Uterine Corpus Endometrioid Carcinoma: Correlation between copy number variation genes and molecular subtypes
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
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 98 peak regions and 10 molecular subtypes across 492 patients, 578 significant findings detected with Q value < 0.25.

  • Amp Peak 1(1p35.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 2(1p34.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 3(1p22.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • Amp Peak 4(1q21.3) cnvs correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 5(1q22) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 6(1q42.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • Amp Peak 7(2p23.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 8(2q13) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 9(3p25.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 10(3p14.1) cnvs correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 11(3q26.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 12(3q26.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 13(4p16.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 14(5p15.33) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 15(5q35.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 16(6p24.2) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 17(6q25.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 18(7q22.1) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 19(8p11.21) cnvs correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 20(8q24.21) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • Amp Peak 22(9p24.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 23(9q34.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 24(10q22.2) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 25(11p11.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 26(11q13.2) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 27(12p12.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 28(12q13.11) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 29(12q13.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 30(13q34) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 31(14q24.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 32(14q32.33) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 33(16p11.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 34(17q11.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 35(17q12) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 36(17q25.1) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 37(18p11.31) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 38(18q11.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 39(19p13.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 40(19p13.11) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 41(19q12) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 42(20p13) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 43(20q11.21) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 44(20q13.12) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 45(20q13.33) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 46(22q12.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 47(Xp11.23) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 48(Xq28) cnvs correlated to 'CN_CNMF'.

  • Del Peak 1(1p36.21) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 2(1p36.11) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 4(2p25.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • Del Peak 5(2q22.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 6(2q37.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • Del Peak 7(3p14.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 8(3q13.31) cnvs correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • Del Peak 9(4p16.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 10(4p15.31) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 11(4q22.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 12(4q34.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 13(5q11.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 14(6q26) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 15(7p22.3) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 16(7q11.22) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 17(7q31.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 18(7q36.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 19(8p23.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 20(9p23) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 21(9q34.11) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 22(10q23.31) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 23(11p15.5) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 24(11q14.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 25(11q25) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 26(12q23.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 27(12q24.33) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 28(13q11) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 29(13q14.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 30(14q13.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 31(15q15.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 32(15q23) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 33(16p13.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 34(16q21) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 35(16q23.1) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 36(17p13.3) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 37(17p12) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 38(17p11.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 39(17q11.2) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 40(17q21.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 41(18q23) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 42(19p13.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 43(19p12) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 44(19q13.43) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 45(20p12.1) cnvs correlated to 'CN_CNMF'.

  • Del Peak 46(22q11.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 47(22q12.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 48(22q13.31) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 49(22q13.32) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 50(Xp21.1) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 98 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 578 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 Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test
Amp Peak 11(3q26 2) 155 (32%) 337 5.21e-06
(0.00249) 		4.74e-05
(0.021) 		3.77e-61
(3.62e-58) 		1.95e-17
(1.58e-14) 		0.000353
(0.141) 		0.0154
(1.00) 		1.91e-25
(1.71e-22) 		3.67e-25
(3.28e-22) 		3.04e-23
(2.67e-20) 		1.97e-24
(1.76e-21)
Del Peak 21(9q34 11) 122 (25%) 370 0.000102
(0.0436) 		1.21e-05
(0.0057) 		5.04e-52
(4.79e-49) 		1.94e-11
(1.28e-08) 		0.000384
(0.153) 		0.0316
(1.00) 		1.13e-17
(9.2e-15) 		4.84e-24
(4.3e-21) 		9.24e-17
(7.26e-14) 		1.37e-12
(9.59e-10)
Del Peak 42(19p13 3) 141 (29%) 351 5.64e-07
(0.000285) 		4.25e-06
(0.00205) 		6e-78
(5.76e-75) 		7.23e-31
(6.61e-28) 		8.99e-06
(0.00427) 		0.0146
(1.00) 		4.05e-36
(3.77e-33) 		1.96e-36
(1.82e-33) 		1.12e-34
(1.04e-31) 		3.01e-34
(2.78e-31)
Amp Peak 12(3q26 2) 144 (29%) 348 2.42e-05
(0.0109) 		0.000168
(0.0703) 		8.96e-60
(8.59e-57) 		8.25e-19
(6.9e-16) 		0.0015
(0.54) 		0.0249
(1.00) 		1.89e-25
(1.69e-22) 		7.53e-26
(6.78e-23) 		1.25e-21
(1.08e-18) 		1.33e-23
(1.18e-20)
Amp Peak 16(6p24 2) 101 (21%) 391 0.00043
(0.171) 		0.00524
(1.00) 		1.36e-39
(1.27e-36) 		2.35e-11
(1.55e-08) 		0.000177
(0.0737) 		0.059
(1.00) 		6.92e-16
(5.35e-13) 		1.49e-14
(1.12e-11) 		1.09e-14
(8.2e-12) 		1.87e-15
(1.43e-12)
Amp Peak 21(8q24 21) 196 (40%) 296 0.00043
(0.171) 		0.00524
(1.00) 		8.36e-35
(7.76e-32) 		1.24e-05
(0.00577) 		7.26e-07
(0.000364) 		0.141
(1.00) 		1.82e-08
(1.01e-05) 		1.7e-11
(1.13e-08) 		9.65e-11
(6.16e-08) 		1.06e-12
(7.43e-10)
Amp Peak 36(17q25 1) 90 (18%) 402 0.000566
(0.219) 		0.000109
(0.0462) 		4.44e-41
(4.16e-38) 		1.36e-11
(9.1e-09) 		0.00741
(1.00) 		0.193
(1.00) 		2.59e-12
(1.79e-09) 		3.88e-13
(2.76e-10) 		3.74e-13
(2.67e-10) 		2.28e-14
(1.7e-11)
Amp Peak 39(19p13 2) 84 (17%) 408 0.000102
(0.0436) 		1.21e-05
(0.0057) 		2.95e-46
(2.78e-43) 		1.22e-09
(7.36e-07) 		0.15
(1.00) 		0.0408
(1.00) 		1.09e-18
(9.09e-16) 		1.76e-18
(1.46e-15) 		8.33e-18
(6.8e-15) 		7.96e-13
(5.61e-10)
Del Peak 37(17p12) 121 (25%) 371 0.000566
(0.219) 		0.000109
(0.0462) 		2.57e-58
(2.46e-55) 		8.75e-16
(6.74e-13) 		0.00125
(0.455) 		0.681
(1.00) 		2.64e-25
(2.36e-22) 		5.65e-29
(5.13e-26) 		2.26e-21
(1.94e-18) 		3.14e-17
(2.53e-14)
Del Peak 38(17p11 2) 106 (22%) 386 0.000235
(0.097) 		5.66e-05
(0.025) 		3.67e-52
(3.49e-49) 		8.82e-14
(6.42e-11) 		0.0247
(1.00) 		0.378
(1.00) 		1.28e-19
(1.08e-16) 		5.19e-24
(4.61e-21) 		3.61e-18
(2.96e-15) 		8.96e-13
(6.31e-10)
Del Peak 40(17q21 2) 101 (21%) 391 0.000102
(0.0436) 		1.21e-05
(0.0057) 		2.03e-48
(1.91e-45) 		1.41e-09
(8.39e-07) 		0.00327
(1.00) 		0.168
(1.00) 		1.38e-14
(1.03e-11) 		7.99e-19
(6.7e-16) 		1.26e-13
(9.1e-11) 		4.18e-09
(2.43e-06)
Del Peak 48(22q13 31) 122 (25%) 370 1.8e-05
(0.00826) 		2.4e-06
(0.00117) 		9.61e-55
(9.17e-52) 		4.79e-13
(3.4e-10) 		0.0018
(0.632) 		0.153
(1.00) 		8.88e-20
(7.52e-17) 		1.44e-23
(1.28e-20) 		1.1e-17
(8.9e-15) 		1.56e-14
(1.17e-11)
Del Peak 49(22q13 32) 128 (26%) 364 0.000102
(0.0436) 		1.21e-05
(0.0057) 		4.93e-53
(4.7e-50) 		2.04e-12
(1.41e-09) 		0.00148
(0.534) 		0.0786
(1.00) 		2.93e-18
(2.41e-15) 		1.21e-21
(1.05e-18) 		4.44e-17
(3.56e-14) 		3.8e-14
(2.8e-11)
Amp Peak 1(1p35 2) 50 (10%) 442 0.0191
(1.00) 		0.0435
(1.00) 		3.5e-20
(3e-17) 		4.77e-07
(0.000243) 		0.0001
(0.0429) 		0.267
(1.00) 		1.22e-09
(7.36e-07) 		8.4e-12
(5.67e-09) 		4.44e-07
(0.000227) 		1.13e-08
(6.42e-06)
Amp Peak 20(8q24 21) 188 (38%) 304 0.00236
(0.814) 		0.028
(1.00) 		1.54e-35
(1.43e-32) 		6.2e-07
(0.000312) 		8.75e-05
(0.0379) 		0.504
(1.00) 		3.35e-09
(1.96e-06) 		1.26e-11
(8.46e-09) 		1.13e-09
(6.84e-07) 		2.01e-13
(1.45e-10)
Amp Peak 26(11q13 2) 68 (14%) 424 0.000235
(0.097) 		0.00101
(0.379) 		5.92e-22
(5.16e-19) 		0.000204
(0.0843) 		0.0148
(1.00) 		1
(1.00) 		9.44e-06
(0.00447) 		5.58e-08
(3.02e-05) 		1.53e-05
(0.00709) 		6.81e-05
(0.0299)
Amp Peak 40(19p13 11) 83 (17%) 409 0.000235
(0.097) 		0.00101
(0.379) 		1.47e-45
(1.38e-42) 		5.98e-12
(4.05e-09) 		0.199
(1.00) 		0.309
(1.00) 		5e-17
(3.99e-14) 		5.37e-18
(4.4e-15) 		1.3e-17
(1.05e-14) 		5.03e-16
(3.91e-13)
Amp Peak 41(19q12) 101 (21%) 391 0.000566
(0.219) 		0.00261
(0.891) 		9.02e-49
(8.52e-46) 		5.85e-17
(4.66e-14) 		0.00289
(0.98) 		0.212
(1.00) 		2.87e-21
(2.47e-18) 		2.66e-20
(2.28e-17) 		6.63e-25
(5.92e-22) 		1.23e-22
(1.08e-19)
Amp Peak 43(20q11 21) 130 (26%) 362 0.000496
(0.195) 		0.000861
(0.325) 		6.65e-49
(6.3e-46) 		5.01e-12
(3.41e-09) 		0.00156
(0.553) 		0.205
(1.00) 		5.71e-16
(4.43e-13) 		1.02e-14
(7.66e-12) 		2.08e-17
(1.68e-14) 		5.66e-20
(4.82e-17)
Del Peak 15(7p22 3) 68 (14%) 424 0.0015
(0.54) 		0.000248
(0.101) 		4.17e-31
(3.82e-28) 		2.43e-10
(1.51e-07) 		0.0312
(1.00) 		0.0935
(1.00) 		5.12e-14
(3.76e-11) 		4.07e-15
(3.1e-12) 		5.6e-14
(4.11e-11) 		4.5e-11
(2.92e-08)
Del Peak 34(16q21) 140 (28%) 352 0.00197
(0.69) 		0.000451
(0.179) 		1.05e-56
(1e-53) 		2.95e-18
(2.42e-15) 		0.0797
(1.00) 		1
(1.00) 		9.4e-18
(7.66e-15) 		6.63e-16
(5.13e-13) 		4.38e-19
(3.68e-16) 		8.48e-19
(7.09e-16)
Del Peak 35(16q23 1) 150 (30%) 342 0.00942
(1.00) 		0.000168
(0.0703) 		2.34e-57
(2.24e-54) 		2.43e-17
(1.96e-14) 		0.0275
(1.00) 		0.369
(1.00) 		7.07e-19
(5.94e-16) 		1.83e-14
(1.37e-11) 		1.52e-19
(1.29e-16) 		3.19e-22
(2.78e-19)
Del Peak 36(17p13 3) 106 (22%) 386 0.00197
(0.69) 		0.000451
(0.179) 		7.29e-49
(6.9e-46) 		2.59e-11
(1.71e-08) 		0.000824
(0.313) 		0.665
(1.00) 		7.12e-17
(5.63e-14) 		1.58e-19
(1.34e-16) 		2.25e-14
(1.67e-11) 		4.41e-11
(2.87e-08)
Del Peak 39(17q11 2) 96 (20%) 396 0.0015
(0.54) 		0.000248
(0.101) 		6.26e-44
(5.88e-41) 		1.13e-07
(6.03e-05) 		0.013
(1.00) 		0.647
(1.00) 		2.47e-14
(1.83e-11) 		4.51e-17
(3.61e-14) 		1.1e-10
(7.03e-08) 		1.81e-07
(9.5e-05)
Del Peak 44(19q13 43) 60 (12%) 432 0.00197
(0.69) 		0.000451
(0.179) 		2.7e-23
(2.38e-20) 		2.56e-09
(1.51e-06) 		0.0782
(1.00) 		0.56
(1.00) 		1.28e-09
(7.71e-07) 		2.47e-09
(1.46e-06) 		2.76e-10
(1.7e-07) 		4.04e-11
(2.64e-08)
Del Peak 50(Xp21 1) 81 (16%) 411 0.0015
(0.54) 		0.000248
(0.101) 		4.23e-33
(3.9e-30) 		3.85e-09
(2.25e-06) 		0.00541
(1.00) 		0.244
(1.00) 		1.34e-10
(8.45e-08) 		3.09e-11
(2.03e-08) 		3.2e-12
(2.21e-09) 		4.81e-10
(2.95e-07)
Amp Peak 2(1p34 2) 63 (13%) 429 0.0015
(0.54) 		0.00379
(1.00) 		2.06e-28
(1.87e-25) 		1.36e-08
(7.7e-06) 		0.00924
(1.00) 		0.56
(1.00) 		7.8e-12
(5.27e-09) 		4.95e-14
(3.64e-11) 		9.39e-13
(6.6e-10) 		3.55e-13
(2.54e-10)
Amp Peak 7(2p23 2) 111 (23%) 381 0.465
(1.00) 		0.497
(1.00) 		5.04e-28
(4.56e-25) 		1.59e-10
(1e-07) 		0.00451
(1.00) 		0.558
(1.00) 		3.63e-06
(0.00176) 		5.02e-06
(0.00241) 		7.34e-10
(4.47e-07) 		1.56e-12
(1.09e-09)
Amp Peak 8(2q13) 107 (22%) 385 0.0698
(1.00) 		0.18
(1.00) 		2.77e-33
(2.56e-30) 		1.95e-12
(1.36e-09) 		0.0025
(0.858) 		0.153
(1.00) 		8.42e-11
(5.42e-08) 		1.53e-10
(9.67e-08) 		8.86e-17
(6.97e-14) 		6.16e-17
(4.9e-14)
Amp Peak 9(3p25 1) 70 (14%) 422 0.0403
(1.00) 		0.212
(1.00) 		4.11e-24
(3.66e-21) 		3.75e-06
(0.00182) 		0.075
(1.00) 		0.438
(1.00) 		6.49e-08
(3.51e-05) 		1.78e-08
(9.95e-06) 		0.000147
(0.0618) 		5.97e-07
(0.000301)
Amp Peak 13(4p16 3) 45 (9%) 447 0.00677
(1.00) 		0.0133
(1.00) 		1.64e-21
(1.42e-18) 		0.000532
(0.209) 		0.0898
(1.00) 		0.00285
(0.969) 		5.2e-10
(3.18e-07) 		6.95e-11
(4.49e-08) 		8.29e-09
(4.73e-06) 		3.67e-08
(2.02e-05)
Amp Peak 14(5p15 33) 77 (16%) 415 0.112
(1.00) 		0.16
(1.00) 		4.71e-32
(4.33e-29) 		3.4e-12
(2.34e-09) 		0.221
(1.00) 		0.612
(1.00) 		3.21e-14
(2.37e-11) 		2.37e-12
(1.64e-09) 		5.86e-14
(4.29e-11) 		9.29e-14
(6.73e-11)
Amp Peak 15(5q35 3) 48 (10%) 444 0.176
(1.00) 		0.0543
(1.00) 		8.67e-20
(7.36e-17) 		0.000639
(0.245) 		0.237
(1.00) 		0.731
(1.00) 		3.18e-07
(0.000165) 		6.98e-05
(0.0306) 		1.41e-08
(7.93e-06) 		0.000561
(0.218)
Amp Peak 17(6q25 1) 76 (15%) 416 0.563
(1.00) 		0.539
(1.00) 		7.52e-22
(6.53e-19) 		2.64e-06
(0.00129) 		0.318
(1.00) 		0.0698
(1.00) 		4.97e-07
(0.000252) 		1.03e-08
(5.88e-06) 		1.58e-05
(0.00729) 		3.2e-05
(0.0143)
Amp Peak 22(9p24 2) 57 (12%) 435 0.0831
(1.00) 		0.0503
(1.00) 		2.87e-22
(2.51e-19) 		4.87e-07
(0.000247) 		0.000874
(0.33) 		0.00457
(1.00) 		2.97e-09
(1.74e-06) 		1.17e-10
(7.42e-08) 		2.66e-10
(1.65e-07) 		1.4e-07
(7.37e-05)
Amp Peak 23(9q34 3) 32 (7%) 460 0.208
(1.00) 		0.185
(1.00) 		3.79e-12
(2.6e-09) 		9.56e-05
(0.0411) 		0.336
(1.00) 		0.507
(1.00) 		2.14e-05
(0.00976) 		3.98e-06
(0.00193) 		2.02e-05
(0.00929) 		1.3e-05
(0.00607)
Amp Peak 25(11p11 2) 45 (9%) 447 0.00677
(1.00) 		0.00103
(0.38) 		1.32e-16
(1.03e-13) 		5.97e-05
(0.0263) 		0.0122
(1.00) 		0.789
(1.00) 		2.37e-05
(0.0107) 		9.28e-05
(0.04) 		9.86e-06
(0.00466) 		1.22e-06
(0.000605)
Amp Peak 27(12p12 1) 81 (16%) 411 0.541
(1.00) 		0.407
(1.00) 		5.1e-15
(3.88e-12) 		1.13e-07
(6e-05) 		0.536
(1.00) 		0.659
(1.00) 		4.17e-05
(0.0185) 		2.11e-05
(0.00964) 		8.98e-08
(4.8e-05) 		8.64e-08
(4.62e-05)
Amp Peak 28(12q13 11) 79 (16%) 413 0.32
(1.00) 		0.342
(1.00) 		6.74e-17
(5.34e-14) 		3.67e-08
(2.02e-05) 		0.449
(1.00) 		0.157
(1.00) 		2.19e-06
(0.00107) 		1.95e-06
(0.00096) 		4.31e-09
(2.5e-06) 		1.12e-08
(6.35e-06)
Amp Peak 29(12q13 2) 87 (18%) 405 0.155
(1.00) 		0.335
(1.00) 		1.75e-17
(1.42e-14) 		1.94e-07
(0.000101) 		0.315
(1.00) 		0.36
(1.00) 		1.66e-08
(9.29e-06) 		6.54e-08
(3.52e-05) 		1.96e-08
(1.09e-05) 		4.63e-09
(2.68e-06)
Amp Peak 30(13q34) 49 (10%) 443 0.176
(1.00) 		0.371
(1.00) 		4.18e-20
(3.57e-17) 		1.98e-06
(0.000971) 		0.241
(1.00) 		0.0546
(1.00) 		8.41e-12
(5.67e-09) 		1.37e-07
(7.23e-05) 		4.89e-09
(2.82e-06) 		1.21e-09
(7.32e-07)
Amp Peak 31(14q24 3) 56 (11%) 436 0.112
(1.00) 		0.0414
(1.00) 		6.04e-18
(4.94e-15) 		1.7e-05
(0.00783) 		0.153
(1.00) 		0.393
(1.00) 		4.85e-08
(2.64e-05) 		1.14e-10
(7.27e-08) 		8.36e-09
(4.76e-06) 		8.16e-09
(4.67e-06)
Amp Peak 32(14q32 33) 70 (14%) 422 0.491
(1.00) 		0.407
(1.00) 		4.26e-22
(3.72e-19) 		1.04e-06
(0.000518) 		0.426
(1.00) 		0.789
(1.00) 		3.54e-05
(0.0158) 		4.77e-08
(2.61e-05) 		2.41e-07
(0.000125) 		1.59e-08
(8.9e-06)
Amp Peak 33(16p11 2) 55 (11%) 437 0.0191
(1.00) 		0.00403
(1.00) 		5.49e-21
(4.72e-18) 		3.26e-05
(0.0146) 		0.138
(1.00) 		0.126
(1.00) 		1.31e-09
(7.84e-07) 		1.78e-09
(1.06e-06) 		1.33e-09
(7.95e-07) 		7.91e-07
(0.000395)
Amp Peak 34(17q11 2) 63 (13%) 429 0.0191
(1.00) 		0.0435
(1.00) 		1.72e-26
(1.55e-23) 		2.13e-11
(1.41e-08) 		0.0201
(1.00) 		0.0052
(1.00) 		1.25e-10
(7.94e-08) 		4.81e-10
(2.95e-07) 		8.65e-15
(6.55e-12) 		7.05e-15
(5.34e-12)
Amp Peak 35(17q12) 64 (13%) 428 0.193
(1.00) 		0.0648
(1.00) 		5.56e-23
(4.88e-20) 		1.42e-12
(9.91e-10) 		0.0111
(1.00) 		0.438
(1.00) 		3.77e-13
(2.69e-10) 		2.74e-10
(1.69e-07) 		7.79e-14
(5.69e-11) 		3.16e-16
(2.46e-13)
Amp Peak 37(18p11 31) 81 (16%) 411 0.0244
(1.00) 		0.128
(1.00) 		2.43e-33
(2.25e-30) 		5.53e-12
(3.75e-09) 		0.0101
(1.00) 		0.0197
(1.00) 		1.45e-11
(9.66e-09) 		1.9e-13
(1.37e-10) 		6.39e-18
(5.22e-15) 		1.86e-19
(1.57e-16)
Amp Peak 38(18q11 2) 62 (13%) 430 0.193
(1.00) 		0.0648
(1.00) 		4.94e-27
(4.47e-24) 		3.19e-10
(1.97e-07) 		0.156
(1.00) 		0.0444
(1.00) 		1.17e-07
(6.21e-05) 		4.53e-08
(2.48e-05) 		1.73e-13
(1.25e-10) 		8.49e-12
(5.71e-09)
Amp Peak 42(20p13) 104 (21%) 388 0.0191
(1.00) 		0.0435
(1.00) 		1.63e-33
(1.51e-30) 		1.8e-09
(1.07e-06) 		0.0828
(1.00) 		0.386
(1.00) 		3.74e-11
(2.45e-08) 		6.9e-11
(4.46e-08) 		1.84e-11
(1.22e-08) 		3.94e-12
(2.7e-09)
Amp Peak 44(20q13 12) 136 (28%) 356 0.0227
(1.00) 		0.00379
(1.00) 		2.71e-49
(2.57e-46) 		1.81e-13
(1.3e-10) 		0.00478
(1.00) 		0.105
(1.00) 		3.32e-15
(2.54e-12) 		5.03e-15
(3.83e-12) 		2.06e-17
(1.67e-14) 		8.82e-17
(6.95e-14)
Amp Peak 45(20q13 33) 134 (27%) 358 0.00538
(1.00) 		0.0108
(1.00) 		1.54e-46
(1.45e-43) 		1.43e-10
(9e-08) 		0.0674
(1.00) 		0.686
(1.00) 		5.7e-13
(4.04e-10) 		8.5e-14
(6.2e-11) 		2.8e-16
(2.18e-13) 		2.45e-14
(1.82e-11)
Amp Peak 46(22q12 2) 54 (11%) 438 0.0591
(1.00) 		0.133
(1.00) 		2.31e-18
(1.9e-15) 		1.88e-14
(1.4e-11) 		0.181
(1.00) 		0.0546
(1.00) 		6.35e-13
(4.49e-10) 		8.42e-11
(5.42e-08) 		2.12e-18
(1.75e-15) 		5.47e-18
(4.48e-15)
Del Peak 1(1p36 21) 65 (13%) 427 0.00538
(1.00) 		0.0108
(1.00) 		1.79e-23
(1.58e-20) 		3.67e-07
(0.000189) 		0.00518
(1.00) 		0.267
(1.00) 		1.55e-11
(1.03e-08) 		7.33e-09
(4.21e-06) 		2.72e-08
(1.5e-05) 		4.31e-09
(2.5e-06)
Del Peak 2(1p36 11) 78 (16%) 414 0.0729
(1.00) 		0.0133
(1.00) 		9.91e-33
(9.11e-30) 		6.98e-11
(4.5e-08) 		0.0339
(1.00) 		0.393
(1.00) 		1.96e-12
(1.36e-09) 		3.18e-11
(2.09e-08) 		9.44e-15
(7.13e-12) 		2.47e-12
(1.71e-09)
Del Peak 5(2q22 1) 44 (9%) 448 0.0191
(1.00) 		0.00403
(1.00) 		2.7e-20
(2.31e-17) 		0.000179
(0.0747) 		0.0907
(1.00) 		0.0831
(1.00) 		1.55e-08
(8.7e-06) 		7.77e-08
(4.16e-05) 		1.24e-06
(0.000614) 		0.000232
(0.096)
Del Peak 7(3p14 2) 69 (14%) 423 0.00677
(1.00) 		0.0133
(1.00) 		5.91e-31
(5.41e-28) 		1.22e-09
(7.36e-07) 		0.000952
(0.358) 		0.0197
(1.00) 		3.77e-15
(2.88e-12) 		1.8e-14
(1.34e-11) 		4.35e-13
(3.09e-10) 		1.08e-09
(6.6e-07)
Del Peak 9(4p16 3) 87 (18%) 405 0.0227
(1.00) 		0.00379
(1.00) 		1.41e-30
(1.29e-27) 		1.74e-12
(1.21e-09) 		0.0096
(1.00) 		0.244
(1.00) 		1.57e-10
(9.87e-08) 		9.13e-11
(5.85e-08) 		4.51e-17
(3.61e-14) 		6.66e-12
(4.51e-09)
Del Peak 10(4p15 31) 90 (18%) 402 0.0227
(1.00) 		0.00379
(1.00) 		4.15e-35
(3.86e-32) 		9.13e-14
(6.63e-11) 		0.0203
(1.00) 		0.346
(1.00) 		3.81e-11
(2.49e-08) 		4.36e-11
(2.84e-08) 		9.25e-19
(7.72e-16) 		3.31e-12
(2.28e-09)
Del Peak 11(4q22 1) 99 (20%) 393 0.00538
(1.00) 		0.00101
(0.379) 		1.04e-46
(9.79e-44) 		2.05e-18
(1.7e-15) 		0.0252
(1.00) 		0.102
(1.00) 		1.1e-16
(8.66e-14) 		1.16e-18
(9.7e-16) 		1.74e-23
(1.54e-20) 		4.21e-20
(3.59e-17)
Del Peak 12(4q34 3) 115 (23%) 377 0.00538
(1.00) 		0.00101
(0.379) 		1.43e-51
(1.36e-48) 		2.7e-15
(2.07e-12) 		0.0599
(1.00) 		0.521
(1.00) 		1.31e-18
(1.09e-15) 		8.83e-20
(7.49e-17) 		1.7e-21
(1.47e-18) 		3.61e-19
(3.04e-16)
Del Peak 13(5q11 2) 100 (20%) 392 0.0227
(1.00) 		0.00379
(1.00) 		8.55e-49
(8.09e-46) 		1.18e-16
(9.29e-14) 		0.000858
(0.325) 		0.01
(1.00) 		7.39e-17
(5.84e-14) 		3.24e-17
(2.61e-14) 		9.56e-18
(7.79e-15) 		6.92e-17
(5.48e-14)
Del Peak 14(6q26) 44 (9%) 448 0.352
(1.00) 		0.133
(1.00) 		9.63e-15
(7.27e-12) 		5.19e-08
(2.82e-05) 		0.675
(1.00) 		0.301
(1.00) 		2.29e-06
(0.00112) 		7.75e-05
(0.0338) 		2.39e-09
(1.41e-06) 		4.18e-07
(0.000214)
Del Peak 16(7q11 22) 39 (8%) 453 3.24e-21
(2.79e-18) 		2.35e-07
(0.000122) 		0.0668
(1.00) 		0.00669
(1.00) 		4.89e-09
(2.82e-06) 		1.5e-09
(8.92e-07) 		4.6e-06
(0.00221) 		0.000302
(0.121)
Del Peak 17(7q31 1) 48 (10%) 444 0.176
(1.00) 		0.0543
(1.00) 		5.75e-27
(5.19e-24) 		2.41e-09
(1.42e-06) 		0.0899
(1.00) 		0.0192
(1.00) 		3.26e-14
(2.41e-11) 		3.17e-13
(2.27e-10) 		2.27e-10
(1.41e-07) 		1.51e-08
(8.5e-06)
Del Peak 18(7q36 3) 57 (12%) 435 0.0882
(1.00) 		0.257
(1.00) 		9.35e-30
(8.53e-27) 		1.75e-10
(1.1e-07) 		0.0187
(1.00) 		0.000655
(0.251) 		1.29e-18
(1.08e-15) 		5.93e-16
(4.6e-13) 		7.64e-13
(5.4e-10) 		2.45e-10
(1.52e-07)
Del Peak 19(8p23 2) 103 (21%) 389 0.00677
(1.00) 		0.00103
(0.38) 		1.03e-40
(9.66e-38) 		1.24e-21
(1.07e-18) 		0.0469
(1.00) 		0.378
(1.00) 		6.45e-17
(5.12e-14) 		5.05e-19
(4.24e-16) 		2.66e-26
(2.39e-23) 		6.08e-24
(5.39e-21)
Del Peak 20(9p23) 65 (13%) 427 0.352
(1.00) 		0.133
(1.00) 		1.01e-22
(8.89e-20) 		1.84e-06
(0.000907) 		0.0369
(1.00) 		0.295
(1.00) 		1.93e-07
(0.000101) 		1.29e-09
(7.75e-07) 		7.54e-08
(4.05e-05) 		7.09e-08
(3.81e-05)
Del Peak 22(10q23 31) 70 (14%) 422 0.176
(1.00) 		0.0543
(1.00) 		1.2e-29
(1.09e-26) 		5.19e-08
(2.82e-05) 		0.116
(1.00) 		0.796
(1.00) 		3.39e-07
(0.000175) 		1.88e-07
(9.85e-05) 		3.63e-10
(2.23e-07) 		1.21e-07
(6.4e-05)
Del Peak 23(11p15 5) 93 (19%) 399 0.352
(1.00) 		0.133
(1.00) 		7.81e-40
(7.3e-37) 		3.91e-17
(3.13e-14) 		0.452
(1.00) 		0.309
(1.00) 		4.92e-14
(3.63e-11) 		4.77e-16
(3.71e-13) 		5.84e-17
(4.66e-14) 		6.31e-15
(4.79e-12)
Del Peak 24(11q14 1) 63 (13%) 429 7.36e-22
(6.4e-19) 		1.39e-09
(8.33e-07) 		0.328
(1.00) 		0.393
(1.00) 		2.82e-08
(1.56e-05) 		2.31e-10
(1.44e-07) 		3.3e-10
(2.03e-07) 		7.81e-13
(5.51e-10)
Del Peak 25(11q25) 84 (17%) 408 4.75e-28
(4.3e-25) 		1.41e-13
(1.02e-10) 		0.134
(1.00) 		0.804
(1.00) 		3.31e-08
(1.82e-05) 		5.43e-12
(3.69e-09) 		5.32e-14
(3.91e-11) 		7.44e-16
(5.74e-13)
Del Peak 26(12q23 1) 48 (10%) 444 2.41e-20
(2.07e-17) 		8.82e-11
(5.66e-08) 		0.0349
(1.00) 		0.00949
(1.00) 		3.97e-07
(0.000204) 		1.13e-07
(6e-05) 		1.55e-10
(9.75e-08) 		3.33e-09
(1.95e-06)
Del Peak 27(12q24 33) 59 (12%) 433 1.03e-25
(9.3e-23) 		2.32e-11
(1.53e-08) 		0.0355
(1.00) 		0.106
(1.00) 		1.07e-11
(7.16e-09) 		2.32e-09
(1.37e-06) 		8.99e-14
(6.54e-11) 		4.51e-11
(2.92e-08)
Del Peak 28(13q11) 86 (17%) 406 0.455
(1.00) 		0.0133
(1.00) 		1.94e-29
(1.76e-26) 		3.97e-09
(2.31e-06) 		0.162
(1.00) 		0.126
(1.00) 		4.78e-07
(0.000243) 		1.7e-11
(1.13e-08) 		1.66e-10
(1.04e-07) 		7.21e-10
(4.4e-07)
Del Peak 29(13q14 2) 94 (19%) 398 0.687
(1.00) 		0.0435
(1.00) 		2.43e-32
(2.23e-29) 		5.16e-08
(2.81e-05) 		0.0746
(1.00) 		0.102
(1.00) 		1.16e-06
(0.000579) 		9.57e-11
(6.12e-08) 		2.51e-08
(1.39e-05) 		3.96e-07
(0.000204)
Del Peak 30(14q13 1) 62 (13%) 430 0.0191
(1.00) 		0.00403
(1.00) 		1.28e-22
(1.12e-19) 		1.27e-10
(8.07e-08) 		0.0681
(1.00) 		0.106
(1.00) 		7.68e-09
(4.4e-06) 		1.63e-10
(1.02e-07) 		1.21e-08
(6.83e-06) 		1.06e-10
(6.78e-08)
Del Peak 31(15q15 1) 124 (25%) 368 0.0227
(1.00) 		0.00379
(1.00) 		1.37e-55
(1.31e-52) 		1.41e-18
(1.17e-15) 		0.00247
(0.849) 		0.205
(1.00) 		3.76e-17
(3.02e-14) 		8.64e-22
(7.5e-19) 		5.54e-23
(4.87e-20) 		2.1e-18
(1.73e-15)
Del Peak 32(15q23) 100 (20%) 392 0.00677
(1.00) 		0.00103
(0.38) 		7.28e-42
(6.83e-39) 		1.94e-18
(1.61e-15) 		0.104
(1.00) 		0.812
(1.00) 		1.46e-12
(1.02e-09) 		9.7e-15
(7.31e-12) 		2.08e-16
(1.63e-13) 		1.35e-15
(1.04e-12)
Del Peak 33(16p13 3) 81 (16%) 411 0.0015
(0.54) 		0.00379
(1.00) 		1.59e-37
(1.48e-34) 		1.53e-14
(1.14e-11) 		0.0547
(1.00) 		0.176
(1.00) 		8.49e-14
(6.2e-11) 		1.28e-11
(8.59e-09) 		2.16e-15
(1.66e-12) 		1.19e-16
(9.3e-14)
Del Peak 41(18q23) 91 (18%) 401 0.193
(1.00) 		0.504
(1.00) 		6.45e-34
(5.96e-31) 		4.64e-12
(3.16e-09) 		0.0427
(1.00) 		0.0354
(1.00) 		4.88e-11
(3.16e-08) 		2.72e-13
(1.95e-10) 		3.61e-12
(2.47e-09) 		4.4e-12
(3e-09)
Del Peak 43(19p12) 49 (10%) 443 1.3e-15
(1e-12) 		6.64e-07
(0.000333) 		0.21
(1.00) 		0.507
(1.00) 		2.14e-05
(0.00976) 		3.98e-06
(0.00193) 		8.82e-07
(0.00044) 		8.4e-05
(0.0364)
Del Peak 46(22q11 1) 81 (16%) 411 0.00677
(1.00) 		0.00103
(0.38) 		2.26e-29
(2.06e-26) 		0.000115
(0.0484) 		0.451
(1.00) 		0.796
(1.00) 		1.25e-07
(6.59e-05) 		1.85e-09
(1.09e-06) 		3.04e-07
(0.000158) 		0.000135
(0.0569)
Del Peak 47(22q12 1) 87 (18%) 405 0.00677
(1.00) 		0.00103
(0.38) 		1.54e-31
(1.41e-28) 		2.1e-05
(0.00961) 		0.267
(1.00) 		0.627
(1.00) 		4.79e-09
(2.77e-06) 		1.31e-11
(8.73e-09) 		4.74e-08
(2.59e-05) 		7.64e-06
(0.00364)
Amp Peak 19(8p11 21) 146 (30%) 346 0.00161
(0.569) 		0.0161
(1.00) 		1.7e-23
(1.51e-20) 		0.011
(1.00) 		0.00111
(0.404) 		0.719
(1.00) 		0.000553
(0.216) 		2.25e-05
(0.0102) 		0.000294
(0.118) 		7.57e-06
(0.00361)
Del Peak 4(2p25 3) 24 (5%) 468 6.48e-09
(3.72e-06) 		0.00054
(0.211) 		0.268
(1.00) 		0.652
(1.00) 		8.8e-05
(0.038) 		0.000323
(0.129) 		0.000578
(0.222) 		0.0035
(1.00)
Del Peak 6(2q37 3) 49 (10%) 443 7.94e-17
(6.26e-14) 		4.56e-05
(0.0202) 		0.276
(1.00) 		0.507
(1.00) 		1.36e-05
(0.00632) 		1.43e-06
(0.000705) 		5.39e-05
(0.0238) 		0.00101
(0.379)
Amp Peak 5(1q22) 232 (47%) 260 0.0177
(1.00) 		0.0229
(1.00) 		4.26e-15
(3.25e-12) 		0.000289
(0.117) 		0.132
(1.00) 		0.179
(1.00) 		0.0112
(1.00) 		0.0445
(1.00) 		1.43e-05
(0.00664) 		1.18e-05
(0.00558)
Amp Peak 10(3p14 1) 56 (11%) 436 0.86
(1.00) 		0.623
(1.00) 		7.51e-20
(6.38e-17) 		0.000802
(0.305) 		0.0521
(1.00) 		0.373
(1.00) 		3.18e-05
(0.0143) 		2.55e-05
(0.0115) 		0.014
(1.00) 		7.39e-05
(0.0323)
Amp Peak 4(1q21 3) 220 (45%) 272 0.0177
(1.00) 		0.0229
(1.00) 		1.7e-13
(1.23e-10) 		0.00951
(1.00) 		0.317
(1.00) 		0.135
(1.00) 		0.011
(1.00) 		0.0901
(1.00) 		2.21e-05
(0.01) 		7.79e-05
(0.0339)
Del Peak 8(3q13 31) 28 (6%) 464 0.0591
(1.00) 		0.133
(1.00) 		1.44e-12
(1e-09) 		0.00461
(1.00) 		0.0559
(1.00) 		1
(1.00) 		0.000246
(0.1) 		0.000744
(0.284) 		5.71e-07
(0.000288) 		0.00118
(0.431)
Amp Peak 3(1p22 3) 81 (16%) 411 0.0238
(1.00) 		0.115
(1.00) 		1.91e-08
(1.06e-05) 		0.0153
(1.00) 		0.737
(1.00) 		0.28
(1.00) 		0.00612
(1.00) 		0.0107
(1.00) 		4.94e-06
(0.00237) 		0.0027
(0.92)
Amp Peak 6(1q42 3) 203 (41%) 289 0.0221
(1.00) 		0.0243
(1.00) 		1.74e-07
(9.13e-05) 		0.132
(1.00) 		0.631
(1.00) 		0.0696
(1.00) 		0.0321
(1.00) 		0.0775
(1.00) 		0.000282
(0.114) 		0.0265
(1.00)
Amp Peak 18(7q22 1) 82 (17%) 410 0.311
(1.00) 		0.558
(1.00) 		5.12e-20
(4.36e-17) 		0.00694
(1.00) 		0.74
(1.00) 		1
(1.00) 		0.00365
(1.00) 		0.0317
(1.00) 		0.00232
(0.806) 		0.00177
(0.621)
Amp Peak 24(10q22 2) 132 (27%) 360 0.00691
(1.00) 		0.116
(1.00) 		1.77e-08
(9.88e-06) 		0.389
(1.00) 		0.273
(1.00) 		0.414
(1.00) 		0.276
(1.00) 		0.0148
(1.00) 		0.891
(1.00) 		0.122
(1.00)
Amp Peak 47(Xp11 23) 84 (17%) 408 0.491
(1.00) 		0.407
(1.00) 		1.88e-25
(1.69e-22) 		0.00847
(1.00) 		0.783
(1.00) 		0.399
(1.00) 		0.155
(1.00) 		0.134
(1.00) 		0.00235
(0.814) 		0.00468
(1.00)
Amp Peak 48(Xq28) 85 (17%) 407 0.0698
(1.00) 		0.18
(1.00) 		4.98e-24
(4.42e-21) 		0.0269
(1.00) 		0.128
(1.00) 		0.535
(1.00) 		0.118
(1.00) 		0.202
(1.00) 		0.00702
(1.00) 		0.0114
(1.00)
Del Peak 45(20p12 1) 30 (6%) 462 1
(1.00) 		1
(1.00) 		0.000182
(0.0754) 		0.0794
(1.00) 		0.0877
(1.00) 		0.507
(1.00) 		0.101
(1.00) 		0.00996
(1.00) 		0.0398
(1.00) 		0.0528
(1.00)
Del Peak 3(1q43) 9 (2%) 483 0.00131
(0.475) 		0.174
(1.00) 		0.376
(1.00) 		0.00486
(1.00) 		0.0431
(1.00) 		0.121
(1.00) 		0.122
(1.00)
'Amp Peak 1(1p35.2) mutation analysis' versus 'CN_CNMF'

