Correlation between copy number variation genes (focal events) and molecular subtypes
Overview
Introduction

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

Summary

Testing the association between copy number variation 100 focal events and 12 molecular subtypes across 539 patients, 960 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1p35.2 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_1p34.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_1p22.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_1q21.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_1q22 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_1q44 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_2p24.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_2q13 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_3p25.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_3p14.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_3q26.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_3q26.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_4p16.3 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_5p15.33 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_5q35.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_6p24.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_6p22.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_6q25.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_7q31.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_8p11.22 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_8p11.21 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_8q24.21 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_8q24.21 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_9p24.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_9q34.3 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_10q22.2 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_11p11.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_11q13.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_11q14.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_12p12.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_12q13.11 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_12q13.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_13q34 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_14q24.3 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_14q32.33 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_15q26.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_16p11.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_17q11.2 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_17q12 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_17q25.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_18p11.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_18q11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_19p13.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_19q12 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_20p13 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_20q11.21 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_20q13.12 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_20q13.33 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_22q12.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_xp11.23 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_xq28 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_1p36.21 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_1p36.11 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_2p25.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_2q22.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_2q37.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_3p14.2 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3q13.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_4p16.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_4p15.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_4q22.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_4q34.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_5q12.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_6q26 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_7p22.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_7q11.22 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_7q31.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_7q36.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_8p23.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_8p21.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_9p23 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_9q21.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_9q34.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_10q23.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_11p15.5 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_11q14.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_11q25 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_12q23.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_12q24.33 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_13q11 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_13q14.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_14q13.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_15q15.1 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_15q23 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_16p13.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_16q21 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_16q22.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_16q23.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_17p13.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_17p11.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_17q11.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_17q21.31 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_18q21.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_18q23 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_19p13.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_19p12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_19q13.43 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_20p12.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_22q13.32 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_xp21.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 100 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 960 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
amp 3q26 2 175 (32%) 364 9e-05
(0.000158) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00018
(0.000305) 		0.00778
(0.011) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05)
amp 3q26 2 164 (30%) 375 0.00029
(0.000483) 		2e-05
(3.7e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00049
(0.000795) 		0.0154
(0.0207) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05)
amp 8q24 21 215 (40%) 324 0.00288
(0.00426) 		0.00599
(0.00858) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00751
(0.0106) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05)
amp 19p13 2 99 (18%) 440 0.00359
(0.00525) 		0.00012
(0.000208) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0195
(0.026) 		0.00038
(0.000626) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05)
amp 19q12 121 (22%) 418 0.00485
(0.00703) 		4e-05
(7.12e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00475
(0.00689) 		0.00145
(0.00223) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05)
del 5q12 1 111 (21%) 428 0.0134
(0.0183) 		0.0092
(0.0128) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00027
(0.000452) 		0.014
(0.0189) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05)
del 7p22 3 72 (13%) 467 0.00014
(0.00024) 		0.00162
(0.00247) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00744
(0.0106) 		0.0217
(0.0287) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0001
(0.000174) 		3e-05
(5.43e-05)
del 8p23 2 119 (22%) 420 0.002
(0.00303) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0444
(0.0559) 		0.0163
(0.0219) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05)
del 8p21 2 117 (22%) 422 0.00218
(0.00328) 		2e-05
(3.7e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0203
(0.027) 		0.00174
(0.00265) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05)
del 19p13 3 154 (29%) 385 1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		4e-05
(7.12e-05) 		0.0117
(0.0161) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05)
amp 1p34 2 73 (14%) 466 0.0128
(0.0174) 		0.00101
(0.00158) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.02
(0.0265) 		0.105
(0.125) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00186
(0.00282) 		1e-05
(1.92e-05)
amp 2q13 119 (22%) 420 0.16
(0.185) 		0.0293
(0.0381) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0024
(0.00359) 		0.0344
(0.0441) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05)
amp 6p24 2 117 (22%) 422 0.00309
(0.00456) 		0.00075
(0.00119) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0001
(0.000174) 		0.218
(0.245) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		3e-05
(5.43e-05) 		4e-05
(7.12e-05)
amp 8p11 21 162 (30%) 377 0.0105
(0.0146) 		0.0306
(0.0397) 		1e-05
(1.92e-05) 		0.00309
(0.00456) 		0.00105
(0.00164) 		0.0517
(0.0643) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		3e-05
(5.43e-05) 		1e-05
(1.92e-05) 		5e-05
(8.88e-05) 		0.00208
(0.00314)
amp 8q24 21 209 (39%) 330 0.0123
(0.0168) 		0.0738
(0.0897) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		4e-05
(7.12e-05) 		0.0255
(0.0333) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		2e-05
(3.7e-05) 		1e-05
(1.92e-05)
amp 11p11 2 51 (9%) 488 0.00214
(0.00323) 		0.0072
(0.0102) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0285
(0.0372) 		0.0799
(0.0966) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0232
(0.0305) 		0.0412
(0.0522)
amp 17q25 1 105 (19%) 434 1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00557
(0.008) 		0.107
(0.128) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		6e-05
(0.000106)
amp 20q11 21 152 (28%) 387 0.00054
(0.000872) 		2e-05
(3.7e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00044
(0.00072) 		0.108
(0.128) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05)
amp 20q13 12 152 (28%) 387 0.0134
(0.0183) 		0.0102
(0.0141) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00531
(0.00764) 		0.332
(0.364) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05)
amp 20q13 33 153 (28%) 386 0.00883
(0.0123) 		0.00159
(0.00242) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0453
(0.057) 		0.61
(0.645) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05)
del 1p36 21 71 (13%) 468 0.0237
(0.0311) 		0.00176
(0.00267) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00492
(0.00712) 		0.27
(0.299) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00119
(0.00184) 		0.00016
(0.000273)
del 2q22 1 48 (9%) 491 0.0385
(0.049) 		0.00067
(0.00107) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0564
(0.0697) 		0.0114
(0.0157) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00099
(0.00155) 		0.00103
(0.00161)
del 4p16 3 94 (17%) 445 0.013
(0.0177) 		0.00114
(0.00177) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00421
(0.00613) 		0.409
(0.442) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		8e-05
(0.000141) 		3e-05
(5.43e-05)
del 4p15 2 98 (18%) 441 0.0136
(0.0184) 		0.0095
(0.0132) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00789
(0.0111) 		0.496
(0.531) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05)
del 4q22 1 106 (20%) 433 0.00365
(0.00533) 		0.00017
(0.000289) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0145
(0.0196) 		0.226
(0.253) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05)
del 9q21 2 129 (24%) 410 4e-05
(7.12e-05) 		2e-05
(3.7e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00029
(0.000483) 		0.699
(0.729) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00034
(0.00056) 		2e-05
(3.7e-05)
del 9q34 2 132 (24%) 407 1e-05
(1.92e-05) 		4e-05
(7.12e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00048
(0.000782) 		0.342
(0.373) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00012
(0.000208) 		1e-05
(1.92e-05)
del 16p13 3 92 (17%) 447 0.0127
(0.0174) 		0.0102
(0.0141) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0635
(0.0779) 		0.0474
(0.0594) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05)
del 16q23 1 166 (31%) 373 0.00267
(0.00398) 		0.00025
(0.000419) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0363
(0.0463) 		0.9
(0.919) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05)
del 17p13 3 122 (23%) 417 0.00078
(0.00124) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00127
(0.00196) 		0.479
(0.513) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		3e-05
(5.43e-05) 		4e-05
(7.12e-05)
del 17p11 2 128 (24%) 411 0.00083
(0.00131) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00349
(0.00511) 		0.143
(0.166) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		2e-05
(3.7e-05) 		1e-05
(1.92e-05)
del 17q11 2 105 (19%) 434 0.00057
(0.000918) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0192
(0.0257) 		0.822
(0.846) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00336
(0.00494) 		0.00315
(0.00464)
del 17q21 31 114 (21%) 425 1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0046
(0.00668) 		0.395
(0.428) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00014
(0.00024) 		0.001
(0.00157)
del 22q13 32 141 (26%) 398 3e-05
(5.43e-05) 		3e-05
(5.43e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00126
(0.00195) 		0.132
(0.155) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		2e-05
(3.7e-05) 		1e-05
(1.92e-05)
del xp21 1 88 (16%) 451 0.00062
(0.000993) 		0.00112
(0.00175) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00245
(0.00366) 		0.822
(0.846) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00015
(0.000257) 		1e-05
(1.92e-05)
amp 1p35 2 56 (10%) 483 0.0511
(0.0637) 		0.00032
(0.00053) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00074
(0.00118) 		0.14
(0.163) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0351
(0.0449) 		0.00014
(0.00024)
amp 1p22 3 96 (18%) 443 0.0197
(0.0262) 		0.0154
(0.0207) 		1e-05
(1.92e-05) 		0.00054
(0.000872) 		0.896
(0.917) 		0.848
(0.872) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00032
(0.00053) 		1e-05
(1.92e-05)
amp 1q21 3 242 (45%) 297 0.0141
(0.0191) 		0.00585
(0.00839) 		1e-05
(1.92e-05) 		0.00025
(0.000419) 		0.415
(0.448) 		0.301
(0.332) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00433
(0.0063) 		2e-05
(3.7e-05)
amp 4p16 3 53 (10%) 486 0.0509
(0.0635) 		0.00797
(0.0112) 		1e-05
(1.92e-05) 		2e-05
(3.7e-05) 		0.0902
(0.108) 		0.0012
(0.00186) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00148
(0.00227) 		0.00045
(0.000736)
amp 9p24 2 65 (12%) 474 0.13
(0.152) 		0.087
(0.105) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00154
(0.00235) 		0.00846
(0.0118) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00019
(0.000321) 		0.00021
(0.000354)
amp 16p11 2 66 (12%) 473 0.00831
(0.0117) 		0.0051
(0.00736) 		1e-05
(1.92e-05) 		2e-05
(3.7e-05) 		0.062
(0.0762) 		0.098
(0.117) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00281
(0.00417) 		0.00048
(0.000782)
amp 17q11 2 71 (13%) 468 0.152
(0.176) 		0.0495
(0.0619) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00761
(0.0108) 		0.068
(0.0829) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		2e-05
(3.7e-05)
amp 17q12 75 (14%) 464 0.106
(0.126) 		0.00223
(0.00335) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00577
(0.00828) 		0.0541
(0.0669) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		9e-05
(0.000158) 		1e-05
(1.92e-05)
del 1p36 11 83 (15%) 456 0.0508
(0.0634) 		0.00719
(0.0102) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0228
(0.0299) 		0.616
(0.65) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00104
(0.00162) 		1e-05
(1.92e-05)
del 3p14 2 79 (15%) 460 0.051
(0.0636) 		0.00747
(0.0106) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00322
(0.00474) 		0.0728
(0.0886) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00034
(0.00056) 		1e-05
(1.92e-05)
del 4q34 3 130 (24%) 409 0.00396
(0.00577) 		0.00013
(0.000224) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0632
(0.0776) 		0.572
(0.606) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05)
del 7q11 22 41 (8%) 498 1e-05
(1.92e-05) 		2e-05
(3.7e-05) 		0.0383
(0.0488) 		0.0156
(0.0209) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0074
(0.0105) 		0.00129
(0.00199)
del 7q36 1 63 (12%) 476 0.334
(0.365) 		0.0793
(0.0959) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0113
(0.0156) 		0.00349
(0.00511) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0001
(0.000174) 		2e-05
(3.7e-05)
del 9p23 79 (15%) 460 0.38
(0.413) 		0.0304
(0.0394) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0173
(0.0231) 		0.397
(0.429) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0217
(0.0287) 		0.00654
(0.00934)
del 12q23 1 56 (10%) 483 1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0362
(0.0462) 		0.0221
(0.0292) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0001
(0.000174) 		1e-05
(1.92e-05)
del 12q24 33 66 (12%) 473 1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0422
(0.0533) 		0.0388
(0.0493) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		4e-05
(7.12e-05) 		1e-05
(1.92e-05)
del 14q13 1 73 (14%) 466 0.00832
(0.0117) 		0.00505
(0.00729) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0601
(0.074) 		0.178
(0.203) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0009
(0.00142) 		1e-05
(1.92e-05)
del 15q15 1 140 (26%) 399 0.0516
(0.0642) 		0.011
(0.0152) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00273
(0.00406) 		0.291
(0.322) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05)
del 15q23 115 (21%) 424 0.00199
(0.00302) 		0.00043
(0.000705) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.117
(0.138) 		0.741
(0.767) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05)
del 16q21 154 (29%) 385 0.00083
(0.00131) 		3e-05
(5.43e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0907
(0.108) 		0.541
(0.576) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05)
del 16q22 3 158 (29%) 381 0.033
(0.0425) 		0.0102
(0.0141) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.077
(0.0934) 		0.866
(0.888) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		4e-05
(7.12e-05) 		1e-05
(1.92e-05)
del 19q13 43 67 (12%) 472 0.00071
(0.00113) 		3e-05
(5.43e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.105
(0.125) 		0.187
(0.213) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0109
(0.0151) 		1e-05
(1.92e-05)
amp 1q22 256 (47%) 283 0.0227
(0.0299) 		0.0103
(0.0143) 		1e-05
(1.92e-05) 		4e-05
(7.12e-05) 		0.199
(0.224) 		0.201
(0.226) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0524
(0.065) 		0.0001
(0.000174)
amp 2p24 3 121 (22%) 418 0.683
(0.714) 		0.132
(0.155) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0473
(0.0593) 		0.246
(0.274) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00023
(0.000387) 		0.00068
(0.00109)
amp 3p25 1 82 (15%) 457 0.192
(0.217) 		0.0523
(0.0649) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0334
(0.0429) 		0.298
(0.329) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		7e-05
(0.000124) 		0.00115
(0.00179)
amp 5p15 33 89 (17%) 450 0.233
(0.26) 		0.0435
(0.0548) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.293
(0.323) 		0.449
(0.483) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05)
amp 6p22 3 107 (20%) 432 0.187
(0.213) 		0.115
(0.136) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.022
(0.029) 		0.645
(0.677) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05)
amp 9q34 3 39 (7%) 500 0.241
(0.269) 		0.0148
(0.02) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.329
(0.361) 		0.693
(0.723) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		2e-05
(3.7e-05) 		1e-05
(1.92e-05) 		0.0431
(0.0544) 		0.0028
(0.00416)
amp 11q13 2 74 (14%) 465 0.0023
(0.00345) 		0.00775
(0.011) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0826
(0.0997) 		0.189
(0.214) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		2e-05
(3.7e-05) 		1e-05
(1.92e-05) 		0.0579
(0.0714) 		0.00924
(0.0129)
amp 13q34 58 (11%) 481 0.69
(0.721) 		0.167
(0.193) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.224
(0.251) 		0.0291
(0.0378) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00046
(0.000751) 		3e-05
(5.43e-05)
amp 18p11 31 96 (18%) 443 0.155
(0.18) 		0.0564
(0.0697) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00528
(0.00761) 		0.0876
(0.105) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05)
amp 18q11 2 69 (13%) 470 0.108
(0.128) 		0.181
(0.207) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.179
(0.205) 		0.0226
(0.0298) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05)
amp 20p13 117 (22%) 422 0.153
(0.177) 		0.049
(0.0613) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.122
(0.144) 		0.27
(0.299) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00058
(0.000933) 		1e-05
(1.92e-05)
amp 22q12 2 62 (12%) 477 0.381
(0.413) 		0.195
(0.22) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.114
(0.135) 		0.00493
(0.00713) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05)
del 6q26 46 (9%) 493 0.377
(0.41) 		0.0291
(0.0378) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.714
(0.743) 		0.13
(0.152) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00078
(0.00124) 		6e-05
(0.000106)
del 7q31 1 55 (10%) 484 0.138
(0.161) 		0.168
(0.193) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0604
(0.0743) 		0.0118
(0.0162) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00022
(0.000371) 		0.00049
(0.000795)
del 13q11 98 (18%) 441 0.332
(0.364) 		0.0399
(0.0506) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.189
(0.214) 		0.809
(0.836) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0256
(0.0334) 		0.00688
(0.00982)
del 18q21 2 91 (17%) 448 0.617
(0.65) 		0.251
(0.279) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0427
(0.0539) 		0.725
(0.753) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00202
(0.00305) 		3e-05
(5.43e-05)
del 18q23 98 (18%) 441 0.617
(0.65) 		0.252
(0.281) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0401
(0.0508) 		0.869
(0.89) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00033
(0.000545) 		0.00017
(0.000289)
amp 1q44 218 (40%) 321 0.0308
(0.0398) 		0.0377
(0.0481) 		1e-05
(1.92e-05) 		0.037
(0.0471) 		0.737
(0.763) 		0.107
(0.127) 		0.00155
(0.00237) 		0.00095
(0.0015) 		2e-05
(3.7e-05) 		0.00615
(0.0088) 		0.866
(0.888) 		0.0668
(0.0816)
amp 3p14 1 65 (12%) 474 0.539
(0.574) 		0.514
(0.549) 		1e-05
(1.92e-05) 		0.0003
(0.000499) 		0.0331
(0.0426) 		0.664
(0.695) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		4e-05
(7.12e-05) 		1e-05
(1.92e-05) 		0.00349
(0.00511) 		0.173
(0.198)
amp 5q35 3 57 (11%) 482 0.136
(0.159) 		0.17
(0.195) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.123
(0.144) 		0.933
(0.952) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00061
(0.000979) 		0.0013
(0.002)
amp 6q25 1 88 (16%) 451 0.284
(0.315) 		1
(1.00) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0888
(0.106) 		0.458
(0.491) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		8e-05
(0.000141) 		0.031
(0.04)
amp 7q31 2 93 (17%) 446 0.534
(0.569) 		0.436
(0.47) 		1e-05
(1.92e-05) 		0.00011
(0.000191) 		0.647
(0.679) 		0.495
(0.53) 		0.00031
(0.000515) 		0.00013
(0.000224) 		0.00132
(0.00203) 		0.0112
(0.0154) 		0.0218
(0.0288) 		0.0146
(0.0196)
amp 11q14 1 59 (11%) 480 0.381
(0.413) 		0.196
(0.221) 		1e-05
(1.92e-05) 		2e-05
(3.7e-05) 		0.455
(0.489) 		0.183
(0.209) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		8e-05
(0.000141) 		2e-05
(3.7e-05) 		0.0171
(0.0229) 		0.0237
(0.0311)
amp 12p12 1 93 (17%) 446 0.328
(0.361) 		0.543
(0.577) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.523
(0.558) 		0.989
(1.00) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00041
(0.000673) 		2e-05
(3.7e-05)
amp 12q13 11 87 (16%) 452 0.376
(0.41) 		0.204
(0.23) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.561
(0.595) 		0.66
(0.692) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00115
(0.00179) 		0.0003
(0.000499)
amp 12q13 2 100 (19%) 439 0.181
(0.207) 		0.0868
(0.105) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.334
(0.365) 		0.612
(0.647) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		2e-05
(3.7e-05) 		9e-05
(0.000158)
amp 14q24 3 64 (12%) 475 0.06
(0.0739) 		0.0103
(0.0143) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.054
(0.0669) 		0.269
(0.298) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		3e-05
(5.43e-05) 		1e-05
(1.92e-05) 		0.0648
(0.0793) 		0.0459
(0.0576)
amp 14q32 33 79 (15%) 460 0.434
(0.468) 		0.316
(0.347) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.079
(0.0956) 		0.633
(0.665) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		2e-05
(3.7e-05) 		1e-05
(1.92e-05) 		0.00269
(0.004) 		0.0267
(0.0349)
amp xp11 23 90 (17%) 449 0.354
(0.385) 		0.812
(0.838) 		1e-05
(1.92e-05) 		0.00019
(0.000321) 		0.727
(0.754) 		0.863
(0.886) 		0.00028
(0.000468) 		0.00053
(0.000858) 		0.00016
(0.000273) 		0.00228
(0.00342) 		0.00839
(0.0118) 		0.00955
(0.0133)
amp xq28 93 (17%) 446 0.0853
(0.103) 		0.0264
(0.0345) 		1e-05
(1.92e-05) 		0.0307
(0.0398) 		0.224
(0.251) 		0.73
(0.756) 		0.00082
(0.0013) 		0.00252
(0.00376) 		0.0024
(0.00359) 		0.0128
(0.0175) 		0.0174
(0.0233) 		0.163
(0.187)
del 10q23 31 77 (14%) 462 0.137
(0.16) 		0.167
(0.193) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0697
(0.0849) 		1
(1.00) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00061
(0.000979) 		2e-05
(3.7e-05)
del 11p15 5 106 (20%) 433 0.381
(0.413) 		0.194
(0.219) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.286
(0.316) 		0.0678
(0.0827) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05)
del 11q14 1 70 (13%) 469 1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.502
(0.537) 		0.584
(0.618) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		2e-05
(3.7e-05)
del 11q25 93 (17%) 446 1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.111
(0.132) 		1
(1.00) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05)
del 13q14 2 107 (20%) 432 0.617
(0.65) 		0.065
(0.0795) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0775
(0.0939) 		0.696
(0.726) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.0218
(0.0288) 		0.00291
(0.0043)
del 19p12 58 (11%) 481 1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.354
(0.385) 		0.456
(0.49) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.033
(0.0425) 		3e-05
(5.43e-05)
del 3q13 31 43 (8%) 496 0.618
(0.65) 		0.184
(0.21) 		1e-05
(1.92e-05) 		0.00055
(0.000887) 		0.155
(0.179) 		0.14
(0.163) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		3e-05
(5.43e-05) 		0.0154
(0.0207) 		0.308
(0.34)
amp 15q26 3 38 (7%) 501 1e-05
(1.92e-05) 		0.0089
(0.0124) 		0.0755
(0.0917) 		0.718
(0.746) 		1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.00018
(0.000305) 		0.00013
(0.000224) 		0.122
(0.144) 		0.163
(0.187)
del 2p25 3 26 (5%) 513 1e-05
(1.92e-05) 		0.00014
(0.00024) 		0.266
(0.295) 		0.0924
(0.11) 		5e-05
(8.88e-05) 		0.00016
(0.000273) 		0.00149
(0.00228) 		0.00049
(0.000795) 		0.175
(0.2) 		0.143
(0.166)
del 2q37 3 53 (10%) 486 1e-05
(1.92e-05) 		1e-05
(1.92e-05) 		0.247
(0.275) 		0.815
(0.84) 		1e-05
(1.92e-05) 		2e-05
(3.7e-05) 		1e-05
(1.92e-05) 		0.00071
(0.00113) 		0.198
(0.223) 		0.126
(0.148)
del 20p12 1 36 (7%) 503 1
(1.00) 		0.513
(0.548) 		1e-05
(1.92e-05) 		0.0441
(0.0555) 		0.141
(0.164) 		0.556
(0.59) 		0.00023
(0.000387) 		0.00136
(0.00209) 		0.00039
(0.000641) 		0.00098
(0.00154) 		0.0874
(0.105) 		0.188
(0.214)
amp 10q22 2 143 (27%) 396 0.0321
(0.0415) 		0.115
(0.136) 		1e-05
(1.92e-05) 		0.184
(0.21) 		0.31
(0.341) 		0.553
(0.587) 		0.0139
(0.0189) 		0.00284
(0.00421) 		0.854
(0.878) 		0.0131
(0.0178) 		0.977
(0.997) 		0.19
(0.215)
amp 8p11 22 126 (23%) 413 0.0877
(0.105) 		0.226
(0.253) 		1e-05
(1.92e-05) 		1
(1.00) 		0.0356
(0.0456) 		0.422
(0.456) 		0.118
(0.14) 		0.00787
(0.0111) 		0.702
(0.731) 		0.0353
(0.0452) 		0.724
(0.752) 		0.747
(0.773)
'amp_1p35.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.00053

