = 7.86e-14 (Fisher's exact test), Q value = 6.2e-11

Table S8. Gene #8: 'Amp Peak 8(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 8(8Q24.21) CNV	119	73	23	24
AMP PEAK 8(8Q24.21) WILD-TYPE	51	114	9	0

Figure S8. Get High-res Image Gene #8: 'Amp Peak 8(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 9(11p15.5)' versus 'MRNA_CNMF'

P value = 6.09e-06 (Fisher's exact test), Q value = 0.0042

Table S9. Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 9(11P15.5) CNV	1	18	3	12
AMP PEAK 9(11P15.5) WILD-TYPE	34	43	26	9

Figure S9. Get High-res Image Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 9(11p15.5)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000343 (Fisher's exact test), Q value = 0.21

Table S10. Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
AMP PEAK 9(11P15.5) CNV	14	2	18
AMP PEAK 9(11P15.5) WILD-TYPE	42	41	29

Figure S10. Get High-res Image Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 9(11p15.5)' versus 'CN_CNMF'

P value = 1.54e-09 (Fisher's exact test), Q value = 1.1e-06

Table S11. Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 9(11P15.5) CNV	54	17	14	1
AMP PEAK 9(11P15.5) WILD-TYPE	116	170	18	23

Figure S11. Get High-res Image Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 9(11p15.5)' versus 'METHLYATION_CNMF'

P value = 4.01e-05 (Fisher's exact test), Q value = 0.027

Table S12. Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	83	64
AMP PEAK 9(11P15.5) CNV	33	5	10
AMP PEAK 9(11P15.5) WILD-TYPE	74	78	54

Figure S12. Get High-res Image Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 9(11p15.5)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.43e-07 (Chi-square test), Q value = 0.00052

Table S13. Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	22	49	62	46	42
AMP PEAK 9(11P15.5) CNV	13	11	4	4	8
AMP PEAK 9(11P15.5) WILD-TYPE	9	38	58	42	34

Figure S13. Get High-res Image Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 11(13q12.13)' versus 'MRNA_CNMF'

P value = 1.58e-06 (Fisher's exact test), Q value = 0.0011

Table S14. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 11(13Q12.13) CNV	15	51	10	16
AMP PEAK 11(13Q12.13) WILD-TYPE	20	10	19	5

Figure S14. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 11(13q12.13)' versus 'MRNA_CHIERARCHICAL'

P value = 2.07e-06 (Fisher's exact test), Q value = 0.0014

Table S15. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
AMP PEAK 11(13Q12.13) CNV	39	14	39
AMP PEAK 11(13Q12.13) WILD-TYPE	17	29	8

Figure S15. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 11(13q12.13)' versus 'CN_CNMF'

P value = 5.04e-36 (Fisher's exact test), Q value = 4.1e-33

Table S16. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 11(13Q12.13) CNV	158	57	18	17
AMP PEAK 11(13Q12.13) WILD-TYPE	12	130	14	7

Figure S16. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 11(13q12.13)' versus 'METHLYATION_CNMF'

P value = 0.000318 (Fisher's exact test), Q value = 0.2

Table S17. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	83	64
AMP PEAK 11(13Q12.13) CNV	80	40	34
AMP PEAK 11(13Q12.13) WILD-TYPE	27	43	30

Figure S17. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 11(13q12.13)' versus 'MRNASEQ_CNMF'

P value = 1.27e-06 (Fisher's exact test), Q value = 0.00089

Table S18. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
AMP PEAK 11(13Q12.13) CNV	22	46	26	16
AMP PEAK 11(13Q12.13) WILD-TYPE	9	13	21	38

Figure S18. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 11(13q12.13)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000196 (Fisher's exact test), Q value = 0.13

Table S19. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
AMP PEAK 11(13Q12.13) CNV	16	43	51
AMP PEAK 11(13Q12.13) WILD-TYPE	33	19	29

Figure S19. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 11(13q12.13)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.46e-05 (Fisher's exact test), Q value = 0.017

Table S20. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	79	65
AMP PEAK 11(13Q12.13) CNV	32	61	42
AMP PEAK 11(13Q12.13) WILD-TYPE	45	18	23

Figure S20. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 11(13q12.13)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.2e-08 (Chi-square test), Q value = 8.7e-06

Table S21. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	22	49	62	46	42
AMP PEAK 11(13Q12.13) CNV	12	40	18	32	33
AMP PEAK 11(13Q12.13) WILD-TYPE	10	9	44	14	9

Figure S21. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 12(13q22.1)' versus 'MRNA_CHIERARCHICAL'

P value = 4.41e-05 (Fisher's exact test), Q value = 0.029

Table S22. Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
AMP PEAK 12(13Q22.1) CNV	39	15	37
AMP PEAK 12(13Q22.1) WILD-TYPE	17	28	10

Figure S22. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 12(13q22.1)' versus 'CN_CNMF'

P value = 7.2e-33 (Fisher's exact test), Q value = 5.8e-30

Table S23. Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 12(13Q22.1) CNV	158	63	17	16
AMP PEAK 12(13Q22.1) WILD-TYPE	12	124	15	8

Figure S23. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 12(13q22.1)' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.13

Table S24. Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	83	64
AMP PEAK 12(13Q22.1) CNV	82	42	34
AMP PEAK 12(13Q22.1) WILD-TYPE	25	41	30

Figure S24. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 12(13q22.1)' versus 'MRNASEQ_CNMF'

P value = 1.15e-06 (Fisher's exact test), Q value = 8e-04

Table S25. Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
AMP PEAK 12(13Q22.1) CNV	22	49	25	19
AMP PEAK 12(13Q22.1) WILD-TYPE	9	10	22	35

Figure S25. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 12(13q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.67e-05 (Fisher's exact test), Q value = 0.051

Table S26. Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
AMP PEAK 12(13Q22.1) CNV	17	46	52
AMP PEAK 12(13Q22.1) WILD-TYPE	32	16	28

Figure S26. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 12(13q22.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.61e-05 (Fisher's exact test), Q value = 0.024

Table S27. Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	79	65
AMP PEAK 12(13Q22.1) CNV	34	62	44
AMP PEAK 12(13Q22.1) WILD-TYPE	43	17	21

Figure S27. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 12(13q22.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.29e-07 (Chi-square test), Q value = 0.00044

Table S28. Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	22	49	62	46	42
AMP PEAK 12(13Q22.1) CNV	14	39	21	33	33
AMP PEAK 12(13Q22.1) WILD-TYPE	8	10	41	13	9

Figure S28. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 13(16p11.2)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000129 (Fisher's exact test), Q value = 0.084

Table S29. Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
AMP PEAK 13(16P11.2) CNV	13	6	25
AMP PEAK 13(16P11.2) WILD-TYPE	43	37	22

Figure S29. Get High-res Image Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 13(16p11.2)' versus 'CN_CNMF'

P value = 8.55e-19 (Fisher's exact test), Q value = 6.8e-16

Table S30. Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 13(16P11.2) CNV	88	18	8	2
AMP PEAK 13(16P11.2) WILD-TYPE	82	169	24	22

Figure S30. Get High-res Image Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 13(16p11.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.15e-06 (Chi-square test), Q value = 0.0015

Table S31. Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	22	49	62	46	42
AMP PEAK 13(16P11.2) CNV	9	21	3	9	19
AMP PEAK 13(16P11.2) WILD-TYPE	13	28	59	37	23

Figure S31. Get High-res Image Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 14(16q12.1)' versus 'MRNA_CNMF'

P value = 0.000126 (Fisher's exact test), Q value = 0.082

Table S32. Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 14(16Q12.1) CNV	4	22	2	11
AMP PEAK 14(16Q12.1) WILD-TYPE	31	39	27	10