P value = 3.5e-20 (Chi-square test), Q value = 3e-17

Table S1.  Gene #1: 'Amp Peak 1(1p35.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 1(1P35.2) MUTATED 0 7 42 1 0
AMP PEAK 1(1P35.2) WILD-TYPE 290 33 97 16 6

Figure S1.  Get High-res Image Gene #1: 'Amp Peak 1(1p35.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 1(1p35.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.77e-07 (Fisher's exact test), Q value = 0.00024

Table S2.  Gene #1: 'Amp Peak 1(1p35.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 1(1P35.2) MUTATED 31 4 5
AMP PEAK 1(1P35.2) WILD-TYPE 112 81 144

Figure S2.  Get High-res Image Gene #1: 'Amp Peak 1(1p35.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 1(1p35.2) mutation analysis' versus 'RPPA_CNMF'

P value = 1e-04 (Chi-square test), Q value = 0.043

Table S3.  Gene #1: 'Amp Peak 1(1p35.2) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
AMP PEAK 1(1P35.2) MUTATED 1 10 2 0 0 2
AMP PEAK 1(1P35.2) WILD-TYPE 40 27 37 12 41 22

Figure S3.  Get High-res Image Gene #1: 'Amp Peak 1(1p35.2) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Amp Peak 1(1p35.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.22e-09 (Fisher's exact test), Q value = 7.4e-07

Table S4.  Gene #1: 'Amp Peak 1(1p35.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 1(1P35.2) MUTATED 27 1 1
AMP PEAK 1(1P35.2) WILD-TYPE 115 106 112

Figure S4.  Get High-res Image Gene #1: 'Amp Peak 1(1p35.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 1(1p35.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.4e-12 (Fisher's exact test), Q value = 5.7e-09

Table S5.  Gene #1: 'Amp Peak 1(1p35.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 1(1P35.2) MUTATED 0 0 0 29
AMP PEAK 1(1P35.2) WILD-TYPE 65 92 65 111

Figure S5.  Get High-res Image Gene #1: 'Amp Peak 1(1p35.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 1(1p35.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.44e-07 (Fisher's exact test), Q value = 0.00023

Table S6.  Gene #1: 'Amp Peak 1(1p35.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 1(1P35.2) MUTATED 37 5 6
AMP PEAK 1(1P35.2) WILD-TYPE 157 141 133

Figure S6.  Get High-res Image Gene #1: 'Amp Peak 1(1p35.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 1(1p35.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.13e-08 (Chi-square test), Q value = 6.4e-06

Table S7.  Gene #1: 'Amp Peak 1(1p35.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 1(1P35.2) MUTATED 1 33 1 1 6 6
AMP PEAK 1(1P35.2) WILD-TYPE 55 109 73 22 33 139

Figure S7.  Get High-res Image Gene #1: 'Amp Peak 1(1p35.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 2(1p34.2) mutation analysis' versus 'CN_CNMF'

P value = 2.06e-28 (Chi-square test), Q value = 1.9e-25

Table S8.  Gene #2: 'Amp Peak 2(1p34.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 2(1P34.2) MUTATED 1 5 56 1 0
AMP PEAK 2(1P34.2) WILD-TYPE 289 35 83 16 6

Figure S8.  Get High-res Image Gene #2: 'Amp Peak 2(1p34.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 2(1p34.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.36e-08 (Fisher's exact test), Q value = 7.7e-06

Table S9.  Gene #2: 'Amp Peak 2(1p34.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 2(1P34.2) MUTATED 37 12 4
AMP PEAK 2(1P34.2) WILD-TYPE 106 73 145

Figure S9.  Get High-res Image Gene #2: 'Amp Peak 2(1p34.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 2(1p34.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.8e-12 (Fisher's exact test), Q value = 5.3e-09

Table S10.  Gene #2: 'Amp Peak 2(1p34.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 2(1P34.2) MUTATED 34 2 1
AMP PEAK 2(1P34.2) WILD-TYPE 108 105 112

Figure S10.  Get High-res Image Gene #2: 'Amp Peak 2(1p34.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 2(1p34.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.95e-14 (Fisher's exact test), Q value = 3.6e-11

Table S11.  Gene #2: 'Amp Peak 2(1p34.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 2(1P34.2) MUTATED 0 0 1 36
AMP PEAK 2(1P34.2) WILD-TYPE 65 92 64 104

Figure S11.  Get High-res Image Gene #2: 'Amp Peak 2(1p34.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 2(1p34.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 9.39e-13 (Fisher's exact test), Q value = 6.6e-10

Table S12.  Gene #2: 'Amp Peak 2(1p34.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 2(1P34.2) MUTATED 51 4 6
AMP PEAK 2(1P34.2) WILD-TYPE 143 142 133

Figure S12.  Get High-res Image Gene #2: 'Amp Peak 2(1p34.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 2(1p34.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.55e-13 (Chi-square test), Q value = 2.5e-10

Table S13.  Gene #2: 'Amp Peak 2(1p34.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 2(1P34.2) MUTATED 3 44 2 1 7 4
AMP PEAK 2(1P34.2) WILD-TYPE 53 98 72 22 32 141

Figure S13.  Get High-res Image Gene #2: 'Amp Peak 2(1p34.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 1.91e-08 (Chi-square test), Q value = 1.1e-05

Table S14.  Gene #3: 'Amp Peak 3(1p22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 3(1P22.3) MUTATED 30 5 39 2 5
AMP PEAK 3(1P22.3) WILD-TYPE 260 35 100 15 1

Figure S14.  Get High-res Image Gene #3: 'Amp Peak 3(1p22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 4.94e-06 (Fisher's exact test), Q value = 0.0024

Table S15.  Gene #3: 'Amp Peak 3(1p22.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 3(1P22.3) MUTATED 44 7 27
AMP PEAK 3(1P22.3) WILD-TYPE 150 139 112

Figure S15.  Get High-res Image Gene #3: 'Amp Peak 3(1p22.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 4(1q21.3) mutation analysis' versus 'CN_CNMF'

P value = 1.7e-13 (Chi-square test), Q value = 1.2e-10

Table S16.  Gene #4: 'Amp Peak 4(1q21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 4(1Q21.3) MUTATED 87 26 88 13 6
AMP PEAK 4(1Q21.3) WILD-TYPE 203 14 51 4 0

Figure S16.  Get High-res Image Gene #4: 'Amp Peak 4(1q21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 4(1q21.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.21e-05 (Fisher's exact test), Q value = 0.01

Table S17.  Gene #4: 'Amp Peak 4(1q21.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 4(1Q21.3) MUTATED 99 42 72
AMP PEAK 4(1Q21.3) WILD-TYPE 95 104 67

Figure S17.  Get High-res Image Gene #4: 'Amp Peak 4(1q21.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 4(1q21.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.79e-05 (Chi-square test), Q value = 0.034

Table S18.  Gene #4: 'Amp Peak 4(1q21.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 4(1Q21.3) MUTATED 28 82 34 4 18 47
AMP PEAK 4(1Q21.3) WILD-TYPE 28 60 40 19 21 98

Figure S18.  Get High-res Image Gene #4: 'Amp Peak 4(1q21.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 5(1q22) mutation analysis' versus 'CN_CNMF'

P value = 4.26e-15 (Chi-square test), Q value = 3.2e-12

Table S19.  Gene #5: 'Amp Peak 5(1q22) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 5(1Q22) MUTATED 91 26 96 13 6
AMP PEAK 5(1Q22) WILD-TYPE 199 14 43 4 0

Figure S19.  Get High-res Image Gene #5: 'Amp Peak 5(1q22) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 5(1q22) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000289 (Fisher's exact test), Q value = 0.12

Table S20.  Gene #5: 'Amp Peak 5(1q22) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 5(1Q22) MUTATED 84 34 54
AMP PEAK 5(1Q22) WILD-TYPE 59 51 95

Figure S20.  Get High-res Image Gene #5: 'Amp Peak 5(1q22) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 5(1q22) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.43e-05 (Fisher's exact test), Q value = 0.0066

Table S21.  Gene #5: 'Amp Peak 5(1q22) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 5(1Q22) MUTATED 105 45 75
AMP PEAK 5(1Q22) WILD-TYPE 89 101 64

Figure S21.  Get High-res Image Gene #5: 'Amp Peak 5(1q22) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 5(1q22) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.18e-05 (Chi-square test), Q value = 0.0056

Table S22.  Gene #5: 'Amp Peak 5(1q22) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 5(1Q22) MUTATED 28 88 35 4 20 50
AMP PEAK 5(1Q22) WILD-TYPE 28 54 39 19 19 95

Figure S22.  Get High-res Image Gene #5: 'Amp Peak 5(1q22) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 6(1q42.3) mutation analysis' versus 'CN_CNMF'

P value = 1.74e-07 (Chi-square test), Q value = 9.1e-05

Table S23.  Gene #6: 'Amp Peak 6(1q42.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 6(1Q42.3) MUTATED 90 24 72 11 6
AMP PEAK 6(1Q42.3) WILD-TYPE 200 16 67 6 0

Figure S23.  Get High-res Image Gene #6: 'Amp Peak 6(1q42.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 6(1q42.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000282 (Fisher's exact test), Q value = 0.11

Table S24.  Gene #6: 'Amp Peak 6(1q42.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 6(1Q42.3) MUTATED 76 46 76
AMP PEAK 6(1Q42.3) WILD-TYPE 118 100 63

Figure S24.  Get High-res Image Gene #6: 'Amp Peak 6(1q42.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 7(2p23.2) mutation analysis' versus 'CN_CNMF'

P value = 5.04e-28 (Chi-square test), Q value = 4.6e-25

Table S25.  Gene #7: 'Amp Peak 7(2p23.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 7(2P23.2) MUTATED 14 23 67 6 1
AMP PEAK 7(2P23.2) WILD-TYPE 276 17 72 11 5

Figure S25.  Get High-res Image Gene #7: 'Amp Peak 7(2p23.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 7(2p23.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.59e-10 (Fisher's exact test), Q value = 1e-07

Table S26.  Gene #7: 'Amp Peak 7(2p23.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 7(2P23.2) MUTATED 59 13 14
AMP PEAK 7(2P23.2) WILD-TYPE 84 72 135

Figure S26.  Get High-res Image Gene #7: 'Amp Peak 7(2p23.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 7(2p23.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.63e-06 (Fisher's exact test), Q value = 0.0018

Table S27.  Gene #7: 'Amp Peak 7(2p23.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 7(2P23.2) MUTATED 46 10 14
AMP PEAK 7(2P23.2) WILD-TYPE 96 97 99

Figure S27.  Get High-res Image Gene #7: 'Amp Peak 7(2p23.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 7(2p23.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.02e-06 (Fisher's exact test), Q value = 0.0024

Table S28.  Gene #7: 'Amp Peak 7(2p23.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 7(2P23.2) MUTATED 8 7 9 46
AMP PEAK 7(2P23.2) WILD-TYPE 57 85 56 94

Figure S28.  Get High-res Image Gene #7: 'Amp Peak 7(2p23.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 7(2p23.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 7.34e-10 (Fisher's exact test), Q value = 4.5e-07

Table S29.  Gene #7: 'Amp Peak 7(2p23.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 7(2P23.2) MUTATED 73 16 19
AMP PEAK 7(2P23.2) WILD-TYPE 121 130 120

Figure S29.  Get High-res Image Gene #7: 'Amp Peak 7(2p23.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 7(2p23.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.56e-12 (Chi-square test), Q value = 1.1e-09

Table S30.  Gene #7: 'Amp Peak 7(2p23.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 7(2P23.2) MUTATED 4 64 12 2 10 16
AMP PEAK 7(2P23.2) WILD-TYPE 52 78 62 21 29 129

Figure S30.  Get High-res Image Gene #7: 'Amp Peak 7(2p23.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 8(2q13) mutation analysis' versus 'CN_CNMF'

P value = 2.77e-33 (Chi-square test), Q value = 2.6e-30

Table S31.  Gene #8: 'Amp Peak 8(2q13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 8(2Q13) MUTATED 8 19 74 5 1
AMP PEAK 8(2Q13) WILD-TYPE 282 21 65 12 5

Figure S31.  Get High-res Image Gene #8: 'Amp Peak 8(2q13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 8(2q13) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.95e-12 (Fisher's exact test), Q value = 1.4e-09

Table S32.  Gene #8: 'Amp Peak 8(2q13) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 8(2Q13) MUTATED 58 16 9
AMP PEAK 8(2Q13) WILD-TYPE 85 69 140

Figure S32.  Get High-res Image Gene #8: 'Amp Peak 8(2q13) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 8(2q13) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 8.42e-11 (Fisher's exact test), Q value = 5.4e-08

Table S33.  Gene #8: 'Amp Peak 8(2q13) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 8(2Q13) MUTATED 50 7 8
AMP PEAK 8(2Q13) WILD-TYPE 92 100 105

Figure S33.  Get High-res Image Gene #8: 'Amp Peak 8(2q13) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 8(2q13) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.53e-10 (Fisher's exact test), Q value = 9.7e-08

Table S34.  Gene #8: 'Amp Peak 8(2q13) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 8(2Q13) MUTATED 6 5 4 50
AMP PEAK 8(2Q13) WILD-TYPE 59 87 61 90

Figure S34.  Get High-res Image Gene #8: 'Amp Peak 8(2q13) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 8(2q13) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 8.86e-17 (Fisher's exact test), Q value = 7e-14

Table S35.  Gene #8: 'Amp Peak 8(2q13) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 8(2Q13) MUTATED 80 10 14
AMP PEAK 8(2Q13) WILD-TYPE 114 136 125

Figure S35.  Get High-res Image Gene #8: 'Amp Peak 8(2q13) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 8(2q13) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.16e-17 (Chi-square test), Q value = 4.9e-14

Table S36.  Gene #8: 'Amp Peak 8(2q13) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 8(2Q13) MUTATED 5 68 6 2 9 14
AMP PEAK 8(2Q13) WILD-TYPE 51 74 68 21 30 131

Figure S36.  Get High-res Image Gene #8: 'Amp Peak 8(2q13) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 9(3p25.1) mutation analysis' versus 'CN_CNMF'

P value = 4.11e-24 (Chi-square test), Q value = 3.7e-21

Table S37.  Gene #9: 'Amp Peak 9(3p25.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 9(3P25.1) MUTATED 4 5 50 9 2
AMP PEAK 9(3P25.1) WILD-TYPE 286 35 89 8 4

Figure S37.  Get High-res Image Gene #9: 'Amp Peak 9(3p25.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 9(3p25.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.75e-06 (Fisher's exact test), Q value = 0.0018

Table S38.  Gene #9: 'Amp Peak 9(3p25.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 9(3P25.1) MUTATED 35 14 7
AMP PEAK 9(3P25.1) WILD-TYPE 108 71 142

Figure S38.  Get High-res Image Gene #9: 'Amp Peak 9(3p25.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 9(3p25.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.49e-08 (Fisher's exact test), Q value = 3.5e-05

Table S39.  Gene #9: 'Amp Peak 9(3p25.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 9(3P25.1) MUTATED 35 7 3
AMP PEAK 9(3P25.1) WILD-TYPE 107 100 110

Figure S39.  Get High-res Image Gene #9: 'Amp Peak 9(3p25.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 9(3p25.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.78e-08 (Fisher's exact test), Q value = 1e-05

Table S40.  Gene #9: 'Amp Peak 9(3p25.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 9(3P25.1) MUTATED 0 3 8 34
AMP PEAK 9(3P25.1) WILD-TYPE 65 89 57 106

Figure S40.  Get High-res Image Gene #9: 'Amp Peak 9(3p25.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 9(3p25.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000147 (Fisher's exact test), Q value = 0.062

Table S41.  Gene #9: 'Amp Peak 9(3p25.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 9(3P25.1) MUTATED 43 11 13
AMP PEAK 9(3P25.1) WILD-TYPE 151 135 126

Figure S41.  Get High-res Image Gene #9: 'Amp Peak 9(3p25.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 9(3p25.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.97e-07 (Chi-square test), Q value = 3e-04

Table S42.  Gene #9: 'Amp Peak 9(3p25.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 9(3P25.1) MUTATED 4 40 3 3 6 11
AMP PEAK 9(3P25.1) WILD-TYPE 52 102 71 20 33 134

Figure S42.  Get High-res Image Gene #9: 'Amp Peak 9(3p25.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 10(3p14.1) mutation analysis' versus 'CN_CNMF'

P value = 7.51e-20 (Chi-square test), Q value = 6.4e-17

Table S43.  Gene #10: 'Amp Peak 10(3p14.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 10(3P14.1) MUTATED 4 5 35 10 2
AMP PEAK 10(3P14.1) WILD-TYPE 286 35 104 7 4

Figure S43.  Get High-res Image Gene #10: 'Amp Peak 10(3p14.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 10(3p14.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.18e-05 (Fisher's exact test), Q value = 0.014

Table S44.  Gene #10: 'Amp Peak 10(3p14.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 10(3P14.1) MUTATED 25 7 2
AMP PEAK 10(3P14.1) WILD-TYPE 117 100 111

Figure S44.  Get High-res Image Gene #10: 'Amp Peak 10(3p14.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 10(3p14.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.55e-05 (Fisher's exact test), Q value = 0.011

Table S45.  Gene #10: 'Amp Peak 10(3p14.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 10(3P14.1) MUTATED 0 3 7 24
AMP PEAK 10(3P14.1) WILD-TYPE 65 89 58 116

Figure S45.  Get High-res Image Gene #10: 'Amp Peak 10(3p14.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 10(3p14.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.39e-05 (Chi-square test), Q value = 0.032

Table S46.  Gene #10: 'Amp Peak 10(3p14.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 10(3P14.1) MUTATED 2 30 1 3 6 12
AMP PEAK 10(3P14.1) WILD-TYPE 54 112 73 20 33 133

Figure S46.  Get High-res Image Gene #10: 'Amp Peak 10(3p14.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 11(3q26.2) mutation analysis' versus 'MRNA_CNMF'

P value = 5.21e-06 (Fisher's exact test), Q value = 0.0025

Table S47.  Gene #11: 'Amp Peak 11(3q26.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
AMP PEAK 11(3Q26.2) MUTATED 0 12 1 0
AMP PEAK 11(3Q26.2) WILD-TYPE 13 6 13 8

Figure S47.  Get High-res Image Gene #11: 'Amp Peak 11(3q26.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 11(3q26.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 4.74e-05 (Fisher's exact test), Q value = 0.021

Table S48.  Gene #11: 'Amp Peak 11(3q26.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
AMP PEAK 11(3Q26.2) MUTATED 1 1 11
AMP PEAK 11(3Q26.2) WILD-TYPE 19 14 7

Figure S48.  Get High-res Image Gene #11: 'Amp Peak 11(3q26.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 11(3q26.2) mutation analysis' versus 'CN_CNMF'

P value = 3.77e-61 (Chi-square test), Q value = 3.6e-58

Table S49.  Gene #11: 'Amp Peak 11(3q26.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 11(3Q26.2) MUTATED 13 10 116 12 4
AMP PEAK 11(3Q26.2) WILD-TYPE 277 30 23 5 2

Figure S49.  Get High-res Image Gene #11: 'Amp Peak 11(3q26.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 11(3q26.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.95e-17 (Fisher's exact test), Q value = 1.6e-14

Table S50.  Gene #11: 'Amp Peak 11(3q26.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 11(3Q26.2) MUTATED 86 24 19
AMP PEAK 11(3Q26.2) WILD-TYPE 57 61 130

Figure S50.  Get High-res Image Gene #11: 'Amp Peak 11(3q26.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 11(3q26.2) mutation analysis' versus 'RPPA_CNMF'

P value = 0.000353 (Chi-square test), Q value = 0.14

Table S51.  Gene #11: 'Amp Peak 11(3q26.2) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
AMP PEAK 11(3Q26.2) MUTATED 11 15 4 1 1 6
AMP PEAK 11(3Q26.2) WILD-TYPE 30 22 35 11 40 18

Figure S51.  Get High-res Image Gene #11: 'Amp Peak 11(3q26.2) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Amp Peak 11(3q26.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.91e-25 (Fisher's exact test), Q value = 1.7e-22

Table S52.  Gene #11: 'Amp Peak 11(3q26.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 11(3Q26.2) MUTATED 80 12 4
AMP PEAK 11(3Q26.2) WILD-TYPE 62 95 109

Figure S52.  Get High-res Image Gene #11: 'Amp Peak 11(3q26.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 11(3q26.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.67e-25 (Fisher's exact test), Q value = 3.3e-22

Table S53.  Gene #11: 'Amp Peak 11(3q26.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 11(3Q26.2) MUTATED 0 6 12 78
AMP PEAK 11(3Q26.2) WILD-TYPE 65 86 53 62

Figure S53.  Get High-res Image Gene #11: 'Amp Peak 11(3q26.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 11(3q26.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.04e-23 (Fisher's exact test), Q value = 2.7e-20

Table S54.  Gene #11: 'Amp Peak 11(3q26.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 11(3Q26.2) MUTATED 111 23 16
AMP PEAK 11(3Q26.2) WILD-TYPE 83 123 123

Figure S54.  Get High-res Image Gene #11: 'Amp Peak 11(3q26.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 11(3q26.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.97e-24 (Chi-square test), Q value = 1.8e-21

Table S55.  Gene #11: 'Amp Peak 11(3q26.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 11(3Q26.2) MUTATED 5 91 4 8 16 26
AMP PEAK 11(3Q26.2) WILD-TYPE 51 51 70 15 23 119

Figure S55.  Get High-res Image Gene #11: 'Amp Peak 11(3q26.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 12(3q26.2) mutation analysis' versus 'MRNA_CNMF'

P value = 2.42e-05 (Fisher's exact test), Q value = 0.011

Table S56.  Gene #12: 'Amp Peak 12(3q26.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
AMP PEAK 12(3Q26.2) MUTATED 0 11 1 0
AMP PEAK 12(3Q26.2) WILD-TYPE 13 7 13 8

Figure S56.  Get High-res Image Gene #12: 'Amp Peak 12(3q26.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 12(3q26.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000168 (Fisher's exact test), Q value = 0.07

Table S57.  Gene #12: 'Amp Peak 12(3q26.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
AMP PEAK 12(3Q26.2) MUTATED 1 1 10
AMP PEAK 12(3Q26.2) WILD-TYPE 19 14 8

Figure S57.  Get High-res Image Gene #12: 'Amp Peak 12(3q26.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 12(3q26.2) mutation analysis' versus 'CN_CNMF'

P value = 8.96e-60 (Chi-square test), Q value = 8.6e-57

Table S58.  Gene #12: 'Amp Peak 12(3q26.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 12(3Q26.2) MUTATED 9 9 110 12 4
AMP PEAK 12(3Q26.2) WILD-TYPE 281 31 29 5 2

Figure S58.  Get High-res Image Gene #12: 'Amp Peak 12(3q26.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 12(3q26.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.25e-19 (Fisher's exact test), Q value = 6.9e-16

Table S59.  Gene #12: 'Amp Peak 12(3q26.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 12(3Q26.2) MUTATED 84 20 16
AMP PEAK 12(3Q26.2) WILD-TYPE 59 65 133

Figure S59.  Get High-res Image Gene #12: 'Amp Peak 12(3q26.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 12(3q26.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.89e-25 (Fisher's exact test), Q value = 1.7e-22

Table S60.  Gene #12: 'Amp Peak 12(3q26.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 12(3Q26.2) MUTATED 78 10 4
AMP PEAK 12(3Q26.2) WILD-TYPE 64 97 109

Figure S60.  Get High-res Image Gene #12: 'Amp Peak 12(3q26.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 12(3q26.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.53e-26 (Fisher's exact test), Q value = 6.8e-23

Table S61.  Gene #12: 'Amp Peak 12(3q26.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 12(3Q26.2) MUTATED 0 5 10 77
AMP PEAK 12(3Q26.2) WILD-TYPE 65 87 55 63

Figure S61.  Get High-res Image Gene #12: 'Amp Peak 12(3q26.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 12(3q26.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.25e-21 (Fisher's exact test), Q value = 1.1e-18

