Correlation between copy number variation genes and molecular subtypes
Breast Invasive Carcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C12R3PMR
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Breast Invasive Carcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C12R3PMR
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 64 peak regions and 10 molecular subtypes across 913 patients, 463 significant findings detected with Q value < 0.25.

  • Amp Peak 1(1p22.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 2(1q21.3) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • Amp Peak 3(1q44) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • Amp Peak 4(3p26.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 5(3q26.32) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 6(4q13.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 7(6p23) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 8(6q21) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 9(8p11.23) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 10(8p11.21) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 11(8q24.21) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 12(10p15.1) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 13(10q22.3) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 14(11p13) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 15(11q13.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • Amp Peak 16(11q14.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 17(12p13.33) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 18(12q15) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 19(13q12.3) cnvs correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 20(13q34) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 21(14q21.1) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • Amp Peak 22(15q26.3) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 23(17q12) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 24(17q23.1) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 25(19q12) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 26(19q13.42) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • Amp Peak 27(20q13.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 1(1p36.13) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 2(1p22.1) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 3(2q37.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 4(3p14.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 5(4p16.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 6(4q35.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 7(5q11.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 8(5q21.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 9(6p25.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 10(6q15) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 11(6q27) cnvs correlated to 'CN_CNMF'.

  • Del Peak 12(7p22.3) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 13(7q36.1) cnvs correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 14(8p23.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 15(8p11.21) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 16(9p21.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 17(9q21.11) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 18(10q23.31) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 19(10q26.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 20(11p15.5) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 21(11q13.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 22(11q23.2) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 23(11q25) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • Del Peak 24(12p13.1) cnvs correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 25(12q24.21) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 26(13q14.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 27(14q24.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 28(15q13.1) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 29(16q24.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 30(17p12) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 31(17q21.31) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 32(18q23) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 33(19p13.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 34(19q13.32) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 35(20p13) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 36(21q11.2) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • Del Peak 37(22q13.32) cnvs correlated to 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 64 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 463 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
nCNV (%) nWild-Type Chi-square test Fisher's exact test Chi-square test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
Amp Peak 1(1p22 3) 0 (0%) 705 1.29e-13
(6.27e-11) 		6.67e-12
(3e-09) 		6.61e-18
(3.63e-15) 		1.95e-17
(1.06e-14) 		0.000139
(0.0318) 		1.28e-07
(4.5e-05) 		9.25e-16
(4.88e-13) 		2.4e-16
(1.28e-13) 		1.36e-13
(6.57e-11) 		1.36e-15
(7.14e-13)
Amp Peak 5(3q26 32) 0 (0%) 625 6.88e-11
(2.96e-08) 		7.83e-10
(3.2e-07) 		8.72e-36
(5.38e-33) 		8.01e-17
(4.32e-14) 		7.16e-07
(0.000231) 		2.92e-06
(0.000863) 		4.31e-22
(2.52e-19) 		5.88e-21
(3.36e-18) 		1.63e-15
(8.53e-13) 		6.39e-24
(3.78e-21)
Amp Peak 7(6p23) 0 (0%) 670 3.59e-07
(0.00012) 		1.92e-07
(6.59e-05) 		5.65e-34
(3.48e-31) 		2.44e-17
(1.33e-14) 		1.98e-06
(0.000593) 		8.42e-05
(0.0201) 		1.01e-13
(4.93e-11) 		3.56e-11
(1.56e-08) 		1.52e-18
(8.5e-16) 		2.51e-15
(1.29e-12)
Amp Peak 8(6q21) 0 (0%) 743 8.2e-14
(4.03e-11) 		4.54e-10
(1.87e-07) 		1.67e-39
(1.04e-36) 		4.11e-13
(1.95e-10) 		1.04e-08
(4e-06) 		4.64e-07
(0.000153) 		7.59e-22
(4.42e-19) 		2.72e-18
(1.51e-15) 		3.42e-19
(1.93e-16) 		4.33e-23
(2.55e-20)
Amp Peak 11(8q24 21) 0 (0%) 329 1.17e-16
(6.3e-14) 		2.62e-07
(8.88e-05) 		2.63e-43
(1.65e-40) 		1.7e-27
(1.02e-24) 		4.58e-08
(1.66e-05) 		9.36e-07
(0.000297) 		3.47e-21
(1.99e-18) 		5.54e-15
(2.83e-12) 		1.31e-21
(7.6e-19) 		2.37e-19
(1.34e-16)
Amp Peak 12(10p15 1) 0 (0%) 655 1.72e-21
(9.93e-19) 		1.06e-18
(5.92e-16) 		9.95e-35
(6.13e-32) 		1.93e-26
(1.16e-23) 		7e-11
(3e-08) 		2.33e-12
(1.07e-09) 		2.05e-28
(1.24e-25) 		1.17e-28
(7.06e-26) 		6.23e-28
(3.76e-25) 		1.2e-30
(7.31e-28)
Amp Peak 17(12p13 33) 0 (0%) 675 1.91e-12
(8.84e-10) 		2.53e-11
(1.11e-08) 		1.68e-28
(1.01e-25) 		7.29e-17
(3.94e-14) 		2.7e-08
(9.98e-06) 		2.37e-07
(8.07e-05) 		1.67e-17
(9.11e-15) 		1.45e-15
(7.57e-13) 		9.18e-22
(5.32e-19) 		5.5e-18
(3.04e-15)
Amp Peak 20(13q34) 0 (0%) 754 9.14e-10
(3.72e-07) 		5.78e-09
(2.28e-06) 		1.51e-17
(8.24e-15) 		1.33e-14
(6.7e-12) 		8.21e-06
(0.00226) 		5.1e-08
(1.84e-05) 		8.44e-14
(4.14e-11) 		1.17e-14
(5.9e-12) 		1.41e-13
(6.83e-11) 		5.59e-20
(3.17e-17)
Amp Peak 25(19q12) 0 (0%) 680 2.12e-12
(9.74e-10) 		9.11e-11
(3.9e-08) 		1.28e-21
(7.43e-19) 		4.2e-12
(1.91e-09) 		6.19e-07
(0.000202) 		9.68e-07
(0.000306) 		1.11e-15
(5.84e-13) 		2.08e-15
(1.08e-12) 		6.49e-13
(3.04e-10) 		2.82e-18
(1.57e-15)
Del Peak 3(2q37 3) 0 (0%) 648 1.39e-06
(0.000432) 		3.78e-08
(1.38e-05) 		1.57e-20
(8.99e-18) 		2.61e-10
(1.09e-07) 		1.03e-08
(3.96e-06) 		1.11e-07
(3.92e-05) 		1.81e-11
(8.04e-09) 		2.03e-08
(7.56e-06) 		4.66e-11
(2.02e-08) 		2.63e-07
(8.9e-05)
Del Peak 4(3p14 3) 0 (0%) 635 1.06e-10
(4.51e-08) 		3.11e-08
(1.14e-05) 		2.93e-33
(1.8e-30) 		5.78e-13
(2.72e-10) 		1.18e-09
(4.77e-07) 		5.21e-06
(0.00148) 		4.61e-18
(2.56e-15) 		4.42e-13
(2.09e-10) 		2.29e-19
(1.3e-16) 		2.57e-14
(1.28e-11)
Del Peak 5(4p16 3) 0 (0%) 632 5.63e-11
(2.44e-08) 		6.3e-12
(2.84e-09) 		1.98e-26
(1.18e-23) 		8.41e-13
(3.94e-10) 		4.6e-07
(0.000152) 		1.62e-06
(0.000497) 		9.75e-24
(5.75e-21) 		2.14e-18
(1.19e-15) 		9.97e-15
(5.05e-12) 		4.7e-18
(2.6e-15)
Del Peak 6(4q35 2) 0 (0%) 630 3.17e-06
(0.000922) 		9.81e-07
(0.000309) 		2.71e-37
(1.68e-34) 		1.66e-13
(8e-11) 		1.51e-08
(5.71e-06) 		1.78e-06
(0.000537) 		2.22e-21
(1.28e-18) 		3.79e-14
(1.87e-11) 		2.84e-13
(1.36e-10) 		6.73e-18
(3.7e-15)
Del Peak 7(5q11 2) 0 (0%) 679 1.17e-27
(7.04e-25) 		6.11e-25
(3.63e-22) 		5.91e-60
(3.78e-57) 		1.43e-39
(8.94e-37) 		3.33e-16
(1.77e-13) 		7.43e-19
(4.18e-16) 		1.33e-40
(8.35e-38) 		1.7e-43
(1.07e-40) 		8.36e-40
(5.24e-37) 		5.41e-49
(3.43e-46)
Del Peak 8(5q21 3) 0 (0%) 688 1.36e-29
(8.28e-27) 		1e-26
(5.98e-24) 		6.13e-70
(3.92e-67) 		3.25e-51
(2.07e-48) 		2.6e-15
(1.34e-12) 		8.97e-16
(4.75e-13) 		5.88e-48
(3.73e-45) 		1.06e-47
(6.73e-45) 		1.28e-39
(8.02e-37) 		1.67e-54
(1.07e-51)
Del Peak 18(10q23 31) 0 (0%) 652 4.09e-05
(0.0103) 		9.57e-05
(0.0225) 		3.83e-20
(2.18e-17) 		4.75e-12
(2.16e-09) 		1.9e-07
(6.53e-05) 		7.37e-05
(0.0178) 		1.06e-11
(4.75e-09) 		6.91e-09
(2.69e-06) 		5.47e-09
(2.17e-06) 		3.97e-09
(1.58e-06)
Del Peak 19(10q26 3) 0 (0%) 649 2.88e-08
(1.06e-05) 		1.49e-07
(5.2e-05) 		2.23e-22
(1.31e-19) 		2.07e-12
(9.53e-10) 		3.06e-08
(1.13e-05) 		8.25e-07
(0.000264) 		1.77e-15
(9.22e-13) 		1.17e-12
(5.44e-10) 		7.81e-12
(3.5e-09) 		3.48e-15
(1.79e-12)
Del Peak 20(11p15 5) 0 (0%) 651 1.34e-06
(0.000418) 		1.62e-07
(5.62e-05) 		5.01e-36
(3.1e-33) 		1.96e-12
(9.01e-10) 		1.27e-09
(5.13e-07) 		1.65e-06
(0.000502) 		8.07e-18
(4.42e-15) 		5.07e-13
(2.39e-10) 		3.87e-15
(1.98e-12) 		1.42e-16
(7.61e-14)
Del Peak 25(12q24 21) 0 (0%) 739 9.6e-11
(4.1e-08) 		2.5e-10
(1.04e-07) 		2.33e-15
(1.2e-12) 		2.68e-14
(1.33e-11) 		0.000209
(0.0458) 		1.05e-06
(0.00033) 		6.55e-16
(3.47e-13) 		3.47e-13
(1.65e-10) 		1.17e-08
(4.46e-06) 		3.27e-13
(1.56e-10)
Del Peak 27(14q24 3) 0 (0%) 619 4e-13
(1.9e-10) 		1.56e-08
(5.89e-06) 		8.6e-37
(5.32e-34) 		3.5e-14
(1.73e-11) 		5.29e-07
(0.000174) 		5.53e-06
(0.00157) 		3.86e-15
(1.98e-12) 		3.04e-13
(1.45e-10) 		5.44e-18
(3.01e-15) 		1.52e-16
(8.14e-14)
Del Peak 28(15q13 1) 0 (0%) 598 3.46e-07
(0.000116) 		7.57e-08
(2.69e-05) 		6.74e-31
(4.12e-28) 		1.2e-11
(5.33e-09) 		0.000193
(0.0427) 		2.32e-05
(0.0061) 		6.07e-15
(3.09e-12) 		2.32e-14
(1.16e-11) 		6.32e-19
(3.56e-16) 		1.96e-18
(1.1e-15)
Del Peak 29(16q24 3) 0 (0%) 326 1.6e-16
(8.57e-14) 		2.51e-14
(1.25e-11) 		1.66e-14
(8.33e-12) 		4.47e-13
(2.11e-10) 		1.14e-09
(4.64e-07) 		3.45e-11
(1.51e-08) 		2.82e-16
(1.5e-13) 		4.62e-21
(2.65e-18) 		9.22e-15
(4.68e-12) 		8.49e-22
(4.93e-19)
Del Peak 31(17q21 31) 0 (0%) 598 1.07e-14
(5.4e-12) 		3.91e-07
(0.00013) 		5.42e-22
(3.17e-19) 		1.19e-11
(5.32e-09) 		1.86e-11
(8.21e-09) 		3.12e-11
(1.37e-08) 		2.86e-21
(1.64e-18) 		8.32e-17
(4.48e-14) 		1.14e-12
(5.32e-10) 		1.76e-11
(7.82e-09)
Del Peak 33(19p13 3) 0 (0%) 608 5.99e-11
(2.59e-08) 		4.57e-08
(1.66e-05) 		1.25e-44
(7.91e-42) 		6.53e-18
(3.6e-15) 		3.03e-06
(0.000888) 		3.39e-05
(0.00861) 		1.19e-12
(5.53e-10) 		5.4e-10
(2.22e-07) 		9.67e-16
(5.1e-13) 		6.54e-17
(3.55e-14)
Del Peak 34(19q13 32) 0 (0%) 730 1.57e-06
(0.000484) 		8.8e-05
(0.0208) 		4.48e-20
(2.55e-17) 		1.52e-10
(6.42e-08) 		0.000783
(0.144) 		4.95e-05
(0.0122) 		5.28e-09
(2.1e-06) 		6.75e-09
(2.64e-06) 		3.6e-10
(1.5e-07) 		5.78e-12
(2.61e-09)
Amp Peak 27(20q13 2) 0 (0%) 448 1.35e-09
(5.42e-07) 		0.000278
(0.0581) 		9.78e-50
(6.22e-47) 		5.18e-25
(3.07e-22) 		0.000604
(0.117) 		0.0154
(1.00) 		6.68e-09
(2.62e-06) 		2.14e-07
(7.31e-05) 		7.41e-10
(3.03e-07) 		1.16e-06
(0.000364)
Amp Peak 6(4q13 3) 0 (0%) 770 5.63e-05
(0.0137) 		0.00023
(0.0495) 		7.87e-14
(3.87e-11) 		3.97e-07
(0.000131) 		0.0471
(1.00) 		0.524
(1.00) 		7e-06
(0.00195) 		2.4e-05
(0.00628) 		0.00138
(0.246) 		1.11e-07
(3.92e-05)
Amp Peak 18(12q15) 0 (0%) 678 1.81e-08
(6.79e-06) 		0.000131
(0.0301) 		1.86e-25
(1.11e-22) 		1.49e-13
(7.21e-11) 		0.188
(1.00) 		0.0652
(1.00) 		6.02e-06
(0.00169) 		1.71e-05
(0.00456) 		9.16e-08
(3.25e-05) 		0.000644
(0.124)
Amp Peak 22(15q26 3) 0 (0%) 747 3.31e-07
(0.000111) 		0.00679
(0.978) 		1.88e-15
(9.76e-13) 		0.000326
(0.0669) 		0.000153
(0.0345) 		0.0384
(1.00) 		2.07e-08
(7.72e-06) 		7.98e-06
(0.0022) 		5.92e-08
(2.11e-05) 		7.56e-09
(2.93e-06)
Del Peak 1(1p36 13) 0 (0%) 533 3.27e-05
(0.00837) 		0.000651
(0.124) 		6.02e-32
(3.68e-29) 		2.81e-09
(1.12e-06) 		0.00726
(1.00) 		0.0805
(1.00) 		1.11e-05
(0.00299) 		6.02e-05
(0.0146) 		2.37e-07
(8.07e-05) 		0.00056
(0.11)
Del Peak 14(8p23 2) 0 (0%) 432 1.08e-09
(4.4e-07) 		2.53e-05
(0.00661) 		7.63e-31
(4.65e-28) 		1.19e-13
(5.8e-11) 		0.00955
(1.00) 		0.0341
(1.00) 		2.05e-11
(9.03e-09) 		3.71e-08
(1.36e-05) 		5.68e-06
(0.00161) 		4.79e-12
(2.17e-09)
Del Peak 16(9p21 3) 0 (0%) 606 2.43e-06
(0.000721) 		0.00076
(0.141) 		1.11e-29
(6.76e-27) 		2.21e-15
(1.14e-12) 		0.00341
(0.543) 		0.444
(1.00) 		7.31e-07
(0.000235) 		2.64e-07
(8.9e-05) 		4.02e-06
(0.00116) 		4.15e-12
(1.89e-09)
Del Peak 17(9q21 11) 0 (0%) 667 0.00255
(0.426) 		0.00029
(0.0603) 		3.41e-16
(1.81e-13) 		1.19e-10
(5.06e-08) 		1.04e-05
(0.00281) 		0.00653
(0.954) 		2.41e-06
(0.000718) 		8.3e-06
(0.00227) 		1.41e-08
(5.34e-06) 		9.33e-13
(4.36e-10)
Del Peak 26(13q14 2) 0 (0%) 500 2.15e-05
(0.00572) 		4.23e-05
(0.0106) 		7.07e-28
(4.25e-25) 		1.81e-08
(6.79e-06) 		0.538
(1.00) 		0.111
(1.00) 		1.55e-07
(5.38e-05) 		6.39e-06
(0.00178) 		3.86e-10
(1.6e-07) 		1.12e-07
(3.93e-05)
Del Peak 35(20p13) 0 (0%) 779 8.81e-06
(0.0024) 		0.000158
(0.0354) 		2.59e-13
(1.24e-10) 		7.15e-09
(2.78e-06) 		0.00154
(0.269) 		0.0119
(1.00) 		2.44e-10
(1.02e-07) 		7.06e-10
(2.89e-07) 		2.69e-12
(1.23e-09) 		1.91e-13
(9.17e-11)
Amp Peak 13(10q22 3) 0 (0%) 781 2.2e-05
(0.00582) 		0.0681
(1.00) 		8.18e-09
(3.16e-06) 		0.000149
(0.0337) 		0.0025
(0.423) 		0.0211
(1.00) 		1.83e-07
(6.31e-05) 		0.000689
(0.129) 		3.75e-05
(0.00949) 		0.000675
(0.127)
Del Peak 10(6q15) 0 (0%) 612 1.55e-06
(0.000478) 		0.00137
(0.246) 		6.83e-28
(4.11e-25) 		3.78e-08
(1.38e-05) 		0.456
(1.00) 		0.0875
(1.00) 		2.69e-05
(0.00692) 		0.000262
(0.055) 		0.0136
(1.00) 		5.04e-05
(0.0124)
Del Peak 12(7p22 3) 0 (0%) 795 0.00298
(0.482) 		0.000366
(0.0742) 		2.06e-15
(1.07e-12) 		5.89e-07
(0.000193) 		0.0214
(1.00) 		0.00553
(0.829) 		8.07e-09
(3.12e-06) 		5.39e-08
(1.93e-05) 		3.96e-11
(1.72e-08) 		1.38e-10
(5.86e-08)
Del Peak 30(17p12) 0 (0%) 367 2.14e-10
(8.99e-08) 		0.166
(1.00) 		9.33e-23
(5.49e-20) 		7.4e-07
(0.000238) 		8.07e-05
(0.0194) 		0.00775
(1.00) 		0.000586
(0.114) 		0.121
(1.00) 		0.000255
(0.0541) 		0.000127
(0.0293)
Amp Peak 2(1q21 3) 0 (0%) 254 1.54e-07
(5.37e-05) 		0.00185
(0.322) 		6.45e-09
(2.54e-06) 		1.66e-06
(0.000504) 		0.0586
(1.00) 		0.00703
(1.00) 		0.000167
(0.0373) 		0.000205
(0.045) 		0.00102
(0.184) 		0.00262
(0.434)
Amp Peak 4(3p26 1) 0 (0%) 725 0.0124
(1.00) 		0.00803
(1.00) 		1.01e-13
(4.93e-11) 		2.95e-06
(0.000868) 		0.00573
(0.848) 		0.00869
(1.00) 		5.11e-09
(2.03e-06) 		6.57e-07
(0.000213) 		5.97e-06
(0.00168) 		1.18e-08
(4.49e-06)
Amp Peak 21(14q21 1) 0 (0%) 732 0.000259
(0.0547) 		0.00478
(0.721) 		1.97e-09
(7.89e-07) 		5.16e-05
(0.0127) 		0.0823
(1.00) 		0.0385
(1.00) 		3.92e-05
(0.00987) 		2.45e-06
(0.000725) 		1.94e-06
(0.000584) 		0.0693
(1.00)
Amp Peak 23(17q12) 0 (0%) 618 1.49e-14
(7.49e-12) 		0.0003
(0.0618) 		7.29e-34
(4.48e-31) 		5.76e-09
(2.28e-06) 		0.049
(1.00) 		0.00821
(1.00) 		0.000101
(0.0237) 		0.000454
(0.0903) 		0.0148
(1.00) 		0.0196
(1.00)
Amp Peak 24(17q23 1) 0 (0%) 539 2.42e-14
(1.21e-11) 		0.00149
(0.263) 		6.19e-38
(3.84e-35) 		1.45e-10
(6.12e-08) 		0.191
(1.00) 		0.334
(1.00) 		0.000644
(0.124) 		0.00575
(0.848) 		3.1e-07
(0.000104) 		3.57e-06
(0.00103)
Del Peak 32(18q23) 0 (0%) 620 0.000347
(0.0709) 		0.149
(1.00) 		1.32e-15
(6.95e-13) 		1.2e-08
(4.56e-06) 		0.00413
(0.64) 		0.581
(1.00) 		2.54e-05
(0.00661) 		0.00371
(0.585) 		0.000375
(0.0757) 		0.000143
(0.0324)
Amp Peak 9(8p11 23) 0 (0%) 567 1.64e-06
(0.000501) 		0.00561
(0.836) 		1.44e-24
(8.5e-22) 		1.22e-12
(5.64e-10) 		0.0399
(1.00) 		0.00473
(0.718) 		0.000227
(0.049) 		3.34e-05
(0.00851) 		0.0447
(1.00) 		0.0332
(1.00)
Amp Peak 14(11p13) 0 (0%) 721 0.311
(1.00) 		0.148
(1.00) 		1.84e-10
(7.73e-08) 		4.84e-05
(0.012) 		0.105
(1.00) 		0.229
(1.00) 		2.61e-05
(0.00675) 		0.0204
(1.00) 		1.33e-06
(0.000417) 		1.91e-08
(7.15e-06)
Amp Peak 16(11q14 1) 0 (0%) 679 0.12
(1.00) 		0.101
(1.00) 		1.8e-19
(1.02e-16) 		7.93e-06
(0.0022) 		0.148
(1.00) 		0.199
(1.00) 		8.57e-05
(0.0203) 		0.00146
(0.259) 		8.98e-07
(0.000285) 		1.39e-05
(0.00372)
Del Peak 2(1p22 1) 0 (0%) 608 0.00234
(0.4) 		8.39e-05
(0.0201) 		5.77e-22
(3.36e-19) 		0.00103
(0.186) 		0.0231
(1.00) 		0.049
(1.00) 		0.000574
(0.113) 		3.06e-06
(0.000892) 		0.0125
(1.00) 		0.0329
(1.00)
Del Peak 13(7q36 1) 0 (0%) 739 0.0129
(1.00) 		0.043
(1.00) 		5.25e-10
(2.16e-07) 		0.0897
(1.00) 		0.551
(1.00) 		0.0562
(1.00) 		0.000414
(0.0831) 		0.000496
(0.0983) 		5.26e-08
(1.89e-05) 		1.6e-06
(0.000491)
Del Peak 15(8p11 21) 0 (0%) 740 0.000126
(0.0292) 		0.0141
(1.00) 		6.19e-11
(2.67e-08) 		0.0474
(1.00) 		0.0465
(1.00) 		0.0191
(1.00) 		0.000593
(0.115) 		0.000914
(0.167) 		0.00401
(0.625) 		6.26e-06
(0.00175)
Amp Peak 10(8p11 21) 0 (0%) 559 0.0144
(1.00) 		0.0422
(1.00) 		1.01e-22
(5.92e-20) 		4.03e-08
(1.46e-05) 		0.791
(1.00) 		0.633
(1.00) 		0.000224
(0.0487) 		0.000104
(0.0242) 		0.0361
(1.00) 		0.0215
(1.00)
Amp Peak 19(13q12 3) 0 (0%) 785 0.0708
(1.00) 		0.0557
(1.00) 		2.22e-05
(0.00586) 		0.00895
(1.00) 		0.0155
(1.00) 		0.142
(1.00) 		2.63e-05
(0.00679) 		0.00269
(0.441) 		0.000196
(0.0433) 		0.00043
(0.086)
Amp Peak 26(19q13 42) 0 (0%) 678 0.000775
(0.143) 		0.0212
(1.00) 		2.5e-14
(1.25e-11) 		6.23e-07
(0.000202) 		0.00233
(0.4) 		0.0549
(1.00) 		0.00264
(0.436) 		0.029
(1.00) 		4.27e-06
(0.00123) 		0.00441
(0.675)
Del Peak 22(11q23 2) 0 (0%) 464 2.08e-08
(7.72e-06) 		0.0296
(1.00) 		3.22e-42
(2.02e-39) 		7.68e-12
(3.45e-09) 		0.975
(1.00) 		0.475
(1.00) 		0.00305
(0.491) 		0.00254
(0.426) 		0.0196
(1.00) 		0.000137
(0.0314)
Del Peak 24(12p13 1) 0 (0%) 756 0.0439
(1.00) 		0.14
(1.00) 		0.000979
(0.178) 		0.0149
(1.00) 		0.222
(1.00) 		0.042
(1.00) 		0.00021
(0.0458) 		0.0137
(1.00) 		8.03e-05
(0.0194) 		8.68e-06
(0.00237)
Amp Peak 3(1q44) 0 (0%) 258 3.9e-06
(0.00113) 		0.263
(1.00) 		1.37e-07
(4.8e-05) 		9.22e-06
(0.0025) 		0.864
(1.00) 		0.324
(1.00) 		0.206
(1.00) 		0.383
(1.00) 		0.711
(1.00) 		0.0277
(1.00)
Amp Peak 15(11q13 3) 0 (0%) 564 0.00319
(0.511) 		0.0336
(1.00) 		4.91e-41
(3.08e-38) 		4e-10
(1.66e-07) 		0.966
(1.00) 		0.146
(1.00) 		0.0453
(1.00) 		0.168
(1.00) 		0.000292
(0.0604) 		0.0396
(1.00)
Del Peak 23(11q25) 0 (0%) 492 0.000243
(0.052) 		0.96
(1.00) 		6.15e-38
(3.83e-35) 		9.89e-09
(3.81e-06) 		0.126
(1.00) 		0.707
(1.00) 		0.355
(1.00) 		0.351
(1.00) 		0.093
(1.00) 		0.0331
(1.00)
Del Peak 36(21q11 2) 0 (0%) 731 0.000252
(0.0538) 		0.0342
(1.00) 		4.31e-11
(1.87e-08) 		2.01e-06
(0.000602) 		0.225
(1.00) 		0.502
(1.00) 		0.0581
(1.00) 		0.197
(1.00) 		0.0142
(1.00) 		0.0194
(1.00)
Del Peak 9(6p25 3) 0 (0%) 743 0.318
(1.00) 		0.522
(1.00) 		8.51e-07
(0.000271) 		4.71e-05
(0.0117) 		0.439
(1.00) 		0.597
(1.00) 		0.00292
(0.477) 		0.00786
(1.00) 		0.299
(1.00) 		0.0417
(1.00)
Del Peak 21(11q13 1) 0 (0%) 719 0.00185
(0.322) 		0.0584
(1.00) 		3.51e-17
(1.91e-14) 		4.39e-06
(0.00125) 		0.331
(1.00) 		0.393
(1.00) 		0.00823
(1.00) 		0.0169
(1.00) 		0.596
(1.00) 		0.0297
(1.00)
Del Peak 11(6q27) 0 (0%) 599 0.0183
(1.00) 		0.61
(1.00) 		2.87e-14
(1.42e-11) 		0.00375
(0.589) 		0.113
(1.00) 		0.796
(1.00) 		0.341
(1.00) 		0.561
(1.00) 		0.393
(1.00) 		0.115
(1.00)
Del Peak 37(22q13 32) 0 (0%) 503 0.164
(1.00) 		0.0438
(1.00) 		0.063
(1.00) 		0.000674
(0.127) 		0.121
(1.00) 		0.0218
(1.00) 		0.00661
(0.959) 		0.00247
(0.419) 		0.00438
(0.674) 		0.492
(1.00)
'Amp Peak 1(1p22.3)' versus 'MRNA_CNMF'