Figure S32. Get High-res Image Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 14(16q12.1)' versus 'MRNA_CHIERARCHICAL'

P value = 2.53e-05 (Fisher's exact test), Q value = 0.017

Table S33. Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
AMP PEAK 14(16Q12.1) CNV	13	3	23
AMP PEAK 14(16Q12.1) WILD-TYPE	43	40	24

Figure S33. Get High-res Image Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 14(16q12.1)' versus 'CN_CNMF'

P value = 1.67e-20 (Fisher's exact test), Q value = 1.3e-17

Table S34. Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 14(16Q12.1) CNV	82	12	7	1
AMP PEAK 14(16Q12.1) WILD-TYPE	88	175	25	23

Figure S34. Get High-res Image Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 14(16q12.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000237 (Fisher's exact test), Q value = 0.15

Table S35. Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	79	65
AMP PEAK 14(16Q12.1) CNV	7	26	21
AMP PEAK 14(16Q12.1) WILD-TYPE	70	53	44

Figure S35. Get High-res Image Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 14(16q12.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.23e-07 (Chi-square test), Q value = 0.00037

Table S36. Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	22	49	62	46	42
AMP PEAK 14(16Q12.1) CNV	9	19	2	6	18
AMP PEAK 14(16Q12.1) WILD-TYPE	13	30	60	40	24

Figure S36. Get High-res Image Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 15(17q12)' versus 'CN_CNMF'

P value = 7.53e-07 (Fisher's exact test), Q value = 0.00053

Table S37. Gene #15: 'Amp Peak 15(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 15(17Q12) CNV	62	23	8	8
AMP PEAK 15(17Q12) WILD-TYPE	108	164	24	16

Figure S37. Get High-res Image Gene #15: 'Amp Peak 15(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 15(17q12)' versus 'MRNASEQ_CNMF'

P value = 4.59e-05 (Fisher's exact test), Q value = 0.03

Table S38. Gene #15: 'Amp Peak 15(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
AMP PEAK 15(17Q12) CNV	8	26	6	5
AMP PEAK 15(17Q12) WILD-TYPE	23	33	41	49

Figure S38. Get High-res Image Gene #15: 'Amp Peak 15(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 16(17q24.1)' versus 'CN_CNMF'

P value = 1.61e-08 (Fisher's exact test), Q value = 1.2e-05

Table S39. Gene #16: 'Amp Peak 16(17q24.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 16(17Q24.1) CNV	59	17	8	8
AMP PEAK 16(17Q24.1) WILD-TYPE	111	170	24	16

Figure S39. Get High-res Image Gene #16: 'Amp Peak 16(17q24.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 16(17q24.1)' versus 'MRNASEQ_CNMF'

P value = 6.04e-06 (Fisher's exact test), Q value = 0.0042

Table S40. Gene #16: 'Amp Peak 16(17q24.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
AMP PEAK 16(17Q24.1) CNV	9	26	4	5
AMP PEAK 16(17Q24.1) WILD-TYPE	22	33	43	49

Figure S40. Get High-res Image Gene #16: 'Amp Peak 16(17q24.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 17(19p13.2)' versus 'CN_CNMF'

P value = 4.82e-05 (Fisher's exact test), Q value = 0.032

Table S41. Gene #17: 'Amp Peak 17(19p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 17(19P13.2) CNV	39	13	8	5
AMP PEAK 17(19P13.2) WILD-TYPE	131	174	24	19

Figure S41. Get High-res Image Gene #17: 'Amp Peak 17(19p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 19(20p12.3)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000356 (Fisher's exact test), Q value = 0.22

Table S42. Gene #19: 'Amp Peak 19(20p12.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
AMP PEAK 19(20P12.3) CNV	33	10	28
AMP PEAK 19(20P12.3) WILD-TYPE	23	33	19

Figure S42. Get High-res Image Gene #19: 'Amp Peak 19(20p12.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 19(20p12.3)' versus 'CN_CNMF'

P value = 1.86e-12 (Fisher's exact test), Q value = 1.4e-09

Table S43. Gene #19: 'Amp Peak 19(20p12.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 19(20P12.3) CNV	83	58	31	12
AMP PEAK 19(20P12.3) WILD-TYPE	87	129	1	12

Figure S43. Get High-res Image Gene #19: 'Amp Peak 19(20p12.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 20(20p11.23)' versus 'CN_CNMF'

P value = 1.26e-16 (Fisher's exact test), Q value = 1e-13

Table S44. Gene #20: 'Amp Peak 20(20p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 20(20P11.23) CNV	102	58	32	13
AMP PEAK 20(20P11.23) WILD-TYPE	68	129	0	11

Figure S44. Get High-res Image Gene #20: 'Amp Peak 20(20p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 20(20p11.23)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.072

Table S45. Gene #20: 'Amp Peak 20(20p11.23)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	79	65
AMP PEAK 20(20P11.23) CNV	23	50	34
AMP PEAK 20(20P11.23) WILD-TYPE	54	29	31

Figure S45. Get High-res Image Gene #20: 'Amp Peak 20(20p11.23)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 20(20p11.23)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000249 (Chi-square test), Q value = 0.16

Table S46. Gene #20: 'Amp Peak 20(20p11.23)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	22	49	62	46	42
AMP PEAK 20(20P11.23) CNV	11	28	15	26	27
AMP PEAK 20(20P11.23) WILD-TYPE	11	21	47	20	15

Figure S46. Get High-res Image Gene #20: 'Amp Peak 20(20p11.23)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 21(20p11.21)' versus 'MRNA_CHIERARCHICAL'

P value = 1.6e-05 (Fisher's exact test), Q value = 0.011

Table S47. Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
AMP PEAK 21(20P11.21) CNV	38	11	32
AMP PEAK 21(20P11.21) WILD-TYPE	18	32	15

Figure S47. Get High-res Image Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 21(20p11.21)' versus 'CN_CNMF'

P value = 4e-23 (Fisher's exact test), Q value = 3.2e-20

Table S48. Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 21(20P11.21) CNV	126	58	32	14
AMP PEAK 21(20P11.21) WILD-TYPE	44	129	0	10

Figure S48. Get High-res Image Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 21(20p11.21)' versus 'MRNASEQ_CNMF'

P value = 2.41e-07 (Fisher's exact test), Q value = 0.00017

Table S49. Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
AMP PEAK 21(20P11.21) CNV	19	44	24	12
AMP PEAK 21(20P11.21) WILD-TYPE	12	15	23	42

Figure S49. Get High-res Image Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 21(20p11.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.39e-06 (Fisher's exact test), Q value = 0.00097

Table S50. Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
AMP PEAK 21(20P11.21) CNV	10	40	49
AMP PEAK 21(20P11.21) WILD-TYPE	39	22	31

Figure S50. Get High-res Image Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 21(20p11.21)' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.09e-07 (Fisher's exact test), Q value = 0.00043

Table S51. Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	79	65
AMP PEAK 21(20P11.21) CNV	25	58	41
AMP PEAK 21(20P11.21) WILD-TYPE	52	21	24

Figure S51. Get High-res Image Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 21(20p11.21)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.56e-08 (Chi-square test), Q value = 1.1e-05

Table S52. Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	22	49	62	46	42
AMP PEAK 21(20P11.21) CNV	15	34	14	28	33
AMP PEAK 21(20P11.21) WILD-TYPE	7	15	48	18	9

Figure S52. Get High-res Image Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 22(20q11.21)' versus 'MRNA_CNMF'

P value = 3.87e-10 (Fisher's exact test), Q value = 2.9e-07

Table S53. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S53. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 22(20q11.21)' versus 'MRNA_CHIERARCHICAL'