Table S62.  Gene #12: 'Amp Peak 12(3q26.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 12(3Q26.2) MUTATED 104 19 16
AMP PEAK 12(3Q26.2) WILD-TYPE 90 127 123

Figure S62.  Get High-res Image Gene #12: 'Amp Peak 12(3q26.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 12(3q26.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.33e-23 (Chi-square test), Q value = 1.2e-20

Table S63.  Gene #12: 'Amp Peak 12(3q26.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 12(3Q26.2) MUTATED 6 86 3 8 15 21
AMP PEAK 12(3Q26.2) WILD-TYPE 50 56 71 15 24 124

Figure S63.  Get High-res Image Gene #12: 'Amp Peak 12(3q26.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 13(4p16.3) mutation analysis' versus 'CN_CNMF'

P value = 1.64e-21 (Chi-square test), Q value = 1.4e-18

Table S64.  Gene #13: 'Amp Peak 13(4p16.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 13(4P16.3) MUTATED 2 1 42 0 0
AMP PEAK 13(4P16.3) WILD-TYPE 288 39 97 17 6

Figure S64.  Get High-res Image Gene #13: 'Amp Peak 13(4p16.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 13(4p16.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000532 (Fisher's exact test), Q value = 0.21

Table S65.  Gene #13: 'Amp Peak 13(4p16.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 13(4P16.3) MUTATED 21 10 4
AMP PEAK 13(4P16.3) WILD-TYPE 122 75 145

Figure S65.  Get High-res Image Gene #13: 'Amp Peak 13(4p16.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 13(4p16.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.2e-10 (Fisher's exact test), Q value = 3.2e-07

Table S66.  Gene #13: 'Amp Peak 13(4p16.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 13(4P16.3) MUTATED 28 1 1
AMP PEAK 13(4P16.3) WILD-TYPE 114 106 112

Figure S66.  Get High-res Image Gene #13: 'Amp Peak 13(4p16.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 13(4p16.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.95e-11 (Fisher's exact test), Q value = 4.5e-08

Table S67.  Gene #13: 'Amp Peak 13(4p16.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 13(4P16.3) MUTATED 1 0 0 29
AMP PEAK 13(4P16.3) WILD-TYPE 64 92 65 111

Figure S67.  Get High-res Image Gene #13: 'Amp Peak 13(4p16.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 13(4p16.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 8.29e-09 (Fisher's exact test), Q value = 4.7e-06

Table S68.  Gene #13: 'Amp Peak 13(4p16.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 13(4P16.3) MUTATED 36 3 4
AMP PEAK 13(4P16.3) WILD-TYPE 158 143 135

Figure S68.  Get High-res Image Gene #13: 'Amp Peak 13(4p16.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 13(4p16.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.67e-08 (Chi-square test), Q value = 2e-05

Table S69.  Gene #13: 'Amp Peak 13(4p16.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 13(4P16.3) MUTATED 3 31 0 1 3 5
AMP PEAK 13(4P16.3) WILD-TYPE 53 111 74 22 36 140

Figure S69.  Get High-res Image Gene #13: 'Amp Peak 13(4p16.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 14(5p15.33) mutation analysis' versus 'CN_CNMF'

P value = 4.71e-32 (Chi-square test), Q value = 4.3e-29

Table S70.  Gene #14: 'Amp Peak 14(5p15.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 14(5P15.33) MUTATED 4 5 66 1 1
AMP PEAK 14(5P15.33) WILD-TYPE 286 35 73 16 5

Figure S70.  Get High-res Image Gene #14: 'Amp Peak 14(5p15.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 14(5p15.33) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.4e-12 (Fisher's exact test), Q value = 2.3e-09

Table S71.  Gene #14: 'Amp Peak 14(5p15.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 14(5P15.33) MUTATED 47 12 4
AMP PEAK 14(5P15.33) WILD-TYPE 96 73 145

Figure S71.  Get High-res Image Gene #14: 'Amp Peak 14(5p15.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 14(5p15.33) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.21e-14 (Fisher's exact test), Q value = 2.4e-11

Table S72.  Gene #14: 'Amp Peak 14(5p15.33) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 14(5P15.33) MUTATED 42 0 6
AMP PEAK 14(5P15.33) WILD-TYPE 100 107 107

Figure S72.  Get High-res Image Gene #14: 'Amp Peak 14(5p15.33) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 14(5p15.33) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.37e-12 (Fisher's exact test), Q value = 1.6e-09

Table S73.  Gene #14: 'Amp Peak 14(5p15.33) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 14(5P15.33) MUTATED 3 0 4 41
AMP PEAK 14(5P15.33) WILD-TYPE 62 92 61 99

Figure S73.  Get High-res Image Gene #14: 'Amp Peak 14(5p15.33) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 14(5p15.33) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 5.86e-14 (Fisher's exact test), Q value = 4.3e-11

Table S74.  Gene #14: 'Amp Peak 14(5p15.33) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 14(5P15.33) MUTATED 59 3 13
AMP PEAK 14(5P15.33) WILD-TYPE 135 143 126

Figure S74.  Get High-res Image Gene #14: 'Amp Peak 14(5p15.33) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 14(5p15.33) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.29e-14 (Chi-square test), Q value = 6.7e-11

Table S75.  Gene #14: 'Amp Peak 14(5p15.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 14(5P15.33) MUTATED 4 49 4 3 11 4
AMP PEAK 14(5P15.33) WILD-TYPE 52 93 70 20 28 141

Figure S75.  Get High-res Image Gene #14: 'Amp Peak 14(5p15.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 15(5q35.3) mutation analysis' versus 'CN_CNMF'

P value = 8.67e-20 (Chi-square test), Q value = 7.4e-17

Table S76.  Gene #15: 'Amp Peak 15(5q35.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 15(5Q35.3) MUTATED 2 3 42 0 1
AMP PEAK 15(5Q35.3) WILD-TYPE 288 37 97 17 5

Figure S76.  Get High-res Image Gene #15: 'Amp Peak 15(5q35.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 15(5q35.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000639 (Fisher's exact test), Q value = 0.25

Table S77.  Gene #15: 'Amp Peak 15(5q35.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 15(5Q35.3) MUTATED 25 10 6
AMP PEAK 15(5Q35.3) WILD-TYPE 118 75 143

Figure S77.  Get High-res Image Gene #15: 'Amp Peak 15(5q35.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 15(5q35.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.18e-07 (Fisher's exact test), Q value = 0.00016

Table S78.  Gene #15: 'Amp Peak 15(5q35.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 15(5Q35.3) MUTATED 23 0 4
AMP PEAK 15(5Q35.3) WILD-TYPE 119 107 109

Figure S78.  Get High-res Image Gene #15: 'Amp Peak 15(5q35.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 15(5q35.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.98e-05 (Fisher's exact test), Q value = 0.031

Table S79.  Gene #15: 'Amp Peak 15(5q35.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 15(5Q35.3) MUTATED 2 0 5 20
AMP PEAK 15(5Q35.3) WILD-TYPE 63 92 60 120

Figure S79.  Get High-res Image Gene #15: 'Amp Peak 15(5q35.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 15(5q35.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.41e-08 (Fisher's exact test), Q value = 7.9e-06

Table S80.  Gene #15: 'Amp Peak 15(5q35.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 15(5Q35.3) MUTATED 38 3 6
AMP PEAK 15(5Q35.3) WILD-TYPE 156 143 133

Figure S80.  Get High-res Image Gene #15: 'Amp Peak 15(5q35.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 15(5q35.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000561 (Chi-square test), Q value = 0.22

Table S81.  Gene #15: 'Amp Peak 15(5q35.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 15(5Q35.3) MUTATED 5 27 4 0 4 7
AMP PEAK 15(5Q35.3) WILD-TYPE 51 115 70 23 35 138

Figure S81.  Get High-res Image Gene #15: 'Amp Peak 15(5q35.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 16(6p24.2) mutation analysis' versus 'MRNA_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.17

Table S82.  Gene #16: 'Amp Peak 16(6p24.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
AMP PEAK 16(6P24.2) MUTATED 0 10 2 0
AMP PEAK 16(6P24.2) WILD-TYPE 13 8 12 8

Figure S82.  Get High-res Image Gene #16: 'Amp Peak 16(6p24.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 16(6p24.2) mutation analysis' versus 'CN_CNMF'

P value = 1.36e-39 (Chi-square test), Q value = 1.3e-36

Table S83.  Gene #16: 'Amp Peak 16(6p24.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 16(6P24.2) MUTATED 8 3 80 9 1
AMP PEAK 16(6P24.2) WILD-TYPE 282 37 59 8 5

Figure S83.  Get High-res Image Gene #16: 'Amp Peak 16(6p24.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 16(6p24.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.35e-11 (Fisher's exact test), Q value = 1.6e-08

Table S84.  Gene #16: 'Amp Peak 16(6p24.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 16(6P24.2) MUTATED 57 17 10
AMP PEAK 16(6P24.2) WILD-TYPE 86 68 139

Figure S84.  Get High-res Image Gene #16: 'Amp Peak 16(6p24.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 16(6p24.2) mutation analysis' versus 'RPPA_CNMF'

P value = 0.000177 (Chi-square test), Q value = 0.074

Table S85.  Gene #16: 'Amp Peak 16(6p24.2) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
AMP PEAK 16(6P24.2) MUTATED 4 12 2 1 0 2
AMP PEAK 16(6P24.2) WILD-TYPE 37 25 37 11 41 22

Figure S85.  Get High-res Image Gene #16: 'Amp Peak 16(6p24.2) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Amp Peak 16(6p24.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.92e-16 (Fisher's exact test), Q value = 5.3e-13

Table S86.  Gene #16: 'Amp Peak 16(6p24.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 16(6P24.2) MUTATED 52 7 2
AMP PEAK 16(6P24.2) WILD-TYPE 90 100 111

Figure S86.  Get High-res Image Gene #16: 'Amp Peak 16(6p24.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 16(6p24.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.49e-14 (Fisher's exact test), Q value = 1.1e-11

Table S87.  Gene #16: 'Amp Peak 16(6p24.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 16(6P24.2) MUTATED 0 6 4 51
AMP PEAK 16(6P24.2) WILD-TYPE 65 86 61 89

Figure S87.  Get High-res Image Gene #16: 'Amp Peak 16(6p24.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 16(6p24.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.09e-14 (Fisher's exact test), Q value = 8.2e-12

Table S88.  Gene #16: 'Amp Peak 16(6p24.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 16(6P24.2) MUTATED 74 11 12
AMP PEAK 16(6P24.2) WILD-TYPE 120 135 127

Figure S88.  Get High-res Image Gene #16: 'Amp Peak 16(6p24.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 16(6p24.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.87e-15 (Chi-square test), Q value = 1.4e-12

Table S89.  Gene #16: 'Amp Peak 16(6p24.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 16(6P24.2) MUTATED 4 62 3 5 10 13
AMP PEAK 16(6P24.2) WILD-TYPE 52 80 71 18 29 132

Figure S89.  Get High-res Image Gene #16: 'Amp Peak 16(6p24.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 17(6q25.1) mutation analysis' versus 'CN_CNMF'

P value = 7.52e-22 (Chi-square test), Q value = 6.5e-19

Table S90.  Gene #17: 'Amp Peak 17(6q25.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 17(6Q25.1) MUTATED 8 5 53 8 2
AMP PEAK 17(6Q25.1) WILD-TYPE 282 35 86 9 4

Figure S90.  Get High-res Image Gene #17: 'Amp Peak 17(6q25.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 17(6q25.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.64e-06 (Fisher's exact test), Q value = 0.0013

Table S91.  Gene #17: 'Amp Peak 17(6q25.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 17(6Q25.1) MUTATED 43 11 12
AMP PEAK 17(6Q25.1) WILD-TYPE 100 74 137

Figure S91.  Get High-res Image Gene #17: 'Amp Peak 17(6q25.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 17(6q25.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.97e-07 (Fisher's exact test), Q value = 0.00025

Table S92.  Gene #17: 'Amp Peak 17(6q25.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 17(6Q25.1) MUTATED 36 7 5
AMP PEAK 17(6Q25.1) WILD-TYPE 106 100 108

Figure S92.  Get High-res Image Gene #17: 'Amp Peak 17(6q25.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 17(6q25.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.03e-08 (Fisher's exact test), Q value = 5.9e-06

Table S93.  Gene #17: 'Amp Peak 17(6q25.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 17(6Q25.1) MUTATED 0 5 6 37
AMP PEAK 17(6Q25.1) WILD-TYPE 65 87 59 103

Figure S93.  Get High-res Image Gene #17: 'Amp Peak 17(6q25.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 17(6q25.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.58e-05 (Fisher's exact test), Q value = 0.0073

Table S94.  Gene #17: 'Amp Peak 17(6q25.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 17(6Q25.1) MUTATED 49 14 12
AMP PEAK 17(6Q25.1) WILD-TYPE 145 132 127

Figure S94.  Get High-res Image Gene #17: 'Amp Peak 17(6q25.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 17(6q25.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.2e-05 (Chi-square test), Q value = 0.014

Table S95.  Gene #17: 'Amp Peak 17(6q25.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 17(6Q25.1) MUTATED 3 38 5 4 10 15
AMP PEAK 17(6Q25.1) WILD-TYPE 53 104 69 19 29 130

Figure S95.  Get High-res Image Gene #17: 'Amp Peak 17(6q25.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 18(7q22.1) mutation analysis' versus 'CN_CNMF'

P value = 5.12e-20 (Chi-square test), Q value = 4.4e-17

Table S96.  Gene #18: 'Amp Peak 18(7q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 18(7Q22.1) MUTATED 12 22 39 7 2
AMP PEAK 18(7Q22.1) WILD-TYPE 278 18 100 10 4

Figure S96.  Get High-res Image Gene #18: 'Amp Peak 18(7q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 19(8p11.21) mutation analysis' versus 'CN_CNMF'

P value = 1.7e-23 (Chi-square test), Q value = 1.5e-20

Table S97.  Gene #19: 'Amp Peak 19(8p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 19(8P11.21) MUTATED 38 20 69 17 2
AMP PEAK 19(8P11.21) WILD-TYPE 252 20 70 0 4

Figure S97.  Get High-res Image Gene #19: 'Amp Peak 19(8p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 19(8p11.21) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000553 (Fisher's exact test), Q value = 0.22

Table S98.  Gene #19: 'Amp Peak 19(8p11.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 19(8P11.21) MUTATED 54 19 24
AMP PEAK 19(8P11.21) WILD-TYPE 88 88 89

Figure S98.  Get High-res Image Gene #19: 'Amp Peak 19(8p11.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 19(8p11.21) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.25e-05 (Fisher's exact test), Q value = 0.01

Table S99.  Gene #19: 'Amp Peak 19(8p11.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 19(8P11.21) MUTATED 12 15 12 58
AMP PEAK 19(8P11.21) WILD-TYPE 53 77 53 82

Figure S99.  Get High-res Image Gene #19: 'Amp Peak 19(8p11.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 19(8p11.21) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000294 (Fisher's exact test), Q value = 0.12

Table S100.  Gene #19: 'Amp Peak 19(8p11.21) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 19(8P11.21) MUTATED 77 30 35
AMP PEAK 19(8P11.21) WILD-TYPE 117 116 104

Figure S100.  Get High-res Image Gene #19: 'Amp Peak 19(8p11.21) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 19(8p11.21) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.57e-06 (Chi-square test), Q value = 0.0036

Table S101.  Gene #19: 'Amp Peak 19(8p11.21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 19(8P11.21) MUTATED 11 61 12 12 14 32
AMP PEAK 19(8P11.21) WILD-TYPE 45 81 62 11 25 113

Figure S101.  Get High-res Image Gene #19: 'Amp Peak 19(8p11.21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 20(8q24.21) mutation analysis' versus 'CN_CNMF'

P value = 1.54e-35 (Chi-square test), Q value = 1.4e-32

Table S102.  Gene #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 20(8Q24.21) MUTATED 44 23 101 17 3
AMP PEAK 20(8Q24.21) WILD-TYPE 246 17 38 0 3

Figure S102.  Get High-res Image Gene #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 20(8q24.21) mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.2e-07 (Fisher's exact test), Q value = 0.00031

Table S103.  Gene #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 20(8Q24.21) MUTATED 84 33 42
AMP PEAK 20(8Q24.21) WILD-TYPE 59 52 107

Figure S103.  Get High-res Image Gene #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 20(8q24.21) mutation analysis' versus 'RPPA_CNMF'

P value = 8.75e-05 (Chi-square test), Q value = 0.038

Table S104.  Gene #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
AMP PEAK 20(8Q24.21) MUTATED 12 14 8 2 2 14
AMP PEAK 20(8Q24.21) WILD-TYPE 29 23 31 10 39 10

Figure S104.  Get High-res Image Gene #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Amp Peak 20(8q24.21) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.35e-09 (Fisher's exact test), Q value = 2e-06

Table S105.  Gene #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 20(8Q24.21) MUTATED 74 20 25
AMP PEAK 20(8Q24.21) WILD-TYPE 68 87 88

Figure S105.  Get High-res Image Gene #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 20(8q24.21) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.26e-11 (Fisher's exact test), Q value = 8.5e-09

Table S106.  Gene #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 20(8Q24.21) MUTATED 13 15 13 78
AMP PEAK 20(8Q24.21) WILD-TYPE 52 77 52 62

Figure S106.  Get High-res Image Gene #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 20(8q24.21) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.13e-09 (Fisher's exact test), Q value = 6.8e-07

Table S107.  Gene #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 20(8Q24.21) MUTATED 108 37 39
AMP PEAK 20(8Q24.21) WILD-TYPE 86 109 100

Figure S107.  Get High-res Image Gene #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 20(8q24.21) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.01e-13 (Chi-square test), Q value = 1.4e-10

Table S108.  Gene #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 20(8Q24.21) MUTATED 11 88 14 13 20 38
AMP PEAK 20(8Q24.21) WILD-TYPE 45 54 60 10 19 107

Figure S108.  Get High-res Image Gene #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 0.00043 (Fisher's exact test), Q value = 0.17

Table S109.  Gene #21: 'Amp Peak 21(8q24.21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
AMP PEAK 21(8Q24.21) MUTATED 0 10 2 0
AMP PEAK 21(8Q24.21) WILD-TYPE 13 8 12 8

Figure S109.  Get High-res Image Gene #21: 'Amp Peak 21(8q24.21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 8.36e-35 (Chi-square test), Q value = 7.8e-32

Table S110.  Gene #21: 'Amp Peak 21(8q24.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 21(8Q24.21) MUTATED 49 23 104 17 3
AMP PEAK 21(8Q24.21) WILD-TYPE 241 17 35 0 3

Figure S110.  Get High-res Image Gene #21: 'Amp Peak 21(8q24.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 1.24e-05 (Fisher's exact test), Q value = 0.0058

Table S111.  Gene #21: 'Amp Peak 21(8q24.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 21(8Q24.21) MUTATED 84 34 47
AMP PEAK 21(8Q24.21) WILD-TYPE 59 51 102

Figure S111.  Get High-res Image Gene #21: 'Amp Peak 21(8q24.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 7.26e-07 (Chi-square test), Q value = 0.00036

Table S112.  Gene #21: 'Amp Peak 21(8q24.21) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
AMP PEAK 21(8Q24.21) MUTATED 12 17 7 2 2 16
AMP PEAK 21(8Q24.21) WILD-TYPE 29 20 32 10 39 8

Figure S112.  Get High-res Image Gene #21: 'Amp Peak 21(8q24.21) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

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

P value = 1.82e-08 (Fisher's exact test), Q value = 1e-05

Table S113.  Gene #21: 'Amp Peak 21(8q24.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 21(8Q24.21) MUTATED 76 25 25
AMP PEAK 21(8Q24.21) WILD-TYPE 66 82 88

Figure S113.  Get High-res Image Gene #21: 'Amp Peak 21(8q24.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 1.7e-11 (Fisher's exact test), Q value = 1.1e-08

Table S114.  Gene #21: 'Amp Peak 21(8q24.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 21(8Q24.21) MUTATED 13 20 12 81
AMP PEAK 21(8Q24.21) WILD-TYPE 52 72 53 59

Figure S114.  Get High-res Image Gene #21: 'Amp Peak 21(8q24.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 9.65e-11 (Fisher's exact test), Q value = 6.2e-08

Table S115.  Gene #21: 'Amp Peak 21(8q24.21) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 21(8Q24.21) MUTATED 113 38 40
AMP PEAK 21(8Q24.21) WILD-TYPE 81 108 99

Figure S115.  Get High-res Image Gene #21: 'Amp Peak 21(8q24.21) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

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

P value = 1.06e-12 (Chi-square test), Q value = 7.4e-10

Table S116.  Gene #21: 'Amp Peak 21(8q24.21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 21(8Q24.21) MUTATED 11 89 16 14 20 41
AMP PEAK 21(8Q24.21) WILD-TYPE 45 53 58 9 19 104

Figure S116.  Get High-res Image Gene #21: 'Amp Peak 21(8q24.21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 22(9p24.2) mutation analysis' versus 'CN_CNMF'

P value = 2.87e-22 (Chi-square test), Q value = 2.5e-19

Table S117.  Gene #22: 'Amp Peak 22(9p24.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 22(9P24.2) MUTATED 5 3 49 0 0
AMP PEAK 22(9P24.2) WILD-TYPE 285 37 90 17 6

Figure S117.  Get High-res Image Gene #22: 'Amp Peak 22(9p24.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 22(9p24.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.87e-07 (Fisher's exact test), Q value = 0.00025

Table S118.  Gene #22: 'Amp Peak 22(9p24.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 22(9P24.2) MUTATED 33 7 5
AMP PEAK 22(9P24.2) WILD-TYPE 110 78 144

Figure S118.  Get High-res Image Gene #22: 'Amp Peak 22(9p24.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 22(9p24.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.97e-09 (Fisher's exact test), Q value = 1.7e-06

Table S119.  Gene #22: 'Amp Peak 22(9p24.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 22(9P24.2) MUTATED 32 2 3
AMP PEAK 22(9P24.2) WILD-TYPE 110 105 110

Figure S119.  Get High-res Image Gene #22: 'Amp Peak 22(9p24.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 22(9p24.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.17e-10 (Fisher's exact test), Q value = 7.4e-08

Table S120.  Gene #22: 'Amp Peak 22(9p24.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 22(9P24.2) MUTATED 0 0 5 32
AMP PEAK 22(9P24.2) WILD-TYPE 65 92 60 108

Figure S120.  Get High-res Image Gene #22: 'Amp Peak 22(9p24.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 22(9p24.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.66e-10 (Fisher's exact test), Q value = 1.6e-07

Table S121.  Gene #22: 'Amp Peak 22(9p24.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 22(9P24.2) MUTATED 44 2 10
AMP PEAK 22(9P24.2) WILD-TYPE 150 144 129

Figure S121.  Get High-res Image Gene #22: 'Amp Peak 22(9p24.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 22(9p24.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.4e-07 (Chi-square test), Q value = 7.4e-05

Table S122.  Gene #22: 'Amp Peak 22(9p24.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 22(9P24.2) MUTATED 4 34 3 3 8 4
AMP PEAK 22(9P24.2) WILD-TYPE 52 108 71 20 31 141

Figure S122.  Get High-res Image Gene #22: 'Amp Peak 22(9p24.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 23(9q34.3) mutation analysis' versus 'CN_CNMF'

P value = 3.79e-12 (Chi-square test), Q value = 2.6e-09

Table S123.  Gene #23: 'Amp Peak 23(9q34.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 23(9Q34.3) MUTATED 3 1 28 0 0
AMP PEAK 23(9Q34.3) WILD-TYPE 287 39 111 17 6

Figure S123.  Get High-res Image Gene #23: 'Amp Peak 23(9q34.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 23(9q34.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.56e-05 (Fisher's exact test), Q value = 0.041

Table S124.  Gene #23: 'Amp Peak 23(9q34.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 23(9Q34.3) MUTATED 17 5 1
AMP PEAK 23(9Q34.3) WILD-TYPE 126 80 148

Figure S124.  Get High-res Image Gene #23: 'Amp Peak 23(9q34.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 23(9q34.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.14e-05 (Fisher's exact test), Q value = 0.0098

Table S125.  Gene #23: 'Amp Peak 23(9q34.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 23(9Q34.3) MUTATED 20 1 3
AMP PEAK 23(9Q34.3) WILD-TYPE 122 106 110

Figure S125.  Get High-res Image Gene #23: 'Amp Peak 23(9q34.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 23(9q34.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.98e-06 (Fisher's exact test), Q value = 0.0019

Table S126.  Gene #23: 'Amp Peak 23(9q34.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 23(9Q34.3) MUTATED 2 0 1 21
AMP PEAK 23(9Q34.3) WILD-TYPE 63 92 64 119

Figure S126.  Get High-res Image Gene #23: 'Amp Peak 23(9q34.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 23(9q34.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.02e-05 (Fisher's exact test), Q value = 0.0093

Table S127.  Gene #23: 'Amp Peak 23(9q34.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 23(9Q34.3) MUTATED 22 1 4
AMP PEAK 23(9Q34.3) WILD-TYPE 172 145 135

Figure S127.  Get High-res Image Gene #23: 'Amp Peak 23(9q34.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 23(9q34.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.3e-05 (Chi-square test), Q value = 0.0061

Table S128.  Gene #23: 'Amp Peak 23(9q34.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 23(9Q34.3) MUTATED 0 20 1 1 3 2
AMP PEAK 23(9Q34.3) WILD-TYPE 56 122 73 22 36 143

Figure S128.  Get High-res Image Gene #23: 'Amp Peak 23(9q34.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 24(10q22.2) mutation analysis' versus 'CN_CNMF'

P value = 1.77e-08 (Chi-square test), Q value = 9.9e-06

Table S129.  Gene #24: 'Amp Peak 24(10q22.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 24(10Q22.2) MUTATED 48 18 53 10 3
AMP PEAK 24(10Q22.2) WILD-TYPE 242 22 86 7 3

Figure S129.  Get High-res Image Gene #24: 'Amp Peak 24(10q22.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 25(11p11.2) mutation analysis' versus 'CN_CNMF'

P value = 1.32e-16 (Chi-square test), Q value = 1e-13

Table S130.  Gene #25: 'Amp Peak 25(11p11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 25(11P11.2) MUTATED 1 6 37 1 0
AMP PEAK 25(11P11.2) WILD-TYPE 289 34 102 16 6

Figure S130.  Get High-res Image Gene #25: 'Amp Peak 25(11p11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 25(11p11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.97e-05 (Fisher's exact test), Q value = 0.026

Table S131.  Gene #25: 'Amp Peak 25(11p11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 25(11P11.2) MUTATED 21 12 3
AMP PEAK 25(11P11.2) WILD-TYPE 122 73 146

Figure S131.  Get High-res Image Gene #25: 'Amp Peak 25(11p11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 25(11p11.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.37e-05 (Fisher's exact test), Q value = 0.011

Table S132.  Gene #25: 'Amp Peak 25(11p11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 25(11P11.2) MUTATED 23 4 2
AMP PEAK 25(11P11.2) WILD-TYPE 119 103 111

Figure S132.  Get High-res Image Gene #25: 'Amp Peak 25(11p11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 25(11p11.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.28e-05 (Fisher's exact test), Q value = 0.04

Table S133.  Gene #25: 'Amp Peak 25(11p11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 25(11P11.2) MUTATED 1 3 2 23
AMP PEAK 25(11P11.2) WILD-TYPE 64 89 63 117

Figure S133.  Get High-res Image Gene #25: 'Amp Peak 25(11p11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 25(11p11.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 9.86e-06 (Fisher's exact test), Q value = 0.0047

Table S134.  Gene #25: 'Amp Peak 25(11p11.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 25(11P11.2) MUTATED 33 6 5
AMP PEAK 25(11P11.2) WILD-TYPE 161 140 134

Figure S134.  Get High-res Image Gene #25: 'Amp Peak 25(11p11.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 25(11p11.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.22e-06 (Chi-square test), Q value = 0.00061

Table S135.  Gene #25: 'Amp Peak 25(11p11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 25(11P11.2) MUTATED 3 30 2 1 3 5
AMP PEAK 25(11P11.2) WILD-TYPE 53 112 72 22 36 140

Figure S135.  Get High-res Image Gene #25: 'Amp Peak 25(11p11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 26(11q13.2) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000235 (Fisher's exact test), Q value = 0.097

Table S136.  Gene #26: 'Amp Peak 26(11q13.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
AMP PEAK 26(11Q13.2) MUTATED 0 8 0 0
AMP PEAK 26(11Q13.2) WILD-TYPE 13 10 14 8

Figure S136.  Get High-res Image Gene #26: 'Amp Peak 26(11q13.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 26(11q13.2) mutation analysis' versus 'CN_CNMF'

P value = 5.92e-22 (Chi-square test), Q value = 5.2e-19

Table S137.  Gene #26: 'Amp Peak 26(11q13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 26(11Q13.2) MUTATED 6 8 53 1 0
AMP PEAK 26(11Q13.2) WILD-TYPE 284 32 86 16 6

Figure S137.  Get High-res Image Gene #26: 'Amp Peak 26(11q13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 26(11q13.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000204 (Fisher's exact test), Q value = 0.084

Table S138.  Gene #26: 'Amp Peak 26(11q13.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 26(11Q13.2) MUTATED 32 13 9
AMP PEAK 26(11Q13.2) WILD-TYPE 111 72 140

Figure S138.  Get High-res Image Gene #26: 'Amp Peak 26(11q13.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 26(11q13.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 9.44e-06 (Fisher's exact test), Q value = 0.0045

Table S139.  Gene #26: 'Amp Peak 26(11q13.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 26(11Q13.2) MUTATED 32 7 5
AMP PEAK 26(11Q13.2) WILD-TYPE 110 100 108

Figure S139.  Get High-res Image Gene #26: 'Amp Peak 26(11q13.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 26(11q13.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.58e-08 (Fisher's exact test), Q value = 3e-05

Table S140.  Gene #26: 'Amp Peak 26(11q13.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 26(11Q13.2) MUTATED 1 6 2 35
AMP PEAK 26(11Q13.2) WILD-TYPE 64 86 63 105

Figure S140.  Get High-res Image Gene #26: 'Amp Peak 26(11q13.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 26(11q13.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.53e-05 (Fisher's exact test), Q value = 0.0071

Table S141.  Gene #26: 'Amp Peak 26(11q13.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 26(11Q13.2) MUTATED 43 13 8
AMP PEAK 26(11Q13.2) WILD-TYPE 151 133 131

Figure S141.  Get High-res Image Gene #26: 'Amp Peak 26(11q13.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 26(11q13.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.81e-05 (Chi-square test), Q value = 0.03

Table S142.  Gene #26: 'Amp Peak 26(11q13.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 26(11Q13.2) MUTATED 5 36 3 2 4 14
AMP PEAK 26(11Q13.2) WILD-TYPE 51 106 71 21 35 131

Figure S142.  Get High-res Image Gene #26: 'Amp Peak 26(11q13.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 27(12p12.1) mutation analysis' versus 'CN_CNMF'

P value = 5.1e-15 (Chi-square test), Q value = 3.9e-12

Table S143.  Gene #27: 'Amp Peak 27(12p12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 27(12P12.1) MUTATED 15 12 49 2 3
AMP PEAK 27(12P12.1) WILD-TYPE 275 28 90 15 3

Figure S143.  Get High-res Image Gene #27: 'Amp Peak 27(12p12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 27(12p12.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.13e-07 (Fisher's exact test), Q value = 6e-05

Table S144.  Gene #27: 'Amp Peak 27(12p12.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 27(12P12.1) MUTATED 44 13 9
AMP PEAK 27(12P12.1) WILD-TYPE 99 72 140

Figure S144.  Get High-res Image Gene #27: 'Amp Peak 27(12p12.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 27(12p12.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.17e-05 (Fisher's exact test), Q value = 0.019

Table S145.  Gene #27: 'Amp Peak 27(12p12.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 27(12P12.1) MUTATED 33 9 6
AMP PEAK 27(12P12.1) WILD-TYPE 109 98 107

Figure S145.  Get High-res Image Gene #27: 'Amp Peak 27(12p12.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 27(12p12.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.11e-05 (Fisher's exact test), Q value = 0.0096

Table S146.  Gene #27: 'Amp Peak 27(12p12.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 27(12P12.1) MUTATED 1 8 6 33
AMP PEAK 27(12P12.1) WILD-TYPE 64 84 59 107

Figure S146.  Get High-res Image Gene #27: 'Amp Peak 27(12p12.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 27(12p12.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 8.98e-08 (Fisher's exact test), Q value = 4.8e-05

Table S147.  Gene #27: 'Amp Peak 27(12p12.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 27(12P12.1) MUTATED 56 12 13
AMP PEAK 27(12P12.1) WILD-TYPE 138 134 126