Table S1.  Gene #1: 'amp_1p35.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
AMP PEAK 1(1P35.2) MUTATED 1 5 0 0 0
AMP PEAK 1(1P35.2) WILD-TYPE 13 4 7 7 16

Figure S1.  Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_1p35.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S2.  Gene #1: 'amp_1p35.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 1(1P35.2) MUTATED 54 0 1 0 1
AMP PEAK 1(1P35.2) WILD-TYPE 115 305 18 9 36

Figure S2.  Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1p35.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S3.  Gene #1: 'amp_1p35.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 1(1P35.2) MUTATED 35 4 6
AMP PEAK 1(1P35.2) WILD-TYPE 130 85 165

Figure S3.  Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1p35.2' versus 'RPPA_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.0012

Table S4.  Gene #1: 'amp_1p35.2' versus Molecular Subtype #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 2 10 2 0 0 3
AMP PEAK 1(1P35.2) WILD-TYPE 39 27 37 12 41 21

Figure S4.  Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_1p35.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S5.  Gene #1: 'amp_1p35.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 1(1P35.2) MUTATED 49 0 6
AMP PEAK 1(1P35.2) WILD-TYPE 185 153 144

Figure S5.  Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1p35.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S6.  Gene #1: 'amp_1p35.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 1(1P35.2) MUTATED 36 0 7 0 7 5 0
AMP PEAK 1(1P35.2) WILD-TYPE 87 53 40 65 101 61 75

Figure S6.  Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1p35.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S7.  Gene #1: 'amp_1p35.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 1(1P35.2) MUTATED 42 6 5
AMP PEAK 1(1P35.2) WILD-TYPE 181 144 152

Figure S7.  Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1p35.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S8.  Gene #1: 'amp_1p35.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 1(1P35.2) MUTATED 18 0 5 30
AMP PEAK 1(1P35.2) WILD-TYPE 201 58 132 86

Figure S8.  Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1p35.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0351 (Fisher's exact test), Q value = 0.045

Table S9.  Gene #1: 'amp_1p35.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 1(1P35.2) MUTATED 26 6 10
AMP PEAK 1(1P35.2) WILD-TYPE 146 90 120

Figure S9.  Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1p35.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00024

Table S10.  Gene #1: 'amp_1p35.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 1(1P35.2) MUTATED 28 6 8
AMP PEAK 1(1P35.2) WILD-TYPE 116 109 131

Figure S10.  Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1p34.2' versus 'MRNA_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.017

Table S11.  Gene #2: 'amp_1p34.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
AMP PEAK 2(1P34.2) MUTATED 1 6 0 0
AMP PEAK 2(1P34.2) WILD-TYPE 13 11 12 10

Figure S11.  Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1p34.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00101 (Fisher's exact test), Q value = 0.0016

Table S12.  Gene #2: 'amp_1p34.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
AMP PEAK 2(1P34.2) MUTATED 2 5 0 0 0
AMP PEAK 2(1P34.2) WILD-TYPE 12 4 7 7 16

Figure S12.  Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_1p34.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S13.  Gene #2: 'amp_1p34.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 2(1P34.2) MUTATED 71 0 1 0 1
AMP PEAK 2(1P34.2) WILD-TYPE 98 305 18 9 36

Figure S13.  Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1p34.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S14.  Gene #2: 'amp_1p34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 2(1P34.2) MUTATED 48 10 5
AMP PEAK 2(1P34.2) WILD-TYPE 117 79 166

Figure S14.  Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1p34.2' versus 'RPPA_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.027

Table S15.  Gene #2: 'amp_1p34.2' versus Molecular Subtype #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 2(1P34.2) MUTATED 2 7 2 0 0 3
AMP PEAK 2(1P34.2) WILD-TYPE 39 30 37 12 41 21

Figure S15.  Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_1p34.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S16.  Gene #2: 'amp_1p34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 2(1P34.2) MUTATED 65 1 6
AMP PEAK 2(1P34.2) WILD-TYPE 169 152 144

Figure S16.  Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1p34.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S17.  Gene #2: 'amp_1p34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 2(1P34.2) MUTATED 49 0 10 0 8 5 0
AMP PEAK 2(1P34.2) WILD-TYPE 74 53 37 65 100 61 75

Figure S17.  Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1p34.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S18.  Gene #2: 'amp_1p34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 2(1P34.2) MUTATED 61 6 4
AMP PEAK 2(1P34.2) WILD-TYPE 162 144 153

Figure S18.  Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1p34.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S19.  Gene #2: 'amp_1p34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 2(1P34.2) MUTATED 23 0 4 44
AMP PEAK 2(1P34.2) WILD-TYPE 196 58 133 72

Figure S19.  Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1p34.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00186 (Fisher's exact test), Q value = 0.0028

Table S20.  Gene #2: 'amp_1p34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 2(1P34.2) MUTATED 38 10 11
AMP PEAK 2(1P34.2) WILD-TYPE 134 86 119

Figure S20.  Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1p34.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S21.  Gene #2: 'amp_1p34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 2(1P34.2) MUTATED 39 5 15
AMP PEAK 2(1P34.2) WILD-TYPE 105 110 124

Figure S21.  Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1p22.3' versus 'MRNA_CNMF'

P value = 0.0197 (Fisher's exact test), Q value = 0.026

Table S22.  Gene #3: 'amp_1p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
AMP PEAK 3(1P22.3) MUTATED 5 5 0 0
AMP PEAK 3(1P22.3) WILD-TYPE 9 12 12 10

Figure S22.  Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1p22.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0154 (Fisher's exact test), Q value = 0.021

Table S23.  Gene #3: 'amp_1p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
AMP PEAK 3(1P22.3) MUTATED 2 4 1 3 0
AMP PEAK 3(1P22.3) WILD-TYPE 12 5 6 4 16

Figure S23.  Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_1p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S24.  Gene #3: 'amp_1p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 3(1P22.3) MUTATED 53 30 2 7 4
AMP PEAK 3(1P22.3) WILD-TYPE 116 275 17 2 33

Figure S24.  Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1p22.3' versus 'METHLYATION_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.00087