P value = 7.28e-12 (Fisher's exact test), Q value = 5.6e-09

Table S54. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
AMP PEAK 22(20Q11.21) CNV	50	13	42
AMP PEAK 22(20Q11.21) WILD-TYPE	6	30	5

Figure S54. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 22(20q11.21)' versus 'CN_CNMF'

P value = 1.54e-43 (Fisher's exact test), Q value = 1.2e-40

Table S55. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 22(20Q11.21) CNV	167	74	32	23
AMP PEAK 22(20Q11.21) WILD-TYPE	3	113	0	1

Figure S55. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 22(20q11.21)' versus 'METHLYATION_CNMF'

P value = 6.22e-10 (Fisher's exact test), Q value = 4.6e-07

Table S56. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	83	64
AMP PEAK 22(20Q11.21) CNV	98	43	41
AMP PEAK 22(20Q11.21) WILD-TYPE	9	40	23

Figure S56. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 22(20q11.21)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000108 (Fisher's exact test), Q value = 0.071

Table S57. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
AMP PEAK 22(20Q11.21) CNV	13	29	53	133
AMP PEAK 22(20Q11.21) WILD-TYPE	13	27	10	47

Figure S57. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 22(20q11.21)' versus 'MRNASEQ_CNMF'

P value = 1.47e-14 (Fisher's exact test), Q value = 1.2e-11

Table S58. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
AMP PEAK 22(20Q11.21) CNV	23	58	34	17
AMP PEAK 22(20Q11.21) WILD-TYPE	8	1	13	37

Figure S58. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 22(20q11.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.85e-12 (Fisher's exact test), Q value = 3e-09

Table S59. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
AMP PEAK 22(20Q11.21) CNV	14	56	62
AMP PEAK 22(20Q11.21) WILD-TYPE	35	6	18

Figure S59. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 22(20q11.21)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.45e-10 (Fisher's exact test), Q value = 1.1e-07

Table S60. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	79	65
AMP PEAK 22(20Q11.21) CNV	34	71	54
AMP PEAK 22(20Q11.21) WILD-TYPE	43	8	11

Figure S60. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 22(20q11.21)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.33e-19 (Chi-square test), Q value = 5.9e-16

Table S61. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	22	49	62	46	42
AMP PEAK 22(20Q11.21) CNV	20	45	16	40	38
AMP PEAK 22(20Q11.21) WILD-TYPE	2	4	46	6	4

Figure S61. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 23(20q12)' versus 'MRNA_CNMF'

P value = 4.29e-11 (Fisher's exact test), Q value = 3.2e-08

Table S62. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S62. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 23(20q12)' versus 'MRNA_CHIERARCHICAL'

P value = 4.99e-12 (Fisher's exact test), Q value = 3.8e-09

Table S63. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
AMP PEAK 23(20Q12) CNV	49	12	42
AMP PEAK 23(20Q12) WILD-TYPE	7	31	5

Figure S63. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 23(20q12)' versus 'CN_CNMF'

P value = 6.28e-43 (Fisher's exact test), Q value = 5.1e-40

Table S64. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 23(20Q12) CNV	167	75	32	23
AMP PEAK 23(20Q12) WILD-TYPE	3	112	0	1

Figure S64. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 23(20q12)' versus 'METHLYATION_CNMF'

P value = 4.37e-09 (Fisher's exact test), Q value = 3.2e-06

Table S65. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	83	64
AMP PEAK 23(20Q12) CNV	98	45	42
AMP PEAK 23(20Q12) WILD-TYPE	9	38	22

Figure S65. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 23(20q12)' versus 'RPPA_CHIERARCHICAL'

P value = 2.18e-05 (Fisher's exact test), Q value = 0.015

Table S66. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
AMP PEAK 23(20Q12) CNV	13	29	55	132
AMP PEAK 23(20Q12) WILD-TYPE	13	27	8	48

Figure S66. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 23(20q12)' versus 'MRNASEQ_CNMF'

P value = 5.48e-14 (Fisher's exact test), Q value = 4.3e-11

Table S67. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
AMP PEAK 23(20Q12) CNV	23	58	35	18
AMP PEAK 23(20Q12) WILD-TYPE	8	1	12	36

Figure S67. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 23(20q12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.34e-11 (Fisher's exact test), Q value = 1e-08

Table S68. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
AMP PEAK 23(20Q12) CNV	15	56	63
AMP PEAK 23(20Q12) WILD-TYPE	34	6	17

Figure S68. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 23(20q12)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.88e-11 (Fisher's exact test), Q value = 1.4e-08

Table S69. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	79	65
AMP PEAK 23(20Q12) CNV	34	72	55
AMP PEAK 23(20Q12) WILD-TYPE	43	7	10

Figure S69. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 23(20q12)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.03e-18 (Chi-square test), Q value = 8.2e-16

Table S70. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	22	49	62	46	42
AMP PEAK 23(20Q12) CNV	20	46	17	40	38
AMP PEAK 23(20Q12) WILD-TYPE	2	3	45	6	4

Figure S70. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 24(20q13.32)' versus 'MRNA_CNMF'

P value = 7.91e-10 (Fisher's exact test), Q value = 5.8e-07

Table S71. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 24(20Q13.32) CNV	13	58	17	18
AMP PEAK 24(20Q13.32) WILD-TYPE	22	3	12	3

Figure S71. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 24(20q13.32)' versus 'MRNA_CHIERARCHICAL'

P value = 2.34e-12 (Fisher's exact test), Q value = 1.8e-09

Table S72. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
AMP PEAK 24(20Q13.32) CNV	51	13	42
AMP PEAK 24(20Q13.32) WILD-TYPE	5	30	5

Figure S72. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 24(20q13.32)' versus 'CN_CNMF'

P value = 3.18e-43 (Fisher's exact test), Q value = 2.6e-40

Table S73. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 24(20Q13.32) CNV	168	77	32	23
AMP PEAK 24(20Q13.32) WILD-TYPE	2	110	0	1

Figure S73. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 24(20q13.32)' versus 'METHLYATION_CNMF'

P value = 4.37e-09 (Fisher's exact test), Q value = 3.2e-06

Table S74. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	83	64
AMP PEAK 24(20Q13.32) CNV	98	45	42
AMP PEAK 24(20Q13.32) WILD-TYPE	9	38	22

Figure S74. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 24(20q13.32)' versus 'RPPA_CHIERARCHICAL'

P value = 1.3e-05 (Fisher's exact test), Q value = 0.0089

Table S75. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
AMP PEAK 24(20Q13.32) CNV	13	29	55	135
AMP PEAK 24(20Q13.32) WILD-TYPE	13	27	8	45

Figure S75. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 24(20q13.32)' versus 'MRNASEQ_CNMF'

P value = 5.48e-14 (Fisher's exact test), Q value = 4.3e-11

Table S76. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
AMP PEAK 24(20Q13.32) CNV	23	58	35	18
AMP PEAK 24(20Q13.32) WILD-TYPE	8	1	12	36

Figure S76. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 24(20q13.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.34e-11 (Fisher's exact test), Q value = 1e-08

Table S77. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
AMP PEAK 24(20Q13.32) CNV	15	56	63
AMP PEAK 24(20Q13.32) WILD-TYPE	34	6	17

Figure S77. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 24(20q13.32)' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.8e-11 (Fisher's exact test), Q value = 5.1e-08

Table S78. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	79	65
AMP PEAK 24(20Q13.32) CNV	35	72	55
AMP PEAK 24(20Q13.32) WILD-TYPE	42	7	10

Figure S78. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 24(20q13.32)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.03e-18 (Chi-square test), Q value = 4.8e-15