Figure S147.  Get High-res Image Gene #27: 'Amp Peak 27(12p12.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 27(12p12.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.64e-08 (Chi-square test), Q value = 4.6e-05

Table S148.  Gene #27: 'Amp Peak 27(12p12.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 27(12P12.1) MUTATED 4 44 7 1 12 13
AMP PEAK 27(12P12.1) WILD-TYPE 52 98 67 22 27 132

Figure S148.  Get High-res Image Gene #27: 'Amp Peak 27(12p12.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 28(12q13.11) mutation analysis' versus 'CN_CNMF'

P value = 6.74e-17 (Chi-square test), Q value = 5.3e-14

Table S149.  Gene #28: 'Amp Peak 28(12q13.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 28(12Q13.11) MUTATED 12 13 49 2 3
AMP PEAK 28(12Q13.11) WILD-TYPE 278 27 90 15 3

Figure S149.  Get High-res Image Gene #28: 'Amp Peak 28(12q13.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 28(12q13.11) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.67e-08 (Fisher's exact test), Q value = 2e-05

Table S150.  Gene #28: 'Amp Peak 28(12q13.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 28(12Q13.11) MUTATED 42 15 7
AMP PEAK 28(12Q13.11) WILD-TYPE 101 70 142

Figure S150.  Get High-res Image Gene #28: 'Amp Peak 28(12q13.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 28(12q13.11) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.19e-06 (Fisher's exact test), Q value = 0.0011

Table S151.  Gene #28: 'Amp Peak 28(12q13.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 28(12Q13.11) MUTATED 34 7 5
AMP PEAK 28(12Q13.11) WILD-TYPE 108 100 108

Figure S151.  Get High-res Image Gene #28: 'Amp Peak 28(12q13.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 28(12q13.11) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.95e-06 (Fisher's exact test), Q value = 0.00096

Table S152.  Gene #28: 'Amp Peak 28(12q13.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 28(12Q13.11) MUTATED 1 6 5 34
AMP PEAK 28(12Q13.11) WILD-TYPE 64 86 60 106

Figure S152.  Get High-res Image Gene #28: 'Amp Peak 28(12q13.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 28(12q13.11) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.31e-09 (Fisher's exact test), Q value = 2.5e-06

Table S153.  Gene #28: 'Amp Peak 28(12q13.11) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 28(12Q13.11) MUTATED 57 11 11
AMP PEAK 28(12Q13.11) WILD-TYPE 137 135 128

Figure S153.  Get High-res Image Gene #28: 'Amp Peak 28(12q13.11) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 28(12q13.11) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.12e-08 (Chi-square test), Q value = 6.4e-06

Table S154.  Gene #28: 'Amp Peak 28(12q13.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 28(12Q13.11) MUTATED 3 46 5 2 10 13
AMP PEAK 28(12Q13.11) WILD-TYPE 53 96 69 21 29 132

Figure S154.  Get High-res Image Gene #28: 'Amp Peak 28(12q13.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 29(12q13.2) mutation analysis' versus 'CN_CNMF'

P value = 1.75e-17 (Chi-square test), Q value = 1.4e-14

Table S155.  Gene #29: 'Amp Peak 29(12q13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 29(12Q13.2) MUTATED 15 13 54 2 3
AMP PEAK 29(12Q13.2) WILD-TYPE 275 27 85 15 3

Figure S155.  Get High-res Image Gene #29: 'Amp Peak 29(12q13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 29(12q13.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.94e-07 (Fisher's exact test), Q value = 1e-04

Table S156.  Gene #29: 'Amp Peak 29(12q13.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 29(12Q13.2) MUTATED 46 13 11
AMP PEAK 29(12Q13.2) WILD-TYPE 97 72 138

Figure S156.  Get High-res Image Gene #29: 'Amp Peak 29(12q13.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 29(12q13.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.66e-08 (Fisher's exact test), Q value = 9.3e-06

Table S157.  Gene #29: 'Amp Peak 29(12q13.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 29(12Q13.2) MUTATED 40 7 5
AMP PEAK 29(12Q13.2) WILD-TYPE 102 100 108

Figure S157.  Get High-res Image Gene #29: 'Amp Peak 29(12q13.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 29(12q13.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.54e-08 (Fisher's exact test), Q value = 3.5e-05

Table S158.  Gene #29: 'Amp Peak 29(12q13.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 29(12Q13.2) MUTATED 1 6 6 39
AMP PEAK 29(12Q13.2) WILD-TYPE 64 86 59 101

Figure S158.  Get High-res Image Gene #29: 'Amp Peak 29(12q13.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 29(12q13.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.96e-08 (Fisher's exact test), Q value = 1.1e-05

Table S159.  Gene #29: 'Amp Peak 29(12q13.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 29(12Q13.2) MUTATED 59 15 11
AMP PEAK 29(12Q13.2) WILD-TYPE 135 131 128

Figure S159.  Get High-res Image Gene #29: 'Amp Peak 29(12q13.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 29(12q13.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.63e-09 (Chi-square test), Q value = 2.7e-06

Table S160.  Gene #29: 'Amp Peak 29(12q13.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 29(12Q13.2) MUTATED 3 49 5 1 10 17
AMP PEAK 29(12Q13.2) WILD-TYPE 53 93 69 22 29 128

Figure S160.  Get High-res Image Gene #29: 'Amp Peak 29(12q13.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 30(13q34) mutation analysis' versus 'CN_CNMF'

P value = 4.18e-20 (Chi-square test), Q value = 3.6e-17

Table S161.  Gene #30: 'Amp Peak 30(13q34) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 30(13Q34) MUTATED 4 0 43 1 1
AMP PEAK 30(13Q34) WILD-TYPE 286 40 96 16 5

Figure S161.  Get High-res Image Gene #30: 'Amp Peak 30(13q34) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 30(13q34) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.98e-06 (Fisher's exact test), Q value = 0.00097

Table S162.  Gene #30: 'Amp Peak 30(13q34) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 30(13Q34) MUTATED 30 10 4
AMP PEAK 30(13Q34) WILD-TYPE 113 75 145

Figure S162.  Get High-res Image Gene #30: 'Amp Peak 30(13q34) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 30(13q34) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 8.41e-12 (Fisher's exact test), Q value = 5.7e-09

Table S163.  Gene #30: 'Amp Peak 30(13q34) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 30(13Q34) MUTATED 31 2 0
AMP PEAK 30(13Q34) WILD-TYPE 111 105 113

Figure S163.  Get High-res Image Gene #30: 'Amp Peak 30(13q34) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 30(13q34) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.37e-07 (Fisher's exact test), Q value = 7.2e-05

Table S164.  Gene #30: 'Amp Peak 30(13q34) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 30(13Q34) MUTATED 0 2 3 28
AMP PEAK 30(13Q34) WILD-TYPE 65 90 62 112

Figure S164.  Get High-res Image Gene #30: 'Amp Peak 30(13q34) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 30(13q34) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.89e-09 (Fisher's exact test), Q value = 2.8e-06

Table S165.  Gene #30: 'Amp Peak 30(13q34) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 30(13Q34) MUTATED 40 4 5
AMP PEAK 30(13Q34) WILD-TYPE 154 142 134

Figure S165.  Get High-res Image Gene #30: 'Amp Peak 30(13q34) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 30(13q34) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.21e-09 (Chi-square test), Q value = 7.3e-07

Table S166.  Gene #30: 'Amp Peak 30(13q34) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 30(13Q34) MUTATED 2 35 0 1 5 6
AMP PEAK 30(13Q34) WILD-TYPE 54 107 74 22 34 139

Figure S166.  Get High-res Image Gene #30: 'Amp Peak 30(13q34) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 31(14q24.3) mutation analysis' versus 'CN_CNMF'

P value = 6.04e-18 (Chi-square test), Q value = 4.9e-15

Table S167.  Gene #31: 'Amp Peak 31(14q24.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 31(14Q24.3) MUTATED 4 5 44 3 0
AMP PEAK 31(14Q24.3) WILD-TYPE 286 35 95 14 6

Figure S167.  Get High-res Image Gene #31: 'Amp Peak 31(14q24.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 31(14q24.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.7e-05 (Fisher's exact test), Q value = 0.0078

Table S168.  Gene #31: 'Amp Peak 31(14q24.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 31(14Q24.3) MUTATED 31 9 6
AMP PEAK 31(14Q24.3) WILD-TYPE 112 76 143

Figure S168.  Get High-res Image Gene #31: 'Amp Peak 31(14q24.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 31(14q24.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.85e-08 (Fisher's exact test), Q value = 2.6e-05

Table S169.  Gene #31: 'Amp Peak 31(14q24.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 31(14Q24.3) MUTATED 29 5 1
AMP PEAK 31(14Q24.3) WILD-TYPE 113 102 112

Figure S169.  Get High-res Image Gene #31: 'Amp Peak 31(14q24.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 31(14q24.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.14e-10 (Fisher's exact test), Q value = 7.3e-08

Table S170.  Gene #31: 'Amp Peak 31(14q24.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 31(14Q24.3) MUTATED 0 3 0 32
AMP PEAK 31(14Q24.3) WILD-TYPE 65 89 65 108

Figure S170.  Get High-res Image Gene #31: 'Amp Peak 31(14q24.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 31(14q24.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 8.36e-09 (Fisher's exact test), Q value = 4.8e-06

Table S171.  Gene #31: 'Amp Peak 31(14q24.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 31(14Q24.3) MUTATED 42 7 4
AMP PEAK 31(14Q24.3) WILD-TYPE 152 139 135

Figure S171.  Get High-res Image Gene #31: 'Amp Peak 31(14q24.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 31(14q24.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.16e-09 (Chi-square test), Q value = 4.7e-06

Table S172.  Gene #31: 'Amp Peak 31(14q24.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 31(14Q24.3) MUTATED 3 36 0 1 5 8
AMP PEAK 31(14Q24.3) WILD-TYPE 53 106 74 22 34 137

Figure S172.  Get High-res Image Gene #31: 'Amp Peak 31(14q24.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 32(14q32.33) mutation analysis' versus 'CN_CNMF'

P value = 4.26e-22 (Chi-square test), Q value = 3.7e-19

Table S173.  Gene #32: 'Amp Peak 32(14q32.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 32(14Q32.33) MUTATED 6 6 54 4 0
AMP PEAK 32(14Q32.33) WILD-TYPE 284 34 85 13 6

Figure S173.  Get High-res Image Gene #32: 'Amp Peak 32(14q32.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 32(14q32.33) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.04e-06 (Fisher's exact test), Q value = 0.00052

Table S174.  Gene #32: 'Amp Peak 32(14q32.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 32(14Q32.33) MUTATED 37 14 7
AMP PEAK 32(14Q32.33) WILD-TYPE 106 71 142

Figure S174.  Get High-res Image Gene #32: 'Amp Peak 32(14q32.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 32(14q32.33) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.54e-05 (Fisher's exact test), Q value = 0.016

Table S175.  Gene #32: 'Amp Peak 32(14q32.33) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 32(14Q32.33) MUTATED 28 6 4
AMP PEAK 32(14Q32.33) WILD-TYPE 114 101 109

Figure S175.  Get High-res Image Gene #32: 'Amp Peak 32(14q32.33) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 32(14q32.33) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.77e-08 (Fisher's exact test), Q value = 2.6e-05

Table S176.  Gene #32: 'Amp Peak 32(14q32.33) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 32(14Q32.33) MUTATED 1 3 2 32
AMP PEAK 32(14Q32.33) WILD-TYPE 64 89 63 108

Figure S176.  Get High-res Image Gene #32: 'Amp Peak 32(14q32.33) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 32(14q32.33) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.41e-07 (Fisher's exact test), Q value = 0.00013

Table S177.  Gene #32: 'Amp Peak 32(14q32.33) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 32(14Q32.33) MUTATED 48 13 7
AMP PEAK 32(14Q32.33) WILD-TYPE 146 133 132

Figure S177.  Get High-res Image Gene #32: 'Amp Peak 32(14q32.33) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 32(14q32.33) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.59e-08 (Chi-square test), Q value = 8.9e-06

Table S178.  Gene #32: 'Amp Peak 32(14q32.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 32(14Q32.33) MUTATED 3 43 3 2 5 12
AMP PEAK 32(14Q32.33) WILD-TYPE 53 99 71 21 34 133

Figure S178.  Get High-res Image Gene #32: 'Amp Peak 32(14q32.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 33(16p11.2) mutation analysis' versus 'CN_CNMF'

P value = 5.49e-21 (Chi-square test), Q value = 4.7e-18

Table S179.  Gene #33: 'Amp Peak 33(16p11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 33(16P11.2) MUTATED 2 6 46 1 0
AMP PEAK 33(16P11.2) WILD-TYPE 288 34 93 16 6

Figure S179.  Get High-res Image Gene #33: 'Amp Peak 33(16p11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 33(16p11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.26e-05 (Fisher's exact test), Q value = 0.015

Table S180.  Gene #33: 'Amp Peak 33(16p11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 33(16P11.2) MUTATED 30 10 6
AMP PEAK 33(16P11.2) WILD-TYPE 113 75 143

Figure S180.  Get High-res Image Gene #33: 'Amp Peak 33(16p11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 33(16p11.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.31e-09 (Fisher's exact test), Q value = 7.8e-07

Table S181.  Gene #33: 'Amp Peak 33(16p11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 33(16P11.2) MUTATED 32 1 4
AMP PEAK 33(16P11.2) WILD-TYPE 110 106 109

Figure S181.  Get High-res Image Gene #33: 'Amp Peak 33(16p11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 33(16p11.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.78e-09 (Fisher's exact test), Q value = 1.1e-06

Table S182.  Gene #33: 'Amp Peak 33(16p11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 33(16P11.2) MUTATED 3 0 2 32
AMP PEAK 33(16P11.2) WILD-TYPE 62 92 63 108

Figure S182.  Get High-res Image Gene #33: 'Amp Peak 33(16p11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 33(16p11.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.33e-09 (Fisher's exact test), Q value = 7.9e-07

Table S183.  Gene #33: 'Amp Peak 33(16p11.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 33(16P11.2) MUTATED 42 3 7
AMP PEAK 33(16P11.2) WILD-TYPE 152 143 132

Figure S183.  Get High-res Image Gene #33: 'Amp Peak 33(16p11.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 33(16p11.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.91e-07 (Chi-square test), Q value = 4e-04

Table S184.  Gene #33: 'Amp Peak 33(16p11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 33(16P11.2) MUTATED 4 34 4 2 2 6
AMP PEAK 33(16P11.2) WILD-TYPE 52 108 70 21 37 139

Figure S184.  Get High-res Image Gene #33: 'Amp Peak 33(16p11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 34(17q11.2) mutation analysis' versus 'CN_CNMF'

P value = 1.72e-26 (Chi-square test), Q value = 1.6e-23

Table S185.  Gene #34: 'Amp Peak 34(17q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 34(17Q11.2) MUTATED 4 1 55 2 1
AMP PEAK 34(17Q11.2) WILD-TYPE 286 39 84 15 5

Figure S185.  Get High-res Image Gene #34: 'Amp Peak 34(17q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 34(17q11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.13e-11 (Fisher's exact test), Q value = 1.4e-08

Table S186.  Gene #34: 'Amp Peak 34(17q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 34(17Q11.2) MUTATED 42 9 3
AMP PEAK 34(17Q11.2) WILD-TYPE 101 76 146

Figure S186.  Get High-res Image Gene #34: 'Amp Peak 34(17q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 34(17q11.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.25e-10 (Fisher's exact test), Q value = 7.9e-08

Table S187.  Gene #34: 'Amp Peak 34(17q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 34(17Q11.2) MUTATED 31 2 1
AMP PEAK 34(17Q11.2) WILD-TYPE 111 105 112

Figure S187.  Get High-res Image Gene #34: 'Amp Peak 34(17q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 34(17q11.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.81e-10 (Fisher's exact test), Q value = 2.9e-07

Table S188.  Gene #34: 'Amp Peak 34(17q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 34(17Q11.2) MUTATED 0 0 4 30
AMP PEAK 34(17Q11.2) WILD-TYPE 65 92 61 110

Figure S188.  Get High-res Image Gene #34: 'Amp Peak 34(17q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 34(17q11.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 8.65e-15 (Fisher's exact test), Q value = 6.5e-12

Table S189.  Gene #34: 'Amp Peak 34(17q11.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 34(17Q11.2) MUTATED 52 2 6
AMP PEAK 34(17Q11.2) WILD-TYPE 142 144 133

Figure S189.  Get High-res Image Gene #34: 'Amp Peak 34(17q11.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 34(17q11.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.05e-15 (Chi-square test), Q value = 5.3e-12

Table S190.  Gene #34: 'Amp Peak 34(17q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 34(17Q11.2) MUTATED 3 45 1 1 7 3
AMP PEAK 34(17Q11.2) WILD-TYPE 53 97 73 22 32 142

Figure S190.  Get High-res Image Gene #34: 'Amp Peak 34(17q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 35(17q12) mutation analysis' versus 'CN_CNMF'

P value = 5.56e-23 (Chi-square test), Q value = 4.9e-20

Table S191.  Gene #35: 'Amp Peak 35(17q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 35(17Q12) MUTATED 6 2 53 2 1
AMP PEAK 35(17Q12) WILD-TYPE 284 38 86 15 5

Figure S191.  Get High-res Image Gene #35: 'Amp Peak 35(17q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 35(17q12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.42e-12 (Fisher's exact test), Q value = 9.9e-10

Table S192.  Gene #35: 'Amp Peak 35(17q12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 35(17Q12) MUTATED 42 8 2
AMP PEAK 35(17Q12) WILD-TYPE 101 77 147

Figure S192.  Get High-res Image Gene #35: 'Amp Peak 35(17q12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 35(17q12) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.77e-13 (Fisher's exact test), Q value = 2.7e-10

Table S193.  Gene #35: 'Amp Peak 35(17q12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 35(17Q12) MUTATED 37 2 1
AMP PEAK 35(17Q12) WILD-TYPE 105 105 112

Figure S193.  Get High-res Image Gene #35: 'Amp Peak 35(17q12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 35(17q12) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.74e-10 (Fisher's exact test), Q value = 1.7e-07

Table S194.  Gene #35: 'Amp Peak 35(17q12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 35(17Q12) MUTATED 0 1 5 34
AMP PEAK 35(17Q12) WILD-TYPE 65 91 60 106

Figure S194.  Get High-res Image Gene #35: 'Amp Peak 35(17q12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 35(17q12) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 7.79e-14 (Fisher's exact test), Q value = 5.7e-11

Table S195.  Gene #35: 'Amp Peak 35(17q12) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 35(17Q12) MUTATED 52 2 8
AMP PEAK 35(17Q12) WILD-TYPE 142 144 131

Figure S195.  Get High-res Image Gene #35: 'Amp Peak 35(17q12) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 35(17q12) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.16e-16 (Chi-square test), Q value = 2.5e-13

Table S196.  Gene #35: 'Amp Peak 35(17q12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 35(17Q12) MUTATED 4 48 2 0 5 3
AMP PEAK 35(17Q12) WILD-TYPE 52 94 72 23 34 142

Figure S196.  Get High-res Image Gene #35: 'Amp Peak 35(17q12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 36(17q25.1) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000566 (Fisher's exact test), Q value = 0.22

Table S197.  Gene #36: 'Amp Peak 36(17q25.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
AMP PEAK 36(17Q25.1) MUTATED 0 9 1 0
AMP PEAK 36(17Q25.1) WILD-TYPE 13 9 13 8

Figure S197.  Get High-res Image Gene #36: 'Amp Peak 36(17q25.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 36(17q25.1) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000109 (Fisher's exact test), Q value = 0.046

Table S198.  Gene #36: 'Amp Peak 36(17q25.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
AMP PEAK 36(17Q25.1) MUTATED 1 0 9
AMP PEAK 36(17Q25.1) WILD-TYPE 19 15 9

Figure S198.  Get High-res Image Gene #36: 'Amp Peak 36(17q25.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 36(17q25.1) mutation analysis' versus 'CN_CNMF'

P value = 4.44e-41 (Chi-square test), Q value = 4.2e-38

Table S199.  Gene #36: 'Amp Peak 36(17q25.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 36(17Q25.1) MUTATED 5 4 79 1 1
AMP PEAK 36(17Q25.1) WILD-TYPE 285 36 60 16 5

Figure S199.  Get High-res Image Gene #36: 'Amp Peak 36(17q25.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 36(17q25.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.36e-11 (Fisher's exact test), Q value = 9.1e-09

Table S200.  Gene #36: 'Amp Peak 36(17q25.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 36(17Q25.1) MUTATED 48 16 5
AMP PEAK 36(17Q25.1) WILD-TYPE 95 69 144

Figure S200.  Get High-res Image Gene #36: 'Amp Peak 36(17q25.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 36(17q25.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.59e-12 (Fisher's exact test), Q value = 1.8e-09

Table S201.  Gene #36: 'Amp Peak 36(17q25.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 36(17Q25.1) MUTATED 44 3 5
AMP PEAK 36(17Q25.1) WILD-TYPE 98 104 108

Figure S201.  Get High-res Image Gene #36: 'Amp Peak 36(17q25.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 36(17q25.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.88e-13 (Fisher's exact test), Q value = 2.8e-10

Table S202.  Gene #36: 'Amp Peak 36(17q25.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 36(17Q25.1) MUTATED 1 1 6 44
AMP PEAK 36(17Q25.1) WILD-TYPE 64 91 59 96

Figure S202.  Get High-res Image Gene #36: 'Amp Peak 36(17q25.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 36(17q25.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.74e-13 (Fisher's exact test), Q value = 2.7e-10

Table S203.  Gene #36: 'Amp Peak 36(17q25.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 36(17Q25.1) MUTATED 66 9 11
AMP PEAK 36(17Q25.1) WILD-TYPE 128 137 128

Figure S203.  Get High-res Image Gene #36: 'Amp Peak 36(17q25.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 36(17q25.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.28e-14 (Chi-square test), Q value = 1.7e-11

Table S204.  Gene #36: 'Amp Peak 36(17q25.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 36(17Q25.1) MUTATED 6 57 4 3 8 8
AMP PEAK 36(17Q25.1) WILD-TYPE 50 85 70 20 31 137

Figure S204.  Get High-res Image Gene #36: 'Amp Peak 36(17q25.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 37(18p11.31) mutation analysis' versus 'CN_CNMF'

P value = 2.43e-33 (Chi-square test), Q value = 2.2e-30

Table S205.  Gene #37: 'Amp Peak 37(18p11.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 37(18P11.31) MUTATED 5 5 69 2 0
AMP PEAK 37(18P11.31) WILD-TYPE 285 35 70 15 6

Figure S205.  Get High-res Image Gene #37: 'Amp Peak 37(18p11.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 37(18p11.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.53e-12 (Fisher's exact test), Q value = 3.8e-09

Table S206.  Gene #37: 'Amp Peak 37(18p11.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 37(18P11.31) MUTATED 49 15 5
AMP PEAK 37(18P11.31) WILD-TYPE 94 70 144

Figure S206.  Get High-res Image Gene #37: 'Amp Peak 37(18p11.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 37(18p11.31) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.45e-11 (Fisher's exact test), Q value = 9.7e-09

Table S207.  Gene #37: 'Amp Peak 37(18p11.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 37(18P11.31) MUTATED 41 4 3
AMP PEAK 37(18P11.31) WILD-TYPE 101 103 110

Figure S207.  Get High-res Image Gene #37: 'Amp Peak 37(18p11.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 37(18p11.31) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.9e-13 (Fisher's exact test), Q value = 1.4e-10

Table S208.  Gene #37: 'Amp Peak 37(18p11.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 37(18P11.31) MUTATED 1 3 1 43
AMP PEAK 37(18P11.31) WILD-TYPE 64 89 64 97

Figure S208.  Get High-res Image Gene #37: 'Amp Peak 37(18p11.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 37(18p11.31) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 6.39e-18 (Fisher's exact test), Q value = 5.2e-15

Table S209.  Gene #37: 'Amp Peak 37(18p11.31) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 37(18P11.31) MUTATED 67 7 5
AMP PEAK 37(18P11.31) WILD-TYPE 127 139 134

Figure S209.  Get High-res Image Gene #37: 'Amp Peak 37(18p11.31) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 37(18p11.31) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.86e-19 (Chi-square test), Q value = 1.6e-16

Table S210.  Gene #37: 'Amp Peak 37(18p11.31) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 37(18P11.31) MUTATED 1 59 2 1 7 9
AMP PEAK 37(18P11.31) WILD-TYPE 55 83 72 22 32 136

Figure S210.  Get High-res Image Gene #37: 'Amp Peak 37(18p11.31) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 38(18q11.2) mutation analysis' versus 'CN_CNMF'

P value = 4.94e-27 (Chi-square test), Q value = 4.5e-24

Table S211.  Gene #38: 'Amp Peak 38(18q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 38(18Q11.2) MUTATED 3 3 55 1 0
AMP PEAK 38(18Q11.2) WILD-TYPE 287 37 84 16 6

Figure S211.  Get High-res Image Gene #38: 'Amp Peak 38(18q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 38(18q11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.19e-10 (Fisher's exact test), Q value = 2e-07

Table S212.  Gene #38: 'Amp Peak 38(18q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 38(18Q11.2) MUTATED 36 15 2
AMP PEAK 38(18Q11.2) WILD-TYPE 107 70 147

Figure S212.  Get High-res Image Gene #38: 'Amp Peak 38(18q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 38(18q11.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.17e-07 (Fisher's exact test), Q value = 6.2e-05

Table S213.  Gene #38: 'Amp Peak 38(18q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 38(18Q11.2) MUTATED 28 2 3
AMP PEAK 38(18Q11.2) WILD-TYPE 114 105 110

Figure S213.  Get High-res Image Gene #38: 'Amp Peak 38(18q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 38(18q11.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.53e-08 (Fisher's exact test), Q value = 2.5e-05

Table S214.  Gene #38: 'Amp Peak 38(18q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 38(18Q11.2) MUTATED 1 2 1 29
AMP PEAK 38(18Q11.2) WILD-TYPE 64 90 64 111

Figure S214.  Get High-res Image Gene #38: 'Amp Peak 38(18q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 38(18q11.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.73e-13 (Fisher's exact test), Q value = 1.2e-10

Table S215.  Gene #38: 'Amp Peak 38(18q11.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 38(18Q11.2) MUTATED 51 3 6
AMP PEAK 38(18Q11.2) WILD-TYPE 143 143 133

Figure S215.  Get High-res Image Gene #38: 'Amp Peak 38(18q11.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 38(18q11.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.49e-12 (Chi-square test), Q value = 5.7e-09

Table S216.  Gene #38: 'Amp Peak 38(18q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 38(18Q11.2) MUTATED 4 42 2 1 7 4
AMP PEAK 38(18Q11.2) WILD-TYPE 52 100 72 22 32 141

Figure S216.  Get High-res Image Gene #38: 'Amp Peak 38(18q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 39(19p13.2) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.044

Table S217.  Gene #39: 'Amp Peak 39(19p13.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
AMP PEAK 39(19P13.2) MUTATED 0 9 0 0
AMP PEAK 39(19P13.2) WILD-TYPE 13 9 14 8

Figure S217.  Get High-res Image Gene #39: 'Amp Peak 39(19p13.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 39(19p13.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.21e-05 (Fisher's exact test), Q value = 0.0057

Table S218.  Gene #39: 'Amp Peak 39(19p13.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
AMP PEAK 39(19P13.2) MUTATED 0 0 9
AMP PEAK 39(19P13.2) WILD-TYPE 20 15 9

Figure S218.  Get High-res Image Gene #39: 'Amp Peak 39(19p13.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 39(19p13.2) mutation analysis' versus 'CN_CNMF'

P value = 2.95e-46 (Chi-square test), Q value = 2.8e-43

Table S219.  Gene #39: 'Amp Peak 39(19p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 39(19P13.2) MUTATED 0 3 79 2 0
AMP PEAK 39(19P13.2) WILD-TYPE 290 37 60 15 6

Figure S219.  Get High-res Image Gene #39: 'Amp Peak 39(19p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 39(19p13.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.22e-09 (Fisher's exact test), Q value = 7.4e-07

Table S220.  Gene #39: 'Amp Peak 39(19p13.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 39(19P13.2) MUTATED 46 19 7
AMP PEAK 39(19P13.2) WILD-TYPE 97 66 142

Figure S220.  Get High-res Image Gene #39: 'Amp Peak 39(19p13.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 39(19p13.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.09e-18 (Fisher's exact test), Q value = 9.1e-16

Table S221.  Gene #39: 'Amp Peak 39(19p13.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 39(19P13.2) MUTATED 49 1 2
AMP PEAK 39(19P13.2) WILD-TYPE 93 106 111

Figure S221.  Get High-res Image Gene #39: 'Amp Peak 39(19p13.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 39(19p13.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.76e-18 (Fisher's exact test), Q value = 1.5e-15

Table S222.  Gene #39: 'Amp Peak 39(19p13.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 39(19P13.2) MUTATED 1 0 2 49
AMP PEAK 39(19P13.2) WILD-TYPE 64 92 63 91

Figure S222.  Get High-res Image Gene #39: 'Amp Peak 39(19p13.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 39(19p13.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 8.33e-18 (Fisher's exact test), Q value = 6.8e-15

Table S223.  Gene #39: 'Amp Peak 39(19p13.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 39(19P13.2) MUTATED 68 8 5
AMP PEAK 39(19P13.2) WILD-TYPE 126 138 134

Figure S223.  Get High-res Image Gene #39: 'Amp Peak 39(19p13.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 39(19p13.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.96e-13 (Chi-square test), Q value = 5.6e-10

Table S224.  Gene #39: 'Amp Peak 39(19p13.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 39(19P13.2) MUTATED 3 53 3 3 8 11
AMP PEAK 39(19P13.2) WILD-TYPE 53 89 71 20 31 134

Figure S224.  Get High-res Image Gene #39: 'Amp Peak 39(19p13.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 40(19p13.11) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000235 (Fisher's exact test), Q value = 0.097

Table S225.  Gene #40: 'Amp Peak 40(19p13.11) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
AMP PEAK 40(19P13.11) MUTATED 0 8 0 0
AMP PEAK 40(19P13.11) WILD-TYPE 13 10 14 8

Figure S225.  Get High-res Image Gene #40: 'Amp Peak 40(19p13.11) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 40(19p13.11) mutation analysis' versus 'CN_CNMF'

P value = 1.47e-45 (Chi-square test), Q value = 1.4e-42

Table S226.  Gene #40: 'Amp Peak 40(19p13.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 40(19P13.11) MUTATED 0 2 78 2 1
AMP PEAK 40(19P13.11) WILD-TYPE 290 38 61 15 5

Figure S226.  Get High-res Image Gene #40: 'Amp Peak 40(19p13.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 40(19p13.11) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.98e-12 (Fisher's exact test), Q value = 4.1e-09

Table S227.  Gene #40: 'Amp Peak 40(19p13.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 40(19P13.11) MUTATED 49 16 5
AMP PEAK 40(19P13.11) WILD-TYPE 94 69 144

Figure S227.  Get High-res Image Gene #40: 'Amp Peak 40(19p13.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 40(19p13.11) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5e-17 (Fisher's exact test), Q value = 4e-14

Table S228.  Gene #40: 'Amp Peak 40(19p13.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 40(19P13.11) MUTATED 47 1 3
AMP PEAK 40(19P13.11) WILD-TYPE 95 106 110

Figure S228.  Get High-res Image Gene #40: 'Amp Peak 40(19p13.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 40(19p13.11) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.37e-18 (Fisher's exact test), Q value = 4.4e-15

Table S229.  Gene #40: 'Amp Peak 40(19p13.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 40(19P13.11) MUTATED 1 0 2 48
AMP PEAK 40(19P13.11) WILD-TYPE 64 92 63 92

Figure S229.  Get High-res Image Gene #40: 'Amp Peak 40(19p13.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 40(19p13.11) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.3e-17 (Fisher's exact test), Q value = 1.1e-14

Table S230.  Gene #40: 'Amp Peak 40(19p13.11) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 40(19P13.11) MUTATED 68 7 6
AMP PEAK 40(19P13.11) WILD-TYPE 126 139 133

Figure S230.  Get High-res Image Gene #40: 'Amp Peak 40(19p13.11) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 40(19p13.11) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.03e-16 (Chi-square test), Q value = 3.9e-13

Table S231.  Gene #40: 'Amp Peak 40(19p13.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 40(19P13.11) MUTATED 2 56 3 2 9 9
AMP PEAK 40(19P13.11) WILD-TYPE 54 86 71 21 30 136

Figure S231.  Get High-res Image Gene #40: 'Amp Peak 40(19p13.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 41(19q12) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000566 (Fisher's exact test), Q value = 0.22