P value = 1.29e-13 (Chi-square test), Q value = 6.3e-11

Table S1.  Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
AMP PEAK 1(1P22.3) CNV 16 2 3 51 16 2 24 2
AMP PEAK 1(1P22.3) WILD-TYPE 108 34 20 44 56 18 79 38

Figure S1.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 1(1p22.3)' versus 'MRNA_CHIERARCHICAL'

P value = 6.67e-12 (Fisher's exact test), Q value = 3e-09

Table S2.  Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
AMP PEAK 1(1P22.3) CNV 13 57 46
AMP PEAK 1(1P22.3) WILD-TYPE 127 68 202

Figure S2.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 1(1p22.3)' versus 'CN_CNMF'

P value = 6.61e-18 (Chi-square test), Q value = 3.6e-15

Table S3.  Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
AMP PEAK 1(1P22.3) CNV 47 26 29 90 16
AMP PEAK 1(1P22.3) WILD-TYPE 300 196 43 133 33

Figure S3.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 1(1p22.3)' versus 'METHLYATION_CNMF'

P value = 1.95e-17 (Chi-square test), Q value = 1.1e-14

Table S4.  Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
AMP PEAK 1(1P22.3) CNV 57 21 22 17 2 17
AMP PEAK 1(1P22.3) WILD-TYPE 44 118 71 120 38 80

Figure S4.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 1(1p22.3)' versus 'RPPA_CNMF'

P value = 0.000139 (Fisher's exact test), Q value = 0.032

Table S5.  Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 1(1P22.3) CNV 52 28 16
AMP PEAK 1(1P22.3) WILD-TYPE 95 105 101

Figure S5.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 1(1p22.3)' versus 'RPPA_CHIERARCHICAL'

P value = 1.28e-07 (Fisher's exact test), Q value = 4.5e-05

Table S6.  Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 1(1P22.3) CNV 32 12 52
AMP PEAK 1(1P22.3) WILD-TYPE 129 98 74

Figure S6.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 1(1p22.3)' versus 'MRNASEQ_CNMF'

P value = 9.25e-16 (Fisher's exact test), Q value = 4.9e-13

Table S7.  Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
AMP PEAK 1(1P22.3) CNV 96 13 73
AMP PEAK 1(1P22.3) WILD-TYPE 138 135 373

Figure S7.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 1(1p22.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.4e-16 (Fisher's exact test), Q value = 1.3e-13

Table S8.  Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
AMP PEAK 1(1P22.3) CNV 23 70 89
AMP PEAK 1(1P22.3) WILD-TYPE 193 338 115

Figure S8.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 1(1p22.3)' versus 'MIRSEQ_CNMF'

P value = 1.36e-13 (Fisher's exact test), Q value = 6.6e-11

Table S9.  Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 1(1P22.3) CNV 39 59 103
AMP PEAK 1(1P22.3) WILD-TYPE 195 333 152

Figure S9.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 1(1p22.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.36e-15 (Fisher's exact test), Q value = 7.1e-13

Table S10.  Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 1(1P22.3) CNV 54 46 101
AMP PEAK 1(1P22.3) WILD-TYPE 308 238 134

Figure S10.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 2(1q21.3)' versus 'MRNA_CNMF'

P value = 1.54e-07 (Chi-square test), Q value = 5.4e-05

Table S11.  Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
AMP PEAK 2(1Q21.3) CNV 77 19 16 88 54 10 85 30
AMP PEAK 2(1Q21.3) WILD-TYPE 47 17 7 7 18 10 18 10

Figure S11.  Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 2(1q21.3)' versus 'CN_CNMF'

P value = 6.45e-09 (Chi-square test), Q value = 2.5e-06

Table S12.  Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
AMP PEAK 2(1Q21.3) CNV 219 167 72 167 34
AMP PEAK 2(1Q21.3) WILD-TYPE 128 55 0 56 15

Figure S12.  Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 2(1q21.3)' versus 'METHLYATION_CNMF'

P value = 1.66e-06 (Chi-square test), Q value = 5e-04

Table S13.  Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
AMP PEAK 2(1Q21.3) CNV 85 110 74 90 21 55
AMP PEAK 2(1Q21.3) WILD-TYPE 16 29 19 47 19 42

Figure S13.  Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 2(1q21.3)' versus 'MRNASEQ_CNMF'

P value = 0.000167 (Fisher's exact test), Q value = 0.037

Table S14.  Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
AMP PEAK 2(1Q21.3) CNV 191 94 313
AMP PEAK 2(1Q21.3) WILD-TYPE 43 54 133

Figure S14.  Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 2(1q21.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000205 (Fisher's exact test), Q value = 0.045

Table S15.  Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
AMP PEAK 2(1Q21.3) CNV 137 295 166
AMP PEAK 2(1Q21.3) WILD-TYPE 79 113 38

Figure S15.  Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 2(1q21.3)' versus 'MIRSEQ_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.18

Table S16.  Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 2(1Q21.3) CNV 153 277 204
AMP PEAK 2(1Q21.3) WILD-TYPE 81 115 51

Figure S16.  Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 3(1q44)' versus 'MRNA_CNMF'

P value = 3.9e-06 (Chi-square test), Q value = 0.0011

Table S17.  Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
AMP PEAK 3(1Q44) CNV 72 19 16 78 57 11 86 33
AMP PEAK 3(1Q44) WILD-TYPE 52 17 7 17 15 9 17 7

Figure S17.  Get High-res Image Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 3(1q44)' versus 'CN_CNMF'

P value = 1.37e-07 (Chi-square test), Q value = 4.8e-05

Table S18.  Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
AMP PEAK 3(1Q44) CNV 226 165 72 160 32
AMP PEAK 3(1Q44) WILD-TYPE 121 57 0 63 17

Figure S18.  Get High-res Image Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 3(1q44)' versus 'METHLYATION_CNMF'

P value = 9.22e-06 (Chi-square test), Q value = 0.0025

Table S19.  Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
AMP PEAK 3(1Q44) CNV 74 113 79 85 24 57
AMP PEAK 3(1Q44) WILD-TYPE 27 26 14 52 16 40

Figure S19.  Get High-res Image Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 4(3p26.1)' versus 'CN_CNMF'

P value = 1.01e-13 (Chi-square test), Q value = 4.9e-11

Table S20.  Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
AMP PEAK 4(3P26.1) CNV 25 55 20 75 13
AMP PEAK 4(3P26.1) WILD-TYPE 322 167 52 148 36

Figure S20.  Get High-res Image Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 4(3p26.1)' versus 'METHLYATION_CNMF'

P value = 2.95e-06 (Chi-square test), Q value = 0.00087

Table S21.  Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
AMP PEAK 4(3P26.1) CNV 31 9 22 30 3 11
AMP PEAK 4(3P26.1) WILD-TYPE 70 130 71 107 37 86

Figure S21.  Get High-res Image Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 4(3p26.1)' versus 'MRNASEQ_CNMF'

P value = 5.11e-09 (Fisher's exact test), Q value = 2e-06

Table S22.  Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
AMP PEAK 4(3P26.1) CNV 75 10 90
AMP PEAK 4(3P26.1) WILD-TYPE 159 138 356

Figure S22.  Get High-res Image Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 4(3p26.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.57e-07 (Fisher's exact test), Q value = 0.00021

Table S23.  Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
AMP PEAK 4(3P26.1) CNV 21 94 60
AMP PEAK 4(3P26.1) WILD-TYPE 195 314 144

Figure S23.  Get High-res Image Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 4(3p26.1)' versus 'MIRSEQ_CNMF'

P value = 5.97e-06 (Fisher's exact test), Q value = 0.0017

Table S24.  Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 4(3P26.1) CNV 30 71 77
AMP PEAK 4(3P26.1) WILD-TYPE 204 321 178

Figure S24.  Get High-res Image Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 4(3p26.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.18e-08 (Fisher's exact test), Q value = 4.5e-06

Table S25.  Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 4(3P26.1) CNV 71 31 76
AMP PEAK 4(3P26.1) WILD-TYPE 291 253 159

Figure S25.  Get High-res Image Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 5(3q26.32)' versus 'MRNA_CNMF'

P value = 6.88e-11 (Chi-square test), Q value = 3e-08

Table S26.  Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
AMP PEAK 5(3Q26.32) CNV 39 11 4 58 34 9 19 4
AMP PEAK 5(3Q26.32) WILD-TYPE 85 25 19 37 38 11 84 36

Figure S26.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 5(3q26.32)' versus 'MRNA_CHIERARCHICAL'

P value = 7.83e-10 (Fisher's exact test), Q value = 3.2e-07

Table S27.  Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
AMP PEAK 5(3Q26.32) CNV 27 71 80
AMP PEAK 5(3Q26.32) WILD-TYPE 113 54 168

Figure S27.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 5(3q26.32)' versus 'CN_CNMF'

P value = 8.72e-36 (Chi-square test), Q value = 5.4e-33

Table S28.  Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
AMP PEAK 5(3Q26.32) CNV 35 77 24 138 14
AMP PEAK 5(3Q26.32) WILD-TYPE 312 145 48 85 35

Figure S28.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 5(3q26.32)' versus 'METHLYATION_CNMF'

P value = 8.01e-17 (Chi-square test), Q value = 4.3e-14

Table S29.  Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
AMP PEAK 5(3Q26.32) CNV 63 15 29 41 9 17
AMP PEAK 5(3Q26.32) WILD-TYPE 38 124 64 96 31 80

Figure S29.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 5(3q26.32)' versus 'RPPA_CNMF'

P value = 7.16e-07 (Fisher's exact test), Q value = 0.00023

Table S30.  Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 5(3Q26.32) CNV 76 35 28
AMP PEAK 5(3Q26.32) WILD-TYPE 71 98 89

Figure S30.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 5(3q26.32)' versus 'RPPA_CHIERARCHICAL'

P value = 2.92e-06 (Fisher's exact test), Q value = 0.00086

Table S31.  Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 5(3Q26.32) CNV 48 25 66
AMP PEAK 5(3Q26.32) WILD-TYPE 113 85 60

Figure S31.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 5(3q26.32)' versus 'MRNASEQ_CNMF'

P value = 4.31e-22 (Fisher's exact test), Q value = 2.5e-19

Table S32.  Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
AMP PEAK 5(3Q26.32) CNV 136 21 117
AMP PEAK 5(3Q26.32) WILD-TYPE 98 127 329

Figure S32.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 5(3q26.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.88e-21 (Fisher's exact test), Q value = 3.4e-18

Table S33.  Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
AMP PEAK 5(3Q26.32) CNV 35 118 121
AMP PEAK 5(3Q26.32) WILD-TYPE 181 290 83

Figure S33.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 5(3q26.32)' versus 'MIRSEQ_CNMF'

P value = 1.63e-15 (Fisher's exact test), Q value = 8.5e-13

Table S34.  Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 5(3Q26.32) CNV 46 100 132
AMP PEAK 5(3Q26.32) WILD-TYPE 188 292 123

Figure S34.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 5(3q26.32)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.39e-24 (Fisher's exact test), Q value = 3.8e-21

Table S35.  Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 5(3Q26.32) CNV 95 47 136
AMP PEAK 5(3Q26.32) WILD-TYPE 267 237 99

Figure S35.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 6(4q13.3)' versus 'MRNA_CNMF'

P value = 5.63e-05 (Chi-square test), Q value = 0.014

Table S36.  Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
AMP PEAK 6(4Q13.3) CNV 31 2 3 19 18 4 3 3
AMP PEAK 6(4Q13.3) WILD-TYPE 93 34 20 76 54 16 100 37

Figure S36.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 6(4q13.3)' versus 'MRNA_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.049

Table S37.  Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
AMP PEAK 6(4Q13.3) CNV 9 29 45
AMP PEAK 6(4Q13.3) WILD-TYPE 131 96 203

Figure S37.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 6(4q13.3)' versus 'CN_CNMF'

P value = 7.87e-14 (Chi-square test), Q value = 3.9e-11

Table S38.  Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
AMP PEAK 6(4Q13.3) CNV 21 59 2 55 6
AMP PEAK 6(4Q13.3) WILD-TYPE 326 163 70 168 43

Figure S38.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 6(4q13.3)' versus 'METHLYATION_CNMF'

P value = 3.97e-07 (Chi-square test), Q value = 0.00013

Table S39.  Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
AMP PEAK 6(4Q13.3) CNV 24 4 11 34 4 9
AMP PEAK 6(4Q13.3) WILD-TYPE 77 135 82 103 36 88

Figure S39.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 6(4q13.3)' versus 'MRNASEQ_CNMF'

P value = 7e-06 (Fisher's exact test), Q value = 0.0019

Table S40.  Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
AMP PEAK 6(4Q13.3) CNV 57 9 71
AMP PEAK 6(4Q13.3) WILD-TYPE 177 139 375

Figure S40.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 6(4q13.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.4e-05 (Fisher's exact test), Q value = 0.0063

Table S41.  Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
AMP PEAK 6(4Q13.3) CNV 20 64 53
AMP PEAK 6(4Q13.3) WILD-TYPE 196 344 151

Figure S41.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 6(4q13.3)' versus 'MIRSEQ_CNMF'

P value = 0.00138 (Fisher's exact test), Q value = 0.25

Table S42.  Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 6(4Q13.3) CNV 26 56 58
AMP PEAK 6(4Q13.3) WILD-TYPE 208 336 197

Figure S42.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 6(4q13.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.11e-07 (Fisher's exact test), Q value = 3.9e-05

Table S43.  Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 6(4Q13.3) CNV 55 23 62
AMP PEAK 6(4Q13.3) WILD-TYPE 307 261 173

Figure S43.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 7(6p23)' versus 'MRNA_CNMF'

P value = 3.59e-07 (Chi-square test), Q value = 0.00012

Table S44.  Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
AMP PEAK 7(6P23) CNV 30 6 3 48 27 8 18 6
AMP PEAK 7(6P23) WILD-TYPE 94 30 20 47 45 12 85 34

Figure S44.  Get High-res Image Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 7(6p23)' versus 'MRNA_CHIERARCHICAL'

P value = 1.92e-07 (Fisher's exact test), Q value = 6.6e-05

Table S45.  Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
AMP PEAK 7(6P23) CNV 22 58 66
AMP PEAK 7(6P23) WILD-TYPE 118 67 182

Figure S45.  Get High-res Image Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 7(6p23)' versus 'CN_CNMF'

P value = 5.65e-34 (Chi-square test), Q value = 3.5e-31

Table S46.  Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
AMP PEAK 7(6P23) CNV 25 57 21 123 17
AMP PEAK 7(6P23) WILD-TYPE 322 165 51 100 32

Figure S46.  Get High-res Image Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 7(6p23)' versus 'METHLYATION_CNMF'

P value = 2.44e-17 (Chi-square test), Q value = 1.3e-14

Table S47.  Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
AMP PEAK 7(6P23) CNV 54 11 22 48 2 14
AMP PEAK 7(6P23) WILD-TYPE 47 128 71 89 38 83

Figure S47.  Get High-res Image Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 7(6p23)' versus 'RPPA_CNMF'

P value = 1.98e-06 (Fisher's exact test), Q value = 0.00059

Table S48.  Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 7(6P23) CNV 64 25 23
AMP PEAK 7(6P23) WILD-TYPE 83 108 94

Figure S48.  Get High-res Image Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 7(6p23)' versus 'RPPA_CHIERARCHICAL'

P value = 8.42e-05 (Fisher's exact test), Q value = 0.02

Table S49.  Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 7(6P23) CNV 34 24 54
AMP PEAK 7(6P23) WILD-TYPE 127 86 72

Figure S49.  Get High-res Image Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 7(6p23)' versus 'MRNASEQ_CNMF'

P value = 1.01e-13 (Fisher's exact test), Q value = 4.9e-11

Table S50.  Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
AMP PEAK 7(6P23) CNV 105 17 101
AMP PEAK 7(6P23) WILD-TYPE 129 131 345

Figure S50.  Get High-res Image Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 7(6p23)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.56e-11 (Fisher's exact test), Q value = 1.6e-08

Table S51.  Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
AMP PEAK 7(6P23) CNV 31 102 90
AMP PEAK 7(6P23) WILD-TYPE 185 306 114

Figure S51.  Get High-res Image Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 7(6p23)' versus 'MIRSEQ_CNMF'

P value = 1.52e-18 (Fisher's exact test), Q value = 8.5e-16

Table S52.  Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 7(6P23) CNV 31 76 119
AMP PEAK 7(6P23) WILD-TYPE 203 316 136

Figure S52.  Get High-res Image Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 7(6p23)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.51e-15 (Fisher's exact test), Q value = 1.3e-12

Table S53.  Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 7(6P23) CNV 88 35 103
AMP PEAK 7(6P23) WILD-TYPE 274 249 132

Figure S53.  Get High-res Image Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 8(6q21)' versus 'MRNA_CNMF'

P value = 8.2e-14 (Chi-square test), Q value = 4e-11

Table S54.  Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
AMP PEAK 8(6Q21) CNV 11 1 4 41 25 9 11 2
AMP PEAK 8(6Q21) WILD-TYPE 113 35 19 54 47 11 92 38

Figure S54.  Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 8(6q21)' versus 'MRNA_CHIERARCHICAL'

P value = 4.54e-10 (Fisher's exact test), Q value = 1.9e-07

Table S55.  Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
AMP PEAK 8(6Q21) CNV 11 50 43
AMP PEAK 8(6Q21) WILD-TYPE 129 75 205

Figure S55.  Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 8(6q21)' versus 'CN_CNMF'

P value = 1.67e-39 (Chi-square test), Q value = 1e-36

Table S56.  Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
AMP PEAK 8(6Q21) CNV 20 20 15 109 6
AMP PEAK 8(6Q21) WILD-TYPE 327 202 57 114 43

Figure S56.  Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 8(6q21)' versus 'METHLYATION_CNMF'

P value = 4.11e-13 (Chi-square test), Q value = 2e-10

Table S57.  Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
AMP PEAK 8(6Q21) CNV 42 5 16 19 2 17
AMP PEAK 8(6Q21) WILD-TYPE 59 134 77 118 38 80

Figure S57.  Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 8(6q21)' versus 'RPPA_CNMF'

P value = 1.04e-08 (Fisher's exact test), Q value = 4e-06

Table S58.  Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 8(6Q21) CNV 54 12 16
AMP PEAK 8(6Q21) WILD-TYPE 93 121 101

Figure S58.  Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 8(6q21)' versus 'RPPA_CHIERARCHICAL'

P value = 4.64e-07 (Fisher's exact test), Q value = 0.00015

Table S59.  Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 8(6Q21) CNV 20 15 47
AMP PEAK 8(6Q21) WILD-TYPE 141 95 79

Figure S59.  Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 8(6q21)' versus 'MRNASEQ_CNMF'

