Correlation between copy number variation genes and molecular subtypes
Breast Invasive Carcinoma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1RJ4GMS
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1RJ4GMS
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 63 peak regions and 10 molecular subtypes across 891 patients, 442 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_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

  • Amp Peak 4(3p26.1) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  '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 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 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',  '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' and 'METHLYATION_CNMF'.

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

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

  • 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_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

  • Amp Peak 23(17p11.2) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 24(17q12) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 25(17q23.1) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • Amp Peak 26(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 27(19q13.42) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 28(20q13.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • Del Peak 2(1p21.2) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 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_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

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

  • Del Peak 17(9q21.11) cnvs correlated to 'MRNA_CNMF',  '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(11q23.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 22(12p13.1) cnvs correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 23(12q24.31) 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 24(13q14.2) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 25(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 26(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 27(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 28(17p12) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 29(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 30(18q23) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 31(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 32(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 33(20p13) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 34(21q11.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 35(22q13.32) cnvs correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 63 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 442 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 Fisher's exact 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) 203 (23%) 688 1.49e-06
(0.000475) 		6.58e-12
(2.99e-09) 		3.43e-16
(1.8e-13) 		7.13e-14
(3.49e-11) 		0.000151
(0.0345) 		1.74e-07
(6.06e-05) 		2.3e-15
(1.18e-12) 		8.7e-17
(4.64e-14) 		2.72e-14
(1.34e-11) 		3.24e-18
(1.78e-15)
Amp Peak 5(3q26 32) 286 (32%) 605 4.54e-11
(2.02e-08) 		1.51e-10
(6.48e-08) 		2.58e-37
(1.58e-34) 		3.92e-15
(1.98e-12) 		1.21e-06
(0.000389) 		5.9e-06
(0.0017) 		1.95e-23
(1.13e-20) 		1.71e-20
(9.68e-18) 		2.8e-16
(1.48e-13) 		6.24e-21
(3.55e-18)
Amp Peak 7(6p23) 235 (26%) 656 5.85e-11
(2.57e-08) 		6.05e-09
(2.36e-06) 		8.38e-33
(5.07e-30) 		2.58e-15
(1.32e-12) 		1e-06
(0.000323) 		7.41e-05
(0.0181) 		1.87e-14
(9.36e-12) 		6.83e-11
(2.99e-08) 		9.53e-19
(5.27e-16) 		2.91e-16
(1.54e-13)
Amp Peak 8(6q21) 165 (19%) 726 2.8e-15
(1.43e-12) 		6.15e-10
(2.55e-07) 		1.01e-39
(6.21e-37) 		1.09e-11
(4.95e-09) 		1.04e-08
(3.95e-06) 		4.91e-07
(0.000162) 		6.64e-24
(3.87e-21) 		2.22e-18
(1.22e-15) 		3.13e-21
(1.78e-18) 		2.86e-26
(1.69e-23)
Amp Peak 11(8q24 21) 573 (64%) 318 3.61e-10
(1.52e-07) 		2.03e-10
(8.62e-08) 		1.77e-45
(1.1e-42) 		5.57e-23
(3.22e-20) 		3.68e-08
(1.34e-05) 		5.27e-07
(0.000174) 		2.34e-20
(1.31e-17) 		6.88e-13
(3.27e-10) 		3.18e-24
(1.86e-21) 		1.55e-19
(8.65e-17)
Amp Peak 12(10p15 1) 253 (28%) 638 7.97e-17
(4.26e-14) 		4.18e-19
(2.32e-16) 		4.58e-35
(2.79e-32) 		9.02e-24
(5.24e-21) 		1.43e-10
(6.14e-08) 		1.46e-12
(6.88e-10) 		2.52e-29
(1.51e-26) 		3.1e-28
(1.85e-25) 		1.73e-27
(1.03e-24) 		6.45e-35
(3.93e-32)
Amp Peak 17(12p13 33) 232 (26%) 659 1.74e-10
(7.43e-08) 		1.35e-13
(6.57e-11) 		3.32e-28
(1.98e-25) 		4.4e-15
(2.22e-12) 		6.79e-08
(2.42e-05) 		3.08e-07
(0.000104) 		1.79e-17
(9.7e-15) 		2.09e-15
(1.08e-12) 		4.16e-22
(2.39e-19) 		3.45e-19
(1.92e-16)
Amp Peak 20(13q34) 157 (18%) 734 0.0011
(0.211) 		8.57e-10
(3.53e-07) 		1.9e-20
(1.07e-17) 		2.37e-12
(1.1e-09) 		4.1e-06
(0.0012) 		2.88e-08
(1.06e-05) 		3.54e-16
(1.86e-13) 		3.05e-15
(1.55e-12) 		2.36e-15
(1.21e-12) 		1.26e-19
(7.04e-17)
Amp Peak 26(19q12) 231 (26%) 660 5.61e-08
(2.03e-05) 		5.55e-12
(2.53e-09) 		1.81e-24
(1.06e-21) 		1.37e-08
(5.21e-06) 		6.56e-07
(0.000216) 		1.51e-06
(0.000478) 		3.87e-14
(1.91e-11) 		4.67e-17
(2.51e-14) 		2.36e-12
(1.1e-09) 		1.69e-17
(9.15e-15)
Del Peak 3(2q37 3) 263 (30%) 628 7.69e-07
(0.00025) 		5.89e-09
(2.3e-06) 		5.27e-20
(2.96e-17) 		4.74e-10
(1.97e-07) 		1.32e-08
(5e-06) 		1.53e-07
(5.33e-05) 		3.19e-11
(1.42e-08) 		2.2e-07
(7.55e-05) 		3.3e-12
(1.52e-09) 		2.58e-07
(8.82e-05)
Del Peak 4(3p14 3) 274 (31%) 617 2.23e-13
(1.08e-10) 		8.42e-09
(3.25e-06) 		2.26e-32
(1.37e-29) 		4.65e-12
(2.13e-09) 		2.21e-09
(8.82e-07) 		1.2e-05
(0.00336) 		1.63e-16
(8.67e-14) 		5.37e-11
(2.37e-08) 		9.81e-20
(5.49e-17) 		2.27e-14
(1.13e-11)
Del Peak 5(4p16 3) 279 (31%) 612 1.39e-10
(5.97e-08) 		3.16e-12
(1.47e-09) 		2.46e-27
(1.46e-24) 		8.82e-12
(4.01e-09) 		6.65e-07
(0.000218) 		3.22e-06
(0.000969) 		2.72e-22
(1.57e-19) 		5.6e-18
(3.06e-15) 		1.12e-14
(5.6e-12) 		3.71e-15
(1.88e-12)
Del Peak 6(4q35 2) 280 (31%) 611 7.12e-10
(2.94e-07) 		1.92e-07
(6.65e-05) 		7.04e-36
(4.3e-33) 		5.96e-14
(2.92e-11) 		3.47e-08
(1.27e-05) 		2.09e-06
(0.000651) 		3.04e-21
(1.73e-18) 		1.18e-15
(6.12e-13) 		1e-15
(5.23e-13) 		2.34e-17
(1.26e-14)
Del Peak 7(5q11 2) 231 (26%) 660 8.07e-22
(4.63e-19) 		5.58e-26
(3.28e-23) 		3.42e-62
(2.15e-59) 		3.27e-36
(2e-33) 		1.99e-15
(1.02e-12) 		1.27e-18
(7.04e-16) 		3.1e-41
(1.92e-38) 		8.36e-44
(5.19e-41) 		6.02e-41
(3.72e-38) 		2.35e-49
(1.47e-46)
Del Peak 8(5q21 3) 223 (25%) 668 5.18e-25
(3.03e-22) 		1.83e-27
(1.09e-24) 		2.4e-74
(1.51e-71) 		1.41e-50
(8.82e-48) 		5.76e-15
(2.9e-12) 		2.82e-15
(1.44e-12) 		2.89e-48
(1.8e-45) 		5.1e-49
(3.18e-46) 		2.74e-40
(1.69e-37) 		2.29e-53
(1.44e-50)
Del Peak 18(10q23 31) 258 (29%) 633 4.65e-07
(0.000155) 		9.23e-05
(0.0221) 		1.31e-18
(7.21e-16) 		5.14e-11
(2.27e-08) 		5.69e-08
(2.05e-05) 		2.15e-05
(0.00578) 		2.38e-12
(1.11e-09) 		6.39e-08
(2.29e-05) 		4.41e-09
(1.73e-06) 		4.12e-09
(1.63e-06)
Del Peak 19(10q26 3) 259 (29%) 632 1.75e-09
(7e-07) 		3.68e-07
(0.000124) 		1.02e-19
(5.69e-17) 		1.24e-10
(5.38e-08) 		2.12e-08
(7.97e-06) 		1.92e-07
(6.65e-05) 		1.56e-15
(8.08e-13) 		2.26e-10
(9.58e-08) 		1.66e-13
(8.04e-11) 		1.91e-12
(8.96e-10)
Del Peak 20(11p15 5) 259 (29%) 632 5.04e-11
(2.23e-08) 		6.22e-08
(2.24e-05) 		3e-30
(1.8e-27) 		1.01e-09
(4.12e-07) 		2.51e-09
(9.98e-07) 		3.81e-06
(0.00114) 		1.05e-16
(5.57e-14) 		3.64e-12
(1.68e-09) 		7.33e-17
(3.92e-14) 		7.13e-17
(3.82e-14)
Del Peak 23(12q24 31) 162 (18%) 729 1.7e-10
(7.3e-08) 		9.29e-11
(4.05e-08) 		1.9e-19
(1.06e-16) 		2.87e-13
(1.38e-10) 		1.44e-05
(0.00399) 		7.16e-07
(0.000234) 		6.91e-17
(3.71e-14) 		2.16e-16
(1.14e-13) 		3.28e-12
(1.52e-09) 		3.24e-12
(1.5e-09)
Del Peak 25(14q24 3) 286 (32%) 605 2.58e-07
(8.82e-05) 		1.05e-09
(4.29e-07) 		6.75e-33
(4.09e-30) 		4.58e-13
(2.19e-10) 		2.51e-07
(8.62e-05) 		2.89e-06
(0.00088) 		1.99e-14
(9.91e-12) 		1.1e-12
(5.22e-10) 		8.25e-18
(4.51e-15) 		1.23e-20
(6.98e-18)
Del Peak 26(15q13 1) 310 (35%) 581 2.12e-06
(0.000657) 		3.26e-08
(1.2e-05) 		9.29e-31
(5.6e-28) 		5.25e-12
(2.4e-09) 		0.000316
(0.0683) 		4.78e-05
(0.012) 		3.27e-15
(1.66e-12) 		1.43e-12
(6.74e-10) 		1.02e-15
(5.32e-13) 		2.67e-21
(1.53e-18)
Del Peak 27(16q24 3) 575 (65%) 316 1.76e-12
(8.28e-10) 		5.68e-13
(2.7e-10) 		6.56e-11
(2.88e-08) 		4.16e-10
(1.74e-07) 		1.71e-09
(6.89e-07) 		2.08e-11
(9.36e-09) 		3.34e-18
(1.83e-15) 		1.19e-17
(6.49e-15) 		5.67e-14
(2.79e-11) 		1.99e-20
(1.12e-17)
Del Peak 29(17q21 31) 312 (35%) 579 2.35e-12
(1.1e-09) 		3.82e-07
(0.000128) 		9.31e-23
(5.37e-20) 		4.98e-14
(2.45e-11) 		1.55e-11
(7e-09) 		5.88e-11
(2.58e-08) 		1.21e-20
(6.87e-18) 		1.17e-15
(6.1e-13) 		1.78e-14
(8.9e-12) 		2.77e-16
(1.47e-13)
Del Peak 31(19p13 3) 301 (34%) 590 1.08e-09
(4.39e-07) 		9.68e-09
(3.72e-06) 		3.97e-43
(2.46e-40) 		4.05e-17
(2.18e-14) 		2.67e-06
(0.000821) 		4.31e-05
(0.011) 		3.11e-13
(1.49e-10) 		2.3e-09
(9.16e-07) 		9.07e-16
(4.73e-13) 		2.14e-14
(1.07e-11)
Del Peak 32(19q13 32) 180 (20%) 711 3.03e-05
(0.00806) 		8.29e-06
(0.00237) 		1.77e-17
(9.6e-15) 		3.07e-11
(1.37e-08) 		0.000469
(0.0989) 		4.52e-05
(0.0114) 		4.4e-09
(1.73e-06) 		1.39e-06
(0.000444) 		1.37e-10
(5.94e-08) 		2.46e-08
(9.16e-06)
Amp Peak 22(15q26 3) 162 (18%) 729 3.16e-07
(0.000107) 		0.000286
(0.0624) 		2.36e-14
(1.17e-11) 		0.00091
(0.18) 		0.000168
(0.038) 		0.0263
(1.00) 		5.25e-08
(1.91e-05) 		3.29e-05
(0.00865) 		1.37e-07
(4.8e-05) 		4.18e-10
(1.74e-07)
Del Peak 17(9q21 11) 239 (27%) 652 0.000914
(0.18) 		1.98e-05
(0.00536) 		9.57e-18
(5.22e-15) 		9.77e-10
(4.01e-07) 		1.44e-05
(0.00399) 		0.00515
(0.788) 		2.82e-06
(0.000862) 		8.67e-05
(0.0209) 		8.68e-09
(3.34e-06) 		1.35e-09
(5.45e-07)
Amp Peak 4(3p26 1) 182 (20%) 709 0.000534
(0.11) 		3.45e-05
(0.00902) 		5.1e-13
(2.43e-10) 		3.28e-07
(0.00011) 		0.0063
(0.926) 		0.00638
(0.931) 		5.03e-10
(2.09e-07) 		3.45e-05
(0.00902) 		1.01e-08
(3.86e-06) 		2.95e-06
(0.000894)
Amp Peak 6(4q13 3) 141 (16%) 750 0.00085
(0.17) 		0.000555
(0.114) 		3.34e-16
(1.76e-13) 		8.72e-07
(0.000282) 		0.0838
(1.00) 		0.562
(1.00) 		1.01e-05
(0.00286) 		0.000523
(0.109) 		0.000649
(0.132) 		2.8e-07
(9.52e-05)
Amp Peak 28(20q13 2) 455 (51%) 436 2.58e-08
(9.54e-06) 		1.22e-06
(0.000391) 		3.23e-49
(2.02e-46) 		2.07e-20
(1.16e-17) 		0.000494
(0.104) 		0.00994
(1.00) 		1.17e-09
(4.75e-07) 		0.0185
(1.00) 		3.02e-11
(1.35e-08) 		2.29e-08
(8.58e-06)
Del Peak 12(7p22 3) 117 (13%) 774 0.000233
(0.0513) 		0.000547
(0.113) 		7.09e-16
(3.71e-13) 		1.54e-05
(0.00424) 		0.0222
(1.00) 		0.00556
(0.834) 		7.93e-09
(3.07e-06) 		3.72e-06
(0.00111) 		3.9e-10
(1.63e-07) 		3.62e-09
(1.43e-06)
Del Peak 14(8p23 2) 469 (53%) 422 3.44e-05
(0.00902) 		2.92e-06
(0.000886) 		1.15e-30
(6.91e-28) 		2.92e-10
(1.23e-07) 		0.0112
(1.00) 		0.03
(1.00) 		2.38e-11
(1.07e-08) 		2.01e-06
(0.000626) 		5.35e-08
(1.94e-05) 		1.5e-09
(6.03e-07)
Del Peak 33(20p13) 132 (15%) 759 0.00206
(0.36) 		1.42e-05
(0.00396) 		9.52e-14
(4.64e-11) 		3.97e-07
(0.000133) 		0.00085
(0.17) 		0.00683
(0.99) 		1.8e-10
(7.68e-08) 		2.57e-08
(9.53e-06) 		1.06e-11
(4.79e-09) 		1.74e-09
(7e-07)
Del Peak 16(9p21 3) 298 (33%) 593 1.01e-05
(0.00287) 		3.96e-06
(0.00117) 		7.63e-29
(4.57e-26) 		2.76e-14
(1.36e-11) 		0.00342
(0.543) 		0.338
(1.00) 		1.14e-07
(4.02e-05) 		0.00183
(0.323) 		9.58e-10
(3.94e-07) 		5.19e-05
(0.013)
Del Peak 24(13q14 2) 407 (46%) 484 0.0102
(1.00) 		3.07e-05
(0.00814) 		2.43e-28
(1.46e-25) 		2.51e-06
(0.000773) 		0.559
(1.00) 		0.104
(1.00) 		1.34e-07
(4.69e-05) 		3.45e-05
(0.00902) 		1.55e-08
(5.87e-06) 		2.62e-05
(0.00701)
Amp Peak 2(1q21 3) 645 (72%) 246 0.0199
(1.00) 		0.000122
(0.0282) 		1.02e-10
(4.46e-08) 		0.000194
(0.0435) 		0.0717
(1.00) 		0.00817
(1.00) 		0.000292
(0.0634) 		0.00104
(0.2) 		3.95e-05
(0.0101) 		0.0043
(0.671)
Amp Peak 13(10q22 3) 129 (14%) 762 5.45e-05
(0.0135) 		0.0536
(1.00) 		1.01e-09
(4.12e-07) 		0.000226
(0.0499) 		0.00279
(0.458) 		0.0146
(1.00) 		9.93e-08
(3.51e-05) 		0.00171
(0.304) 		5.17e-06
(0.00149) 		0.000147
(0.0337)
Amp Peak 16(11q14 1) 220 (25%) 671 0.0143
(1.00) 		0.0783
(1.00) 		4.58e-13
(2.19e-10) 		3.14e-05
(0.0083) 		0.0703
(1.00) 		0.189
(1.00) 		0.000112
(0.0261) 		0.00121
(0.23) 		4.64e-07
(0.000155) 		7.01e-05
(0.0172)
Amp Peak 18(12q15) 228 (26%) 663 1.75e-06
(0.000551) 		6.29e-08
(2.26e-05) 		1.6e-25
(9.36e-23) 		1.64e-13
(7.95e-11) 		0.187
(1.00) 		0.0724
(1.00) 		1.17e-05
(0.00331) 		0.0105
(1.00) 		6.14e-09
(2.39e-06) 		0.175
(1.00)
Amp Peak 21(14q21 1) 179 (20%) 712 0.0123
(1.00) 		0.00043
(0.0911) 		1.03e-13
(5.04e-11) 		3.91e-06
(0.00116) 		0.127
(1.00) 		0.0459
(1.00) 		1.65e-05
(0.00453) 		0.00123
(0.232) 		0.000113
(0.0264) 		0.0261
(1.00)
Amp Peak 24(17q12) 289 (32%) 602 0.000108
(0.0256) 		1.51e-05
(0.00418) 		9.14e-37
(5.6e-34) 		8.72e-08
(3.09e-05) 		0.0476
(1.00) 		0.00547
(0.826) 		6.59e-05
(0.0162) 		0.0253
(1.00) 		0.00163
(0.295) 		0.000416
(0.0885)
Amp Peak 25(17q23 1) 367 (41%) 524 0.000367
(0.0788) 		5.11e-05
(0.0128) 		4.12e-40
(2.54e-37) 		4.73e-09
(1.86e-06) 		0.189
(1.00) 		0.462
(1.00) 		0.000199
(0.0443) 		0.327
(1.00) 		1.72e-06
(0.000541) 		0.0445
(1.00)
Del Peak 28(17p12) 537 (60%) 354 4.01e-06
(0.00118) 		0.054
(1.00) 		1.35e-21
(7.75e-19) 		2.15e-07
(7.43e-05) 		0.000114
(0.0264) 		0.00818
(1.00) 		0.00285
(0.461) 		0.0986
(1.00) 		1.49e-06
(0.000474) 		1.81e-06
(0.000567)
Del Peak 30(18q23) 290 (33%) 601 6.04e-06
(0.00173) 		0.0272
(1.00) 		3.87e-12
(1.78e-09) 		1.02e-08
(3.88e-06) 		0.00601
(0.896) 		0.596
(1.00) 		2.74e-05
(0.00731) 		0.0396
(1.00) 		4.31e-05
(0.011) 		0.000169
(0.0381)
Amp Peak 14(11p13) 186 (21%) 705 0.0017
(0.304) 		0.112
(1.00) 		3.3e-08
(1.21e-05) 		0.000751
(0.152) 		0.0969
(1.00) 		0.14
(1.00) 		8.03e-05
(0.0194) 		0.0282
(1.00) 		3.5e-05
(0.00904) 		1.39e-05
(0.00391)
Amp Peak 27(19q13 42) 232 (26%) 659 0.000202
(0.0449) 		0.00138
(0.26) 		5.8e-15
(2.92e-12) 		4.71e-06
(0.00137) 		0.00161
(0.294) 		0.0495
(1.00) 		0.00459
(0.711) 		0.0242
(1.00) 		1.89e-05
(0.00513) 		9.44e-05
(0.0225)
Del Peak 1(1p36 13) 373 (42%) 518 0.00609
(0.901) 		3.17e-06
(0.000959) 		3e-33
(1.82e-30) 		6.69e-08
(2.39e-05) 		0.00536
(0.815) 		0.0639
(1.00) 		4.33e-06
(0.00126) 		0.0028
(0.458) 		3.4e-11
(1.51e-08) 		0.104
(1.00)
Del Peak 10(6q15) 293 (33%) 598 0.0795
(1.00) 		0.000985
(0.191) 		1.45e-26
(8.57e-24) 		1.07e-07
(3.79e-05) 		0.396
(1.00) 		0.105
(1.00) 		1.98e-05
(0.00536) 		8e-05
(0.0194) 		0.0529
(1.00) 		0.00161
(0.294)
Del Peak 13(7q36 1) 173 (19%) 718 0.000562
(0.115) 		0.00776
(1.00) 		2.34e-08
(8.73e-06) 		0.069
(1.00) 		0.606
(1.00) 		0.0735
(1.00) 		0.000824
(0.166) 		0.0438
(1.00) 		7.75e-09
(3.01e-06) 		1.57e-06
(0.000496)
Amp Peak 10(8p11 21) 345 (39%) 546 0.259
(1.00) 		0.153
(1.00) 		3e-25
(1.76e-22) 		3.77e-05
(0.0097) 		0.78
(1.00) 		0.68
(1.00) 		5.22e-05
(0.013) 		0.000134
(0.0309) 		0.0372
(1.00) 		0.207
(1.00)
Del Peak 2(1p21 2) 301 (34%) 590 0.0114
(1.00) 		0.000109
(0.0257) 		4.04e-23
(2.34e-20) 		8.77e-05
(0.021) 		0.00164
(0.296) 		0.0112
(1.00) 		0.000366
(0.0788) 		0.00139
(0.261) 		0.00221
(0.38) 		0.00388
(0.609)
Del Peak 15(8p11 21) 170 (19%) 721 0.000175
(0.0394) 		0.00259
(0.433) 		1.12e-10
(4.84e-08) 		0.019
(1.00) 		0.036
(1.00) 		0.0184
(1.00) 		0.000996
(0.192) 		0.0393
(1.00) 		0.0213
(1.00) 		4.97e-06
(0.00144)
Amp Peak 9(8p11 23) 335 (38%) 556 0.041
(1.00) 		0.00826
(1.00) 		3.12e-26
(1.84e-23) 		2.47e-10
(1.05e-07) 		0.0486
(1.00) 		0.00925
(1.00) 		1.76e-05
(0.0048) 		0.00266
(0.438) 		0.16
(1.00) 		0.0374
(1.00)
Amp Peak 19(13q12 3) 125 (14%) 766 0.00885
(1.00) 		0.0282
(1.00) 		9.35e-06
(0.00266) 		0.0195
(1.00) 		0.00907
(1.00) 		0.106
(1.00) 		2.18e-06
(0.000674) 		0.0151
(1.00) 		3.53e-06
(0.00106) 		0.00505
(0.777)
Amp Peak 3(1q44) 642 (72%) 249 0.387
(1.00) 		0.067
(1.00) 		2.17e-08
(8.12e-06) 		0.000527
(0.11) 		0.928
(1.00) 		0.345
(1.00) 		0.335
(1.00) 		0.533
(1.00) 		0.417
(1.00) 		0.64
(1.00)
Amp Peak 15(11q13 3) 340 (38%) 551 0.231
(1.00) 		0.0253
(1.00) 		6.2e-34
(3.77e-31) 		1.83e-08
(6.89e-06) 		0.957
(1.00) 		0.174
(1.00) 		0.0424
(1.00) 		0.32
(1.00) 		0.00213
(0.368) 		0.119
(1.00)
Del Peak 9(6p25 3) 167 (19%) 724 0.918
(1.00) 		0.542
(1.00) 		4.07e-06
(0.0012) 		5.56e-05
(0.0137) 		0.469
(1.00) 		0.587
(1.00) 		0.00221
(0.38) 		0.0616
(1.00) 		0.0403
(1.00) 		0.103
(1.00)
Del Peak 21(11q23 2) 442 (50%) 449 0.00819
(1.00) 		0.0832
(1.00) 		3.59e-26
(2.11e-23) 		3.17e-10
(1.33e-07) 		0.919
(1.00) 		0.507
(1.00) 		0.00141
(0.263) 		0.00262
(0.434) 		0.0106
(1.00) 		0.00307
(0.49)
Del Peak 22(12p13 1) 156 (18%) 735 0.0316
(1.00) 		0.067
(1.00) 		0.00226
(0.384) 		0.0154
(1.00) 		0.244
(1.00) 		0.0506
(1.00) 		0.00145
(0.269) 		0.0173
(1.00) 		0.000962
(0.188) 		9.45e-05
(0.0225)
Del Peak 34(21q11 2) 181 (20%) 710 0.00209
(0.364) 		0.0593
(1.00) 		1.38e-12
(6.53e-10) 		0.000275
(0.0602) 		0.309
(1.00) 		0.504
(1.00) 		0.0105
(1.00) 		0.235
(1.00) 		0.0172
(1.00) 		0.0735
(1.00)
Amp Peak 23(17p11 2) 124 (14%) 767 0.151
(1.00) 		0.0305
(1.00) 		7.6e-07
(0.000248) 		0.00299
(0.482) 		0.358
(1.00) 		0.613
(1.00) 		0.00236
(0.397) 		0.0707
(1.00) 		0.183
(1.00) 		0.342
(1.00)
Del Peak 11(6q27) 303 (34%) 588 0.148
(1.00) 		0.398
(1.00) 		3.04e-13
(1.46e-10) 		0.00234
(0.396) 		0.0524
(1.00) 		0.581
(1.00) 		0.486
(1.00) 		0.52
(1.00) 		0.159
(1.00) 		0.611
(1.00)
Del Peak 35(22q13 32) 399 (45%) 492 0.0703
(1.00) 		0.109
(1.00) 		0.000936
(0.183) 		0.00146
(0.269) 		0.111
(1.00) 		0.0188
(1.00) 		0.00201
(0.354) 		0.0208
(1.00) 		0.00342
(0.543) 		0.169
(1.00)
'Amp Peak 1(1p22.3) mutation analysis' versus 'MRNA_CNMF'