Table S79. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	22	49	62	46	42
AMP PEAK 24(20Q13.32) CNV	20	46	18	40	38
AMP PEAK 24(20Q13.32) WILD-TYPE	2	3	44	6	4

Figure S79. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 1(1p36.11)' versus 'MRNA_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.097

Table S80. Gene #25: 'Del Peak 1(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) CNV	9	35	4	10
DEL PEAK 1(1P36.11) WILD-TYPE	26	26	25	11

Figure S80. Get High-res Image Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 1(1p36.11)' versus 'CN_CNMF'

P value = 6.32e-17 (Fisher's exact test), Q value = 5e-14

Table S81. Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 1(1P36.11) CNV	91	28	22	9
DEL PEAK 1(1P36.11) WILD-TYPE	79	159	10	15

Figure S81. Get High-res Image Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 1(1p36.11)' versus 'METHLYATION_CNMF'

P value = 0.000328 (Fisher's exact test), Q value = 0.21

Table S82. Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	83	64
DEL PEAK 1(1P36.11) CNV	50	16	21
DEL PEAK 1(1P36.11) WILD-TYPE	57	67	43

Figure S82. Get High-res Image Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 1(1p36.11)' versus 'MRNASEQ_CNMF'

P value = 0.000347 (Fisher's exact test), Q value = 0.22

Table S83. Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 1(1P36.11) CNV	11	31	17	8
DEL PEAK 1(1P36.11) WILD-TYPE	20	28	30	46

Figure S83. Get High-res Image Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 1(1p36.11)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.25e-05 (Chi-square test), Q value = 0.0086

Table S84. Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	22	49	62	46	42
DEL PEAK 1(1P36.11) CNV	15	21	7	18	14
DEL PEAK 1(1P36.11) WILD-TYPE	7	28	55	28	28

Figure S84. Get High-res Image Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 2(1p33)' versus 'CN_CNMF'

P value = 1.09e-11 (Fisher's exact test), Q value = 8.3e-09

Table S85. Gene #26: 'Del Peak 2(1p33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 2(1P33) CNV	69	20	15	3
DEL PEAK 2(1P33) WILD-TYPE	101	167	17	21

Figure S85. Get High-res Image Gene #26: 'Del Peak 2(1p33)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 2(1p33)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.25e-05 (Chi-square test), Q value = 0.022

Table S86. Gene #26: 'Del Peak 2(1p33)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	22	49	62	46	42
DEL PEAK 2(1P33) CNV	13	17	5	10	10
DEL PEAK 2(1P33) WILD-TYPE	9	32	57	36	32

Figure S86. Get High-res Image Gene #26: 'Del Peak 2(1p33)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 3(1p13.1)' versus 'CN_CNMF'

P value = 6.85e-10 (Fisher's exact test), Q value = 5.1e-07

Table S87. Gene #27: 'Del Peak 3(1p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 3(1P13.1) CNV	66	23	13	1
DEL PEAK 3(1P13.1) WILD-TYPE	104	164	19	23

Figure S87. Get High-res Image Gene #27: 'Del Peak 3(1p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 4(1q43)' versus 'CN_CNMF'

P value = 6.98e-06 (Fisher's exact test), Q value = 0.0048

Table S88. Gene #28: 'Del Peak 4(1q43)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 4(1Q43) CNV	32	7	5	0
DEL PEAK 4(1Q43) WILD-TYPE	138	180	27	24

Figure S88. Get High-res Image Gene #28: 'Del Peak 4(1q43)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 9(4p16.2)' versus 'CN_CNMF'

P value = 1.16e-12 (Fisher's exact test), Q value = 9e-10

Table S89. Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 9(4P16.2) CNV	73	23	19	6
DEL PEAK 9(4P16.2) WILD-TYPE	97	164	13	18

Figure S89. Get High-res Image Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 9(4p16.2)' versus 'MRNASEQ_CNMF'

P value = 0.000237 (Fisher's exact test), Q value = 0.15

Table S90. Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 9(4P16.2) CNV	9	24	16	4
DEL PEAK 9(4P16.2) WILD-TYPE	22	35	31	50

Figure S90. Get High-res Image Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 9(4p16.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000107 (Fisher's exact test), Q value = 0.07

Table S91. Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
DEL PEAK 9(4P16.2) CNV	3	23	27
DEL PEAK 9(4P16.2) WILD-TYPE	46	39	53

Figure S91. Get High-res Image Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 10(4q22.1)' versus 'MRNA_CNMF'

P value = 0.000383 (Fisher's exact test), Q value = 0.24

Table S92. Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S92. Get High-res Image Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 10(4q22.1)' versus 'CN_CNMF'

P value = 8.5e-12 (Fisher's exact test), Q value = 6.5e-09

Table S93. Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 10(4Q22.1) CNV	77	28	18	3
DEL PEAK 10(4Q22.1) WILD-TYPE	93	159	14	21

Figure S93. Get High-res Image Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 10(4q22.1)' versus 'MRNASEQ_CNMF'

P value = 9.23e-05 (Fisher's exact test), Q value = 0.061

Table S94. Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 10(4Q22.1) CNV	9	28	15	5
DEL PEAK 10(4Q22.1) WILD-TYPE	22	31	32	49

Figure S94. Get High-res Image Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 10(4q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.81e-05 (Fisher's exact test), Q value = 0.019

Table S95. Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
DEL PEAK 10(4Q22.1) CNV	3	25	29
DEL PEAK 10(4Q22.1) WILD-TYPE	46	37	51

Figure S95. Get High-res Image Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 11(4q35.1)' versus 'CN_CNMF'

P value = 1.05e-13 (Fisher's exact test), Q value = 8.2e-11

Table S96. Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 11(4Q35.1) CNV	88	28	16	5
DEL PEAK 11(4Q35.1) WILD-TYPE	82	159	16	19

Figure S96. Get High-res Image Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 11(4q35.1)' versus 'METHLYATION_CNMF'

P value = 1.63e-05 (Fisher's exact test), Q value = 0.011

Table S97. Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	83	64
DEL PEAK 11(4Q35.1) CNV	47	11	21
DEL PEAK 11(4Q35.1) WILD-TYPE	60	72	43

Figure S97. Get High-res Image Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 11(4q35.1)' versus 'MRNASEQ_CNMF'

P value = 0.000239 (Fisher's exact test), Q value = 0.15

Table S98. Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 11(4Q35.1) CNV	11	30	15	7
DEL PEAK 11(4Q35.1) WILD-TYPE	20	29	32	47

Figure S98. Get High-res Image Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 12(5q11.2)' versus 'CN_CNMF'

P value = 4.94e-09 (Fisher's exact test), Q value = 3.6e-06

Table S99. Gene #36: 'Del Peak 12(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 12(5Q11.2) CNV	60	16	9	6
DEL PEAK 12(5Q11.2) WILD-TYPE	110	171	23	18

Figure S99. Get High-res Image Gene #36: 'Del Peak 12(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 13(5q21.3)' versus 'CN_CNMF'

P value = 1.14e-09 (Fisher's exact test), Q value = 8.4e-07

Table S100. Gene #37: 'Del Peak 13(5q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 13(5Q21.3) CNV	71	24	14	8
DEL PEAK 13(5Q21.3) WILD-TYPE	99	163	18	16

Figure S100. Get High-res Image Gene #37: 'Del Peak 13(5q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 14(5q23.1)' versus 'CN_CNMF'

P value = 1.57e-08 (Fisher's exact test), Q value = 1.1e-05

Table S101. Gene #38: 'Del Peak 14(5q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 14(5Q23.1) CNV	64	22	13	8
DEL PEAK 14(5Q23.1) WILD-TYPE	106	165	19	16

Figure S101. Get High-res Image Gene #38: 'Del Peak 14(5q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 15(6p25.3)' versus 'CN_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.067