P value = 7.59e-22 (Fisher's exact test), Q value = 4.4e-19

Table S60.  Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
AMP PEAK 8(6Q21) CNV 95 9 51
AMP PEAK 8(6Q21) WILD-TYPE 139 139 395

Figure S60.  Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 8(6q21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.72e-18 (Fisher's exact test), Q value = 1.5e-15

Table S61.  Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
AMP PEAK 8(6Q21) CNV 15 58 82
AMP PEAK 8(6Q21) WILD-TYPE 201 350 122

Figure S61.  Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 8(6q21)' versus 'MIRSEQ_CNMF'

P value = 3.42e-19 (Fisher's exact test), Q value = 1.9e-16

Table S62.  Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 8(6Q21) CNV 21 41 95
AMP PEAK 8(6Q21) WILD-TYPE 213 351 160

Figure S62.  Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 8(6q21)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.33e-23 (Fisher's exact test), Q value = 2.6e-20

Table S63.  Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 8(6Q21) CNV 41 21 95
AMP PEAK 8(6Q21) WILD-TYPE 321 263 140

Figure S63.  Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 9(8p11.23)' versus 'MRNA_CNMF'

P value = 1.64e-06 (Chi-square test), Q value = 5e-04

Table S64.  Gene #9: 'Amp Peak 9(8p11.23)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
AMP PEAK 9(8P11.23) CNV 76 17 12 30 23 5 34 9
AMP PEAK 9(8P11.23) WILD-TYPE 48 19 11 65 49 15 69 31

Figure S64.  Get High-res Image Gene #9: 'Amp Peak 9(8p11.23)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 9(8p11.23)' versus 'CN_CNMF'

P value = 1.44e-24 (Chi-square test), Q value = 8.5e-22

Table S65.  Gene #9: 'Amp Peak 9(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
AMP PEAK 9(8P11.23) CNV 94 111 32 61 48
AMP PEAK 9(8P11.23) WILD-TYPE 253 111 40 162 1

Figure S65.  Get High-res Image Gene #9: 'Amp Peak 9(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 9(8p11.23)' versus 'METHLYATION_CNMF'

P value = 1.22e-12 (Chi-square test), Q value = 5.6e-10

Table S66.  Gene #9: 'Amp Peak 9(8p11.23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
AMP PEAK 9(8P11.23) CNV 32 28 37 88 12 29
AMP PEAK 9(8P11.23) WILD-TYPE 69 111 56 49 28 68

Figure S66.  Get High-res Image Gene #9: 'Amp Peak 9(8p11.23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 9(8p11.23)' versus 'MRNASEQ_CNMF'

P value = 0.000227 (Fisher's exact test), Q value = 0.049

Table S67.  Gene #9: 'Amp Peak 9(8p11.23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
AMP PEAK 9(8P11.23) CNV 78 43 202
AMP PEAK 9(8P11.23) WILD-TYPE 156 105 244

Figure S67.  Get High-res Image Gene #9: 'Amp Peak 9(8p11.23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 9(8p11.23)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.34e-05 (Fisher's exact test), Q value = 0.0085

Table S68.  Gene #9: 'Amp Peak 9(8p11.23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
AMP PEAK 9(8P11.23) CNV 67 191 65
AMP PEAK 9(8P11.23) WILD-TYPE 149 217 139

Figure S68.  Get High-res Image Gene #9: 'Amp Peak 9(8p11.23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 10(8p11.21)' versus 'CN_CNMF'

P value = 1.01e-22 (Chi-square test), Q value = 5.9e-20

Table S69.  Gene #10: 'Amp Peak 10(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
AMP PEAK 10(8P11.21) CNV 91 94 39 81 49
AMP PEAK 10(8P11.21) WILD-TYPE 256 128 33 142 0

Figure S69.  Get High-res Image Gene #10: 'Amp Peak 10(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 10(8p11.21)' versus 'METHLYATION_CNMF'

P value = 4.03e-08 (Chi-square test), Q value = 1.5e-05

Table S70.  Gene #10: 'Amp Peak 10(8p11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
AMP PEAK 10(8P11.21) CNV 51 29 35 74 10 32
AMP PEAK 10(8P11.21) WILD-TYPE 50 110 58 63 30 65

Figure S70.  Get High-res Image Gene #10: 'Amp Peak 10(8p11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 10(8p11.21)' versus 'MRNASEQ_CNMF'

P value = 0.000224 (Fisher's exact test), Q value = 0.049

Table S71.  Gene #10: 'Amp Peak 10(8p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
AMP PEAK 10(8P11.21) CNV 104 37 185
AMP PEAK 10(8P11.21) WILD-TYPE 130 111 261

Figure S71.  Get High-res Image Gene #10: 'Amp Peak 10(8p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 10(8p11.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000104 (Fisher's exact test), Q value = 0.024

Table S72.  Gene #10: 'Amp Peak 10(8p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
AMP PEAK 10(8P11.21) CNV 59 179 88
AMP PEAK 10(8P11.21) WILD-TYPE 157 229 116

Figure S72.  Get High-res Image Gene #10: 'Amp Peak 10(8p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 11(8q24.21)' versus 'MRNA_CNMF'

P value = 1.17e-16 (Chi-square test), Q value = 6.3e-14

Table S73.  Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
AMP PEAK 11(8Q24.21) CNV 101 21 17 83 56 17 42 14
AMP PEAK 11(8Q24.21) WILD-TYPE 23 15 6 12 16 3 61 26

Figure S73.  Get High-res Image Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 11(8q24.21)' versus 'MRNA_CHIERARCHICAL'

P value = 2.62e-07 (Fisher's exact test), Q value = 8.9e-05

Table S74.  Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
AMP PEAK 11(8Q24.21) CNV 73 104 174
AMP PEAK 11(8Q24.21) WILD-TYPE 67 21 74

Figure S74.  Get High-res Image Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 11(8q24.21)' versus 'CN_CNMF'

P value = 2.63e-43 (Chi-square test), Q value = 1.7e-40

Table S75.  Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
AMP PEAK 11(8Q24.21) CNV 132 163 39 203 47
AMP PEAK 11(8Q24.21) WILD-TYPE 215 59 33 20 2

Figure S75.  Get High-res Image Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 11(8q24.21)' versus 'METHLYATION_CNMF'

P value = 1.7e-27 (Chi-square test), Q value = 1e-24

Table S76.  Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
AMP PEAK 11(8Q24.21) CNV 91 36 62 108 17 50
AMP PEAK 11(8Q24.21) WILD-TYPE 10 103 31 29 23 47

Figure S76.  Get High-res Image Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 11(8q24.21)' versus 'RPPA_CNMF'

P value = 4.58e-08 (Fisher's exact test), Q value = 1.7e-05

Table S77.  Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 11(8Q24.21) CNV 125 72 76
AMP PEAK 11(8Q24.21) WILD-TYPE 22 61 41

Figure S77.  Get High-res Image Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 11(8q24.21)' versus 'RPPA_CHIERARCHICAL'

P value = 9.36e-07 (Fisher's exact test), Q value = 3e-04

Table S78.  Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 11(8Q24.21) CNV 102 63 108
AMP PEAK 11(8Q24.21) WILD-TYPE 59 47 18

Figure S78.  Get High-res Image Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 11(8q24.21)' versus 'MRNASEQ_CNMF'

P value = 3.47e-21 (Fisher's exact test), Q value = 2e-18

Table S79.  Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
AMP PEAK 11(8Q24.21) CNV 202 59 278
AMP PEAK 11(8Q24.21) WILD-TYPE 32 89 168

Figure S79.  Get High-res Image Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 11(8q24.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.54e-15 (Fisher's exact test), Q value = 2.8e-12

Table S80.  Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
AMP PEAK 11(8Q24.21) CNV 101 267 171
AMP PEAK 11(8Q24.21) WILD-TYPE 115 141 33

Figure S80.  Get High-res Image Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 11(8q24.21)' versus 'MIRSEQ_CNMF'

P value = 1.31e-21 (Fisher's exact test), Q value = 7.6e-19

Table S81.  Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 11(8Q24.21) CNV 111 233 221
AMP PEAK 11(8Q24.21) WILD-TYPE 123 159 34

Figure S81.  Get High-res Image Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 11(8q24.21)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.37e-19 (Fisher's exact test), Q value = 1.3e-16

Table S82.  Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 11(8Q24.21) CNV 222 140 203
AMP PEAK 11(8Q24.21) WILD-TYPE 140 144 32

Figure S82.  Get High-res Image Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 12(10p15.1)' versus 'MRNA_CNMF'

P value = 1.72e-21 (Chi-square test), Q value = 9.9e-19

Table S83.  Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
AMP PEAK 12(10P15.1) CNV 28 4 4 67 34 6 11 7
AMP PEAK 12(10P15.1) WILD-TYPE 96 32 19 28 38 14 92 33

Figure S83.  Get High-res Image Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 12(10p15.1)' versus 'MRNA_CHIERARCHICAL'

P value = 1.06e-18 (Fisher's exact test), Q value = 5.9e-16

Table S84.  Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
AMP PEAK 12(10P15.1) CNV 24 81 56
AMP PEAK 12(10P15.1) WILD-TYPE 116 44 192

Figure S84.  Get High-res Image Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 12(10p15.1)' versus 'CN_CNMF'

P value = 9.95e-35 (Chi-square test), Q value = 6.1e-32

Table S85.  Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
AMP PEAK 12(10P15.1) CNV 40 55 17 135 11
AMP PEAK 12(10P15.1) WILD-TYPE 307 167 55 88 38

Figure S85.  Get High-res Image Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 12(10p15.1)' versus 'METHLYATION_CNMF'

P value = 1.93e-26 (Chi-square test), Q value = 1.2e-23

Table S86.  Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
AMP PEAK 12(10P15.1) CNV 67 6 23 33 2 24
AMP PEAK 12(10P15.1) WILD-TYPE 34 133 70 104 38 73

Figure S86.  Get High-res Image Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 12(10p15.1)' versus 'RPPA_CNMF'

P value = 7e-11 (Fisher's exact test), Q value = 3e-08

Table S87.  Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 12(10P15.1) CNV 78 22 29
AMP PEAK 12(10P15.1) WILD-TYPE 69 111 88

Figure S87.  Get High-res Image Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 12(10p15.1)' versus 'RPPA_CHIERARCHICAL'

P value = 2.33e-12 (Fisher's exact test), Q value = 1.1e-09

Table S88.  Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 12(10P15.1) CNV 30 26 73
AMP PEAK 12(10P15.1) WILD-TYPE 131 84 53

Figure S88.  Get High-res Image Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 12(10p15.1)' versus 'MRNASEQ_CNMF'

P value = 2.05e-28 (Fisher's exact test), Q value = 1.2e-25

Table S89.  Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
AMP PEAK 12(10P15.1) CNV 135 22 81
AMP PEAK 12(10P15.1) WILD-TYPE 99 126 365

Figure S89.  Get High-res Image Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 12(10p15.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.17e-28 (Fisher's exact test), Q value = 7.1e-26

Table S90.  Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
AMP PEAK 12(10P15.1) CNV 33 81 124
AMP PEAK 12(10P15.1) WILD-TYPE 183 327 80

Figure S90.  Get High-res Image Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 12(10p15.1)' versus 'MIRSEQ_CNMF'

P value = 6.23e-28 (Fisher's exact test), Q value = 3.8e-25

Table S91.  Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 12(10P15.1) CNV 38 68 141
AMP PEAK 12(10P15.1) WILD-TYPE 196 324 114

Figure S91.  Get High-res Image Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 12(10p15.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.2e-30 (Fisher's exact test), Q value = 7.3e-28

Table S92.  Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 12(10P15.1) CNV 73 38 136
AMP PEAK 12(10P15.1) WILD-TYPE 289 246 99

Figure S92.  Get High-res Image Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 13(10q22.3)' versus 'MRNA_CNMF'

P value = 2.2e-05 (Chi-square test), Q value = 0.0058

Table S93.  Gene #13: 'Amp Peak 13(10q22.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
AMP PEAK 13(10Q22.3) CNV 17 2 5 18 23 8 8 3
AMP PEAK 13(10Q22.3) WILD-TYPE 107 34 18 77 49 12 95 37

Figure S93.  Get High-res Image Gene #13: 'Amp Peak 13(10q22.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 13(10q22.3)' versus 'CN_CNMF'

P value = 8.18e-09 (Chi-square test), Q value = 3.2e-06

Table S94.  Gene #13: 'Amp Peak 13(10q22.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
AMP PEAK 13(10Q22.3) CNV 23 31 12 59 7
AMP PEAK 13(10Q22.3) WILD-TYPE 324 191 60 164 42

Figure S94.  Get High-res Image Gene #13: 'Amp Peak 13(10q22.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 13(10q22.3)' versus 'METHLYATION_CNMF'

P value = 0.000149 (Chi-square test), Q value = 0.034

Table S95.  Gene #13: 'Amp Peak 13(10q22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
AMP PEAK 13(10Q22.3) CNV 23 5 16 21 2 10
AMP PEAK 13(10Q22.3) WILD-TYPE 78 134 77 116 38 87

Figure S95.  Get High-res Image Gene #13: 'Amp Peak 13(10q22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 13(10q22.3)' versus 'MRNASEQ_CNMF'

P value = 1.83e-07 (Fisher's exact test), Q value = 6.3e-05

Table S96.  Gene #13: 'Amp Peak 13(10q22.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
AMP PEAK 13(10Q22.3) CNV 61 11 52
AMP PEAK 13(10Q22.3) WILD-TYPE 173 137 394

Figure S96.  Get High-res Image Gene #13: 'Amp Peak 13(10q22.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 13(10q22.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000689 (Fisher's exact test), Q value = 0.13

Table S97.  Gene #13: 'Amp Peak 13(10q22.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
AMP PEAK 13(10Q22.3) CNV 20 58 46
AMP PEAK 13(10Q22.3) WILD-TYPE 196 350 158

Figure S97.  Get High-res Image Gene #13: 'Amp Peak 13(10q22.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 13(10q22.3)' versus 'MIRSEQ_CNMF'

P value = 3.75e-05 (Fisher's exact test), Q value = 0.0095

Table S98.  Gene #13: 'Amp Peak 13(10q22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 13(10Q22.3) CNV 21 48 58
AMP PEAK 13(10Q22.3) WILD-TYPE 213 344 197

Figure S98.  Get High-res Image Gene #13: 'Amp Peak 13(10q22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 13(10q22.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000675 (Fisher's exact test), Q value = 0.13

Table S99.  Gene #13: 'Amp Peak 13(10q22.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 13(10Q22.3) CNV 48 28 51
AMP PEAK 13(10Q22.3) WILD-TYPE 314 256 184

Figure S99.  Get High-res Image Gene #13: 'Amp Peak 13(10q22.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 14(11p13)' versus 'CN_CNMF'

P value = 1.84e-10 (Chi-square test), Q value = 7.7e-08

Table S100.  Gene #14: 'Amp Peak 14(11p13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
AMP PEAK 14(11P13) CNV 33 68 13 67 11
AMP PEAK 14(11P13) WILD-TYPE 314 154 59 156 38

Figure S100.  Get High-res Image Gene #14: 'Amp Peak 14(11p13)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 14(11p13)' versus 'METHLYATION_CNMF'

P value = 4.84e-05 (Chi-square test), Q value = 0.012

Table S101.  Gene #14: 'Amp Peak 14(11p13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
AMP PEAK 14(11P13) CNV 27 16 16 44 3 15
AMP PEAK 14(11P13) WILD-TYPE 74 123 77 93 37 82

Figure S101.  Get High-res Image Gene #14: 'Amp Peak 14(11p13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 14(11p13)' versus 'MRNASEQ_CNMF'

P value = 2.61e-05 (Fisher's exact test), Q value = 0.0067

Table S102.  Gene #14: 'Amp Peak 14(11p13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
AMP PEAK 14(11P13) CNV 69 15 99
AMP PEAK 14(11P13) WILD-TYPE 165 133 347

Figure S102.  Get High-res Image Gene #14: 'Amp Peak 14(11p13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 14(11p13)' versus 'MIRSEQ_CNMF'

P value = 1.33e-06 (Fisher's exact test), Q value = 0.00042

Table S103.  Gene #14: 'Amp Peak 14(11p13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 14(11P13) CNV 29 77 80
AMP PEAK 14(11P13) WILD-TYPE 205 315 175

Figure S103.  Get High-res Image Gene #14: 'Amp Peak 14(11p13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 14(11p13)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.91e-08 (Fisher's exact test), Q value = 7.2e-06

Table S104.  Gene #14: 'Amp Peak 14(11p13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 14(11P13) CNV 80 31 75
AMP PEAK 14(11P13) WILD-TYPE 282 253 160

Figure S104.  Get High-res Image Gene #14: 'Amp Peak 14(11p13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 15(11q13.3)' versus 'CN_CNMF'

P value = 4.91e-41 (Chi-square test), Q value = 3.1e-38

Table S105.  Gene #15: 'Amp Peak 15(11q13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
AMP PEAK 15(11Q13.3) CNV 53 163 28 89 16
AMP PEAK 15(11Q13.3) WILD-TYPE 294 59 44 134 33

Figure S105.  Get High-res Image Gene #15: 'Amp Peak 15(11q13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 15(11q13.3)' versus 'METHLYATION_CNMF'

P value = 4e-10 (Chi-square test), Q value = 1.7e-07

Table S106.  Gene #15: 'Amp Peak 15(11q13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
AMP PEAK 15(11Q13.3) CNV 37 31 45 75 11 18
AMP PEAK 15(11Q13.3) WILD-TYPE 64 108 48 62 29 79

Figure S106.  Get High-res Image Gene #15: 'Amp Peak 15(11q13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 15(11q13.3)' versus 'MIRSEQ_CNMF'

P value = 0.000292 (Fisher's exact test), Q value = 0.06

Table S107.  Gene #15: 'Amp Peak 15(11q13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 15(11Q13.3) CNV 64 160 111
AMP PEAK 15(11Q13.3) WILD-TYPE 170 232 144

Figure S107.  Get High-res Image Gene #15: 'Amp Peak 15(11q13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 16(11q14.1)' versus 'CN_CNMF'

P value = 1.8e-19 (Chi-square test), Q value = 1e-16

Table S108.  Gene #16: 'Amp Peak 16(11q14.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
AMP PEAK 16(11Q14.1) CNV 31 89 19 85 10
AMP PEAK 16(11Q14.1) WILD-TYPE 316 133 53 138 39

Figure S108.  Get High-res Image Gene #16: 'Amp Peak 16(11q14.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 16(11q14.1)' versus 'METHLYATION_CNMF'

P value = 7.93e-06 (Chi-square test), Q value = 0.0022

Table S109.  Gene #16: 'Amp Peak 16(11q14.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
AMP PEAK 16(11Q14.1) CNV 38 19 32 32 7 13
AMP PEAK 16(11Q14.1) WILD-TYPE 63 120 61 105 33 84

Figure S109.  Get High-res Image Gene #16: 'Amp Peak 16(11q14.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 16(11q14.1)' versus 'MRNASEQ_CNMF'

P value = 8.57e-05 (Fisher's exact test), Q value = 0.02

Table S110.  Gene #16: 'Amp Peak 16(11q14.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
AMP PEAK 16(11Q14.1) CNV 86 27 107
AMP PEAK 16(11Q14.1) WILD-TYPE 148 121 339

Figure S110.  Get High-res Image Gene #16: 'Amp Peak 16(11q14.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 16(11q14.1)' versus 'MIRSEQ_CNMF'

P value = 8.98e-07 (Fisher's exact test), Q value = 0.00029

Table S111.  Gene #16: 'Amp Peak 16(11q14.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 16(11Q14.1) CNV 40 90 95
AMP PEAK 16(11Q14.1) WILD-TYPE 194 302 160

Figure S111.  Get High-res Image Gene #16: 'Amp Peak 16(11q14.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 16(11q14.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.39e-05 (Fisher's exact test), Q value = 0.0037

Table S112.  Gene #16: 'Amp Peak 16(11q14.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 16(11Q14.1) CNV 89 51 85
AMP PEAK 16(11Q14.1) WILD-TYPE 273 233 150

Figure S112.  Get High-res Image Gene #16: 'Amp Peak 16(11q14.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 17(12p13.33)' versus 'MRNA_CNMF'

P value = 1.91e-12 (Chi-square test), Q value = 8.8e-10

Table S113.  Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
AMP PEAK 17(12P13.33) CNV 37 5 3 53 29 3 13 3
AMP PEAK 17(12P13.33) WILD-TYPE 87 31 20 42 43 17 90 37

Figure S113.  Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 17(12p13.33)' versus 'MRNA_CHIERARCHICAL'

P value = 2.53e-11 (Fisher's exact test), Q value = 1.1e-08

Table S114.  Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
AMP PEAK 17(12P13.33) CNV 15 61 70
AMP PEAK 17(12P13.33) WILD-TYPE 125 64 178

Figure S114.  Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 17(12p13.33)' versus 'CN_CNMF'

P value = 1.68e-28 (Chi-square test), Q value = 1e-25

Table S115.  Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
AMP PEAK 17(12P13.33) CNV 23 68 22 111 14
AMP PEAK 17(12P13.33) WILD-TYPE 324 154 50 112 35

Figure S115.  Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 17(12p13.33)' versus 'METHLYATION_CNMF'

P value = 7.29e-17 (Chi-square test), Q value = 3.9e-14

Table S116.  Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
AMP PEAK 17(12P13.33) CNV 54 13 20 44 2 12
AMP PEAK 17(12P13.33) WILD-TYPE 47 126 73 93 38 85

Figure S116.  Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 17(12p13.33)' versus 'RPPA_CNMF'

P value = 2.7e-08 (Fisher's exact test), Q value = 1e-05

Table S117.  Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 17(12P13.33) CNV 69 31 18
AMP PEAK 17(12P13.33) WILD-TYPE 78 102 99

Figure S117.  Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 17(12p13.33)' versus 'RPPA_CHIERARCHICAL'

P value = 2.37e-07 (Fisher's exact test), Q value = 8.1e-05

Table S118.  Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 17(12P13.33) CNV 43 16 59
AMP PEAK 17(12P13.33) WILD-TYPE 118 94 67

Figure S118.  Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 17(12p13.33)' versus 'MRNASEQ_CNMF'

P value = 1.67e-17 (Fisher's exact test), Q value = 9.1e-15

Table S119.  Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
AMP PEAK 17(12P13.33) CNV 107 12 96
AMP PEAK 17(12P13.33) WILD-TYPE 127 136 350

Figure S119.  Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 17(12p13.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.45e-15 (Fisher's exact test), Q value = 7.6e-13

Table S120.  Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
AMP PEAK 17(12P13.33) CNV 24 97 94
AMP PEAK 17(12P13.33) WILD-TYPE 192 311 110

Figure S120.  Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 17(12p13.33)' versus 'MIRSEQ_CNMF'

P value = 9.18e-22 (Fisher's exact test), Q value = 5.3e-19

Table S121.  Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 17(12P13.33) CNV 27 76 123
AMP PEAK 17(12P13.33) WILD-TYPE 207 316 132

Figure S121.  Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 17(12p13.33)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.5e-18 (Fisher's exact test), Q value = 3e-15

Table S122.  Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 17(12P13.33) CNV 73 41 112
AMP PEAK 17(12P13.33) WILD-TYPE 289 243 123

Figure S122.  Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 18(12q15)' versus 'MRNA_CNMF'

P value = 1.81e-08 (Chi-square test), Q value = 6.8e-06

Table S123.  Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
AMP PEAK 18(12Q15) CNV 56 7 3 20 35 7 16 6
AMP PEAK 18(12Q15) WILD-TYPE 68 29 20 75 37 13 87 34

Figure S123.  Get High-res Image Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 18(12q15)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000131 (Fisher's exact test), Q value = 0.03