P value = 1.49e-06 (Fisher's exact test), Q value = 0.00047

Table S1.  Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
AMP PEAK 1(1P22.3) MUTATED 44 12 59
AMP PEAK 1(1P22.3) WILD-TYPE 212 80 100

Figure S1.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 6.58e-12 (Fisher's exact test), Q value = 3e-09

Table S2.  Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
AMP PEAK 1(1P22.3) MUTATED 55 49 11
AMP PEAK 1(1P22.3) WILD-TYPE 66 203 123

Figure S2.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

P value = 3.43e-16 (Chi-square test), Q value = 1.8e-13

Table S3.  Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
AMP PEAK 1(1P22.3) MUTATED 45 30 26 86 16
AMP PEAK 1(1P22.3) WILD-TYPE 301 46 172 129 40

Figure S3.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 7.13e-14 (Chi-square test), Q value = 3.5e-11

Table S4.  Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
AMP PEAK 1(1P22.3) MUTATED 50 23 18 14 2 14
AMP PEAK 1(1P22.3) WILD-TYPE 46 119 62 109 34 76

Figure S4.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 0.000151 (Fisher's exact test), Q value = 0.035

Table S5.  Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
AMP PEAK 1(1P22.3) MUTATED 52 27 16
AMP PEAK 1(1P22.3) WILD-TYPE 94 102 99

Figure S5.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

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

P value = 1.74e-07 (Fisher's exact test), Q value = 6.1e-05

Table S6.  Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
AMP PEAK 1(1P22.3) MUTATED 31 12 52
AMP PEAK 1(1P22.3) WILD-TYPE 125 96 74

Figure S6.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

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

P value = 2.3e-15 (Fisher's exact test), Q value = 1.2e-12

Table S7.  Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
AMP PEAK 1(1P22.3) MUTATED 96 15 70
AMP PEAK 1(1P22.3) WILD-TYPE 139 140 364

Figure S7.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 8.7e-17 (Fisher's exact test), Q value = 4.6e-14

Table S8.  Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
AMP PEAK 1(1P22.3) MUTATED 71 23 87
AMP PEAK 1(1P22.3) WILD-TYPE 342 193 108

Figure S8.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 2.72e-14 (Fisher's exact test), Q value = 1.3e-11

Table S9.  Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
AMP PEAK 1(1P22.3) MUTATED 32 65 103
AMP PEAK 1(1P22.3) WILD-TYPE 168 358 146

Figure S9.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 3.24e-18 (Fisher's exact test), Q value = 1.8e-15

Table S10.  Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
AMP PEAK 1(1P22.3) MUTATED 96 93 11
AMP PEAK 1(1P22.3) WILD-TYPE 108 516 48

Figure S10.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 2(1q21.3) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000122 (Fisher's exact test), Q value = 0.028

Table S11.  Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
AMP PEAK 2(1Q21.3) MUTATED 103 189 83
AMP PEAK 2(1Q21.3) WILD-TYPE 18 63 51

Figure S11.  Get High-res Image Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

P value = 1.02e-10 (Chi-square test), Q value = 4.5e-08

Table S12.  Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
AMP PEAK 2(1Q21.3) MUTATED 213 76 149 166 41
AMP PEAK 2(1Q21.3) WILD-TYPE 133 0 49 49 15

Figure S12.  Get High-res Image Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.000194 (Chi-square test), Q value = 0.043

Table S13.  Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
AMP PEAK 2(1Q21.3) MUTATED 78 110 65 81 20 53
AMP PEAK 2(1Q21.3) WILD-TYPE 18 32 15 42 16 37

Figure S13.  Get High-res Image Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 0.000292 (Fisher's exact test), Q value = 0.063

Table S14.  Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
AMP PEAK 2(1Q21.3) MUTATED 191 99 305
AMP PEAK 2(1Q21.3) WILD-TYPE 44 56 129

Figure S14.  Get High-res Image Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 0.00104 (Fisher's exact test), Q value = 0.2

Table S15.  Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
AMP PEAK 2(1Q21.3) MUTATED 297 140 158
AMP PEAK 2(1Q21.3) WILD-TYPE 116 76 37

Figure S15.  Get High-res Image Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 3.95e-05 (Fisher's exact test), Q value = 0.01

Table S16.  Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
AMP PEAK 2(1Q21.3) MUTATED 130 294 205
AMP PEAK 2(1Q21.3) WILD-TYPE 70 129 44

Figure S16.  Get High-res Image Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 2.17e-08 (Chi-square test), Q value = 8.1e-06

Table S17.  Gene #3: 'Amp Peak 3(1q44) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
AMP PEAK 3(1Q44) MUTATED 224 76 149 157 36
AMP PEAK 3(1Q44) WILD-TYPE 122 0 49 58 20

Figure S17.  Get High-res Image Gene #3: 'Amp Peak 3(1q44) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.000527 (Chi-square test), Q value = 0.11

Table S18.  Gene #3: 'Amp Peak 3(1q44) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
AMP PEAK 3(1Q44) MUTATED 69 112 69 77 23 56
AMP PEAK 3(1Q44) WILD-TYPE 27 30 11 46 13 34

Figure S18.  Get High-res Image Gene #3: 'Amp Peak 3(1q44) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 4(3p26.1) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000534 (Fisher's exact test), Q value = 0.11

Table S19.  Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
AMP PEAK 4(3P26.1) MUTATED 49 17 56
AMP PEAK 4(3P26.1) WILD-TYPE 207 75 103

Figure S19.  Get High-res Image Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 4(3p26.1) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.45e-05 (Fisher's exact test), Q value = 0.009

Table S20.  Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
AMP PEAK 4(3P26.1) MUTATED 35 73 14
AMP PEAK 4(3P26.1) WILD-TYPE 86 179 120

Figure S20.  Get High-res Image Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

P value = 5.1e-13 (Chi-square test), Q value = 2.4e-10

Table S21.  Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
AMP PEAK 4(3P26.1) MUTATED 26 21 50 72 13
AMP PEAK 4(3P26.1) WILD-TYPE 320 55 148 143 43

Figure S21.  Get High-res Image Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 3.28e-07 (Chi-square test), Q value = 0.00011

Table S22.  Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
AMP PEAK 4(3P26.1) MUTATED 30 7 21 28 3 11
AMP PEAK 4(3P26.1) WILD-TYPE 66 135 59 95 33 79

Figure S22.  Get High-res Image Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 5.03e-10 (Fisher's exact test), Q value = 2.1e-07

Table S23.  Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
AMP PEAK 4(3P26.1) MUTATED 75 9 88
AMP PEAK 4(3P26.1) WILD-TYPE 160 146 346

Figure S23.  Get High-res Image Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 3.45e-05 (Fisher's exact test), Q value = 0.009

Table S24.  Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
AMP PEAK 4(3P26.1) MUTATED 90 25 57
AMP PEAK 4(3P26.1) WILD-TYPE 323 191 138

Figure S24.  Get High-res Image Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 1.01e-08 (Fisher's exact test), Q value = 3.9e-06

Table S25.  Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
AMP PEAK 4(3P26.1) MUTATED 23 69 82
AMP PEAK 4(3P26.1) WILD-TYPE 177 354 167

Figure S25.  Get High-res Image Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 2.95e-06 (Fisher's exact test), Q value = 0.00089

Table S26.  Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
AMP PEAK 4(3P26.1) MUTATED 64 94 16
AMP PEAK 4(3P26.1) WILD-TYPE 140 515 43

Figure S26.  Get High-res Image Gene #4: 'Amp Peak 4(3p26.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 4.54e-11 (Fisher's exact test), Q value = 2e-08

Table S27.  Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
AMP PEAK 5(3Q26.32) MUTATED 65 23 91
AMP PEAK 5(3Q26.32) WILD-TYPE 191 69 68

Figure S27.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 1.51e-10 (Fisher's exact test), Q value = 6.5e-08

Table S28.  Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
AMP PEAK 5(3Q26.32) MUTATED 70 85 24
AMP PEAK 5(3Q26.32) WILD-TYPE 51 167 110

Figure S28.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

P value = 2.58e-37 (Chi-square test), Q value = 1.6e-34

Table S29.  Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
AMP PEAK 5(3Q26.32) MUTATED 33 27 75 135 16
AMP PEAK 5(3Q26.32) WILD-TYPE 313 49 123 80 40

Figure S29.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 3.92e-15 (Chi-square test), Q value = 2e-12

Table S30.  Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
AMP PEAK 5(3Q26.32) MUTATED 59 16 28 36 9 17
AMP PEAK 5(3Q26.32) WILD-TYPE 37 126 52 87 27 73

Figure S30.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 1.21e-06 (Fisher's exact test), Q value = 0.00039

Table S31.  Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
AMP PEAK 5(3Q26.32) MUTATED 76 35 28
AMP PEAK 5(3Q26.32) WILD-TYPE 70 94 87

Figure S31.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

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

P value = 5.9e-06 (Fisher's exact test), Q value = 0.0017

Table S32.  Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
AMP PEAK 5(3Q26.32) MUTATED 48 25 66
AMP PEAK 5(3Q26.32) WILD-TYPE 108 83 60

Figure S32.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

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

P value = 1.95e-23 (Fisher's exact test), Q value = 1.1e-20

Table S33.  Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
AMP PEAK 5(3Q26.32) MUTATED 137 19 119
AMP PEAK 5(3Q26.32) WILD-TYPE 98 136 315

Figure S33.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 1.71e-20 (Fisher's exact test), Q value = 9.7e-18

Table S34.  Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
AMP PEAK 5(3Q26.32) MUTATED 116 40 119
AMP PEAK 5(3Q26.32) WILD-TYPE 297 176 76

Figure S34.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 2.8e-16 (Fisher's exact test), Q value = 1.5e-13

Table S35.  Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
AMP PEAK 5(3Q26.32) MUTATED 45 100 133
AMP PEAK 5(3Q26.32) WILD-TYPE 155 323 116

Figure S35.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 6.24e-21 (Fisher's exact test), Q value = 3.6e-18

Table S36.  Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
AMP PEAK 5(3Q26.32) MUTATED 121 136 21
AMP PEAK 5(3Q26.32) WILD-TYPE 83 473 38

Figure S36.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 0.00085 (Fisher's exact test), Q value = 0.17

Table S37.  Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
AMP PEAK 6(4Q13.3) MUTATED 34 8 40
AMP PEAK 6(4Q13.3) WILD-TYPE 222 84 119

Figure S37.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 0.000555 (Fisher's exact test), Q value = 0.11

Table S38.  Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
AMP PEAK 6(4Q13.3) MUTATED 28 45 9
AMP PEAK 6(4Q13.3) WILD-TYPE 93 207 125

Figure S38.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

P value = 3.34e-16 (Chi-square test), Q value = 1.8e-13

Table S39.  Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
AMP PEAK 6(4Q13.3) MUTATED 19 2 58 54 8
AMP PEAK 6(4Q13.3) WILD-TYPE 327 74 140 161 48

Figure S39.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 8.72e-07 (Chi-square test), Q value = 0.00028

Table S40.  Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
AMP PEAK 6(4Q13.3) MUTATED 25 5 11 30 4 8
AMP PEAK 6(4Q13.3) WILD-TYPE 71 137 69 93 32 82

Figure S40.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 1.01e-05 (Fisher's exact test), Q value = 0.0029

Table S41.  Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
AMP PEAK 6(4Q13.3) MUTATED 57 10 69
AMP PEAK 6(4Q13.3) WILD-TYPE 178 145 365

Figure S41.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 0.000523 (Fisher's exact test), Q value = 0.11

Table S42.  Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
AMP PEAK 6(4Q13.3) MUTATED 60 26 50
AMP PEAK 6(4Q13.3) WILD-TYPE 353 190 145

Figure S42.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 0.000649 (Fisher's exact test), Q value = 0.13

Table S43.  Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
AMP PEAK 6(4Q13.3) MUTATED 26 54 59
AMP PEAK 6(4Q13.3) WILD-TYPE 174 369 190

Figure S43.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 2.8e-07 (Fisher's exact test), Q value = 9.5e-05

Table S44.  Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
AMP PEAK 6(4Q13.3) MUTATED 57 70 12
AMP PEAK 6(4Q13.3) WILD-TYPE 147 539 47

Figure S44.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 5.85e-11 (Fisher's exact test), Q value = 2.6e-08

Table S45.  Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
AMP PEAK 7(6P23) MUTATED 51 15 78
AMP PEAK 7(6P23) WILD-TYPE 205 77 81

Figure S45.  Get High-res Image Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 6.05e-09 (Fisher's exact test), Q value = 2.4e-06

Table S46.  Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
AMP PEAK 7(6P23) MUTATED 57 70 17
AMP PEAK 7(6P23) WILD-TYPE 64 182 117

Figure S46.  Get High-res Image Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

P value = 8.38e-33 (Chi-square test), Q value = 5.1e-30

Table S47.  Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
AMP PEAK 7(6P23) MUTATED 23 18 62 116 16
AMP PEAK 7(6P23) WILD-TYPE 323 58 136 99 40

Figure S47.  Get High-res Image Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 2.58e-15 (Chi-square test), Q value = 1.3e-12

Table S48.  Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
AMP PEAK 7(6P23) MUTATED 47 11 20 45 2 11
AMP PEAK 7(6P23) WILD-TYPE 49 131 60 78 34 79

Figure S48.  Get High-res Image Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 1e-06 (Fisher's exact test), Q value = 0.00032

Table S49.  Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
AMP PEAK 7(6P23) MUTATED 64 23 23
AMP PEAK 7(6P23) WILD-TYPE 82 106 92

Figure S49.  Get High-res Image Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

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

P value = 7.41e-05 (Fisher's exact test), Q value = 0.018

Table S50.  Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
AMP PEAK 7(6P23) MUTATED 32 24 54
AMP PEAK 7(6P23) WILD-TYPE 124 84 72

Figure S50.  Get High-res Image Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

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

P value = 1.87e-14 (Fisher's exact test), Q value = 9.4e-12

Table S51.  Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
AMP PEAK 7(6P23) MUTATED 105 16 100
AMP PEAK 7(6P23) WILD-TYPE 130 139 334

Figure S51.  Get High-res Image Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 6.83e-11 (Fisher's exact test), Q value = 3e-08

Table S52.  Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
AMP PEAK 7(6P23) MUTATED 96 36 89
AMP PEAK 7(6P23) WILD-TYPE 317 180 106

Figure S52.  Get High-res Image Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 9.53e-19 (Fisher's exact test), Q value = 5.3e-16

Table S53.  Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
AMP PEAK 7(6P23) MUTATED 29 76 118
AMP PEAK 7(6P23) WILD-TYPE 171 347 131

Figure S53.  Get High-res Image Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 2.91e-16 (Fisher's exact test), Q value = 1.5e-13

Table S54.  Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
AMP PEAK 7(6P23) MUTATED 97 106 20
AMP PEAK 7(6P23) WILD-TYPE 107 503 39

Figure S54.  Get High-res Image Gene #7: 'Amp Peak 7(6p23) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 2.8e-15 (Fisher's exact test), Q value = 1.4e-12

Table S55.  Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
AMP PEAK 8(6Q21) MUTATED 24 12 68
AMP PEAK 8(6Q21) WILD-TYPE 232 80 91

Figure S55.  Get High-res Image Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 6.15e-10 (Fisher's exact test), Q value = 2.5e-07

Table S56.  Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
AMP PEAK 8(6Q21) MUTATED 50 42 12
AMP PEAK 8(6Q21) WILD-TYPE 71 210 122