Table S25.  Gene #3: 'amp_1p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 3(1P22.3) MUTATED 44 8 24
AMP PEAK 3(1P22.3) WILD-TYPE 121 81 147

Figure S25.  Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1p22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S26.  Gene #3: 'amp_1p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 3(1P22.3) MUTATED 60 27 8
AMP PEAK 3(1P22.3) WILD-TYPE 174 126 142

Figure S26.  Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1p22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S27.  Gene #3: 'amp_1p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 3(1P22.3) MUTATED 42 7 8 18 13 4 3
AMP PEAK 3(1P22.3) WILD-TYPE 81 46 39 47 95 62 72

Figure S27.  Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1p22.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S28.  Gene #3: 'amp_1p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 3(1P22.3) MUTATED 52 36 7
AMP PEAK 3(1P22.3) WILD-TYPE 171 114 150

Figure S28.  Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1p22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S29.  Gene #3: 'amp_1p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 3(1P22.3) MUTATED 42 8 10 35
AMP PEAK 3(1P22.3) WILD-TYPE 177 50 127 81

Figure S29.  Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1p22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.00053

Table S30.  Gene #3: 'amp_1p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 3(1P22.3) MUTATED 48 13 14
AMP PEAK 3(1P22.3) WILD-TYPE 124 83 116

Figure S30.  Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S31.  Gene #3: 'amp_1p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 3(1P22.3) MUTATED 46 8 21
AMP PEAK 3(1P22.3) WILD-TYPE 98 107 118

Figure S31.  Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q21.3' versus 'MRNA_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.019

Table S32.  Gene #4: 'amp_1q21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
AMP PEAK 4(1Q21.3) MUTATED 11 12 5 2
AMP PEAK 4(1Q21.3) WILD-TYPE 3 5 7 8

Figure S32.  Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1q21.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00585 (Fisher's exact test), Q value = 0.0084

Table S33.  Gene #4: 'amp_1q21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
AMP PEAK 4(1Q21.3) MUTATED 9 7 6 5 3
AMP PEAK 4(1Q21.3) WILD-TYPE 5 2 1 2 13

Figure S33.  Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S34.  Gene #4: 'amp_1q21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 4(1Q21.3) MUTATED 105 90 13 9 25
AMP PEAK 4(1Q21.3) WILD-TYPE 64 215 6 0 12

Figure S34.  Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.00042

Table S35.  Gene #4: 'amp_1q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 4(1Q21.3) MUTATED 92 31 62
AMP PEAK 4(1Q21.3) WILD-TYPE 73 58 109

Figure S35.  Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S36.  Gene #4: 'amp_1q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 4(1Q21.3) MUTATED 128 72 42
AMP PEAK 4(1Q21.3) WILD-TYPE 106 81 108

Figure S36.  Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S37.  Gene #4: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 4(1Q21.3) MUTATED 81 28 22 32 40 18 21
AMP PEAK 4(1Q21.3) WILD-TYPE 42 25 25 33 68 48 54

Figure S37.  Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S38.  Gene #4: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 4(1Q21.3) MUTATED 113 83 43
AMP PEAK 4(1Q21.3) WILD-TYPE 110 67 114

Figure S38.  Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S39.  Gene #4: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 4(1Q21.3) MUTATED 94 28 43 74
AMP PEAK 4(1Q21.3) WILD-TYPE 125 30 94 42

Figure S39.  Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00433 (Fisher's exact test), Q value = 0.0063

Table S40.  Gene #4: 'amp_1q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 4(1Q21.3) MUTATED 94 40 47
AMP PEAK 4(1Q21.3) WILD-TYPE 78 56 83

Figure S40.  Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.7e-05

Table S41.  Gene #4: 'amp_1q21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 4(1Q21.3) MUTATED 88 37 56
AMP PEAK 4(1Q21.3) WILD-TYPE 56 78 83

Figure S41.  Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q22' versus 'MRNA_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.03

Table S42.  Gene #5: 'amp_1q22' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
AMP PEAK 5(1Q22) MUTATED 11 11 5 2
AMP PEAK 5(1Q22) WILD-TYPE 3 6 7 8

Figure S42.  Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1q22' versus 'MRNA_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.014

Table S43.  Gene #5: 'amp_1q22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
AMP PEAK 5(1Q22) MUTATED 9 6 6 5 3
AMP PEAK 5(1Q22) WILD-TYPE 5 3 1 2 13

Figure S43.  Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_1q22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S44.  Gene #5: 'amp_1q22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 5(1Q22) MUTATED 116 93 13 9 25
AMP PEAK 5(1Q22) WILD-TYPE 53 212 6 0 12

Figure S44.  Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q22' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 7.1e-05

Table S45.  Gene #5: 'amp_1q22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 5(1Q22) MUTATED 100 34 63
AMP PEAK 5(1Q22) WILD-TYPE 65 55 108

Figure S45.  Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q22' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S46.  Gene #5: 'amp_1q22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 5(1Q22) MUTATED 137 73 46
AMP PEAK 5(1Q22) WILD-TYPE 97 80 104

Figure S46.  Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S47.  Gene #5: 'amp_1q22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 5(1Q22) MUTATED 88 28 23 33 41 20 23
AMP PEAK 5(1Q22) WILD-TYPE 35 25 24 32 67 46 52

Figure S47.  Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q22' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S48.  Gene #5: 'amp_1q22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 5(1Q22) MUTATED 121 84 48
AMP PEAK 5(1Q22) WILD-TYPE 102 66 109

Figure S48.  Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S49.  Gene #5: 'amp_1q22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 5(1Q22) MUTATED 93 29 48 83
AMP PEAK 5(1Q22) WILD-TYPE 126 29 89 33

Figure S49.  Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00017

Table S50.  Gene #5: 'amp_1q22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 5(1Q22) MUTATED 89 42 62
AMP PEAK 5(1Q22) WILD-TYPE 55 73 77

Figure S50.  Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q44' versus 'MRNA_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.04

Table S51.  Gene #6: 'amp_1q44' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
AMP PEAK 6(1Q44) MUTATED 10 11 4 2
AMP PEAK 6(1Q44) WILD-TYPE 4 6 8 8

Figure S51.  Get High-res Image Gene #6: 'amp_1q44' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1q44' versus 'MRNA_CHIERARCHICAL'

P value = 0.0377 (Fisher's exact test), Q value = 0.048

Table S52.  Gene #6: 'amp_1q44' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
AMP PEAK 6(1Q44) MUTATED 9 5 5 5 3
AMP PEAK 6(1Q44) WILD-TYPE 5 4 2 2 13

Figure S52.  Get High-res Image Gene #6: 'amp_1q44' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_1q44' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S53.  Gene #6: 'amp_1q44' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 6(1Q44) MUTATED 83 92 10 9 24
AMP PEAK 6(1Q44) WILD-TYPE 86 213 9 0 13

Figure S53.  Get High-res Image Gene #6: 'amp_1q44' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q44' versus 'METHLYATION_CNMF'

P value = 0.037 (Fisher's exact test), Q value = 0.047

Table S54.  Gene #6: 'amp_1q44' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 6(1Q44) MUTATED 74 26 61
AMP PEAK 6(1Q44) WILD-TYPE 91 63 110

Figure S54.  Get High-res Image Gene #6: 'amp_1q44' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q44' versus 'MRNASEQ_CNMF'

P value = 0.00155 (Fisher's exact test), Q value = 0.0024

Table S55.  Gene #6: 'amp_1q44' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 6(1Q44) MUTATED 99 75 44
AMP PEAK 6(1Q44) WILD-TYPE 135 78 106

Figure S55.  Get High-res Image Gene #6: 'amp_1q44' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q44' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00095 (Fisher's exact test), Q value = 0.0015

Table S56.  Gene #6: 'amp_1q44' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 6(1Q44) MUTATED 61 29 16 34 37 21 20
AMP PEAK 6(1Q44) WILD-TYPE 62 24 31 31 71 45 55

Figure S56.  Get High-res Image Gene #6: 'amp_1q44' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q44' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.7e-05

Table S57.  Gene #6: 'amp_1q44' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 6(1Q44) MUTATED 87 85 44
AMP PEAK 6(1Q44) WILD-TYPE 136 65 113

Figure S57.  Get High-res Image Gene #6: 'amp_1q44' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q44' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00615 (Fisher's exact test), Q value = 0.0088

Table S58.  Gene #6: 'amp_1q44' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 6(1Q44) MUTATED 85 30 43 58
AMP PEAK 6(1Q44) WILD-TYPE 134 28 94 58

Figure S58.  Get High-res Image Gene #6: 'amp_1q44' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_2p24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S59.  Gene #7: 'amp_2p24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 7(2P24.3) MUTATED 79 14 12 4 12
AMP PEAK 7(2P24.3) WILD-TYPE 90 291 7 5 25

Figure S59.  Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2p24.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S60.  Gene #7: 'amp_2p24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 7(2P24.3) MUTATED 66 11 19
AMP PEAK 7(2P24.3) WILD-TYPE 99 78 152

Figure S60.  Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2p24.3' versus 'RPPA_CNMF'

P value = 0.0473 (Fisher's exact test), Q value = 0.059

Table S61.  Gene #7: 'amp_2p24.3' versus Molecular Subtype #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 7(2P24.3) MUTATED 4 11 3 1 6 7
AMP PEAK 7(2P24.3) WILD-TYPE 37 26 36 11 35 17

Figure S61.  Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_2p24.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S62.  Gene #7: 'amp_2p24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 7(2P24.3) MUTATED 85 19 17
AMP PEAK 7(2P24.3) WILD-TYPE 149 134 133

Figure S62.  Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2p24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S63.  Gene #7: 'amp_2p24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 7(2P24.3) MUTATED 59 7 14 6 19 10 6
AMP PEAK 7(2P24.3) WILD-TYPE 64 46 33 59 89 56 69

Figure S63.  Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_2p24.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S64.  Gene #7: 'amp_2p24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 7(2P24.3) MUTATED 79 21 19
AMP PEAK 7(2P24.3) WILD-TYPE 144 129 138

Figure S64.  Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_2p24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S65.  Gene #7: 'amp_2p24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 7(2P24.3) MUTATED 39 7 18 55
AMP PEAK 7(2P24.3) WILD-TYPE 180 51 119 61

Figure S65.  Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_2p24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00039

Table S66.  Gene #7: 'amp_2p24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 7(2P24.3) MUTATED 56 20 16
AMP PEAK 7(2P24.3) WILD-TYPE 116 76 114

Figure S66.  Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_2p24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00068 (Fisher's exact test), Q value = 0.0011

Table S67.  Gene #7: 'amp_2p24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 7(2P24.3) MUTATED 46 14 32
AMP PEAK 7(2P24.3) WILD-TYPE 98 101 107

Figure S67.  Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_2q13' versus 'MRNA_CHIERARCHICAL'

P value = 0.0293 (Fisher's exact test), Q value = 0.038

Table S68.  Gene #8: 'amp_2q13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
AMP PEAK 8(2Q13) MUTATED 3 5 1 0 1
AMP PEAK 8(2Q13) WILD-TYPE 11 4 6 7 15

Figure S68.  Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_2q13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S69.  Gene #8: 'amp_2q13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 8(2Q13) MUTATED 90 8 9 3 9
AMP PEAK 8(2Q13) WILD-TYPE 79 297 10 6 28

Figure S69.  Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2q13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S70.  Gene #8: 'amp_2q13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 8(2Q13) MUTATED 72 14 10
AMP PEAK 8(2Q13) WILD-TYPE 93 75 161

Figure S70.  Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2q13' versus 'RPPA_CNMF'

P value = 0.0024 (Fisher's exact test), Q value = 0.0036

Table S71.  Gene #8: 'amp_2q13' versus Molecular Subtype #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 8(2Q13) MUTATED 5 12 1 1 4 7
AMP PEAK 8(2Q13) WILD-TYPE 36 25 38 11 37 17

Figure S71.  Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_2q13' versus 'RPPA_CHIERARCHICAL'

P value = 0.0344 (Fisher's exact test), Q value = 0.044

Table S72.  Gene #8: 'amp_2q13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
AMP PEAK 8(2Q13) MUTATED 13 8 3 6
AMP PEAK 8(2Q13) WILD-TYPE 54 59 40 11

Figure S72.  Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_2q13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S73.  Gene #8: 'amp_2q13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 8(2Q13) MUTATED 98 11 9
AMP PEAK 8(2Q13) WILD-TYPE 136 142 141

Figure S73.  Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2q13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S74.  Gene #8: 'amp_2q13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 8(2Q13) MUTATED 73 5 13 2 15 6 4
AMP PEAK 8(2Q13) WILD-TYPE 50 48 34 63 93 60 71

Figure S74.  Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_2q13' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S75.  Gene #8: 'amp_2q13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 8(2Q13) MUTATED 92 16 9
AMP PEAK 8(2Q13) WILD-TYPE 131 134 148

Figure S75.  Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_2q13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S76.  Gene #8: 'amp_2q13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 8(2Q13) MUTATED 37 5 10 65
AMP PEAK 8(2Q13) WILD-TYPE 182 53 127 51

Figure S76.  Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_2q13' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S77.  Gene #8: 'amp_2q13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 8(2Q13) MUTATED 61 22 11
AMP PEAK 8(2Q13) WILD-TYPE 111 74 119

Figure S77.  Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_2q13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S78.  Gene #8: 'amp_2q13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 8(2Q13) MUTATED 51 8 35
AMP PEAK 8(2Q13) WILD-TYPE 93 107 104

Figure S78.  Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3p25.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S79.  Gene #9: 'amp_3p25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 9(3P25.1) MUTATED 62 4 1 3 12
AMP PEAK 9(3P25.1) WILD-TYPE 107 301 18 6 25

Figure S79.  Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3p25.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S80.  Gene #9: 'amp_3p25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 9(3P25.1) MUTATED 44 14 10
AMP PEAK 9(3P25.1) WILD-TYPE 121 75 161

Figure S80.  Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3p25.1' versus 'RPPA_CNMF'

P value = 0.0334 (Fisher's exact test), Q value = 0.043

Table S81.  Gene #9: 'amp_3p25.1' versus Molecular Subtype #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 9(3P25.1) MUTATED 6 7 3 1 0 1
AMP PEAK 9(3P25.1) WILD-TYPE 35 30 36 11 41 23

Figure S81.  Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_3p25.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S82.  Gene #9: 'amp_3p25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 9(3P25.1) MUTATED 66 4 12
AMP PEAK 9(3P25.1) WILD-TYPE 168 149 138

Figure S82.  Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3p25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S83.  Gene #9: 'amp_3p25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 9(3P25.1) MUTATED 41 0 13 4 15 5 4
AMP PEAK 9(3P25.1) WILD-TYPE 82 53 34 61 93 61 71

Figure S83.  Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3p25.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S84.  Gene #9: 'amp_3p25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 9(3P25.1) MUTATED 58 11 11
AMP PEAK 9(3P25.1) WILD-TYPE 165 139 146