Table S124.  Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
AMP PEAK 18(12Q15) CNV 27 29 94
AMP PEAK 18(12Q15) WILD-TYPE 113 96 154

Figure S124.  Get High-res Image Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 18(12q15)' versus 'CN_CNMF'

P value = 1.86e-25 (Chi-square test), Q value = 1.1e-22

Table S125.  Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
AMP PEAK 18(12Q15) CNV 26 106 26 65 12
AMP PEAK 18(12Q15) WILD-TYPE 321 116 46 158 37

Figure S125.  Get High-res Image Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 18(12q15)' versus 'METHLYATION_CNMF'

P value = 1.49e-13 (Chi-square test), Q value = 7.2e-11

Table S126.  Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
AMP PEAK 18(12Q15) CNV 17 18 19 66 6 11
AMP PEAK 18(12Q15) WILD-TYPE 84 121 74 71 34 86

Figure S126.  Get High-res Image Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 18(12q15)' versus 'MRNASEQ_CNMF'

P value = 6.02e-06 (Fisher's exact test), Q value = 0.0017

Table S127.  Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
AMP PEAK 18(12Q15) CNV 63 18 142
AMP PEAK 18(12Q15) WILD-TYPE 171 130 304

Figure S127.  Get High-res Image Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 18(12q15)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.71e-05 (Fisher's exact test), Q value = 0.0046

Table S128.  Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
AMP PEAK 18(12Q15) CNV 37 138 48
AMP PEAK 18(12Q15) WILD-TYPE 179 270 156

Figure S128.  Get High-res Image Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 18(12q15)' versus 'MIRSEQ_CNMF'

P value = 9.16e-08 (Fisher's exact test), Q value = 3.3e-05

Table S129.  Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 18(12Q15) CNV 29 118 79
AMP PEAK 18(12Q15) WILD-TYPE 205 274 176

Figure S129.  Get High-res Image Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 18(12q15)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000644 (Fisher's exact test), Q value = 0.12

Table S130.  Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 18(12Q15) CNV 112 51 63
AMP PEAK 18(12Q15) WILD-TYPE 250 233 172

Figure S130.  Get High-res Image Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 19(13q12.3)' versus 'CN_CNMF'

P value = 2.22e-05 (Chi-square test), Q value = 0.0059

Table S131.  Gene #19: 'Amp Peak 19(13q12.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
AMP PEAK 19(13Q12.3) CNV 23 38 13 46 8
AMP PEAK 19(13Q12.3) WILD-TYPE 324 184 59 177 41

Figure S131.  Get High-res Image Gene #19: 'Amp Peak 19(13q12.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 19(13q12.3)' versus 'MRNASEQ_CNMF'

P value = 2.63e-05 (Fisher's exact test), Q value = 0.0068

Table S132.  Gene #19: 'Amp Peak 19(13q12.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
AMP PEAK 19(13Q12.3) CNV 45 6 70
AMP PEAK 19(13Q12.3) WILD-TYPE 189 142 376

Figure S132.  Get High-res Image Gene #19: 'Amp Peak 19(13q12.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 19(13q12.3)' versus 'MIRSEQ_CNMF'

P value = 0.000196 (Fisher's exact test), Q value = 0.043

Table S133.  Gene #19: 'Amp Peak 19(13q12.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 19(13Q12.3) CNV 17 55 51
AMP PEAK 19(13Q12.3) WILD-TYPE 217 337 204

Figure S133.  Get High-res Image Gene #19: 'Amp Peak 19(13q12.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 19(13q12.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.086

Table S134.  Gene #19: 'Amp Peak 19(13q12.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 19(13Q12.3) CNV 51 24 48
AMP PEAK 19(13Q12.3) WILD-TYPE 311 260 187

Figure S134.  Get High-res Image Gene #19: 'Amp Peak 19(13q12.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 20(13q34)' versus 'MRNA_CNMF'

P value = 9.14e-10 (Chi-square test), Q value = 3.7e-07

Table S135.  Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
AMP PEAK 20(13Q34) CNV 19 3 3 42 10 4 15 0
AMP PEAK 20(13Q34) WILD-TYPE 105 33 20 53 62 16 88 40

Figure S135.  Get High-res Image Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 20(13q34)' versus 'MRNA_CHIERARCHICAL'

P value = 5.78e-09 (Fisher's exact test), Q value = 2.3e-06

Table S136.  Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
AMP PEAK 20(13Q34) CNV 12 47 37
AMP PEAK 20(13Q34) WILD-TYPE 128 78 211

Figure S136.  Get High-res Image Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 20(13q34)' versus 'CN_CNMF'

P value = 1.51e-17 (Chi-square test), Q value = 8.2e-15

Table S137.  Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
AMP PEAK 20(13Q34) CNV 28 33 9 83 6
AMP PEAK 20(13Q34) WILD-TYPE 319 189 63 140 43

Figure S137.  Get High-res Image Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 20(13q34)' versus 'METHLYATION_CNMF'

P value = 1.33e-14 (Chi-square test), Q value = 6.7e-12

Table S138.  Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
AMP PEAK 20(13Q34) CNV 44 8 13 20 1 12
AMP PEAK 20(13Q34) WILD-TYPE 57 131 80 117 39 85

Figure S138.  Get High-res Image Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 20(13q34)' versus 'RPPA_CNMF'

P value = 8.21e-06 (Fisher's exact test), Q value = 0.0023

Table S139.  Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 20(13Q34) CNV 48 22 11
AMP PEAK 20(13Q34) WILD-TYPE 99 111 106

Figure S139.  Get High-res Image Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 20(13q34)' versus 'RPPA_CHIERARCHICAL'

P value = 5.1e-08 (Fisher's exact test), Q value = 1.8e-05

Table S140.  Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 20(13Q34) CNV 25 9 47
AMP PEAK 20(13Q34) WILD-TYPE 136 101 79

Figure S140.  Get High-res Image Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 20(13q34)' versus 'MRNASEQ_CNMF'

P value = 8.44e-14 (Fisher's exact test), Q value = 4.1e-11

Table S141.  Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
AMP PEAK 20(13Q34) CNV 77 7 59
AMP PEAK 20(13Q34) WILD-TYPE 157 141 387

Figure S141.  Get High-res Image Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 20(13q34)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.17e-14 (Fisher's exact test), Q value = 5.9e-12

Table S142.  Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
AMP PEAK 20(13Q34) CNV 15 55 73
AMP PEAK 20(13Q34) WILD-TYPE 201 353 131

Figure S142.  Get High-res Image Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 20(13q34)' versus 'MIRSEQ_CNMF'

P value = 1.41e-13 (Fisher's exact test), Q value = 6.8e-11

Table S143.  Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 20(13Q34) CNV 25 44 86
AMP PEAK 20(13Q34) WILD-TYPE 209 348 169

Figure S143.  Get High-res Image Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 20(13q34)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.59e-20 (Fisher's exact test), Q value = 3.2e-17

Table S144.  Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 20(13Q34) CNV 47 19 89
AMP PEAK 20(13Q34) WILD-TYPE 315 265 146

Figure S144.  Get High-res Image Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 21(14q21.1)' versus 'MRNA_CNMF'

P value = 0.000259 (Chi-square test), Q value = 0.055

Table S145.  Gene #21: 'Amp Peak 21(14q21.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
AMP PEAK 21(14Q21.1) CNV 35 7 5 11 26 6 20 1
AMP PEAK 21(14Q21.1) WILD-TYPE 89 29 18 84 46 14 83 39

Figure S145.  Get High-res Image Gene #21: 'Amp Peak 21(14q21.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 21(14q21.1)' versus 'CN_CNMF'

P value = 1.97e-09 (Chi-square test), Q value = 7.9e-07

Table S146.  Gene #21: 'Amp Peak 21(14q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
AMP PEAK 21(14Q21.1) CNV 34 73 15 49 10
AMP PEAK 21(14Q21.1) WILD-TYPE 313 149 57 174 39

Figure S146.  Get High-res Image Gene #21: 'Amp Peak 21(14q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 21(14q21.1)' versus 'METHLYATION_CNMF'

P value = 5.16e-05 (Chi-square test), Q value = 0.013

Table S147.  Gene #21: 'Amp Peak 21(14q21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
AMP PEAK 21(14Q21.1) CNV 13 18 23 41 4 9
AMP PEAK 21(14Q21.1) WILD-TYPE 88 121 70 96 36 88

Figure S147.  Get High-res Image Gene #21: 'Amp Peak 21(14q21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 21(14q21.1)' versus 'MRNASEQ_CNMF'

P value = 3.92e-05 (Fisher's exact test), Q value = 0.0099

Table S148.  Gene #21: 'Amp Peak 21(14q21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
AMP PEAK 21(14Q21.1) CNV 42 15 117
AMP PEAK 21(14Q21.1) WILD-TYPE 192 133 329

Figure S148.  Get High-res Image Gene #21: 'Amp Peak 21(14q21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 21(14q21.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.45e-06 (Fisher's exact test), Q value = 0.00072

Table S149.  Gene #21: 'Amp Peak 21(14q21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
AMP PEAK 21(14Q21.1) CNV 27 115 32
AMP PEAK 21(14Q21.1) WILD-TYPE 189 293 172

Figure S149.  Get High-res Image Gene #21: 'Amp Peak 21(14q21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 21(14q21.1)' versus 'MIRSEQ_CNMF'

P value = 1.94e-06 (Fisher's exact test), Q value = 0.00058

Table S150.  Gene #21: 'Amp Peak 21(14q21.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 21(14Q21.1) CNV 21 95 58
AMP PEAK 21(14Q21.1) WILD-TYPE 213 297 197

Figure S150.  Get High-res Image Gene #21: 'Amp Peak 21(14q21.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 22(15q26.3)' versus 'MRNA_CNMF'

P value = 3.31e-07 (Chi-square test), Q value = 0.00011

Table S151.  Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
AMP PEAK 22(15Q26.3) CNV 32 7 2 32 16 8 4 2
AMP PEAK 22(15Q26.3) WILD-TYPE 92 29 21 63 56 12 99 38

Figure S151.  Get High-res Image Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 22(15q26.3)' versus 'CN_CNMF'

P value = 1.88e-15 (Chi-square test), Q value = 9.8e-13

Table S152.  Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
AMP PEAK 22(15Q26.3) CNV 30 47 6 79 4
AMP PEAK 22(15Q26.3) WILD-TYPE 317 175 66 144 45

Figure S152.  Get High-res Image Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 22(15q26.3)' versus 'METHLYATION_CNMF'

P value = 0.000326 (Chi-square test), Q value = 0.067

Table S153.  Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
AMP PEAK 22(15Q26.3) CNV 26 6 17 26 6 14
AMP PEAK 22(15Q26.3) WILD-TYPE 75 133 76 111 34 83

Figure S153.  Get High-res Image Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 22(15q26.3)' versus 'RPPA_CNMF'

P value = 0.000153 (Fisher's exact test), Q value = 0.035

Table S154.  Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 22(15Q26.3) CNV 47 18 17
AMP PEAK 22(15Q26.3) WILD-TYPE 100 115 100

Figure S154.  Get High-res Image Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 22(15q26.3)' versus 'MRNASEQ_CNMF'

P value = 2.07e-08 (Fisher's exact test), Q value = 7.7e-06

Table S155.  Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
AMP PEAK 22(15Q26.3) CNV 70 10 74
AMP PEAK 22(15Q26.3) WILD-TYPE 164 138 372

Figure S155.  Get High-res Image Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 22(15q26.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.98e-06 (Fisher's exact test), Q value = 0.0022

Table S156.  Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
AMP PEAK 22(15Q26.3) CNV 24 70 60
AMP PEAK 22(15Q26.3) WILD-TYPE 192 338 144

Figure S156.  Get High-res Image Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 22(15q26.3)' versus 'MIRSEQ_CNMF'

P value = 5.92e-08 (Fisher's exact test), Q value = 2.1e-05

Table S157.  Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 22(15Q26.3) CNV 31 51 77
AMP PEAK 22(15Q26.3) WILD-TYPE 203 341 178

Figure S157.  Get High-res Image Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 22(15q26.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.56e-09 (Fisher's exact test), Q value = 2.9e-06

Table S158.  Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 22(15Q26.3) CNV 59 28 72
AMP PEAK 22(15Q26.3) WILD-TYPE 303 256 163

Figure S158.  Get High-res Image Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 23(17q12)' versus 'MRNA_CNMF'

P value = 1.49e-14 (Chi-square test), Q value = 7.5e-12

Table S159.  Gene #23: 'Amp Peak 23(17q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
AMP PEAK 23(17Q12) CNV 52 12 8 19 49 7 14 4
AMP PEAK 23(17Q12) WILD-TYPE 72 24 15 76 23 13 89 36

Figure S159.  Get High-res Image Gene #23: 'Amp Peak 23(17q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 23(17q12)' versus 'MRNA_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.062

Table S160.  Gene #23: 'Amp Peak 23(17q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
AMP PEAK 23(17Q12) CNV 28 39 98
AMP PEAK 23(17Q12) WILD-TYPE 112 86 150

Figure S160.  Get High-res Image Gene #23: 'Amp Peak 23(17q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 23(17q12)' versus 'CN_CNMF'

P value = 7.29e-34 (Chi-square test), Q value = 4.5e-31

Table S161.  Gene #23: 'Amp Peak 23(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
AMP PEAK 23(17Q12) CNV 55 146 22 57 15
AMP PEAK 23(17Q12) WILD-TYPE 292 76 50 166 34

Figure S161.  Get High-res Image Gene #23: 'Amp Peak 23(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 23(17q12)' versus 'METHLYATION_CNMF'

P value = 5.76e-09 (Chi-square test), Q value = 2.3e-06

Table S162.  Gene #23: 'Amp Peak 23(17q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
AMP PEAK 23(17Q12) CNV 27 24 40 69 11 21
AMP PEAK 23(17Q12) WILD-TYPE 74 115 53 68 29 76

Figure S162.  Get High-res Image Gene #23: 'Amp Peak 23(17q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 23(17q12)' versus 'MRNASEQ_CNMF'

P value = 0.000101 (Fisher's exact test), Q value = 0.024

Table S163.  Gene #23: 'Amp Peak 23(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
AMP PEAK 23(17Q12) CNV 89 28 159
AMP PEAK 23(17Q12) WILD-TYPE 145 120 287

Figure S163.  Get High-res Image Gene #23: 'Amp Peak 23(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 23(17q12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000454 (Fisher's exact test), Q value = 0.09

Table S164.  Gene #23: 'Amp Peak 23(17q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
AMP PEAK 23(17Q12) CNV 50 157 69
AMP PEAK 23(17Q12) WILD-TYPE 166 251 135

Figure S164.  Get High-res Image Gene #23: 'Amp Peak 23(17q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 24(17q23.1)' versus 'MRNA_CNMF'

P value = 2.42e-14 (Chi-square test), Q value = 1.2e-11

Table S165.  Gene #24: 'Amp Peak 24(17q23.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
AMP PEAK 24(17Q23.1) CNV 81 17 8 29 43 11 16 10
AMP PEAK 24(17Q23.1) WILD-TYPE 43 19 15 66 29 9 87 30

Figure S165.  Get High-res Image Gene #24: 'Amp Peak 24(17q23.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 24(17q23.1)' versus 'CN_CNMF'

P value = 6.19e-38 (Chi-square test), Q value = 3.8e-35

Table S166.  Gene #24: 'Amp Peak 24(17q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
AMP PEAK 24(17Q23.1) CNV 66 166 21 102 19
AMP PEAK 24(17Q23.1) WILD-TYPE 281 56 51 121 30

Figure S166.  Get High-res Image Gene #24: 'Amp Peak 24(17q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 24(17q23.1)' versus 'METHLYATION_CNMF'

P value = 1.45e-10 (Chi-square test), Q value = 6.1e-08

Table S167.  Gene #24: 'Amp Peak 24(17q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
AMP PEAK 24(17Q23.1) CNV 42 31 40 85 17 25
AMP PEAK 24(17Q23.1) WILD-TYPE 59 108 53 52 23 72

Figure S167.  Get High-res Image Gene #24: 'Amp Peak 24(17q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 24(17q23.1)' versus 'MRNASEQ_CNMF'

P value = 0.000644 (Fisher's exact test), Q value = 0.12

Table S168.  Gene #24: 'Amp Peak 24(17q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
AMP PEAK 24(17Q23.1) CNV 99 43 209
AMP PEAK 24(17Q23.1) WILD-TYPE 135 105 237

Figure S168.  Get High-res Image Gene #24: 'Amp Peak 24(17q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 24(17q23.1)' versus 'MIRSEQ_CNMF'

P value = 3.1e-07 (Fisher's exact test), Q value = 1e-04

Table S169.  Gene #24: 'Amp Peak 24(17q23.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 24(17Q23.1) CNV 65 167 132
AMP PEAK 24(17Q23.1) WILD-TYPE 169 225 123

Figure S169.  Get High-res Image Gene #24: 'Amp Peak 24(17q23.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 24(17q23.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.57e-06 (Fisher's exact test), Q value = 0.001

Table S170.  Gene #24: 'Amp Peak 24(17q23.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 24(17Q23.1) CNV 175 84 105
AMP PEAK 24(17Q23.1) WILD-TYPE 187 200 130

Figure S170.  Get High-res Image Gene #24: 'Amp Peak 24(17q23.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 25(19q12)' versus 'MRNA_CNMF'

P value = 2.12e-12 (Chi-square test), Q value = 9.7e-10

Table S171.  Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
AMP PEAK 25(19Q12) CNV 30 4 4 56 20 7 14 5
AMP PEAK 25(19Q12) WILD-TYPE 94 32 19 39 52 13 89 35

Figure S171.  Get High-res Image Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 25(19q12)' versus 'MRNA_CHIERARCHICAL'

P value = 9.11e-11 (Fisher's exact test), Q value = 3.9e-08

Table S172.  Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
AMP PEAK 25(19Q12) CNV 22 64 54
AMP PEAK 25(19Q12) WILD-TYPE 118 61 194

Figure S172.  Get High-res Image Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 25(19q12)' versus 'CN_CNMF'

P value = 1.28e-21 (Chi-square test), Q value = 7.4e-19

Table S173.  Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
AMP PEAK 25(19Q12) CNV 41 44 26 108 14
AMP PEAK 25(19Q12) WILD-TYPE 306 178 46 115 35

Figure S173.  Get High-res Image Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 25(19q12)' versus 'METHLYATION_CNMF'

P value = 4.2e-12 (Chi-square test), Q value = 1.9e-09

Table S174.  Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
AMP PEAK 25(19Q12) CNV 53 15 20 34 4 22
AMP PEAK 25(19Q12) WILD-TYPE 48 124 73 103 36 75

Figure S174.  Get High-res Image Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 25(19q12)' versus 'RPPA_CNMF'

P value = 6.19e-07 (Fisher's exact test), Q value = 2e-04

Table S175.  Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 25(19Q12) CNV 64 23 23
AMP PEAK 25(19Q12) WILD-TYPE 83 110 94

Figure S175.  Get High-res Image Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 25(19q12)' versus 'RPPA_CHIERARCHICAL'

P value = 9.68e-07 (Fisher's exact test), Q value = 0.00031

Table S176.  Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 25(19Q12) CNV 29 24 57
AMP PEAK 25(19Q12) WILD-TYPE 132 86 69

Figure S176.  Get High-res Image Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 25(19q12)' versus 'MRNASEQ_CNMF'

P value = 1.11e-15 (Fisher's exact test), Q value = 5.8e-13

Table S177.  Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
AMP PEAK 25(19Q12) CNV 109 26 79
AMP PEAK 25(19Q12) WILD-TYPE 125 122 367

Figure S177.  Get High-res Image Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 25(19q12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.08e-15 (Fisher's exact test), Q value = 1.1e-12

Table S178.  Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
AMP PEAK 25(19Q12) CNV 37 78 99
AMP PEAK 25(19Q12) WILD-TYPE 179 330 105

Figure S178.  Get High-res Image Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 25(19q12)' versus 'MIRSEQ_CNMF'

P value = 6.49e-13 (Fisher's exact test), Q value = 3e-10

Table S179.  Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 25(19Q12) CNV 45 71 111
AMP PEAK 25(19Q12) WILD-TYPE 189 321 144

Figure S179.  Get High-res Image Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 25(19q12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.82e-18 (Fisher's exact test), Q value = 1.6e-15

Table S180.  Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 25(19Q12) CNV 65 48 114
AMP PEAK 25(19Q12) WILD-TYPE 297 236 121

Figure S180.  Get High-res Image Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 26(19q13.42)' versus 'MRNA_CNMF'

P value = 0.000775 (Chi-square test), Q value = 0.14

Table S181.  Gene #26: 'Amp Peak 26(19q13.42)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
AMP PEAK 26(19Q13.42) CNV 38 8 5 37 22 10 15 6
AMP PEAK 26(19Q13.42) WILD-TYPE 86 28 18 58 50 10 88 34

Figure S181.  Get High-res Image Gene #26: 'Amp Peak 26(19q13.42)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 26(19q13.42)' versus 'CN_CNMF'

P value = 2.5e-14 (Chi-square test), Q value = 1.2e-11

Table S182.  Gene #26: 'Amp Peak 26(19q13.42)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
AMP PEAK 26(19Q13.42) CNV 41 59 27 92 16
AMP PEAK 26(19Q13.42) WILD-TYPE 306 163 45 131 33

Figure S182.  Get High-res Image Gene #26: 'Amp Peak 26(19q13.42)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 26(19q13.42)' versus 'METHLYATION_CNMF'

P value = 6.23e-07 (Chi-square test), Q value = 2e-04

Table S183.  Gene #26: 'Amp Peak 26(19q13.42)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
AMP PEAK 26(19Q13.42) CNV 34 15 25 51 5 17
AMP PEAK 26(19Q13.42) WILD-TYPE 67 124 68 86 35 80

Figure S183.  Get High-res Image Gene #26: 'Amp Peak 26(19q13.42)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 26(19q13.42)' versus 'MIRSEQ_CNMF'

P value = 4.27e-06 (Fisher's exact test), Q value = 0.0012

Table S184.  Gene #26: 'Amp Peak 26(19q13.42)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 26(19Q13.42) CNV 43 91 95
AMP PEAK 26(19Q13.42) WILD-TYPE 191 301 160

Figure S184.  Get High-res Image Gene #26: 'Amp Peak 26(19q13.42)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 27(20q13.2)' versus 'MRNA_CNMF'

P value = 1.35e-09 (Chi-square test), Q value = 5.4e-07

Table S185.  Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
AMP PEAK 27(20Q13.2) CNV 87 18 10 51 49 15 34 10
AMP PEAK 27(20Q13.2) WILD-TYPE 37 18 13 44 23 5 69 30

Figure S185.  Get High-res Image Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 27(20q13.2)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000278 (Fisher's exact test), Q value = 0.058

Table S186.  Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
AMP PEAK 27(20Q13.2) CNV 55 69 150
AMP PEAK 27(20Q13.2) WILD-TYPE 85 56 98

Figure S186.  Get High-res Image Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 27(20q13.2)' versus 'CN_CNMF'

P value = 9.78e-50 (Chi-square test), Q value = 6.2e-47

Table S187.  Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
AMP PEAK 27(20Q13.2) CNV 67 170 43 158 27
AMP PEAK 27(20Q13.2) WILD-TYPE 280 52 29 65 22

Figure S187.  Get High-res Image Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 27(20q13.2)' versus 'METHLYATION_CNMF'

P value = 5.18e-25 (Chi-square test), Q value = 3.1e-22

Table S188.  Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
AMP PEAK 27(20Q13.2) CNV 61 28 48 111 12 32
AMP PEAK 27(20Q13.2) WILD-TYPE 40 111 45 26 28 65