Table S102. Gene #39: 'Del Peak 15(6p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 15(6P25.3) CNV	13	23	9	9
DEL PEAK 15(6P25.3) WILD-TYPE	157	164	23	15

Figure S102. Get High-res Image Gene #39: 'Del Peak 15(6p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 18(8p23.3)' versus 'MRNA_CHIERARCHICAL'

P value = 6.76e-05 (Fisher's exact test), Q value = 0.045

Table S103. Gene #42: 'Del Peak 18(8p23.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
DEL PEAK 18(8P23.3) CNV	19	11	32
DEL PEAK 18(8P23.3) WILD-TYPE	37	32	15

Figure S103. Get High-res Image Gene #42: 'Del Peak 18(8p23.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 18(8p23.3)' versus 'CN_CNMF'

P value = 6.84e-26 (Fisher's exact test), Q value = 5.5e-23

Table S104. Gene #42: 'Del Peak 18(8p23.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 18(8P23.3) CNV	119	32	6	14
DEL PEAK 18(8P23.3) WILD-TYPE	51	155	26	10

Figure S104. Get High-res Image Gene #42: 'Del Peak 18(8p23.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 18(8p23.3)' versus 'METHLYATION_CNMF'

P value = 7.25e-07 (Fisher's exact test), Q value = 0.00051

Table S105. Gene #42: 'Del Peak 18(8p23.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	83	64
DEL PEAK 18(8P23.3) CNV	64	19	22
DEL PEAK 18(8P23.3) WILD-TYPE	43	64	42

Figure S105. Get High-res Image Gene #42: 'Del Peak 18(8p23.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 18(8p23.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.49e-05 (Fisher's exact test), Q value = 0.01

Table S106. Gene #42: 'Del Peak 18(8p23.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	79	65
DEL PEAK 18(8P23.3) CNV	16	43	33
DEL PEAK 18(8P23.3) WILD-TYPE	61	36	32

Figure S106. Get High-res Image Gene #42: 'Del Peak 18(8p23.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 18(8p23.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000112 (Chi-square test), Q value = 0.073

Table S107. Gene #42: 'Del Peak 18(8p23.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	22	49	62	46	42
DEL PEAK 18(8P23.3) CNV	13	25	11	19	24
DEL PEAK 18(8P23.3) WILD-TYPE	9	24	51	27	18

Figure S107. Get High-res Image Gene #42: 'Del Peak 18(8p23.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 19(8p22)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000174 (Fisher's exact test), Q value = 0.11

Table S108. Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
DEL PEAK 19(8P22) CNV	25	9	30
DEL PEAK 19(8P22) WILD-TYPE	31	34	17

Figure S108. Get High-res Image Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 19(8p22)' versus 'CN_CNMF'

P value = 2.41e-30 (Fisher's exact test), Q value = 1.9e-27

Table S109. Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 19(8P22) CNV	129	33	8	15
DEL PEAK 19(8P22) WILD-TYPE	41	154	24	9

Figure S109. Get High-res Image Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 19(8p22)' versus 'METHLYATION_CNMF'

P value = 7.14e-08 (Fisher's exact test), Q value = 5.1e-05

Table S110. Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	83	64
DEL PEAK 19(8P22) CNV	71	22	24
DEL PEAK 19(8P22) WILD-TYPE	36	61	40

Figure S110. Get High-res Image Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 19(8p22)' versus 'RPPA_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.084

Table S111. Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
DEL PEAK 19(8P22) CNV	5	15	38	82
DEL PEAK 19(8P22) WILD-TYPE	21	41	25	98

Figure S111. Get High-res Image Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 19(8p22)' versus 'MRNASEQ_CNMF'

P value = 2.16e-05 (Fisher's exact test), Q value = 0.015

Table S112. Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 19(8P22) CNV	17	38	21	11
DEL PEAK 19(8P22) WILD-TYPE	14	21	26	43

Figure S112. Get High-res Image Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 19(8p22)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.99e-05 (Fisher's exact test), Q value = 0.014

Table S113. Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	79	65
DEL PEAK 19(8P22) CNV	20	47	37
DEL PEAK 19(8P22) WILD-TYPE	57	32	28

Figure S113. Get High-res Image Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 19(8p22)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.73e-05 (Chi-square test), Q value = 0.012

Table S114. Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	22	49	62	46	42
DEL PEAK 19(8P22) CNV	14	29	13	21	27
DEL PEAK 19(8P22) WILD-TYPE	8	20	49	25	15

Figure S114. Get High-res Image Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 20(8p11.22)' versus 'CN_CNMF'

P value = 8.88e-09 (Fisher's exact test), Q value = 6.4e-06

Table S115. Gene #44: 'Del Peak 20(8p11.22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 20(8P11.22) CNV	58	18	3	1
DEL PEAK 20(8P11.22) WILD-TYPE	112	169	29	23

Figure S115. Get High-res Image Gene #44: 'Del Peak 20(8p11.22)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 21(8p11.21)' versus 'CN_CNMF'

P value = 5.81e-07 (Fisher's exact test), Q value = 0.00041

Table S116. Gene #45: 'Del Peak 21(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 21(8P11.21) CNV	35	7	1	0
DEL PEAK 21(8P11.21) WILD-TYPE	135	180	31	24

Figure S116. Get High-res Image Gene #45: 'Del Peak 21(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 22(9p21.3)' versus 'CN_CNMF'

P value = 4.51e-05 (Fisher's exact test), Q value = 0.03

Table S117. Gene #46: 'Del Peak 22(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 22(9P21.3) CNV	35	10	7	4
DEL PEAK 22(9P21.3) WILD-TYPE	135	177	25	20

Figure S117. Get High-res Image Gene #46: 'Del Peak 22(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 23(10p15.3)' versus 'CN_CNMF'

P value = 2.25e-08 (Fisher's exact test), Q value = 1.6e-05

Table S118. Gene #47: 'Del Peak 23(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 23(10P15.3) CNV	38	12	15	3
DEL PEAK 23(10P15.3) WILD-TYPE	132	175	17	21

Figure S118. Get High-res Image Gene #47: 'Del Peak 23(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 24(10q21.1)' versus 'CN_CNMF'

P value = 2.24e-11 (Fisher's exact test), Q value = 1.7e-08

Table S119. Gene #48: 'Del Peak 24(10q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 24(10Q21.1) CNV	48	12	17	5
DEL PEAK 24(10Q21.1) WILD-TYPE	122	175	15	19

Figure S119. Get High-res Image Gene #48: 'Del Peak 24(10q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 25(10q23.31)' versus 'CN_CNMF'

P value = 3.46e-07 (Fisher's exact test), Q value = 0.00025

Table S120. Gene #49: 'Del Peak 25(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 25(10Q23.31) CNV	53	21	15	5
DEL PEAK 25(10Q23.31) WILD-TYPE	117	166	17	19

Figure S120. Get High-res Image Gene #49: 'Del Peak 25(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 26(10q25.2)' versus 'CN_CNMF'

P value = 1.91e-11 (Fisher's exact test), Q value = 1.5e-08

Table S121. Gene #50: 'Del Peak 26(10q25.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 26(10Q25.2) CNV	57	16	17	3
DEL PEAK 26(10Q25.2) WILD-TYPE	113	171	15	21

Figure S121. Get High-res Image Gene #50: 'Del Peak 26(10q25.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 26(10q25.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.81e-05 (Fisher's exact test), Q value = 0.012

Table S122. Gene #50: 'Del Peak 26(10q25.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	79	65
DEL PEAK 26(10Q25.2) CNV	4	26	17
DEL PEAK 26(10Q25.2) WILD-TYPE	73	53	48

Figure S122. Get High-res Image Gene #50: 'Del Peak 26(10q25.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 27(12p13.2)' versus 'CN_CNMF'