Figure S84.  Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3p25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S85.  Gene #9: 'amp_3p25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 9(3P25.1) MUTATED 24 0 13 43
AMP PEAK 9(3P25.1) WILD-TYPE 195 58 124 73

Figure S85.  Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3p25.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00012

Table S86.  Gene #9: 'amp_3p25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 9(3P25.1) MUTATED 40 18 7
AMP PEAK 9(3P25.1) WILD-TYPE 132 78 123

Figure S86.  Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3p25.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00115 (Fisher's exact test), Q value = 0.0018

Table S87.  Gene #9: 'amp_3p25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 9(3P25.1) MUTATED 35 9 21
AMP PEAK 9(3P25.1) WILD-TYPE 109 106 118

Figure S87.  Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3p14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S88.  Gene #10: 'amp_3p14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 10(3P14.1) MUTATED 46 3 1 3 12
AMP PEAK 10(3P14.1) WILD-TYPE 123 302 18 6 25

Figure S88.  Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3p14.1' versus 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 5e-04

Table S89.  Gene #10: 'amp_3p14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 10(3P14.1) MUTATED 35 10 11
AMP PEAK 10(3P14.1) WILD-TYPE 130 79 160

Figure S89.  Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3p14.1' versus 'RPPA_CNMF'

P value = 0.0331 (Fisher's exact test), Q value = 0.043

Table S90.  Gene #10: 'amp_3p14.1' versus Molecular Subtype #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 10(3P14.1) MUTATED 4 6 2 1 0 0
AMP PEAK 10(3P14.1) WILD-TYPE 37 31 37 11 41 24

Figure S90.  Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_3p14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S91.  Gene #10: 'amp_3p14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 10(3P14.1) MUTATED 49 4 12
AMP PEAK 10(3P14.1) WILD-TYPE 185 149 138

Figure S91.  Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3p14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S92.  Gene #10: 'amp_3p14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 10(3P14.1) MUTATED 29 0 9 4 14 4 5
AMP PEAK 10(3P14.1) WILD-TYPE 94 53 38 61 94 62 70

Figure S92.  Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3p14.1' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 7.1e-05

Table S93.  Gene #10: 'amp_3p14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 10(3P14.1) MUTATED 44 10 10
AMP PEAK 10(3P14.1) WILD-TYPE 179 140 147

Figure S93.  Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3p14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S94.  Gene #10: 'amp_3p14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 10(3P14.1) MUTATED 20 0 13 31
AMP PEAK 10(3P14.1) WILD-TYPE 199 58 124 85

Figure S94.  Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3p14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00349 (Fisher's exact test), Q value = 0.0051

Table S95.  Gene #10: 'amp_3p14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 10(3P14.1) MUTATED 28 17 7
AMP PEAK 10(3P14.1) WILD-TYPE 144 79 123

Figure S95.  Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'MRNA_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00016

Table S96.  Gene #11: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
AMP PEAK 11(3Q26.2) MUTATED 1 11 1 0
AMP PEAK 11(3Q26.2) WILD-TYPE 13 6 11 10

Figure S96.  Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S97.  Gene #11: 'amp_3q26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
AMP PEAK 11(3Q26.2) MUTATED 4 8 1 0 0
AMP PEAK 11(3Q26.2) WILD-TYPE 10 1 6 7 16

Figure S97.  Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S98.  Gene #11: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 11(3Q26.2) MUTATED 141 11 3 5 15
AMP PEAK 11(3Q26.2) WILD-TYPE 28 294 16 4 22

Figure S98.  Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S99.  Gene #11: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 11(3Q26.2) MUTATED 102 25 23
AMP PEAK 11(3Q26.2) WILD-TYPE 63 64 148

Figure S99.  Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'RPPA_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00031

Table S100.  Gene #11: 'amp_3q26.2' versus Molecular Subtype #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 S100.  Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_3q26.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00778 (Fisher's exact test), Q value = 0.011

Table S101.  Gene #11: 'amp_3q26.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
AMP PEAK 11(3Q26.2) MUTATED 21 10 3 4
AMP PEAK 11(3Q26.2) WILD-TYPE 46 57 40 13

Figure S101.  Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_3q26.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S102.  Gene #11: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 11(3Q26.2) MUTATED 143 7 24
AMP PEAK 11(3Q26.2) WILD-TYPE 91 146 126

Figure S102.  Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S103.  Gene #11: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 11(3Q26.2) MUTATED 95 0 26 5 26 14 8
AMP PEAK 11(3Q26.2) WILD-TYPE 28 53 21 60 82 52 67

Figure S103.  Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S104.  Gene #11: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 11(3Q26.2) MUTATED 131 19 21
AMP PEAK 11(3Q26.2) WILD-TYPE 92 131 136

Figure S104.  Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S105.  Gene #11: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 11(3Q26.2) MUTATED 61 0 24 86
AMP PEAK 11(3Q26.2) WILD-TYPE 158 58 113 30

Figure S105.  Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S106.  Gene #11: 'amp_3q26.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 11(3Q26.2) MUTATED 85 33 25
AMP PEAK 11(3Q26.2) WILD-TYPE 87 63 105

Figure S106.  Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S107.  Gene #11: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 11(3Q26.2) MUTATED 78 20 45
AMP PEAK 11(3Q26.2) WILD-TYPE 66 95 94

Figure S107.  Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.2' versus 'MRNA_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.00048

Table S108.  Gene #12: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
AMP PEAK 12(3Q26.2) MUTATED 1 10 1 0
AMP PEAK 12(3Q26.2) WILD-TYPE 13 7 11 10

Figure S108.  Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.2' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.7e-05

Table S109.  Gene #12: 'amp_3q26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
AMP PEAK 12(3Q26.2) MUTATED 3 8 1 0 0
AMP PEAK 12(3Q26.2) WILD-TYPE 11 1 6 7 16

Figure S109.  Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S110.  Gene #12: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 12(3Q26.2) MUTATED 135 7 3 5 14
AMP PEAK 12(3Q26.2) WILD-TYPE 34 298 16 4 23

Figure S110.  Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S111.  Gene #12: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 12(3Q26.2) MUTATED 101 20 20
AMP PEAK 12(3Q26.2) WILD-TYPE 64 69 151

Figure S111.  Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'RPPA_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.00079

Table S112.  Gene #12: 'amp_3q26.2' versus Molecular Subtype #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 12(3Q26.2) MUTATED 11 13 4 1 1 7
AMP PEAK 12(3Q26.2) WILD-TYPE 30 24 35 11 40 17

Figure S112.  Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_3q26.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0154 (Fisher's exact test), Q value = 0.021

Table S113.  Gene #12: 'amp_3q26.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
AMP PEAK 12(3Q26.2) MUTATED 19 10 3 5
AMP PEAK 12(3Q26.2) WILD-TYPE 48 57 40 12

Figure S113.  Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_3q26.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S114.  Gene #12: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 12(3Q26.2) MUTATED 136 7 20
AMP PEAK 12(3Q26.2) WILD-TYPE 98 146 130

Figure S114.  Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S115.  Gene #12: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 12(3Q26.2) MUTATED 92 0 24 5 24 11 7
AMP PEAK 12(3Q26.2) WILD-TYPE 31 53 23 60 84 55 68

Figure S115.  Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S116.  Gene #12: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 12(3Q26.2) MUTATED 123 19 18
AMP PEAK 12(3Q26.2) WILD-TYPE 100 131 139

Figure S116.  Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S117.  Gene #12: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 12(3Q26.2) MUTATED 57 0 20 83
AMP PEAK 12(3Q26.2) WILD-TYPE 162 58 117 33

Figure S117.  Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S118.  Gene #12: 'amp_3q26.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 12(3Q26.2) MUTATED 84 28 22
AMP PEAK 12(3Q26.2) WILD-TYPE 88 68 108

Figure S118.  Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S119.  Gene #12: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 12(3Q26.2) MUTATED 77 16 41
AMP PEAK 12(3Q26.2) WILD-TYPE 67 99 98

Figure S119.  Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4p16.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00797 (Fisher's exact test), Q value = 0.011

Table S120.  Gene #13: 'amp_4p16.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
AMP PEAK 13(4P16.3) MUTATED 2 4 0 0 0
AMP PEAK 13(4P16.3) WILD-TYPE 12 5 7 7 16

Figure S120.  Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_4p16.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S121.  Gene #13: 'amp_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 13(4P16.3) MUTATED 50 2 0 0 1
AMP PEAK 13(4P16.3) WILD-TYPE 119 303 19 9 36

Figure S121.  Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_4p16.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.7e-05

Table S122.  Gene #13: 'amp_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 13(4P16.3) MUTATED 30 8 6
AMP PEAK 13(4P16.3) WILD-TYPE 135 81 165

Figure S122.  Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_4p16.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0012 (Fisher's exact test), Q value = 0.0019

Table S123.  Gene #13: 'amp_4p16.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
AMP PEAK 13(4P16.3) MUTATED 10 0 1 1
AMP PEAK 13(4P16.3) WILD-TYPE 57 67 42 16

Figure S123.  Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_4p16.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S124.  Gene #13: 'amp_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 13(4P16.3) MUTATED 49 1 2
AMP PEAK 13(4P16.3) WILD-TYPE 185 152 148

Figure S124.  Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S125.  Gene #13: 'amp_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 13(4P16.3) MUTATED 39 0 3 0 8 1 1
AMP PEAK 13(4P16.3) WILD-TYPE 84 53 44 65 100 65 74

Figure S125.  Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_4p16.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S126.  Gene #13: 'amp_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 13(4P16.3) MUTATED 44 3 4
AMP PEAK 13(4P16.3) WILD-TYPE 179 147 153

Figure S126.  Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S127.  Gene #13: 'amp_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 13(4P16.3) MUTATED 13 0 4 34
AMP PEAK 13(4P16.3) WILD-TYPE 206 58 133 82

Figure S127.  Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00148 (Fisher's exact test), Q value = 0.0023

Table S128.  Gene #13: 'amp_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 13(4P16.3) MUTATED 29 7 6
AMP PEAK 13(4P16.3) WILD-TYPE 143 89 124

Figure S128.  Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.00074

Table S129.  Gene #13: 'amp_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 13(4P16.3) MUTATED 26 4 12
AMP PEAK 13(4P16.3) WILD-TYPE 118 111 127

Figure S129.  Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.0435 (Fisher's exact test), Q value = 0.055

Table S130.  Gene #14: 'amp_5p15.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
AMP PEAK 14(5P15.33) MUTATED 2 4 1 1 0
AMP PEAK 14(5P15.33) WILD-TYPE 12 5 6 6 16

Figure S130.  Get High-res Image Gene #14: 'amp_5p15.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S131.  Gene #14: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 14(5P15.33) MUTATED 80 4 4 1 0
AMP PEAK 14(5P15.33) WILD-TYPE 89 301 15 8 37

Figure S131.  Get High-res Image Gene #14: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S132.  Gene #14: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 14(5P15.33) MUTATED 58 11 7
AMP PEAK 14(5P15.33) WILD-TYPE 107 78 164

Figure S132.  Get High-res Image Gene #14: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S133.  Gene #14: 'amp_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 14(5P15.33) MUTATED 79 5 4
AMP PEAK 14(5P15.33) WILD-TYPE 155 148 146

Figure S133.  Get High-res Image Gene #14: 'amp_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S134.  Gene #14: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 14(5P15.33) MUTATED 54 3 13 2 11 5 0
AMP PEAK 14(5P15.33) WILD-TYPE 69 50 34 63 97 61 75

Figure S134.  Get High-res Image Gene #14: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S135.  Gene #14: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 14(5P15.33) MUTATED 71 12 5
AMP PEAK 14(5P15.33) WILD-TYPE 152 138 152

Figure S135.  Get High-res Image Gene #14: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S136.  Gene #14: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 14(5P15.33) MUTATED 28 3 5 52
AMP PEAK 14(5P15.33) WILD-TYPE 191 55 132 64

Figure S136.  Get High-res Image Gene #14: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S137.  Gene #14: 'amp_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 14(5P15.33) MUTATED 54 15 6
AMP PEAK 14(5P15.33) WILD-TYPE 118 81 124

Figure S137.  Get High-res Image Gene #14: 'amp_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S138.  Gene #14: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 14(5P15.33) MUTATED 47 4 24
AMP PEAK 14(5P15.33) WILD-TYPE 97 111 115

Figure S138.  Get High-res Image Gene #14: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5q35.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S139.  Gene #15: 'amp_5q35.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 15(5Q35.3) MUTATED 51 1 4 1 0
AMP PEAK 15(5Q35.3) WILD-TYPE 118 304 15 8 37

Figure S139.  Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5q35.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S140.  Gene #15: 'amp_5q35.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 15(5Q35.3) MUTATED 35 9 6
AMP PEAK 15(5Q35.3) WILD-TYPE 130 80 165

Figure S140.  Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_5q35.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S141.  Gene #15: 'amp_5q35.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 15(5Q35.3) MUTATED 50 4 3
AMP PEAK 15(5Q35.3) WILD-TYPE 184 149 147

Figure S141.  Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5q35.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S142.  Gene #15: 'amp_5q35.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 15(5Q35.3) MUTATED 35 2 9 1 7 2 1
AMP PEAK 15(5Q35.3) WILD-TYPE 88 51 38 64 101 64 74

Figure S142.  Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5q35.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S143.  Gene #15: 'amp_5q35.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 15(5Q35.3) MUTATED 44 8 4
AMP PEAK 15(5Q35.3) WILD-TYPE 179 142 153

Figure S143.  Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_5q35.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S144.  Gene #15: 'amp_5q35.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 15(5Q35.3) MUTATED 18 3 4 31
AMP PEAK 15(5Q35.3) WILD-TYPE 201 55 133 85

Figure S144.  Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5q35.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.00098

Table S145.  Gene #15: 'amp_5q35.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 15(5Q35.3) MUTATED 30 13 5
AMP PEAK 15(5Q35.3) WILD-TYPE 142 83 125

Figure S145.  Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_5q35.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0013 (Fisher's exact test), Q value = 0.002

Table S146.  Gene #15: 'amp_5q35.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 15(5Q35.3) MUTATED 27 5 16
AMP PEAK 15(5Q35.3) WILD-TYPE 117 110 123

Figure S146.  Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6p24.2' versus 'MRNA_CNMF'

P value = 0.00309 (Fisher's exact test), Q value = 0.0046

Table S147.  Gene #16: 'amp_6p24.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
AMP PEAK 16(6P24.2) MUTATED 1 9 2 0
AMP PEAK 16(6P24.2) WILD-TYPE 13 8 10 10

Figure S147.  Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_6p24.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00075 (Fisher's exact test), Q value = 0.0012

Table S148.  Gene #16: 'amp_6p24.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
AMP PEAK 16(6P24.2) MUTATED 3 7 0 0 2
AMP PEAK 16(6P24.2) WILD-TYPE 11 2 7 7 14

Figure S148.  Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_6p24.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S149.  Gene #16: 'amp_6p24.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 16(6P24.2) MUTATED 95 8 1 1 12
AMP PEAK 16(6P24.2) WILD-TYPE 74 297 18 8 25