Figure S56.  Get High-res Image Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

P value = 1.01e-39 (Chi-square test), Q value = 6.2e-37

Table S57.  Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
AMP PEAK 8(6Q21) MUTATED 21 13 18 107 6
AMP PEAK 8(6Q21) WILD-TYPE 325 63 180 108 50

Figure S57.  Get High-res Image Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 1.09e-11 (Chi-square test), Q value = 4.9e-09

Table S58.  Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
AMP PEAK 8(6Q21) MUTATED 37 3 16 18 2 16
AMP PEAK 8(6Q21) WILD-TYPE 59 139 64 105 34 74

Figure S58.  Get High-res Image Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 1.04e-08 (Fisher's exact test), Q value = 3.9e-06

Table S59.  Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
AMP PEAK 8(6Q21) MUTATED 54 12 15
AMP PEAK 8(6Q21) WILD-TYPE 92 117 100

Figure S59.  Get High-res Image Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

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

P value = 4.91e-07 (Fisher's exact test), Q value = 0.00016

Table S60.  Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
AMP PEAK 8(6Q21) MUTATED 20 14 47
AMP PEAK 8(6Q21) WILD-TYPE 136 94 79

Figure S60.  Get High-res Image Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

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

P value = 6.64e-24 (Fisher's exact test), Q value = 3.9e-21

Table S61.  Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
AMP PEAK 8(6Q21) MUTATED 97 7 51
AMP PEAK 8(6Q21) WILD-TYPE 138 148 383

Figure S61.  Get High-res Image Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 2.22e-18 (Fisher's exact test), Q value = 1.2e-15

Table S62.  Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
AMP PEAK 8(6Q21) MUTATED 57 17 81
AMP PEAK 8(6Q21) WILD-TYPE 356 199 114

Figure S62.  Get High-res Image Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 3.13e-21 (Fisher's exact test), Q value = 1.8e-18

Table S63.  Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
AMP PEAK 8(6Q21) MUTATED 24 36 96
AMP PEAK 8(6Q21) WILD-TYPE 176 387 153

Figure S63.  Get High-res Image Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 2.86e-26 (Fisher's exact test), Q value = 1.7e-23

Table S64.  Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
AMP PEAK 8(6Q21) MUTATED 88 52 16
AMP PEAK 8(6Q21) WILD-TYPE 116 557 43

Figure S64.  Get High-res Image Gene #8: 'Amp Peak 8(6q21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 3.12e-26 (Chi-square test), Q value = 1.8e-23

Table S65.  Gene #9: 'Amp Peak 9(8p11.23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
AMP PEAK 9(8P11.23) MUTATED 92 34 95 59 55
AMP PEAK 9(8P11.23) WILD-TYPE 254 42 103 156 1

Figure S65.  Get High-res Image Gene #9: 'Amp Peak 9(8p11.23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 2.47e-10 (Chi-square test), Q value = 1e-07

Table S66.  Gene #9: 'Amp Peak 9(8p11.23) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
AMP PEAK 9(8P11.23) MUTATED 31 34 33 79 11 26
AMP PEAK 9(8P11.23) WILD-TYPE 65 108 47 44 25 64

Figure S66.  Get High-res Image Gene #9: 'Amp Peak 9(8p11.23) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 1.76e-05 (Fisher's exact test), Q value = 0.0048

Table S67.  Gene #9: 'Amp Peak 9(8p11.23) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
AMP PEAK 9(8P11.23) MUTATED 76 43 200
AMP PEAK 9(8P11.23) WILD-TYPE 159 112 234

Figure S67.  Get High-res Image Gene #9: 'Amp Peak 9(8p11.23) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 3e-25 (Chi-square test), Q value = 1.8e-22

Table S68.  Gene #10: 'Amp Peak 10(8p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
AMP PEAK 10(8P11.21) MUTATED 88 40 81 80 56
AMP PEAK 10(8P11.21) WILD-TYPE 258 36 117 135 0

Figure S68.  Get High-res Image Gene #10: 'Amp Peak 10(8p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 3.77e-05 (Chi-square test), Q value = 0.0097

Table S69.  Gene #10: 'Amp Peak 10(8p11.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
AMP PEAK 10(8P11.21) MUTATED 45 35 30 65 10 30
AMP PEAK 10(8P11.21) WILD-TYPE 51 107 50 58 26 60

Figure S69.  Get High-res Image Gene #10: 'Amp Peak 10(8p11.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 5.22e-05 (Fisher's exact test), Q value = 0.013

Table S70.  Gene #10: 'Amp Peak 10(8p11.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
AMP PEAK 10(8P11.21) MUTATED 102 37 184
AMP PEAK 10(8P11.21) WILD-TYPE 133 118 250

Figure S70.  Get High-res Image Gene #10: 'Amp Peak 10(8p11.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 0.000134 (Fisher's exact test), Q value = 0.031

Table S71.  Gene #10: 'Amp Peak 10(8p11.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
AMP PEAK 10(8P11.21) MUTATED 179 59 85
AMP PEAK 10(8P11.21) WILD-TYPE 234 157 110

Figure S71.  Get High-res Image Gene #10: 'Amp Peak 10(8p11.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 3.61e-10 (Fisher's exact test), Q value = 1.5e-07

Table S72.  Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
AMP PEAK 11(8Q24.21) MUTATED 154 53 139
AMP PEAK 11(8Q24.21) WILD-TYPE 102 39 20

Figure S72.  Get High-res Image Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 2.03e-10 (Fisher's exact test), Q value = 8.6e-08

Table S73.  Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
AMP PEAK 11(8Q24.21) MUTATED 104 178 64
AMP PEAK 11(8Q24.21) WILD-TYPE 17 74 70

Figure S73.  Get High-res Image Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

P value = 1.77e-45 (Chi-square test), Q value = 1.1e-42

Table S74.  Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
AMP PEAK 11(8Q24.21) MUTATED 129 43 152 196 53
AMP PEAK 11(8Q24.21) WILD-TYPE 217 33 46 19 3

Figure S74.  Get High-res Image Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 5.57e-23 (Chi-square test), Q value = 3.2e-20

Table S75.  Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
AMP PEAK 11(8Q24.21) MUTATED 85 42 56 96 16 46
AMP PEAK 11(8Q24.21) WILD-TYPE 11 100 24 27 20 44

Figure S75.  Get High-res Image Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 3.68e-08 (Fisher's exact test), Q value = 1.3e-05

Table S76.  Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
AMP PEAK 11(8Q24.21) MUTATED 124 69 74
AMP PEAK 11(8Q24.21) WILD-TYPE 22 60 41

Figure S76.  Get High-res Image Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

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

P value = 5.27e-07 (Fisher's exact test), Q value = 0.00017

Table S77.  Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
AMP PEAK 11(8Q24.21) MUTATED 98 61 108
AMP PEAK 11(8Q24.21) WILD-TYPE 58 47 18

Figure S77.  Get High-res Image Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

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

P value = 2.34e-20 (Fisher's exact test), Q value = 1.3e-17

Table S78.  Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
AMP PEAK 11(8Q24.21) MUTATED 200 61 275
AMP PEAK 11(8Q24.21) WILD-TYPE 35 94 159

Figure S78.  Get High-res Image Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 6.88e-13 (Fisher's exact test), Q value = 3.3e-10

Table S79.  Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
AMP PEAK 11(8Q24.21) MUTATED 261 110 165
AMP PEAK 11(8Q24.21) WILD-TYPE 152 106 30

Figure S79.  Get High-res Image Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 3.18e-24 (Fisher's exact test), Q value = 1.9e-21

Table S80.  Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
AMP PEAK 11(8Q24.21) MUTATED 97 240 221
AMP PEAK 11(8Q24.21) WILD-TYPE 103 183 28

Figure S80.  Get High-res Image Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 1.55e-19 (Fisher's exact test), Q value = 8.7e-17

Table S81.  Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
AMP PEAK 11(8Q24.21) MUTATED 179 333 46
AMP PEAK 11(8Q24.21) WILD-TYPE 25 276 13

Figure S81.  Get High-res Image Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 7.97e-17 (Fisher's exact test), Q value = 4.3e-14

Table S82.  Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
AMP PEAK 12(10P15.1) MUTATED 43 25 91
AMP PEAK 12(10P15.1) WILD-TYPE 213 67 68

Figure S82.  Get High-res Image Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 4.18e-19 (Fisher's exact test), Q value = 2.3e-16

Table S83.  Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
AMP PEAK 12(10P15.1) MUTATED 79 60 20
AMP PEAK 12(10P15.1) WILD-TYPE 42 192 114

Figure S83.  Get High-res Image Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

P value = 4.58e-35 (Chi-square test), Q value = 2.8e-32

Table S84.  Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
AMP PEAK 12(10P15.1) MUTATED 37 20 53 131 12
AMP PEAK 12(10P15.1) WILD-TYPE 309 56 145 84 44

Figure S84.  Get High-res Image Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 9.02e-24 (Chi-square test), Q value = 5.2e-21

Table S85.  Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
AMP PEAK 12(10P15.1) MUTATED 61 5 23 29 2 24
AMP PEAK 12(10P15.1) WILD-TYPE 35 137 57 94 34 66

Figure S85.  Get High-res Image Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 1.43e-10 (Fisher's exact test), Q value = 6.1e-08

Table S86.  Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
AMP PEAK 12(10P15.1) MUTATED 77 21 29
AMP PEAK 12(10P15.1) WILD-TYPE 69 108 86

Figure S86.  Get High-res Image Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

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

P value = 1.46e-12 (Fisher's exact test), Q value = 6.9e-10

Table S87.  Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
AMP PEAK 12(10P15.1) MUTATED 28 26 73
AMP PEAK 12(10P15.1) WILD-TYPE 128 82 53

Figure S87.  Get High-res Image Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

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

P value = 2.52e-29 (Fisher's exact test), Q value = 1.5e-26

Table S88.  Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
AMP PEAK 12(10P15.1) MUTATED 136 22 78
AMP PEAK 12(10P15.1) WILD-TYPE 99 133 356

Figure S88.  Get High-res Image Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 3.1e-28 (Fisher's exact test), Q value = 1.9e-25

Table S89.  Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
AMP PEAK 12(10P15.1) MUTATED 72 44 120
AMP PEAK 12(10P15.1) WILD-TYPE 341 172 75

Figure S89.  Get High-res Image Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 1.73e-27 (Fisher's exact test), Q value = 1e-24

Table S90.  Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
AMP PEAK 12(10P15.1) MUTATED 43 64 137
AMP PEAK 12(10P15.1) WILD-TYPE 157 359 112

Figure S90.  Get High-res Image Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 6.45e-35 (Fisher's exact test), Q value = 3.9e-32

Table S91.  Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
AMP PEAK 12(10P15.1) MUTATED 126 95 23
AMP PEAK 12(10P15.1) WILD-TYPE 78 514 36

Figure S91.  Get High-res Image Gene #12: 'Amp Peak 12(10p15.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 5.45e-05 (Fisher's exact test), Q value = 0.014

Table S92.  Gene #13: 'Amp Peak 13(10q22.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
AMP PEAK 13(10Q22.3) MUTATED 25 15 42
AMP PEAK 13(10Q22.3) WILD-TYPE 231 77 117

Figure S92.  Get High-res Image Gene #13: 'Amp Peak 13(10q22.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 1.01e-09 (Chi-square test), Q value = 4.1e-07

Table S93.  Gene #13: 'Amp Peak 13(10q22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
AMP PEAK 13(10Q22.3) MUTATED 21 14 28 58 8
AMP PEAK 13(10Q22.3) WILD-TYPE 325 62 170 157 48

Figure S93.  Get High-res Image Gene #13: 'Amp Peak 13(10q22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.000226 (Chi-square test), Q value = 0.05

Table S94.  Gene #13: 'Amp Peak 13(10q22.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
AMP PEAK 13(10Q22.3) MUTATED 23 6 14 19 2 10
AMP PEAK 13(10Q22.3) WILD-TYPE 73 136 66 104 34 80

Figure S94.  Get High-res Image Gene #13: 'Amp Peak 13(10q22.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 9.93e-08 (Fisher's exact test), Q value = 3.5e-05

Table S95.  Gene #13: 'Amp Peak 13(10q22.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
AMP PEAK 13(10Q22.3) MUTATED 61 11 50
AMP PEAK 13(10Q22.3) WILD-TYPE 174 144 384

Figure S95.  Get High-res Image Gene #13: 'Amp Peak 13(10q22.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 5.17e-06 (Fisher's exact test), Q value = 0.0015

Table S96.  Gene #13: 'Amp Peak 13(10q22.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
AMP PEAK 13(10Q22.3) MUTATED 17 49 59
AMP PEAK 13(10Q22.3) WILD-TYPE 183 374 190

Figure S96.  Get High-res Image Gene #13: 'Amp Peak 13(10q22.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 0.000147 (Fisher's exact test), Q value = 0.034

Table S97.  Gene #13: 'Amp Peak 13(10q22.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
AMP PEAK 13(10Q22.3) MUTATED 41 68 16
AMP PEAK 13(10Q22.3) WILD-TYPE 163 541 43

Figure S97.  Get High-res Image Gene #13: 'Amp Peak 13(10q22.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 3.3e-08 (Chi-square test), Q value = 1.2e-05

Table S98.  Gene #14: 'Amp Peak 14(11p13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
AMP PEAK 14(11P13) MUTATED 37 15 58 64 12
AMP PEAK 14(11P13) WILD-TYPE 309 61 140 151 44

Figure S98.  Get High-res Image Gene #14: 'Amp Peak 14(11p13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.000751 (Chi-square test), Q value = 0.15

Table S99.  Gene #14: 'Amp Peak 14(11p13) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
AMP PEAK 14(11P13) MUTATED 27 18 15 38 3 15
AMP PEAK 14(11P13) WILD-TYPE 69 124 65 85 33 75

Figure S99.  Get High-res Image Gene #14: 'Amp Peak 14(11p13) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 8.03e-05 (Fisher's exact test), Q value = 0.019

Table S100.  Gene #14: 'Amp Peak 14(11p13) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
AMP PEAK 14(11P13) MUTATED 70 18 92
AMP PEAK 14(11P13) WILD-TYPE 165 137 342

Figure S100.  Get High-res Image Gene #14: 'Amp Peak 14(11p13) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 3.5e-05 (Fisher's exact test), Q value = 0.009

Table S101.  Gene #14: 'Amp Peak 14(11p13) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
AMP PEAK 14(11P13) MUTATED 28 78 76
AMP PEAK 14(11P13) WILD-TYPE 172 345 173

Figure S101.  Get High-res Image Gene #14: 'Amp Peak 14(11p13) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 1.39e-05 (Fisher's exact test), Q value = 0.0039

Table S102.  Gene #14: 'Amp Peak 14(11p13) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
AMP PEAK 14(11P13) MUTATED 61 101 20
AMP PEAK 14(11P13) WILD-TYPE 143 508 39

Figure S102.  Get High-res Image Gene #14: 'Amp Peak 14(11p13) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 6.2e-34 (Chi-square test), Q value = 3.8e-31

Table S103.  Gene #15: 'Amp Peak 15(11q13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
AMP PEAK 15(11Q13.3) MUTATED 63 29 145 83 20
AMP PEAK 15(11Q13.3) WILD-TYPE 283 47 53 132 36

Figure S103.  Get High-res Image Gene #15: 'Amp Peak 15(11q13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 1.83e-08 (Chi-square test), Q value = 6.9e-06

Table S104.  Gene #15: 'Amp Peak 15(11q13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
AMP PEAK 15(11Q13.3) MUTATED 34 35 41 67 11 18
AMP PEAK 15(11Q13.3) WILD-TYPE 62 107 39 56 25 72

Figure S104.  Get High-res Image Gene #15: 'Amp Peak 15(11q13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 4.58e-13 (Chi-square test), Q value = 2.2e-10

Table S105.  Gene #16: 'Amp Peak 16(11q14.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
AMP PEAK 16(11Q14.1) MUTATED 39 17 71 79 14
AMP PEAK 16(11Q14.1) WILD-TYPE 307 59 127 136 42

Figure S105.  Get High-res Image Gene #16: 'Amp Peak 16(11q14.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 3.14e-05 (Chi-square test), Q value = 0.0083

Table S106.  Gene #16: 'Amp Peak 16(11q14.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
AMP PEAK 16(11Q14.1) MUTATED 33 20 30 25 6 13
AMP PEAK 16(11Q14.1) WILD-TYPE 63 122 50 98 30 77

Figure S106.  Get High-res Image Gene #16: 'Amp Peak 16(11q14.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 0.000112 (Fisher's exact test), Q value = 0.026

Table S107.  Gene #16: 'Amp Peak 16(11q14.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
AMP PEAK 16(11Q14.1) MUTATED 83 27 100
AMP PEAK 16(11Q14.1) WILD-TYPE 152 128 334

Figure S107.  Get High-res Image Gene #16: 'Amp Peak 16(11q14.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 16(11q14.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00121 (Fisher's exact test), Q value = 0.23

Table S108.  Gene #16: 'Amp Peak 16(11q14.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
AMP PEAK 16(11Q14.1) MUTATED 97 44 69
AMP PEAK 16(11Q14.1) WILD-TYPE 316 172 126

Figure S108.  Get High-res Image Gene #16: 'Amp Peak 16(11q14.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

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

Table S109.  Gene #16: 'Amp Peak 16(11q14.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
AMP PEAK 16(11Q14.1) MUTATED 32 89 91
AMP PEAK 16(11Q14.1) WILD-TYPE 168 334 158

Figure S109.  Get High-res Image Gene #16: 'Amp Peak 16(11q14.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 7.01e-05 (Fisher's exact test), Q value = 0.017

Table S110.  Gene #16: 'Amp Peak 16(11q14.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
AMP PEAK 16(11Q14.1) MUTATED 66 123 23
AMP PEAK 16(11Q14.1) WILD-TYPE 138 486 36

Figure S110.  Get High-res Image Gene #16: 'Amp Peak 16(11q14.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 1.74e-10 (Fisher's exact test), Q value = 7.4e-08

Table S111.  Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
AMP PEAK 17(12P13.33) MUTATED 53 14 77
AMP PEAK 17(12P13.33) WILD-TYPE 203 78 82

Figure S111.  Get High-res Image Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 1.35e-13 (Fisher's exact test), Q value = 6.6e-11

Table S112.  Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
AMP PEAK 17(12P13.33) MUTATED 61 72 11
AMP PEAK 17(12P13.33) WILD-TYPE 60 180 123

Figure S112.  Get High-res Image Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

P value = 3.32e-28 (Chi-square test), Q value = 2e-25

Table S113.  Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
AMP PEAK 17(12P13.33) MUTATED 23 22 64 107 16
AMP PEAK 17(12P13.33) WILD-TYPE 323 54 134 108 40

Figure S113.  Get High-res Image Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 4.4e-15 (Chi-square test), Q value = 2.2e-12

Table S114.  Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
AMP PEAK 17(12P13.33) MUTATED 49 13 19 40 2 10
AMP PEAK 17(12P13.33) WILD-TYPE 47 129 61 83 34 80

Figure S114.  Get High-res Image Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 6.79e-08 (Fisher's exact test), Q value = 2.4e-05

Table S115.  Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
AMP PEAK 17(12P13.33) MUTATED 68 30 18
AMP PEAK 17(12P13.33) WILD-TYPE 78 99 97

Figure S115.  Get High-res Image Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

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

P value = 3.08e-07 (Fisher's exact test), Q value = 1e-04

Table S116.  Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
AMP PEAK 17(12P13.33) MUTATED 41 16 59
AMP PEAK 17(12P13.33) WILD-TYPE 115 92 67

Figure S116.  Get High-res Image Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

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

P value = 1.79e-17 (Fisher's exact test), Q value = 9.7e-15

Table S117.  Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
AMP PEAK 17(12P13.33) MUTATED 106 12 95
AMP PEAK 17(12P13.33) WILD-TYPE 129 143 339

Figure S117.  Get High-res Image Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 2.09e-15 (Fisher's exact test), Q value = 1.1e-12

Table S118.  Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
AMP PEAK 17(12P13.33) MUTATED 95 26 92
AMP PEAK 17(12P13.33) WILD-TYPE 318 190 103

Figure S118.  Get High-res Image Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 4.16e-22 (Fisher's exact test), Q value = 2.4e-19

Table S119.  Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
AMP PEAK 17(12P13.33) MUTATED 26 75 123
AMP PEAK 17(12P13.33) WILD-TYPE 174 348 126

Figure S119.  Get High-res Image Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 3.45e-19 (Fisher's exact test), Q value = 1.9e-16

Table S120.  Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
AMP PEAK 17(12P13.33) MUTATED 104 105 15
AMP PEAK 17(12P13.33) WILD-TYPE 100 504 44

Figure S120.  Get High-res Image Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 1.75e-06 (Fisher's exact test), Q value = 0.00055

Table S121.  Gene #18: 'Amp Peak 18(12q15) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
AMP PEAK 18(12Q15) MUTATED 72 10 64
AMP PEAK 18(12Q15) WILD-TYPE 184 82 95

Figure S121.  Get High-res Image Gene #18: 'Amp Peak 18(12q15) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 6.29e-08 (Fisher's exact test), Q value = 2.3e-05

Table S122.  Gene #18: 'Amp Peak 18(12q15) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
AMP PEAK 18(12Q15) MUTATED 28 100 18
AMP PEAK 18(12Q15) WILD-TYPE 93 152 116