Table S232.  Gene #41: 'Amp Peak 41(19q12) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
AMP PEAK 41(19Q12) MUTATED 0 9 1 0
AMP PEAK 41(19Q12) WILD-TYPE 13 9 13 8

Figure S232.  Get High-res Image Gene #41: 'Amp Peak 41(19q12) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 41(19q12) mutation analysis' versus 'CN_CNMF'

P value = 9.02e-49 (Chi-square test), Q value = 8.5e-46

Table S233.  Gene #41: 'Amp Peak 41(19q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 41(19Q12) MUTATED 4 4 89 4 0
AMP PEAK 41(19Q12) WILD-TYPE 286 36 50 13 6

Figure S233.  Get High-res Image Gene #41: 'Amp Peak 41(19q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 41(19q12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.85e-17 (Fisher's exact test), Q value = 4.7e-14

Table S234.  Gene #41: 'Amp Peak 41(19q12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 41(19Q12) MUTATED 62 19 5
AMP PEAK 41(19Q12) WILD-TYPE 81 66 144

Figure S234.  Get High-res Image Gene #41: 'Amp Peak 41(19q12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 41(19q12) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.87e-21 (Fisher's exact test), Q value = 2.5e-18

Table S235.  Gene #41: 'Amp Peak 41(19q12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 41(19Q12) MUTATED 56 2 2
AMP PEAK 41(19Q12) WILD-TYPE 86 105 111

Figure S235.  Get High-res Image Gene #41: 'Amp Peak 41(19q12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 41(19q12) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.66e-20 (Fisher's exact test), Q value = 2.3e-17

Table S236.  Gene #41: 'Amp Peak 41(19q12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 41(19Q12) MUTATED 1 0 4 55
AMP PEAK 41(19Q12) WILD-TYPE 64 92 61 85

Figure S236.  Get High-res Image Gene #41: 'Amp Peak 41(19q12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 41(19q12) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 6.63e-25 (Fisher's exact test), Q value = 5.9e-22

Table S237.  Gene #41: 'Amp Peak 41(19q12) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 41(19Q12) MUTATED 84 7 6
AMP PEAK 41(19Q12) WILD-TYPE 110 139 133

Figure S237.  Get High-res Image Gene #41: 'Amp Peak 41(19q12) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 41(19q12) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.23e-22 (Chi-square test), Q value = 1.1e-19

Table S238.  Gene #41: 'Amp Peak 41(19q12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 41(19Q12) MUTATED 3 70 2 2 9 11
AMP PEAK 41(19Q12) WILD-TYPE 53 72 72 21 30 134

Figure S238.  Get High-res Image Gene #41: 'Amp Peak 41(19q12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 42(20p13) mutation analysis' versus 'CN_CNMF'

P value = 1.63e-33 (Chi-square test), Q value = 1.5e-30

Table S239.  Gene #42: 'Amp Peak 42(20p13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 42(20P13) MUTATED 8 18 74 2 2
AMP PEAK 42(20P13) WILD-TYPE 282 22 65 15 4

Figure S239.  Get High-res Image Gene #42: 'Amp Peak 42(20p13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 42(20p13) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.8e-09 (Fisher's exact test), Q value = 1.1e-06

Table S240.  Gene #42: 'Amp Peak 42(20p13) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 42(20P13) MUTATED 59 17 15
AMP PEAK 42(20P13) WILD-TYPE 84 68 134

Figure S240.  Get High-res Image Gene #42: 'Amp Peak 42(20p13) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 42(20p13) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.74e-11 (Fisher's exact test), Q value = 2.4e-08

Table S241.  Gene #42: 'Amp Peak 42(20p13) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 42(20P13) MUTATED 52 7 9
AMP PEAK 42(20P13) WILD-TYPE 90 100 104

Figure S241.  Get High-res Image Gene #42: 'Amp Peak 42(20p13) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 42(20p13) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.9e-11 (Fisher's exact test), Q value = 4.5e-08

Table S242.  Gene #42: 'Amp Peak 42(20p13) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 42(20P13) MUTATED 6 5 5 52
AMP PEAK 42(20P13) WILD-TYPE 59 87 60 88

Figure S242.  Get High-res Image Gene #42: 'Amp Peak 42(20p13) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 42(20p13) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.84e-11 (Fisher's exact test), Q value = 1.2e-08

Table S243.  Gene #42: 'Amp Peak 42(20p13) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 42(20P13) MUTATED 73 15 15
AMP PEAK 42(20P13) WILD-TYPE 121 131 124

Figure S243.  Get High-res Image Gene #42: 'Amp Peak 42(20p13) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 42(20p13) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.94e-12 (Chi-square test), Q value = 2.7e-09

Table S244.  Gene #42: 'Amp Peak 42(20p13) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 42(20P13) MUTATED 7 59 8 1 14 14
AMP PEAK 42(20P13) WILD-TYPE 49 83 66 22 25 131

Figure S244.  Get High-res Image Gene #42: 'Amp Peak 42(20p13) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 43(20q11.21) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000496 (Fisher's exact test), Q value = 0.19

Table S245.  Gene #43: 'Amp Peak 43(20q11.21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
AMP PEAK 43(20Q11.21) MUTATED 1 9 0 0
AMP PEAK 43(20Q11.21) WILD-TYPE 12 9 14 8

Figure S245.  Get High-res Image Gene #43: 'Amp Peak 43(20q11.21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 43(20q11.21) mutation analysis' versus 'CN_CNMF'

P value = 6.65e-49 (Chi-square test), Q value = 6.3e-46

Table S246.  Gene #43: 'Amp Peak 43(20q11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 43(20Q11.21) MUTATED 7 24 94 3 2
AMP PEAK 43(20Q11.21) WILD-TYPE 283 16 45 14 4

Figure S246.  Get High-res Image Gene #43: 'Amp Peak 43(20q11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 43(20q11.21) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.01e-12 (Fisher's exact test), Q value = 3.4e-09

Table S247.  Gene #43: 'Amp Peak 43(20q11.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 43(20Q11.21) MUTATED 72 20 19
AMP PEAK 43(20Q11.21) WILD-TYPE 71 65 130

Figure S247.  Get High-res Image Gene #43: 'Amp Peak 43(20q11.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 43(20q11.21) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.71e-16 (Fisher's exact test), Q value = 4.4e-13

Table S248.  Gene #43: 'Amp Peak 43(20q11.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 43(20Q11.21) MUTATED 62 8 7
AMP PEAK 43(20Q11.21) WILD-TYPE 80 99 106

Figure S248.  Get High-res Image Gene #43: 'Amp Peak 43(20q11.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 43(20q11.21) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.02e-14 (Fisher's exact test), Q value = 7.7e-12

Table S249.  Gene #43: 'Amp Peak 43(20q11.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 43(20Q11.21) MUTATED 5 5 6 61
AMP PEAK 43(20Q11.21) WILD-TYPE 60 87 59 79

Figure S249.  Get High-res Image Gene #43: 'Amp Peak 43(20q11.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 43(20q11.21) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.08e-17 (Fisher's exact test), Q value = 1.7e-14

Table S250.  Gene #43: 'Amp Peak 43(20q11.21) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 43(20Q11.21) MUTATED 93 19 15
AMP PEAK 43(20Q11.21) WILD-TYPE 101 127 124

Figure S250.  Get High-res Image Gene #43: 'Amp Peak 43(20q11.21) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 43(20q11.21) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.66e-20 (Chi-square test), Q value = 4.8e-17

Table S251.  Gene #43: 'Amp Peak 43(20q11.21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 43(20Q11.21) MUTATED 4 80 8 2 12 21
AMP PEAK 43(20Q11.21) WILD-TYPE 52 62 66 21 27 124

Figure S251.  Get High-res Image Gene #43: 'Amp Peak 43(20q11.21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 44(20q13.12) mutation analysis' versus 'CN_CNMF'

P value = 2.71e-49 (Chi-square test), Q value = 2.6e-46

Table S252.  Gene #44: 'Amp Peak 44(20q13.12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 44(20Q13.12) MUTATED 9 25 96 3 3
AMP PEAK 44(20Q13.12) WILD-TYPE 281 15 43 14 3

Figure S252.  Get High-res Image Gene #44: 'Amp Peak 44(20q13.12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 44(20q13.12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.81e-13 (Fisher's exact test), Q value = 1.3e-10

Table S253.  Gene #44: 'Amp Peak 44(20q13.12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 44(20Q13.12) MUTATED 79 20 22
AMP PEAK 44(20Q13.12) WILD-TYPE 64 65 127

Figure S253.  Get High-res Image Gene #44: 'Amp Peak 44(20q13.12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 44(20q13.12) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.32e-15 (Fisher's exact test), Q value = 2.5e-12

Table S254.  Gene #44: 'Amp Peak 44(20q13.12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 44(20Q13.12) MUTATED 64 9 9
AMP PEAK 44(20Q13.12) WILD-TYPE 78 98 104

Figure S254.  Get High-res Image Gene #44: 'Amp Peak 44(20q13.12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 44(20q13.12) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.03e-15 (Fisher's exact test), Q value = 3.8e-12

Table S255.  Gene #44: 'Amp Peak 44(20q13.12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 44(20Q13.12) MUTATED 5 6 7 64
AMP PEAK 44(20Q13.12) WILD-TYPE 60 86 58 76

Figure S255.  Get High-res Image Gene #44: 'Amp Peak 44(20q13.12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 44(20q13.12) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.06e-17 (Fisher's exact test), Q value = 1.7e-14

Table S256.  Gene #44: 'Amp Peak 44(20q13.12) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 44(20Q13.12) MUTATED 97 21 17
AMP PEAK 44(20Q13.12) WILD-TYPE 97 125 122

Figure S256.  Get High-res Image Gene #44: 'Amp Peak 44(20q13.12) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 44(20q13.12) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.82e-17 (Chi-square test), Q value = 6.9e-14

Table S257.  Gene #44: 'Amp Peak 44(20q13.12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 44(20Q13.12) MUTATED 6 78 9 3 16 23
AMP PEAK 44(20Q13.12) WILD-TYPE 50 64 65 20 23 122

Figure S257.  Get High-res Image Gene #44: 'Amp Peak 44(20q13.12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 45(20q13.33) mutation analysis' versus 'CN_CNMF'

P value = 1.54e-46 (Chi-square test), Q value = 1.4e-43

Table S258.  Gene #45: 'Amp Peak 45(20q13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 45(20Q13.33) MUTATED 10 27 91 3 3
AMP PEAK 45(20Q13.33) WILD-TYPE 280 13 48 14 3

Figure S258.  Get High-res Image Gene #45: 'Amp Peak 45(20q13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 45(20q13.33) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.43e-10 (Fisher's exact test), Q value = 9e-08

Table S259.  Gene #45: 'Amp Peak 45(20q13.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 45(20Q13.33) MUTATED 73 21 23
AMP PEAK 45(20Q13.33) WILD-TYPE 70 64 126

Figure S259.  Get High-res Image Gene #45: 'Amp Peak 45(20q13.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 45(20q13.33) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.7e-13 (Fisher's exact test), Q value = 4e-10

Table S260.  Gene #45: 'Amp Peak 45(20q13.33) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 45(20Q13.33) MUTATED 61 9 11
AMP PEAK 45(20Q13.33) WILD-TYPE 81 98 102

Figure S260.  Get High-res Image Gene #45: 'Amp Peak 45(20q13.33) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 45(20q13.33) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.5e-14 (Fisher's exact test), Q value = 6.2e-11

Table S261.  Gene #45: 'Amp Peak 45(20q13.33) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 45(20Q13.33) MUTATED 5 6 8 62
AMP PEAK 45(20Q13.33) WILD-TYPE 60 86 57 78

Figure S261.  Get High-res Image Gene #45: 'Amp Peak 45(20q13.33) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 45(20q13.33) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.8e-16 (Fisher's exact test), Q value = 2.2e-13

Table S262.  Gene #45: 'Amp Peak 45(20q13.33) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 45(20Q13.33) MUTATED 94 22 16
AMP PEAK 45(20Q13.33) WILD-TYPE 100 124 123

Figure S262.  Get High-res Image Gene #45: 'Amp Peak 45(20q13.33) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 45(20q13.33) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.45e-14 (Chi-square test), Q value = 1.8e-11

Table S263.  Gene #45: 'Amp Peak 45(20q13.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 45(20Q13.33) MUTATED 6 73 11 3 17 22
AMP PEAK 45(20Q13.33) WILD-TYPE 50 69 63 20 22 123

Figure S263.  Get High-res Image Gene #45: 'Amp Peak 45(20q13.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 46(22q12.2) mutation analysis' versus 'CN_CNMF'

P value = 2.31e-18 (Chi-square test), Q value = 1.9e-15

Table S264.  Gene #46: 'Amp Peak 46(22q12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 46(22Q12.2) MUTATED 4 4 44 1 1
AMP PEAK 46(22Q12.2) WILD-TYPE 286 36 95 16 5

Figure S264.  Get High-res Image Gene #46: 'Amp Peak 46(22q12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 46(22q12.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.88e-14 (Fisher's exact test), Q value = 1.4e-11

Table S265.  Gene #46: 'Amp Peak 46(22q12.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 46(22Q12.2) MUTATED 40 8 0
AMP PEAK 46(22Q12.2) WILD-TYPE 103 77 149

Figure S265.  Get High-res Image Gene #46: 'Amp Peak 46(22q12.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 46(22q12.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.35e-13 (Fisher's exact test), Q value = 4.5e-10

Table S266.  Gene #46: 'Amp Peak 46(22q12.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 46(22Q12.2) MUTATED 32 0 1
AMP PEAK 46(22Q12.2) WILD-TYPE 110 107 112

Figure S266.  Get High-res Image Gene #46: 'Amp Peak 46(22q12.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 46(22q12.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.42e-11 (Fisher's exact test), Q value = 5.4e-08

Table S267.  Gene #46: 'Amp Peak 46(22q12.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 46(22Q12.2) MUTATED 1 0 1 31
AMP PEAK 46(22Q12.2) WILD-TYPE 64 92 64 109

Figure S267.  Get High-res Image Gene #46: 'Amp Peak 46(22q12.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 46(22q12.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.12e-18 (Fisher's exact test), Q value = 1.7e-15

Table S268.  Gene #46: 'Amp Peak 46(22q12.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
AMP PEAK 46(22Q12.2) MUTATED 50 0 3
AMP PEAK 46(22Q12.2) WILD-TYPE 144 146 136

Figure S268.  Get High-res Image Gene #46: 'Amp Peak 46(22q12.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Amp Peak 46(22q12.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.47e-18 (Chi-square test), Q value = 4.5e-15

Table S269.  Gene #46: 'Amp Peak 46(22q12.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
AMP PEAK 46(22Q12.2) MUTATED 2 45 1 0 4 1
AMP PEAK 46(22Q12.2) WILD-TYPE 54 97 73 23 35 144

Figure S269.  Get High-res Image Gene #46: 'Amp Peak 46(22q12.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 47(Xp11.23) mutation analysis' versus 'CN_CNMF'

P value = 1.88e-25 (Chi-square test), Q value = 1.7e-22

Table S270.  Gene #47: 'Amp Peak 47(Xp11.23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 47(XP11.23) MUTATED 10 16 42 14 2
AMP PEAK 47(XP11.23) WILD-TYPE 280 24 97 3 4

Figure S270.  Get High-res Image Gene #47: 'Amp Peak 47(Xp11.23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 48(Xq28) mutation analysis' versus 'CN_CNMF'

P value = 4.98e-24 (Chi-square test), Q value = 4.4e-21

Table S271.  Gene #48: 'Amp Peak 48(Xq28) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 48(XQ28) MUTATED 12 16 41 14 2
AMP PEAK 48(XQ28) WILD-TYPE 278 24 98 3 4

Figure S271.  Get High-res Image Gene #48: 'Amp Peak 48(Xq28) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 1(1p36.21) mutation analysis' versus 'CN_CNMF'

P value = 1.79e-23 (Chi-square test), Q value = 1.6e-20

Table S272.  Gene #49: 'Del Peak 1(1p36.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 1(1P36.21) MUTATED 3 7 51 1 3
DEL PEAK 1(1P36.21) WILD-TYPE 287 33 88 16 3

Figure S272.  Get High-res Image Gene #49: 'Del Peak 1(1p36.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 1(1p36.21) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.67e-07 (Fisher's exact test), Q value = 0.00019

Table S273.  Gene #49: 'Del Peak 1(1p36.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 1(1P36.21) MUTATED 34 15 5
DEL PEAK 1(1P36.21) WILD-TYPE 109 70 144

Figure S273.  Get High-res Image Gene #49: 'Del Peak 1(1p36.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 1(1p36.21) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.55e-11 (Fisher's exact test), Q value = 1e-08

Table S274.  Gene #49: 'Del Peak 1(1p36.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 1(1P36.21) MUTATED 35 0 5
DEL PEAK 1(1P36.21) WILD-TYPE 107 107 108

Figure S274.  Get High-res Image Gene #49: 'Del Peak 1(1p36.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 1(1p36.21) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.33e-09 (Fisher's exact test), Q value = 4.2e-06

Table S275.  Gene #49: 'Del Peak 1(1p36.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 1(1P36.21) MUTATED 2 0 6 32
DEL PEAK 1(1P36.21) WILD-TYPE 63 92 59 108

Figure S275.  Get High-res Image Gene #49: 'Del Peak 1(1p36.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 1(1p36.21) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.72e-08 (Fisher's exact test), Q value = 1.5e-05

Table S276.  Gene #49: 'Del Peak 1(1p36.21) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 1(1P36.21) MUTATED 46 7 8
DEL PEAK 1(1P36.21) WILD-TYPE 148 139 131

Figure S276.  Get High-res Image Gene #49: 'Del Peak 1(1p36.21) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 1(1p36.21) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.31e-09 (Chi-square test), Q value = 2.5e-06

Table S277.  Gene #49: 'Del Peak 1(1p36.21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 1(1P36.21) MUTATED 3 39 3 2 8 6
DEL PEAK 1(1P36.21) WILD-TYPE 53 103 71 21 31 139

Figure S277.  Get High-res Image Gene #49: 'Del Peak 1(1p36.21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 2(1p36.11) mutation analysis' versus 'CN_CNMF'

P value = 9.91e-33 (Chi-square test), Q value = 9.1e-30

Table S278.  Gene #50: 'Del Peak 2(1p36.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 2(1P36.11) MUTATED 2 7 65 1 3
DEL PEAK 2(1P36.11) WILD-TYPE 288 33 74 16 3

Figure S278.  Get High-res Image Gene #50: 'Del Peak 2(1p36.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 2(1p36.11) mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.98e-11 (Fisher's exact test), Q value = 4.5e-08

Table S279.  Gene #50: 'Del Peak 2(1p36.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 2(1P36.11) MUTATED 48 15 6
DEL PEAK 2(1P36.11) WILD-TYPE 95 70 143

Figure S279.  Get High-res Image Gene #50: 'Del Peak 2(1p36.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 2(1p36.11) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.96e-12 (Fisher's exact test), Q value = 1.4e-09

Table S280.  Gene #50: 'Del Peak 2(1p36.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 2(1P36.11) MUTATED 37 0 5
DEL PEAK 2(1P36.11) WILD-TYPE 105 107 108

Figure S280.  Get High-res Image Gene #50: 'Del Peak 2(1p36.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 2(1p36.11) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.18e-11 (Fisher's exact test), Q value = 2.1e-08

Table S281.  Gene #50: 'Del Peak 2(1p36.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 2(1P36.11) MUTATED 1 0 5 36
DEL PEAK 2(1P36.11) WILD-TYPE 64 92 60 104

Figure S281.  Get High-res Image Gene #50: 'Del Peak 2(1p36.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 2(1p36.11) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 9.44e-15 (Fisher's exact test), Q value = 7.1e-12

Table S282.  Gene #50: 'Del Peak 2(1p36.11) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 2(1P36.11) MUTATED 61 7 6
DEL PEAK 2(1P36.11) WILD-TYPE 133 139 133

Figure S282.  Get High-res Image Gene #50: 'Del Peak 2(1p36.11) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 2(1p36.11) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.47e-12 (Chi-square test), Q value = 1.7e-09

Table S283.  Gene #50: 'Del Peak 2(1p36.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 2(1P36.11) MUTATED 4 47 3 3 11 6
DEL PEAK 2(1P36.11) WILD-TYPE 52 95 71 20 28 139

Figure S283.  Get High-res Image Gene #50: 'Del Peak 2(1p36.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 4(2p25.3) mutation analysis' versus 'CN_CNMF'

P value = 6.48e-09 (Chi-square test), Q value = 3.7e-06

Table S284.  Gene #52: 'Del Peak 4(2p25.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 4(2P25.3) MUTATED 2 1 21 0 0
DEL PEAK 4(2P25.3) WILD-TYPE 288 39 118 17 6

Figure S284.  Get High-res Image Gene #52: 'Del Peak 4(2p25.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 4(2p25.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.21

Table S285.  Gene #52: 'Del Peak 4(2p25.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 4(2P25.3) MUTATED 17 4 2
DEL PEAK 4(2P25.3) WILD-TYPE 126 81 147

Figure S285.  Get High-res Image Gene #52: 'Del Peak 4(2p25.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 4(2p25.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 8.8e-05 (Fisher's exact test), Q value = 0.038

Table S286.  Gene #52: 'Del Peak 4(2p25.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 4(2P25.3) MUTATED 13 0 1
DEL PEAK 4(2P25.3) WILD-TYPE 129 107 112

Figure S286.  Get High-res Image Gene #52: 'Del Peak 4(2p25.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 4(2p25.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000323 (Fisher's exact test), Q value = 0.13

Table S287.  Gene #52: 'Del Peak 4(2p25.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 4(2P25.3) MUTATED 1 0 0 13
DEL PEAK 4(2P25.3) WILD-TYPE 64 92 65 127

Figure S287.  Get High-res Image Gene #52: 'Del Peak 4(2p25.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 4(2p25.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000578 (Fisher's exact test), Q value = 0.22

Table S288.  Gene #52: 'Del Peak 4(2p25.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 4(2P25.3) MUTATED 19 3 2
DEL PEAK 4(2P25.3) WILD-TYPE 175 143 137

Figure S288.  Get High-res Image Gene #52: 'Del Peak 4(2p25.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 5(2q22.1) mutation analysis' versus 'CN_CNMF'

P value = 2.7e-20 (Chi-square test), Q value = 2.3e-17

Table S289.  Gene #53: 'Del Peak 5(2q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 5(2Q22.1) MUTATED 0 4 40 0 0
DEL PEAK 5(2Q22.1) WILD-TYPE 290 36 99 17 6

Figure S289.  Get High-res Image Gene #53: 'Del Peak 5(2q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 5(2q22.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000179 (Fisher's exact test), Q value = 0.075

Table S290.  Gene #53: 'Del Peak 5(2q22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 5(2Q22.1) MUTATED 23 10 4
DEL PEAK 5(2Q22.1) WILD-TYPE 120 75 145

Figure S290.  Get High-res Image Gene #53: 'Del Peak 5(2q22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 5(2q22.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.55e-08 (Fisher's exact test), Q value = 8.7e-06

Table S291.  Gene #53: 'Del Peak 5(2q22.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 5(2Q22.1) MUTATED 22 1 0
DEL PEAK 5(2Q22.1) WILD-TYPE 120 106 113

Figure S291.  Get High-res Image Gene #53: 'Del Peak 5(2q22.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 5(2q22.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.77e-08 (Fisher's exact test), Q value = 4.2e-05

Table S292.  Gene #53: 'Del Peak 5(2q22.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 5(2Q22.1) MUTATED 0 0 1 22
DEL PEAK 5(2Q22.1) WILD-TYPE 65 92 64 118

Figure S292.  Get High-res Image Gene #53: 'Del Peak 5(2q22.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 5(2q22.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.24e-06 (Fisher's exact test), Q value = 0.00061

Table S293.  Gene #53: 'Del Peak 5(2q22.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 5(2Q22.1) MUTATED 33 4 5
DEL PEAK 5(2Q22.1) WILD-TYPE 161 142 134

Figure S293.  Get High-res Image Gene #53: 'Del Peak 5(2q22.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 5(2q22.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000232 (Chi-square test), Q value = 0.096

Table S294.  Gene #53: 'Del Peak 5(2q22.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 5(2Q22.1) MUTATED 4 22 0 3 7 6
DEL PEAK 5(2Q22.1) WILD-TYPE 52 120 74 20 32 139

Figure S294.  Get High-res Image Gene #53: 'Del Peak 5(2q22.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 6(2q37.3) mutation analysis' versus 'CN_CNMF'

P value = 7.94e-17 (Chi-square test), Q value = 6.3e-14

Table S295.  Gene #54: 'Del Peak 6(2q37.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 6(2Q37.3) MUTATED 3 7 39 0 0
DEL PEAK 6(2Q37.3) WILD-TYPE 287 33 100 17 6

Figure S295.  Get High-res Image Gene #54: 'Del Peak 6(2q37.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 6(2q37.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.56e-05 (Fisher's exact test), Q value = 0.02

Table S296.  Gene #54: 'Del Peak 6(2q37.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 6(2Q37.3) MUTATED 31 6 8
DEL PEAK 6(2Q37.3) WILD-TYPE 112 79 141

Figure S296.  Get High-res Image Gene #54: 'Del Peak 6(2q37.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 6(2q37.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.36e-05 (Fisher's exact test), Q value = 0.0063

Table S297.  Gene #54: 'Del Peak 6(2q37.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 6(2Q37.3) MUTATED 21 2 2
DEL PEAK 6(2Q37.3) WILD-TYPE 121 105 111

Figure S297.  Get High-res Image Gene #54: 'Del Peak 6(2q37.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 6(2q37.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.43e-06 (Fisher's exact test), Q value = 7e-04

Table S298.  Gene #54: 'Del Peak 6(2q37.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 6(2Q37.3) MUTATED 0 0 4 21
DEL PEAK 6(2Q37.3) WILD-TYPE 65 92 61 119

Figure S298.  Get High-res Image Gene #54: 'Del Peak 6(2q37.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 6(2q37.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 5.39e-05 (Fisher's exact test), Q value = 0.024

Table S299.  Gene #54: 'Del Peak 6(2q37.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 6(2Q37.3) MUTATED 34 8 6
DEL PEAK 6(2Q37.3) WILD-TYPE 160 138 133

Figure S299.  Get High-res Image Gene #54: 'Del Peak 6(2q37.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 7(3p14.2) mutation analysis' versus 'CN_CNMF'

P value = 5.91e-31 (Chi-square test), Q value = 5.4e-28

Table S300.  Gene #55: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 7(3P14.2) MUTATED 1 8 60 0 0
DEL PEAK 7(3P14.2) WILD-TYPE 289 32 79 17 6

Figure S300.  Get High-res Image Gene #55: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 7(3p14.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.22e-09 (Fisher's exact test), Q value = 7.4e-07

Table S301.  Gene #55: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 7(3P14.2) MUTATED 40 14 4
DEL PEAK 7(3P14.2) WILD-TYPE 103 71 145

Figure S301.  Get High-res Image Gene #55: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 7(3p14.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.77e-15 (Fisher's exact test), Q value = 2.9e-12

Table S302.  Gene #55: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 7(3P14.2) MUTATED 41 2 1
DEL PEAK 7(3P14.2) WILD-TYPE 101 105 112

Figure S302.  Get High-res Image Gene #55: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 7(3p14.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.8e-14 (Fisher's exact test), Q value = 1.3e-11

Table S303.  Gene #55: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 7(3P14.2) MUTATED 0 1 2 41
DEL PEAK 7(3P14.2) WILD-TYPE 65 91 63 99

Figure S303.  Get High-res Image Gene #55: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 7(3p14.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.35e-13 (Fisher's exact test), Q value = 3.1e-10

Table S304.  Gene #55: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 7(3P14.2) MUTATED 55 5 7
DEL PEAK 7(3P14.2) WILD-TYPE 139 141 132

Figure S304.  Get High-res Image Gene #55: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 7(3p14.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.08e-09 (Chi-square test), Q value = 6.6e-07

Table S305.  Gene #55: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 7(3P14.2) MUTATED 3 41 2 3 10 8
DEL PEAK 7(3P14.2) WILD-TYPE 53 101 72 20 29 137

Figure S305.  Get High-res Image Gene #55: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 8(3q13.31) mutation analysis' versus 'CN_CNMF'

P value = 1.44e-12 (Chi-square test), Q value = 1e-09

Table S306.  Gene #56: 'Del Peak 8(3q13.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 8(3Q13.31) MUTATED 1 1 26 0 0
DEL PEAK 8(3Q13.31) WILD-TYPE 289 39 113 17 6

Figure S306.  Get High-res Image Gene #56: 'Del Peak 8(3q13.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 8(3q13.31) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000246 (Fisher's exact test), Q value = 0.1

Table S307.  Gene #56: 'Del Peak 8(3q13.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 8(3Q13.31) MUTATED 12 0 1
DEL PEAK 8(3Q13.31) WILD-TYPE 130 107 112

Figure S307.  Get High-res Image Gene #56: 'Del Peak 8(3q13.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 8(3q13.31) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 5.71e-07 (Fisher's exact test), Q value = 0.00029

Table S308.  Gene #56: 'Del Peak 8(3q13.31) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 8(3Q13.31) MUTATED 24 2 1
DEL PEAK 8(3Q13.31) WILD-TYPE 170 144 138

Figure S308.  Get High-res Image Gene #56: 'Del Peak 8(3q13.31) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 9(4p16.3) mutation analysis' versus 'CN_CNMF'

P value = 1.41e-30 (Chi-square test), Q value = 1.3e-27

Table S309.  Gene #57: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 9(4P16.3) MUTATED 4 12 67 3 1
DEL PEAK 9(4P16.3) WILD-TYPE 286 28 72 14 5

Figure S309.  Get High-res Image Gene #57: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 9(4p16.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.74e-12 (Fisher's exact test), Q value = 1.2e-09

Table S310.  Gene #57: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 9(4P16.3) MUTATED 54 14 7
DEL PEAK 9(4P16.3) WILD-TYPE 89 71 142

Figure S310.  Get High-res Image Gene #57: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 9(4p16.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.57e-10 (Fisher's exact test), Q value = 9.9e-08

Table S311.  Gene #57: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 9(4P16.3) MUTATED 40 4 4
DEL PEAK 9(4P16.3) WILD-TYPE 102 103 109

Figure S311.  Get High-res Image Gene #57: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 9(4p16.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.13e-11 (Fisher's exact test), Q value = 5.9e-08

Table S312.  Gene #57: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 9(4P16.3) MUTATED 1 2 5 40
DEL PEAK 9(4P16.3) WILD-TYPE 64 90 60 100

Figure S312.  Get High-res Image Gene #57: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 9(4p16.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.51e-17 (Fisher's exact test), Q value = 3.6e-14

Table S313.  Gene #57: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 9(4P16.3) MUTATED 68 8 6
DEL PEAK 9(4P16.3) WILD-TYPE 126 138 133

Figure S313.  Get High-res Image Gene #57: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 9(4p16.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.66e-12 (Chi-square test), Q value = 4.5e-09

Table S314.  Gene #57: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 9(4P16.3) MUTATED 4 49 3 3 13 10
DEL PEAK 9(4P16.3) WILD-TYPE 52 93 71 20 26 135

Figure S314.  Get High-res Image Gene #57: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 10(4p15.31) mutation analysis' versus 'CN_CNMF'

P value = 4.15e-35 (Chi-square test), Q value = 3.9e-32

Table S315.  Gene #58: 'Del Peak 10(4p15.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 10(4P15.31) MUTATED 3 12 72 3 0
DEL PEAK 10(4P15.31) WILD-TYPE 287 28 67 14 6

Figure S315.  Get High-res Image Gene #58: 'Del Peak 10(4p15.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 10(4p15.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.13e-14 (Fisher's exact test), Q value = 6.6e-11

Table S316.  Gene #58: 'Del Peak 10(4p15.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 10(4P15.31) MUTATED 56 16 6
DEL PEAK 10(4P15.31) WILD-TYPE 87 69 143

Figure S316.  Get High-res Image Gene #58: 'Del Peak 10(4p15.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 10(4p15.31) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.81e-11 (Fisher's exact test), Q value = 2.5e-08

Table S317.  Gene #58: 'Del Peak 10(4p15.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 10(4P15.31) MUTATED 40 3 4
DEL PEAK 10(4P15.31) WILD-TYPE 102 104 109

Figure S317.  Get High-res Image Gene #58: 'Del Peak 10(4p15.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 10(4p15.31) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.36e-11 (Fisher's exact test), Q value = 2.8e-08

Table S318.  Gene #58: 'Del Peak 10(4p15.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 10(4P15.31) MUTATED 1 2 4 40
DEL PEAK 10(4P15.31) WILD-TYPE 64 90 61 100

Figure S318.  Get High-res Image Gene #58: 'Del Peak 10(4p15.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 10(4p15.31) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 9.25e-19 (Fisher's exact test), Q value = 7.7e-16