Figure S149.  Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p24.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S150.  Gene #16: 'amp_6p24.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 16(6P24.2) MUTATED 73 15 12
AMP PEAK 16(6P24.2) WILD-TYPE 92 74 159

Figure S150.  Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6p24.2' versus 'RPPA_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00017

Table S151.  Gene #16: 'amp_6p24.2' versus Molecular Subtype #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 5 13 2 1 0 3
AMP PEAK 16(6P24.2) WILD-TYPE 36 24 37 11 41 21

Figure S151.  Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_6p24.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S152.  Gene #16: 'amp_6p24.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 16(6P24.2) MUTATED 97 5 15
AMP PEAK 16(6P24.2) WILD-TYPE 137 148 135

Figure S152.  Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6p24.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S153.  Gene #16: 'amp_6p24.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 16(6P24.2) MUTATED 68 0 11 5 19 8 6
AMP PEAK 16(6P24.2) WILD-TYPE 55 53 36 60 89 58 69

Figure S153.  Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6p24.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S154.  Gene #16: 'amp_6p24.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 16(6P24.2) MUTATED 84 18 12
AMP PEAK 16(6P24.2) WILD-TYPE 139 132 145

Figure S154.  Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_6p24.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S155.  Gene #16: 'amp_6p24.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 16(6P24.2) MUTATED 42 0 12 60
AMP PEAK 16(6P24.2) WILD-TYPE 177 58 125 56

Figure S155.  Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6p24.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 5.4e-05

Table S156.  Gene #16: 'amp_6p24.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 16(6P24.2) MUTATED 58 24 14
AMP PEAK 16(6P24.2) WILD-TYPE 114 72 116

Figure S156.  Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_6p24.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 7.1e-05

Table S157.  Gene #16: 'amp_6p24.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 16(6P24.2) MUTATED 51 13 32
AMP PEAK 16(6P24.2) WILD-TYPE 93 102 107

Figure S157.  Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S158.  Gene #17: 'amp_6p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 17(6P22.3) MUTATED 86 7 1 1 12
AMP PEAK 17(6P22.3) WILD-TYPE 83 298 18 8 25

Figure S158.  Get High-res Image Gene #17: 'amp_6p22.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S159.  Gene #17: 'amp_6p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 17(6P22.3) MUTATED 70 15 10
AMP PEAK 17(6P22.3) WILD-TYPE 95 74 161

Figure S159.  Get High-res Image Gene #17: 'amp_6p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6p22.3' versus 'RPPA_CNMF'

P value = 0.022 (Fisher's exact test), Q value = 0.029

Table S160.  Gene #17: 'amp_6p22.3' versus Molecular Subtype #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 17(6P22.3) MUTATED 4 8 2 1 0 2
AMP PEAK 17(6P22.3) WILD-TYPE 37 29 37 11 41 22

Figure S160.  Get High-res Image Gene #17: 'amp_6p22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_6p22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S161.  Gene #17: 'amp_6p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 17(6P22.3) MUTATED 88 5 14
AMP PEAK 17(6P22.3) WILD-TYPE 146 148 136

Figure S161.  Get High-res Image Gene #17: 'amp_6p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6p22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S162.  Gene #17: 'amp_6p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 17(6P22.3) MUTATED 61 0 12 5 16 7 6
AMP PEAK 17(6P22.3) WILD-TYPE 62 53 35 60 92 59 69

Figure S162.  Get High-res Image Gene #17: 'amp_6p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6p22.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S163.  Gene #17: 'amp_6p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 17(6P22.3) MUTATED 80 15 11
AMP PEAK 17(6P22.3) WILD-TYPE 143 135 146

Figure S163.  Get High-res Image Gene #17: 'amp_6p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_6p22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S164.  Gene #17: 'amp_6p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 17(6P22.3) MUTATED 39 0 11 56
AMP PEAK 17(6P22.3) WILD-TYPE 180 58 126 60

Figure S164.  Get High-res Image Gene #17: 'amp_6p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6p22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S165.  Gene #17: 'amp_6p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 17(6P22.3) MUTATED 58 21 12
AMP PEAK 17(6P22.3) WILD-TYPE 114 75 118

Figure S165.  Get High-res Image Gene #17: 'amp_6p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_6p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S166.  Gene #17: 'amp_6p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 17(6P22.3) MUTATED 50 11 30
AMP PEAK 17(6P22.3) WILD-TYPE 94 104 109

Figure S166.  Get High-res Image Gene #17: 'amp_6p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q25.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S167.  Gene #18: 'amp_6q25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 18(6Q25.1) MUTATED 65 7 3 2 11
AMP PEAK 18(6Q25.1) WILD-TYPE 104 298 16 7 26

Figure S167.  Get High-res Image Gene #18: 'amp_6q25.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6q25.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S168.  Gene #18: 'amp_6q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 18(6Q25.1) MUTATED 55 10 14
AMP PEAK 18(6Q25.1) WILD-TYPE 110 79 157

Figure S168.  Get High-res Image Gene #18: 'amp_6q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6q25.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S169.  Gene #18: 'amp_6q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 18(6Q25.1) MUTATED 63 7 17
AMP PEAK 18(6Q25.1) WILD-TYPE 171 146 133

Figure S169.  Get High-res Image Gene #18: 'amp_6q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6q25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S170.  Gene #18: 'amp_6q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 18(6Q25.1) MUTATED 40 0 9 6 15 11 6
AMP PEAK 18(6Q25.1) WILD-TYPE 83 53 38 59 93 55 69

Figure S170.  Get High-res Image Gene #18: 'amp_6q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6q25.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S171.  Gene #18: 'amp_6q25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 18(6Q25.1) MUTATED 57 19 12
AMP PEAK 18(6Q25.1) WILD-TYPE 166 131 145

Figure S171.  Get High-res Image Gene #18: 'amp_6q25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_6q25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S172.  Gene #18: 'amp_6q25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 18(6Q25.1) MUTATED 39 1 12 36
AMP PEAK 18(6Q25.1) WILD-TYPE 180 57 125 80

Figure S172.  Get High-res Image Gene #18: 'amp_6q25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6q25.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00014

Table S173.  Gene #18: 'amp_6q25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 18(6Q25.1) MUTATED 48 17 11
AMP PEAK 18(6Q25.1) WILD-TYPE 124 79 119

Figure S173.  Get High-res Image Gene #18: 'amp_6q25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_6q25.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.031 (Fisher's exact test), Q value = 0.04

Table S174.  Gene #18: 'amp_6q25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 18(6Q25.1) MUTATED 37 15 24
AMP PEAK 18(6Q25.1) WILD-TYPE 107 100 115

Figure S174.  Get High-res Image Gene #18: 'amp_6q25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S175.  Gene #19: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 19(7Q31.2) MUTATED 53 15 13 2 10
AMP PEAK 19(7Q31.2) WILD-TYPE 116 290 6 7 27

Figure S175.  Get High-res Image Gene #19: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q31.2' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00019

Table S176.  Gene #19: 'amp_7q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 19(7Q31.2) MUTATED 45 8 21
AMP PEAK 19(7Q31.2) WILD-TYPE 120 81 150

Figure S176.  Get High-res Image Gene #19: 'amp_7q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.00051

Table S177.  Gene #19: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 19(7Q31.2) MUTATED 58 17 18
AMP PEAK 19(7Q31.2) WILD-TYPE 176 136 132

Figure S177.  Get High-res Image Gene #19: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00022

Table S178.  Gene #19: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 19(7Q31.2) MUTATED 34 8 13 2 19 10 7
AMP PEAK 19(7Q31.2) WILD-TYPE 89 45 34 63 89 56 68

Figure S178.  Get High-res Image Gene #19: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_CNMF'

P value = 0.00132 (Fisher's exact test), Q value = 0.002

Table S179.  Gene #19: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 19(7Q31.2) MUTATED 54 23 16
AMP PEAK 19(7Q31.2) WILD-TYPE 169 127 141

Figure S179.  Get High-res Image Gene #19: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.015

Table S180.  Gene #19: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 19(7Q31.2) MUTATED 35 10 16 32
AMP PEAK 19(7Q31.2) WILD-TYPE 184 48 121 84

Figure S180.  Get High-res Image Gene #19: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.029

Table S181.  Gene #19: 'amp_7q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 19(7Q31.2) MUTATED 39 19 14
AMP PEAK 19(7Q31.2) WILD-TYPE 133 77 116

Figure S181.  Get High-res Image Gene #19: 'amp_7q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0146 (Fisher's exact test), Q value = 0.02

Table S182.  Gene #19: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 19(7Q31.2) MUTATED 35 12 25
AMP PEAK 19(7Q31.2) WILD-TYPE 109 103 114

Figure S182.  Get High-res Image Gene #19: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S183.  Gene #20: 'amp_8p11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 20(8P11.22) MUTATED 50 29 8 2 37
AMP PEAK 20(8P11.22) WILD-TYPE 119 276 11 7 0

Figure S183.  Get High-res Image Gene #20: 'amp_8p11.22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.22' versus 'RPPA_CNMF'

P value = 0.0356 (Fisher's exact test), Q value = 0.046

Table S184.  Gene #20: 'amp_8p11.22' versus Molecular Subtype #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(8P11.22) MUTATED 8 11 5 2 2 7
AMP PEAK 20(8P11.22) WILD-TYPE 33 26 34 10 39 17

Figure S184.  Get High-res Image Gene #20: 'amp_8p11.22' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8p11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00787 (Fisher's exact test), Q value = 0.011

Table S185.  Gene #20: 'amp_8p11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 20(8P11.22) MUTATED 30 9 9 9 36 22 11
AMP PEAK 20(8P11.22) WILD-TYPE 93 44 38 56 72 44 64

Figure S185.  Get High-res Image Gene #20: 'amp_8p11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0353 (Fisher's exact test), Q value = 0.045

Table S186.  Gene #20: 'amp_8p11.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 20(8P11.22) MUTATED 61 6 32 25
AMP PEAK 20(8P11.22) WILD-TYPE 158 52 105 91

Figure S186.  Get High-res Image Gene #20: 'amp_8p11.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MRNA_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.015

Table S187.  Gene #21: 'amp_8p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
AMP PEAK 21(8P11.21) MUTATED 1 8 2 0
AMP PEAK 21(8P11.21) WILD-TYPE 13 9 10 10

Figure S187.  Get High-res Image Gene #21: 'amp_8p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8p11.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.0306 (Fisher's exact test), Q value = 0.04

Table S188.  Gene #21: 'amp_8p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
AMP PEAK 21(8P11.21) MUTATED 4 5 0 0 2
AMP PEAK 21(8P11.21) WILD-TYPE 10 4 7 7 14

Figure S188.  Get High-res Image Gene #21: 'amp_8p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S189.  Gene #21: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 21(8P11.21) MUTATED 87 29 8 2 36
AMP PEAK 21(8P11.21) WILD-TYPE 82 276 11 7 1

Figure S189.  Get High-res Image Gene #21: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'METHLYATION_CNMF'

P value = 0.00309 (Fisher's exact test), Q value = 0.0046

Table S190.  Gene #21: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 21(8P11.21) MUTATED 69 27 42
AMP PEAK 21(8P11.21) WILD-TYPE 96 62 129

Figure S190.  Get High-res Image Gene #21: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8p11.21' versus 'RPPA_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.0016

Table S191.  Gene #21: 'amp_8p11.21' versus Molecular Subtype #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(8P11.21) MUTATED 8 12 5 2 2 11
AMP PEAK 21(8P11.21) WILD-TYPE 33 25 34 10 39 13

Figure S191.  Get High-res Image Gene #21: 'amp_8p11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S192.  Gene #21: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 21(8P11.21) MUTATED 100 29 33
AMP PEAK 21(8P11.21) WILD-TYPE 134 124 117

Figure S192.  Get High-res Image Gene #21: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S193.  Gene #21: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 21(8P11.21) MUTATED 59 9 19 10 34 20 11
AMP PEAK 21(8P11.21) WILD-TYPE 64 44 28 55 74 46 64

Figure S193.  Get High-res Image Gene #21: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 5.4e-05

Table S194.  Gene #21: 'amp_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 21(8P11.21) MUTATED 91 35 33
AMP PEAK 21(8P11.21) WILD-TYPE 132 115 124

Figure S194.  Get High-res Image Gene #21: 'amp_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S195.  Gene #21: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 21(8P11.21) MUTATED 62 6 31 60
AMP PEAK 21(8P11.21) WILD-TYPE 157 52 106 56

Figure S195.  Get High-res Image Gene #21: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 8.9e-05

Table S196.  Gene #21: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 21(8P11.21) MUTATED 75 30 26
AMP PEAK 21(8P11.21) WILD-TYPE 97 66 104

Figure S196.  Get High-res Image Gene #21: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00208 (Fisher's exact test), Q value = 0.0031

Table S197.  Gene #21: 'amp_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 21(8P11.21) MUTATED 62 26 43
AMP PEAK 21(8P11.21) WILD-TYPE 82 89 96

Figure S197.  Get High-res Image Gene #21: 'amp_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNA_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.017

Table S198.  Gene #22: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
AMP PEAK 22(8Q24.21) MUTATED 1 8 3 0
AMP PEAK 22(8Q24.21) WILD-TYPE 13 9 9 10

Figure S198.  Get High-res Image Gene #22: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S199.  Gene #22: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 22(8Q24.21) MUTATED 126 35 8 3 37
AMP PEAK 22(8Q24.21) WILD-TYPE 43 270 11 6 0

Figure S199.  Get High-res Image Gene #22: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S200.  Gene #22: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 22(8Q24.21) MUTATED 101 32 48
AMP PEAK 22(8Q24.21) WILD-TYPE 64 57 123

Figure S200.  Get High-res Image Gene #22: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 7.1e-05

Table S201.  Gene #22: 'amp_8q24.21' versus Molecular Subtype #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 22(8Q24.21) MUTATED 12 14 8 2 2 14
AMP PEAK 22(8Q24.21) WILD-TYPE 29 23 31 10 39 10

Figure S201.  Get High-res Image Gene #22: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8q24.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.0255 (Fisher's exact test), Q value = 0.033

Table S202.  Gene #22: 'amp_8q24.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
AMP PEAK 22(8Q24.21) MUTATED 19 18 6 9
AMP PEAK 22(8Q24.21) WILD-TYPE 48 49 37 8

Figure S202.  Get High-res Image Gene #22: 'amp_8q24.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S203.  Gene #22: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 22(8Q24.21) MUTATED 140 29 39
AMP PEAK 22(8Q24.21) WILD-TYPE 94 124 111

Figure S203.  Get High-res Image Gene #22: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S204.  Gene #22: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 22(8Q24.21) MUTATED 86 10 27 8 39 26 12
AMP PEAK 22(8Q24.21) WILD-TYPE 37 43 20 57 69 40 63

Figure S204.  Get High-res Image Gene #22: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S205.  Gene #22: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 22(8Q24.21) MUTATED 130 38 38
AMP PEAK 22(8Q24.21) WILD-TYPE 93 112 119