Figure S122.  Get High-res Image Gene #18: 'Amp Peak 18(12q15) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

P value = 1.6e-25 (Chi-square test), Q value = 9.4e-23

Table S123.  Gene #18: 'Amp Peak 18(12q15) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
AMP PEAK 18(12Q15) MUTATED 30 25 101 60 12
AMP PEAK 18(12Q15) WILD-TYPE 316 51 97 155 44

Figure S123.  Get High-res Image Gene #18: 'Amp Peak 18(12q15) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 1.64e-13 (Chi-square test), Q value = 8e-11

Table S124.  Gene #18: 'Amp Peak 18(12q15) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
AMP PEAK 18(12Q15) MUTATED 17 19 17 62 6 10
AMP PEAK 18(12Q15) WILD-TYPE 79 123 63 61 30 80

Figure S124.  Get High-res Image Gene #18: 'Amp Peak 18(12q15) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 1.17e-05 (Fisher's exact test), Q value = 0.0033

Table S125.  Gene #18: 'Amp Peak 18(12q15) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
AMP PEAK 18(12Q15) MUTATED 61 20 138
AMP PEAK 18(12Q15) WILD-TYPE 174 135 296

Figure S125.  Get High-res Image Gene #18: 'Amp Peak 18(12q15) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 6.14e-09 (Fisher's exact test), Q value = 2.4e-06

Table S126.  Gene #18: 'Amp Peak 18(12q15) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
AMP PEAK 18(12Q15) MUTATED 21 115 85
AMP PEAK 18(12Q15) WILD-TYPE 179 308 164

Figure S126.  Get High-res Image Gene #18: 'Amp Peak 18(12q15) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 9.35e-06 (Chi-square test), Q value = 0.0027

Table S127.  Gene #19: 'Amp Peak 19(13q12.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
AMP PEAK 19(13Q12.3) MUTATED 22 15 34 44 10
AMP PEAK 19(13Q12.3) WILD-TYPE 324 61 164 171 46

Figure S127.  Get High-res Image Gene #19: 'Amp Peak 19(13q12.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 2.18e-06 (Fisher's exact test), Q value = 0.00067

Table S128.  Gene #19: 'Amp Peak 19(13q12.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
AMP PEAK 19(13Q12.3) MUTATED 45 5 70
AMP PEAK 19(13Q12.3) WILD-TYPE 190 150 364

Figure S128.  Get High-res Image Gene #19: 'Amp Peak 19(13q12.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 3.53e-06 (Fisher's exact test), Q value = 0.0011

Table S129.  Gene #19: 'Amp Peak 19(13q12.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
AMP PEAK 19(13Q12.3) MUTATED 12 54 55
AMP PEAK 19(13Q12.3) WILD-TYPE 188 369 194

Figure S129.  Get High-res Image Gene #19: 'Amp Peak 19(13q12.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 0.0011 (Fisher's exact test), Q value = 0.21

Table S130.  Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
AMP PEAK 20(13Q34) MUTATED 35 15 45
AMP PEAK 20(13Q34) WILD-TYPE 221 77 114

Figure S130.  Get High-res Image Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 8.57e-10 (Fisher's exact test), Q value = 3.5e-07

Table S131.  Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
AMP PEAK 20(13Q34) MUTATED 46 40 9
AMP PEAK 20(13Q34) WILD-TYPE 75 212 125

Figure S131.  Get High-res Image Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

P value = 1.9e-20 (Chi-square test), Q value = 1.1e-17

Table S132.  Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
AMP PEAK 20(13Q34) MUTATED 26 11 28 85 7
AMP PEAK 20(13Q34) WILD-TYPE 320 65 170 130 49

Figure S132.  Get High-res Image Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 2.37e-12 (Chi-square test), Q value = 1.1e-09

Table S133.  Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
AMP PEAK 20(13Q34) MUTATED 40 9 11 18 1 11
AMP PEAK 20(13Q34) WILD-TYPE 56 133 69 105 35 79

Figure S133.  Get High-res Image Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 4.1e-06 (Fisher's exact test), Q value = 0.0012

Table S134.  Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
AMP PEAK 20(13Q34) MUTATED 48 22 10
AMP PEAK 20(13Q34) WILD-TYPE 98 107 105

Figure S134.  Get High-res Image Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

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

P value = 2.88e-08 (Fisher's exact test), Q value = 1.1e-05

Table S135.  Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
AMP PEAK 20(13Q34) MUTATED 25 8 47
AMP PEAK 20(13Q34) WILD-TYPE 131 100 79

Figure S135.  Get High-res Image Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

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

P value = 3.54e-16 (Fisher's exact test), Q value = 1.9e-13

Table S136.  Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
AMP PEAK 20(13Q34) MUTATED 79 5 58
AMP PEAK 20(13Q34) WILD-TYPE 156 150 376

Figure S136.  Get High-res Image Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 3.05e-15 (Fisher's exact test), Q value = 1.5e-12

Table S137.  Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
AMP PEAK 20(13Q34) MUTATED 51 18 73
AMP PEAK 20(13Q34) WILD-TYPE 362 198 122

Figure S137.  Get High-res Image Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 2.36e-15 (Fisher's exact test), Q value = 1.2e-12

Table S138.  Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
AMP PEAK 20(13Q34) MUTATED 24 42 87
AMP PEAK 20(13Q34) WILD-TYPE 176 381 162

Figure S138.  Get High-res Image Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 1.26e-19 (Fisher's exact test), Q value = 7e-17

Table S139.  Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
AMP PEAK 20(13Q34) MUTATED 81 59 13
AMP PEAK 20(13Q34) WILD-TYPE 123 550 46

Figure S139.  Get High-res Image Gene #20: 'Amp Peak 20(13q34) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 21(14q21.1) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.091

Table S140.  Gene #21: 'Amp Peak 21(14q21.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
AMP PEAK 21(14Q21.1) MUTATED 18 73 19
AMP PEAK 21(14Q21.1) WILD-TYPE 103 179 115

Figure S140.  Get High-res Image Gene #21: 'Amp Peak 21(14q21.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

P value = 1.03e-13 (Chi-square test), Q value = 5e-11

Table S141.  Gene #21: 'Amp Peak 21(14q21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
AMP PEAK 21(14Q21.1) MUTATED 31 19 75 43 11
AMP PEAK 21(14Q21.1) WILD-TYPE 315 57 123 172 45

Figure S141.  Get High-res Image Gene #21: 'Amp Peak 21(14q21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 3.91e-06 (Chi-square test), Q value = 0.0012

Table S142.  Gene #21: 'Amp Peak 21(14q21.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
AMP PEAK 21(14Q21.1) MUTATED 14 17 24 38 4 7
AMP PEAK 21(14Q21.1) WILD-TYPE 82 125 56 85 32 83

Figure S142.  Get High-res Image Gene #21: 'Amp Peak 21(14q21.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 21(14q21.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.65e-05 (Fisher's exact test), Q value = 0.0045

Table S143.  Gene #21: 'Amp Peak 21(14q21.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
AMP PEAK 21(14Q21.1) MUTATED 41 16 116
AMP PEAK 21(14Q21.1) WILD-TYPE 194 139 318

Figure S143.  Get High-res Image Gene #21: 'Amp Peak 21(14q21.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 21(14q21.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00123 (Fisher's exact test), Q value = 0.23

Table S144.  Gene #21: 'Amp Peak 21(14q21.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
AMP PEAK 21(14Q21.1) MUTATED 108 36 29
AMP PEAK 21(14Q21.1) WILD-TYPE 305 180 166

Figure S144.  Get High-res Image Gene #21: 'Amp Peak 21(14q21.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 21(14q21.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000113 (Fisher's exact test), Q value = 0.026

Table S145.  Gene #21: 'Amp Peak 21(14q21.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
AMP PEAK 21(14Q21.1) MUTATED 20 92 61
AMP PEAK 21(14Q21.1) WILD-TYPE 180 331 188

Figure S145.  Get High-res Image Gene #21: 'Amp Peak 21(14q21.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 22(15q26.3) mutation analysis' versus 'MRNA_CNMF'

P value = 3.16e-07 (Fisher's exact test), Q value = 0.00011

Table S146.  Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
AMP PEAK 22(15Q26.3) MUTATED 36 10 55
AMP PEAK 22(15Q26.3) WILD-TYPE 220 82 104

Figure S146.  Get High-res Image Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 22(15q26.3) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000286 (Fisher's exact test), Q value = 0.062

Table S147.  Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
AMP PEAK 22(15Q26.3) MUTATED 38 48 15
AMP PEAK 22(15Q26.3) WILD-TYPE 83 204 119

Figure S147.  Get High-res Image Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 22(15q26.3) mutation analysis' versus 'CN_CNMF'

P value = 2.36e-14 (Chi-square test), Q value = 1.2e-11

Table S148.  Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
AMP PEAK 22(15Q26.3) MUTATED 29 8 44 75 6
AMP PEAK 22(15Q26.3) WILD-TYPE 317 68 154 140 50

Figure S148.  Get High-res Image Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 22(15q26.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.00091 (Chi-square test), Q value = 0.18

Table S149.  Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
AMP PEAK 22(15Q26.3) MUTATED 24 7 14 25 6 14
AMP PEAK 22(15Q26.3) WILD-TYPE 72 135 66 98 30 76

Figure S149.  Get High-res Image Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 22(15q26.3) mutation analysis' versus 'RPPA_CNMF'

P value = 0.000168 (Fisher's exact test), Q value = 0.038

Table S150.  Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
AMP PEAK 22(15Q26.3) MUTATED 46 17 16
AMP PEAK 22(15Q26.3) WILD-TYPE 100 112 99

Figure S150.  Get High-res Image Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Amp Peak 22(15q26.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.25e-08 (Fisher's exact test), Q value = 1.9e-05

Table S151.  Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
AMP PEAK 22(15Q26.3) MUTATED 69 11 72
AMP PEAK 22(15Q26.3) WILD-TYPE 166 144 362

Figure S151.  Get High-res Image Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 22(15q26.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.29e-05 (Fisher's exact test), Q value = 0.0087

Table S152.  Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
AMP PEAK 22(15Q26.3) MUTATED 65 29 58
AMP PEAK 22(15Q26.3) WILD-TYPE 348 187 137

Figure S152.  Get High-res Image Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 22(15q26.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.37e-07 (Fisher's exact test), Q value = 4.8e-05

Table S153.  Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
AMP PEAK 22(15Q26.3) MUTATED 25 56 74
AMP PEAK 22(15Q26.3) WILD-TYPE 175 367 175

Figure S153.  Get High-res Image Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 22(15q26.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.18e-10 (Fisher's exact test), Q value = 1.7e-07

Table S154.  Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
AMP PEAK 22(15Q26.3) MUTATED 68 75 12
AMP PEAK 22(15Q26.3) WILD-TYPE 136 534 47

Figure S154.  Get High-res Image Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 23(17p11.2) mutation analysis' versus 'CN_CNMF'

P value = 7.6e-07 (Chi-square test), Q value = 0.00025

Table S155.  Gene #23: 'Amp Peak 23(17p11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
AMP PEAK 23(17P11.2) MUTATED 25 14 44 26 15
AMP PEAK 23(17P11.2) WILD-TYPE 321 62 154 189 41

Figure S155.  Get High-res Image Gene #23: 'Amp Peak 23(17p11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 24(17q12) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000108 (Fisher's exact test), Q value = 0.026

Table S156.  Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
AMP PEAK 24(17Q12) MUTATED 77 16 68
AMP PEAK 24(17Q12) WILD-TYPE 179 76 91

Figure S156.  Get High-res Image Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 24(17q12) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.51e-05 (Fisher's exact test), Q value = 0.0042

Table S157.  Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
AMP PEAK 24(17Q12) MUTATED 37 101 23
AMP PEAK 24(17Q12) WILD-TYPE 84 151 111

Figure S157.  Get High-res Image Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 24(17q12) mutation analysis' versus 'CN_CNMF'

P value = 9.14e-37 (Chi-square test), Q value = 5.6e-34

Table S158.  Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
AMP PEAK 24(17Q12) MUTATED 58 24 138 48 21
AMP PEAK 24(17Q12) WILD-TYPE 288 52 60 167 35

Figure S158.  Get High-res Image Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 24(17q12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.72e-08 (Chi-square test), Q value = 3.1e-05

Table S159.  Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
AMP PEAK 24(17Q12) MUTATED 25 30 35 63 11 18
AMP PEAK 24(17Q12) WILD-TYPE 71 112 45 60 25 72

Figure S159.  Get High-res Image Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 24(17q12) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.59e-05 (Fisher's exact test), Q value = 0.016

Table S160.  Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
AMP PEAK 24(17Q12) MUTATED 88 29 156
AMP PEAK 24(17Q12) WILD-TYPE 147 126 278

Figure S160.  Get High-res Image Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 24(17q12) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000416 (Fisher's exact test), Q value = 0.089

Table S161.  Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
AMP PEAK 24(17Q12) MUTATED 66 183 33
AMP PEAK 24(17Q12) WILD-TYPE 138 426 26

Figure S161.  Get High-res Image Gene #24: 'Amp Peak 24(17q12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 25(17q23.1) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000367 (Fisher's exact test), Q value = 0.079

Table S162.  Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
AMP PEAK 25(17Q23.1) MUTATED 107 23 80
AMP PEAK 25(17Q23.1) WILD-TYPE 149 69 79

Figure S162.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 25(17q23.1) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 5.11e-05 (Fisher's exact test), Q value = 0.013

Table S163.  Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
AMP PEAK 25(17Q23.1) MUTATED 46 127 37
AMP PEAK 25(17Q23.1) WILD-TYPE 75 125 97

Figure S163.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 25(17q23.1) mutation analysis' versus 'CN_CNMF'

P value = 4.12e-40 (Chi-square test), Q value = 2.5e-37

Table S164.  Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
AMP PEAK 25(17Q23.1) MUTATED 69 23 158 93 24
AMP PEAK 25(17Q23.1) WILD-TYPE 277 53 40 122 32

Figure S164.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 25(17q23.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.73e-09 (Chi-square test), Q value = 1.9e-06

Table S165.  Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
AMP PEAK 25(17Q23.1) MUTATED 37 37 36 78 16 24
AMP PEAK 25(17Q23.1) WILD-TYPE 59 105 44 45 20 66

Figure S165.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 25(17q23.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000199 (Fisher's exact test), Q value = 0.044

Table S166.  Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
AMP PEAK 25(17Q23.1) MUTATED 98 44 205
AMP PEAK 25(17Q23.1) WILD-TYPE 137 111 229

Figure S166.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 25(17q23.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.72e-06 (Fisher's exact test), Q value = 0.00054

Table S167.  Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
AMP PEAK 25(17Q23.1) MUTATED 60 165 133
AMP PEAK 25(17Q23.1) WILD-TYPE 140 258 116

Figure S167.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 26(19q12) mutation analysis' versus 'MRNA_CNMF'

P value = 5.61e-08 (Fisher's exact test), Q value = 2e-05

Table S168.  Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
AMP PEAK 26(19Q12) MUTATED 44 26 69
AMP PEAK 26(19Q12) WILD-TYPE 212 66 90

Figure S168.  Get High-res Image Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 26(19q12) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 5.55e-12 (Fisher's exact test), Q value = 2.5e-09

Table S169.  Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
AMP PEAK 26(19Q12) MUTATED 64 56 19
AMP PEAK 26(19Q12) WILD-TYPE 57 196 115

Figure S169.  Get High-res Image Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 26(19q12) mutation analysis' versus 'CN_CNMF'

P value = 1.81e-24 (Chi-square test), Q value = 1.1e-21

Table S170.  Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
AMP PEAK 26(19Q12) MUTATED 35 28 44 108 16
AMP PEAK 26(19Q12) WILD-TYPE 311 48 154 107 40

Figure S170.  Get High-res Image Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 26(19q12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.37e-08 (Chi-square test), Q value = 5.2e-06

Table S171.  Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
AMP PEAK 26(19Q12) MUTATED 46 17 17 31 4 21
AMP PEAK 26(19Q12) WILD-TYPE 50 125 63 92 32 69

Figure S171.  Get High-res Image Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 26(19q12) mutation analysis' versus 'RPPA_CNMF'

P value = 6.56e-07 (Fisher's exact test), Q value = 0.00022

Table S172.  Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
AMP PEAK 26(19Q12) MUTATED 64 23 22
AMP PEAK 26(19Q12) WILD-TYPE 82 106 93

Figure S172.  Get High-res Image Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Amp Peak 26(19q12) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 1.51e-06 (Fisher's exact test), Q value = 0.00048

Table S173.  Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
AMP PEAK 26(19Q12) MUTATED 29 23 57
AMP PEAK 26(19Q12) WILD-TYPE 127 85 69

Figure S173.  Get High-res Image Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 26(19q12) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.87e-14 (Fisher's exact test), Q value = 1.9e-11

Table S174.  Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
AMP PEAK 26(19Q12) MUTATED 107 27 80
AMP PEAK 26(19Q12) WILD-TYPE 128 128 354

Figure S174.  Get High-res Image Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 26(19q12) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.67e-17 (Fisher's exact test), Q value = 2.5e-14

Table S175.  Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
AMP PEAK 26(19Q12) MUTATED 75 40 99
AMP PEAK 26(19Q12) WILD-TYPE 338 176 96

Figure S175.  Get High-res Image Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 26(19q12) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.36e-12 (Fisher's exact test), Q value = 1.1e-09

Table S176.  Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
AMP PEAK 26(19Q12) MUTATED 43 75 108
AMP PEAK 26(19Q12) WILD-TYPE 157 348 141

Figure S176.  Get High-res Image Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 26(19q12) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.69e-17 (Fisher's exact test), Q value = 9.2e-15

Table S177.  Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
AMP PEAK 26(19Q12) MUTATED 101 107 18
AMP PEAK 26(19Q12) WILD-TYPE 103 502 41

Figure S177.  Get High-res Image Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 27(19q13.42) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000202 (Fisher's exact test), Q value = 0.045

Table S178.  Gene #27: 'Amp Peak 27(19q13.42) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
AMP PEAK 27(19Q13.42) MUTATED 54 22 63
AMP PEAK 27(19Q13.42) WILD-TYPE 202 70 96

Figure S178.  Get High-res Image Gene #27: 'Amp Peak 27(19q13.42) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 27(19q13.42) mutation analysis' versus 'CN_CNMF'

P value = 5.8e-15 (Chi-square test), Q value = 2.9e-12

Table S179.  Gene #27: 'Amp Peak 27(19q13.42) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
AMP PEAK 27(19Q13.42) MUTATED 38 29 62 87 16
AMP PEAK 27(19Q13.42) WILD-TYPE 308 47 136 128 40

Figure S179.  Get High-res Image Gene #27: 'Amp Peak 27(19q13.42) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 27(19q13.42) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.71e-06 (Chi-square test), Q value = 0.0014

Table S180.  Gene #27: 'Amp Peak 27(19q13.42) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
AMP PEAK 27(19Q13.42) MUTATED 31 18 22 48 5 16
AMP PEAK 27(19Q13.42) WILD-TYPE 65 124 58 75 31 74

Figure S180.  Get High-res Image Gene #27: 'Amp Peak 27(19q13.42) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 27(19q13.42) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0051

Table S181.  Gene #27: 'Amp Peak 27(19q13.42) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
AMP PEAK 27(19Q13.42) MUTATED 36 100 91
AMP PEAK 27(19Q13.42) WILD-TYPE 164 323 158

Figure S181.  Get High-res Image Gene #27: 'Amp Peak 27(19q13.42) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 27(19q13.42) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.44e-05 (Fisher's exact test), Q value = 0.022

Table S182.  Gene #27: 'Amp Peak 27(19q13.42) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
AMP PEAK 27(19Q13.42) MUTATED 71 133 23
AMP PEAK 27(19Q13.42) WILD-TYPE 133 476 36

Figure S182.  Get High-res Image Gene #27: 'Amp Peak 27(19q13.42) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 28(20q13.2) mutation analysis' versus 'MRNA_CNMF'

P value = 2.58e-08 (Fisher's exact test), Q value = 9.5e-06

Table S183.  Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
AMP PEAK 28(20Q13.2) MUTATED 128 30 111
AMP PEAK 28(20Q13.2) WILD-TYPE 128 62 48

Figure S183.  Get High-res Image Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 28(20q13.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.22e-06 (Fisher's exact test), Q value = 0.00039

Table S184.  Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
AMP PEAK 28(20Q13.2) MUTATED 67 156 46
AMP PEAK 28(20Q13.2) WILD-TYPE 54 96 88

Figure S184.  Get High-res Image Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 28(20q13.2) mutation analysis' versus 'CN_CNMF'

P value = 3.23e-49 (Chi-square test), Q value = 2e-46

Table S185.  Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
AMP PEAK 28(20Q13.2) MUTATED 71 44 163 146 31
AMP PEAK 28(20Q13.2) WILD-TYPE 275 32 35 69 25

Figure S185.  Get High-res Image Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 28(20q13.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.07e-20 (Chi-square test), Q value = 1.2e-17

Table S186.  Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
AMP PEAK 28(20Q13.2) MUTATED 56 35 44 100 12 30
AMP PEAK 28(20Q13.2) WILD-TYPE 40 107 36 23 24 60