Figure S188.  Get High-res Image Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 27(20q13.2)' versus 'RPPA_CNMF'

P value = 0.000604 (Fisher's exact test), Q value = 0.12

Table S189.  Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 27(20Q13.2) CNV 99 67 53
AMP PEAK 27(20Q13.2) WILD-TYPE 48 66 64

Figure S189.  Get High-res Image Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 27(20q13.2)' versus 'MRNASEQ_CNMF'

P value = 6.68e-09 (Fisher's exact test), Q value = 2.6e-06

Table S190.  Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
AMP PEAK 27(20Q13.2) CNV 140 45 253
AMP PEAK 27(20Q13.2) WILD-TYPE 94 103 193

Figure S190.  Get High-res Image Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 27(20q13.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.14e-07 (Fisher's exact test), Q value = 7.3e-05

Table S191.  Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
AMP PEAK 27(20Q13.2) CNV 80 245 113
AMP PEAK 27(20Q13.2) WILD-TYPE 136 163 91

Figure S191.  Get High-res Image Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 27(20q13.2)' versus 'MIRSEQ_CNMF'

P value = 7.41e-10 (Fisher's exact test), Q value = 3e-07

Table S192.  Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 27(20Q13.2) CNV 80 214 159
AMP PEAK 27(20Q13.2) WILD-TYPE 154 178 96

Figure S192.  Get High-res Image Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 27(20q13.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00036

Table S193.  Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 27(20Q13.2) CNV 205 110 138
AMP PEAK 27(20Q13.2) WILD-TYPE 157 174 97

Figure S193.  Get High-res Image Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 1(1p36.13)' versus 'MRNA_CNMF'

P value = 3.27e-05 (Chi-square test), Q value = 0.0084

Table S194.  Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
DEL PEAK 1(1P36.13) CNV 65 11 7 40 46 7 30 12
DEL PEAK 1(1P36.13) WILD-TYPE 59 25 16 55 26 13 73 28

Figure S194.  Get High-res Image Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 1(1p36.13)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000651 (Fisher's exact test), Q value = 0.12

Table S195.  Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
DEL PEAK 1(1P36.13) CNV 43 50 125
DEL PEAK 1(1P36.13) WILD-TYPE 97 75 123

Figure S195.  Get High-res Image Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 1(1p36.13)' versus 'CN_CNMF'

P value = 6.02e-32 (Chi-square test), Q value = 3.7e-29

Table S196.  Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 1(1P36.13) CNV 58 135 47 120 20
DEL PEAK 1(1P36.13) WILD-TYPE 289 87 25 103 29

Figure S196.  Get High-res Image Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 1(1p36.13)' versus 'METHLYATION_CNMF'

P value = 2.81e-09 (Chi-square test), Q value = 1.1e-06

Table S197.  Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 1(1P36.13) CNV 46 33 50 76 11 25
DEL PEAK 1(1P36.13) WILD-TYPE 55 106 43 61 29 72

Figure S197.  Get High-res Image Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 1(1p36.13)' versus 'MRNASEQ_CNMF'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.003

Table S198.  Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 1(1P36.13) CNV 105 37 207
DEL PEAK 1(1P36.13) WILD-TYPE 129 111 239

Figure S198.  Get High-res Image Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 1(1p36.13)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.02e-05 (Fisher's exact test), Q value = 0.015

Table S199.  Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
DEL PEAK 1(1P36.13) CNV 68 201 80
DEL PEAK 1(1P36.13) WILD-TYPE 148 207 124

Figure S199.  Get High-res Image Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 1(1p36.13)' versus 'MIRSEQ_CNMF'

P value = 2.37e-07 (Fisher's exact test), Q value = 8.1e-05

Table S200.  Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 1(1P36.13) CNV 64 168 131
DEL PEAK 1(1P36.13) WILD-TYPE 170 224 124

Figure S200.  Get High-res Image Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 1(1p36.13)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.11

Table S201.  Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 1(1P36.13) CNV 168 91 104
DEL PEAK 1(1P36.13) WILD-TYPE 194 193 131

Figure S201.  Get High-res Image Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 2(1p22.1)' versus 'MRNA_CHIERARCHICAL'

P value = 8.39e-05 (Fisher's exact test), Q value = 0.02

Table S202.  Gene #29: 'Del Peak 2(1p22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
DEL PEAK 2(1P22.1) CNV 40 30 110
DEL PEAK 2(1P22.1) WILD-TYPE 100 95 138

Figure S202.  Get High-res Image Gene #29: 'Del Peak 2(1p22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 2(1p22.1)' versus 'CN_CNMF'

P value = 5.77e-22 (Chi-square test), Q value = 3.4e-19

Table S203.  Gene #29: 'Del Peak 2(1p22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 2(1P22.1) CNV 61 117 45 70 12
DEL PEAK 2(1P22.1) WILD-TYPE 286 105 27 153 37

Figure S203.  Get High-res Image Gene #29: 'Del Peak 2(1p22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 2(1p22.1)' versus 'METHLYATION_CNMF'

P value = 0.00103 (Chi-square test), Q value = 0.19

Table S204.  Gene #29: 'Del Peak 2(1p22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 2(1P22.1) CNV 25 35 40 56 13 21
DEL PEAK 2(1P22.1) WILD-TYPE 76 104 53 81 27 76

Figure S204.  Get High-res Image Gene #29: 'Del Peak 2(1p22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 2(1p22.1)' versus 'MRNASEQ_CNMF'

P value = 0.000574 (Fisher's exact test), Q value = 0.11

Table S205.  Gene #29: 'Del Peak 2(1p22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 2(1P22.1) CNV 68 38 180
DEL PEAK 2(1P22.1) WILD-TYPE 166 110 266

Figure S205.  Get High-res Image Gene #29: 'Del Peak 2(1p22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 2(1p22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.06e-06 (Fisher's exact test), Q value = 0.00089

Table S206.  Gene #29: 'Del Peak 2(1p22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
DEL PEAK 2(1P22.1) CNV 64 174 48
DEL PEAK 2(1P22.1) WILD-TYPE 152 234 156

Figure S206.  Get High-res Image Gene #29: 'Del Peak 2(1p22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 3(2q37.3)' versus 'MRNA_CNMF'

P value = 1.39e-06 (Chi-square test), Q value = 0.00043

Table S207.  Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
DEL PEAK 3(2Q37.3) CNV 43 10 5 46 28 6 22 0
DEL PEAK 3(2Q37.3) WILD-TYPE 81 26 18 49 44 14 81 40

Figure S207.  Get High-res Image Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 3(2q37.3)' versus 'MRNA_CHIERARCHICAL'

P value = 3.78e-08 (Fisher's exact test), Q value = 1.4e-05

Table S208.  Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
DEL PEAK 3(2Q37.3) CNV 20 58 82
DEL PEAK 3(2Q37.3) WILD-TYPE 120 67 166

Figure S208.  Get High-res Image Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 3(2q37.3)' versus 'CN_CNMF'

P value = 1.57e-20 (Chi-square test), Q value = 9e-18

Table S209.  Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 3(2Q37.3) CNV 39 76 26 108 16
DEL PEAK 3(2Q37.3) WILD-TYPE 308 146 46 115 33

Figure S209.  Get High-res Image Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 3(2q37.3)' versus 'METHLYATION_CNMF'

P value = 2.61e-10 (Chi-square test), Q value = 1.1e-07

Table S210.  Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 3(2Q37.3) CNV 44 19 25 53 4 12
DEL PEAK 3(2Q37.3) WILD-TYPE 57 120 68 84 36 85

Figure S210.  Get High-res Image Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 3(2q37.3)' versus 'RPPA_CNMF'

P value = 1.03e-08 (Fisher's exact test), Q value = 4e-06

Table S211.  Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 3(2Q37.3) CNV 70 38 16
DEL PEAK 3(2Q37.3) WILD-TYPE 77 95 101

Figure S211.  Get High-res Image Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 3(2q37.3)' versus 'RPPA_CHIERARCHICAL'

P value = 1.11e-07 (Fisher's exact test), Q value = 3.9e-05

Table S212.  Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 3(2Q37.3) CNV 56 13 55
DEL PEAK 3(2Q37.3) WILD-TYPE 105 97 71

Figure S212.  Get High-res Image Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 3(2q37.3)' versus 'MRNASEQ_CNMF'

P value = 1.81e-11 (Fisher's exact test), Q value = 8e-09

Table S213.  Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 3(2Q37.3) CNV 103 17 126
DEL PEAK 3(2Q37.3) WILD-TYPE 131 131 320

Figure S213.  Get High-res Image Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 3(2q37.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.03e-08 (Fisher's exact test), Q value = 7.6e-06

Table S214.  Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
DEL PEAK 3(2Q37.3) CNV 35 125 86
DEL PEAK 3(2Q37.3) WILD-TYPE 181 283 118

Figure S214.  Get High-res Image Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 3(2q37.3)' versus 'MIRSEQ_CNMF'

P value = 4.66e-11 (Fisher's exact test), Q value = 2e-08

Table S215.  Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 3(2Q37.3) CNV 43 99 116
DEL PEAK 3(2Q37.3) WILD-TYPE 191 293 139

Figure S215.  Get High-res Image Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 3(2q37.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.63e-07 (Fisher's exact test), Q value = 8.9e-05

Table S216.  Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 3(2Q37.3) CNV 110 53 95
DEL PEAK 3(2Q37.3) WILD-TYPE 252 231 140

Figure S216.  Get High-res Image Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 4(3p14.3)' versus 'MRNA_CNMF'

P value = 1.06e-10 (Chi-square test), Q value = 4.5e-08

Table S217.  Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
DEL PEAK 4(3P14.3) CNV 39 11 4 50 34 9 8 8
DEL PEAK 4(3P14.3) WILD-TYPE 85 25 19 45 38 11 95 32

Figure S217.  Get High-res Image Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 4(3p14.3)' versus 'MRNA_CHIERARCHICAL'

P value = 3.11e-08 (Fisher's exact test), Q value = 1.1e-05

Table S218.  Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
DEL PEAK 4(3P14.3) CNV 36 67 60
DEL PEAK 4(3P14.3) WILD-TYPE 104 58 188

Figure S218.  Get High-res Image Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 4(3p14.3)' versus 'CN_CNMF'

P value = 2.93e-33 (Chi-square test), Q value = 1.8e-30

Table S219.  Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 4(3P14.3) CNV 44 80 12 134 8
DEL PEAK 4(3P14.3) WILD-TYPE 303 142 60 89 41

Figure S219.  Get High-res Image Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 4(3p14.3)' versus 'METHLYATION_CNMF'

P value = 5.78e-13 (Chi-square test), Q value = 2.7e-10

Table S220.  Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 4(3P14.3) CNV 49 9 35 51 12 18
DEL PEAK 4(3P14.3) WILD-TYPE 52 130 58 86 28 79

Figure S220.  Get High-res Image Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 4(3p14.3)' versus 'RPPA_CNMF'

P value = 1.18e-09 (Fisher's exact test), Q value = 4.8e-07

Table S221.  Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 4(3P14.3) CNV 79 25 32
DEL PEAK 4(3P14.3) WILD-TYPE 68 108 85

Figure S221.  Get High-res Image Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 4(3p14.3)' versus 'RPPA_CHIERARCHICAL'

P value = 5.21e-06 (Fisher's exact test), Q value = 0.0015

Table S222.  Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 4(3P14.3) CNV 40 31 65
DEL PEAK 4(3P14.3) WILD-TYPE 121 79 61

Figure S222.  Get High-res Image Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 4(3p14.3)' versus 'MRNASEQ_CNMF'

P value = 4.61e-18 (Fisher's exact test), Q value = 2.6e-15

Table S223.  Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 4(3P14.3) CNV 127 28 102
DEL PEAK 4(3P14.3) WILD-TYPE 107 120 344

Figure S223.  Get High-res Image Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 4(3p14.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.42e-13 (Fisher's exact test), Q value = 2.1e-10

Table S224.  Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
DEL PEAK 4(3P14.3) CNV 45 105 107
DEL PEAK 4(3P14.3) WILD-TYPE 171 303 97

Figure S224.  Get High-res Image Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 4(3p14.3)' versus 'MIRSEQ_CNMF'

P value = 2.29e-19 (Fisher's exact test), Q value = 1.3e-16

Table S225.  Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 4(3P14.3) CNV 45 87 136
DEL PEAK 4(3P14.3) WILD-TYPE 189 305 119

Figure S225.  Get High-res Image Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 4(3p14.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.57e-14 (Fisher's exact test), Q value = 1.3e-11

Table S226.  Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 4(3P14.3) CNV 100 51 117
DEL PEAK 4(3P14.3) WILD-TYPE 262 233 118

Figure S226.  Get High-res Image Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 5(4p16.3)' versus 'MRNA_CNMF'

P value = 5.63e-11 (Chi-square test), Q value = 2.4e-08

Table S227.  Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
DEL PEAK 5(4P16.3) CNV 28 10 4 55 37 7 21 5
DEL PEAK 5(4P16.3) WILD-TYPE 96 26 19 40 35 13 82 35

Figure S227.  Get High-res Image Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 5(4p16.3)' versus 'MRNA_CHIERARCHICAL'

P value = 6.3e-12 (Fisher's exact test), Q value = 2.8e-09

Table S228.  Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
DEL PEAK 5(4P16.3) CNV 24 72 71
DEL PEAK 5(4P16.3) WILD-TYPE 116 53 177

Figure S228.  Get High-res Image Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 5(4p16.3)' versus 'CN_CNMF'

P value = 1.98e-26 (Chi-square test), Q value = 1.2e-23

Table S229.  Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 5(4P16.3) CNV 55 52 31 130 13
DEL PEAK 5(4P16.3) WILD-TYPE 292 170 41 93 36

Figure S229.  Get High-res Image Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 5(4p16.3)' versus 'METHLYATION_CNMF'

P value = 8.41e-13 (Chi-square test), Q value = 3.9e-10

Table S230.  Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 5(4P16.3) CNV 62 30 27 28 5 25
DEL PEAK 5(4P16.3) WILD-TYPE 39 109 66 109 35 72

Figure S230.  Get High-res Image Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 5(4p16.3)' versus 'RPPA_CNMF'

P value = 4.6e-07 (Fisher's exact test), Q value = 0.00015

Table S231.  Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 5(4P16.3) CNV 75 39 24
DEL PEAK 5(4P16.3) WILD-TYPE 72 94 93

Figure S231.  Get High-res Image Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 5(4p16.3)' versus 'RPPA_CHIERARCHICAL'

P value = 1.62e-06 (Fisher's exact test), Q value = 5e-04

Table S232.  Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 5(4P16.3) CNV 48 24 66
DEL PEAK 5(4P16.3) WILD-TYPE 113 86 60

Figure S232.  Get High-res Image Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 5(4p16.3)' versus 'MRNASEQ_CNMF'

P value = 9.75e-24 (Fisher's exact test), Q value = 5.8e-21

Table S233.  Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 5(4P16.3) CNV 134 20 104
DEL PEAK 5(4P16.3) WILD-TYPE 100 128 342

Figure S233.  Get High-res Image Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 5(4p16.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.14e-18 (Fisher's exact test), Q value = 1.2e-15

Table S234.  Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
DEL PEAK 5(4P16.3) CNV 38 105 115
DEL PEAK 5(4P16.3) WILD-TYPE 178 303 89

Figure S234.  Get High-res Image Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 5(4p16.3)' versus 'MIRSEQ_CNMF'

P value = 9.97e-15 (Fisher's exact test), Q value = 5.1e-12

Table S235.  Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 5(4P16.3) CNV 48 94 129
DEL PEAK 5(4P16.3) WILD-TYPE 186 298 126

Figure S235.  Get High-res Image Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 5(4p16.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.7e-18 (Fisher's exact test), Q value = 2.6e-15

Table S236.  Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 5(4P16.3) CNV 93 52 126
DEL PEAK 5(4P16.3) WILD-TYPE 269 232 109

Figure S236.  Get High-res Image Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 6(4q35.2)' versus 'MRNA_CNMF'

P value = 3.17e-06 (Chi-square test), Q value = 0.00092

Table S237.  Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
DEL PEAK 6(4Q35.2) CNV 27 10 7 50 30 10 23 8
DEL PEAK 6(4Q35.2) WILD-TYPE 97 26 16 45 42 10 80 32

Figure S237.  Get High-res Image Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 6(4q35.2)' versus 'MRNA_CHIERARCHICAL'

P value = 9.81e-07 (Fisher's exact test), Q value = 0.00031

Table S238.  Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
DEL PEAK 6(4Q35.2) CNV 29 63 73
DEL PEAK 6(4Q35.2) WILD-TYPE 111 62 175

Figure S238.  Get High-res Image Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 6(4q35.2)' versus 'CN_CNMF'

P value = 2.71e-37 (Chi-square test), Q value = 1.7e-34

Table S239.  Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 6(4Q35.2) CNV 53 42 36 141 11
DEL PEAK 6(4Q35.2) WILD-TYPE 294 180 36 82 38

Figure S239.  Get High-res Image Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 6(4q35.2)' versus 'METHLYATION_CNMF'

P value = 1.66e-13 (Chi-square test), Q value = 8e-11

Table S240.  Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 6(4Q35.2) CNV 63 29 23 26 7 29
DEL PEAK 6(4Q35.2) WILD-TYPE 38 110 70 111 33 68

Figure S240.  Get High-res Image Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 6(4q35.2)' versus 'RPPA_CNMF'

P value = 1.51e-08 (Fisher's exact test), Q value = 5.7e-06

Table S241.  Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 6(4Q35.2) CNV 78 35 24
DEL PEAK 6(4Q35.2) WILD-TYPE 69 98 93

Figure S241.  Get High-res Image Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 6(4q35.2)' versus 'RPPA_CHIERARCHICAL'

P value = 1.78e-06 (Fisher's exact test), Q value = 0.00054

Table S242.  Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 6(4Q35.2) CNV 46 25 66
DEL PEAK 6(4Q35.2) WILD-TYPE 115 85 60

Figure S242.  Get High-res Image Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 6(4q35.2)' versus 'MRNASEQ_CNMF'

P value = 2.22e-21 (Fisher's exact test), Q value = 1.3e-18

Table S243.  Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 6(4Q35.2) CNV 131 21 107
DEL PEAK 6(4Q35.2) WILD-TYPE 103 127 339

Figure S243.  Get High-res Image Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 6(4q35.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.79e-14 (Fisher's exact test), Q value = 1.9e-11

Table S244.  Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
DEL PEAK 6(4Q35.2) CNV 43 107 109
DEL PEAK 6(4Q35.2) WILD-TYPE 173 301 95

Figure S244.  Get High-res Image Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 6(4q35.2)' versus 'MIRSEQ_CNMF'

P value = 2.84e-13 (Fisher's exact test), Q value = 1.4e-10

Table S245.  Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 6(4Q35.2) CNV 48 97 126
DEL PEAK 6(4Q35.2) WILD-TYPE 186 295 129

Figure S245.  Get High-res Image Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 6(4q35.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.73e-18 (Fisher's exact test), Q value = 3.7e-15

Table S246.  Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 6(4Q35.2) CNV 87 57 127
DEL PEAK 6(4Q35.2) WILD-TYPE 275 227 108

Figure S246.  Get High-res Image Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 7(5q11.2)' versus 'MRNA_CNMF'

P value = 1.17e-27 (Chi-square test), Q value = 7e-25

Table S247.  Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
DEL PEAK 7(5Q11.2) CNV 19 5 2 68 25 3 8 4
DEL PEAK 7(5Q11.2) WILD-TYPE 105 31 21 27 47 17 95 36

Figure S247.  Get High-res Image Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 7(5q11.2)' versus 'MRNA_CHIERARCHICAL'

P value = 6.11e-25 (Fisher's exact test), Q value = 3.6e-22

Table S248.  Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
DEL PEAK 7(5Q11.2) CNV 14 79 41
DEL PEAK 7(5Q11.2) WILD-TYPE 126 46 207

Figure S248.  Get High-res Image Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 7(5q11.2)' versus 'CN_CNMF'

P value = 5.91e-60 (Chi-square test), Q value = 3.8e-57

Table S249.  Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 7(5Q11.2) CNV 35 29 8 152 10
DEL PEAK 7(5Q11.2) WILD-TYPE 312 193 64 71 39

Figure S249.  Get High-res Image Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 7(5q11.2)' versus 'METHLYATION_CNMF'

P value = 1.43e-39 (Chi-square test), Q value = 8.9e-37

Table S250.  Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 7(5Q11.2) CNV 78 4 15 28 5 22
DEL PEAK 7(5Q11.2) WILD-TYPE 23 135 78 109 35 75

Figure S250.  Get High-res Image Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 7(5q11.2)' versus 'RPPA_CNMF'

P value = 3.33e-16 (Fisher's exact test), Q value = 1.8e-13

Table S251.  Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 7(5Q11.2) CNV 78 13 23
DEL PEAK 7(5Q11.2) WILD-TYPE 69 120 94

Figure S251.  Get High-res Image Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 7(5q11.2)' versus 'RPPA_CHIERARCHICAL'

P value = 7.43e-19 (Fisher's exact test), Q value = 4.2e-16

Table S252.  Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 7(5Q11.2) CNV 26 13 75
DEL PEAK 7(5Q11.2) WILD-TYPE 135 97 51

Figure S252.  Get High-res Image Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 7(5q11.2)' versus 'MRNASEQ_CNMF'

P value = 1.33e-40 (Fisher's exact test), Q value = 8.3e-38

Table S253.  Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 7(5Q11.2) CNV 140 11 67
DEL PEAK 7(5Q11.2) WILD-TYPE 94 137 379

Figure S253.  Get High-res Image Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 7(5q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.7e-43 (Fisher's exact test), Q value = 1.1e-40

Table S254.  Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
DEL PEAK 7(5Q11.2) CNV 19 67 132
DEL PEAK 7(5Q11.2) WILD-TYPE 197 341 72

Figure S254.  Get High-res Image Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 7(5q11.2)' versus 'MIRSEQ_CNMF'

P value = 8.36e-40 (Fisher's exact test), Q value = 5.2e-37

Table S255.  Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 7(5Q11.2) CNV 32 45 145
DEL PEAK 7(5Q11.2) WILD-TYPE 202 347 110

Figure S255.  Get High-res Image Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 7(5q11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.41e-49 (Fisher's exact test), Q value = 3.4e-46

Table S256.  Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 7(5Q11.2) CNV 63 16 143
DEL PEAK 7(5Q11.2) WILD-TYPE 299 268 92

Figure S256.  Get High-res Image Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 8(5q21.3)' versus 'MRNA_CNMF'

P value = 1.36e-29 (Chi-square test), Q value = 8.3e-27

Table S257.  Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
DEL PEAK 8(5Q21.3) CNV 19 5 2 69 24 5 7 2
DEL PEAK 8(5Q21.3) WILD-TYPE 105 31 21 26 48 15 96 38

Figure S257.  Get High-res Image Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 8(5q21.3)' versus 'MRNA_CHIERARCHICAL'

P value = 1e-26 (Fisher's exact test), Q value = 6e-24

Table S258.  Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
DEL PEAK 8(5Q21.3) CNV 12 80 41
DEL PEAK 8(5Q21.3) WILD-TYPE 128 45 207

Figure S258.  Get High-res Image Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 8(5q21.3)' versus 'CN_CNMF'

P value = 6.13e-70 (Chi-square test), Q value = 3.9e-67

Table S259.  Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 8(5Q21.3) CNV 28 25 7 156 9
DEL PEAK 8(5Q21.3) WILD-TYPE 319 197 65 67 40

Figure S259.  Get High-res Image Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 8(5q21.3)' versus 'METHLYATION_CNMF'

P value = 3.25e-51 (Chi-square test), Q value = 2.1e-48

Table S260.  Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 8(5Q21.3) CNV 84 4 10 23 3 22
DEL PEAK 8(5Q21.3) WILD-TYPE 17 135 83 114 37 75