Figure S205.  Get High-res Image Gene #22: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S206.  Gene #22: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 22(8Q24.21) MUTATED 83 6 35 82
AMP PEAK 22(8Q24.21) WILD-TYPE 136 52 102 34

Figure S206.  Get High-res Image Gene #22: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.7e-05

Table S207.  Gene #22: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 22(8Q24.21) MUTATED 95 41 33
AMP PEAK 22(8Q24.21) WILD-TYPE 77 55 97

Figure S207.  Get High-res Image Gene #22: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S208.  Gene #22: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 22(8Q24.21) MUTATED 83 30 56
AMP PEAK 22(8Q24.21) WILD-TYPE 61 85 83

Figure S208.  Get High-res Image Gene #22: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNA_CNMF'

P value = 0.00288 (Fisher's exact test), Q value = 0.0043

Table S209.  Gene #23: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
AMP PEAK 23(8Q24.21) MUTATED 1 9 2 0
AMP PEAK 23(8Q24.21) WILD-TYPE 13 8 10 10

Figure S209.  Get High-res Image Gene #23: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8q24.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.00599 (Fisher's exact test), Q value = 0.0086

Table S210.  Gene #23: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
AMP PEAK 23(8Q24.21) MUTATED 4 6 0 0 2
AMP PEAK 23(8Q24.21) WILD-TYPE 10 3 7 7 14

Figure S210.  Get High-res Image Gene #23: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S211.  Gene #23: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 23(8Q24.21) MUTATED 127 40 8 3 37
AMP PEAK 23(8Q24.21) WILD-TYPE 42 265 11 6 0

Figure S211.  Get High-res Image Gene #23: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S212.  Gene #23: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 23(8Q24.21) MUTATED 101 31 53
AMP PEAK 23(8Q24.21) WILD-TYPE 64 58 118

Figure S212.  Get High-res Image Gene #23: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S213.  Gene #23: 'amp_8q24.21' versus Molecular Subtype #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 23(8Q24.21) MUTATED 12 17 7 2 2 16
AMP PEAK 23(8Q24.21) WILD-TYPE 29 20 32 10 39 8

Figure S213.  Get High-res Image Gene #23: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8q24.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.00751 (Fisher's exact test), Q value = 0.011

Table S214.  Gene #23: 'amp_8q24.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
AMP PEAK 23(8Q24.21) MUTATED 23 16 7 10
AMP PEAK 23(8Q24.21) WILD-TYPE 44 51 36 7

Figure S214.  Get High-res Image Gene #23: 'amp_8q24.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S215.  Gene #23: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 23(8Q24.21) MUTATED 142 32 40
AMP PEAK 23(8Q24.21) WILD-TYPE 92 121 110

Figure S215.  Get High-res Image Gene #23: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S216.  Gene #23: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 23(8Q24.21) MUTATED 91 11 25 9 39 25 14
AMP PEAK 23(8Q24.21) WILD-TYPE 32 42 22 56 69 41 61

Figure S216.  Get High-res Image Gene #23: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S217.  Gene #23: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 23(8Q24.21) MUTATED 135 38 38
AMP PEAK 23(8Q24.21) WILD-TYPE 88 112 119

Figure S217.  Get High-res Image Gene #23: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S218.  Gene #23: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 23(8Q24.21) MUTATED 83 7 38 83
AMP PEAK 23(8Q24.21) WILD-TYPE 136 51 99 33

Figure S218.  Get High-res Image Gene #23: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S219.  Gene #23: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 23(8Q24.21) MUTATED 98 40 36
AMP PEAK 23(8Q24.21) WILD-TYPE 74 56 94

Figure S219.  Get High-res Image Gene #23: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S220.  Gene #23: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 23(8Q24.21) MUTATED 88 32 54
AMP PEAK 23(8Q24.21) WILD-TYPE 56 83 85

Figure S220.  Get High-res Image Gene #23: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9p24.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S221.  Gene #24: 'amp_9p24.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 24(9P24.2) MUTATED 59 4 1 0 1
AMP PEAK 24(9P24.2) WILD-TYPE 110 301 18 9 36

Figure S221.  Get High-res Image Gene #24: 'amp_9p24.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_9p24.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S222.  Gene #24: 'amp_9p24.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 24(9P24.2) MUTATED 42 7 5
AMP PEAK 24(9P24.2) WILD-TYPE 123 82 166

Figure S222.  Get High-res Image Gene #24: 'amp_9p24.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_9p24.2' versus 'RPPA_CNMF'

P value = 0.00154 (Fisher's exact test), Q value = 0.0024

Table S223.  Gene #24: 'amp_9p24.2' versus Molecular Subtype #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 24(9P24.2) MUTATED 5 9 0 0 1 1
AMP PEAK 24(9P24.2) WILD-TYPE 36 28 39 12 40 23

Figure S223.  Get High-res Image Gene #24: 'amp_9p24.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_9p24.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00846 (Fisher's exact test), Q value = 0.012

Table S224.  Gene #24: 'amp_9p24.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
AMP PEAK 24(9P24.2) MUTATED 12 2 2 0
AMP PEAK 24(9P24.2) WILD-TYPE 55 65 41 17

Figure S224.  Get High-res Image Gene #24: 'amp_9p24.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_9p24.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S225.  Gene #24: 'amp_9p24.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 24(9P24.2) MUTATED 57 3 5
AMP PEAK 24(9P24.2) WILD-TYPE 177 150 145

Figure S225.  Get High-res Image Gene #24: 'amp_9p24.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_9p24.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S226.  Gene #24: 'amp_9p24.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 24(9P24.2) MUTATED 41 0 6 2 12 4 0
AMP PEAK 24(9P24.2) WILD-TYPE 82 53 41 63 96 62 75

Figure S226.  Get High-res Image Gene #24: 'amp_9p24.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_9p24.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S227.  Gene #24: 'amp_9p24.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 24(9P24.2) MUTATED 54 8 2
AMP PEAK 24(9P24.2) WILD-TYPE 169 142 155

Figure S227.  Get High-res Image Gene #24: 'amp_9p24.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_9p24.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S228.  Gene #24: 'amp_9p24.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 24(9P24.2) MUTATED 21 2 3 38
AMP PEAK 24(9P24.2) WILD-TYPE 198 56 134 78

Figure S228.  Get High-res Image Gene #24: 'amp_9p24.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_9p24.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00032

Table S229.  Gene #24: 'amp_9p24.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 24(9P24.2) MUTATED 35 11 6
AMP PEAK 24(9P24.2) WILD-TYPE 137 85 124

Figure S229.  Get High-res Image Gene #24: 'amp_9p24.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_9p24.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00035

Table S230.  Gene #24: 'amp_9p24.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 24(9P24.2) MUTATED 31 5 16
AMP PEAK 24(9P24.2) WILD-TYPE 113 110 123

Figure S230.  Get High-res Image Gene #24: 'amp_9p24.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9q34.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0148 (Fisher's exact test), Q value = 0.02

Table S231.  Gene #25: 'amp_9q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
AMP PEAK 25(9Q34.3) MUTATED 0 4 1 0 1
AMP PEAK 25(9Q34.3) WILD-TYPE 14 5 6 7 15

Figure S231.  Get High-res Image Gene #25: 'amp_9q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_9q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S232.  Gene #25: 'amp_9q34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 25(9Q34.3) MUTATED 35 2 0 1 1
AMP PEAK 25(9Q34.3) WILD-TYPE 134 303 19 8 36

Figure S232.  Get High-res Image Gene #25: 'amp_9q34.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_9q34.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S233.  Gene #25: 'amp_9q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 25(9Q34.3) MUTATED 22 6 2
AMP PEAK 25(9Q34.3) WILD-TYPE 143 83 169

Figure S233.  Get High-res Image Gene #25: 'amp_9q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_9q34.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S234.  Gene #25: 'amp_9q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 25(9Q34.3) MUTATED 34 3 1
AMP PEAK 25(9Q34.3) WILD-TYPE 200 150 149

Figure S234.  Get High-res Image Gene #25: 'amp_9q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_9q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S235.  Gene #25: 'amp_9q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 25(9Q34.3) MUTATED 30 2 2 0 2 2 0
AMP PEAK 25(9Q34.3) WILD-TYPE 93 51 45 65 106 64 75

Figure S235.  Get High-res Image Gene #25: 'amp_9q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_9q34.3' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.7e-05

Table S236.  Gene #25: 'amp_9q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 25(9Q34.3) MUTATED 28 4 3
AMP PEAK 25(9Q34.3) WILD-TYPE 195 146 154

Figure S236.  Get High-res Image Gene #25: 'amp_9q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_9q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S237.  Gene #25: 'amp_9q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 25(9Q34.3) MUTATED 10 1 2 22
AMP PEAK 25(9Q34.3) WILD-TYPE 209 57 135 94

Figure S237.  Get High-res Image Gene #25: 'amp_9q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_9q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0431 (Fisher's exact test), Q value = 0.054

Table S238.  Gene #25: 'amp_9q34.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 25(9Q34.3) MUTATED 16 10 4
AMP PEAK 25(9Q34.3) WILD-TYPE 156 86 126

Figure S238.  Get High-res Image Gene #25: 'amp_9q34.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_9q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0028 (Fisher's exact test), Q value = 0.0042

Table S239.  Gene #25: 'amp_9q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 25(9Q34.3) MUTATED 18 2 10
AMP PEAK 25(9Q34.3) WILD-TYPE 126 113 129

Figure S239.  Get High-res Image Gene #25: 'amp_9q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10q22.2' versus 'MRNA_CNMF'

P value = 0.0321 (Fisher's exact test), Q value = 0.041

Table S240.  Gene #26: 'amp_10q22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
AMP PEAK 26(10Q22.2) MUTATED 2 7 8 2
AMP PEAK 26(10Q22.2) WILD-TYPE 12 10 4 8

Figure S240.  Get High-res Image Gene #26: 'amp_10q22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_10q22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S241.  Gene #26: 'amp_10q22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 26(10Q22.2) MUTATED 66 45 8 4 20
AMP PEAK 26(10Q22.2) WILD-TYPE 103 260 11 5 17

Figure S241.  Get High-res Image Gene #26: 'amp_10q22.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10q22.2' versus 'MRNASEQ_CNMF'

P value = 0.0139 (Fisher's exact test), Q value = 0.019

Table S242.  Gene #26: 'amp_10q22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 26(10Q22.2) MUTATED 74 28 40
AMP PEAK 26(10Q22.2) WILD-TYPE 160 125 110

Figure S242.  Get High-res Image Gene #26: 'amp_10q22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_10q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00284 (Fisher's exact test), Q value = 0.0042

Table S243.  Gene #26: 'amp_10q22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 26(10Q22.2) MUTATED 49 15 10 10 22 21 15
AMP PEAK 26(10Q22.2) WILD-TYPE 74 38 37 55 86 45 60

Figure S243.  Get High-res Image Gene #26: 'amp_10q22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10q22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 0.018

Table S244.  Gene #26: 'amp_10q22.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 26(10Q22.2) MUTATED 43 19 39 40
AMP PEAK 26(10Q22.2) WILD-TYPE 176 39 98 76

Figure S244.  Get High-res Image Gene #26: 'amp_10q22.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11p11.2' versus 'MRNA_CNMF'

P value = 0.00214 (Fisher's exact test), Q value = 0.0032

Table S245.  Gene #27: 'amp_11p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
AMP PEAK 27(11P11.2) MUTATED 0 6 0 0
AMP PEAK 27(11P11.2) WILD-TYPE 14 11 12 10

Figure S245.  Get High-res Image Gene #27: 'amp_11p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0072 (Fisher's exact test), Q value = 0.01

Table S246.  Gene #27: 'amp_11p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
AMP PEAK 27(11P11.2) MUTATED 2 4 0 0 0
AMP PEAK 27(11P11.2) WILD-TYPE 12 5 7 7 16

Figure S246.  Get High-res Image Gene #27: 'amp_11p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S247.  Gene #27: 'amp_11p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 27(11P11.2) MUTATED 43 1 4 0 3
AMP PEAK 27(11P11.2) WILD-TYPE 126 304 15 9 34

Figure S247.  Get High-res Image Gene #27: 'amp_11p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S248.  Gene #27: 'amp_11p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 27(11P11.2) MUTATED 30 9 4
AMP PEAK 27(11P11.2) WILD-TYPE 135 80 167

Figure S248.  Get High-res Image Gene #27: 'amp_11p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11p11.2' versus 'RPPA_CNMF'

P value = 0.0285 (Fisher's exact test), Q value = 0.037

Table S249.  Gene #27: 'amp_11p11.2' versus Molecular Subtype #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 27(11P11.2) MUTATED 4 4 1 0 1 6
AMP PEAK 27(11P11.2) WILD-TYPE 37 33 38 12 40 18

Figure S249.  Get High-res Image Gene #27: 'amp_11p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_11p11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S250.  Gene #27: 'amp_11p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 27(11P11.2) MUTATED 42 3 6
AMP PEAK 27(11P11.2) WILD-TYPE 192 150 144

Figure S250.  Get High-res Image Gene #27: 'amp_11p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S251.  Gene #27: 'amp_11p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 27(11P11.2) MUTATED 35 1 2 2 6 4 1
AMP PEAK 27(11P11.2) WILD-TYPE 88 52 45 63 102 62 74

Figure S251.  Get High-res Image Gene #27: 'amp_11p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11p11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S252.  Gene #27: 'amp_11p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 27(11P11.2) MUTATED 40 4 6
AMP PEAK 27(11P11.2) WILD-TYPE 183 146 151

Figure S252.  Get High-res Image Gene #27: 'amp_11p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S253.  Gene #27: 'amp_11p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 27(11P11.2) MUTATED 14 1 4 31
AMP PEAK 27(11P11.2) WILD-TYPE 205 57 133 85

Figure S253.  Get High-res Image Gene #27: 'amp_11p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0232 (Fisher's exact test), Q value = 0.03

Table S254.  Gene #27: 'amp_11p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 27(11P11.2) MUTATED 24 10 6
AMP PEAK 27(11P11.2) WILD-TYPE 148 86 124

Figure S254.  Get High-res Image Gene #27: 'amp_11p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_11p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0412 (Fisher's exact test), Q value = 0.052

Table S255.  Gene #27: 'amp_11p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 27(11P11.2) MUTATED 18 5 17
AMP PEAK 27(11P11.2) WILD-TYPE 126 110 122

Figure S255.  Get High-res Image Gene #27: 'amp_11p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q13.2' versus 'MRNA_CNMF'

P value = 0.0023 (Fisher's exact test), Q value = 0.0034

Table S256.  Gene #28: 'amp_11q13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
AMP PEAK 28(11Q13.2) MUTATED 0 6 0 0
AMP PEAK 28(11Q13.2) WILD-TYPE 14 11 12 10