Figure S186.  Get High-res Image Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 28(20q13.2) mutation analysis' versus 'RPPA_CNMF'

P value = 0.000494 (Fisher's exact test), Q value = 0.1

Table S187.  Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
AMP PEAK 28(20Q13.2) MUTATED 98 65 51
AMP PEAK 28(20Q13.2) WILD-TYPE 48 64 64

Figure S187.  Get High-res Image Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Amp Peak 28(20q13.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.17e-09 (Fisher's exact test), Q value = 4.8e-07

Table S188.  Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
AMP PEAK 28(20Q13.2) MUTATED 138 46 250
AMP PEAK 28(20Q13.2) WILD-TYPE 97 109 184

Figure S188.  Get High-res Image Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 28(20q13.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.02e-11 (Fisher's exact test), Q value = 1.4e-08

Table S189.  Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
AMP PEAK 28(20Q13.2) MUTATED 67 215 165
AMP PEAK 28(20Q13.2) WILD-TYPE 133 208 84

Figure S189.  Get High-res Image Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 28(20q13.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.29e-08 (Fisher's exact test), Q value = 8.6e-06

Table S190.  Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
AMP PEAK 28(20Q13.2) MUTATED 117 281 49
AMP PEAK 28(20Q13.2) WILD-TYPE 87 328 10

Figure S190.  Get High-res Image Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 1(1p36.13) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.17e-06 (Fisher's exact test), Q value = 0.00096

Table S191.  Gene #29: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
DEL PEAK 1(1P36.13) MUTATED 50 132 35
DEL PEAK 1(1P36.13) WILD-TYPE 71 120 99

Figure S191.  Get High-res Image Gene #29: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 1(1p36.13) mutation analysis' versus 'CN_CNMF'

P value = 3e-33 (Chi-square test), Q value = 1.8e-30

Table S192.  Gene #29: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 1(1P36.13) MUTATED 60 52 129 109 23
DEL PEAK 1(1P36.13) WILD-TYPE 286 24 69 106 33

Figure S192.  Get High-res Image Gene #29: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 1(1p36.13) mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.69e-08 (Chi-square test), Q value = 2.4e-05

Table S193.  Gene #29: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 1(1P36.13) MUTATED 41 39 45 69 10 23
DEL PEAK 1(1P36.13) WILD-TYPE 55 103 35 54 26 67

Figure S193.  Get High-res Image Gene #29: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 1(1p36.13) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.33e-06 (Fisher's exact test), Q value = 0.0013

Table S194.  Gene #29: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
DEL PEAK 1(1P36.13) MUTATED 104 39 206
DEL PEAK 1(1P36.13) WILD-TYPE 131 116 228

Figure S194.  Get High-res Image Gene #29: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 1(1p36.13) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.4e-11 (Fisher's exact test), Q value = 1.5e-08

Table S195.  Gene #29: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
DEL PEAK 1(1P36.13) MUTATED 45 179 135
DEL PEAK 1(1P36.13) WILD-TYPE 155 244 114

Figure S195.  Get High-res Image Gene #29: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 2(1p21.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000109 (Fisher's exact test), Q value = 0.026

Table S196.  Gene #30: 'Del Peak 2(1p21.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
DEL PEAK 2(1P21.2) MUTATED 31 111 35
DEL PEAK 2(1P21.2) WILD-TYPE 90 141 99

Figure S196.  Get High-res Image Gene #30: 'Del Peak 2(1p21.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 2(1p21.2) mutation analysis' versus 'CN_CNMF'

P value = 4.04e-23 (Chi-square test), Q value = 2.3e-20

Table S197.  Gene #30: 'Del Peak 2(1p21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 2(1P21.2) MUTATED 60 51 104 69 17
DEL PEAK 2(1P21.2) WILD-TYPE 286 25 94 146 39

Figure S197.  Get High-res Image Gene #30: 'Del Peak 2(1p21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 2(1p21.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.77e-05 (Chi-square test), Q value = 0.021

Table S198.  Gene #30: 'Del Peak 2(1p21.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 2(1P21.2) MUTATED 28 33 38 53 11 19
DEL PEAK 2(1P21.2) WILD-TYPE 68 109 42 70 25 71

Figure S198.  Get High-res Image Gene #30: 'Del Peak 2(1p21.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 2(1p21.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000366 (Fisher's exact test), Q value = 0.079

Table S199.  Gene #30: 'Del Peak 2(1p21.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
DEL PEAK 2(1P21.2) MUTATED 70 38 175
DEL PEAK 2(1P21.2) WILD-TYPE 165 117 259

Figure S199.  Get High-res Image Gene #30: 'Del Peak 2(1p21.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 3(2q37.3) mutation analysis' versus 'MRNA_CNMF'

P value = 7.69e-07 (Fisher's exact test), Q value = 0.00025

Table S200.  Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
DEL PEAK 3(2Q37.3) MUTATED 65 19 76
DEL PEAK 3(2Q37.3) WILD-TYPE 191 73 83

Figure S200.  Get High-res Image Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 3(2q37.3) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 5.89e-09 (Fisher's exact test), Q value = 2.3e-06

Table S201.  Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
DEL PEAK 3(2Q37.3) MUTATED 58 84 18
DEL PEAK 3(2Q37.3) WILD-TYPE 63 168 116

Figure S201.  Get High-res Image Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 3(2q37.3) mutation analysis' versus 'CN_CNMF'

P value = 5.27e-20 (Chi-square test), Q value = 3e-17

Table S202.  Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 3(2Q37.3) MUTATED 40 29 69 103 22
DEL PEAK 3(2Q37.3) WILD-TYPE 306 47 129 112 34

Figure S202.  Get High-res Image Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 3(2q37.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.74e-10 (Chi-square test), Q value = 2e-07

Table S203.  Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 3(2Q37.3) MUTATED 43 21 24 48 4 10
DEL PEAK 3(2Q37.3) WILD-TYPE 53 121 56 75 32 80

Figure S203.  Get High-res Image Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 3(2q37.3) mutation analysis' versus 'RPPA_CNMF'

P value = 1.32e-08 (Fisher's exact test), Q value = 5e-06

Table S204.  Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
DEL PEAK 3(2Q37.3) MUTATED 70 37 16
DEL PEAK 3(2Q37.3) WILD-TYPE 76 92 99

Figure S204.  Get High-res Image Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 3(2q37.3) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 1.53e-07 (Fisher's exact test), Q value = 5.3e-05

Table S205.  Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
DEL PEAK 3(2Q37.3) MUTATED 55 13 55
DEL PEAK 3(2Q37.3) WILD-TYPE 101 95 71

Figure S205.  Get High-res Image Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 3(2q37.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.19e-11 (Fisher's exact test), Q value = 1.4e-08

Table S206.  Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
DEL PEAK 3(2Q37.3) MUTATED 102 18 126
DEL PEAK 3(2Q37.3) WILD-TYPE 133 137 308

Figure S206.  Get High-res Image Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 3(2q37.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.2e-07 (Fisher's exact test), Q value = 7.6e-05

Table S207.  Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
DEL PEAK 3(2Q37.3) MUTATED 128 37 81
DEL PEAK 3(2Q37.3) WILD-TYPE 285 179 114

Figure S207.  Get High-res Image Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 3(2q37.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.3e-12 (Fisher's exact test), Q value = 1.5e-09

Table S208.  Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
DEL PEAK 3(2Q37.3) MUTATED 31 110 114
DEL PEAK 3(2Q37.3) WILD-TYPE 169 313 135

Figure S208.  Get High-res Image Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 3(2q37.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.58e-07 (Fisher's exact test), Q value = 8.8e-05

Table S209.  Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
DEL PEAK 3(2Q37.3) MUTATED 84 144 27
DEL PEAK 3(2Q37.3) WILD-TYPE 120 465 32

Figure S209.  Get High-res Image Gene #31: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 4(3p14.3) mutation analysis' versus 'MRNA_CNMF'

P value = 2.23e-13 (Fisher's exact test), Q value = 1.1e-10

Table S210.  Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
DEL PEAK 4(3P14.3) MUTATED 49 27 88
DEL PEAK 4(3P14.3) WILD-TYPE 207 65 71

Figure S210.  Get High-res Image Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 4(3p14.3) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 8.42e-09 (Fisher's exact test), Q value = 3.3e-06

Table S211.  Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
DEL PEAK 4(3P14.3) MUTATED 67 66 31
DEL PEAK 4(3P14.3) WILD-TYPE 54 186 103

Figure S211.  Get High-res Image Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 4(3p14.3) mutation analysis' versus 'CN_CNMF'

P value = 2.26e-32 (Chi-square test), Q value = 1.4e-29

Table S212.  Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 4(3P14.3) MUTATED 47 11 75 130 11
DEL PEAK 4(3P14.3) WILD-TYPE 299 65 123 85 45

Figure S212.  Get High-res Image Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 4(3p14.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.65e-12 (Chi-square test), Q value = 2.1e-09

Table S213.  Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 4(3P14.3) MUTATED 48 12 31 46 12 17
DEL PEAK 4(3P14.3) WILD-TYPE 48 130 49 77 24 73

Figure S213.  Get High-res Image Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 4(3p14.3) mutation analysis' versus 'RPPA_CNMF'

P value = 2.21e-09 (Fisher's exact test), Q value = 8.8e-07

Table S214.  Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
DEL PEAK 4(3P14.3) MUTATED 79 25 32
DEL PEAK 4(3P14.3) WILD-TYPE 67 104 83

Figure S214.  Get High-res Image Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 4(3p14.3) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 1.2e-05 (Fisher's exact test), Q value = 0.0034

Table S215.  Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
DEL PEAK 4(3P14.3) MUTATED 40 31 65
DEL PEAK 4(3P14.3) WILD-TYPE 116 77 61

Figure S215.  Get High-res Image Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 4(3p14.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.63e-16 (Fisher's exact test), Q value = 8.7e-14

Table S216.  Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
DEL PEAK 4(3P14.3) MUTATED 125 28 105
DEL PEAK 4(3P14.3) WILD-TYPE 110 127 329

Figure S216.  Get High-res Image Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 4(3p14.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.37e-11 (Fisher's exact test), Q value = 2.4e-08

Table S217.  Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
DEL PEAK 4(3P14.3) MUTATED 103 54 101
DEL PEAK 4(3P14.3) WILD-TYPE 310 162 94

Figure S217.  Get High-res Image Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 4(3p14.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 9.81e-20 (Fisher's exact test), Q value = 5.5e-17

Table S218.  Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
DEL PEAK 4(3P14.3) MUTATED 44 88 135
DEL PEAK 4(3P14.3) WILD-TYPE 156 335 114

Figure S218.  Get High-res Image Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 4(3p14.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.27e-14 (Fisher's exact test), Q value = 1.1e-11

Table S219.  Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
DEL PEAK 4(3P14.3) MUTATED 105 137 25
DEL PEAK 4(3P14.3) WILD-TYPE 99 472 34

Figure S219.  Get High-res Image Gene #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 5(4p16.3) mutation analysis' versus 'MRNA_CNMF'

P value = 1.39e-10 (Fisher's exact test), Q value = 6e-08

Table S220.  Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
DEL PEAK 5(4P16.3) MUTATED 53 31 84
DEL PEAK 5(4P16.3) WILD-TYPE 203 61 75

Figure S220.  Get High-res Image Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 5(4p16.3) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.16e-12 (Fisher's exact test), Q value = 1.5e-09

Table S221.  Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
DEL PEAK 5(4P16.3) MUTATED 72 72 24
DEL PEAK 5(4P16.3) WILD-TYPE 49 180 110

Figure S221.  Get High-res Image Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 5(4p16.3) mutation analysis' versus 'CN_CNMF'

P value = 2.46e-27 (Chi-square test), Q value = 1.5e-24

Table S222.  Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 5(4P16.3) MUTATED 49 39 53 123 15
DEL PEAK 5(4P16.3) WILD-TYPE 297 37 145 92 41

Figure S222.  Get High-res Image Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 5(4p16.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.82e-12 (Chi-square test), Q value = 4e-09

Table S223.  Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 5(4P16.3) MUTATED 58 28 26 27 5 21
DEL PEAK 5(4P16.3) WILD-TYPE 38 114 54 96 31 69

Figure S223.  Get High-res Image Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 5(4p16.3) mutation analysis' versus 'RPPA_CNMF'

P value = 6.65e-07 (Fisher's exact test), Q value = 0.00022

Table S224.  Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
DEL PEAK 5(4P16.3) MUTATED 75 39 24
DEL PEAK 5(4P16.3) WILD-TYPE 71 90 91

Figure S224.  Get High-res Image Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 5(4p16.3) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 3.22e-06 (Fisher's exact test), Q value = 0.00097

Table S225.  Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
DEL PEAK 5(4P16.3) MUTATED 48 24 66
DEL PEAK 5(4P16.3) WILD-TYPE 108 84 60

Figure S225.  Get High-res Image Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 5(4p16.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.72e-22 (Fisher's exact test), Q value = 1.6e-19

Table S226.  Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
DEL PEAK 5(4P16.3) MUTATED 133 22 104
DEL PEAK 5(4P16.3) WILD-TYPE 102 133 330

Figure S226.  Get High-res Image Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 5(4p16.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.6e-18 (Fisher's exact test), Q value = 3.1e-15

Table S227.  Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
DEL PEAK 5(4P16.3) MUTATED 110 38 111
DEL PEAK 5(4P16.3) WILD-TYPE 303 178 84

Figure S227.  Get High-res Image Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 5(4p16.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.12e-14 (Fisher's exact test), Q value = 5.6e-12

Table S228.  Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
DEL PEAK 5(4P16.3) MUTATED 40 103 127
DEL PEAK 5(4P16.3) WILD-TYPE 160 320 122

Figure S228.  Get High-res Image Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 5(4p16.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.71e-15 (Fisher's exact test), Q value = 1.9e-12

Table S229.  Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
DEL PEAK 5(4P16.3) MUTATED 108 138 24
DEL PEAK 5(4P16.3) WILD-TYPE 96 471 35

Figure S229.  Get High-res Image Gene #33: 'Del Peak 5(4p16.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 6(4q35.2) mutation analysis' versus 'MRNA_CNMF'

P value = 7.12e-10 (Fisher's exact test), Q value = 2.9e-07

Table S230.  Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
DEL PEAK 6(4Q35.2) MUTATED 55 26 83
DEL PEAK 6(4Q35.2) WILD-TYPE 201 66 76

Figure S230.  Get High-res Image Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 6(4q35.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.92e-07 (Fisher's exact test), Q value = 6.7e-05

Table S231.  Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
DEL PEAK 6(4Q35.2) MUTATED 63 74 27
DEL PEAK 6(4Q35.2) WILD-TYPE 58 178 107

Figure S231.  Get High-res Image Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 6(4q35.2) mutation analysis' versus 'CN_CNMF'

P value = 7.04e-36 (Chi-square test), Q value = 4.3e-33

Table S232.  Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 6(4Q35.2) MUTATED 50 41 44 134 11
DEL PEAK 6(4Q35.2) WILD-TYPE 296 35 154 81 45

Figure S232.  Get High-res Image Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 6(4q35.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.96e-14 (Chi-square test), Q value = 2.9e-11

Table S233.  Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 6(4Q35.2) MUTATED 61 26 24 23 7 25
DEL PEAK 6(4Q35.2) WILD-TYPE 35 116 56 100 29 65

Figure S233.  Get High-res Image Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 6(4q35.2) mutation analysis' versus 'RPPA_CNMF'

P value = 3.47e-08 (Fisher's exact test), Q value = 1.3e-05

Table S234.  Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
DEL PEAK 6(4Q35.2) MUTATED 77 34 24
DEL PEAK 6(4Q35.2) WILD-TYPE 69 95 91

Figure S234.  Get High-res Image Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 6(4q35.2) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 2.09e-06 (Fisher's exact test), Q value = 0.00065

Table S235.  Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
DEL PEAK 6(4Q35.2) MUTATED 44 25 66
DEL PEAK 6(4Q35.2) WILD-TYPE 112 83 60

Figure S235.  Get High-res Image Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 6(4q35.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.04e-21 (Fisher's exact test), Q value = 1.7e-18

Table S236.  Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
DEL PEAK 6(4Q35.2) MUTATED 131 22 105
DEL PEAK 6(4Q35.2) WILD-TYPE 104 133 329

Figure S236.  Get High-res Image Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 6(4q35.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.18e-15 (Fisher's exact test), Q value = 6.1e-13

Table S237.  Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
DEL PEAK 6(4Q35.2) MUTATED 108 42 108
DEL PEAK 6(4Q35.2) WILD-TYPE 305 174 87

Figure S237.  Get High-res Image Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 6(4q35.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1e-15 (Fisher's exact test), Q value = 5.2e-13

Table S238.  Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
DEL PEAK 6(4Q35.2) MUTATED 38 102 128
DEL PEAK 6(4Q35.2) WILD-TYPE 162 321 121

Figure S238.  Get High-res Image Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 6(4q35.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.34e-17 (Fisher's exact test), Q value = 1.3e-14

Table S239.  Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
DEL PEAK 6(4Q35.2) MUTATED 111 133 24
DEL PEAK 6(4Q35.2) WILD-TYPE 93 476 35

Figure S239.  Get High-res Image Gene #34: 'Del Peak 6(4q35.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 7(5q11.2) mutation analysis' versus 'MRNA_CNMF'

P value = 8.07e-22 (Fisher's exact test), Q value = 4.6e-19

Table S240.  Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
DEL PEAK 7(5Q11.2) MUTATED 26 22 86
DEL PEAK 7(5Q11.2) WILD-TYPE 230 70 73

Figure S240.  Get High-res Image Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 7(5q11.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 5.58e-26 (Fisher's exact test), Q value = 3.3e-23

Table S241.  Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
DEL PEAK 7(5Q11.2) MUTATED 79 41 14
DEL PEAK 7(5Q11.2) WILD-TYPE 42 211 120

Figure S241.  Get High-res Image Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 7(5q11.2) mutation analysis' versus 'CN_CNMF'

P value = 3.42e-62 (Chi-square test), Q value = 2.1e-59

Table S242.  Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 7(5Q11.2) MUTATED 31 6 29 150 15
DEL PEAK 7(5Q11.2) WILD-TYPE 315 70 169 65 41

Figure S242.  Get High-res Image Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 7(5q11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.27e-36 (Chi-square test), Q value = 2e-33

Table S243.  Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 7(5Q11.2) MUTATED 72 3 14 26 4 21
DEL PEAK 7(5Q11.2) WILD-TYPE 24 139 66 97 32 69

Figure S243.  Get High-res Image Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 7(5q11.2) mutation analysis' versus 'RPPA_CNMF'

P value = 1.99e-15 (Fisher's exact test), Q value = 1e-12

Table S244.  Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
DEL PEAK 7(5Q11.2) MUTATED 77 13 23
DEL PEAK 7(5Q11.2) WILD-TYPE 69 116 92

Figure S244.  Get High-res Image Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 7(5q11.2) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 1.27e-18 (Fisher's exact test), Q value = 7e-16

Table S245.  Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
DEL PEAK 7(5Q11.2) MUTATED 25 13 75
DEL PEAK 7(5Q11.2) WILD-TYPE 131 95 51

Figure S245.  Get High-res Image Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 7(5q11.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.1e-41 (Fisher's exact test), Q value = 1.9e-38

Table S246.  Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
DEL PEAK 7(5Q11.2) MUTATED 141 11 66
DEL PEAK 7(5Q11.2) WILD-TYPE 94 144 368

Figure S246.  Get High-res Image Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 7(5q11.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.36e-44 (Fisher's exact test), Q value = 5.2e-41

Table S247.  Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
DEL PEAK 7(5Q11.2) MUTATED 65 23 130
DEL PEAK 7(5Q11.2) WILD-TYPE 348 193 65

Figure S247.  Get High-res Image Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 7(5q11.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 6.02e-41 (Fisher's exact test), Q value = 3.7e-38

Table S248.  Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
DEL PEAK 7(5Q11.2) MUTATED 28 48 144
DEL PEAK 7(5Q11.2) WILD-TYPE 172 375 105

Figure S248.  Get High-res Image Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 7(5q11.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.35e-49 (Fisher's exact test), Q value = 1.5e-46

Table S249.  Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
DEL PEAK 7(5Q11.2) MUTATED 134 69 17
DEL PEAK 7(5Q11.2) WILD-TYPE 70 540 42

Figure S249.  Get High-res Image Gene #35: 'Del Peak 7(5q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 8(5q21.3) mutation analysis' versus 'MRNA_CNMF'

P value = 5.18e-25 (Fisher's exact test), Q value = 3e-22

Table S250.  Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
DEL PEAK 8(5Q21.3) MUTATED 23 22 89
DEL PEAK 8(5Q21.3) WILD-TYPE 233 70 70

Figure S250.  Get High-res Image Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 8(5q21.3) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.83e-27 (Fisher's exact test), Q value = 1.1e-24

Table S251.  Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
DEL PEAK 8(5Q21.3) MUTATED 80 42 12
DEL PEAK 8(5Q21.3) WILD-TYPE 41 210 122

Figure S251.  Get High-res Image Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 8(5q21.3) mutation analysis' versus 'CN_CNMF'

P value = 2.4e-74 (Chi-square test), Q value = 1.5e-71

Table S252.  Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 8(5Q21.3) MUTATED 23 6 25 156 13
DEL PEAK 8(5Q21.3) WILD-TYPE 323 70 173 59 43