Table S319.  Gene #58: 'Del Peak 10(4p15.31) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 10(4P15.31) MUTATED 72 8 6
DEL PEAK 10(4P15.31) WILD-TYPE 122 138 133

Figure S319.  Get High-res Image Gene #58: 'Del Peak 10(4p15.31) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 10(4p15.31) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.31e-12 (Chi-square test), Q value = 2.3e-09

Table S320.  Gene #58: 'Del Peak 10(4p15.31) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 10(4P15.31) MUTATED 7 52 3 3 12 9
DEL PEAK 10(4P15.31) WILD-TYPE 49 90 71 20 27 136

Figure S320.  Get High-res Image Gene #58: 'Del Peak 10(4p15.31) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 11(4q22.1) mutation analysis' versus 'CN_CNMF'

P value = 1.04e-46 (Chi-square test), Q value = 9.8e-44

Table S321.  Gene #59: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 11(4Q22.1) MUTATED 2 9 86 1 1
DEL PEAK 11(4Q22.1) WILD-TYPE 288 31 53 16 5

Figure S321.  Get High-res Image Gene #59: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 11(4q22.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.05e-18 (Fisher's exact test), Q value = 1.7e-15

Table S322.  Gene #59: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 11(4Q22.1) MUTATED 63 17 4
DEL PEAK 11(4Q22.1) WILD-TYPE 80 68 145

Figure S322.  Get High-res Image Gene #59: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 11(4q22.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.1e-16 (Fisher's exact test), Q value = 8.7e-14

Table S323.  Gene #59: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 11(4Q22.1) MUTATED 50 2 4
DEL PEAK 11(4Q22.1) WILD-TYPE 92 105 109

Figure S323.  Get High-res Image Gene #59: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 11(4q22.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.16e-18 (Fisher's exact test), Q value = 9.7e-16

Table S324.  Gene #59: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 11(4Q22.1) MUTATED 1 1 2 52
DEL PEAK 11(4Q22.1) WILD-TYPE 64 91 63 88

Figure S324.  Get High-res Image Gene #59: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 11(4q22.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.74e-23 (Fisher's exact test), Q value = 1.5e-20

Table S325.  Gene #59: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 11(4Q22.1) MUTATED 81 7 6
DEL PEAK 11(4Q22.1) WILD-TYPE 113 139 133

Figure S325.  Get High-res Image Gene #59: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 11(4q22.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.21e-20 (Chi-square test), Q value = 3.6e-17

Table S326.  Gene #59: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 11(4Q22.1) MUTATED 5 64 2 2 13 8
DEL PEAK 11(4Q22.1) WILD-TYPE 51 78 72 21 26 137

Figure S326.  Get High-res Image Gene #59: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 12(4q34.3) mutation analysis' versus 'CN_CNMF'

P value = 1.43e-51 (Chi-square test), Q value = 1.4e-48

Table S327.  Gene #60: 'Del Peak 12(4q34.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 12(4Q34.3) MUTATED 6 10 97 1 1
DEL PEAK 12(4Q34.3) WILD-TYPE 284 30 42 16 5

Figure S327.  Get High-res Image Gene #60: 'Del Peak 12(4q34.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 12(4q34.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.7e-15 (Fisher's exact test), Q value = 2.1e-12

Table S328.  Gene #60: 'Del Peak 12(4q34.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 12(4Q34.3) MUTATED 66 23 9
DEL PEAK 12(4Q34.3) WILD-TYPE 77 62 140

Figure S328.  Get High-res Image Gene #60: 'Del Peak 12(4q34.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 12(4q34.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.31e-18 (Fisher's exact test), Q value = 1.1e-15

Table S329.  Gene #60: 'Del Peak 12(4q34.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 12(4Q34.3) MUTATED 59 3 6
DEL PEAK 12(4Q34.3) WILD-TYPE 83 104 107

Figure S329.  Get High-res Image Gene #60: 'Del Peak 12(4q34.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 12(4q34.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.83e-20 (Fisher's exact test), Q value = 7.5e-17

Table S330.  Gene #60: 'Del Peak 12(4q34.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 12(4Q34.3) MUTATED 1 1 7 59
DEL PEAK 12(4Q34.3) WILD-TYPE 64 91 58 81

Figure S330.  Get High-res Image Gene #60: 'Del Peak 12(4q34.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 12(4q34.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.7e-21 (Fisher's exact test), Q value = 1.5e-18

Table S331.  Gene #60: 'Del Peak 12(4q34.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 12(4Q34.3) MUTATED 88 8 14
DEL PEAK 12(4Q34.3) WILD-TYPE 106 138 125

Figure S331.  Get High-res Image Gene #60: 'Del Peak 12(4q34.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 12(4q34.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.61e-19 (Chi-square test), Q value = 3e-16

Table S332.  Gene #60: 'Del Peak 12(4q34.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 12(4Q34.3) MUTATED 9 69 3 4 15 10
DEL PEAK 12(4Q34.3) WILD-TYPE 47 73 71 19 24 135

Figure S332.  Get High-res Image Gene #60: 'Del Peak 12(4q34.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 13(5q11.2) mutation analysis' versus 'CN_CNMF'

P value = 8.55e-49 (Chi-square test), Q value = 8.1e-46

Table S333.  Gene #61: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 13(5Q11.2) MUTATED 0 11 87 2 0
DEL PEAK 13(5Q11.2) WILD-TYPE 290 29 52 15 6

Figure S333.  Get High-res Image Gene #61: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 13(5q11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.18e-16 (Fisher's exact test), Q value = 9.3e-14

Table S334.  Gene #61: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 13(5Q11.2) MUTATED 63 16 6
DEL PEAK 13(5Q11.2) WILD-TYPE 80 69 143

Figure S334.  Get High-res Image Gene #61: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 13(5q11.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.39e-17 (Fisher's exact test), Q value = 5.8e-14

Table S335.  Gene #61: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 13(5Q11.2) MUTATED 49 2 3
DEL PEAK 13(5Q11.2) WILD-TYPE 93 105 110

Figure S335.  Get High-res Image Gene #61: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 13(5q11.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.24e-17 (Fisher's exact test), Q value = 2.6e-14

Table S336.  Gene #61: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 13(5Q11.2) MUTATED 0 1 4 49
DEL PEAK 13(5Q11.2) WILD-TYPE 65 91 61 91

Figure S336.  Get High-res Image Gene #61: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 13(5q11.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 9.56e-18 (Fisher's exact test), Q value = 7.8e-15

Table S337.  Gene #61: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 13(5Q11.2) MUTATED 78 10 10
DEL PEAK 13(5Q11.2) WILD-TYPE 116 136 129

Figure S337.  Get High-res Image Gene #61: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 13(5q11.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.92e-17 (Chi-square test), Q value = 5.5e-14

Table S338.  Gene #61: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 13(5Q11.2) MUTATED 4 61 3 4 15 11
DEL PEAK 13(5Q11.2) WILD-TYPE 52 81 71 19 24 134

Figure S338.  Get High-res Image Gene #61: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 14(6q26) mutation analysis' versus 'CN_CNMF'

P value = 9.63e-15 (Chi-square test), Q value = 7.3e-12

Table S339.  Gene #62: 'Del Peak 14(6q26) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 14(6Q26) MUTATED 4 4 36 0 0
DEL PEAK 14(6Q26) WILD-TYPE 286 36 103 17 6

Figure S339.  Get High-res Image Gene #62: 'Del Peak 14(6q26) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 14(6q26) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.19e-08 (Fisher's exact test), Q value = 2.8e-05

Table S340.  Gene #62: 'Del Peak 14(6q26) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 14(6Q26) MUTATED 27 10 1
DEL PEAK 14(6Q26) WILD-TYPE 116 75 148

Figure S340.  Get High-res Image Gene #62: 'Del Peak 14(6q26) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 14(6q26) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.29e-06 (Fisher's exact test), Q value = 0.0011

Table S341.  Gene #62: 'Del Peak 14(6q26) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 14(6Q26) MUTATED 21 1 2
DEL PEAK 14(6Q26) WILD-TYPE 121 106 111

Figure S341.  Get High-res Image Gene #62: 'Del Peak 14(6q26) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 14(6q26) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.75e-05 (Fisher's exact test), Q value = 0.034

Table S342.  Gene #62: 'Del Peak 14(6q26) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 14(6Q26) MUTATED 2 1 1 20
DEL PEAK 14(6Q26) WILD-TYPE 63 91 64 120

Figure S342.  Get High-res Image Gene #62: 'Del Peak 14(6q26) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 14(6q26) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.39e-09 (Fisher's exact test), Q value = 1.4e-06

Table S343.  Gene #62: 'Del Peak 14(6q26) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 14(6Q26) MUTATED 36 3 3
DEL PEAK 14(6Q26) WILD-TYPE 158 143 136

Figure S343.  Get High-res Image Gene #62: 'Del Peak 14(6q26) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 14(6q26) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.18e-07 (Chi-square test), Q value = 0.00021

Table S344.  Gene #62: 'Del Peak 14(6q26) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 14(6Q26) MUTATED 3 27 0 1 7 4
DEL PEAK 14(6Q26) WILD-TYPE 53 115 74 22 32 141

Figure S344.  Get High-res Image Gene #62: 'Del Peak 14(6q26) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 15(7p22.3) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000248 (Fisher's exact test), Q value = 0.1

Table S345.  Gene #63: 'Del Peak 15(7p22.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
DEL PEAK 15(7P22.3) MUTATED 0 0 7
DEL PEAK 15(7P22.3) WILD-TYPE 20 15 11

Figure S345.  Get High-res Image Gene #63: 'Del Peak 15(7p22.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 15(7p22.3) mutation analysis' versus 'CN_CNMF'

P value = 4.17e-31 (Chi-square test), Q value = 3.8e-28

Table S346.  Gene #63: 'Del Peak 15(7p22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 15(7P22.3) MUTATED 4 2 61 0 1
DEL PEAK 15(7P22.3) WILD-TYPE 286 38 78 17 5

Figure S346.  Get High-res Image Gene #63: 'Del Peak 15(7p22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 15(7p22.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.43e-10 (Fisher's exact test), Q value = 1.5e-07

Table S347.  Gene #63: 'Del Peak 15(7p22.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 15(7P22.3) MUTATED 42 12 4
DEL PEAK 15(7P22.3) WILD-TYPE 101 73 145

Figure S347.  Get High-res Image Gene #63: 'Del Peak 15(7p22.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 15(7p22.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.12e-14 (Fisher's exact test), Q value = 3.8e-11

Table S348.  Gene #63: 'Del Peak 15(7p22.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 15(7P22.3) MUTATED 41 2 2
DEL PEAK 15(7P22.3) WILD-TYPE 101 105 111

Figure S348.  Get High-res Image Gene #63: 'Del Peak 15(7p22.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 15(7p22.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.07e-15 (Fisher's exact test), Q value = 3.1e-12

Table S349.  Gene #63: 'Del Peak 15(7p22.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 15(7P22.3) MUTATED 2 0 1 42
DEL PEAK 15(7P22.3) WILD-TYPE 63 92 64 98

Figure S349.  Get High-res Image Gene #63: 'Del Peak 15(7p22.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 15(7p22.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 5.6e-14 (Fisher's exact test), Q value = 4.1e-11

Table S350.  Gene #63: 'Del Peak 15(7p22.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 15(7P22.3) MUTATED 56 6 5
DEL PEAK 15(7P22.3) WILD-TYPE 138 140 134

Figure S350.  Get High-res Image Gene #63: 'Del Peak 15(7p22.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 15(7p22.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.5e-11 (Chi-square test), Q value = 2.9e-08

Table S351.  Gene #63: 'Del Peak 15(7p22.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 15(7P22.3) MUTATED 5 45 1 2 6 8
DEL PEAK 15(7P22.3) WILD-TYPE 51 97 73 21 33 137

Figure S351.  Get High-res Image Gene #63: 'Del Peak 15(7p22.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 16(7q11.22) mutation analysis' versus 'CN_CNMF'

P value = 3.24e-21 (Chi-square test), Q value = 2.8e-18

Table S352.  Gene #64: 'Del Peak 16(7q11.22) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 16(7Q11.22) MUTATED 0 0 38 0 1
DEL PEAK 16(7Q11.22) WILD-TYPE 290 40 101 17 5

Figure S352.  Get High-res Image Gene #64: 'Del Peak 16(7q11.22) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 16(7q11.22) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.35e-07 (Fisher's exact test), Q value = 0.00012

Table S353.  Gene #64: 'Del Peak 16(7q11.22) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 16(7Q11.22) MUTATED 25 9 1
DEL PEAK 16(7Q11.22) WILD-TYPE 118 76 148

Figure S353.  Get High-res Image Gene #64: 'Del Peak 16(7q11.22) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 16(7q11.22) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.89e-09 (Fisher's exact test), Q value = 2.8e-06

Table S354.  Gene #64: 'Del Peak 16(7q11.22) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 16(7Q11.22) MUTATED 23 1 0
DEL PEAK 16(7Q11.22) WILD-TYPE 119 106 113

Figure S354.  Get High-res Image Gene #64: 'Del Peak 16(7q11.22) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 16(7q11.22) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.5e-09 (Fisher's exact test), Q value = 8.9e-07

Table S355.  Gene #64: 'Del Peak 16(7q11.22) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 16(7Q11.22) MUTATED 0 0 0 24
DEL PEAK 16(7Q11.22) WILD-TYPE 65 92 65 116

Figure S355.  Get High-res Image Gene #64: 'Del Peak 16(7q11.22) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 16(7q11.22) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.6e-06 (Fisher's exact test), Q value = 0.0022

Table S356.  Gene #64: 'Del Peak 16(7q11.22) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 16(7Q11.22) MUTATED 30 4 4
DEL PEAK 16(7Q11.22) WILD-TYPE 164 142 135

Figure S356.  Get High-res Image Gene #64: 'Del Peak 16(7q11.22) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 16(7q11.22) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000302 (Chi-square test), Q value = 0.12

Table S357.  Gene #64: 'Del Peak 16(7q11.22) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 16(7Q11.22) MUTATED 4 23 0 1 4 6
DEL PEAK 16(7Q11.22) WILD-TYPE 52 119 74 22 35 139

Figure S357.  Get High-res Image Gene #64: 'Del Peak 16(7q11.22) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 17(7q31.1) mutation analysis' versus 'CN_CNMF'

P value = 5.75e-27 (Chi-square test), Q value = 5.2e-24

Table S358.  Gene #65: 'Del Peak 17(7q31.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 17(7Q31.1) MUTATED 0 0 47 0 1
DEL PEAK 17(7Q31.1) WILD-TYPE 290 40 92 17 5

Figure S358.  Get High-res Image Gene #65: 'Del Peak 17(7q31.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 17(7q31.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.41e-09 (Fisher's exact test), Q value = 1.4e-06

Table S359.  Gene #65: 'Del Peak 17(7q31.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 17(7Q31.1) MUTATED 31 10 1
DEL PEAK 17(7Q31.1) WILD-TYPE 112 75 148

Figure S359.  Get High-res Image Gene #65: 'Del Peak 17(7q31.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 17(7q31.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.26e-14 (Fisher's exact test), Q value = 2.4e-11

Table S360.  Gene #65: 'Del Peak 17(7q31.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 17(7Q31.1) MUTATED 32 0 0
DEL PEAK 17(7Q31.1) WILD-TYPE 110 107 113

Figure S360.  Get High-res Image Gene #65: 'Del Peak 17(7q31.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 17(7q31.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.17e-13 (Fisher's exact test), Q value = 2.3e-10

Table S361.  Gene #65: 'Del Peak 17(7q31.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 17(7Q31.1) MUTATED 0 0 0 32
DEL PEAK 17(7Q31.1) WILD-TYPE 65 92 65 108

Figure S361.  Get High-res Image Gene #65: 'Del Peak 17(7q31.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 17(7q31.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.27e-10 (Fisher's exact test), Q value = 1.4e-07

Table S362.  Gene #65: 'Del Peak 17(7q31.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 17(7Q31.1) MUTATED 40 3 4
DEL PEAK 17(7Q31.1) WILD-TYPE 154 143 135

Figure S362.  Get High-res Image Gene #65: 'Del Peak 17(7q31.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 17(7q31.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.51e-08 (Chi-square test), Q value = 8.5e-06

Table S363.  Gene #65: 'Del Peak 17(7q31.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 17(7Q31.1) MUTATED 3 33 0 2 4 5
DEL PEAK 17(7Q31.1) WILD-TYPE 53 109 74 21 35 140

Figure S363.  Get High-res Image Gene #65: 'Del Peak 17(7q31.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 18(7q36.3) mutation analysis' versus 'CN_CNMF'

P value = 9.35e-30 (Chi-square test), Q value = 8.5e-27

Table S364.  Gene #66: 'Del Peak 18(7q36.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 18(7Q36.3) MUTATED 1 1 54 0 1
DEL PEAK 18(7Q36.3) WILD-TYPE 289 39 85 17 5

Figure S364.  Get High-res Image Gene #66: 'Del Peak 18(7q36.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 18(7q36.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.75e-10 (Fisher's exact test), Q value = 1.1e-07

Table S365.  Gene #66: 'Del Peak 18(7q36.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 18(7Q36.3) MUTATED 34 12 1
DEL PEAK 18(7Q36.3) WILD-TYPE 109 73 148

Figure S365.  Get High-res Image Gene #66: 'Del Peak 18(7q36.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 18(7q36.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.29e-18 (Fisher's exact test), Q value = 1.1e-15

Table S366.  Gene #66: 'Del Peak 18(7q36.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 18(7Q36.3) MUTATED 41 0 0
DEL PEAK 18(7Q36.3) WILD-TYPE 101 107 113

Figure S366.  Get High-res Image Gene #66: 'Del Peak 18(7q36.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 18(7q36.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.93e-16 (Fisher's exact test), Q value = 4.6e-13

Table S367.  Gene #66: 'Del Peak 18(7q36.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 18(7Q36.3) MUTATED 0 0 1 40
DEL PEAK 18(7Q36.3) WILD-TYPE 65 92 64 100

Figure S367.  Get High-res Image Gene #66: 'Del Peak 18(7q36.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 18(7q36.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 7.64e-13 (Fisher's exact test), Q value = 5.4e-10

Table S368.  Gene #66: 'Del Peak 18(7q36.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 18(7Q36.3) MUTATED 48 3 5
DEL PEAK 18(7Q36.3) WILD-TYPE 146 143 134

Figure S368.  Get High-res Image Gene #66: 'Del Peak 18(7q36.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 18(7q36.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.45e-10 (Chi-square test), Q value = 1.5e-07

Table S369.  Gene #66: 'Del Peak 18(7q36.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 18(7Q36.3) MUTATED 5 38 0 1 7 5
DEL PEAK 18(7Q36.3) WILD-TYPE 51 104 74 22 32 140

Figure S369.  Get High-res Image Gene #66: 'Del Peak 18(7q36.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 19(8p23.2) mutation analysis' versus 'CN_CNMF'

P value = 1.03e-40 (Chi-square test), Q value = 9.7e-38

Table S370.  Gene #67: 'Del Peak 19(8p23.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 19(8P23.2) MUTATED 9 6 85 2 1
DEL PEAK 19(8P23.2) WILD-TYPE 281 34 54 15 5

Figure S370.  Get High-res Image Gene #67: 'Del Peak 19(8p23.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 19(8p23.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.24e-21 (Fisher's exact test), Q value = 1.1e-18

Table S371.  Gene #67: 'Del Peak 19(8p23.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 19(8P23.2) MUTATED 68 18 3
DEL PEAK 19(8P23.2) WILD-TYPE 75 67 146

Figure S371.  Get High-res Image Gene #67: 'Del Peak 19(8p23.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 19(8p23.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.45e-17 (Fisher's exact test), Q value = 5.1e-14

Table S372.  Gene #67: 'Del Peak 19(8p23.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 19(8P23.2) MUTATED 52 2 5
DEL PEAK 19(8P23.2) WILD-TYPE 90 105 108

Figure S372.  Get High-res Image Gene #67: 'Del Peak 19(8p23.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 19(8p23.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.05e-19 (Fisher's exact test), Q value = 4.2e-16

Table S373.  Gene #67: 'Del Peak 19(8p23.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 19(8P23.2) MUTATED 1 1 3 54
DEL PEAK 19(8P23.2) WILD-TYPE 64 91 62 86

Figure S373.  Get High-res Image Gene #67: 'Del Peak 19(8p23.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 19(8p23.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.66e-26 (Fisher's exact test), Q value = 2.4e-23

Table S374.  Gene #67: 'Del Peak 19(8p23.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 19(8P23.2) MUTATED 87 7 6
DEL PEAK 19(8P23.2) WILD-TYPE 107 139 133

Figure S374.  Get High-res Image Gene #67: 'Del Peak 19(8p23.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 19(8p23.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.08e-24 (Chi-square test), Q value = 5.4e-21

Table S375.  Gene #67: 'Del Peak 19(8p23.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 19(8P23.2) MUTATED 6 72 3 3 10 6
DEL PEAK 19(8P23.2) WILD-TYPE 50 70 71 20 29 139

Figure S375.  Get High-res Image Gene #67: 'Del Peak 19(8p23.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 20(9p23) mutation analysis' versus 'CN_CNMF'

P value = 1.01e-22 (Chi-square test), Q value = 8.9e-20

Table S376.  Gene #68: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 20(9P23) MUTATED 2 12 49 2 0
DEL PEAK 20(9P23) WILD-TYPE 288 28 90 15 6

Figure S376.  Get High-res Image Gene #68: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 20(9p23) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.84e-06 (Fisher's exact test), Q value = 0.00091

Table S377.  Gene #68: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 20(9P23) MUTATED 32 18 6
DEL PEAK 20(9P23) WILD-TYPE 111 67 143

Figure S377.  Get High-res Image Gene #68: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 20(9p23) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.93e-07 (Fisher's exact test), Q value = 1e-04

Table S378.  Gene #68: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 20(9P23) MUTATED 29 3 3
DEL PEAK 20(9P23) WILD-TYPE 113 104 110

Figure S378.  Get High-res Image Gene #68: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 20(9p23) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.29e-09 (Fisher's exact test), Q value = 7.7e-07

Table S379.  Gene #68: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 20(9P23) MUTATED 0 1 3 31
DEL PEAK 20(9P23) WILD-TYPE 65 91 62 109

Figure S379.  Get High-res Image Gene #68: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 20(9p23) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 7.54e-08 (Fisher's exact test), Q value = 4e-05

Table S380.  Gene #68: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 20(9P23) MUTATED 45 15 4
DEL PEAK 20(9P23) WILD-TYPE 149 131 135

Figure S380.  Get High-res Image Gene #68: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 20(9p23) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.09e-08 (Chi-square test), Q value = 3.8e-05

Table S381.  Gene #68: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 20(9P23) MUTATED 1 38 1 2 8 14
DEL PEAK 20(9P23) WILD-TYPE 55 104 73 21 31 131

Figure S381.  Get High-res Image Gene #68: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 21(9q34.11) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.044

Table S382.  Gene #69: 'Del Peak 21(9q34.11) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
DEL PEAK 21(9Q34.11) MUTATED 0 9 0 0
DEL PEAK 21(9Q34.11) WILD-TYPE 13 9 14 8

Figure S382.  Get High-res Image Gene #69: 'Del Peak 21(9q34.11) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 21(9q34.11) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.21e-05 (Fisher's exact test), Q value = 0.0057

Table S383.  Gene #69: 'Del Peak 21(9q34.11) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
DEL PEAK 21(9Q34.11) MUTATED 0 0 9
DEL PEAK 21(9Q34.11) WILD-TYPE 20 15 9

Figure S383.  Get High-res Image Gene #69: 'Del Peak 21(9q34.11) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 21(9q34.11) mutation analysis' versus 'CN_CNMF'

P value = 5.04e-52 (Chi-square test), Q value = 4.8e-49

Table S384.  Gene #69: 'Del Peak 21(9q34.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 21(9Q34.11) MUTATED 5 18 97 1 1
DEL PEAK 21(9Q34.11) WILD-TYPE 285 22 42 16 5

Figure S384.  Get High-res Image Gene #69: 'Del Peak 21(9q34.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 21(9q34.11) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.94e-11 (Fisher's exact test), Q value = 1.3e-08

Table S385.  Gene #69: 'Del Peak 21(9q34.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 21(9Q34.11) MUTATED 64 25 14
DEL PEAK 21(9Q34.11) WILD-TYPE 79 60 135

Figure S385.  Get High-res Image Gene #69: 'Del Peak 21(9q34.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 21(9q34.11) mutation analysis' versus 'RPPA_CNMF'

P value = 0.000384 (Chi-square test), Q value = 0.15

Table S386.  Gene #69: 'Del Peak 21(9q34.11) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
DEL PEAK 21(9Q34.11) MUTATED 8 14 2 2 1 6
DEL PEAK 21(9Q34.11) WILD-TYPE 33 23 37 10 40 18

Figure S386.  Get High-res Image Gene #69: 'Del Peak 21(9q34.11) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 21(9q34.11) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.13e-17 (Fisher's exact test), Q value = 9.2e-15

Table S387.  Gene #69: 'Del Peak 21(9q34.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 21(9Q34.11) MUTATED 63 6 7
DEL PEAK 21(9Q34.11) WILD-TYPE 79 101 106

Figure S387.  Get High-res Image Gene #69: 'Del Peak 21(9q34.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 21(9q34.11) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.84e-24 (Fisher's exact test), Q value = 4.3e-21

Table S388.  Gene #69: 'Del Peak 21(9q34.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 21(9Q34.11) MUTATED 0 2 7 67
DEL PEAK 21(9Q34.11) WILD-TYPE 65 90 58 73

Figure S388.  Get High-res Image Gene #69: 'Del Peak 21(9q34.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 21(9q34.11) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 9.24e-17 (Fisher's exact test), Q value = 7.3e-14

Table S389.  Gene #69: 'Del Peak 21(9q34.11) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 21(9Q34.11) MUTATED 87 20 11
DEL PEAK 21(9Q34.11) WILD-TYPE 107 126 128

Figure S389.  Get High-res Image Gene #69: 'Del Peak 21(9q34.11) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 21(9q34.11) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.37e-12 (Chi-square test), Q value = 9.6e-10

Table S390.  Gene #69: 'Del Peak 21(9q34.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 21(9Q34.11) MUTATED 7 65 5 6 15 20
DEL PEAK 21(9Q34.11) WILD-TYPE 49 77 69 17 24 125

Figure S390.  Get High-res Image Gene #69: 'Del Peak 21(9q34.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 22(10q23.31) mutation analysis' versus 'CN_CNMF'

P value = 1.2e-29 (Chi-square test), Q value = 1.1e-26

Table S391.  Gene #70: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 22(10Q23.31) MUTATED 5 4 61 0 0
DEL PEAK 22(10Q23.31) WILD-TYPE 285 36 78 17 6

Figure S391.  Get High-res Image Gene #70: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 22(10q23.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.19e-08 (Fisher's exact test), Q value = 2.8e-05

Table S392.  Gene #70: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 22(10Q23.31) MUTATED 39 16 6
DEL PEAK 22(10Q23.31) WILD-TYPE 104 69 143

Figure S392.  Get High-res Image Gene #70: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 22(10q23.31) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.39e-07 (Fisher's exact test), Q value = 0.00017

Table S393.  Gene #70: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 22(10Q23.31) MUTATED 30 4 3
DEL PEAK 22(10Q23.31) WILD-TYPE 112 103 110

Figure S393.  Get High-res Image Gene #70: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 22(10q23.31) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.88e-07 (Fisher's exact test), Q value = 9.9e-05

Table S394.  Gene #70: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 22(10Q23.31) MUTATED 0 2 6 29
DEL PEAK 22(10Q23.31) WILD-TYPE 65 90 59 111

Figure S394.  Get High-res Image Gene #70: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 22(10q23.31) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.63e-10 (Fisher's exact test), Q value = 2.2e-07

Table S395.  Gene #70: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 22(10Q23.31) MUTATED 53 8 8
DEL PEAK 22(10Q23.31) WILD-TYPE 141 138 131

Figure S395.  Get High-res Image Gene #70: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 22(10q23.31) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.21e-07 (Chi-square test), Q value = 6.4e-05

Table S396.  Gene #70: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 22(10Q23.31) MUTATED 3 41 5 3 8 9
DEL PEAK 22(10Q23.31) WILD-TYPE 53 101 69 20 31 136

Figure S396.  Get High-res Image Gene #70: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 23(11p15.5) mutation analysis' versus 'CN_CNMF'

P value = 7.81e-40 (Chi-square test), Q value = 7.3e-37

Table S397.  Gene #71: 'Del Peak 23(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 23(11P15.5) MUTATED 1 11 77 2 2
DEL PEAK 23(11P15.5) WILD-TYPE 289 29 62 15 4

Figure S397.  Get High-res Image Gene #71: 'Del Peak 23(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 23(11p15.5) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.91e-17 (Fisher's exact test), Q value = 3.1e-14

Table S398.  Gene #71: 'Del Peak 23(11p15.5) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 23(11P15.5) MUTATED 60 19 4
DEL PEAK 23(11P15.5) WILD-TYPE 83 66 145

Figure S398.  Get High-res Image Gene #71: 'Del Peak 23(11p15.5) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 23(11p15.5) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.92e-14 (Fisher's exact test), Q value = 3.6e-11

Table S399.  Gene #71: 'Del Peak 23(11p15.5) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 23(11P15.5) MUTATED 43 2 3
DEL PEAK 23(11P15.5) WILD-TYPE 99 105 110

Figure S399.  Get High-res Image Gene #71: 'Del Peak 23(11p15.5) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 23(11p15.5) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.77e-16 (Fisher's exact test), Q value = 3.7e-13

Table S400.  Gene #71: 'Del Peak 23(11p15.5) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 23(11P15.5) MUTATED 1 1 1 45
DEL PEAK 23(11P15.5) WILD-TYPE 64 91 64 95

Figure S400.  Get High-res Image Gene #71: 'Del Peak 23(11p15.5) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 23(11p15.5) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 5.84e-17 (Fisher's exact test), Q value = 4.7e-14

Table S401.  Gene #71: 'Del Peak 23(11p15.5) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 23(11P15.5) MUTATED 73 11 7
DEL PEAK 23(11P15.5) WILD-TYPE 121 135 132

Figure S401.  Get High-res Image Gene #71: 'Del Peak 23(11p15.5) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 23(11p15.5) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.31e-15 (Chi-square test), Q value = 4.8e-12

Table S402.  Gene #71: 'Del Peak 23(11p15.5) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 23(11P15.5) MUTATED 3 57 2 2 13 14
DEL PEAK 23(11P15.5) WILD-TYPE 53 85 72 21 26 131

Figure S402.  Get High-res Image Gene #71: 'Del Peak 23(11p15.5) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 24(11q14.1) mutation analysis' versus 'CN_CNMF'

P value = 7.36e-22 (Chi-square test), Q value = 6.4e-19

Table S403.  Gene #72: 'Del Peak 24(11q14.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 24(11Q14.1) MUTATED 1 11 47 2 2
DEL PEAK 24(11Q14.1) WILD-TYPE 289 29 92 15 4

Figure S403.  Get High-res Image Gene #72: 'Del Peak 24(11q14.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 24(11q14.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.39e-09 (Fisher's exact test), Q value = 8.3e-07

Table S404.  Gene #72: 'Del Peak 24(11q14.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 24(11Q14.1) MUTATED 40 13 4
DEL PEAK 24(11Q14.1) WILD-TYPE 103 72 145

Figure S404.  Get High-res Image Gene #72: 'Del Peak 24(11q14.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 24(11q14.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.82e-08 (Fisher's exact test), Q value = 1.6e-05

Table S405.  Gene #72: 'Del Peak 24(11q14.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 24(11Q14.1) MUTATED 28 2 2
DEL PEAK 24(11Q14.1) WILD-TYPE 114 105 111

Figure S405.  Get High-res Image Gene #72: 'Del Peak 24(11q14.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 24(11q14.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.31e-10 (Fisher's exact test), Q value = 1.4e-07

Table S406.  Gene #72: 'Del Peak 24(11q14.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 24(11Q14.1) MUTATED 1 0 1 30
DEL PEAK 24(11Q14.1) WILD-TYPE 64 92 64 110

Figure S406.  Get High-res Image Gene #72: 'Del Peak 24(11q14.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 24(11q14.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.3e-10 (Fisher's exact test), Q value = 2e-07

Table S407.  Gene #72: 'Del Peak 24(11q14.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 24(11Q14.1) MUTATED 48 9 4
DEL PEAK 24(11Q14.1) WILD-TYPE 146 137 135

Figure S407.  Get High-res Image Gene #72: 'Del Peak 24(11q14.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 24(11q14.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.81e-13 (Chi-square test), Q value = 5.5e-10