Figure S260.  Get High-res Image Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 8(5q21.3)' versus 'RPPA_CNMF'

P value = 2.6e-15 (Fisher's exact test), Q value = 1.3e-12

Table S261.  Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 8(5Q21.3) CNV 76 13 23
DEL PEAK 8(5Q21.3) WILD-TYPE 71 120 94

Figure S261.  Get High-res Image Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 8(5q21.3)' versus 'RPPA_CHIERARCHICAL'

P value = 8.97e-16 (Fisher's exact test), Q value = 4.7e-13

Table S262.  Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 8(5Q21.3) CNV 26 15 71
DEL PEAK 8(5Q21.3) WILD-TYPE 135 95 55

Figure S262.  Get High-res Image Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 8(5q21.3)' versus 'MRNASEQ_CNMF'

P value = 5.88e-48 (Fisher's exact test), Q value = 3.7e-45

Table S263.  Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 8(5Q21.3) CNV 143 8 57
DEL PEAK 8(5Q21.3) WILD-TYPE 91 140 389

Figure S263.  Get High-res Image Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 8(5q21.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.06e-47 (Fisher's exact test), Q value = 6.7e-45

Table S264.  Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
DEL PEAK 8(5Q21.3) CNV 18 57 133
DEL PEAK 8(5Q21.3) WILD-TYPE 198 351 71

Figure S264.  Get High-res Image Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 8(5q21.3)' versus 'MIRSEQ_CNMF'

P value = 1.28e-39 (Fisher's exact test), Q value = 8e-37

Table S265.  Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 8(5Q21.3) CNV 31 42 142
DEL PEAK 8(5Q21.3) WILD-TYPE 203 350 113

Figure S265.  Get High-res Image Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 8(5q21.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.67e-54 (Fisher's exact test), Q value = 1.1e-51

Table S266.  Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 8(5Q21.3) CNV 55 14 146
DEL PEAK 8(5Q21.3) WILD-TYPE 307 270 89

Figure S266.  Get High-res Image Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 9(6p25.3)' versus 'CN_CNMF'

P value = 8.51e-07 (Chi-square test), Q value = 0.00027

Table S267.  Gene #36: 'Del Peak 9(6p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 9(6P25.3) CNV 35 63 12 47 13
DEL PEAK 9(6P25.3) WILD-TYPE 312 159 60 176 36

Figure S267.  Get High-res Image Gene #36: 'Del Peak 9(6p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 9(6p25.3)' versus 'METHLYATION_CNMF'

P value = 4.71e-05 (Chi-square test), Q value = 0.012

Table S268.  Gene #36: 'Del Peak 9(6p25.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 9(6P25.3) CNV 24 13 19 41 2 14
DEL PEAK 9(6P25.3) WILD-TYPE 77 126 74 96 38 83

Figure S268.  Get High-res Image Gene #36: 'Del Peak 9(6p25.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 10(6q15)' versus 'MRNA_CNMF'

P value = 1.55e-06 (Chi-square test), Q value = 0.00048

Table S269.  Gene #37: 'Del Peak 10(6q15)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
DEL PEAK 10(6Q15) CNV 64 13 7 17 29 4 22 16
DEL PEAK 10(6Q15) WILD-TYPE 60 23 16 78 43 16 81 24

Figure S269.  Get High-res Image Gene #37: 'Del Peak 10(6q15)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 10(6q15)' versus 'MRNA_CHIERARCHICAL'

P value = 0.00137 (Fisher's exact test), Q value = 0.25

Table S270.  Gene #37: 'Del Peak 10(6q15)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
DEL PEAK 10(6Q15) CNV 49 26 97
DEL PEAK 10(6Q15) WILD-TYPE 91 99 151

Figure S270.  Get High-res Image Gene #37: 'Del Peak 10(6q15)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 10(6q15)' versus 'CN_CNMF'

P value = 6.83e-28 (Chi-square test), Q value = 4.1e-25

Table S271.  Gene #37: 'Del Peak 10(6q15)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 10(6Q15) CNV 73 133 19 45 31
DEL PEAK 10(6Q15) WILD-TYPE 274 89 53 178 18

Figure S271.  Get High-res Image Gene #37: 'Del Peak 10(6q15)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 10(6q15)' versus 'METHLYATION_CNMF'

P value = 3.78e-08 (Chi-square test), Q value = 1.4e-05

Table S272.  Gene #37: 'Del Peak 10(6q15)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 10(6Q15) CNV 19 43 34 70 7 19
DEL PEAK 10(6Q15) WILD-TYPE 82 96 59 67 33 78

Figure S272.  Get High-res Image Gene #37: 'Del Peak 10(6q15)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 10(6q15)' versus 'MRNASEQ_CNMF'

P value = 2.69e-05 (Fisher's exact test), Q value = 0.0069

Table S273.  Gene #37: 'Del Peak 10(6q15)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 10(6Q15) CNV 56 43 181
DEL PEAK 10(6Q15) WILD-TYPE 178 105 265

Figure S273.  Get High-res Image Gene #37: 'Del Peak 10(6q15)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 10(6q15)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000262 (Fisher's exact test), Q value = 0.055

Table S274.  Gene #37: 'Del Peak 10(6q15)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
DEL PEAK 10(6Q15) CNV 66 164 50
DEL PEAK 10(6Q15) WILD-TYPE 150 244 154

Figure S274.  Get High-res Image Gene #37: 'Del Peak 10(6q15)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 10(6q15)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.04e-05 (Fisher's exact test), Q value = 0.012

Table S275.  Gene #37: 'Del Peak 10(6q15)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 10(6Q15) CNV 150 86 58
DEL PEAK 10(6Q15) WILD-TYPE 212 198 177

Figure S275.  Get High-res Image Gene #37: 'Del Peak 10(6q15)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 11(6q27)' versus 'CN_CNMF'

P value = 2.87e-14 (Chi-square test), Q value = 1.4e-11

Table S276.  Gene #38: 'Del Peak 11(6q27)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 11(6Q27) CNV 76 112 19 76 31
DEL PEAK 11(6Q27) WILD-TYPE 271 110 53 147 18

Figure S276.  Get High-res Image Gene #38: 'Del Peak 11(6q27)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 12(7p22.3)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000366 (Fisher's exact test), Q value = 0.074

Table S277.  Gene #39: 'Del Peak 12(7p22.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
DEL PEAK 12(7P22.3) CNV 8 27 40
DEL PEAK 12(7P22.3) WILD-TYPE 132 98 208

Figure S277.  Get High-res Image Gene #39: 'Del Peak 12(7p22.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 12(7p22.3)' versus 'CN_CNMF'

P value = 2.06e-15 (Chi-square test), Q value = 1.1e-12

Table S278.  Gene #39: 'Del Peak 12(7p22.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 12(7P22.3) CNV 11 47 3 54 3
DEL PEAK 12(7P22.3) WILD-TYPE 336 175 69 169 46

Figure S278.  Get High-res Image Gene #39: 'Del Peak 12(7p22.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 12(7p22.3)' versus 'METHLYATION_CNMF'

P value = 5.89e-07 (Chi-square test), Q value = 0.00019

Table S279.  Gene #39: 'Del Peak 12(7p22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 12(7P22.3) CNV 25 6 12 18 2 2
DEL PEAK 12(7P22.3) WILD-TYPE 76 133 81 119 38 95

Figure S279.  Get High-res Image Gene #39: 'Del Peak 12(7p22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 12(7p22.3)' versus 'MRNASEQ_CNMF'

P value = 8.07e-09 (Fisher's exact test), Q value = 3.1e-06

Table S280.  Gene #39: 'Del Peak 12(7p22.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 12(7P22.3) CNV 55 4 56
DEL PEAK 12(7P22.3) WILD-TYPE 179 144 390

Figure S280.  Get High-res Image Gene #39: 'Del Peak 12(7p22.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 12(7p22.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.39e-08 (Fisher's exact test), Q value = 1.9e-05

Table S281.  Gene #39: 'Del Peak 12(7p22.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
DEL PEAK 12(7P22.3) CNV 9 60 46
DEL PEAK 12(7P22.3) WILD-TYPE 207 348 158

Figure S281.  Get High-res Image Gene #39: 'Del Peak 12(7p22.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 12(7p22.3)' versus 'MIRSEQ_CNMF'

P value = 3.96e-11 (Fisher's exact test), Q value = 1.7e-08

Table S282.  Gene #39: 'Del Peak 12(7p22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 12(7P22.3) CNV 7 48 59
DEL PEAK 12(7P22.3) WILD-TYPE 227 344 196

Figure S282.  Get High-res Image Gene #39: 'Del Peak 12(7p22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 12(7p22.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.38e-10 (Fisher's exact test), Q value = 5.9e-08

Table S283.  Gene #39: 'Del Peak 12(7p22.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 12(7P22.3) CNV 46 12 56
DEL PEAK 12(7P22.3) WILD-TYPE 316 272 179

Figure S283.  Get High-res Image Gene #39: 'Del Peak 12(7p22.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 13(7q36.1)' versus 'CN_CNMF'

P value = 5.25e-10 (Chi-square test), Q value = 2.2e-07

Table S284.  Gene #40: 'Del Peak 13(7q36.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 13(7Q36.1) CNV 32 61 13 64 4
DEL PEAK 13(7Q36.1) WILD-TYPE 315 161 59 159 45

Figure S284.  Get High-res Image Gene #40: 'Del Peak 13(7q36.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 13(7q36.1)' versus 'MRNASEQ_CNMF'

P value = 0.000414 (Fisher's exact test), Q value = 0.083

Table S285.  Gene #40: 'Del Peak 13(7q36.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 13(7Q36.1) CNV 65 17 87
DEL PEAK 13(7Q36.1) WILD-TYPE 169 131 359

Figure S285.  Get High-res Image Gene #40: 'Del Peak 13(7q36.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 13(7q36.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000496 (Fisher's exact test), Q value = 0.098

Table S286.  Gene #40: 'Del Peak 13(7q36.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
DEL PEAK 13(7Q36.1) CNV 25 95 49
DEL PEAK 13(7Q36.1) WILD-TYPE 191 313 155

Figure S286.  Get High-res Image Gene #40: 'Del Peak 13(7q36.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 13(7q36.1)' versus 'MIRSEQ_CNMF'

P value = 5.26e-08 (Fisher's exact test), Q value = 1.9e-05

Table S287.  Gene #40: 'Del Peak 13(7q36.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 13(7Q36.1) CNV 23 69 77
DEL PEAK 13(7Q36.1) WILD-TYPE 211 323 178

Figure S287.  Get High-res Image Gene #40: 'Del Peak 13(7q36.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 13(7q36.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.6e-06 (Fisher's exact test), Q value = 0.00049

Table S288.  Gene #40: 'Del Peak 13(7q36.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 13(7Q36.1) CNV 73 30 66
DEL PEAK 13(7Q36.1) WILD-TYPE 289 254 169

Figure S288.  Get High-res Image Gene #40: 'Del Peak 13(7q36.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 14(8p23.2)' versus 'MRNA_CNMF'

P value = 1.08e-09 (Chi-square test), Q value = 4.4e-07

Table S289.  Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
DEL PEAK 14(8P23.2) CNV 81 16 13 64 47 13 26 17
DEL PEAK 14(8P23.2) WILD-TYPE 43 20 10 31 25 7 77 23

Figure S289.  Get High-res Image Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 14(8p23.2)' versus 'MRNA_CHIERARCHICAL'

P value = 2.53e-05 (Fisher's exact test), Q value = 0.0066

Table S290.  Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
DEL PEAK 14(8P23.2) CNV 57 86 134
DEL PEAK 14(8P23.2) WILD-TYPE 83 39 114

Figure S290.  Get High-res Image Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 14(8p23.2)' versus 'CN_CNMF'

P value = 7.63e-31 (Chi-square test), Q value = 4.7e-28

Table S291.  Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 14(8P23.2) CNV 117 148 15 161 40
DEL PEAK 14(8P23.2) WILD-TYPE 230 74 57 62 9

Figure S291.  Get High-res Image Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 14(8p23.2)' versus 'METHLYATION_CNMF'

P value = 1.19e-13 (Chi-square test), Q value = 5.8e-11

Table S292.  Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 14(8P23.2) CNV 68 35 48 95 18 41
DEL PEAK 14(8P23.2) WILD-TYPE 33 104 45 42 22 56

Figure S292.  Get High-res Image Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 14(8p23.2)' versus 'MRNASEQ_CNMF'

P value = 2.05e-11 (Fisher's exact test), Q value = 9e-09

Table S293.  Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 14(8P23.2) CNV 162 49 232
DEL PEAK 14(8P23.2) WILD-TYPE 72 99 214

Figure S293.  Get High-res Image Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 14(8p23.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.71e-08 (Fisher's exact test), Q value = 1.4e-05

Table S294.  Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
DEL PEAK 14(8P23.2) CNV 84 222 137
DEL PEAK 14(8P23.2) WILD-TYPE 132 186 67

Figure S294.  Get High-res Image Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 14(8p23.2)' versus 'MIRSEQ_CNMF'

P value = 5.68e-06 (Fisher's exact test), Q value = 0.0016

Table S295.  Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 14(8P23.2) CNV 98 203 163
DEL PEAK 14(8P23.2) WILD-TYPE 136 189 92

Figure S295.  Get High-res Image Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 14(8p23.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.79e-12 (Fisher's exact test), Q value = 2.2e-09

Table S296.  Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 14(8P23.2) CNV 189 110 165
DEL PEAK 14(8P23.2) WILD-TYPE 173 174 70

Figure S296.  Get High-res Image Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 15(8p11.21)' versus 'MRNA_CNMF'

P value = 0.000126 (Chi-square test), Q value = 0.029

Table S297.  Gene #42: 'Del Peak 15(8p11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
DEL PEAK 15(8P11.21) CNV 24 5 4 21 27 7 7 7
DEL PEAK 15(8P11.21) WILD-TYPE 100 31 19 74 45 13 96 33

Figure S297.  Get High-res Image Gene #42: 'Del Peak 15(8p11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 15(8p11.21)' versus 'CN_CNMF'

P value = 6.19e-11 (Chi-square test), Q value = 2.7e-08

Table S298.  Gene #42: 'Del Peak 15(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 15(8P11.21) CNV 45 47 7 74 0
DEL PEAK 15(8P11.21) WILD-TYPE 302 175 65 149 49

Figure S298.  Get High-res Image Gene #42: 'Del Peak 15(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 15(8p11.21)' versus 'MRNASEQ_CNMF'

P value = 0.000593 (Fisher's exact test), Q value = 0.12

Table S299.  Gene #42: 'Del Peak 15(8p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 15(8P11.21) CNV 64 18 79
DEL PEAK 15(8P11.21) WILD-TYPE 170 130 367

Figure S299.  Get High-res Image Gene #42: 'Del Peak 15(8p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 15(8p11.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000914 (Fisher's exact test), Q value = 0.17

Table S300.  Gene #42: 'Del Peak 15(8p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
DEL PEAK 15(8P11.21) CNV 28 77 56
DEL PEAK 15(8P11.21) WILD-TYPE 188 331 148

Figure S300.  Get High-res Image Gene #42: 'Del Peak 15(8p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 15(8p11.21)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.26e-06 (Fisher's exact test), Q value = 0.0018

Table S301.  Gene #42: 'Del Peak 15(8p11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 15(8P11.21) CNV 72 32 66
DEL PEAK 15(8P11.21) WILD-TYPE 290 252 169

Figure S301.  Get High-res Image Gene #42: 'Del Peak 15(8p11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 16(9p21.3)' versus 'MRNA_CNMF'

P value = 2.43e-06 (Chi-square test), Q value = 0.00072

Table S302.  Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
DEL PEAK 16(9P21.3) CNV 62 13 9 29 38 8 23 5
DEL PEAK 16(9P21.3) WILD-TYPE 62 23 14 66 34 12 80 35

Figure S302.  Get High-res Image Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 16(9p21.3)' versus 'MRNA_CHIERARCHICAL'

P value = 0.00076 (Fisher's exact test), Q value = 0.14

Table S303.  Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
DEL PEAK 16(9P21.3) CNV 35 43 109
DEL PEAK 16(9P21.3) WILD-TYPE 105 82 139

Figure S303.  Get High-res Image Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 16(9p21.3)' versus 'CN_CNMF'

P value = 1.11e-29 (Chi-square test), Q value = 6.8e-27

Table S304.  Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 16(9P21.3) CNV 44 122 17 110 14
DEL PEAK 16(9P21.3) WILD-TYPE 303 100 55 113 35

Figure S304.  Get High-res Image Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 16(9p21.3)' versus 'METHLYATION_CNMF'

P value = 2.21e-15 (Chi-square test), Q value = 1.1e-12

Table S305.  Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 16(9P21.3) CNV 37 14 38 72 8 15
DEL PEAK 16(9P21.3) WILD-TYPE 64 125 55 65 32 82

Figure S305.  Get High-res Image Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 16(9p21.3)' versus 'MRNASEQ_CNMF'

P value = 7.31e-07 (Fisher's exact test), Q value = 0.00024

Table S306.  Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 16(9P21.3) CNV 95 25 168
DEL PEAK 16(9P21.3) WILD-TYPE 139 123 278

Figure S306.  Get High-res Image Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 16(9p21.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.64e-07 (Fisher's exact test), Q value = 8.9e-05

Table S307.  Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
DEL PEAK 16(9P21.3) CNV 43 165 80
DEL PEAK 16(9P21.3) WILD-TYPE 173 243 124

Figure S307.  Get High-res Image Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 16(9p21.3)' versus 'MIRSEQ_CNMF'

P value = 4.02e-06 (Fisher's exact test), Q value = 0.0012

Table S308.  Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 16(9P21.3) CNV 51 134 109
DEL PEAK 16(9P21.3) WILD-TYPE 183 258 146

Figure S308.  Get High-res Image Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 16(9p21.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.15e-12 (Fisher's exact test), Q value = 1.9e-09

Table S309.  Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 16(9P21.3) CNV 146 49 99
DEL PEAK 16(9P21.3) WILD-TYPE 216 235 136

Figure S309.  Get High-res Image Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 17(9q21.11)' versus 'MRNA_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.06

Table S310.  Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
DEL PEAK 17(9Q21.11) CNV 24 47 81
DEL PEAK 17(9Q21.11) WILD-TYPE 116 78 167

Figure S310.  Get High-res Image Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 17(9q21.11)' versus 'CN_CNMF'

P value = 3.41e-16 (Chi-square test), Q value = 1.8e-13

Table S311.  Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 17(9Q21.11) CNV 41 77 17 97 14
DEL PEAK 17(9Q21.11) WILD-TYPE 306 145 55 126 35

Figure S311.  Get High-res Image Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 17(9q21.11)' versus 'METHLYATION_CNMF'

P value = 1.19e-10 (Chi-square test), Q value = 5.1e-08

Table S312.  Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 17(9Q21.11) CNV 38 10 23 54 4 18
DEL PEAK 17(9Q21.11) WILD-TYPE 63 129 70 83 36 79

Figure S312.  Get High-res Image Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 17(9q21.11)' versus 'RPPA_CNMF'

P value = 1.04e-05 (Fisher's exact test), Q value = 0.0028

Table S313.  Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 17(9Q21.11) CNV 65 32 22
DEL PEAK 17(9Q21.11) WILD-TYPE 82 101 95

Figure S313.  Get High-res Image Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 17(9q21.11)' versus 'MRNASEQ_CNMF'

P value = 2.41e-06 (Fisher's exact test), Q value = 0.00072

Table S314.  Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 17(9Q21.11) CNV 86 20 123
DEL PEAK 17(9Q21.11) WILD-TYPE 148 128 323

Figure S314.  Get High-res Image Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 17(9q21.11)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.3e-06 (Fisher's exact test), Q value = 0.0023

Table S315.  Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
DEL PEAK 17(9Q21.11) CNV 35 120 74
DEL PEAK 17(9Q21.11) WILD-TYPE 181 288 130

Figure S315.  Get High-res Image Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 17(9q21.11)' versus 'MIRSEQ_CNMF'

P value = 1.41e-08 (Fisher's exact test), Q value = 5.3e-06

Table S316.  Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 17(9Q21.11) CNV 39 93 102
DEL PEAK 17(9Q21.11) WILD-TYPE 195 299 153

Figure S316.  Get High-res Image Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 17(9q21.11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.33e-13 (Fisher's exact test), Q value = 4.4e-10

Table S317.  Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 17(9Q21.11) CNV 102 36 96
DEL PEAK 17(9Q21.11) WILD-TYPE 260 248 139

Figure S317.  Get High-res Image Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 18(10q23.31)' versus 'MRNA_CNMF'

P value = 4.09e-05 (Chi-square test), Q value = 0.01

Table S318.  Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
DEL PEAK 18(10Q23.31) CNV 36 7 7 45 20 7 22 2
DEL PEAK 18(10Q23.31) WILD-TYPE 88 29 16 50 52 13 81 38

Figure S318.  Get High-res Image Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 18(10q23.31)' versus 'MRNA_CHIERARCHICAL'

P value = 9.57e-05 (Fisher's exact test), Q value = 0.022

Table S319.  Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
DEL PEAK 18(10Q23.31) CNV 26 53 67
DEL PEAK 18(10Q23.31) WILD-TYPE 114 72 181

Figure S319.  Get High-res Image Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 18(10q23.31)' versus 'CN_CNMF'

P value = 3.83e-20 (Chi-square test), Q value = 2.2e-17

Table S320.  Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 18(10Q23.31) CNV 45 72 17 113 14
DEL PEAK 18(10Q23.31) WILD-TYPE 302 150 55 110 35

Figure S320.  Get High-res Image Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 18(10q23.31)' versus 'METHLYATION_CNMF'

P value = 4.75e-12 (Chi-square test), Q value = 2.2e-09

Table S321.  Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 18(10Q23.31) CNV 55 22 23 53 7 15
DEL PEAK 18(10Q23.31) WILD-TYPE 46 117 70 84 33 82

Figure S321.  Get High-res Image Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 18(10q23.31)' versus 'RPPA_CNMF'

P value = 1.9e-07 (Fisher's exact test), Q value = 6.5e-05

Table S322.  Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 18(10Q23.31) CNV 67 30 19
DEL PEAK 18(10Q23.31) WILD-TYPE 80 103 98

Figure S322.  Get High-res Image Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 18(10q23.31)' versus 'RPPA_CHIERARCHICAL'

P value = 7.37e-05 (Fisher's exact test), Q value = 0.018

Table S323.  Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 18(10Q23.31) CNV 45 18 53
DEL PEAK 18(10Q23.31) WILD-TYPE 116 92 73

Figure S323.  Get High-res Image Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 18(10q23.31)' versus 'MRNASEQ_CNMF'

P value = 1.06e-11 (Fisher's exact test), Q value = 4.7e-09

Table S324.  Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 18(10Q23.31) CNV 108 21 115
DEL PEAK 18(10Q23.31) WILD-TYPE 126 127 331

Figure S324.  Get High-res Image Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 18(10q23.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.91e-09 (Fisher's exact test), Q value = 2.7e-06

Table S325.  Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
DEL PEAK 18(10Q23.31) CNV 39 113 92
DEL PEAK 18(10Q23.31) WILD-TYPE 177 295 112

Figure S325.  Get High-res Image Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 18(10q23.31)' versus 'MIRSEQ_CNMF'

P value = 5.47e-09 (Fisher's exact test), Q value = 2.2e-06

Table S326.  Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 18(10Q23.31) CNV 49 92 111
DEL PEAK 18(10Q23.31) WILD-TYPE 185 300 144

Figure S326.  Get High-res Image Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 18(10q23.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.97e-09 (Fisher's exact test), Q value = 1.6e-06

Table S327.  Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 18(10Q23.31) CNV 97 53 102
DEL PEAK 18(10Q23.31) WILD-TYPE 265 231 133