Figure S252.  Get High-res Image Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 8(5q21.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.41e-50 (Chi-square test), Q value = 8.8e-48

Table S253.  Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 8(5Q21.3) MUTATED 80 2 9 21 2 21
DEL PEAK 8(5Q21.3) WILD-TYPE 16 140 71 102 34 69

Figure S253.  Get High-res Image Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 8(5q21.3) mutation analysis' versus 'RPPA_CNMF'

P value = 5.76e-15 (Fisher's exact test), Q value = 2.9e-12

Table S254.  Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
DEL PEAK 8(5Q21.3) MUTATED 76 13 23
DEL PEAK 8(5Q21.3) WILD-TYPE 70 116 92

Figure S254.  Get High-res Image Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 8(5q21.3) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 2.82e-15 (Fisher's exact test), Q value = 1.4e-12

Table S255.  Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
DEL PEAK 8(5Q21.3) MUTATED 26 15 71
DEL PEAK 8(5Q21.3) WILD-TYPE 130 93 55

Figure S255.  Get High-res Image Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 8(5q21.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.89e-48 (Fisher's exact test), Q value = 1.8e-45

Table S256.  Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
DEL PEAK 8(5Q21.3) MUTATED 144 8 57
DEL PEAK 8(5Q21.3) WILD-TYPE 91 147 377

Figure S256.  Get High-res Image Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 8(5q21.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.1e-49 (Fisher's exact test), Q value = 3.2e-46

Table S257.  Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
DEL PEAK 8(5Q21.3) MUTATED 55 22 132
DEL PEAK 8(5Q21.3) WILD-TYPE 358 194 63

Figure S257.  Get High-res Image Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 8(5q21.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.74e-40 (Fisher's exact test), Q value = 1.7e-37

Table S258.  Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
DEL PEAK 8(5Q21.3) MUTATED 27 46 141
DEL PEAK 8(5Q21.3) WILD-TYPE 173 377 108

Figure S258.  Get High-res Image Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 8(5q21.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.29e-53 (Fisher's exact test), Q value = 1.4e-50

Table S259.  Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
DEL PEAK 8(5Q21.3) MUTATED 136 63 15
DEL PEAK 8(5Q21.3) WILD-TYPE 68 546 44

Figure S259.  Get High-res Image Gene #36: 'Del Peak 8(5q21.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 9(6p25.3) mutation analysis' versus 'CN_CNMF'

P value = 4.07e-06 (Chi-square test), Q value = 0.0012

Table S260.  Gene #37: 'Del Peak 9(6p25.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 9(6P25.3) MUTATED 37 15 58 44 13
DEL PEAK 9(6P25.3) WILD-TYPE 309 61 140 171 43

Figure S260.  Get High-res Image Gene #37: 'Del Peak 9(6p25.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 9(6p25.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.56e-05 (Chi-square test), Q value = 0.014

Table S261.  Gene #37: 'Del Peak 9(6p25.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 9(6P25.3) MUTATED 23 16 16 39 2 11
DEL PEAK 9(6P25.3) WILD-TYPE 73 126 64 84 34 79

Figure S261.  Get High-res Image Gene #37: 'Del Peak 9(6p25.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 10(6q15) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000985 (Fisher's exact test), Q value = 0.19

Table S262.  Gene #38: 'Del Peak 10(6q15) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
DEL PEAK 10(6Q15) MUTATED 25 100 43
DEL PEAK 10(6Q15) WILD-TYPE 96 152 91

Figure S262.  Get High-res Image Gene #38: 'Del Peak 10(6q15) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 10(6q15) mutation analysis' versus 'CN_CNMF'

P value = 1.45e-26 (Chi-square test), Q value = 8.6e-24

Table S263.  Gene #38: 'Del Peak 10(6q15) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 10(6Q15) MUTATED 78 25 117 37 36
DEL PEAK 10(6Q15) WILD-TYPE 268 51 81 178 20

Figure S263.  Get High-res Image Gene #38: 'Del Peak 10(6q15) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 10(6q15) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.07e-07 (Chi-square test), Q value = 3.8e-05

Table S264.  Gene #38: 'Del Peak 10(6q15) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 10(6Q15) MUTATED 19 49 27 64 6 17
DEL PEAK 10(6Q15) WILD-TYPE 77 93 53 59 30 73

Figure S264.  Get High-res Image Gene #38: 'Del Peak 10(6q15) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 10(6q15) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.98e-05 (Fisher's exact test), Q value = 0.0054

Table S265.  Gene #38: 'Del Peak 10(6q15) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
DEL PEAK 10(6Q15) MUTATED 55 46 176
DEL PEAK 10(6Q15) WILD-TYPE 180 109 258

Figure S265.  Get High-res Image Gene #38: 'Del Peak 10(6q15) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 10(6q15) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.019

Table S266.  Gene #38: 'Del Peak 10(6q15) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
DEL PEAK 10(6Q15) MUTATED 166 66 45
DEL PEAK 10(6Q15) WILD-TYPE 247 150 150

Figure S266.  Get High-res Image Gene #38: 'Del Peak 10(6q15) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 11(6q27) mutation analysis' versus 'CN_CNMF'

P value = 3.04e-13 (Chi-square test), Q value = 1.5e-10

Table S267.  Gene #39: 'Del Peak 11(6q27) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 11(6Q27) MUTATED 77 23 97 70 36
DEL PEAK 11(6Q27) WILD-TYPE 269 53 101 145 20

Figure S267.  Get High-res Image Gene #39: 'Del Peak 11(6q27) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 12(7p22.3) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000233 (Fisher's exact test), Q value = 0.051

Table S268.  Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
DEL PEAK 12(7P22.3) MUTATED 30 6 38
DEL PEAK 12(7P22.3) WILD-TYPE 226 86 121

Figure S268.  Get High-res Image Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 12(7p22.3) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000547 (Fisher's exact test), Q value = 0.11

Table S269.  Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
DEL PEAK 12(7P22.3) MUTATED 27 39 8
DEL PEAK 12(7P22.3) WILD-TYPE 94 213 126

Figure S269.  Get High-res Image Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 12(7p22.3) mutation analysis' versus 'CN_CNMF'

P value = 7.09e-16 (Chi-square test), Q value = 3.7e-13

Table S270.  Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 12(7P22.3) MUTATED 12 3 44 54 4
DEL PEAK 12(7P22.3) WILD-TYPE 334 73 154 161 52

Figure S270.  Get High-res Image Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 12(7p22.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.54e-05 (Chi-square test), Q value = 0.0042

Table S271.  Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 12(7P22.3) MUTATED 22 7 12 17 2 2
DEL PEAK 12(7P22.3) WILD-TYPE 74 135 68 106 34 88

Figure S271.  Get High-res Image Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 12(7p22.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.93e-09 (Fisher's exact test), Q value = 3.1e-06

Table S272.  Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
DEL PEAK 12(7P22.3) MUTATED 54 4 56
DEL PEAK 12(7P22.3) WILD-TYPE 181 151 378

Figure S272.  Get High-res Image Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 12(7p22.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.72e-06 (Fisher's exact test), Q value = 0.0011

Table S273.  Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
DEL PEAK 12(7P22.3) MUTATED 59 12 43
DEL PEAK 12(7P22.3) WILD-TYPE 354 204 152

Figure S273.  Get High-res Image Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 12(7p22.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.9e-10 (Fisher's exact test), Q value = 1.6e-07

Table S274.  Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
DEL PEAK 12(7P22.3) MUTATED 9 43 61
DEL PEAK 12(7P22.3) WILD-TYPE 191 380 188

Figure S274.  Get High-res Image Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 12(7p22.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.62e-09 (Fisher's exact test), Q value = 1.4e-06

Table S275.  Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
DEL PEAK 12(7P22.3) MUTATED 51 50 12
DEL PEAK 12(7P22.3) WILD-TYPE 153 559 47

Figure S275.  Get High-res Image Gene #40: 'Del Peak 12(7p22.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 13(7q36.1) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000562 (Fisher's exact test), Q value = 0.11

Table S276.  Gene #41: 'Del Peak 13(7q36.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
DEL PEAK 13(7Q36.1) MUTATED 43 11 48
DEL PEAK 13(7Q36.1) WILD-TYPE 213 81 111

Figure S276.  Get High-res Image Gene #41: 'Del Peak 13(7q36.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 13(7q36.1) mutation analysis' versus 'CN_CNMF'

P value = 2.34e-08 (Chi-square test), Q value = 8.7e-06

Table S277.  Gene #41: 'Del Peak 13(7q36.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 13(7Q36.1) MUTATED 39 13 56 61 4
DEL PEAK 13(7Q36.1) WILD-TYPE 307 63 142 154 52

Figure S277.  Get High-res Image Gene #41: 'Del Peak 13(7q36.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 13(7q36.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000824 (Fisher's exact test), Q value = 0.17

Table S278.  Gene #41: 'Del Peak 13(7q36.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
DEL PEAK 13(7Q36.1) MUTATED 65 19 85
DEL PEAK 13(7Q36.1) WILD-TYPE 170 136 349

Figure S278.  Get High-res Image Gene #41: 'Del Peak 13(7q36.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 13(7q36.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 7.75e-09 (Fisher's exact test), Q value = 3e-06

Table S279.  Gene #41: 'Del Peak 13(7q36.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
DEL PEAK 13(7Q36.1) MUTATED 22 65 80
DEL PEAK 13(7Q36.1) WILD-TYPE 178 358 169

Figure S279.  Get High-res Image Gene #41: 'Del Peak 13(7q36.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 13(7q36.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.57e-06 (Fisher's exact test), Q value = 5e-04

Table S280.  Gene #41: 'Del Peak 13(7q36.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
DEL PEAK 13(7Q36.1) MUTATED 55 90 22
DEL PEAK 13(7Q36.1) WILD-TYPE 149 519 37

Figure S280.  Get High-res Image Gene #41: 'Del Peak 13(7q36.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 14(8p23.2) mutation analysis' versus 'MRNA_CNMF'

P value = 3.44e-05 (Fisher's exact test), Q value = 0.009

Table S281.  Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
DEL PEAK 14(8P23.2) MUTATED 122 42 109
DEL PEAK 14(8P23.2) WILD-TYPE 134 50 50

Figure S281.  Get High-res Image Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 14(8p23.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 2.92e-06 (Fisher's exact test), Q value = 0.00089

Table S282.  Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
DEL PEAK 14(8P23.2) MUTATED 85 136 52
DEL PEAK 14(8P23.2) WILD-TYPE 36 116 82

Figure S282.  Get High-res Image Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 14(8p23.2) mutation analysis' versus 'CN_CNMF'

P value = 1.15e-30 (Chi-square test), Q value = 6.9e-28

Table S283.  Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 14(8P23.2) MUTATED 115 18 139 154 43
DEL PEAK 14(8P23.2) WILD-TYPE 231 58 59 61 13

Figure S283.  Get High-res Image Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 14(8p23.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.92e-10 (Chi-square test), Q value = 1.2e-07

Table S284.  Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 14(8P23.2) MUTATED 64 42 42 83 17 36
DEL PEAK 14(8P23.2) WILD-TYPE 32 100 38 40 19 54

Figure S284.  Get High-res Image Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 14(8p23.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.38e-11 (Fisher's exact test), Q value = 1.1e-08

Table S285.  Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
DEL PEAK 14(8P23.2) MUTATED 160 50 230
DEL PEAK 14(8P23.2) WILD-TYPE 75 105 204

Figure S285.  Get High-res Image Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 14(8p23.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.01e-06 (Fisher's exact test), Q value = 0.00063

Table S286.  Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
DEL PEAK 14(8P23.2) MUTATED 218 91 131
DEL PEAK 14(8P23.2) WILD-TYPE 195 125 64

Figure S286.  Get High-res Image Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 14(8p23.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 5.35e-08 (Fisher's exact test), Q value = 1.9e-05

Table S287.  Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
DEL PEAK 14(8P23.2) MUTATED 86 203 168
DEL PEAK 14(8P23.2) WILD-TYPE 114 220 81

Figure S287.  Get High-res Image Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 14(8p23.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.5e-09 (Fisher's exact test), Q value = 6e-07

Table S288.  Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
DEL PEAK 14(8P23.2) MUTATED 143 277 37
DEL PEAK 14(8P23.2) WILD-TYPE 61 332 22

Figure S288.  Get High-res Image Gene #42: 'Del Peak 14(8p23.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 15(8p11.21) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000175 (Fisher's exact test), Q value = 0.039

Table S289.  Gene #43: 'Del Peak 15(8p11.21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
DEL PEAK 15(8P11.21) MUTATED 34 18 48
DEL PEAK 15(8P11.21) WILD-TYPE 222 74 111

Figure S289.  Get High-res Image Gene #43: 'Del Peak 15(8p11.21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 15(8p11.21) mutation analysis' versus 'CN_CNMF'

P value = 1.12e-10 (Chi-square test), Q value = 4.8e-08

Table S290.  Gene #43: 'Del Peak 15(8p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 15(8P11.21) MUTATED 40 9 50 69 2
DEL PEAK 15(8P11.21) WILD-TYPE 306 67 148 146 54

Figure S290.  Get High-res Image Gene #43: 'Del Peak 15(8p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 15(8p11.21) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000996 (Fisher's exact test), Q value = 0.19

Table S291.  Gene #43: 'Del Peak 15(8p11.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
DEL PEAK 15(8P11.21) MUTATED 63 19 77
DEL PEAK 15(8P11.21) WILD-TYPE 172 136 357

Figure S291.  Get High-res Image Gene #43: 'Del Peak 15(8p11.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 15(8p11.21) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.97e-06 (Fisher's exact test), Q value = 0.0014

Table S292.  Gene #43: 'Del Peak 15(8p11.21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
DEL PEAK 15(8P11.21) MUTATED 57 91 20
DEL PEAK 15(8P11.21) WILD-TYPE 147 518 39

Figure S292.  Get High-res Image Gene #43: 'Del Peak 15(8p11.21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 16(9p21.3) mutation analysis' versus 'MRNA_CNMF'

P value = 1.01e-05 (Fisher's exact test), Q value = 0.0029

Table S293.  Gene #44: 'Del Peak 16(9p21.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
DEL PEAK 16(9P21.3) MUTATED 86 19 79
DEL PEAK 16(9P21.3) WILD-TYPE 170 73 80

Figure S293.  Get High-res Image Gene #44: 'Del Peak 16(9p21.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 16(9p21.3) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.96e-06 (Fisher's exact test), Q value = 0.0012

Table S294.  Gene #44: 'Del Peak 16(9p21.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
DEL PEAK 16(9P21.3) MUTATED 43 114 27
DEL PEAK 16(9P21.3) WILD-TYPE 78 138 107

Figure S294.  Get High-res Image Gene #44: 'Del Peak 16(9p21.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 16(9p21.3) mutation analysis' versus 'CN_CNMF'

P value = 7.63e-29 (Chi-square test), Q value = 4.6e-26

Table S295.  Gene #44: 'Del Peak 16(9p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 16(9P21.3) MUTATED 46 23 117 98 14
DEL PEAK 16(9P21.3) WILD-TYPE 300 53 81 117 42

Figure S295.  Get High-res Image Gene #44: 'Del Peak 16(9p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 16(9p21.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.76e-14 (Chi-square test), Q value = 1.4e-11

Table S296.  Gene #44: 'Del Peak 16(9p21.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 16(9P21.3) MUTATED 39 17 34 64 7 13
DEL PEAK 16(9P21.3) WILD-TYPE 57 125 46 59 29 77

Figure S296.  Get High-res Image Gene #44: 'Del Peak 16(9p21.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 16(9p21.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.14e-07 (Fisher's exact test), Q value = 4e-05

Table S297.  Gene #44: 'Del Peak 16(9p21.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
DEL PEAK 16(9P21.3) MUTATED 94 25 167
DEL PEAK 16(9P21.3) WILD-TYPE 141 130 267

Figure S297.  Get High-res Image Gene #44: 'Del Peak 16(9p21.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 16(9p21.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 9.58e-10 (Fisher's exact test), Q value = 3.9e-07

Table S298.  Gene #44: 'Del Peak 16(9p21.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
DEL PEAK 16(9P21.3) MUTATED 35 140 114
DEL PEAK 16(9P21.3) WILD-TYPE 165 283 135

Figure S298.  Get High-res Image Gene #44: 'Del Peak 16(9p21.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 16(9p21.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.19e-05 (Fisher's exact test), Q value = 0.013

Table S299.  Gene #44: 'Del Peak 16(9p21.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
DEL PEAK 16(9P21.3) MUTATED 86 174 29
DEL PEAK 16(9P21.3) WILD-TYPE 118 435 30

Figure S299.  Get High-res Image Gene #44: 'Del Peak 16(9p21.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 17(9q21.11) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000914 (Fisher's exact test), Q value = 0.18

Table S300.  Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
DEL PEAK 17(9Q21.11) MUTATED 68 18 64
DEL PEAK 17(9Q21.11) WILD-TYPE 188 74 95

Figure S300.  Get High-res Image Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 17(9q21.11) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.98e-05 (Fisher's exact test), Q value = 0.0054

Table S301.  Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
DEL PEAK 17(9Q21.11) MUTATED 47 83 20
DEL PEAK 17(9Q21.11) WILD-TYPE 74 169 114

Figure S301.  Get High-res Image Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 17(9q21.11) mutation analysis' versus 'CN_CNMF'

P value = 9.57e-18 (Chi-square test), Q value = 5.2e-15

Table S302.  Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 17(9Q21.11) MUTATED 36 22 76 90 15
DEL PEAK 17(9Q21.11) WILD-TYPE 310 54 122 125 41

Figure S302.  Get High-res Image Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 17(9q21.11) mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.77e-10 (Chi-square test), Q value = 4e-07

Table S303.  Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 17(9Q21.11) MUTATED 37 13 17 49 4 16
DEL PEAK 17(9Q21.11) WILD-TYPE 59 129 63 74 32 74

Figure S303.  Get High-res Image Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 17(9q21.11) mutation analysis' versus 'RPPA_CNMF'

P value = 1.44e-05 (Fisher's exact test), Q value = 0.004

Table S304.  Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
DEL PEAK 17(9Q21.11) MUTATED 64 32 21
DEL PEAK 17(9Q21.11) WILD-TYPE 82 97 94

Figure S304.  Get High-res Image Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 17(9q21.11) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.82e-06 (Fisher's exact test), Q value = 0.00086

Table S305.  Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
DEL PEAK 17(9Q21.11) MUTATED 85 21 122
DEL PEAK 17(9Q21.11) WILD-TYPE 150 134 312

Figure S305.  Get High-res Image Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 17(9q21.11) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.67e-05 (Fisher's exact test), Q value = 0.021

Table S306.  Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
DEL PEAK 17(9Q21.11) MUTATED 117 39 72
DEL PEAK 17(9Q21.11) WILD-TYPE 296 177 123

Figure S306.  Get High-res Image Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 17(9q21.11) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 8.68e-09 (Fisher's exact test), Q value = 3.3e-06

Table S307.  Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
DEL PEAK 17(9Q21.11) MUTATED 31 101 100
DEL PEAK 17(9Q21.11) WILD-TYPE 169 322 149

Figure S307.  Get High-res Image Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 17(9q21.11) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.35e-09 (Fisher's exact test), Q value = 5.5e-07

Table S308.  Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
DEL PEAK 17(9Q21.11) MUTATED 88 124 20
DEL PEAK 17(9Q21.11) WILD-TYPE 116 485 39

Figure S308.  Get High-res Image Gene #45: 'Del Peak 17(9q21.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 18(10q23.31) mutation analysis' versus 'MRNA_CNMF'

P value = 4.65e-07 (Fisher's exact test), Q value = 0.00015

Table S309.  Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
DEL PEAK 18(10Q23.31) MUTATED 51 23 71
DEL PEAK 18(10Q23.31) WILD-TYPE 205 69 88

Figure S309.  Get High-res Image Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 18(10q23.31) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 9.23e-05 (Fisher's exact test), Q value = 0.022

Table S310.  Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
DEL PEAK 18(10Q23.31) MUTATED 53 65 27
DEL PEAK 18(10Q23.31) WILD-TYPE 68 187 107

Figure S310.  Get High-res Image Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 18(10q23.31) mutation analysis' versus 'CN_CNMF'

P value = 1.31e-18 (Chi-square test), Q value = 7.2e-16

Table S311.  Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 18(10Q23.31) MUTATED 45 19 72 105 17
DEL PEAK 18(10Q23.31) WILD-TYPE 301 57 126 110 39

Figure S311.  Get High-res Image Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 18(10q23.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.14e-11 (Chi-square test), Q value = 2.3e-08

Table S312.  Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 18(10Q23.31) MUTATED 51 19 26 48 7 16
DEL PEAK 18(10Q23.31) WILD-TYPE 45 123 54 75 29 74

Figure S312.  Get High-res Image Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 18(10q23.31) mutation analysis' versus 'RPPA_CNMF'

P value = 5.69e-08 (Fisher's exact test), Q value = 2.1e-05

Table S313.  Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
DEL PEAK 18(10Q23.31) MUTATED 67 30 17
DEL PEAK 18(10Q23.31) WILD-TYPE 79 99 98

Figure S313.  Get High-res Image Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 18(10q23.31) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 2.15e-05 (Fisher's exact test), Q value = 0.0058

Table S314.  Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
DEL PEAK 18(10Q23.31) MUTATED 45 16 53
DEL PEAK 18(10Q23.31) WILD-TYPE 111 92 73