P value = 9.87e-08 (Fisher's exact test), Q value = 7.1e-05

Table S123. Gene #51: 'Del Peak 27(12p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 27(12P13.2) CNV	34	4	5	1
DEL PEAK 27(12P13.2) WILD-TYPE	136	183	27	23

Figure S123. Get High-res Image Gene #51: 'Del Peak 27(12p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 28(13q14.13)' versus 'CN_CNMF'

P value = 0.000128 (Fisher's exact test), Q value = 0.083

Table S124. Gene #52: 'Del Peak 28(13q14.13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 28(13Q14.13) CNV	1	9	6	2
DEL PEAK 28(13Q14.13) WILD-TYPE	169	178	26	22

Figure S124. Get High-res Image Gene #52: 'Del Peak 28(13q14.13)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 29(14q32.11)' versus 'MRNA_CNMF'

P value = 1.58e-06 (Fisher's exact test), Q value = 0.0011

Table S125. Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 29(14Q32.11) CNV	8	36	2	10
DEL PEAK 29(14Q32.11) WILD-TYPE	27	25	27	11

Figure S125. Get High-res Image Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 29(14q32.11)' versus 'MRNA_CHIERARCHICAL'

P value = 3.23e-05 (Fisher's exact test), Q value = 0.022

Table S126. Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
DEL PEAK 29(14Q32.11) CNV	22	6	28
DEL PEAK 29(14Q32.11) WILD-TYPE	34	37	19

Figure S126. Get High-res Image Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 29(14q32.11)' versus 'CN_CNMF'

P value = 1.61e-20 (Fisher's exact test), Q value = 1.3e-17

Table S127. Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 29(14Q32.11) CNV	98	22	10	3
DEL PEAK 29(14Q32.11) WILD-TYPE	72	165	22	21

Figure S127. Get High-res Image Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 29(14q32.11)' versus 'MRNASEQ_CNMF'

P value = 7.3e-05 (Fisher's exact test), Q value = 0.048

Table S128. Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 29(14Q32.11) CNV	11	28	13	5
DEL PEAK 29(14Q32.11) WILD-TYPE	20	31	34	49

Figure S128. Get High-res Image Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 29(14q32.11)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.46e-05 (Fisher's exact test), Q value = 0.017

Table S129. Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	79	65
DEL PEAK 29(14Q32.11) CNV	9	35	19
DEL PEAK 29(14Q32.11) WILD-TYPE	68	44	46

Figure S129. Get High-res Image Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 29(14q32.11)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.39e-05 (Chi-square test), Q value = 0.023

Table S130. Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	22	49	62	46	42
DEL PEAK 29(14Q32.11) CNV	10	21	4	18	10
DEL PEAK 29(14Q32.11) WILD-TYPE	12	28	58	28	32

Figure S130. Get High-res Image Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 30(15q11.2)' versus 'CN_CNMF'

P value = 1.2e-21 (Fisher's exact test), Q value = 9.6e-19

Table S131. Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 30(15Q11.2) CNV	104	29	22	5
DEL PEAK 30(15Q11.2) WILD-TYPE	66	158	10	19

Figure S131. Get High-res Image Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 30(15q11.2)' versus 'MRNASEQ_CNMF'

P value = 2.09e-06 (Fisher's exact test), Q value = 0.0015

Table S132. Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 30(15Q11.2) CNV	13	32	19	5
DEL PEAK 30(15Q11.2) WILD-TYPE	18	27	28	49

Figure S132. Get High-res Image Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 30(15q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000117 (Fisher's exact test), Q value = 0.076

Table S133. Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
DEL PEAK 30(15Q11.2) CNV	6	29	34
DEL PEAK 30(15Q11.2) WILD-TYPE	43	33	46

Figure S133. Get High-res Image Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 30(15q11.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.5e-06 (Chi-square test), Q value = 0.0059

Table S134. Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	22	49	62	46	42
DEL PEAK 30(15Q11.2) CNV	8	30	8	20	18
DEL PEAK 30(15Q11.2) WILD-TYPE	14	19	54	26	24

Figure S134. Get High-res Image Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 31(15q21.1)' versus 'CN_CNMF'

P value = 8.15e-18 (Fisher's exact test), Q value = 6.5e-15

Table S135. Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 31(15Q21.1) CNV	97	30	20	4
DEL PEAK 31(15Q21.1) WILD-TYPE	73	157	12	20

Figure S135. Get High-res Image Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 31(15q21.1)' versus 'MRNASEQ_CNMF'

P value = 2.03e-07 (Fisher's exact test), Q value = 0.00014

Table S136. Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 31(15Q21.1) CNV	12	31	17	3
DEL PEAK 31(15Q21.1) WILD-TYPE	19	28	30	51

Figure S136. Get High-res Image Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 31(15q21.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.05e-05 (Fisher's exact test), Q value = 0.014

Table S137. Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
DEL PEAK 31(15Q21.1) CNV	4	28	31
DEL PEAK 31(15Q21.1) WILD-TYPE	45	34	49

Figure S137. Get High-res Image Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 31(15q21.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000165 (Chi-square test), Q value = 0.11

Table S138. Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	22	49	62	46	42
DEL PEAK 31(15Q21.1) CNV	8	27	8	17	16
DEL PEAK 31(15Q21.1) WILD-TYPE	14	22	54	29	26

Figure S138. Get High-res Image Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 32(15q22.33)' versus 'MRNA_CNMF'

P value = 0.000273 (Fisher's exact test), Q value = 0.17

Table S139. Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 32(15Q22.33) CNV	8	31	3	10
DEL PEAK 32(15Q22.33) WILD-TYPE	27	30	26	11

Figure S139. Get High-res Image Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 32(15q22.33)' versus 'CN_CNMF'

P value = 2.48e-21 (Fisher's exact test), Q value = 2e-18

Table S140. Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 32(15Q22.33) CNV	96	23	21	5
DEL PEAK 32(15Q22.33) WILD-TYPE	74	164	11	19

Figure S140. Get High-res Image Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 32(15q22.33)' versus 'METHLYATION_CNMF'

P value = 0.000336 (Fisher's exact test), Q value = 0.21

Table S141. Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	83	64
DEL PEAK 32(15Q22.33) CNV	50	16	22
DEL PEAK 32(15Q22.33) WILD-TYPE	57	67	42

Figure S141. Get High-res Image Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 32(15q22.33)' versus 'MRNASEQ_CNMF'

P value = 3.07e-08 (Fisher's exact test), Q value = 2.2e-05

Table S142. Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 32(15Q22.33) CNV	13	33	17	3
DEL PEAK 32(15Q22.33) WILD-TYPE	18	26	30	51

Figure S142. Get High-res Image Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 32(15q22.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.55e-06 (Fisher's exact test), Q value = 0.0052

Table S143. Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
DEL PEAK 32(15Q22.33) CNV	4	29	33
DEL PEAK 32(15Q22.33) WILD-TYPE	45	33	47

Figure S143. Get High-res Image Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 32(15q22.33)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.77e-05 (Chi-square test), Q value = 0.012

Table S144. Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	22	49	62	46	42
DEL PEAK 32(15Q22.33) CNV	10	28	7	17	14
DEL PEAK 32(15Q22.33) WILD-TYPE	12	21	55	29	28

Figure S144. Get High-res Image Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 35(17p12)' versus 'MRNA_CNMF'

P value = 2.47e-08 (Fisher's exact test), Q value = 1.8e-05

Table S145. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 35(17P12) CNV	10	49	8	15
DEL PEAK 35(17P12) WILD-TYPE	25	12	21	6

Figure S145. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 35(17p12)' versus 'MRNA_CHIERARCHICAL'