Table S408.  Gene #72: 'Del Peak 24(11q14.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 24(11Q14.1) MUTATED 1 42 0 0 9 9
DEL PEAK 24(11Q14.1) WILD-TYPE 55 100 74 23 30 136

Figure S408.  Get High-res Image Gene #72: 'Del Peak 24(11q14.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 25(11q25) mutation analysis' versus 'CN_CNMF'

P value = 4.75e-28 (Chi-square test), Q value = 4.3e-25

Table S409.  Gene #73: 'Del Peak 25(11q25) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 25(11Q25) MUTATED 4 15 61 2 2
DEL PEAK 25(11Q25) WILD-TYPE 286 25 78 15 4

Figure S409.  Get High-res Image Gene #73: 'Del Peak 25(11q25) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 25(11q25) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.41e-13 (Fisher's exact test), Q value = 1e-10

Table S410.  Gene #73: 'Del Peak 25(11q25) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 25(11Q25) MUTATED 55 14 6
DEL PEAK 25(11Q25) WILD-TYPE 88 71 143

Figure S410.  Get High-res Image Gene #73: 'Del Peak 25(11q25) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 25(11q25) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.31e-08 (Fisher's exact test), Q value = 1.8e-05

Table S411.  Gene #73: 'Del Peak 25(11q25) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 25(11Q25) MUTATED 35 3 6
DEL PEAK 25(11Q25) WILD-TYPE 107 104 107

Figure S411.  Get High-res Image Gene #73: 'Del Peak 25(11q25) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 25(11q25) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.43e-12 (Fisher's exact test), Q value = 3.7e-09

Table S412.  Gene #73: 'Del Peak 25(11q25) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 25(11Q25) MUTATED 1 1 3 39
DEL PEAK 25(11Q25) WILD-TYPE 64 91 62 101

Figure S412.  Get High-res Image Gene #73: 'Del Peak 25(11q25) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 25(11q25) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 5.32e-14 (Fisher's exact test), Q value = 3.9e-11

Table S413.  Gene #73: 'Del Peak 25(11q25) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 25(11Q25) MUTATED 64 11 6
DEL PEAK 25(11Q25) WILD-TYPE 130 135 133

Figure S413.  Get High-res Image Gene #73: 'Del Peak 25(11q25) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 25(11q25) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.44e-16 (Chi-square test), Q value = 5.7e-13

Table S414.  Gene #73: 'Del Peak 25(11q25) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 25(11Q25) MUTATED 2 53 2 2 13 9
DEL PEAK 25(11Q25) WILD-TYPE 54 89 72 21 26 136

Figure S414.  Get High-res Image Gene #73: 'Del Peak 25(11q25) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 26(12q23.1) mutation analysis' versus 'CN_CNMF'

P value = 2.41e-20 (Chi-square test), Q value = 2.1e-17

Table S415.  Gene #74: 'Del Peak 26(12q23.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 26(12Q23.1) MUTATED 0 4 42 2 0
DEL PEAK 26(12Q23.1) WILD-TYPE 290 36 97 15 6

Figure S415.  Get High-res Image Gene #74: 'Del Peak 26(12q23.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 26(12q23.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.82e-11 (Fisher's exact test), Q value = 5.7e-08

Table S416.  Gene #74: 'Del Peak 26(12q23.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 26(12Q23.1) MUTATED 31 9 0
DEL PEAK 26(12Q23.1) WILD-TYPE 112 76 149

Figure S416.  Get High-res Image Gene #74: 'Del Peak 26(12q23.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 26(12q23.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.97e-07 (Fisher's exact test), Q value = 2e-04

Table S417.  Gene #74: 'Del Peak 26(12q23.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 26(12Q23.1) MUTATED 21 1 1
DEL PEAK 26(12Q23.1) WILD-TYPE 121 106 112

Figure S417.  Get High-res Image Gene #74: 'Del Peak 26(12q23.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 26(12q23.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.13e-07 (Fisher's exact test), Q value = 6e-05

Table S418.  Gene #74: 'Del Peak 26(12q23.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 26(12Q23.1) MUTATED 0 1 0 22
DEL PEAK 26(12Q23.1) WILD-TYPE 65 91 65 118

Figure S418.  Get High-res Image Gene #74: 'Del Peak 26(12q23.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 26(12q23.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.55e-10 (Fisher's exact test), Q value = 9.8e-08

Table S419.  Gene #74: 'Del Peak 26(12q23.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 26(12Q23.1) MUTATED 39 3 3
DEL PEAK 26(12Q23.1) WILD-TYPE 155 143 136

Figure S419.  Get High-res Image Gene #74: 'Del Peak 26(12q23.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 26(12q23.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.33e-09 (Chi-square test), Q value = 2e-06

Table S420.  Gene #74: 'Del Peak 26(12q23.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 26(12Q23.1) MUTATED 2 32 1 1 6 3
DEL PEAK 26(12Q23.1) WILD-TYPE 54 110 73 22 33 142

Figure S420.  Get High-res Image Gene #74: 'Del Peak 26(12q23.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 27(12q24.33) mutation analysis' versus 'CN_CNMF'

P value = 1.03e-25 (Chi-square test), Q value = 9.3e-23

Table S421.  Gene #75: 'Del Peak 27(12q24.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 27(12Q24.33) MUTATED 1 4 52 2 0
DEL PEAK 27(12Q24.33) WILD-TYPE 289 36 87 15 6

Figure S421.  Get High-res Image Gene #75: 'Del Peak 27(12q24.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 27(12q24.33) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.32e-11 (Fisher's exact test), Q value = 1.5e-08

Table S422.  Gene #75: 'Del Peak 27(12q24.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 27(12Q24.33) MUTATED 40 12 2
DEL PEAK 27(12Q24.33) WILD-TYPE 103 73 147

Figure S422.  Get High-res Image Gene #75: 'Del Peak 27(12q24.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 27(12q24.33) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.07e-11 (Fisher's exact test), Q value = 7.2e-09

Table S423.  Gene #75: 'Del Peak 27(12q24.33) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 27(12Q24.33) MUTATED 29 1 0
DEL PEAK 27(12Q24.33) WILD-TYPE 113 106 113

Figure S423.  Get High-res Image Gene #75: 'Del Peak 27(12q24.33) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 27(12q24.33) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.32e-09 (Fisher's exact test), Q value = 1.4e-06

Table S424.  Gene #75: 'Del Peak 27(12q24.33) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 27(12Q24.33) MUTATED 0 1 1 28
DEL PEAK 27(12Q24.33) WILD-TYPE 65 91 64 112

Figure S424.  Get High-res Image Gene #75: 'Del Peak 27(12q24.33) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 27(12q24.33) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 8.99e-14 (Fisher's exact test), Q value = 6.5e-11

Table S425.  Gene #75: 'Del Peak 27(12q24.33) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 27(12Q24.33) MUTATED 49 3 4
DEL PEAK 27(12Q24.33) WILD-TYPE 145 143 135

Figure S425.  Get High-res Image Gene #75: 'Del Peak 27(12q24.33) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 27(12q24.33) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.51e-11 (Chi-square test), Q value = 2.9e-08

Table S426.  Gene #75: 'Del Peak 27(12q24.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 27(12Q24.33) MUTATED 4 37 0 3 9 3
DEL PEAK 27(12Q24.33) WILD-TYPE 52 105 74 20 30 142

Figure S426.  Get High-res Image Gene #75: 'Del Peak 27(12q24.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 28(13q11) mutation analysis' versus 'CN_CNMF'

P value = 1.94e-29 (Chi-square test), Q value = 1.8e-26

Table S427.  Gene #76: 'Del Peak 28(13q11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 28(13Q11) MUTATED 4 17 62 2 1
DEL PEAK 28(13Q11) WILD-TYPE 286 23 77 15 5

Figure S427.  Get High-res Image Gene #76: 'Del Peak 28(13q11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 28(13q11) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.97e-09 (Fisher's exact test), Q value = 2.3e-06

Table S428.  Gene #76: 'Del Peak 28(13q11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 28(13Q11) MUTATED 47 17 8
DEL PEAK 28(13Q11) WILD-TYPE 96 68 141

Figure S428.  Get High-res Image Gene #76: 'Del Peak 28(13q11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 28(13q11) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.78e-07 (Fisher's exact test), Q value = 0.00024

Table S429.  Gene #76: 'Del Peak 28(13q11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 28(13Q11) MUTATED 35 5 6
DEL PEAK 28(13Q11) WILD-TYPE 107 102 107

Figure S429.  Get High-res Image Gene #76: 'Del Peak 28(13q11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 28(13q11) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.7e-11 (Fisher's exact test), Q value = 1.1e-08

Table S430.  Gene #76: 'Del Peak 28(13q11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 28(13Q11) MUTATED 1 2 3 40
DEL PEAK 28(13Q11) WILD-TYPE 64 90 62 100

Figure S430.  Get High-res Image Gene #76: 'Del Peak 28(13q11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 28(13q11) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.66e-10 (Fisher's exact test), Q value = 1e-07

Table S431.  Gene #76: 'Del Peak 28(13q11) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 28(13Q11) MUTATED 61 13 9
DEL PEAK 28(13Q11) WILD-TYPE 133 133 130

Figure S431.  Get High-res Image Gene #76: 'Del Peak 28(13q11) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 28(13q11) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.21e-10 (Chi-square test), Q value = 4.4e-07

Table S432.  Gene #76: 'Del Peak 28(13q11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 28(13Q11) MUTATED 3 45 4 5 14 12
DEL PEAK 28(13Q11) WILD-TYPE 53 97 70 18 25 133

Figure S432.  Get High-res Image Gene #76: 'Del Peak 28(13q11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 29(13q14.2) mutation analysis' versus 'CN_CNMF'

P value = 2.43e-32 (Chi-square test), Q value = 2.2e-29

Table S433.  Gene #77: 'Del Peak 29(13q14.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 29(13Q14.2) MUTATED 5 19 67 2 1
DEL PEAK 29(13Q14.2) WILD-TYPE 285 21 72 15 5

Figure S433.  Get High-res Image Gene #77: 'Del Peak 29(13q14.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 29(13q14.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.16e-08 (Fisher's exact test), Q value = 2.8e-05

Table S434.  Gene #77: 'Del Peak 29(13q14.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 29(13Q14.2) MUTATED 48 21 11
DEL PEAK 29(13Q14.2) WILD-TYPE 95 64 138

Figure S434.  Get High-res Image Gene #77: 'Del Peak 29(13q14.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 29(13q14.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00058

Table S435.  Gene #77: 'Del Peak 29(13q14.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 29(13Q14.2) MUTATED 35 5 7
DEL PEAK 29(13Q14.2) WILD-TYPE 107 102 106

Figure S435.  Get High-res Image Gene #77: 'Del Peak 29(13q14.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 29(13q14.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.57e-11 (Fisher's exact test), Q value = 6.1e-08

Table S436.  Gene #77: 'Del Peak 29(13q14.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 29(13Q14.2) MUTATED 2 2 3 40
DEL PEAK 29(13Q14.2) WILD-TYPE 63 90 62 100

Figure S436.  Get High-res Image Gene #77: 'Del Peak 29(13q14.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 29(13q14.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.51e-08 (Fisher's exact test), Q value = 1.4e-05

Table S437.  Gene #77: 'Del Peak 29(13q14.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 29(13Q14.2) MUTATED 62 16 13
DEL PEAK 29(13Q14.2) WILD-TYPE 132 130 126

Figure S437.  Get High-res Image Gene #77: 'Del Peak 29(13q14.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 29(13q14.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.96e-07 (Chi-square test), Q value = 2e-04

Table S438.  Gene #77: 'Del Peak 29(13q14.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 29(13Q14.2) MUTATED 6 45 5 5 14 16
DEL PEAK 29(13Q14.2) WILD-TYPE 50 97 69 18 25 129

Figure S438.  Get High-res Image Gene #77: 'Del Peak 29(13q14.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 30(14q13.1) mutation analysis' versus 'CN_CNMF'

P value = 1.28e-22 (Chi-square test), Q value = 1.1e-19

Table S439.  Gene #78: 'Del Peak 30(14q13.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 30(14Q13.1) MUTATED 2 6 50 2 2
DEL PEAK 30(14Q13.1) WILD-TYPE 288 34 89 15 4

Figure S439.  Get High-res Image Gene #78: 'Del Peak 30(14q13.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 30(14q13.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.27e-10 (Fisher's exact test), Q value = 8.1e-08

Table S440.  Gene #78: 'Del Peak 30(14q13.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 30(14Q13.1) MUTATED 41 7 4
DEL PEAK 30(14Q13.1) WILD-TYPE 102 78 145

Figure S440.  Get High-res Image Gene #78: 'Del Peak 30(14q13.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 30(14q13.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.68e-09 (Fisher's exact test), Q value = 4.4e-06

Table S441.  Gene #78: 'Del Peak 30(14q13.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 30(14Q13.1) MUTATED 31 2 3
DEL PEAK 30(14Q13.1) WILD-TYPE 111 105 110

Figure S441.  Get High-res Image Gene #78: 'Del Peak 30(14q13.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 30(14q13.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.63e-10 (Fisher's exact test), Q value = 1e-07

Table S442.  Gene #78: 'Del Peak 30(14q13.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 30(14Q13.1) MUTATED 1 1 1 33
DEL PEAK 30(14Q13.1) WILD-TYPE 64 91 64 107

Figure S442.  Get High-res Image Gene #78: 'Del Peak 30(14q13.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 30(14q13.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.21e-08 (Fisher's exact test), Q value = 6.8e-06

Table S443.  Gene #78: 'Del Peak 30(14q13.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 30(14Q13.1) MUTATED 45 5 9
DEL PEAK 30(14Q13.1) WILD-TYPE 149 141 130

Figure S443.  Get High-res Image Gene #78: 'Del Peak 30(14q13.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 30(14q13.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.06e-10 (Chi-square test), Q value = 6.8e-08

Table S444.  Gene #78: 'Del Peak 30(14q13.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 30(14Q13.1) MUTATED 3 39 1 1 9 6
DEL PEAK 30(14Q13.1) WILD-TYPE 53 103 73 22 30 139

Figure S444.  Get High-res Image Gene #78: 'Del Peak 30(14q13.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 31(15q15.1) mutation analysis' versus 'CN_CNMF'

P value = 1.37e-55 (Chi-square test), Q value = 1.3e-52

Table S445.  Gene #79: 'Del Peak 31(15q15.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 31(15Q15.1) MUTATED 4 17 100 0 3
DEL PEAK 31(15Q15.1) WILD-TYPE 286 23 39 17 3

Figure S445.  Get High-res Image Gene #79: 'Del Peak 31(15q15.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 31(15q15.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.41e-18 (Fisher's exact test), Q value = 1.2e-15

Table S446.  Gene #79: 'Del Peak 31(15q15.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 31(15Q15.1) MUTATED 74 25 9
DEL PEAK 31(15Q15.1) WILD-TYPE 69 60 140

Figure S446.  Get High-res Image Gene #79: 'Del Peak 31(15q15.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 31(15q15.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.76e-17 (Fisher's exact test), Q value = 3e-14

Table S447.  Gene #79: 'Del Peak 31(15q15.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 31(15Q15.1) MUTATED 60 4 8
DEL PEAK 31(15Q15.1) WILD-TYPE 82 103 105

Figure S447.  Get High-res Image Gene #79: 'Del Peak 31(15q15.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 31(15q15.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.64e-22 (Fisher's exact test), Q value = 7.5e-19

Table S448.  Gene #79: 'Del Peak 31(15q15.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 31(15Q15.1) MUTATED 1 1 7 63
DEL PEAK 31(15Q15.1) WILD-TYPE 64 91 58 77

Figure S448.  Get High-res Image Gene #79: 'Del Peak 31(15q15.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 31(15q15.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 5.54e-23 (Fisher's exact test), Q value = 4.9e-20

Table S449.  Gene #79: 'Del Peak 31(15q15.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 31(15Q15.1) MUTATED 96 13 12
DEL PEAK 31(15Q15.1) WILD-TYPE 98 133 127

Figure S449.  Get High-res Image Gene #79: 'Del Peak 31(15q15.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 31(15q15.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.1e-18 (Chi-square test), Q value = 1.7e-15

Table S450.  Gene #79: 'Del Peak 31(15q15.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 31(15Q15.1) MUTATED 8 73 5 5 16 14
DEL PEAK 31(15Q15.1) WILD-TYPE 48 69 69 18 23 131

Figure S450.  Get High-res Image Gene #79: 'Del Peak 31(15q15.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 32(15q23) mutation analysis' versus 'CN_CNMF'

P value = 7.28e-42 (Chi-square test), Q value = 6.8e-39

Table S451.  Gene #80: 'Del Peak 32(15q23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 32(15Q23) MUTATED 3 14 79 0 4
DEL PEAK 32(15Q23) WILD-TYPE 287 26 60 17 2

Figure S451.  Get High-res Image Gene #80: 'Del Peak 32(15q23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 32(15q23) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.94e-18 (Fisher's exact test), Q value = 1.6e-15

Table S452.  Gene #80: 'Del Peak 32(15q23) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 32(15Q23) MUTATED 65 16 5
DEL PEAK 32(15Q23) WILD-TYPE 78 69 144

Figure S452.  Get High-res Image Gene #80: 'Del Peak 32(15q23) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 32(15q23) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.46e-12 (Fisher's exact test), Q value = 1e-09

Table S453.  Gene #80: 'Del Peak 32(15q23) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 32(15Q23) MUTATED 45 2 7
DEL PEAK 32(15Q23) WILD-TYPE 97 105 106

Figure S453.  Get High-res Image Gene #80: 'Del Peak 32(15q23) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 32(15q23) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.7e-15 (Fisher's exact test), Q value = 7.3e-12

Table S454.  Gene #80: 'Del Peak 32(15q23) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 32(15Q23) MUTATED 1 1 5 47
DEL PEAK 32(15Q23) WILD-TYPE 64 91 60 93

Figure S454.  Get High-res Image Gene #80: 'Del Peak 32(15q23) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 32(15q23) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.08e-16 (Fisher's exact test), Q value = 1.6e-13

Table S455.  Gene #80: 'Del Peak 32(15q23) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 32(15Q23) MUTATED 76 11 10
DEL PEAK 32(15Q23) WILD-TYPE 118 135 129

Figure S455.  Get High-res Image Gene #80: 'Del Peak 32(15q23) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 32(15q23) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.35e-15 (Chi-square test), Q value = 1e-12

Table S456.  Gene #80: 'Del Peak 32(15q23) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 32(15Q23) MUTATED 5 61 5 3 13 10
DEL PEAK 32(15Q23) WILD-TYPE 51 81 69 20 26 135

Figure S456.  Get High-res Image Gene #80: 'Del Peak 32(15q23) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 33(16p13.3) mutation analysis' versus 'CN_CNMF'

P value = 1.59e-37 (Chi-square test), Q value = 1.5e-34

Table S457.  Gene #81: 'Del Peak 33(16p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 33(16P13.3) MUTATED 2 8 71 0 0
DEL PEAK 33(16P13.3) WILD-TYPE 288 32 68 17 6

Figure S457.  Get High-res Image Gene #81: 'Del Peak 33(16p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 33(16p13.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.53e-14 (Fisher's exact test), Q value = 1.1e-11

Table S458.  Gene #81: 'Del Peak 33(16p13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 33(16P13.3) MUTATED 51 17 3
DEL PEAK 33(16P13.3) WILD-TYPE 92 68 146

Figure S458.  Get High-res Image Gene #81: 'Del Peak 33(16p13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 33(16p13.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 8.49e-14 (Fisher's exact test), Q value = 6.2e-11

Table S459.  Gene #81: 'Del Peak 33(16p13.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 33(16P13.3) MUTATED 40 3 1
DEL PEAK 33(16P13.3) WILD-TYPE 102 104 112

Figure S459.  Get High-res Image Gene #81: 'Del Peak 33(16p13.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 33(16p13.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.28e-11 (Fisher's exact test), Q value = 8.6e-09

Table S460.  Gene #81: 'Del Peak 33(16p13.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 33(16P13.3) MUTATED 1 2 2 39
DEL PEAK 33(16P13.3) WILD-TYPE 64 90 63 101

Figure S460.  Get High-res Image Gene #81: 'Del Peak 33(16p13.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 33(16p13.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.16e-15 (Fisher's exact test), Q value = 1.7e-12

Table S461.  Gene #81: 'Del Peak 33(16p13.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 33(16P13.3) MUTATED 64 7 7
DEL PEAK 33(16P13.3) WILD-TYPE 130 139 132

Figure S461.  Get High-res Image Gene #81: 'Del Peak 33(16p13.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 33(16p13.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.19e-16 (Chi-square test), Q value = 9.3e-14

Table S462.  Gene #81: 'Del Peak 33(16p13.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 33(16P13.3) MUTATED 3 53 1 2 12 7
DEL PEAK 33(16P13.3) WILD-TYPE 53 89 73 21 27 138

Figure S462.  Get High-res Image Gene #81: 'Del Peak 33(16p13.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 34(16q21) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000451 (Fisher's exact test), Q value = 0.18

Table S463.  Gene #82: 'Del Peak 34(16q21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
DEL PEAK 34(16Q21) MUTATED 1 0 8
DEL PEAK 34(16Q21) WILD-TYPE 19 15 10

Figure S463.  Get High-res Image Gene #82: 'Del Peak 34(16q21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 34(16q21) mutation analysis' versus 'CN_CNMF'

P value = 1.05e-56 (Chi-square test), Q value = 1e-53

Table S464.  Gene #82: 'Del Peak 34(16q21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 34(16Q21) MUTATED 15 14 111 0 0
DEL PEAK 34(16Q21) WILD-TYPE 275 26 28 17 6

Figure S464.  Get High-res Image Gene #82: 'Del Peak 34(16q21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 34(16q21) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.95e-18 (Fisher's exact test), Q value = 2.4e-15

Table S465.  Gene #82: 'Del Peak 34(16q21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 34(16Q21) MUTATED 80 28 13
DEL PEAK 34(16Q21) WILD-TYPE 63 57 136

Figure S465.  Get High-res Image Gene #82: 'Del Peak 34(16q21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 34(16q21) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 9.4e-18 (Fisher's exact test), Q value = 7.7e-15

Table S466.  Gene #82: 'Del Peak 34(16q21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 34(16Q21) MUTATED 70 7 12
DEL PEAK 34(16Q21) WILD-TYPE 72 100 101

Figure S466.  Get High-res Image Gene #82: 'Del Peak 34(16q21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 34(16q21) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.63e-16 (Fisher's exact test), Q value = 5.1e-13

Table S467.  Gene #82: 'Del Peak 34(16q21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 34(16Q21) MUTATED 9 5 7 68
DEL PEAK 34(16Q21) WILD-TYPE 56 87 58 72

Figure S467.  Get High-res Image Gene #82: 'Del Peak 34(16q21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 34(16q21) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.38e-19 (Fisher's exact test), Q value = 3.7e-16

Table S468.  Gene #82: 'Del Peak 34(16q21) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 34(16Q21) MUTATED 99 16 20
DEL PEAK 34(16Q21) WILD-TYPE 95 130 119

Figure S468.  Get High-res Image Gene #82: 'Del Peak 34(16q21) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 34(16q21) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.48e-19 (Chi-square test), Q value = 7.1e-16

Table S469.  Gene #82: 'Del Peak 34(16q21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 34(16Q21) MUTATED 7 81 10 4 15 18
DEL PEAK 34(16Q21) WILD-TYPE 49 61 64 19 24 127

Figure S469.  Get High-res Image Gene #82: 'Del Peak 34(16q21) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 35(16q23.1) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000168 (Fisher's exact test), Q value = 0.07

Table S470.  Gene #83: 'Del Peak 35(16q23.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
DEL PEAK 35(16Q23.1) MUTATED 1 1 10
DEL PEAK 35(16Q23.1) WILD-TYPE 19 14 8

Figure S470.  Get High-res Image Gene #83: 'Del Peak 35(16q23.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 35(16q23.1) mutation analysis' versus 'CN_CNMF'

P value = 2.34e-57 (Chi-square test), Q value = 2.2e-54

Table S471.  Gene #83: 'Del Peak 35(16q23.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 35(16Q23.1) MUTATED 20 14 116 0 0
DEL PEAK 35(16Q23.1) WILD-TYPE 270 26 23 17 6

Figure S471.  Get High-res Image Gene #83: 'Del Peak 35(16q23.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 35(16q23.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.43e-17 (Fisher's exact test), Q value = 2e-14

Table S472.  Gene #83: 'Del Peak 35(16q23.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 35(16Q23.1) MUTATED 81 29 15
DEL PEAK 35(16Q23.1) WILD-TYPE 62 56 134

Figure S472.  Get High-res Image Gene #83: 'Del Peak 35(16q23.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 35(16q23.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.07e-19 (Fisher's exact test), Q value = 5.9e-16

Table S473.  Gene #83: 'Del Peak 35(16q23.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 35(16Q23.1) MUTATED 76 9 13
DEL PEAK 35(16Q23.1) WILD-TYPE 66 98 100

Figure S473.  Get High-res Image Gene #83: 'Del Peak 35(16q23.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 35(16q23.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.83e-14 (Fisher's exact test), Q value = 1.4e-11

Table S474.  Gene #83: 'Del Peak 35(16q23.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 35(16Q23.1) MUTATED 10 7 10 71
DEL PEAK 35(16Q23.1) WILD-TYPE 55 85 55 69

Figure S474.  Get High-res Image Gene #83: 'Del Peak 35(16q23.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 35(16q23.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.52e-19 (Fisher's exact test), Q value = 1.3e-16

Table S475.  Gene #83: 'Del Peak 35(16q23.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 35(16Q23.1) MUTATED 104 18 22
DEL PEAK 35(16Q23.1) WILD-TYPE 90 128 117

Figure S475.  Get High-res Image Gene #83: 'Del Peak 35(16q23.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 35(16q23.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.19e-22 (Chi-square test), Q value = 2.8e-19

Table S476.  Gene #83: 'Del Peak 35(16q23.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 35(16Q23.1) MUTATED 8 88 10 2 16 20
DEL PEAK 35(16Q23.1) WILD-TYPE 48 54 64 21 23 125

Figure S476.  Get High-res Image Gene #83: 'Del Peak 35(16q23.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 36(17p13.3) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000451 (Fisher's exact test), Q value = 0.18

Table S477.  Gene #84: 'Del Peak 36(17p13.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
DEL PEAK 36(17P13.3) MUTATED 1 0 8
DEL PEAK 36(17P13.3) WILD-TYPE 19 15 10

Figure S477.  Get High-res Image Gene #84: 'Del Peak 36(17p13.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 36(17p13.3) mutation analysis' versus 'CN_CNMF'

P value = 7.29e-49 (Chi-square test), Q value = 6.9e-46

Table S478.  Gene #84: 'Del Peak 36(17p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 36(17P13.3) MUTATED 3 14 89 0 0
DEL PEAK 36(17P13.3) WILD-TYPE 287 26 50 17 6

Figure S478.  Get High-res Image Gene #84: 'Del Peak 36(17p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 36(17p13.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.59e-11 (Fisher's exact test), Q value = 1.7e-08

Table S479.  Gene #84: 'Del Peak 36(17p13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 36(17P13.3) MUTATED 57 21 10
DEL PEAK 36(17P13.3) WILD-TYPE 86 64 139

Figure S479.  Get High-res Image Gene #84: 'Del Peak 36(17p13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 36(17p13.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.12e-17 (Fisher's exact test), Q value = 5.6e-14

Table S480.  Gene #84: 'Del Peak 36(17p13.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 36(17P13.3) MUTATED 54 3 5
DEL PEAK 36(17P13.3) WILD-TYPE 88 104 108

Figure S480.  Get High-res Image Gene #84: 'Del Peak 36(17p13.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 36(17p13.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.58e-19 (Fisher's exact test), Q value = 1.3e-16

Table S481.  Gene #84: 'Del Peak 36(17p13.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 36(17P13.3) MUTATED 1 0 6 55
DEL PEAK 36(17P13.3) WILD-TYPE 64 92 59 85

Figure S481.  Get High-res Image Gene #84: 'Del Peak 36(17p13.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 36(17p13.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.25e-14 (Fisher's exact test), Q value = 1.7e-11

Table S482.  Gene #84: 'Del Peak 36(17p13.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 36(17P13.3) MUTATED 76 16 10
DEL PEAK 36(17P13.3) WILD-TYPE 118 130 129

Figure S482.  Get High-res Image Gene #84: 'Del Peak 36(17p13.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 36(17p13.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.41e-11 (Chi-square test), Q value = 2.9e-08

Table S483.  Gene #84: 'Del Peak 36(17p13.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 36(17P13.3) MUTATED 6 58 4 5 12 17
DEL PEAK 36(17P13.3) WILD-TYPE 50 84 70 18 27 128

Figure S483.  Get High-res Image Gene #84: 'Del Peak 36(17p13.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 37(17p12) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000566 (Fisher's exact test), Q value = 0.22

Table S484.  Gene #85: 'Del Peak 37(17p12) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
DEL PEAK 37(17P12) MUTATED 0 9 1 0
DEL PEAK 37(17P12) WILD-TYPE 13 9 13 8

Figure S484.  Get High-res Image Gene #85: 'Del Peak 37(17p12) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 37(17p12) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000109 (Fisher's exact test), Q value = 0.046

Table S485.  Gene #85: 'Del Peak 37(17p12) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
DEL PEAK 37(17P12) MUTATED 1 0 9
DEL PEAK 37(17P12) WILD-TYPE 19 15 9

Figure S485.  Get High-res Image Gene #85: 'Del Peak 37(17p12) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 37(17p12) mutation analysis' versus 'CN_CNMF'

P value = 2.57e-58 (Chi-square test), Q value = 2.5e-55

Table S486.  Gene #85: 'Del Peak 37(17p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 37(17P12) MUTATED 4 13 103 0 1
DEL PEAK 37(17P12) WILD-TYPE 286 27 36 17 5

Figure S486.  Get High-res Image Gene #85: 'Del Peak 37(17p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 37(17p12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.75e-16 (Fisher's exact test), Q value = 6.7e-13

Table S487.  Gene #85: 'Del Peak 37(17p12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 37(17P12) MUTATED 69 23 10
DEL PEAK 37(17P12) WILD-TYPE 74 62 139

Figure S487.  Get High-res Image Gene #85: 'Del Peak 37(17p12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 37(17p12) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.64e-25 (Fisher's exact test), Q value = 2.4e-22

Table S488.  Gene #85: 'Del Peak 37(17p12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 37(17P12) MUTATED 69 3 4
DEL PEAK 37(17P12) WILD-TYPE 73 104 109

Figure S488.  Get High-res Image Gene #85: 'Del Peak 37(17p12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 37(17p12) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.65e-29 (Fisher's exact test), Q value = 5.1e-26

Table S489.  Gene #85: 'Del Peak 37(17p12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 37(17P12) MUTATED 1 0 4 71
DEL PEAK 37(17P12) WILD-TYPE 64 92 61 69

Figure S489.  Get High-res Image Gene #85: 'Del Peak 37(17p12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 37(17p12) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.26e-21 (Fisher's exact test), Q value = 1.9e-18

Table S490.  Gene #85: 'Del Peak 37(17p12) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 37(17P12) MUTATED 91 17 8
DEL PEAK 37(17P12) WILD-TYPE 103 129 131

Figure S490.  Get High-res Image Gene #85: 'Del Peak 37(17p12) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 37(17p12) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.14e-17 (Chi-square test), Q value = 2.5e-14

Table S491.  Gene #85: 'Del Peak 37(17p12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 37(17P12) MUTATED 5 72 3 5 11 20
DEL PEAK 37(17P12) WILD-TYPE 51 70 71 18 28 125

Figure S491.  Get High-res Image Gene #85: 'Del Peak 37(17p12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 38(17p11.2) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000235 (Fisher's exact test), Q value = 0.097

Table S492.  Gene #86: 'Del Peak 38(17p11.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
DEL PEAK 38(17P11.2) MUTATED 0 8 0 0
DEL PEAK 38(17P11.2) WILD-TYPE 13 10 14 8

Figure S492.  Get High-res Image Gene #86: 'Del Peak 38(17p11.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 38(17p11.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 5.66e-05 (Fisher's exact test), Q value = 0.025

Table S493.  Gene #86: 'Del Peak 38(17p11.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
DEL PEAK 38(17P11.2) MUTATED 0 0 8
DEL PEAK 38(17P11.2) WILD-TYPE 20 15 10

Figure S493.  Get High-res Image Gene #86: 'Del Peak 38(17p11.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 38(17p11.2) mutation analysis' versus 'CN_CNMF'

P value = 3.67e-52 (Chi-square test), Q value = 3.5e-49

Table S494.  Gene #86: 'Del Peak 38(17p11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 38(17P11.2) MUTATED 2 12 92 0 0
DEL PEAK 38(17P11.2) WILD-TYPE 288 28 47 17 6