Figure S327.  Get High-res Image Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 19(10q26.3)' versus 'MRNA_CNMF'

P value = 2.88e-08 (Chi-square test), Q value = 1.1e-05

Table S328.  Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
DEL PEAK 19(10Q26.3) CNV 38 9 8 52 21 6 16 3
DEL PEAK 19(10Q26.3) WILD-TYPE 86 27 15 43 51 14 87 37

Figure S328.  Get High-res Image Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 19(10q26.3)' versus 'MRNA_CHIERARCHICAL'

P value = 1.49e-07 (Fisher's exact test), Q value = 5.2e-05

Table S329.  Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
DEL PEAK 19(10Q26.3) CNV 22 59 72
DEL PEAK 19(10Q26.3) WILD-TYPE 118 66 176

Figure S329.  Get High-res Image Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 19(10q26.3)' versus 'CN_CNMF'

P value = 2.23e-22 (Chi-square test), Q value = 1.3e-19

Table S330.  Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 19(10Q26.3) CNV 45 77 15 116 11
DEL PEAK 19(10Q26.3) WILD-TYPE 302 145 57 107 38

Figure S330.  Get High-res Image Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 19(10q26.3)' versus 'METHLYATION_CNMF'

P value = 2.07e-12 (Chi-square test), Q value = 9.5e-10

Table S331.  Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 19(10Q26.3) CNV 57 18 28 45 8 17
DEL PEAK 19(10Q26.3) WILD-TYPE 44 121 65 92 32 80

Figure S331.  Get High-res Image Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 19(10q26.3)' versus 'RPPA_CNMF'

P value = 3.06e-08 (Fisher's exact test), Q value = 1.1e-05

Table S332.  Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 19(10Q26.3) CNV 72 27 24
DEL PEAK 19(10Q26.3) WILD-TYPE 75 106 93

Figure S332.  Get High-res Image Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 19(10q26.3)' versus 'RPPA_CHIERARCHICAL'

P value = 8.25e-07 (Fisher's exact test), Q value = 0.00026

Table S333.  Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 19(10Q26.3) CNV 45 18 60
DEL PEAK 19(10Q26.3) WILD-TYPE 116 92 66

Figure S333.  Get High-res Image Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 19(10q26.3)' versus 'MRNASEQ_CNMF'

P value = 1.77e-15 (Fisher's exact test), Q value = 9.2e-13

Table S334.  Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 19(10Q26.3) CNV 115 18 114
DEL PEAK 19(10Q26.3) WILD-TYPE 119 130 332

Figure S334.  Get High-res Image Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 19(10q26.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.17e-12 (Fisher's exact test), Q value = 5.4e-10

Table S335.  Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
DEL PEAK 19(10Q26.3) CNV 34 114 99
DEL PEAK 19(10Q26.3) WILD-TYPE 182 294 105

Figure S335.  Get High-res Image Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 19(10q26.3)' versus 'MIRSEQ_CNMF'

P value = 7.81e-12 (Fisher's exact test), Q value = 3.5e-09

Table S336.  Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 19(10Q26.3) CNV 44 92 117
DEL PEAK 19(10Q26.3) WILD-TYPE 190 300 138

Figure S336.  Get High-res Image Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 19(10q26.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.48e-15 (Fisher's exact test), Q value = 1.8e-12

Table S337.  Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 19(10Q26.3) CNV 100 42 111
DEL PEAK 19(10Q26.3) WILD-TYPE 262 242 124

Figure S337.  Get High-res Image Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 20(11p15.5)' versus 'MRNA_CNMF'

P value = 1.34e-06 (Chi-square test), Q value = 0.00042

Table S338.  Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
DEL PEAK 20(11P15.5) CNV 33 8 3 45 32 7 15 8
DEL PEAK 20(11P15.5) WILD-TYPE 91 28 20 50 40 13 88 32

Figure S338.  Get High-res Image Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 20(11p15.5)' versus 'MRNA_CHIERARCHICAL'

P value = 1.62e-07 (Fisher's exact test), Q value = 5.6e-05

Table S339.  Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
DEL PEAK 20(11P15.5) CNV 29 62 60
DEL PEAK 20(11P15.5) WILD-TYPE 111 63 188

Figure S339.  Get High-res Image Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 20(11p15.5)' versus 'CN_CNMF'

P value = 5.01e-36 (Chi-square test), Q value = 3.1e-33

Table S340.  Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 20(11P15.5) CNV 35 69 15 134 9
DEL PEAK 20(11P15.5) WILD-TYPE 312 153 57 89 40

Figure S340.  Get High-res Image Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 20(11p15.5)' versus 'METHLYATION_CNMF'

P value = 1.96e-12 (Chi-square test), Q value = 9e-10

Table S341.  Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 20(11P15.5) CNV 54 15 27 42 10 14
DEL PEAK 20(11P15.5) WILD-TYPE 47 124 66 95 30 83

Figure S341.  Get High-res Image Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 20(11p15.5)' versus 'RPPA_CNMF'

P value = 1.27e-09 (Fisher's exact test), Q value = 5.1e-07

Table S342.  Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 20(11P15.5) CNV 76 26 25
DEL PEAK 20(11P15.5) WILD-TYPE 71 107 92

Figure S342.  Get High-res Image Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 20(11p15.5)' versus 'RPPA_CHIERARCHICAL'

P value = 1.65e-06 (Fisher's exact test), Q value = 5e-04

Table S343.  Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 20(11P15.5) CNV 38 26 63
DEL PEAK 20(11P15.5) WILD-TYPE 123 84 63

Figure S343.  Get High-res Image Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 20(11p15.5)' versus 'MRNASEQ_CNMF'

P value = 8.07e-18 (Fisher's exact test), Q value = 4.4e-15

Table S344.  Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 20(11P15.5) CNV 121 22 100
DEL PEAK 20(11P15.5) WILD-TYPE 113 126 346

Figure S344.  Get High-res Image Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 20(11p15.5)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.07e-13 (Fisher's exact test), Q value = 2.4e-10

Table S345.  Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
DEL PEAK 20(11P15.5) CNV 42 98 103
DEL PEAK 20(11P15.5) WILD-TYPE 174 310 101

Figure S345.  Get High-res Image Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 20(11p15.5)' versus 'MIRSEQ_CNMF'

P value = 3.87e-15 (Fisher's exact test), Q value = 2e-12

Table S346.  Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 20(11P15.5) CNV 43 85 123
DEL PEAK 20(11P15.5) WILD-TYPE 191 307 132

Figure S346.  Get High-res Image Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 20(11p15.5)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.42e-16 (Fisher's exact test), Q value = 7.6e-14

Table S347.  Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 20(11P15.5) CNV 93 43 115
DEL PEAK 20(11P15.5) WILD-TYPE 269 241 120

Figure S347.  Get High-res Image Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 21(11q13.1)' versus 'CN_CNMF'

P value = 3.51e-17 (Chi-square test), Q value = 1.9e-14

Table S348.  Gene #48: 'Del Peak 21(11q13.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 21(11Q13.1) CNV 30 88 23 44 9
DEL PEAK 21(11Q13.1) WILD-TYPE 317 134 49 179 40

Figure S348.  Get High-res Image Gene #48: 'Del Peak 21(11q13.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 21(11q13.1)' versus 'METHLYATION_CNMF'

P value = 4.39e-06 (Chi-square test), Q value = 0.0013

Table S349.  Gene #48: 'Del Peak 21(11q13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 21(11Q13.1) CNV 18 19 26 47 7 8
DEL PEAK 21(11Q13.1) WILD-TYPE 83 120 67 90 33 89

Figure S349.  Get High-res Image Gene #48: 'Del Peak 21(11q13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 22(11q23.2)' versus 'MRNA_CNMF'

P value = 2.08e-08 (Chi-square test), Q value = 7.7e-06

Table S350.  Gene #49: 'Del Peak 22(11q23.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
DEL PEAK 22(11Q23.2) CNV 92 21 12 36 37 11 33 22
DEL PEAK 22(11Q23.2) WILD-TYPE 32 15 11 59 35 9 70 18

Figure S350.  Get High-res Image Gene #49: 'Del Peak 22(11q23.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 22(11q23.2)' versus 'CN_CNMF'

P value = 3.22e-42 (Chi-square test), Q value = 2e-39

Table S351.  Gene #49: 'Del Peak 22(11q23.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 22(11Q23.2) CNV 93 193 35 111 17
DEL PEAK 22(11Q23.2) WILD-TYPE 254 29 37 112 32

Figure S351.  Get High-res Image Gene #49: 'Del Peak 22(11q23.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 22(11q23.2)' versus 'METHLYATION_CNMF'

P value = 7.68e-12 (Chi-square test), Q value = 3.4e-09

Table S352.  Gene #49: 'Del Peak 22(11q23.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 22(11Q23.2) CNV 41 49 57 98 20 29
DEL PEAK 22(11Q23.2) WILD-TYPE 60 90 36 39 20 68

Figure S352.  Get High-res Image Gene #49: 'Del Peak 22(11q23.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 22(11q23.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000137 (Fisher's exact test), Q value = 0.031

Table S353.  Gene #49: 'Del Peak 22(11q23.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 22(11Q23.2) CNV 209 125 100
DEL PEAK 22(11Q23.2) WILD-TYPE 153 159 135

Figure S353.  Get High-res Image Gene #49: 'Del Peak 22(11q23.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 23(11q25)' versus 'MRNA_CNMF'

P value = 0.000243 (Chi-square test), Q value = 0.052

Table S354.  Gene #50: 'Del Peak 23(11q25)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
DEL PEAK 23(11Q25) CNV 79 20 10 44 37 12 31 20
DEL PEAK 23(11Q25) WILD-TYPE 45 16 13 51 35 8 72 20

Figure S354.  Get High-res Image Gene #50: 'Del Peak 23(11q25)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 23(11q25)' versus 'CN_CNMF'

P value = 6.15e-38 (Chi-square test), Q value = 3.8e-35

Table S355.  Gene #50: 'Del Peak 23(11q25)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 23(11Q25) CNV 81 177 34 114 15
DEL PEAK 23(11Q25) WILD-TYPE 266 45 38 109 34

Figure S355.  Get High-res Image Gene #50: 'Del Peak 23(11q25)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 23(11q25)' versus 'METHLYATION_CNMF'

P value = 9.89e-09 (Chi-square test), Q value = 3.8e-06

Table S356.  Gene #50: 'Del Peak 23(11q25)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 23(11Q25) CNV 46 42 53 86 16 28
DEL PEAK 23(11Q25) WILD-TYPE 55 97 40 51 24 69

Figure S356.  Get High-res Image Gene #50: 'Del Peak 23(11q25)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 24(12p13.1)' versus 'CN_CNMF'

P value = 0.000979 (Chi-square test), Q value = 0.18

Table S357.  Gene #51: 'Del Peak 24(12p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 24(12P13.1) CNV 40 46 11 54 6
DEL PEAK 24(12P13.1) WILD-TYPE 307 176 61 169 43

Figure S357.  Get High-res Image Gene #51: 'Del Peak 24(12p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 24(12p13.1)' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.046

Table S358.  Gene #51: 'Del Peak 24(12p13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 24(12P13.1) CNV 63 19 67
DEL PEAK 24(12P13.1) WILD-TYPE 171 129 379

Figure S358.  Get High-res Image Gene #51: 'Del Peak 24(12p13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 24(12p13.1)' versus 'MIRSEQ_CNMF'

P value = 8.03e-05 (Fisher's exact test), Q value = 0.019

Table S359.  Gene #51: 'Del Peak 24(12p13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 24(12P13.1) CNV 30 56 67
DEL PEAK 24(12P13.1) WILD-TYPE 204 336 188

Figure S359.  Get High-res Image Gene #51: 'Del Peak 24(12p13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 24(12p13.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.68e-06 (Fisher's exact test), Q value = 0.0024

Table S360.  Gene #51: 'Del Peak 24(12p13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 24(12P13.1) CNV 60 30 63
DEL PEAK 24(12P13.1) WILD-TYPE 302 254 172

Figure S360.  Get High-res Image Gene #51: 'Del Peak 24(12p13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 25(12q24.21)' versus 'MRNA_CNMF'

P value = 9.6e-11 (Chi-square test), Q value = 4.1e-08

Table S361.  Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
DEL PEAK 25(12Q24.21) CNV 17 5 3 41 22 3 4 5
DEL PEAK 25(12Q24.21) WILD-TYPE 107 31 20 54 50 17 99 35

Figure S361.  Get High-res Image Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 25(12q24.21)' versus 'MRNA_CHIERARCHICAL'

P value = 2.5e-10 (Fisher's exact test), Q value = 1e-07

Table S362.  Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
DEL PEAK 25(12Q24.21) CNV 14 51 35
DEL PEAK 25(12Q24.21) WILD-TYPE 126 74 213

Figure S362.  Get High-res Image Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 25(12q24.21)' versus 'CN_CNMF'

P value = 2.33e-15 (Chi-square test), Q value = 1.2e-12

Table S363.  Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 25(12Q24.21) CNV 38 30 16 85 5
DEL PEAK 25(12Q24.21) WILD-TYPE 309 192 56 138 44

Figure S363.  Get High-res Image Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 25(12q24.21)' versus 'METHLYATION_CNMF'

P value = 2.68e-14 (Chi-square test), Q value = 1.3e-11

Table S364.  Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 25(12Q24.21) CNV 48 13 14 20 2 14
DEL PEAK 25(12Q24.21) WILD-TYPE 53 126 79 117 38 83

Figure S364.  Get High-res Image Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 25(12q24.21)' versus 'RPPA_CNMF'

P value = 0.000209 (Fisher's exact test), Q value = 0.046

Table S365.  Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 25(12Q24.21) CNV 44 14 21
DEL PEAK 25(12Q24.21) WILD-TYPE 103 119 96

Figure S365.  Get High-res Image Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 25(12q24.21)' versus 'RPPA_CHIERARCHICAL'

P value = 1.05e-06 (Fisher's exact test), Q value = 0.00033

Table S366.  Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 25(12Q24.21) CNV 22 12 45
DEL PEAK 25(12Q24.21) WILD-TYPE 139 98 81

Figure S366.  Get High-res Image Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 25(12q24.21)' versus 'MRNASEQ_CNMF'

P value = 6.55e-16 (Fisher's exact test), Q value = 3.5e-13

Table S367.  Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 25(12Q24.21) CNV 86 15 49
DEL PEAK 25(12Q24.21) WILD-TYPE 148 133 397

Figure S367.  Get High-res Image Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 25(12q24.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.47e-13 (Fisher's exact test), Q value = 1.6e-10

Table S368.  Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
DEL PEAK 25(12Q24.21) CNV 23 52 75
DEL PEAK 25(12Q24.21) WILD-TYPE 193 356 129

Figure S368.  Get High-res Image Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 25(12q24.21)' versus 'MIRSEQ_CNMF'

P value = 1.17e-08 (Fisher's exact test), Q value = 4.5e-06

Table S369.  Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 25(12Q24.21) CNV 32 53 81
DEL PEAK 25(12Q24.21) WILD-TYPE 202 339 174

Figure S369.  Get High-res Image Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 25(12q24.21)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.27e-13 (Fisher's exact test), Q value = 1.6e-10

Table S370.  Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 25(12Q24.21) CNV 47 34 85
DEL PEAK 25(12Q24.21) WILD-TYPE 315 250 150

Figure S370.  Get High-res Image Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 26(13q14.2)' versus 'MRNA_CNMF'

P value = 2.15e-05 (Chi-square test), Q value = 0.0057

Table S371.  Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
DEL PEAK 26(13Q14.2) CNV 74 13 7 55 39 9 31 13
DEL PEAK 26(13Q14.2) WILD-TYPE 50 23 16 40 33 11 72 27

Figure S371.  Get High-res Image Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 26(13q14.2)' versus 'MRNA_CHIERARCHICAL'

P value = 4.23e-05 (Fisher's exact test), Q value = 0.011

Table S372.  Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
DEL PEAK 26(13Q14.2) CNV 46 75 120
DEL PEAK 26(13Q14.2) WILD-TYPE 94 50 128

Figure S372.  Get High-res Image Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 26(13q14.2)' versus 'CN_CNMF'

P value = 7.07e-28 (Chi-square test), Q value = 4.3e-25

Table S373.  Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 26(13Q14.2) CNV 73 138 41 130 31
DEL PEAK 26(13Q14.2) WILD-TYPE 274 84 31 93 18

Figure S373.  Get High-res Image Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 26(13q14.2)' versus 'METHLYATION_CNMF'

P value = 1.81e-08 (Chi-square test), Q value = 6.8e-06

Table S374.  Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 26(13Q14.2) CNV 61 39 50 75 11 32
DEL PEAK 26(13Q14.2) WILD-TYPE 40 100 43 62 29 65

Figure S374.  Get High-res Image Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 26(13q14.2)' versus 'MRNASEQ_CNMF'

P value = 1.55e-07 (Fisher's exact test), Q value = 5.4e-05

Table S375.  Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 26(13Q14.2) CNV 136 43 207
DEL PEAK 26(13Q14.2) WILD-TYPE 98 105 239

Figure S375.  Get High-res Image Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 26(13q14.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.39e-06 (Fisher's exact test), Q value = 0.0018

Table S376.  Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
DEL PEAK 26(13Q14.2) CNV 74 194 118
DEL PEAK 26(13Q14.2) WILD-TYPE 142 214 86

Figure S376.  Get High-res Image Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 26(13q14.2)' versus 'MIRSEQ_CNMF'

P value = 3.86e-10 (Fisher's exact test), Q value = 1.6e-07

Table S377.  Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 26(13Q14.2) CNV 69 182 150
DEL PEAK 26(13Q14.2) WILD-TYPE 165 210 105

Figure S377.  Get High-res Image Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 26(13q14.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.12e-07 (Fisher's exact test), Q value = 3.9e-05

Table S378.  Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 26(13Q14.2) CNV 172 94 135
DEL PEAK 26(13Q14.2) WILD-TYPE 190 190 100

Figure S378.  Get High-res Image Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 27(14q24.3)' versus 'MRNA_CNMF'

P value = 4e-13 (Chi-square test), Q value = 1.9e-10

Table S379.  Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
DEL PEAK 27(14Q24.3) CNV 51 8 4 57 22 10 9 8
DEL PEAK 27(14Q24.3) WILD-TYPE 73 28 19 38 50 10 94 32

Figure S379.  Get High-res Image Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 27(14q24.3)' versus 'MRNA_CHIERARCHICAL'

P value = 1.56e-08 (Fisher's exact test), Q value = 5.9e-06

Table S380.  Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
DEL PEAK 27(14Q24.3) CNV 33 69 67
DEL PEAK 27(14Q24.3) WILD-TYPE 107 56 181

Figure S380.  Get High-res Image Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 27(14q24.3)' versus 'CN_CNMF'

P value = 8.6e-37 (Chi-square test), Q value = 5.3e-34

Table S381.  Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 27(14Q24.3) CNV 42 76 14 143 19
DEL PEAK 27(14Q24.3) WILD-TYPE 305 146 58 80 30

Figure S381.  Get High-res Image Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 27(14q24.3)' versus 'METHLYATION_CNMF'

P value = 3.5e-14 (Chi-square test), Q value = 1.7e-11

Table S382.  Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 27(14Q24.3) CNV 60 16 28 53 8 22
DEL PEAK 27(14Q24.3) WILD-TYPE 41 123 65 84 32 75

Figure S382.  Get High-res Image Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 27(14q24.3)' versus 'RPPA_CNMF'

P value = 5.29e-07 (Fisher's exact test), Q value = 0.00017

Table S383.  Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 27(14Q24.3) CNV 74 29 31
DEL PEAK 27(14Q24.3) WILD-TYPE 73 104 86

Figure S383.  Get High-res Image Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 27(14q24.3)' versus 'RPPA_CHIERARCHICAL'

P value = 5.53e-06 (Fisher's exact test), Q value = 0.0016

Table S384.  Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 27(14Q24.3) CNV 45 25 64
DEL PEAK 27(14Q24.3) WILD-TYPE 116 85 62

Figure S384.  Get High-res Image Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 27(14q24.3)' versus 'MRNASEQ_CNMF'

P value = 3.86e-15 (Fisher's exact test), Q value = 2e-12

Table S385.  Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 27(14Q24.3) CNV 124 25 120
DEL PEAK 27(14Q24.3) WILD-TYPE 110 123 326

Figure S385.  Get High-res Image Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 27(14q24.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.04e-13 (Fisher's exact test), Q value = 1.5e-10

Table S386.  Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
DEL PEAK 27(14Q24.3) CNV 41 120 108
DEL PEAK 27(14Q24.3) WILD-TYPE 175 288 96

Figure S386.  Get High-res Image Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 27(14q24.3)' versus 'MIRSEQ_CNMF'

P value = 5.44e-18 (Fisher's exact test), Q value = 3e-15

Table S387.  Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 27(14Q24.3) CNV 51 91 138
DEL PEAK 27(14Q24.3) WILD-TYPE 183 301 117

Figure S387.  Get High-res Image Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 27(14q24.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.52e-16 (Fisher's exact test), Q value = 8.1e-14

Table S388.  Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 27(14Q24.3) CNV 102 53 125
DEL PEAK 27(14Q24.3) WILD-TYPE 260 231 110

Figure S388.  Get High-res Image Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 28(15q13.1)' versus 'MRNA_CNMF'

P value = 3.46e-07 (Chi-square test), Q value = 0.00012

Table S389.  Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
DEL PEAK 28(15Q13.1) CNV 41 11 7 56 33 10 22 7
DEL PEAK 28(15Q13.1) WILD-TYPE 83 25 16 39 39 10 81 33

Figure S389.  Get High-res Image Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 28(15q13.1)' versus 'MRNA_CHIERARCHICAL'

P value = 7.57e-08 (Fisher's exact test), Q value = 2.7e-05

Table S390.  Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
DEL PEAK 28(15Q13.1) CNV 29 68 90
DEL PEAK 28(15Q13.1) WILD-TYPE 111 57 158

Figure S390.  Get High-res Image Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 28(15q13.1)' versus 'CN_CNMF'

P value = 6.74e-31 (Chi-square test), Q value = 4.1e-28

Table S391.  Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 28(15Q13.1) CNV 56 68 35 143 13
DEL PEAK 28(15Q13.1) WILD-TYPE 291 154 37 80 36

Figure S391.  Get High-res Image Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 28(15q13.1)' versus 'METHLYATION_CNMF'

P value = 1.2e-11 (Chi-square test), Q value = 5.3e-09

Table S392.  Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 28(15Q13.1) CNV 63 25 30 52 8 25
DEL PEAK 28(15Q13.1) WILD-TYPE 38 114 63 85 32 72

Figure S392.  Get High-res Image Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 28(15q13.1)' versus 'RPPA_CNMF'

P value = 0.000193 (Fisher's exact test), Q value = 0.043

Table S393.  Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 28(15Q13.1) CNV 76 39 38
DEL PEAK 28(15Q13.1) WILD-TYPE 71 94 79

Figure S393.  Get High-res Image Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 28(15q13.1)' versus 'RPPA_CHIERARCHICAL'

P value = 2.32e-05 (Fisher's exact test), Q value = 0.0061

Table S394.  Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 28(15Q13.1) CNV 54 30 69
DEL PEAK 28(15Q13.1) WILD-TYPE 107 80 57

Figure S394.  Get High-res Image Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 28(15q13.1)' versus 'MRNASEQ_CNMF'

P value = 6.07e-15 (Fisher's exact test), Q value = 3.1e-12

Table S395.  Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 28(15Q13.1) CNV 127 24 137
DEL PEAK 28(15Q13.1) WILD-TYPE 107 124 309

Figure S395.  Get High-res Image Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 28(15q13.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.32e-14 (Fisher's exact test), Q value = 1.2e-11