P value = 4.97e-07 (Fisher's exact test), Q value = 0.00035

Table S146. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
DEL PEAK 35(17P12) CNV	36	10	36
DEL PEAK 35(17P12) WILD-TYPE	20	33	11

Figure S146. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 35(17p12)' versus 'CN_CNMF'

P value = 2.81e-35 (Fisher's exact test), Q value = 2.3e-32

Table S147. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 35(17P12) CNV	146	43	24	16
DEL PEAK 35(17P12) WILD-TYPE	24	144	8	8

Figure S147. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 35(17p12)' versus 'METHLYATION_CNMF'

P value = 2.58e-10 (Fisher's exact test), Q value = 1.9e-07

Table S148. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	83	64
DEL PEAK 35(17P12) CNV	84	27	30
DEL PEAK 35(17P12) WILD-TYPE	23	56	34

Figure S148. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 35(17p12)' versus 'RPPA_CHIERARCHICAL'

P value = 7.42e-05 (Fisher's exact test), Q value = 0.049

Table S149. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
DEL PEAK 35(17P12) CNV	8	19	43	106
DEL PEAK 35(17P12) WILD-TYPE	18	37	20	74

Figure S149. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 35(17p12)' versus 'MRNASEQ_CNMF'

P value = 1.06e-10 (Fisher's exact test), Q value = 7.9e-08

Table S150. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 35(17P12) CNV	20	49	23	11
DEL PEAK 35(17P12) WILD-TYPE	11	10	24	43

Figure S150. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 35(17p12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.2e-08 (Fisher's exact test), Q value = 2.3e-05

Table S151. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
DEL PEAK 35(17P12) CNV	11	48	44
DEL PEAK 35(17P12) WILD-TYPE	38	14	36

Figure S151. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 35(17p12)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.4e-09 (Fisher's exact test), Q value = 1e-06

Table S152. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	79	65
DEL PEAK 35(17P12) CNV	23	63	36
DEL PEAK 35(17P12) WILD-TYPE	54	16	29

Figure S152. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 35(17p12)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.43e-10 (Chi-square test), Q value = 1.8e-07

Table S153. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	22	49	62	46	42
DEL PEAK 35(17P12) CNV	18	32	11	33	28
DEL PEAK 35(17P12) WILD-TYPE	4	17	51	13	14

Figure S153. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 37(18p11.31)' versus 'MRNA_CNMF'

P value = 6.87e-12 (Fisher's exact test), Q value = 5.3e-09

Table S154. Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 37(18P11.31) CNV	6	50	7	15
DEL PEAK 37(18P11.31) WILD-TYPE	29	11	22	6

Figure S154. Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 37(18p11.31)' versus 'MRNA_CHIERARCHICAL'

P value = 7.49e-10 (Fisher's exact test), Q value = 5.5e-07

Table S155. Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
DEL PEAK 37(18P11.31) CNV	36	6	36
DEL PEAK 37(18P11.31) WILD-TYPE	20	37	11

Figure S155. Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 37(18p11.31)' versus 'CN_CNMF'

P value = 1.93e-42 (Fisher's exact test), Q value = 1.6e-39

Table S156. Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 37(18P11.31) CNV	145	34	28	13
DEL PEAK 37(18P11.31) WILD-TYPE	25	153	4	11

Figure S156. Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 37(18p11.31)' versus 'METHLYATION_CNMF'

P value = 1.57e-14 (Fisher's exact test), Q value = 1.2e-11

Table S157. Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	83	64
DEL PEAK 37(18P11.31) CNV	85	19	32
DEL PEAK 37(18P11.31) WILD-TYPE	22	64	32

Figure S157. Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 37(18p11.31)' versus 'MRNASEQ_CNMF'

P value = 3.11e-17 (Fisher's exact test), Q value = 2.5e-14

Table S158. Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 37(18P11.31) CNV	17	52	24	5
DEL PEAK 37(18P11.31) WILD-TYPE	14	7	23	49

Figure S158. Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 37(18p11.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.19e-10 (Fisher's exact test), Q value = 6e-07

Table S159. Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
DEL PEAK 37(18P11.31) CNV	7	45	46
DEL PEAK 37(18P11.31) WILD-TYPE	42	17	34

Figure S159. Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 37(18p11.31)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.44e-11 (Fisher's exact test), Q value = 1.1e-08

Table S160. Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	79	65
DEL PEAK 37(18P11.31) CNV	18	62	35
DEL PEAK 37(18P11.31) WILD-TYPE	59	17	30

Figure S160. Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 37(18p11.31)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.44e-12 (Chi-square test), Q value = 2.7e-09

Table S161. Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	22	49	62	46	42
DEL PEAK 37(18P11.31) CNV	18	33	7	31	26
DEL PEAK 37(18P11.31) WILD-TYPE	4	16	55	15	16

Figure S161. Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 38(18q12.2)' versus 'MRNA_CNMF'

P value = 1.09e-11 (Fisher's exact test), Q value = 8.4e-09

Table S162. Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 38(18Q12.2) CNV	8	53	9	16
DEL PEAK 38(18Q12.2) WILD-TYPE	27	8	20	5

Figure S162. Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 38(18q12.2)' versus 'MRNA_CHIERARCHICAL'

P value = 2.66e-10 (Fisher's exact test), Q value = 2e-07

Table S163. Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
DEL PEAK 38(18Q12.2) CNV	39	8	39
DEL PEAK 38(18Q12.2) WILD-TYPE	17	35	8

Figure S163. Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 38(18q12.2)' versus 'CN_CNMF'

P value = 1.87e-45 (Fisher's exact test), Q value = 1.5e-42

Table S164. Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 38(18Q12.2) CNV	157	44	27	19
DEL PEAK 38(18Q12.2) WILD-TYPE	13	143	5	5

Figure S164. Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 38(18q12.2)' versus 'METHLYATION_CNMF'

P value = 9.4e-17 (Fisher's exact test), Q value = 7.4e-14

Table S165. Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	83	64
DEL PEAK 38(18Q12.2) CNV	95	26	32
DEL PEAK 38(18Q12.2) WILD-TYPE	12	57	32

Figure S165. Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 38(18q12.2)' versus 'MRNASEQ_CNMF'

P value = 7.66e-16 (Fisher's exact test), Q value = 6.1e-13

Table S166. Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 38(18Q12.2) CNV	21	53	28	8
DEL PEAK 38(18Q12.2) WILD-TYPE	10	6	19	46

Figure S166. Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 38(18q12.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.07e-08 (Fisher's exact test), Q value = 7.8e-06

Table S167. Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
DEL PEAK 38(18Q12.2) CNV	11	48	51
DEL PEAK 38(18Q12.2) WILD-TYPE	38	14	29

Figure S167. Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 38(18q12.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.5e-11 (Fisher's exact test), Q value = 6.4e-08

Table S168. Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	79	65
DEL PEAK 38(18Q12.2) CNV	25	67	40
DEL PEAK 38(18Q12.2) WILD-TYPE	52	12	25

Figure S168. Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 38(18q12.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.43e-13 (Chi-square test), Q value = 3.5e-10

Table S169. Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	22	49	62	46	42
DEL PEAK 38(18Q12.2) CNV	18	38	11	35	30
DEL PEAK 38(18Q12.2) WILD-TYPE	4	11	51	11	12

Figure S169. Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 39(18q21.2)' versus 'MRNA_CNMF'

P value = 3.37e-11 (Fisher's exact test), Q value = 2.6e-08

Table S170. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 39(18Q21.2) CNV	8	53	10	16
DEL PEAK 39(18Q21.2) WILD-TYPE	27	8	19	5

Figure S170. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 39(18q21.2)' versus 'MRNA_CHIERARCHICAL'