Figure S256.  Get High-res Image Gene #28: 'amp_11q13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11q13.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00775 (Fisher's exact test), Q value = 0.011

Table S257.  Gene #28: 'amp_11q13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
AMP PEAK 28(11Q13.2) MUTATED 2 4 0 0 0
AMP PEAK 28(11Q13.2) WILD-TYPE 12 5 7 7 16

Figure S257.  Get High-res Image Gene #28: 'amp_11q13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S258.  Gene #28: 'amp_11q13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 28(11Q13.2) MUTATED 59 5 5 0 5
AMP PEAK 28(11Q13.2) WILD-TYPE 110 300 14 9 32

Figure S258.  Get High-res Image Gene #28: 'amp_11q13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S259.  Gene #28: 'amp_11q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 28(11Q13.2) MUTATED 43 8 12
AMP PEAK 28(11Q13.2) WILD-TYPE 122 81 159

Figure S259.  Get High-res Image Gene #28: 'amp_11q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S260.  Gene #28: 'amp_11q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 28(11Q13.2) MUTATED 53 5 15
AMP PEAK 28(11Q13.2) WILD-TYPE 181 148 135

Figure S260.  Get High-res Image Gene #28: 'amp_11q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S261.  Gene #28: 'amp_11q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 28(11Q13.2) MUTATED 39 1 2 2 16 10 3
AMP PEAK 28(11Q13.2) WILD-TYPE 84 52 45 63 92 56 72

Figure S261.  Get High-res Image Gene #28: 'amp_11q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.2' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.7e-05

Table S262.  Gene #28: 'amp_11q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 28(11Q13.2) MUTATED 48 9 15
AMP PEAK 28(11Q13.2) WILD-TYPE 175 141 142

Figure S262.  Get High-res Image Gene #28: 'amp_11q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S263.  Gene #28: 'amp_11q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 28(11Q13.2) MUTATED 28 1 12 31
AMP PEAK 28(11Q13.2) WILD-TYPE 191 57 125 85

Figure S263.  Get High-res Image Gene #28: 'amp_11q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00924 (Fisher's exact test), Q value = 0.013

Table S264.  Gene #28: 'amp_11q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 28(11Q13.2) MUTATED 32 13 14
AMP PEAK 28(11Q13.2) WILD-TYPE 112 102 125

Figure S264.  Get High-res Image Gene #28: 'amp_11q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S265.  Gene #29: 'amp_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 29(11Q14.1) MUTATED 47 3 4 0 5
AMP PEAK 29(11Q14.1) WILD-TYPE 122 302 15 9 32

Figure S265.  Get High-res Image Gene #29: 'amp_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q14.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.7e-05

Table S266.  Gene #29: 'amp_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 29(11Q14.1) MUTATED 35 7 8
AMP PEAK 29(11Q14.1) WILD-TYPE 130 82 163

Figure S266.  Get High-res Image Gene #29: 'amp_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S267.  Gene #29: 'amp_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 29(11Q14.1) MUTATED 44 5 9
AMP PEAK 29(11Q14.1) WILD-TYPE 190 148 141

Figure S267.  Get High-res Image Gene #29: 'amp_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S268.  Gene #29: 'amp_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 29(11Q14.1) MUTATED 33 1 4 2 9 7 2
AMP PEAK 29(11Q14.1) WILD-TYPE 90 52 43 63 99 59 73

Figure S268.  Get High-res Image Gene #29: 'amp_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q14.1' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00014

Table S269.  Gene #29: 'amp_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 29(11Q14.1) MUTATED 40 7 12
AMP PEAK 29(11Q14.1) WILD-TYPE 183 143 145

Figure S269.  Get High-res Image Gene #29: 'amp_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.7e-05

Table S270.  Gene #29: 'amp_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 29(11Q14.1) MUTATED 23 1 8 27
AMP PEAK 29(11Q14.1) WILD-TYPE 196 57 129 89

Figure S270.  Get High-res Image Gene #29: 'amp_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0171 (Fisher's exact test), Q value = 0.023

Table S271.  Gene #29: 'amp_11q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 29(11Q14.1) MUTATED 30 9 9
AMP PEAK 29(11Q14.1) WILD-TYPE 142 87 121

Figure S271.  Get High-res Image Gene #29: 'amp_11q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_11q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0237 (Fisher's exact test), Q value = 0.031

Table S272.  Gene #29: 'amp_11q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 29(11Q14.1) MUTATED 26 9 13
AMP PEAK 29(11Q14.1) WILD-TYPE 118 106 126

Figure S272.  Get High-res Image Gene #29: 'amp_11q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S273.  Gene #30: 'amp_12p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 30(12P12.1) MUTATED 61 16 7 3 6
AMP PEAK 30(12P12.1) WILD-TYPE 108 289 12 6 31

Figure S273.  Get High-res Image Gene #30: 'amp_12p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S274.  Gene #30: 'amp_12p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 30(12P12.1) MUTATED 55 12 10
AMP PEAK 30(12P12.1) WILD-TYPE 110 77 161

Figure S274.  Get High-res Image Gene #30: 'amp_12p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S275.  Gene #30: 'amp_12p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 30(12P12.1) MUTATED 70 11 12
AMP PEAK 30(12P12.1) WILD-TYPE 164 142 138

Figure S275.  Get High-res Image Gene #30: 'amp_12p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S276.  Gene #30: 'amp_12p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 30(12P12.1) MUTATED 48 2 11 6 13 4 9
AMP PEAK 30(12P12.1) WILD-TYPE 75 51 36 59 95 62 66

Figure S276.  Get High-res Image Gene #30: 'amp_12p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S277.  Gene #30: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 30(12P12.1) MUTATED 65 16 12
AMP PEAK 30(12P12.1) WILD-TYPE 158 134 145

Figure S277.  Get High-res Image Gene #30: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S278.  Gene #30: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 30(12P12.1) MUTATED 34 5 12 42
AMP PEAK 30(12P12.1) WILD-TYPE 185 53 125 74

Figure S278.  Get High-res Image Gene #30: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.00067

Table S279.  Gene #30: 'amp_12p12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 30(12P12.1) MUTATED 47 13 14
AMP PEAK 30(12P12.1) WILD-TYPE 125 83 116

Figure S279.  Get High-res Image Gene #30: 'amp_12p12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.7e-05

Table S280.  Gene #30: 'amp_12p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 30(12P12.1) MUTATED 44 10 20
AMP PEAK 30(12P12.1) WILD-TYPE 100 105 119

Figure S280.  Get High-res Image Gene #30: 'amp_12p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q13.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S281.  Gene #31: 'amp_12q13.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 31(12Q13.11) MUTATED 59 13 7 3 5
AMP PEAK 31(12Q13.11) WILD-TYPE 110 292 12 6 32

Figure S281.  Get High-res Image Gene #31: 'amp_12q13.11' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q13.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S282.  Gene #31: 'amp_12q13.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 31(12Q13.11) MUTATED 49 15 7
AMP PEAK 31(12Q13.11) WILD-TYPE 116 74 164

Figure S282.  Get High-res Image Gene #31: 'amp_12q13.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q13.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S283.  Gene #31: 'amp_12q13.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 31(12Q13.11) MUTATED 66 9 11
AMP PEAK 31(12Q13.11) WILD-TYPE 168 144 139

Figure S283.  Get High-res Image Gene #31: 'amp_12q13.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q13.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S284.  Gene #31: 'amp_12q13.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 31(12Q13.11) MUTATED 45 1 12 6 11 4 7
AMP PEAK 31(12Q13.11) WILD-TYPE 78 52 35 59 97 62 68

Figure S284.  Get High-res Image Gene #31: 'amp_12q13.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q13.11' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S285.  Gene #31: 'amp_12q13.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 31(12Q13.11) MUTATED 62 14 11
AMP PEAK 31(12Q13.11) WILD-TYPE 161 136 146

Figure S285.  Get High-res Image Gene #31: 'amp_12q13.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q13.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S286.  Gene #31: 'amp_12q13.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 31(12Q13.11) MUTATED 30 3 11 43
AMP PEAK 31(12Q13.11) WILD-TYPE 189 55 126 73

Figure S286.  Get High-res Image Gene #31: 'amp_12q13.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q13.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00115 (Fisher's exact test), Q value = 0.0018

Table S287.  Gene #31: 'amp_12q13.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 31(12Q13.11) MUTATED 41 14 11
AMP PEAK 31(12Q13.11) WILD-TYPE 131 82 119

Figure S287.  Get High-res Image Gene #31: 'amp_12q13.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12q13.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 5e-04

Table S288.  Gene #31: 'amp_12q13.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 31(12Q13.11) MUTATED 37 9 20
AMP PEAK 31(12Q13.11) WILD-TYPE 107 106 119

Figure S288.  Get High-res Image Gene #31: 'amp_12q13.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S289.  Gene #32: 'amp_12q13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 32(12Q13.2) MUTATED 68 16 6 3 7
AMP PEAK 32(12Q13.2) WILD-TYPE 101 289 13 6 30

Figure S289.  Get High-res Image Gene #32: 'amp_12q13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S290.  Gene #32: 'amp_12q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 32(12Q13.2) MUTATED 55 14 13
AMP PEAK 32(12Q13.2) WILD-TYPE 110 75 158

Figure S290.  Get High-res Image Gene #32: 'amp_12q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S291.  Gene #32: 'amp_12q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 32(12Q13.2) MUTATED 75 9 15
AMP PEAK 32(12Q13.2) WILD-TYPE 159 144 135

Figure S291.  Get High-res Image Gene #32: 'amp_12q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S292.  Gene #32: 'amp_12q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 32(12Q13.2) MUTATED 46 1 16 6 15 7 8
AMP PEAK 32(12Q13.2) WILD-TYPE 77 52 31 59 93 59 67

Figure S292.  Get High-res Image Gene #32: 'amp_12q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q13.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S293.  Gene #32: 'amp_12q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 32(12Q13.2) MUTATED 71 13 14
AMP PEAK 32(12Q13.2) WILD-TYPE 152 137 143

Figure S293.  Get High-res Image Gene #32: 'amp_12q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S294.  Gene #32: 'amp_12q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 32(12Q13.2) MUTATED 33 3 15 47
AMP PEAK 32(12Q13.2) WILD-TYPE 186 55 122 69

Figure S294.  Get High-res Image Gene #32: 'amp_12q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.7e-05

Table S295.  Gene #32: 'amp_12q13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 32(12Q13.2) MUTATED 53 12 13
AMP PEAK 32(12Q13.2) WILD-TYPE 119 84 117

Figure S295.  Get High-res Image Gene #32: 'amp_12q13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00016

Table S296.  Gene #32: 'amp_12q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 32(12Q13.2) MUTATED 44 13 21
AMP PEAK 32(12Q13.2) WILD-TYPE 100 102 118

Figure S296.  Get High-res Image Gene #32: 'amp_12q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S297.  Gene #33: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 33(13Q34) MUTATED 52 3 0 1 2
AMP PEAK 33(13Q34) WILD-TYPE 117 302 19 8 35

Figure S297.  Get High-res Image Gene #33: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q34' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S298.  Gene #33: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 33(13Q34) MUTATED 38 11 4
AMP PEAK 33(13Q34) WILD-TYPE 127 78 167

Figure S298.  Get High-res Image Gene #33: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q34' versus 'RPPA_CHIERARCHICAL'

P value = 0.0291 (Fisher's exact test), Q value = 0.038

Table S299.  Gene #33: 'amp_13q34' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
AMP PEAK 33(13Q34) MUTATED 6 1 0 2
AMP PEAK 33(13Q34) WILD-TYPE 61 66 43 15

Figure S299.  Get High-res Image Gene #33: 'amp_13q34' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_13q34' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S300.  Gene #33: 'amp_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 33(13Q34) MUTATED 52 3 3
AMP PEAK 33(13Q34) WILD-TYPE 182 150 147

Figure S300.  Get High-res Image Gene #33: 'amp_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S301.  Gene #33: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 33(13Q34) MUTATED 46 0 5 2 3 1 1
AMP PEAK 33(13Q34) WILD-TYPE 77 53 42 63 105 65 74

Figure S301.  Get High-res Image Gene #33: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q34' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S302.  Gene #33: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 33(13Q34) MUTATED 52 3 3
AMP PEAK 33(13Q34) WILD-TYPE 171 147 154

Figure S302.  Get High-res Image Gene #33: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S303.  Gene #33: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 33(13Q34) MUTATED 14 0 4 40
AMP PEAK 33(13Q34) WILD-TYPE 205 58 133 76

Figure S303.  Get High-res Image Gene #33: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_13q34' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.00075

Table S304.  Gene #33: 'amp_13q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 33(13Q34) MUTATED 33 13 6
AMP PEAK 33(13Q34) WILD-TYPE 139 83 124

Figure S304.  Get High-res Image Gene #33: 'amp_13q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_13q34' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 5.4e-05

Table S305.  Gene #33: 'amp_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 33(13Q34) MUTATED 32 3 17
AMP PEAK 33(13Q34) WILD-TYPE 112 112 122

Figure S305.  Get High-res Image Gene #33: 'amp_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_14q24.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.014

Table S306.  Gene #34: 'amp_14q24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
AMP PEAK 34(14Q24.3) MUTATED 1 5 0 1 1
AMP PEAK 34(14Q24.3) WILD-TYPE 13 4 7 6 15

Figure S306.  Get High-res Image Gene #34: 'amp_14q24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_14q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S307.  Gene #34: 'amp_14q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 34(14Q24.3) MUTATED 52 4 2 0 6
AMP PEAK 34(14Q24.3) WILD-TYPE 117 301 17 9 31

Figure S307.  Get High-res Image Gene #34: 'amp_14q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_14q24.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S308.  Gene #34: 'amp_14q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 34(14Q24.3) MUTATED 37 9 8
AMP PEAK 34(14Q24.3) WILD-TYPE 128 80 163

Figure S308.  Get High-res Image Gene #34: 'amp_14q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_14q24.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S309.  Gene #34: 'amp_14q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 34(14Q24.3) MUTATED 54 3 7
AMP PEAK 34(14Q24.3) WILD-TYPE 180 150 143

Figure S309.  Get High-res Image Gene #34: 'amp_14q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_14q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S310.  Gene #34: 'amp_14q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 34(14Q24.3) MUTATED 40 1 8 1 9 1 4
AMP PEAK 34(14Q24.3) WILD-TYPE 83 52 39 64 99 65 71

Figure S310.  Get High-res Image Gene #34: 'amp_14q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_14q24.3' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 5.4e-05

Table S311.  Gene #34: 'amp_14q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 34(14Q24.3) MUTATED 44 10 8
AMP PEAK 34(14Q24.3) WILD-TYPE 179 140 149

Figure S311.  Get High-res Image Gene #34: 'amp_14q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_14q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S312.  Gene #34: 'amp_14q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 34(14Q24.3) MUTATED 15 1 9 37
AMP PEAK 34(14Q24.3) WILD-TYPE 204 57 128 79