Table S396.  Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
DEL PEAK 28(15Q13.1) CNV 44 129 115
DEL PEAK 28(15Q13.1) WILD-TYPE 172 279 89

Figure S396.  Get High-res Image Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 28(15q13.1)' versus 'MIRSEQ_CNMF'

P value = 6.32e-19 (Fisher's exact test), Q value = 3.6e-16

Table S397.  Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 28(15Q13.1) CNV 47 110 145
DEL PEAK 28(15Q13.1) WILD-TYPE 187 282 110

Figure S397.  Get High-res Image Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 28(15q13.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.96e-18 (Fisher's exact test), Q value = 1.1e-15

Table S398.  Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 28(15Q13.1) CNV 112 56 134
DEL PEAK 28(15Q13.1) WILD-TYPE 250 228 101

Figure S398.  Get High-res Image Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 29(16q24.3)' versus 'MRNA_CNMF'

P value = 1.6e-16 (Chi-square test), Q value = 8.6e-14

Table S399.  Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
DEL PEAK 29(16Q24.3) CNV 86 26 18 26 45 13 88 34
DEL PEAK 29(16Q24.3) WILD-TYPE 38 10 5 69 27 7 15 6

Figure S399.  Get High-res Image Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 29(16q24.3)' versus 'MRNA_CHIERARCHICAL'

P value = 2.51e-14 (Fisher's exact test), Q value = 1.3e-11

Table S400.  Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
DEL PEAK 29(16Q24.3) CNV 110 45 181
DEL PEAK 29(16Q24.3) WILD-TYPE 30 80 67

Figure S400.  Get High-res Image Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 29(16q24.3)' versus 'CN_CNMF'

P value = 1.66e-14 (Chi-square test), Q value = 8.3e-12

Table S401.  Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 29(16Q24.3) CNV 244 153 59 93 38
DEL PEAK 29(16Q24.3) WILD-TYPE 103 69 13 130 11

Figure S401.  Get High-res Image Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 29(16q24.3)' versus 'METHLYATION_CNMF'

P value = 4.47e-13 (Chi-square test), Q value = 2.1e-10

Table S402.  Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 29(16Q24.3) CNV 37 115 72 83 19 57
DEL PEAK 29(16Q24.3) WILD-TYPE 64 24 21 54 21 40

Figure S402.  Get High-res Image Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 29(16q24.3)' versus 'RPPA_CNMF'

P value = 1.14e-09 (Fisher's exact test), Q value = 4.6e-07

Table S403.  Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 29(16Q24.3) CNV 63 103 84
DEL PEAK 29(16Q24.3) WILD-TYPE 84 30 33

Figure S403.  Get High-res Image Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 29(16q24.3)' versus 'RPPA_CHIERARCHICAL'

P value = 3.45e-11 (Fisher's exact test), Q value = 1.5e-08

Table S404.  Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 29(16Q24.3) CNV 119 83 48
DEL PEAK 29(16Q24.3) WILD-TYPE 42 27 78

Figure S404.  Get High-res Image Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 29(16q24.3)' versus 'MRNASEQ_CNMF'

P value = 2.82e-16 (Fisher's exact test), Q value = 1.5e-13

Table S405.  Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 29(16Q24.3) CNV 99 115 322
DEL PEAK 29(16Q24.3) WILD-TYPE 135 33 124

Figure S405.  Get High-res Image Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 29(16q24.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.62e-21 (Fisher's exact test), Q value = 2.6e-18

Table S406.  Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
DEL PEAK 29(16Q24.3) CNV 173 287 76
DEL PEAK 29(16Q24.3) WILD-TYPE 43 121 128

Figure S406.  Get High-res Image Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 29(16q24.3)' versus 'MIRSEQ_CNMF'

P value = 9.22e-15 (Fisher's exact test), Q value = 4.7e-12

Table S407.  Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 29(16Q24.3) CNV 168 288 112
DEL PEAK 29(16Q24.3) WILD-TYPE 66 104 143

Figure S407.  Get High-res Image Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 29(16q24.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.49e-22 (Fisher's exact test), Q value = 4.9e-19

Table S408.  Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 29(16Q24.3) CNV 239 233 96
DEL PEAK 29(16Q24.3) WILD-TYPE 123 51 139

Figure S408.  Get High-res Image Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 30(17p12)' versus 'MRNA_CNMF'

P value = 2.14e-10 (Chi-square test), Q value = 9e-08

Table S409.  Gene #57: 'Del Peak 30(17p12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
DEL PEAK 30(17P12) CNV 80 27 14 60 60 15 32 24
DEL PEAK 30(17P12) WILD-TYPE 44 9 9 35 12 5 71 16

Figure S409.  Get High-res Image Gene #57: 'Del Peak 30(17p12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 30(17p12)' versus 'CN_CNMF'

P value = 9.33e-23 (Chi-square test), Q value = 5.5e-20

Table S410.  Gene #57: 'Del Peak 30(17p12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 30(17P12) CNV 142 170 35 172 27
DEL PEAK 30(17P12) WILD-TYPE 205 52 37 51 22

Figure S410.  Get High-res Image Gene #57: 'Del Peak 30(17p12)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 30(17p12)' versus 'METHLYATION_CNMF'

P value = 7.4e-07 (Chi-square test), Q value = 0.00024

Table S411.  Gene #57: 'Del Peak 30(17p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 30(17P12) CNV 61 62 64 103 21 46
DEL PEAK 30(17P12) WILD-TYPE 40 77 29 34 19 51

Figure S411.  Get High-res Image Gene #57: 'Del Peak 30(17p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 30(17p12)' versus 'RPPA_CNMF'

P value = 8.07e-05 (Fisher's exact test), Q value = 0.019

Table S412.  Gene #57: 'Del Peak 30(17p12)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 30(17P12) CNV 109 67 65
DEL PEAK 30(17P12) WILD-TYPE 38 66 52

Figure S412.  Get High-res Image Gene #57: 'Del Peak 30(17p12)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 30(17p12)' versus 'MRNASEQ_CNMF'

P value = 0.000586 (Fisher's exact test), Q value = 0.11

Table S413.  Gene #57: 'Del Peak 30(17p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 30(17P12) CNV 166 83 253
DEL PEAK 30(17P12) WILD-TYPE 68 65 193

Figure S413.  Get High-res Image Gene #57: 'Del Peak 30(17p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 30(17p12)' versus 'MIRSEQ_CNMF'

P value = 0.000255 (Fisher's exact test), Q value = 0.054

Table S414.  Gene #57: 'Del Peak 30(17p12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 30(17P12) CNV 133 220 181
DEL PEAK 30(17P12) WILD-TYPE 101 172 74

Figure S414.  Get High-res Image Gene #57: 'Del Peak 30(17p12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 30(17p12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000127 (Fisher's exact test), Q value = 0.029

Table S415.  Gene #57: 'Del Peak 30(17p12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 30(17P12) CNV 219 149 166
DEL PEAK 30(17P12) WILD-TYPE 143 135 69

Figure S415.  Get High-res Image Gene #57: 'Del Peak 30(17p12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 31(17q21.31)' versus 'MRNA_CNMF'

P value = 1.07e-14 (Chi-square test), Q value = 5.4e-12

Table S416.  Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
DEL PEAK 31(17Q21.31) CNV 29 16 7 50 50 9 13 16
DEL PEAK 31(17Q21.31) WILD-TYPE 95 20 16 45 22 11 90 24

Figure S416.  Get High-res Image Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 31(17q21.31)' versus 'MRNA_CHIERARCHICAL'

P value = 3.91e-07 (Fisher's exact test), Q value = 0.00013

Table S417.  Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
DEL PEAK 31(17Q21.31) CNV 45 72 73
DEL PEAK 31(17Q21.31) WILD-TYPE 95 53 175

Figure S417.  Get High-res Image Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 31(17q21.31)' versus 'CN_CNMF'

P value = 5.42e-22 (Chi-square test), Q value = 3.2e-19

Table S418.  Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 31(17Q21.31) CNV 79 69 18 139 10
DEL PEAK 31(17Q21.31) WILD-TYPE 268 153 54 84 39

Figure S418.  Get High-res Image Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 31(17q21.31)' versus 'METHLYATION_CNMF'

P value = 1.19e-11 (Chi-square test), Q value = 5.3e-09

Table S419.  Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 31(17Q21.31) CNV 60 19 36 39 11 28
DEL PEAK 31(17Q21.31) WILD-TYPE 41 120 57 98 29 69

Figure S419.  Get High-res Image Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 31(17q21.31)' versus 'RPPA_CNMF'

P value = 1.86e-11 (Fisher's exact test), Q value = 8.2e-09

Table S420.  Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 31(17Q21.31) CNV 87 25 44
DEL PEAK 31(17Q21.31) WILD-TYPE 60 108 73

Figure S420.  Get High-res Image Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 31(17q21.31)' versus 'RPPA_CHIERARCHICAL'

P value = 3.12e-11 (Fisher's exact test), Q value = 1.4e-08

Table S421.  Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 31(17Q21.31) CNV 42 33 81
DEL PEAK 31(17Q21.31) WILD-TYPE 119 77 45

Figure S421.  Get High-res Image Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 31(17q21.31)' versus 'MRNASEQ_CNMF'

P value = 2.86e-21 (Fisher's exact test), Q value = 1.6e-18

Table S422.  Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 31(17Q21.31) CNV 144 41 109
DEL PEAK 31(17Q21.31) WILD-TYPE 90 107 337

Figure S422.  Get High-res Image Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 31(17q21.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.32e-17 (Fisher's exact test), Q value = 4.5e-14

Table S423.  Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
DEL PEAK 31(17Q21.31) CNV 64 106 124
DEL PEAK 31(17Q21.31) WILD-TYPE 152 302 80

Figure S423.  Get High-res Image Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 31(17q21.31)' versus 'MIRSEQ_CNMF'

P value = 1.14e-12 (Fisher's exact test), Q value = 5.3e-10

Table S424.  Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 31(17Q21.31) CNV 69 102 137
DEL PEAK 31(17Q21.31) WILD-TYPE 165 290 118

Figure S424.  Get High-res Image Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 31(17q21.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.76e-11 (Fisher's exact test), Q value = 7.8e-09

Table S425.  Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 31(17Q21.31) CNV 110 72 126
DEL PEAK 31(17Q21.31) WILD-TYPE 252 212 109

Figure S425.  Get High-res Image Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 32(18q23)' versus 'MRNA_CNMF'

P value = 0.000347 (Chi-square test), Q value = 0.071

Table S426.  Gene #59: 'Del Peak 32(18q23)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
DEL PEAK 32(18Q23) CNV 40 13 4 36 37 6 19 9
DEL PEAK 32(18Q23) WILD-TYPE 84 23 19 59 35 14 84 31

Figure S426.  Get High-res Image Gene #59: 'Del Peak 32(18q23)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 32(18q23)' versus 'CN_CNMF'

P value = 1.32e-15 (Chi-square test), Q value = 7e-13

Table S427.  Gene #59: 'Del Peak 32(18q23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 32(18Q23) CNV 58 84 28 111 12
DEL PEAK 32(18Q23) WILD-TYPE 289 138 44 112 37

Figure S427.  Get High-res Image Gene #59: 'Del Peak 32(18q23)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 32(18q23)' versus 'METHLYATION_CNMF'

P value = 1.2e-08 (Chi-square test), Q value = 4.6e-06

Table S428.  Gene #59: 'Del Peak 32(18q23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 32(18Q23) CNV 40 25 47 59 9 19
DEL PEAK 32(18Q23) WILD-TYPE 61 114 46 78 31 78

Figure S428.  Get High-res Image Gene #59: 'Del Peak 32(18q23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 32(18q23)' versus 'MRNASEQ_CNMF'

P value = 2.54e-05 (Fisher's exact test), Q value = 0.0066

Table S429.  Gene #59: 'Del Peak 32(18q23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 32(18Q23) CNV 102 33 134
DEL PEAK 32(18Q23) WILD-TYPE 132 115 312

Figure S429.  Get High-res Image Gene #59: 'Del Peak 32(18q23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 32(18q23)' versus 'MIRSEQ_CNMF'

P value = 0.000375 (Fisher's exact test), Q value = 0.076

Table S430.  Gene #59: 'Del Peak 32(18q23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 32(18Q23) CNV 60 120 107
DEL PEAK 32(18Q23) WILD-TYPE 174 272 148

Figure S430.  Get High-res Image Gene #59: 'Del Peak 32(18q23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 32(18q23)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000143 (Fisher's exact test), Q value = 0.032

Table S431.  Gene #59: 'Del Peak 32(18q23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 32(18Q23) CNV 113 73 101
DEL PEAK 32(18Q23) WILD-TYPE 249 211 134

Figure S431.  Get High-res Image Gene #59: 'Del Peak 32(18q23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 33(19p13.3)' versus 'MRNA_CNMF'

P value = 5.99e-11 (Chi-square test), Q value = 2.6e-08

Table S432.  Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
DEL PEAK 33(19P13.3) CNV 53 11 6 53 37 6 12 6
DEL PEAK 33(19P13.3) WILD-TYPE 71 25 17 42 35 14 91 34

Figure S432.  Get High-res Image Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 33(19p13.3)' versus 'MRNA_CHIERARCHICAL'

P value = 4.57e-08 (Fisher's exact test), Q value = 1.7e-05

Table S433.  Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
DEL PEAK 33(19P13.3) CNV 26 65 93
DEL PEAK 33(19P13.3) WILD-TYPE 114 60 155

Figure S433.  Get High-res Image Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 33(19p13.3)' versus 'CN_CNMF'

P value = 1.25e-44 (Chi-square test), Q value = 7.9e-42

Table S434.  Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 33(19P13.3) CNV 30 112 11 136 16
DEL PEAK 33(19P13.3) WILD-TYPE 317 110 61 87 33

Figure S434.  Get High-res Image Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 33(19p13.3)' versus 'METHLYATION_CNMF'

P value = 6.53e-18 (Chi-square test), Q value = 3.6e-15

Table S435.  Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 33(19P13.3) CNV 52 9 22 67 6 24
DEL PEAK 33(19P13.3) WILD-TYPE 49 130 71 70 34 73

Figure S435.  Get High-res Image Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 33(19p13.3)' versus 'RPPA_CNMF'

P value = 3.03e-06 (Fisher's exact test), Q value = 0.00089

Table S436.  Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 33(19P13.3) CNV 79 40 31
DEL PEAK 33(19P13.3) WILD-TYPE 68 93 86

Figure S436.  Get High-res Image Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 33(19p13.3)' versus 'RPPA_CHIERARCHICAL'

P value = 3.39e-05 (Fisher's exact test), Q value = 0.0086

Table S437.  Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 33(19P13.3) CNV 51 31 68
DEL PEAK 33(19P13.3) WILD-TYPE 110 79 58

Figure S437.  Get High-res Image Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 33(19p13.3)' versus 'MRNASEQ_CNMF'

P value = 1.19e-12 (Fisher's exact test), Q value = 5.5e-10

Table S438.  Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 33(19P13.3) CNV 121 24 142
DEL PEAK 33(19P13.3) WILD-TYPE 113 124 304

Figure S438.  Get High-res Image Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 33(19p13.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.4e-10 (Fisher's exact test), Q value = 2.2e-07

Table S439.  Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
DEL PEAK 33(19P13.3) CNV 43 142 102
DEL PEAK 33(19P13.3) WILD-TYPE 173 266 102

Figure S439.  Get High-res Image Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 33(19p13.3)' versus 'MIRSEQ_CNMF'

P value = 9.67e-16 (Fisher's exact test), Q value = 5.1e-13

Table S440.  Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 33(19P13.3) CNV 47 111 137
DEL PEAK 33(19P13.3) WILD-TYPE 187 281 118

Figure S440.  Get High-res Image Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 33(19p13.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.54e-17 (Fisher's exact test), Q value = 3.5e-14

Table S441.  Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 33(19P13.3) CNV 124 48 123
DEL PEAK 33(19P13.3) WILD-TYPE 238 236 112

Figure S441.  Get High-res Image Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 34(19q13.32)' versus 'MRNA_CNMF'

P value = 1.57e-06 (Chi-square test), Q value = 0.00048

Table S442.  Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
DEL PEAK 34(19Q13.32) CNV 24 7 3 23 29 1 7 3
DEL PEAK 34(19Q13.32) WILD-TYPE 100 29 20 72 43 19 96 37

Figure S442.  Get High-res Image Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 34(19q13.32)' versus 'MRNA_CHIERARCHICAL'

P value = 8.8e-05 (Fisher's exact test), Q value = 0.021

Table S443.  Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
DEL PEAK 34(19Q13.32) CNV 12 36 49
DEL PEAK 34(19Q13.32) WILD-TYPE 128 89 199

Figure S443.  Get High-res Image Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 34(19q13.32)' versus 'CN_CNMF'

P value = 4.48e-20 (Chi-square test), Q value = 2.6e-17

Table S444.  Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 34(19Q13.32) CNV 22 68 5 79 9
DEL PEAK 34(19Q13.32) WILD-TYPE 325 154 67 144 40

Figure S444.  Get High-res Image Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 34(19q13.32)' versus 'METHLYATION_CNMF'

P value = 1.52e-10 (Chi-square test), Q value = 6.4e-08

Table S445.  Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 34(19Q13.32) CNV 37 6 19 43 5 12
DEL PEAK 34(19Q13.32) WILD-TYPE 64 133 74 94 35 85

Figure S445.  Get High-res Image Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 34(19q13.32)' versus 'RPPA_CNMF'

P value = 0.000783 (Fisher's exact test), Q value = 0.14

Table S446.  Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 34(19Q13.32) CNV 44 20 15
DEL PEAK 34(19Q13.32) WILD-TYPE 103 113 102

Figure S446.  Get High-res Image Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 34(19q13.32)' versus 'RPPA_CHIERARCHICAL'

P value = 4.95e-05 (Fisher's exact test), Q value = 0.012

Table S447.  Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 34(19Q13.32) CNV 27 11 41
DEL PEAK 34(19Q13.32) WILD-TYPE 134 99 85

Figure S447.  Get High-res Image Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 34(19q13.32)' versus 'MRNASEQ_CNMF'

P value = 5.28e-09 (Fisher's exact test), Q value = 2.1e-06

Table S448.  Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 34(19Q13.32) CNV 79 13 82
DEL PEAK 34(19Q13.32) WILD-TYPE 155 135 364

Figure S448.  Get High-res Image Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 34(19q13.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.75e-09 (Fisher's exact test), Q value = 2.6e-06

Table S449.  Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
DEL PEAK 34(19Q13.32) CNV 19 89 66
DEL PEAK 34(19Q13.32) WILD-TYPE 197 319 138

Figure S449.  Get High-res Image Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 34(19q13.32)' versus 'MIRSEQ_CNMF'

P value = 3.6e-10 (Fisher's exact test), Q value = 1.5e-07

Table S450.  Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 34(19Q13.32) CNV 24 66 85
DEL PEAK 34(19Q13.32) WILD-TYPE 210 326 170

Figure S450.  Get High-res Image Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 34(19q13.32)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.78e-12 (Fisher's exact test), Q value = 2.6e-09

Table S451.  Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 34(19Q13.32) CNV 78 22 75
DEL PEAK 34(19Q13.32) WILD-TYPE 284 262 160

Figure S451.  Get High-res Image Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 35(20p13)' versus 'MRNA_CNMF'

P value = 8.81e-06 (Chi-square test), Q value = 0.0024

Table S452.  Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
DEL PEAK 35(20P13) CNV 28 3 1 24 16 3 3 1
DEL PEAK 35(20P13) WILD-TYPE 96 33 22 71 56 17 100 39

Figure S452.  Get High-res Image Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 35(20p13)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000158 (Fisher's exact test), Q value = 0.035

Table S453.  Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
DEL PEAK 35(20P13) CNV 10 32 37
DEL PEAK 35(20P13) WILD-TYPE 130 93 211

Figure S453.  Get High-res Image Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 35(20p13)' versus 'CN_CNMF'

P value = 2.59e-13 (Chi-square test), Q value = 1.2e-10

Table S454.  Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 35(20P13) CNV 18 36 5 61 14
DEL PEAK 35(20P13) WILD-TYPE 329 186 67 162 35

Figure S454.  Get High-res Image Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 35(20p13)' versus 'METHLYATION_CNMF'

P value = 7.15e-09 (Chi-square test), Q value = 2.8e-06

Table S455.  Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 35(20P13) CNV 31 4 11 24 3 7
DEL PEAK 35(20P13) WILD-TYPE 70 135 82 113 37 90

Figure S455.  Get High-res Image Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 35(20p13)' versus 'MRNASEQ_CNMF'

P value = 2.44e-10 (Fisher's exact test), Q value = 1e-07

Table S456.  Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 148 446
DEL PEAK 35(20P13) CNV 64 6 55
DEL PEAK 35(20P13) WILD-TYPE 170 142 391

Figure S456.  Get High-res Image Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 35(20p13)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.06e-10 (Fisher's exact test), Q value = 2.9e-07

Table S457.  Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 216 408 204
DEL PEAK 35(20P13) CNV 11 58 56
DEL PEAK 35(20P13) WILD-TYPE 205 350 148

Figure S457.  Get High-res Image Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 35(20p13)' versus 'MIRSEQ_CNMF'

P value = 2.69e-12 (Fisher's exact test), Q value = 1.2e-09

Table S458.  Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 35(20P13) CNV 15 40 72
DEL PEAK 35(20P13) WILD-TYPE 219 352 183

Figure S458.  Get High-res Image Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 35(20p13)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.91e-13 (Fisher's exact test), Q value = 9.2e-11

Table S459.  Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 35(20P13) CNV 48 13 66
DEL PEAK 35(20P13) WILD-TYPE 314 271 169

Figure S459.  Get High-res Image Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 36(21q11.2)' versus 'MRNA_CNMF'

P value = 0.000252 (Chi-square test), Q value = 0.054

Table S460.  Gene #63: 'Del Peak 36(21q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
DEL PEAK 36(21Q11.2) CNV 38 11 4 15 22 3 10 3
DEL PEAK 36(21Q11.2) WILD-TYPE 86 25 19 80 50 17 93 37

Figure S460.  Get High-res Image Gene #63: 'Del Peak 36(21q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 36(21q11.2)' versus 'CN_CNMF'

P value = 4.31e-11 (Chi-square test), Q value = 1.9e-08

Table S461.  Gene #63: 'Del Peak 36(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
DEL PEAK 36(21Q11.2) CNV 28 66 13 63 12
DEL PEAK 36(21Q11.2) WILD-TYPE 319 156 59 160 37

Figure S461.  Get High-res Image Gene #63: 'Del Peak 36(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 36(21q11.2)' versus 'METHLYATION_CNMF'

P value = 2.01e-06 (Chi-square test), Q value = 6e-04

Table S462.  Gene #63: 'Del Peak 36(21q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 36(21Q11.2) CNV 17 16 18 48 7 9
DEL PEAK 36(21Q11.2) WILD-TYPE 84 123 75 89 33 88

Figure S462.  Get High-res Image Gene #63: 'Del Peak 36(21q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 37(22q13.32)' versus 'METHLYATION_CNMF'

P value = 0.000674 (Chi-square test), Q value = 0.13

Table S463.  Gene #64: 'Del Peak 37(22q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
DEL PEAK 37(22Q13.32) CNV 49 52 42 79 10 36
DEL PEAK 37(22Q13.32) WILD-TYPE 52 87 51 58 30 61

Figure S463.  Get High-res Image Gene #64: 'Del Peak 37(22q13.32)' versus Molecular Subtype #4: 'METHLYATION_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 = BRCA-TP.transferedmergedcluster.txt

  • Number of patients = 913

  • Number of copy number variation regions = 64

  • Number of molecular subtypes = 10

  • Exclude regions that fewer than K tumors have alterations, K = 3

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

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[2] 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)
[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)
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