P value = 1.46e-10 (Fisher's exact test), Q value = 1.1e-07

Table S171. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
DEL PEAK 39(18Q21.2) CNV	40	8	39
DEL PEAK 39(18Q21.2) WILD-TYPE	16	35	8

Figure S171. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 39(18q21.2)' versus 'CN_CNMF'

P value = 1.51e-45 (Fisher's exact test), Q value = 1.2e-42

Table S172. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 39(18Q21.2) CNV	161	51	28	20
DEL PEAK 39(18Q21.2) WILD-TYPE	9	136	4	4

Figure S172. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 39(18q21.2)' versus 'METHLYATION_CNMF'

P value = 5.83e-13 (Fisher's exact test), Q value = 4.5e-10

Table S173. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	83	64
DEL PEAK 39(18Q21.2) CNV	96	35	34
DEL PEAK 39(18Q21.2) WILD-TYPE	11	48	30

Figure S173. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 39(18q21.2)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000225 (Fisher's exact test), Q value = 0.14

Table S174. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
DEL PEAK 39(18Q21.2) CNV	10	24	46	120
DEL PEAK 39(18Q21.2) WILD-TYPE	16	32	17	60

Figure S174. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 39(18q21.2)' versus 'MRNASEQ_CNMF'

P value = 8.74e-13 (Fisher's exact test), Q value = 6.8e-10

Table S175. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 39(18Q21.2) CNV	21	54	29	13
DEL PEAK 39(18Q21.2) WILD-TYPE	10	5	18	41

Figure S175. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 39(18q21.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.14e-07 (Fisher's exact test), Q value = 5e-04

Table S176. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
DEL PEAK 39(18Q21.2) CNV	15	49	53
DEL PEAK 39(18Q21.2) WILD-TYPE	34	13	27

Figure S176. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 39(18q21.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.95e-10 (Fisher's exact test), Q value = 5.1e-07

Table S177. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	79	65
DEL PEAK 39(18Q21.2) CNV	31	70	42
DEL PEAK 39(18Q21.2) WILD-TYPE	46	9	23

Figure S177. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 39(18q21.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.62e-11 (Chi-square test), Q value = 5e-08

Table S178. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	22	49	62	46	42
DEL PEAK 39(18Q21.2) CNV	19	39	17	37	31
DEL PEAK 39(18Q21.2) WILD-TYPE	3	10	45	9	11

Figure S178. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 40(18q22.1)' versus 'MRNA_CNMF'

P value = 8.76e-11 (Fisher's exact test), Q value = 6.6e-08

Table S179. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 40(18Q22.1) CNV	8	53	11	16
DEL PEAK 40(18Q22.1) WILD-TYPE	27	8	18	5

Figure S179. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 40(18q22.1)' versus 'MRNA_CHIERARCHICAL'

P value = 8.34e-10 (Fisher's exact test), Q value = 6.1e-07

Table S180. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
DEL PEAK 40(18Q22.1) CNV	40	9	39
DEL PEAK 40(18Q22.1) WILD-TYPE	16	34	8

Figure S180. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 40(18q22.1)' versus 'CN_CNMF'

P value = 1.58e-47 (Fisher's exact test), Q value = 1.3e-44

Table S181. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 40(18Q22.1) CNV	162	50	29	19
DEL PEAK 40(18Q22.1) WILD-TYPE	8	137	3	5

Figure S181. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 40(18q22.1)' versus 'METHLYATION_CNMF'

P value = 3.42e-13 (Fisher's exact test), Q value = 2.7e-10

Table S182. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	83	64
DEL PEAK 40(18Q22.1) CNV	96	35	33
DEL PEAK 40(18Q22.1) WILD-TYPE	11	48	31

Figure S182. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 40(18q22.1)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000224 (Fisher's exact test), Q value = 0.14

Table S183. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
DEL PEAK 40(18Q22.1) CNV	10	24	45	122
DEL PEAK 40(18Q22.1) WILD-TYPE	16	32	18	58

Figure S183. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 40(18q22.1)' versus 'MRNASEQ_CNMF'

P value = 4.05e-12 (Fisher's exact test), Q value = 3.1e-09

Table S184. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 40(18Q22.1) CNV	21	54	29	14
DEL PEAK 40(18Q22.1) WILD-TYPE	10	5	18	40

Figure S184. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 40(18q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.76e-07 (Fisher's exact test), Q value = 2e-04

Table S185. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
DEL PEAK 40(18Q22.1) CNV	15	50	53
DEL PEAK 40(18Q22.1) WILD-TYPE	34	12	27

Figure S185. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 40(18q22.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.4e-10 (Fisher's exact test), Q value = 1.8e-07

Table S186. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	79	65
DEL PEAK 40(18Q22.1) CNV	30	70	42
DEL PEAK 40(18Q22.1) WILD-TYPE	47	9	23

Figure S186. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 40(18q22.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.72e-11 (Chi-square test), Q value = 5.1e-08

Table S187. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	22	49	62	46	42
DEL PEAK 40(18Q22.1) CNV	19	39	17	38	29
DEL PEAK 40(18Q22.1) WILD-TYPE	3	10	45	8	13

Figure S187. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 42(20p12.1)' versus 'CN_CNMF'

P value = 1.38e-13 (Fisher's exact test), Q value = 1.1e-10

Table S188. Gene #66: 'Del Peak 42(20p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 42(20P12.1) CNV	61	12	0	6
DEL PEAK 42(20P12.1) WILD-TYPE	109	175	32	18

Figure S188. Get High-res Image Gene #66: 'Del Peak 42(20p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 42(20p12.1)' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.097

Table S189. Gene #66: 'Del Peak 42(20p12.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 42(20P12.1) CNV	8	24	7	4
DEL PEAK 42(20P12.1) WILD-TYPE	23	35	40	50

Figure S189. Get High-res Image Gene #66: 'Del Peak 42(20p12.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 43(21q11.2)' versus 'CN_CNMF'

P value = 3.37e-09 (Fisher's exact test), Q value = 2.5e-06

Table S190. Gene #67: 'Del Peak 43(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 43(21Q11.2) CNV	72	30	18	5
DEL PEAK 43(21Q11.2) WILD-TYPE	98	157	14	19

Figure S190. Get High-res Image Gene #67: 'Del Peak 43(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 44(22q13.32)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000232 (Fisher's exact test), Q value = 0.15

Table S191. Gene #68: 'Del Peak 44(22q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
DEL PEAK 44(22Q13.32) CNV	26	6	24
DEL PEAK 44(22Q13.32) WILD-TYPE	30	37	23

Figure S191. Get High-res Image Gene #68: 'Del Peak 44(22q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 44(22q13.32)' versus 'CN_CNMF'

P value = 9.76e-13 (Fisher's exact test), Q value = 7.6e-10

Table S192. Gene #68: 'Del Peak 44(22q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 44(22Q13.32) CNV	85	28	17	8
DEL PEAK 44(22Q13.32) WILD-TYPE	85	159	15	16

Figure S192. Get High-res Image Gene #68: 'Del Peak 44(22q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 44(22q13.32)' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.8e-05 (Fisher's exact test), Q value = 0.058

Table S193. Gene #68: 'Del Peak 44(22q13.32)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	79	65
DEL PEAK 44(22Q13.32) CNV	11	36	21
DEL PEAK 44(22Q13.32) WILD-TYPE	66	43	44

Figure S193. Get High-res Image Gene #68: 'Del Peak 44(22q13.32)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

Methods & Data

Input

Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
Molecular subtype file = COAD-TP.transferedmergedcluster.txt
Number of patients = 413
Number of copy number variation regions = 68
Number of molecular subtypes = 12
Exclude regions 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

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

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[3] 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)

[4] GISTIC_version2

Made with Nozzle