Figure S494.  Get High-res Image Gene #86: 'Del Peak 38(17p11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 38(17p11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.82e-14 (Fisher's exact test), Q value = 6.4e-11

Table S495.  Gene #86: 'Del Peak 38(17p11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 38(17P11.2) MUTATED 62 21 9
DEL PEAK 38(17P11.2) WILD-TYPE 81 64 140

Figure S495.  Get High-res Image Gene #86: 'Del Peak 38(17p11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 38(17p11.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.28e-19 (Fisher's exact test), Q value = 1.1e-16

Table S496.  Gene #86: 'Del Peak 38(17p11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 38(17P11.2) MUTATED 58 3 4
DEL PEAK 38(17P11.2) WILD-TYPE 84 104 109

Figure S496.  Get High-res Image Gene #86: 'Del Peak 38(17p11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 38(17p11.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.19e-24 (Fisher's exact test), Q value = 4.6e-21

Table S497.  Gene #86: 'Del Peak 38(17p11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 38(17P11.2) MUTATED 1 0 3 61
DEL PEAK 38(17P11.2) WILD-TYPE 64 92 62 79

Figure S497.  Get High-res Image Gene #86: 'Del Peak 38(17p11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 38(17p11.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.61e-18 (Fisher's exact test), Q value = 3e-15

Table S498.  Gene #86: 'Del Peak 38(17p11.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 38(17P11.2) MUTATED 80 15 7
DEL PEAK 38(17P11.2) WILD-TYPE 114 131 132

Figure S498.  Get High-res Image Gene #86: 'Del Peak 38(17p11.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 38(17p11.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.96e-13 (Chi-square test), Q value = 6.3e-10

Table S499.  Gene #86: 'Del Peak 38(17p11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 38(17P11.2) MUTATED 5 60 3 5 12 17
DEL PEAK 38(17P11.2) WILD-TYPE 51 82 71 18 27 128

Figure S499.  Get High-res Image Gene #86: 'Del Peak 38(17p11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 39(17q11.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000248 (Fisher's exact test), Q value = 0.1

Table S500.  Gene #87: 'Del Peak 39(17q11.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
DEL PEAK 39(17Q11.2) MUTATED 0 0 7
DEL PEAK 39(17Q11.2) WILD-TYPE 20 15 11

Figure S500.  Get High-res Image Gene #87: 'Del Peak 39(17q11.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 39(17q11.2) mutation analysis' versus 'CN_CNMF'

P value = 6.26e-44 (Chi-square test), Q value = 5.9e-41

Table S501.  Gene #87: 'Del Peak 39(17q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 39(17Q11.2) MUTATED 2 13 81 0 0
DEL PEAK 39(17Q11.2) WILD-TYPE 288 27 58 17 6

Figure S501.  Get High-res Image Gene #87: 'Del Peak 39(17q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 39(17q11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.13e-07 (Fisher's exact test), Q value = 6e-05

Table S502.  Gene #87: 'Del Peak 39(17q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 39(17Q11.2) MUTATED 49 20 12
DEL PEAK 39(17Q11.2) WILD-TYPE 94 65 137

Figure S502.  Get High-res Image Gene #87: 'Del Peak 39(17q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 39(17q11.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.47e-14 (Fisher's exact test), Q value = 1.8e-11

Table S503.  Gene #87: 'Del Peak 39(17q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 39(17Q11.2) MUTATED 50 3 6
DEL PEAK 39(17Q11.2) WILD-TYPE 92 104 107

Figure S503.  Get High-res Image Gene #87: 'Del Peak 39(17q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 39(17q11.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.51e-17 (Fisher's exact test), Q value = 3.6e-14

Table S504.  Gene #87: 'Del Peak 39(17q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 39(17Q11.2) MUTATED 1 1 5 52
DEL PEAK 39(17Q11.2) WILD-TYPE 64 91 60 88

Figure S504.  Get High-res Image Gene #87: 'Del Peak 39(17q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 39(17q11.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.1e-10 (Fisher's exact test), Q value = 7e-08

Table S505.  Gene #87: 'Del Peak 39(17q11.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 39(17Q11.2) MUTATED 65 17 9
DEL PEAK 39(17Q11.2) WILD-TYPE 129 129 130

Figure S505.  Get High-res Image Gene #87: 'Del Peak 39(17q11.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 39(17q11.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.81e-07 (Chi-square test), Q value = 9.5e-05

Table S506.  Gene #87: 'Del Peak 39(17q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 39(17Q11.2) MUTATED 5 46 3 5 13 19
DEL PEAK 39(17Q11.2) WILD-TYPE 51 96 71 18 26 126

Figure S506.  Get High-res Image Gene #87: 'Del Peak 39(17q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 40(17q21.2) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.044

Table S507.  Gene #88: 'Del Peak 40(17q21.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
DEL PEAK 40(17Q21.2) MUTATED 0 9 0 0
DEL PEAK 40(17Q21.2) WILD-TYPE 13 9 14 8

Figure S507.  Get High-res Image Gene #88: 'Del Peak 40(17q21.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 40(17q21.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.21e-05 (Fisher's exact test), Q value = 0.0057

Table S508.  Gene #88: 'Del Peak 40(17q21.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
DEL PEAK 40(17Q21.2) MUTATED 0 0 9
DEL PEAK 40(17Q21.2) WILD-TYPE 20 15 9

Figure S508.  Get High-res Image Gene #88: 'Del Peak 40(17q21.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 40(17q21.2) mutation analysis' versus 'CN_CNMF'

P value = 2.03e-48 (Chi-square test), Q value = 1.9e-45

Table S509.  Gene #88: 'Del Peak 40(17q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 40(17Q21.2) MUTATED 1 12 87 1 0
DEL PEAK 40(17Q21.2) WILD-TYPE 289 28 52 16 6

Figure S509.  Get High-res Image Gene #88: 'Del Peak 40(17q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 40(17q21.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.41e-09 (Fisher's exact test), Q value = 8.4e-07

Table S510.  Gene #88: 'Del Peak 40(17q21.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 40(17Q21.2) MUTATED 53 23 11
DEL PEAK 40(17Q21.2) WILD-TYPE 90 62 138

Figure S510.  Get High-res Image Gene #88: 'Del Peak 40(17q21.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 40(17q21.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.38e-14 (Fisher's exact test), Q value = 1e-11

Table S511.  Gene #88: 'Del Peak 40(17q21.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 40(17Q21.2) MUTATED 49 3 5
DEL PEAK 40(17Q21.2) WILD-TYPE 93 104 108

Figure S511.  Get High-res Image Gene #88: 'Del Peak 40(17q21.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 40(17q21.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.99e-19 (Fisher's exact test), Q value = 6.7e-16

Table S512.  Gene #88: 'Del Peak 40(17q21.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 40(17Q21.2) MUTATED 1 0 4 52
DEL PEAK 40(17Q21.2) WILD-TYPE 64 92 61 88

Figure S512.  Get High-res Image Gene #88: 'Del Peak 40(17q21.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 40(17q21.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.26e-13 (Fisher's exact test), Q value = 9.1e-11

Table S513.  Gene #88: 'Del Peak 40(17q21.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 40(17Q21.2) MUTATED 71 16 8
DEL PEAK 40(17Q21.2) WILD-TYPE 123 130 131

Figure S513.  Get High-res Image Gene #88: 'Del Peak 40(17q21.2) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 40(17q21.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.18e-09 (Chi-square test), Q value = 2.4e-06

Table S514.  Gene #88: 'Del Peak 40(17q21.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 40(17Q21.2) MUTATED 6 52 2 5 11 19
DEL PEAK 40(17Q21.2) WILD-TYPE 50 90 72 18 28 126

Figure S514.  Get High-res Image Gene #88: 'Del Peak 40(17q21.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 41(18q23) mutation analysis' versus 'CN_CNMF'

P value = 6.45e-34 (Chi-square test), Q value = 6e-31

Table S515.  Gene #89: 'Del Peak 41(18q23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 41(18Q23) MUTATED 2 17 68 3 1
DEL PEAK 41(18Q23) WILD-TYPE 288 23 71 14 5

Figure S515.  Get High-res Image Gene #89: 'Del Peak 41(18q23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 41(18q23) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.64e-12 (Fisher's exact test), Q value = 3.2e-09

Table S516.  Gene #89: 'Del Peak 41(18q23) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 41(18Q23) MUTATED 55 15 8
DEL PEAK 41(18Q23) WILD-TYPE 88 70 141

Figure S516.  Get High-res Image Gene #89: 'Del Peak 41(18q23) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 41(18q23) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.88e-11 (Fisher's exact test), Q value = 3.2e-08

Table S517.  Gene #89: 'Del Peak 41(18q23) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 41(18Q23) MUTATED 41 3 5
DEL PEAK 41(18Q23) WILD-TYPE 101 104 108

Figure S517.  Get High-res Image Gene #89: 'Del Peak 41(18q23) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 41(18q23) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.72e-13 (Fisher's exact test), Q value = 2e-10

Table S518.  Gene #89: 'Del Peak 41(18q23) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 41(18Q23) MUTATED 1 1 4 43
DEL PEAK 41(18Q23) WILD-TYPE 64 91 61 97

Figure S518.  Get High-res Image Gene #89: 'Del Peak 41(18q23) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 41(18q23) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.61e-12 (Fisher's exact test), Q value = 2.5e-09

Table S519.  Gene #89: 'Del Peak 41(18q23) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 41(18Q23) MUTATED 66 12 10
DEL PEAK 41(18Q23) WILD-TYPE 128 134 129

Figure S519.  Get High-res Image Gene #89: 'Del Peak 41(18q23) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 41(18q23) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.4e-12 (Chi-square test), Q value = 3e-09

Table S520.  Gene #89: 'Del Peak 41(18q23) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 41(18Q23) MUTATED 6 54 2 4 10 12
DEL PEAK 41(18Q23) WILD-TYPE 50 88 72 19 29 133

Figure S520.  Get High-res Image Gene #89: 'Del Peak 41(18q23) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 42(19p13.3) mutation analysis' versus 'MRNA_CNMF'

P value = 5.64e-07 (Fisher's exact test), Q value = 0.00029

Table S521.  Gene #90: 'Del Peak 42(19p13.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
DEL PEAK 42(19P13.3) MUTATED 0 12 0 0
DEL PEAK 42(19P13.3) WILD-TYPE 13 6 14 8

Figure S521.  Get High-res Image Gene #90: 'Del Peak 42(19p13.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 42(19p13.3) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 4.25e-06 (Fisher's exact test), Q value = 0.002

Table S522.  Gene #90: 'Del Peak 42(19p13.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
DEL PEAK 42(19P13.3) MUTATED 0 1 11
DEL PEAK 42(19P13.3) WILD-TYPE 20 14 7

Figure S522.  Get High-res Image Gene #90: 'Del Peak 42(19p13.3) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 42(19p13.3) mutation analysis' versus 'CN_CNMF'

P value = 6e-78 (Chi-square test), Q value = 5.8e-75

Table S523.  Gene #90: 'Del Peak 42(19p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 42(19P13.3) MUTATED 1 13 124 2 1
DEL PEAK 42(19P13.3) WILD-TYPE 289 27 15 15 5

Figure S523.  Get High-res Image Gene #90: 'Del Peak 42(19p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 42(19p13.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.23e-31 (Fisher's exact test), Q value = 6.6e-28

Table S524.  Gene #90: 'Del Peak 42(19p13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 42(19P13.3) MUTATED 91 24 5
DEL PEAK 42(19P13.3) WILD-TYPE 52 61 144

Figure S524.  Get High-res Image Gene #90: 'Del Peak 42(19p13.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 42(19p13.3) mutation analysis' versus 'RPPA_CNMF'

P value = 8.99e-06 (Chi-square test), Q value = 0.0043

Table S525.  Gene #90: 'Del Peak 42(19p13.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
DEL PEAK 42(19P13.3) MUTATED 6 15 2 0 1 7
DEL PEAK 42(19P13.3) WILD-TYPE 35 22 37 12 40 17

Figure S525.  Get High-res Image Gene #90: 'Del Peak 42(19p13.3) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 42(19p13.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.05e-36 (Fisher's exact test), Q value = 3.8e-33

Table S526.  Gene #90: 'Del Peak 42(19p13.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 42(19P13.3) MUTATED 82 2 2
DEL PEAK 42(19P13.3) WILD-TYPE 60 105 111

Figure S526.  Get High-res Image Gene #90: 'Del Peak 42(19p13.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 42(19p13.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.96e-36 (Fisher's exact test), Q value = 1.8e-33

Table S527.  Gene #90: 'Del Peak 42(19p13.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 42(19P13.3) MUTATED 1 0 3 82
DEL PEAK 42(19P13.3) WILD-TYPE 64 92 62 58

Figure S527.  Get High-res Image Gene #90: 'Del Peak 42(19p13.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 42(19p13.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.12e-34 (Fisher's exact test), Q value = 1e-31

Table S528.  Gene #90: 'Del Peak 42(19p13.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 42(19P13.3) MUTATED 114 11 10
DEL PEAK 42(19P13.3) WILD-TYPE 80 135 129

Figure S528.  Get High-res Image Gene #90: 'Del Peak 42(19p13.3) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 42(19p13.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.01e-34 (Chi-square test), Q value = 2.8e-31

Table S529.  Gene #90: 'Del Peak 42(19p13.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 42(19P13.3) MUTATED 5 95 2 4 15 14
DEL PEAK 42(19P13.3) WILD-TYPE 51 47 72 19 24 131

Figure S529.  Get High-res Image Gene #90: 'Del Peak 42(19p13.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 43(19p12) mutation analysis' versus 'CN_CNMF'

P value = 1.3e-15 (Chi-square test), Q value = 1e-12

Table S530.  Gene #91: 'Del Peak 43(19p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 43(19P12) MUTATED 2 12 33 2 0
DEL PEAK 43(19P12) WILD-TYPE 288 28 106 15 6

Figure S530.  Get High-res Image Gene #91: 'Del Peak 43(19p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 43(19p12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.64e-07 (Fisher's exact test), Q value = 0.00033

Table S531.  Gene #91: 'Del Peak 43(19p12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 43(19P12) MUTATED 29 11 3
DEL PEAK 43(19P12) WILD-TYPE 114 74 146

Figure S531.  Get High-res Image Gene #91: 'Del Peak 43(19p12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 43(19p12) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.14e-05 (Fisher's exact test), Q value = 0.0098

Table S532.  Gene #91: 'Del Peak 43(19p12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 43(19P12) MUTATED 20 1 3
DEL PEAK 43(19P12) WILD-TYPE 122 106 110

Figure S532.  Get High-res Image Gene #91: 'Del Peak 43(19p12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 43(19p12) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.98e-06 (Fisher's exact test), Q value = 0.0019

Table S533.  Gene #91: 'Del Peak 43(19p12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 43(19P12) MUTATED 1 0 2 21
DEL PEAK 43(19P12) WILD-TYPE 64 92 63 119

Figure S533.  Get High-res Image Gene #91: 'Del Peak 43(19p12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 43(19p12) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 8.82e-07 (Fisher's exact test), Q value = 0.00044

Table S534.  Gene #91: 'Del Peak 43(19p12) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 43(19P12) MUTATED 36 5 6
DEL PEAK 43(19P12) WILD-TYPE 158 141 133

Figure S534.  Get High-res Image Gene #91: 'Del Peak 43(19p12) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 43(19p12) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.4e-05 (Chi-square test), Q value = 0.036

Table S535.  Gene #91: 'Del Peak 43(19p12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 43(19P12) MUTATED 5 25 1 2 8 6
DEL PEAK 43(19P12) WILD-TYPE 51 117 73 21 31 139

Figure S535.  Get High-res Image Gene #91: 'Del Peak 43(19p12) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 44(19q13.43) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000451 (Fisher's exact test), Q value = 0.18

Table S536.  Gene #92: 'Del Peak 44(19q13.43) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
DEL PEAK 44(19Q13.43) MUTATED 1 0 8
DEL PEAK 44(19Q13.43) WILD-TYPE 19 15 10

Figure S536.  Get High-res Image Gene #92: 'Del Peak 44(19q13.43) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 44(19q13.43) mutation analysis' versus 'CN_CNMF'

P value = 2.7e-23 (Chi-square test), Q value = 2.4e-20

Table S537.  Gene #92: 'Del Peak 44(19q13.43) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 44(19Q13.43) MUTATED 2 9 49 0 0
DEL PEAK 44(19Q13.43) WILD-TYPE 288 31 90 17 6

Figure S537.  Get High-res Image Gene #92: 'Del Peak 44(19q13.43) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 44(19q13.43) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.56e-09 (Fisher's exact test), Q value = 1.5e-06

Table S538.  Gene #92: 'Del Peak 44(19q13.43) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 44(19Q13.43) MUTATED 34 12 2
DEL PEAK 44(19Q13.43) WILD-TYPE 109 73 147

Figure S538.  Get High-res Image Gene #92: 'Del Peak 44(19q13.43) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 44(19q13.43) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.28e-09 (Fisher's exact test), Q value = 7.7e-07

Table S539.  Gene #92: 'Del Peak 44(19q13.43) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 44(19Q13.43) MUTATED 29 1 2
DEL PEAK 44(19Q13.43) WILD-TYPE 113 106 111

Figure S539.  Get High-res Image Gene #92: 'Del Peak 44(19q13.43) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 44(19q13.43) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.47e-09 (Fisher's exact test), Q value = 1.5e-06

Table S540.  Gene #92: 'Del Peak 44(19q13.43) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 44(19Q13.43) MUTATED 1 0 2 29
DEL PEAK 44(19Q13.43) WILD-TYPE 64 92 63 111

Figure S540.  Get High-res Image Gene #92: 'Del Peak 44(19q13.43) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 44(19q13.43) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.76e-10 (Fisher's exact test), Q value = 1.7e-07

Table S541.  Gene #92: 'Del Peak 44(19q13.43) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 44(19Q13.43) MUTATED 45 5 5
DEL PEAK 44(19Q13.43) WILD-TYPE 149 141 134

Figure S541.  Get High-res Image Gene #92: 'Del Peak 44(19q13.43) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 44(19q13.43) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.04e-11 (Chi-square test), Q value = 2.6e-08

Table S542.  Gene #92: 'Del Peak 44(19q13.43) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 44(19Q13.43) MUTATED 3 38 1 0 8 5
DEL PEAK 44(19Q13.43) WILD-TYPE 53 104 73 23 31 140

Figure S542.  Get High-res Image Gene #92: 'Del Peak 44(19q13.43) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 45(20p12.1) mutation analysis' versus 'CN_CNMF'

P value = 0.000182 (Chi-square test), Q value = 0.075

Table S543.  Gene #93: 'Del Peak 45(20p12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 45(20P12.1) MUTATED 6 6 16 2 0
DEL PEAK 45(20P12.1) WILD-TYPE 284 34 123 15 6

Figure S543.  Get High-res Image Gene #93: 'Del Peak 45(20p12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 46(22q11.1) mutation analysis' versus 'CN_CNMF'

P value = 2.26e-29 (Chi-square test), Q value = 2.1e-26

Table S544.  Gene #94: 'Del Peak 46(22q11.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 46(22Q11.1) MUTATED 3 15 61 1 1
DEL PEAK 46(22Q11.1) WILD-TYPE 287 25 78 16 5

Figure S544.  Get High-res Image Gene #94: 'Del Peak 46(22q11.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 46(22q11.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000115 (Fisher's exact test), Q value = 0.048

Table S545.  Gene #94: 'Del Peak 46(22q11.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 46(22Q11.1) MUTATED 39 18 13
DEL PEAK 46(22Q11.1) WILD-TYPE 104 67 136

Figure S545.  Get High-res Image Gene #94: 'Del Peak 46(22q11.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 46(22q11.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.25e-07 (Fisher's exact test), Q value = 6.6e-05

Table S546.  Gene #94: 'Del Peak 46(22q11.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 46(22Q11.1) MUTATED 34 4 5
DEL PEAK 46(22Q11.1) WILD-TYPE 108 103 108

Figure S546.  Get High-res Image Gene #94: 'Del Peak 46(22q11.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 46(22q11.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.85e-09 (Fisher's exact test), Q value = 1.1e-06

Table S547.  Gene #94: 'Del Peak 46(22q11.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 46(22Q11.1) MUTATED 1 2 4 36
DEL PEAK 46(22Q11.1) WILD-TYPE 64 90 61 104

Figure S547.  Get High-res Image Gene #94: 'Del Peak 46(22q11.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 46(22q11.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.04e-07 (Fisher's exact test), Q value = 0.00016

Table S548.  Gene #94: 'Del Peak 46(22q11.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 46(22Q11.1) MUTATED 53 16 9
DEL PEAK 46(22Q11.1) WILD-TYPE 141 130 130

Figure S548.  Get High-res Image Gene #94: 'Del Peak 46(22q11.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 46(22q11.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000135 (Chi-square test), Q value = 0.057

Table S549.  Gene #94: 'Del Peak 46(22q11.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 46(22Q11.1) MUTATED 5 36 3 5 11 18
DEL PEAK 46(22Q11.1) WILD-TYPE 51 106 71 18 28 127

Figure S549.  Get High-res Image Gene #94: 'Del Peak 46(22q11.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 47(22q12.1) mutation analysis' versus 'CN_CNMF'

P value = 1.54e-31 (Chi-square test), Q value = 1.4e-28

Table S550.  Gene #95: 'Del Peak 47(22q12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 47(22Q12.1) MUTATED 4 13 67 1 2
DEL PEAK 47(22Q12.1) WILD-TYPE 286 27 72 16 4

Figure S550.  Get High-res Image Gene #95: 'Del Peak 47(22q12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 47(22q12.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.1e-05 (Fisher's exact test), Q value = 0.0096

Table S551.  Gene #95: 'Del Peak 47(22q12.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 47(22Q12.1) MUTATED 41 21 13
DEL PEAK 47(22Q12.1) WILD-TYPE 102 64 136

Figure S551.  Get High-res Image Gene #95: 'Del Peak 47(22q12.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 47(22q12.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.79e-09 (Fisher's exact test), Q value = 2.8e-06

Table S552.  Gene #95: 'Del Peak 47(22q12.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 47(22Q12.1) MUTATED 39 4 6
DEL PEAK 47(22Q12.1) WILD-TYPE 103 103 107

Figure S552.  Get High-res Image Gene #95: 'Del Peak 47(22q12.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 47(22q12.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.31e-11 (Fisher's exact test), Q value = 8.7e-09

Table S553.  Gene #95: 'Del Peak 47(22q12.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 47(22Q12.1) MUTATED 2 2 3 42
DEL PEAK 47(22Q12.1) WILD-TYPE 63 90 62 98

Figure S553.  Get High-res Image Gene #95: 'Del Peak 47(22q12.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 47(22q12.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.74e-08 (Fisher's exact test), Q value = 2.6e-05

Table S554.  Gene #95: 'Del Peak 47(22q12.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 47(22Q12.1) MUTATED 57 18 9
DEL PEAK 47(22Q12.1) WILD-TYPE 137 128 130

Figure S554.  Get High-res Image Gene #95: 'Del Peak 47(22q12.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 47(22q12.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.64e-06 (Chi-square test), Q value = 0.0036

Table S555.  Gene #95: 'Del Peak 47(22q12.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 47(22Q12.1) MUTATED 5 42 3 4 11 19
DEL PEAK 47(22Q12.1) WILD-TYPE 51 100 71 19 28 126

Figure S555.  Get High-res Image Gene #95: 'Del Peak 47(22q12.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 48(22q13.31) mutation analysis' versus 'MRNA_CNMF'

P value = 1.8e-05 (Fisher's exact test), Q value = 0.0083

Table S556.  Gene #96: 'Del Peak 48(22q13.31) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
DEL PEAK 48(22Q13.31) MUTATED 0 10 0 0
DEL PEAK 48(22Q13.31) WILD-TYPE 13 8 14 8

Figure S556.  Get High-res Image Gene #96: 'Del Peak 48(22q13.31) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 48(22q13.31) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 2.4e-06 (Fisher's exact test), Q value = 0.0012

Table S557.  Gene #96: 'Del Peak 48(22q13.31) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
DEL PEAK 48(22Q13.31) MUTATED 0 0 10
DEL PEAK 48(22Q13.31) WILD-TYPE 20 15 8

Figure S557.  Get High-res Image Gene #96: 'Del Peak 48(22q13.31) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 48(22q13.31) mutation analysis' versus 'CN_CNMF'

P value = 9.61e-55 (Chi-square test), Q value = 9.2e-52

Table S558.  Gene #96: 'Del Peak 48(22q13.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 48(22Q13.31) MUTATED 4 14 100 1 3
DEL PEAK 48(22Q13.31) WILD-TYPE 286 26 39 16 3

Figure S558.  Get High-res Image Gene #96: 'Del Peak 48(22q13.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 48(22q13.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.79e-13 (Fisher's exact test), Q value = 3.4e-10

Table S559.  Gene #96: 'Del Peak 48(22q13.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 48(22Q13.31) MUTATED 67 24 13
DEL PEAK 48(22Q13.31) WILD-TYPE 76 61 136

Figure S559.  Get High-res Image Gene #96: 'Del Peak 48(22q13.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 48(22q13.31) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 8.88e-20 (Fisher's exact test), Q value = 7.5e-17

Table S560.  Gene #96: 'Del Peak 48(22q13.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 48(22Q13.31) MUTATED 63 4 6
DEL PEAK 48(22Q13.31) WILD-TYPE 79 103 107

Figure S560.  Get High-res Image Gene #96: 'Del Peak 48(22q13.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 48(22q13.31) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.44e-23 (Fisher's exact test), Q value = 1.3e-20

Table S561.  Gene #96: 'Del Peak 48(22q13.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 48(22Q13.31) MUTATED 1 2 4 66
DEL PEAK 48(22Q13.31) WILD-TYPE 64 90 61 74

Figure S561.  Get High-res Image Gene #96: 'Del Peak 48(22q13.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 48(22q13.31) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.1e-17 (Fisher's exact test), Q value = 8.9e-15

Table S562.  Gene #96: 'Del Peak 48(22q13.31) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 48(22Q13.31) MUTATED 87 19 10
DEL PEAK 48(22Q13.31) WILD-TYPE 107 127 129

Figure S562.  Get High-res Image Gene #96: 'Del Peak 48(22q13.31) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 48(22q13.31) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.56e-14 (Chi-square test), Q value = 1.2e-11

Table S563.  Gene #96: 'Del Peak 48(22q13.31) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 48(22Q13.31) MUTATED 7 67 4 4 15 19
DEL PEAK 48(22Q13.31) WILD-TYPE 49 75 70 19 24 126

Figure S563.  Get High-res Image Gene #96: 'Del Peak 48(22q13.31) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 49(22q13.32) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.044

Table S564.  Gene #97: 'Del Peak 49(22q13.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
DEL PEAK 49(22Q13.32) MUTATED 0 9 0 0
DEL PEAK 49(22Q13.32) WILD-TYPE 13 9 14 8

Figure S564.  Get High-res Image Gene #97: 'Del Peak 49(22q13.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 49(22q13.32) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.21e-05 (Fisher's exact test), Q value = 0.0057

Table S565.  Gene #97: 'Del Peak 49(22q13.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
DEL PEAK 49(22Q13.32) MUTATED 0 0 9
DEL PEAK 49(22Q13.32) WILD-TYPE 20 15 9

Figure S565.  Get High-res Image Gene #97: 'Del Peak 49(22q13.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 49(22q13.32) mutation analysis' versus 'CN_CNMF'

P value = 4.93e-53 (Chi-square test), Q value = 4.7e-50

Table S566.  Gene #97: 'Del Peak 49(22q13.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 49(22Q13.32) MUTATED 8 14 102 1 3
DEL PEAK 49(22Q13.32) WILD-TYPE 282 26 37 16 3

Figure S566.  Get High-res Image Gene #97: 'Del Peak 49(22q13.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 49(22q13.32) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.04e-12 (Fisher's exact test), Q value = 1.4e-09

Table S567.  Gene #97: 'Del Peak 49(22q13.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 49(22Q13.32) MUTATED 68 28 15
DEL PEAK 49(22Q13.32) WILD-TYPE 75 57 134

Figure S567.  Get High-res Image Gene #97: 'Del Peak 49(22q13.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 49(22q13.32) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.93e-18 (Fisher's exact test), Q value = 2.4e-15

Table S568.  Gene #97: 'Del Peak 49(22q13.32) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 49(22Q13.32) MUTATED 64 5 8
DEL PEAK 49(22Q13.32) WILD-TYPE 78 102 105

Figure S568.  Get High-res Image Gene #97: 'Del Peak 49(22q13.32) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 49(22q13.32) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.21e-21 (Fisher's exact test), Q value = 1e-18

Table S569.  Gene #97: 'Del Peak 49(22q13.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 49(22Q13.32) MUTATED 2 3 5 67
DEL PEAK 49(22Q13.32) WILD-TYPE 63 89 60 73

Figure S569.  Get High-res Image Gene #97: 'Del Peak 49(22q13.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 49(22q13.32) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.44e-17 (Fisher's exact test), Q value = 3.6e-14

Table S570.  Gene #97: 'Del Peak 49(22q13.32) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 49(22Q13.32) MUTATED 90 21 12
DEL PEAK 49(22Q13.32) WILD-TYPE 104 125 127

Figure S570.  Get High-res Image Gene #97: 'Del Peak 49(22q13.32) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 49(22q13.32) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.8e-14 (Chi-square test), Q value = 2.8e-11

Table S571.  Gene #97: 'Del Peak 49(22q13.32) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 49(22Q13.32) MUTATED 7 69 5 4 16 22
DEL PEAK 49(22Q13.32) WILD-TYPE 49 73 69 19 23 123

Figure S571.  Get High-res Image Gene #97: 'Del Peak 49(22q13.32) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 50(Xp21.1) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000248 (Fisher's exact test), Q value = 0.1

Table S572.  Gene #98: 'Del Peak 50(Xp21.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
DEL PEAK 50(XP21.1) MUTATED 0 0 7
DEL PEAK 50(XP21.1) WILD-TYPE 20 15 11

Figure S572.  Get High-res Image Gene #98: 'Del Peak 50(Xp21.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 50(Xp21.1) mutation analysis' versus 'CN_CNMF'

P value = 4.23e-33 (Chi-square test), Q value = 3.9e-30

Table S573.  Gene #98: 'Del Peak 50(Xp21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 50(XP21.1) MUTATED 2 10 67 2 0
DEL PEAK 50(XP21.1) WILD-TYPE 288 30 72 15 6

Figure S573.  Get High-res Image Gene #98: 'Del Peak 50(Xp21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 50(Xp21.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.85e-09 (Fisher's exact test), Q value = 2.3e-06

Table S574.  Gene #98: 'Del Peak 50(Xp21.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 50(XP21.1) MUTATED 45 15 7
DEL PEAK 50(XP21.1) WILD-TYPE 98 70 142

Figure S574.  Get High-res Image Gene #98: 'Del Peak 50(Xp21.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 50(Xp21.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.34e-10 (Fisher's exact test), Q value = 8.4e-08

Table S575.  Gene #98: 'Del Peak 50(Xp21.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 50(XP21.1) MUTATED 38 2 5
DEL PEAK 50(XP21.1) WILD-TYPE 104 105 108

Figure S575.  Get High-res Image Gene #98: 'Del Peak 50(Xp21.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 50(Xp21.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.09e-11 (Fisher's exact test), Q value = 2e-08

Table S576.  Gene #98: 'Del Peak 50(Xp21.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 50(XP21.1) MUTATED 2 1 3 39
DEL PEAK 50(XP21.1) WILD-TYPE 63 91 62 101

Figure S576.  Get High-res Image Gene #98: 'Del Peak 50(Xp21.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 50(Xp21.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.2e-12 (Fisher's exact test), Q value = 2.2e-09

Table S577.  Gene #98: 'Del Peak 50(Xp21.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 194 146 139
DEL PEAK 50(XP21.1) MUTATED 60 9 8
DEL PEAK 50(XP21.1) WILD-TYPE 134 137 131

Figure S577.  Get High-res Image Gene #98: 'Del Peak 50(Xp21.1) mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Del Peak 50(Xp21.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.81e-10 (Chi-square test), Q value = 2.9e-07

Table S578.  Gene #98: 'Del Peak 50(Xp21.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 142 74 23 39 145
DEL PEAK 50(XP21.1) MUTATED 4 47 3 4 9 10
DEL PEAK 50(XP21.1) WILD-TYPE 52 95 71 19 30 135

Figure S578.  Get High-res Image Gene #98: 'Del Peak 50(Xp21.1) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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 = UCEC-TP.transferedmergedcluster.txt

  • Number of patients = 492

  • Number of copy number variation regions = 98

  • 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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