Figure S314.  Get High-res Image Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 18(10q23.31) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.38e-12 (Fisher's exact test), Q value = 1.1e-09

Table S315.  Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
DEL PEAK 18(10Q23.31) MUTATED 109 21 114
DEL PEAK 18(10Q23.31) WILD-TYPE 126 134 320

Figure S315.  Get High-res Image Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 18(10q23.31) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.39e-08 (Fisher's exact test), Q value = 2.3e-05

Table S316.  Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
DEL PEAK 18(10Q23.31) MUTATED 111 44 89
DEL PEAK 18(10Q23.31) WILD-TYPE 302 172 106

Figure S316.  Get High-res Image Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 18(10q23.31) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.41e-09 (Fisher's exact test), Q value = 1.7e-06

Table S317.  Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
DEL PEAK 18(10Q23.31) MUTATED 41 99 109
DEL PEAK 18(10Q23.31) WILD-TYPE 159 324 140

Figure S317.  Get High-res Image Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 18(10q23.31) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.12e-09 (Fisher's exact test), Q value = 1.6e-06

Table S318.  Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
DEL PEAK 18(10Q23.31) MUTATED 94 139 16
DEL PEAK 18(10Q23.31) WILD-TYPE 110 470 43

Figure S318.  Get High-res Image Gene #46: 'Del Peak 18(10q23.31) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 19(10q26.3) mutation analysis' versus 'MRNA_CNMF'

P value = 1.75e-09 (Fisher's exact test), Q value = 7e-07

Table S319.  Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
DEL PEAK 19(10Q26.3) MUTATED 49 23 77
DEL PEAK 19(10Q26.3) WILD-TYPE 207 69 82

Figure S319.  Get High-res Image Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 19(10q26.3) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.68e-07 (Fisher's exact test), Q value = 0.00012

Table S320.  Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
DEL PEAK 19(10Q26.3) MUTATED 58 68 23
DEL PEAK 19(10Q26.3) WILD-TYPE 63 184 111

Figure S320.  Get High-res Image Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 19(10q26.3) mutation analysis' versus 'CN_CNMF'

P value = 1.02e-19 (Chi-square test), Q value = 5.7e-17

Table S321.  Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 19(10Q26.3) MUTATED 46 17 72 108 16
DEL PEAK 19(10Q26.3) WILD-TYPE 300 59 126 107 40

Figure S321.  Get High-res Image Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 19(10q26.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.24e-10 (Chi-square test), Q value = 5.4e-08

Table S322.  Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 19(10Q26.3) MUTATED 51 18 31 40 8 17
DEL PEAK 19(10Q26.3) WILD-TYPE 45 124 49 83 28 73

Figure S322.  Get High-res Image Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 19(10q26.3) mutation analysis' versus 'RPPA_CNMF'

P value = 2.12e-08 (Fisher's exact test), Q value = 8e-06

Table S323.  Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
DEL PEAK 19(10Q26.3) MUTATED 71 26 22
DEL PEAK 19(10Q26.3) WILD-TYPE 75 103 93

Figure S323.  Get High-res Image Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 19(10q26.3) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 1.92e-07 (Fisher's exact test), Q value = 6.7e-05

Table S324.  Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
DEL PEAK 19(10Q26.3) MUTATED 43 16 60
DEL PEAK 19(10Q26.3) WILD-TYPE 113 92 66

Figure S324.  Get High-res Image Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 19(10q26.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.56e-15 (Fisher's exact test), Q value = 8.1e-13

Table S325.  Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
DEL PEAK 19(10Q26.3) MUTATED 114 18 112
DEL PEAK 19(10Q26.3) WILD-TYPE 121 137 322

Figure S325.  Get High-res Image Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 19(10q26.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.26e-10 (Fisher's exact test), Q value = 9.6e-08

Table S326.  Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
DEL PEAK 19(10Q26.3) MUTATED 112 39 93
DEL PEAK 19(10Q26.3) WILD-TYPE 301 177 102

Figure S326.  Get High-res Image Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 19(10q26.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.66e-13 (Fisher's exact test), Q value = 8e-11

Table S327.  Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
DEL PEAK 19(10Q26.3) MUTATED 39 91 118
DEL PEAK 19(10Q26.3) WILD-TYPE 161 332 131

Figure S327.  Get High-res Image Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 19(10q26.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.91e-12 (Fisher's exact test), Q value = 9e-10

Table S328.  Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
DEL PEAK 19(10Q26.3) MUTATED 96 128 24
DEL PEAK 19(10Q26.3) WILD-TYPE 108 481 35

Figure S328.  Get High-res Image Gene #47: 'Del Peak 19(10q26.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 20(11p15.5) mutation analysis' versus 'MRNA_CNMF'

P value = 5.04e-11 (Fisher's exact test), Q value = 2.2e-08

Table S329.  Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
DEL PEAK 20(11P15.5) MUTATED 47 24 80
DEL PEAK 20(11P15.5) WILD-TYPE 209 68 79

Figure S329.  Get High-res Image Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 20(11p15.5) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 6.22e-08 (Fisher's exact test), Q value = 2.2e-05

Table S330.  Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
DEL PEAK 20(11P15.5) MUTATED 62 60 29
DEL PEAK 20(11P15.5) WILD-TYPE 59 192 105

Figure S330.  Get High-res Image Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 20(11p15.5) mutation analysis' versus 'CN_CNMF'

P value = 3e-30 (Chi-square test), Q value = 1.8e-27

Table S331.  Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 20(11P15.5) MUTATED 40 14 68 124 13
DEL PEAK 20(11P15.5) WILD-TYPE 306 62 130 91 43

Figure S331.  Get High-res Image Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 20(11p15.5) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.01e-09 (Chi-square test), Q value = 4.1e-07

Table S332.  Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 20(11P15.5) MUTATED 48 16 26 38 10 15
DEL PEAK 20(11P15.5) WILD-TYPE 48 126 54 85 26 75

Figure S332.  Get High-res Image Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 20(11p15.5) mutation analysis' versus 'RPPA_CNMF'

P value = 2.51e-09 (Fisher's exact test), Q value = 1e-06

Table S333.  Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
DEL PEAK 20(11P15.5) MUTATED 76 26 25
DEL PEAK 20(11P15.5) WILD-TYPE 70 103 90

Figure S333.  Get High-res Image Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 20(11p15.5) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 3.81e-06 (Fisher's exact test), Q value = 0.0011

Table S334.  Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
DEL PEAK 20(11P15.5) MUTATED 38 26 63
DEL PEAK 20(11P15.5) WILD-TYPE 118 82 63

Figure S334.  Get High-res Image Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 20(11p15.5) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.05e-16 (Fisher's exact test), Q value = 5.6e-14

Table S335.  Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
DEL PEAK 20(11P15.5) MUTATED 119 22 102
DEL PEAK 20(11P15.5) WILD-TYPE 116 133 332

Figure S335.  Get High-res Image Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 20(11p15.5) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.64e-12 (Fisher's exact test), Q value = 1.7e-09

Table S336.  Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
DEL PEAK 20(11P15.5) MUTATED 97 47 99
DEL PEAK 20(11P15.5) WILD-TYPE 316 169 96

Figure S336.  Get High-res Image Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 20(11p15.5) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 7.33e-17 (Fisher's exact test), Q value = 3.9e-14

Table S337.  Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
DEL PEAK 20(11P15.5) MUTATED 38 88 125
DEL PEAK 20(11P15.5) WILD-TYPE 162 335 124

Figure S337.  Get High-res Image Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 20(11p15.5) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.13e-17 (Fisher's exact test), Q value = 3.8e-14

Table S338.  Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
DEL PEAK 20(11P15.5) MUTATED 106 123 22
DEL PEAK 20(11P15.5) WILD-TYPE 98 486 37

Figure S338.  Get High-res Image Gene #48: 'Del Peak 20(11p15.5) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 21(11q23.2) mutation analysis' versus 'CN_CNMF'

P value = 3.59e-26 (Chi-square test), Q value = 2.1e-23

Table S339.  Gene #49: 'Del Peak 21(11q23.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 21(11Q23.2) MUTATED 117 33 164 106 22
DEL PEAK 21(11Q23.2) WILD-TYPE 229 43 34 109 34

Figure S339.  Get High-res Image Gene #49: 'Del Peak 21(11q23.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 21(11q23.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.17e-10 (Chi-square test), Q value = 1.3e-07

Table S340.  Gene #49: 'Del Peak 21(11q23.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 21(11Q23.2) MUTATED 36 57 51 90 20 31
DEL PEAK 21(11Q23.2) WILD-TYPE 60 85 29 33 16 59

Figure S340.  Get High-res Image Gene #49: 'Del Peak 21(11q23.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 22(12p13.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000962 (Fisher's exact test), Q value = 0.19

Table S341.  Gene #50: 'Del Peak 22(12p13.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
DEL PEAK 22(12P13.1) MUTATED 30 60 63
DEL PEAK 22(12P13.1) WILD-TYPE 170 363 186

Figure S341.  Get High-res Image Gene #50: 'Del Peak 22(12p13.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 22(12p13.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.45e-05 (Fisher's exact test), Q value = 0.022

Table S342.  Gene #50: 'Del Peak 22(12p13.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
DEL PEAK 22(12P13.1) MUTATED 50 85 18
DEL PEAK 22(12P13.1) WILD-TYPE 154 524 41

Figure S342.  Get High-res Image Gene #50: 'Del Peak 22(12p13.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 23(12q24.31) mutation analysis' versus 'MRNA_CNMF'

P value = 1.7e-10 (Fisher's exact test), Q value = 7.3e-08

Table S343.  Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
DEL PEAK 23(12Q24.31) MUTATED 21 22 54
DEL PEAK 23(12Q24.31) WILD-TYPE 235 70 105

Figure S343.  Get High-res Image Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 23(12q24.31) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 9.29e-11 (Fisher's exact test), Q value = 4.1e-08

Table S344.  Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
DEL PEAK 23(12Q24.31) MUTATED 50 34 13
DEL PEAK 23(12Q24.31) WILD-TYPE 71 218 121

Figure S344.  Get High-res Image Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 23(12q24.31) mutation analysis' versus 'CN_CNMF'

P value = 1.9e-19 (Chi-square test), Q value = 1.1e-16

Table S345.  Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 23(12Q24.31) MUTATED 34 13 20 86 9
DEL PEAK 23(12Q24.31) WILD-TYPE 312 63 178 129 47

Figure S345.  Get High-res Image Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 23(12q24.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.87e-13 (Chi-square test), Q value = 1.4e-10

Table S346.  Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 23(12Q24.31) MUTATED 43 10 14 14 4 11
DEL PEAK 23(12Q24.31) WILD-TYPE 53 132 66 109 32 79

Figure S346.  Get High-res Image Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 23(12q24.31) mutation analysis' versus 'RPPA_CNMF'

P value = 1.44e-05 (Fisher's exact test), Q value = 0.004

Table S347.  Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
DEL PEAK 23(12Q24.31) MUTATED 46 12 19
DEL PEAK 23(12Q24.31) WILD-TYPE 100 117 96

Figure S347.  Get High-res Image Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 23(12q24.31) mutation analysis' versus 'RPPA_CHIERARCHICAL'

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

Table S348.  Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
DEL PEAK 23(12Q24.31) MUTATED 20 12 45
DEL PEAK 23(12Q24.31) WILD-TYPE 136 96 81

Figure S348.  Get High-res Image Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 23(12q24.31) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.91e-17 (Fisher's exact test), Q value = 3.7e-14

Table S349.  Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
DEL PEAK 23(12Q24.31) MUTATED 85 17 41
DEL PEAK 23(12Q24.31) WILD-TYPE 150 138 393

Figure S349.  Get High-res Image Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 23(12q24.31) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.16e-16 (Fisher's exact test), Q value = 1.1e-13

Table S350.  Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
DEL PEAK 23(12Q24.31) MUTATED 39 29 75
DEL PEAK 23(12Q24.31) WILD-TYPE 374 187 120

Figure S350.  Get High-res Image Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 23(12q24.31) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.28e-12 (Fisher's exact test), Q value = 1.5e-09

Table S351.  Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
DEL PEAK 23(12Q24.31) MUTATED 29 45 83
DEL PEAK 23(12Q24.31) WILD-TYPE 171 378 166

Figure S351.  Get High-res Image Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 23(12q24.31) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.24e-12 (Fisher's exact test), Q value = 1.5e-09

Table S352.  Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
DEL PEAK 23(12Q24.31) MUTATED 69 71 17
DEL PEAK 23(12Q24.31) WILD-TYPE 135 538 42

Figure S352.  Get High-res Image Gene #51: 'Del Peak 23(12q24.31) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 24(13q14.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.07e-05 (Fisher's exact test), Q value = 0.0081

Table S353.  Gene #52: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
DEL PEAK 24(13Q14.2) MUTATED 74 120 44
DEL PEAK 24(13Q14.2) WILD-TYPE 47 132 90

Figure S353.  Get High-res Image Gene #52: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 24(13q14.2) mutation analysis' versus 'CN_CNMF'

P value = 2.43e-28 (Chi-square test), Q value = 1.5e-25

Table S354.  Gene #52: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 24(13Q14.2) MUTATED 74 46 126 126 35
DEL PEAK 24(13Q14.2) WILD-TYPE 272 30 72 89 21

Figure S354.  Get High-res Image Gene #52: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 24(13q14.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.51e-06 (Chi-square test), Q value = 0.00077

Table S355.  Gene #52: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 24(13Q14.2) MUTATED 58 48 47 64 11 29
DEL PEAK 24(13Q14.2) WILD-TYPE 38 94 33 59 25 61

Figure S355.  Get High-res Image Gene #52: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 24(13q14.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.34e-07 (Fisher's exact test), Q value = 4.7e-05

Table S356.  Gene #52: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
DEL PEAK 24(13Q14.2) MUTATED 134 44 205
DEL PEAK 24(13Q14.2) WILD-TYPE 101 111 229

Figure S356.  Get High-res Image Gene #52: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 24(13q14.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.45e-05 (Fisher's exact test), Q value = 0.009

Table S357.  Gene #52: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
DEL PEAK 24(13Q14.2) MUTATED 193 77 113
DEL PEAK 24(13Q14.2) WILD-TYPE 220 139 82

Figure S357.  Get High-res Image Gene #52: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 24(13q14.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.55e-08 (Fisher's exact test), Q value = 5.9e-06

Table S358.  Gene #52: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
DEL PEAK 24(13Q14.2) MUTATED 61 189 146
DEL PEAK 24(13Q14.2) WILD-TYPE 139 234 103

Figure S358.  Get High-res Image Gene #52: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 24(13q14.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.62e-05 (Fisher's exact test), Q value = 0.007

Table S359.  Gene #52: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
DEL PEAK 24(13Q14.2) MUTATED 114 246 36
DEL PEAK 24(13Q14.2) WILD-TYPE 90 363 23

Figure S359.  Get High-res Image Gene #52: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 25(14q24.3) mutation analysis' versus 'MRNA_CNMF'

P value = 2.58e-07 (Fisher's exact test), Q value = 8.8e-05

Table S360.  Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
DEL PEAK 25(14Q24.3) MUTATED 60 28 79
DEL PEAK 25(14Q24.3) WILD-TYPE 196 64 80

Figure S360.  Get High-res Image Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 25(14q24.3) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.05e-09 (Fisher's exact test), Q value = 4.3e-07

Table S361.  Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
DEL PEAK 25(14Q24.3) MUTATED 69 69 29
DEL PEAK 25(14Q24.3) WILD-TYPE 52 183 105

Figure S361.  Get High-res Image Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 25(14q24.3) mutation analysis' versus 'CN_CNMF'

P value = 6.75e-33 (Chi-square test), Q value = 4.1e-30

Table S362.  Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 25(14Q24.3) MUTATED 42 17 72 133 22
DEL PEAK 25(14Q24.3) WILD-TYPE 304 59 126 82 34

Figure S362.  Get High-res Image Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 25(14q24.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.58e-13 (Chi-square test), Q value = 2.2e-10

Table S363.  Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 25(14Q24.3) MUTATED 55 16 27 48 7 20
DEL PEAK 25(14Q24.3) WILD-TYPE 41 126 53 75 29 70

Figure S363.  Get High-res Image Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 25(14q24.3) mutation analysis' versus 'RPPA_CNMF'

P value = 2.51e-07 (Fisher's exact test), Q value = 8.6e-05

Table S364.  Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
DEL PEAK 25(14Q24.3) MUTATED 74 28 29
DEL PEAK 25(14Q24.3) WILD-TYPE 72 101 86

Figure S364.  Get High-res Image Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 25(14q24.3) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 2.89e-06 (Fisher's exact test), Q value = 0.00088

Table S365.  Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
DEL PEAK 25(14Q24.3) MUTATED 44 23 64
DEL PEAK 25(14Q24.3) WILD-TYPE 112 85 62

Figure S365.  Get High-res Image Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 25(14q24.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.99e-14 (Fisher's exact test), Q value = 9.9e-12

Table S366.  Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
DEL PEAK 25(14Q24.3) MUTATED 122 25 121
DEL PEAK 25(14Q24.3) WILD-TYPE 113 130 313

Figure S366.  Get High-res Image Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 25(14q24.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.1e-12 (Fisher's exact test), Q value = 5.2e-10

Table S367.  Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
DEL PEAK 25(14Q24.3) MUTATED 114 48 106
DEL PEAK 25(14Q24.3) WILD-TYPE 299 168 89

Figure S367.  Get High-res Image Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 25(14q24.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 8.25e-18 (Fisher's exact test), Q value = 4.5e-15

Table S368.  Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
DEL PEAK 25(14Q24.3) MUTATED 46 95 135
DEL PEAK 25(14Q24.3) WILD-TYPE 154 328 114

Figure S368.  Get High-res Image Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 25(14q24.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.23e-20 (Fisher's exact test), Q value = 7e-18

Table S369.  Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
DEL PEAK 25(14Q24.3) MUTATED 119 134 23
DEL PEAK 25(14Q24.3) WILD-TYPE 85 475 36

Figure S369.  Get High-res Image Gene #53: 'Del Peak 25(14q24.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 26(15q13.1) mutation analysis' versus 'MRNA_CNMF'

P value = 2.12e-06 (Fisher's exact test), Q value = 0.00066

Table S370.  Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
DEL PEAK 26(15Q13.1) MUTATED 75 28 85
DEL PEAK 26(15Q13.1) WILD-TYPE 181 64 74

Figure S370.  Get High-res Image Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 26(15q13.1) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.26e-08 (Fisher's exact test), Q value = 1.2e-05

Table S371.  Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
DEL PEAK 26(15Q13.1) MUTATED 68 92 28
DEL PEAK 26(15Q13.1) WILD-TYPE 53 160 106

Figure S371.  Get High-res Image Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 26(15q13.1) mutation analysis' versus 'CN_CNMF'

P value = 9.29e-31 (Chi-square test), Q value = 5.6e-28

Table S372.  Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 26(15Q13.1) MUTATED 52 37 69 137 15
DEL PEAK 26(15Q13.1) WILD-TYPE 294 39 129 78 41

Figure S372.  Get High-res Image Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 26(15q13.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.25e-12 (Chi-square test), Q value = 2.4e-09

Table S373.  Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 26(15Q13.1) MUTATED 60 23 27 48 8 23
DEL PEAK 26(15Q13.1) WILD-TYPE 36 119 53 75 28 67

Figure S373.  Get High-res Image Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 26(15q13.1) mutation analysis' versus 'RPPA_CNMF'

P value = 0.000316 (Fisher's exact test), Q value = 0.068

Table S374.  Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
DEL PEAK 26(15Q13.1) MUTATED 76 39 38
DEL PEAK 26(15Q13.1) WILD-TYPE 70 90 77

Figure S374.  Get High-res Image Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 26(15q13.1) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 4.78e-05 (Fisher's exact test), Q value = 0.012

Table S375.  Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
DEL PEAK 26(15Q13.1) MUTATED 54 30 69
DEL PEAK 26(15Q13.1) WILD-TYPE 102 78 57

Figure S375.  Get High-res Image Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 26(15q13.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.27e-15 (Fisher's exact test), Q value = 1.7e-12

Table S376.  Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
DEL PEAK 26(15Q13.1) MUTATED 127 24 138
DEL PEAK 26(15Q13.1) WILD-TYPE 108 131 296

Figure S376.  Get High-res Image Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 26(15q13.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.43e-12 (Fisher's exact test), Q value = 6.7e-10

Table S377.  Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
DEL PEAK 26(15Q13.1) MUTATED 126 52 111
DEL PEAK 26(15Q13.1) WILD-TYPE 287 164 84

Figure S377.  Get High-res Image Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 26(15q13.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.02e-15 (Fisher's exact test), Q value = 5.3e-13

Table S378.  Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
DEL PEAK 26(15Q13.1) MUTATED 40 124 137
DEL PEAK 26(15Q13.1) WILD-TYPE 160 299 112

Figure S378.  Get High-res Image Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 26(15q13.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.67e-21 (Fisher's exact test), Q value = 1.5e-18

Table S379.  Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
DEL PEAK 26(15Q13.1) MUTATED 119 147 35
DEL PEAK 26(15Q13.1) WILD-TYPE 85 462 24

Figure S379.  Get High-res Image Gene #54: 'Del Peak 26(15q13.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 27(16q24.3) mutation analysis' versus 'MRNA_CNMF'

P value = 1.76e-12 (Fisher's exact test), Q value = 8.3e-10

Table S380.  Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
DEL PEAK 27(16Q24.3) MUTATED 204 57 71
DEL PEAK 27(16Q24.3) WILD-TYPE 52 35 88

Figure S380.  Get High-res Image Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 27(16q24.3) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 5.68e-13 (Fisher's exact test), Q value = 2.7e-10

Table S381.  Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
DEL PEAK 27(16Q24.3) MUTATED 45 181 106
DEL PEAK 27(16Q24.3) WILD-TYPE 76 71 28

Figure S381.  Get High-res Image Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 27(16q24.3) mutation analysis' versus 'CN_CNMF'

P value = 6.56e-11 (Chi-square test), Q value = 2.9e-08

Table S382.  Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 27(16Q24.3) MUTATED 245 61 132 96 41
DEL PEAK 27(16Q24.3) WILD-TYPE 101 15 66 119 15

Figure S382.  Get High-res Image Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 27(16q24.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.16e-10 (Chi-square test), Q value = 1.7e-07

Table S383.  Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 27(16Q24.3) MUTATED 40 119 59 71 19 57
DEL PEAK 27(16Q24.3) WILD-TYPE 56 23 21 52 17 33

Figure S383.  Get High-res Image Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 27(16q24.3) mutation analysis' versus 'RPPA_CNMF'

P value = 1.71e-09 (Fisher's exact test), Q value = 6.9e-07

Table S384.  Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
DEL PEAK 27(16Q24.3) MUTATED 63 100 83
DEL PEAK 27(16Q24.3) WILD-TYPE 83 29 32

Figure S384.  Get High-res Image Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 27(16q24.3) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 2.08e-11 (Fisher's exact test), Q value = 9.4e-09

Table S385.  Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
DEL PEAK 27(16Q24.3) MUTATED 116 82 48
DEL PEAK 27(16Q24.3) WILD-TYPE 40 26 78

Figure S385.  Get High-res Image Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 27(16q24.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.34e-18 (Fisher's exact test), Q value = 1.8e-15

Table S386.  Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
DEL PEAK 27(16Q24.3) MUTATED 97 123 314
DEL PEAK 27(16Q24.3) WILD-TYPE 138 32 120

Figure S386.  Get High-res Image Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 27(16q24.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.19e-17 (Fisher's exact test), Q value = 6.5e-15

Table S387.  Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
DEL PEAK 27(16Q24.3) MUTATED 301 159 74
DEL PEAK 27(16Q24.3) WILD-TYPE 112 57 121

Figure S387.  Get High-res Image Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 27(16q24.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 5.67e-14 (Fisher's exact test), Q value = 2.8e-11

Table S388.  Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
DEL PEAK 27(16Q24.3) MUTATED 134 317 112
DEL PEAK 27(16Q24.3) WILD-TYPE 66 106 137

Figure S388.  Get High-res Image Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 27(16q24.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.99e-20 (Fisher's exact test), Q value = 1.1e-17

Table S389.  Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
DEL PEAK 27(16Q24.3) MUTATED 78 454 31
DEL PEAK 27(16Q24.3) WILD-TYPE 126 155 28

Figure S389.  Get High-res Image Gene #55: 'Del Peak 27(16q24.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 28(17p12) mutation analysis' versus 'MRNA_CNMF'

P value = 4.01e-06 (Fisher's exact test), Q value = 0.0012

Table S390.  Gene #56: 'Del Peak 28(17p12) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
DEL PEAK 28(17P12) MUTATED 133 55 121
DEL PEAK 28(17P12) WILD-TYPE 123 37 38

Figure S390.  Get High-res Image Gene #56: 'Del Peak 28(17p12) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 28(17p12) mutation analysis' versus 'CN_CNMF'

P value = 1.35e-21 (Chi-square test), Q value = 7.8e-19

Table S391.  Gene #56: 'Del Peak 28(17p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 28(17P12) MUTATED 146 37 154 167 33
DEL PEAK 28(17P12) WILD-TYPE 200 39 44 48 23

Figure S391.  Get High-res Image Gene #56: 'Del Peak 28(17p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 28(17p12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.15e-07 (Chi-square test), Q value = 7.4e-05

Table S392.  Gene #56: 'Del Peak 28(17p12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 28(17P12) MUTATED 59 63 60 94 20 46
DEL PEAK 28(17P12) WILD-TYPE 37 79 20 29 16 44

Figure S392.  Get High-res Image Gene #56: 'Del Peak 28(17p12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 28(17p12) mutation analysis' versus 'RPPA_CNMF'

P value = 0.000114 (Fisher's exact test), Q value = 0.026

Table S393.  Gene #56: 'Del Peak 28(17p12) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
DEL PEAK 28(17P12) MUTATED 108 65 64
DEL PEAK 28(17P12) WILD-TYPE 38 64 51

Figure S393.  Get High-res Image Gene #56: 'Del Peak 28(17p12) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 28(17p12) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.49e-06 (Fisher's exact test), Q value = 0.00047

Table S394.  Gene #56: 'Del Peak 28(17p12) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
DEL PEAK 28(17P12) MUTATED 110 234 184
DEL PEAK 28(17P12) WILD-TYPE 90 189 65

Figure S394.  Get High-res Image Gene #56: 'Del Peak 28(17p12) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 28(17p12) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.81e-06 (Fisher's exact test), Q value = 0.00057

Table S395.  Gene #56: 'Del Peak 28(17p12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
DEL PEAK 28(17P12) MUTATED 141 338 49
DEL PEAK 28(17P12) WILD-TYPE 63 271 10

Figure S395.  Get High-res Image Gene #56: 'Del Peak 28(17p12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 29(17q21.31) mutation analysis' versus 'MRNA_CNMF'

P value = 2.35e-12 (Fisher's exact test), Q value = 1.1e-09

Table S396.  Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
DEL PEAK 29(17Q21.31) MUTATED 60 36 94
DEL PEAK 29(17Q21.31) WILD-TYPE 196 56 65

Figure S396.  Get High-res Image Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 29(17q21.31) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.82e-07 (Fisher's exact test), Q value = 0.00013

Table S397.  Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
DEL PEAK 29(17Q21.31) MUTATED 71 78 41
DEL PEAK 29(17Q21.31) WILD-TYPE 50 174 93

Figure S397.  Get High-res Image Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 29(17q21.31) mutation analysis' versus 'CN_CNMF'

P value = 9.31e-23 (Chi-square test), Q value = 5.4e-20

Table S398.  Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 29(17Q21.31) MUTATED 80 17 66 137 12
DEL PEAK 29(17Q21.31) WILD-TYPE 266 59 132 78 44

Figure S398.  Get High-res Image Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 29(17q21.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.98e-14 (Chi-square test), Q value = 2.5e-11

Table S399.  Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 29(17Q21.31) MUTATED 60 16 33 38 10 29
DEL PEAK 29(17Q21.31) WILD-TYPE 36 126 47 85 26 61

Figure S399.  Get High-res Image Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 29(17q21.31) mutation analysis' versus 'RPPA_CNMF'

P value = 1.55e-11 (Fisher's exact test), Q value = 7e-09

Table S400.  Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
DEL PEAK 29(17Q21.31) MUTATED 87 24 44
DEL PEAK 29(17Q21.31) WILD-TYPE 59 105 71

Figure S400.  Get High-res Image Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 29(17q21.31) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 5.88e-11 (Fisher's exact test), Q value = 2.6e-08

Table S401.  Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
DEL PEAK 29(17Q21.31) MUTATED 41 33 81
DEL PEAK 29(17Q21.31) WILD-TYPE 115 75 45

Figure S401.  Get High-res Image Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 29(17q21.31) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.21e-20 (Fisher's exact test), Q value = 6.9e-18

Table S402.  Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
DEL PEAK 29(17Q21.31) MUTATED 144 41 109
DEL PEAK 29(17Q21.31) WILD-TYPE 91 114 325

Figure S402.  Get High-res Image Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 29(17q21.31) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.17e-15 (Fisher's exact test), Q value = 6.1e-13

Table S403.  Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
DEL PEAK 29(17Q21.31) MUTATED 100 79 115
DEL PEAK 29(17Q21.31) WILD-TYPE 313 137 80

Figure S403.  Get High-res Image Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 29(17q21.31) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.78e-14 (Fisher's exact test), Q value = 8.9e-12

Table S404.  Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
DEL PEAK 29(17Q21.31) MUTATED 59 108 138
DEL PEAK 29(17Q21.31) WILD-TYPE 141 315 111

Figure S404.  Get High-res Image Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 29(17q21.31) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.77e-16 (Fisher's exact test), Q value = 1.5e-13

Table S405.  Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
DEL PEAK 29(17Q21.31) MUTATED 112 158 35
DEL PEAK 29(17Q21.31) WILD-TYPE 92 451 24

Figure S405.  Get High-res Image Gene #57: 'Del Peak 29(17q21.31) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 30(18q23) mutation analysis' versus 'MRNA_CNMF'

P value = 6.04e-06 (Fisher's exact test), Q value = 0.0017

Table S406.  Gene #58: 'Del Peak 30(18q23) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
DEL PEAK 30(18Q23) MUTATED 67 22 76
DEL PEAK 30(18Q23) WILD-TYPE 189 70 83

Figure S406.  Get High-res Image Gene #58: 'Del Peak 30(18q23) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 30(18q23) mutation analysis' versus 'CN_CNMF'

P value = 3.87e-12 (Chi-square test), Q value = 1.8e-09

Table S407.  Gene #58: 'Del Peak 30(18q23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 30(18Q23) MUTATED 63 30 82 99 16
DEL PEAK 30(18Q23) WILD-TYPE 283 46 116 116 40

Figure S407.  Get High-res Image Gene #58: 'Del Peak 30(18q23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 30(18q23) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.02e-08 (Chi-square test), Q value = 3.9e-06

Table S408.  Gene #58: 'Del Peak 30(18q23) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 30(18Q23) MUTATED 38 28 45 53 9 18
DEL PEAK 30(18Q23) WILD-TYPE 58 114 35 70 27 72

Figure S408.  Get High-res Image Gene #58: 'Del Peak 30(18q23) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 30(18q23) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.74e-05 (Fisher's exact test), Q value = 0.0073

Table S409.  Gene #58: 'Del Peak 30(18q23) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
DEL PEAK 30(18Q23) MUTATED 102 34 134
DEL PEAK 30(18Q23) WILD-TYPE 133 121 300

Figure S409.  Get High-res Image Gene #58: 'Del Peak 30(18q23) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 30(18q23) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.31e-05 (Fisher's exact test), Q value = 0.011

Table S410.  Gene #58: 'Del Peak 30(18q23) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
DEL PEAK 30(18Q23) MUTATED 48 131 108
DEL PEAK 30(18Q23) WILD-TYPE 152 292 141

Figure S410.  Get High-res Image Gene #58: 'Del Peak 30(18q23) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 30(18q23) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000169 (Fisher's exact test), Q value = 0.038

Table S411.  Gene #58: 'Del Peak 30(18q23) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
DEL PEAK 30(18Q23) MUTATED 86 174 27
DEL PEAK 30(18Q23) WILD-TYPE 118 435 32

Figure S411.  Get High-res Image Gene #58: 'Del Peak 30(18q23) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 31(19p13.3) mutation analysis' versus 'MRNA_CNMF'

P value = 1.08e-09 (Fisher's exact test), Q value = 4.4e-07

Table S412.  Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
DEL PEAK 31(19P13.3) MUTATED 69 24 90
DEL PEAK 31(19P13.3) WILD-TYPE 187 68 69

Figure S412.  Get High-res Image Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 31(19p13.3) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 9.68e-09 (Fisher's exact test), Q value = 3.7e-06

Table S413.  Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
DEL PEAK 31(19P13.3) MUTATED 65 94 24
DEL PEAK 31(19P13.3) WILD-TYPE 56 158 110

Figure S413.  Get High-res Image Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 31(19p13.3) mutation analysis' versus 'CN_CNMF'

P value = 3.97e-43 (Chi-square test), Q value = 2.5e-40

Table S414.  Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 31(19P13.3) MUTATED 32 13 108 128 20
DEL PEAK 31(19P13.3) WILD-TYPE 314 63 90 87 36

Figure S414.  Get High-res Image Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 31(19p13.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.05e-17 (Chi-square test), Q value = 2.2e-14

Table S415.  Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 31(19P13.3) MUTATED 49 10 22 63 6 22
DEL PEAK 31(19P13.3) WILD-TYPE 47 132 58 60 30 68

Figure S415.  Get High-res Image Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 31(19p13.3) mutation analysis' versus 'RPPA_CNMF'

P value = 2.67e-06 (Fisher's exact test), Q value = 0.00082

Table S416.  Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
DEL PEAK 31(19P13.3) MUTATED 79 38 31
DEL PEAK 31(19P13.3) WILD-TYPE 67 91 84

Figure S416.  Get High-res Image Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 31(19p13.3) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 4.31e-05 (Fisher's exact test), Q value = 0.011

Table S417.  Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
DEL PEAK 31(19P13.3) MUTATED 49 31 68
DEL PEAK 31(19P13.3) WILD-TYPE 107 77 58

Figure S417.  Get High-res Image Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 31(19p13.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.11e-13 (Fisher's exact test), Q value = 1.5e-10

Table S418.  Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
DEL PEAK 31(19P13.3) MUTATED 120 23 143
DEL PEAK 31(19P13.3) WILD-TYPE 115 132 291

Figure S418.  Get High-res Image Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 31(19p13.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.3e-09 (Fisher's exact test), Q value = 9.2e-07

Table S419.  Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
DEL PEAK 31(19P13.3) MUTATED 139 47 100
DEL PEAK 31(19P13.3) WILD-TYPE 274 169 95

Figure S419.  Get High-res Image Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 31(19p13.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 9.07e-16 (Fisher's exact test), Q value = 4.7e-13

Table S420.  Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
DEL PEAK 31(19P13.3) MUTATED 40 117 135
DEL PEAK 31(19P13.3) WILD-TYPE 160 306 114

Figure S420.  Get High-res Image Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 31(19p13.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.14e-14 (Fisher's exact test), Q value = 1.1e-11

Table S421.  Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
DEL PEAK 31(19P13.3) MUTATED 113 154 25
DEL PEAK 31(19P13.3) WILD-TYPE 91 455 34

Figure S421.  Get High-res Image Gene #59: 'Del Peak 31(19p13.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 32(19q13.32) mutation analysis' versus 'MRNA_CNMF'

P value = 3.03e-05 (Fisher's exact test), Q value = 0.0081

Table S422.  Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
DEL PEAK 32(19Q13.32) MUTATED 34 12 49
DEL PEAK 32(19Q13.32) WILD-TYPE 222 80 110

Figure S422.  Get High-res Image Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 32(19q13.32) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 8.29e-06 (Fisher's exact test), Q value = 0.0024

Table S423.  Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
DEL PEAK 32(19Q13.32) MUTATED 35 51 9
DEL PEAK 32(19Q13.32) WILD-TYPE 86 201 125

Figure S423.  Get High-res Image Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 32(19q13.32) mutation analysis' versus 'CN_CNMF'

P value = 1.77e-17 (Chi-square test), Q value = 9.6e-15

Table S424.  Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 32(19Q13.32) MUTATED 23 8 66 69 14
DEL PEAK 32(19Q13.32) WILD-TYPE 323 68 132 146 42

Figure S424.  Get High-res Image Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 32(19q13.32) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.07e-11 (Chi-square test), Q value = 1.4e-08

Table S425.  Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 32(19Q13.32) MUTATED 37 5 20 39 4 13
DEL PEAK 32(19Q13.32) WILD-TYPE 59 137 60 84 32 77

Figure S425.  Get High-res Image Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 32(19q13.32) mutation analysis' versus 'RPPA_CNMF'

P value = 0.000469 (Fisher's exact test), Q value = 0.099

Table S426.  Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
DEL PEAK 32(19Q13.32) MUTATED 44 18 15
DEL PEAK 32(19Q13.32) WILD-TYPE 102 111 100

Figure S426.  Get High-res Image Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 32(19q13.32) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 4.52e-05 (Fisher's exact test), Q value = 0.011

Table S427.  Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
DEL PEAK 32(19Q13.32) MUTATED 25 11 41
DEL PEAK 32(19Q13.32) WILD-TYPE 131 97 85

Figure S427.  Get High-res Image Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 32(19q13.32) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.4e-09 (Fisher's exact test), Q value = 1.7e-06

Table S428.  Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
DEL PEAK 32(19Q13.32) MUTATED 77 12 83
DEL PEAK 32(19Q13.32) WILD-TYPE 158 143 351

Figure S428.  Get High-res Image Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 32(19q13.32) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.39e-06 (Fisher's exact test), Q value = 0.00044

Table S429.  Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
DEL PEAK 32(19Q13.32) MUTATED 86 24 62
DEL PEAK 32(19Q13.32) WILD-TYPE 327 192 133

Figure S429.  Get High-res Image Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 32(19q13.32) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.37e-10 (Fisher's exact test), Q value = 5.9e-08

Table S430.  Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
DEL PEAK 32(19Q13.32) MUTATED 21 66 85
DEL PEAK 32(19Q13.32) WILD-TYPE 179 357 164

Figure S430.  Get High-res Image Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 32(19q13.32) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.46e-08 (Fisher's exact test), Q value = 9.2e-06

Table S431.  Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
DEL PEAK 32(19Q13.32) MUTATED 59 89 24
DEL PEAK 32(19Q13.32) WILD-TYPE 145 520 35

Figure S431.  Get High-res Image Gene #60: 'Del Peak 32(19q13.32) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 33(20p13) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.42e-05 (Fisher's exact test), Q value = 0.004

Table S432.  Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
DEL PEAK 33(20P13) MUTATED 33 37 8
DEL PEAK 33(20P13) WILD-TYPE 88 215 126

Figure S432.  Get High-res Image Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 33(20p13) mutation analysis' versus 'CN_CNMF'

P value = 9.52e-14 (Chi-square test), Q value = 4.6e-11

Table S433.  Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 33(20P13) MUTATED 18 4 36 61 13
DEL PEAK 33(20P13) WILD-TYPE 328 72 162 154 43

Figure S433.  Get High-res Image Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 33(20p13) mutation analysis' versus 'METHLYATION_CNMF'

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

Table S434.  Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 33(20P13) MUTATED 28 5 11 22 3 7
DEL PEAK 33(20P13) WILD-TYPE 68 137 69 101 33 83

Figure S434.  Get High-res Image Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 33(20p13) mutation analysis' versus 'RPPA_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.17

Table S435.  Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
DEL PEAK 33(20P13) MUTATED 35 10 16
DEL PEAK 33(20P13) WILD-TYPE 111 119 99

Figure S435.  Get High-res Image Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 33(20p13) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.8e-10 (Fisher's exact test), Q value = 7.7e-08

Table S436.  Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
DEL PEAK 33(20P13) MUTATED 64 6 55
DEL PEAK 33(20P13) WILD-TYPE 171 149 379

Figure S436.  Get High-res Image Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 33(20p13) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.57e-08 (Fisher's exact test), Q value = 9.5e-06

Table S437.  Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
DEL PEAK 33(20P13) MUTATED 54 16 55
DEL PEAK 33(20P13) WILD-TYPE 359 200 140

Figure S437.  Get High-res Image Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 33(20p13) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.06e-11 (Fisher's exact test), Q value = 4.8e-09

Table S438.  Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
DEL PEAK 33(20P13) MUTATED 15 39 70
DEL PEAK 33(20P13) WILD-TYPE 185 384 179

Figure S438.  Get High-res Image Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 33(20p13) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.74e-09 (Fisher's exact test), Q value = 7e-07

Table S439.  Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
DEL PEAK 33(20P13) MUTATED 57 57 10
DEL PEAK 33(20P13) WILD-TYPE 147 552 49

Figure S439.  Get High-res Image Gene #61: 'Del Peak 33(20p13) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 34(21q11.2) mutation analysis' versus 'CN_CNMF'

P value = 1.38e-12 (Chi-square test), Q value = 6.5e-10

Table S440.  Gene #62: 'Del Peak 34(21q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 34(21Q11.2) MUTATED 30 13 70 56 12
DEL PEAK 34(21Q11.2) WILD-TYPE 316 63 128 159 44

Figure S440.  Get High-res Image Gene #62: 'Del Peak 34(21q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 34(21q11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000275 (Chi-square test), Q value = 0.06

Table S441.  Gene #62: 'Del Peak 34(21q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
DEL PEAK 34(21Q11.2) MUTATED 17 19 19 41 6 10
DEL PEAK 34(21Q11.2) WILD-TYPE 79 123 61 82 30 80

Figure S441.  Get High-res Image Gene #62: 'Del Peak 34(21q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 35(22q13.32) mutation analysis' versus 'CN_CNMF'

P value = 0.000936 (Chi-square test), Q value = 0.18

Table S442.  Gene #63: 'Del Peak 35(22q13.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
DEL PEAK 35(22Q13.32) MUTATED 130 46 102 95 26
DEL PEAK 35(22Q13.32) WILD-TYPE 216 30 96 120 30

Figure S442.  Get High-res Image Gene #63: 'Del Peak 35(22q13.32) mutation analysis' versus Clinical Feature #3: 'CN_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 = 891

  • Number of copy number variation regions = 63

  • Number of molecular subtypes = 10

  • Exclude regions that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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