Figure S312.  Get High-res Image Gene #34: 'amp_14q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_14q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0459 (Fisher's exact test), Q value = 0.058

Table S313.  Gene #34: 'amp_14q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 34(14Q24.3) MUTATED 23 8 22
AMP PEAK 34(14Q24.3) WILD-TYPE 121 107 117

Figure S313.  Get High-res Image Gene #34: 'amp_14q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_14q32.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S314.  Gene #35: 'amp_14q32.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 35(14Q32.33) MUTATED 67 4 2 0 6
AMP PEAK 35(14Q32.33) WILD-TYPE 102 301 17 9 31

Figure S314.  Get High-res Image Gene #35: 'amp_14q32.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_14q32.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S315.  Gene #35: 'amp_14q32.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 35(14Q32.33) MUTATED 48 11 9
AMP PEAK 35(14Q32.33) WILD-TYPE 117 78 162

Figure S315.  Get High-res Image Gene #35: 'amp_14q32.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_14q32.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S316.  Gene #35: 'amp_14q32.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 35(14Q32.33) MUTATED 61 4 13
AMP PEAK 35(14Q32.33) WILD-TYPE 173 149 137

Figure S316.  Get High-res Image Gene #35: 'amp_14q32.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_14q32.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S317.  Gene #35: 'amp_14q32.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 35(14Q32.33) MUTATED 38 1 12 3 13 7 4
AMP PEAK 35(14Q32.33) WILD-TYPE 85 52 35 62 95 59 71

Figure S317.  Get High-res Image Gene #35: 'amp_14q32.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_14q32.33' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.7e-05

Table S318.  Gene #35: 'amp_14q32.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 35(14Q32.33) MUTATED 56 9 13
AMP PEAK 35(14Q32.33) WILD-TYPE 167 141 144

Figure S318.  Get High-res Image Gene #35: 'amp_14q32.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_14q32.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S319.  Gene #35: 'amp_14q32.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 35(14Q32.33) MUTATED 23 1 11 43
AMP PEAK 35(14Q32.33) WILD-TYPE 196 57 126 73

Figure S319.  Get High-res Image Gene #35: 'amp_14q32.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_14q32.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00269 (Fisher's exact test), Q value = 0.004

Table S320.  Gene #35: 'amp_14q32.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 35(14Q32.33) MUTATED 41 14 12
AMP PEAK 35(14Q32.33) WILD-TYPE 131 82 118

Figure S320.  Get High-res Image Gene #35: 'amp_14q32.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_14q32.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0267 (Fisher's exact test), Q value = 0.035

Table S321.  Gene #35: 'amp_14q32.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 35(14Q32.33) MUTATED 33 12 22
AMP PEAK 35(14Q32.33) WILD-TYPE 111 103 117

Figure S321.  Get High-res Image Gene #35: 'amp_14q32.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_15q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S322.  Gene #36: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 36(15Q26.3) MUTATED 33 2 1 0 2
AMP PEAK 36(15Q26.3) WILD-TYPE 136 303 18 9 35

Figure S322.  Get High-res Image Gene #36: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_15q26.3' versus 'METHLYATION_CNMF'

P value = 0.0089 (Fisher's exact test), Q value = 0.012

Table S323.  Gene #36: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 36(15Q26.3) MUTATED 22 6 7
AMP PEAK 36(15Q26.3) WILD-TYPE 143 83 164

Figure S323.  Get High-res Image Gene #36: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S324.  Gene #36: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 36(15Q26.3) MUTATED 32 3 3
AMP PEAK 36(15Q26.3) WILD-TYPE 202 150 147

Figure S324.  Get High-res Image Gene #36: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S325.  Gene #36: 'amp_15q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 36(15Q26.3) MUTATED 20 1 6 1 8 2 0
AMP PEAK 36(15Q26.3) WILD-TYPE 103 52 41 64 100 64 75

Figure S325.  Get High-res Image Gene #36: 'amp_15q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00031

Table S326.  Gene #36: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 36(15Q26.3) MUTATED 28 7 3
AMP PEAK 36(15Q26.3) WILD-TYPE 195 143 154

Figure S326.  Get High-res Image Gene #36: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_15q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00022

Table S327.  Gene #36: 'amp_15q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 36(15Q26.3) MUTATED 15 1 3 19
AMP PEAK 36(15Q26.3) WILD-TYPE 204 57 134 97

Figure S327.  Get High-res Image Gene #36: 'amp_15q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'MRNA_CNMF'

P value = 0.00831 (Fisher's exact test), Q value = 0.012

Table S328.  Gene #37: 'amp_16p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
AMP PEAK 37(16P11.2) MUTATED 0 5 0 0
AMP PEAK 37(16P11.2) WILD-TYPE 14 12 12 10

Figure S328.  Get High-res Image Gene #37: 'amp_16p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_16p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0051 (Fisher's exact test), Q value = 0.0074

Table S329.  Gene #37: 'amp_16p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
AMP PEAK 37(16P11.2) MUTATED 1 4 0 0 0
AMP PEAK 37(16P11.2) WILD-TYPE 13 5 7 7 16

Figure S329.  Get High-res Image Gene #37: 'amp_16p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_16p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S330.  Gene #37: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 37(16P11.2) MUTATED 61 1 1 0 3
AMP PEAK 37(16P11.2) WILD-TYPE 108 304 18 9 34

Figure S330.  Get High-res Image Gene #37: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_16p11.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.7e-05

Table S331.  Gene #37: 'amp_16p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 37(16P11.2) MUTATED 39 10 8
AMP PEAK 37(16P11.2) WILD-TYPE 126 79 163

Figure S331.  Get High-res Image Gene #37: 'amp_16p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_16p11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S332.  Gene #37: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 37(16P11.2) MUTATED 58 4 4
AMP PEAK 37(16P11.2) WILD-TYPE 176 149 146

Figure S332.  Get High-res Image Gene #37: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_16p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S333.  Gene #37: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 37(16P11.2) MUTATED 46 3 4 1 9 3 0
AMP PEAK 37(16P11.2) WILD-TYPE 77 50 43 64 99 63 75

Figure S333.  Get High-res Image Gene #37: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S334.  Gene #37: 'amp_16p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 37(16P11.2) MUTATED 52 6 5
AMP PEAK 37(16P11.2) WILD-TYPE 171 144 152

Figure S334.  Get High-res Image Gene #37: 'amp_16p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_16p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S335.  Gene #37: 'amp_16p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 37(16P11.2) MUTATED 22 3 4 34
AMP PEAK 37(16P11.2) WILD-TYPE 197 55 133 82

Figure S335.  Get High-res Image Gene #37: 'amp_16p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00281 (Fisher's exact test), Q value = 0.0042

Table S336.  Gene #37: 'amp_16p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 37(16P11.2) MUTATED 33 11 8
AMP PEAK 37(16P11.2) WILD-TYPE 139 85 122

Figure S336.  Get High-res Image Gene #37: 'amp_16p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_16p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00048 (Fisher's exact test), Q value = 0.00078

Table S337.  Gene #37: 'amp_16p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 37(16P11.2) MUTATED 29 5 18
AMP PEAK 37(16P11.2) WILD-TYPE 115 110 121

Figure S337.  Get High-res Image Gene #37: 'amp_16p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0495 (Fisher's exact test), Q value = 0.062

Table S338.  Gene #38: 'amp_17q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
AMP PEAK 38(17Q11.2) MUTATED 2 3 0 0 0
AMP PEAK 38(17Q11.2) WILD-TYPE 12 6 7 7 16

Figure S338.  Get High-res Image Gene #38: 'amp_17q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S339.  Gene #38: 'amp_17q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 38(17Q11.2) MUTATED 64 4 0 1 2
AMP PEAK 38(17Q11.2) WILD-TYPE 105 301 19 8 35

Figure S339.  Get High-res Image Gene #38: 'amp_17q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S340.  Gene #38: 'amp_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 38(17Q11.2) MUTATED 54 6 3
AMP PEAK 38(17Q11.2) WILD-TYPE 111 83 168

Figure S340.  Get High-res Image Gene #38: 'amp_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q11.2' versus 'RPPA_CNMF'

P value = 0.00761 (Fisher's exact test), Q value = 0.011

Table S341.  Gene #38: 'amp_17q11.2' versus Molecular Subtype #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 38(17Q11.2) MUTATED 5 6 0 1 0 1
AMP PEAK 38(17Q11.2) WILD-TYPE 36 31 39 11 41 23

Figure S341.  Get High-res Image Gene #38: 'amp_17q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_17q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S342.  Gene #38: 'amp_17q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 38(17Q11.2) MUTATED 64 2 4
AMP PEAK 38(17Q11.2) WILD-TYPE 170 151 146

Figure S342.  Get High-res Image Gene #38: 'amp_17q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S343.  Gene #38: 'amp_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 38(17Q11.2) MUTATED 50 0 9 2 6 3 0
AMP PEAK 38(17Q11.2) WILD-TYPE 73 53 38 63 102 63 75

Figure S343.  Get High-res Image Gene #38: 'amp_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S344.  Gene #38: 'amp_17q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 38(17Q11.2) MUTATED 57 9 2
AMP PEAK 38(17Q11.2) WILD-TYPE 166 141 155

Figure S344.  Get High-res Image Gene #38: 'amp_17q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S345.  Gene #38: 'amp_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 38(17Q11.2) MUTATED 23 1 2 42
AMP PEAK 38(17Q11.2) WILD-TYPE 196 57 135 74

Figure S345.  Get High-res Image Gene #38: 'amp_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S346.  Gene #38: 'amp_17q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 38(17Q11.2) MUTATED 41 12 5
AMP PEAK 38(17Q11.2) WILD-TYPE 131 84 125

Figure S346.  Get High-res Image Gene #38: 'amp_17q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.7e-05

Table S347.  Gene #38: 'amp_17q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 38(17Q11.2) MUTATED 37 5 16
AMP PEAK 38(17Q11.2) WILD-TYPE 107 110 123

Figure S347.  Get High-res Image Gene #38: 'amp_17q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00223 (Fisher's exact test), Q value = 0.0034

Table S348.  Gene #39: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
AMP PEAK 39(17Q12) MUTATED 0 4 1 0 0
AMP PEAK 39(17Q12) WILD-TYPE 14 5 6 7 16

Figure S348.  Get High-res Image Gene #39: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S349.  Gene #39: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 39(17Q12) MUTATED 67 5 0 1 2
AMP PEAK 39(17Q12) WILD-TYPE 102 300 19 8 35

Figure S349.  Get High-res Image Gene #39: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S350.  Gene #39: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 39(17Q12) MUTATED 53 8 2
AMP PEAK 39(17Q12) WILD-TYPE 112 81 169

Figure S350.  Get High-res Image Gene #39: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q12' versus 'RPPA_CNMF'

P value = 0.00577 (Fisher's exact test), Q value = 0.0083

Table S351.  Gene #39: 'amp_17q12' versus Molecular Subtype #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 39(17Q12) MUTATED 4 5 1 1 0 6
AMP PEAK 39(17Q12) WILD-TYPE 37 32 38 11 41 18

Figure S351.  Get High-res Image Gene #39: 'amp_17q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S352.  Gene #39: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 39(17Q12) MUTATED 70 2 3
AMP PEAK 39(17Q12) WILD-TYPE 164 151 147

Figure S352.  Get High-res Image Gene #39: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S353.  Gene #39: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 39(17Q12) MUTATED 51 0 15 2 5 2 0
AMP PEAK 39(17Q12) WILD-TYPE 72 53 32 63 103 64 75

Figure S353.  Get High-res Image Gene #39: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S354.  Gene #39: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 39(17Q12) MUTATED 63 7 3
AMP PEAK 39(17Q12) WILD-TYPE 160 143 154

Figure S354.  Get High-res Image Gene #39: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S355.  Gene #39: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 39(17Q12) MUTATED 19 2 3 49
AMP PEAK 39(17Q12) WILD-TYPE 200 56 134 67

Figure S355.  Get High-res Image Gene #39: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00016

Table S356.  Gene #39: 'amp_17q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 39(17Q12) MUTATED 40 13 7
AMP PEAK 39(17Q12) WILD-TYPE 132 83 123

Figure S356.  Get High-res Image Gene #39: 'amp_17q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S357.  Gene #39: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 39(17Q12) MUTATED 37 3 20
AMP PEAK 39(17Q12) WILD-TYPE 107 112 119

Figure S357.  Get High-res Image Gene #39: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q25.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S358.  Gene #40: 'amp_17q25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
AMP PEAK 40(17Q25.1) MUTATED 0 10 1 0
AMP PEAK 40(17Q25.1) WILD-TYPE 14 7 11 10

Figure S358.  Get High-res Image Gene #40: 'amp_17q25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q25.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S359.  Gene #40: 'amp_17q25.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
AMP PEAK 40(17Q25.1) MUTATED 2 8 1 0 0
AMP PEAK 40(17Q25.1) WILD-TYPE 12 1 6 7 16

Figure S359.  Get High-res Image Gene #40: 'amp_17q25.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q25.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S360.  Gene #40: 'amp_17q25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 40(17Q25.1) MUTATED 94 5 1 1 4
AMP PEAK 40(17Q25.1) WILD-TYPE 75 300 18 8 33

Figure S360.  Get High-res Image Gene #40: 'amp_17q25.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q25.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S361.  Gene #40: 'amp_17q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 40(17Q25.1) MUTATED 64 15 6
AMP PEAK 40(17Q25.1) WILD-TYPE 101 74 165

Figure S361.  Get High-res Image Gene #40: 'amp_17q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q25.1' versus 'RPPA_CNMF'

P value = 0.00557 (Fisher's exact test), Q value = 0.008

Table S362.  Gene #40: 'amp_17q25.1' versus Molecular Subtype #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 40(17Q25.1) MUTATED 6 9 2 1 1 7
AMP PEAK 40(17Q25.1) WILD-TYPE 35 28 37 11 40 17

Figure S362.  Get High-res Image Gene #40: 'amp_17q25.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_17q25.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S363.  Gene #40: 'amp_17q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 40(17Q25.1) MUTATED 90 5 9
AMP PEAK 40(17Q25.1) WILD-TYPE 144 148 141

Figure S363.  Get High-res Image Gene #40: 'amp_17q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S364.  Gene #40: 'amp_17q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 40(17Q25.1) MUTATED 72 0 13 2 9 7 1
AMP PEAK 40(17Q25.1) WILD-TYPE 51 53 34 63 99 59 74

Figure S364.  Get High-res Image Gene #40: 'amp_17q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q25.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S365.  Gene #40: 'amp_17q25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 40(17Q25.1) MUTATED 82 11 8
AMP PEAK 40(17Q25.1) WILD-TYPE 141 139 149

Figure S365.  Get High-res Image Gene #40: 'amp_17q25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S366.  Gene #40: 'amp_17q25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 40(17Q25.1) MUTATED 35 2 6 58
AMP PEAK 40(17Q25.1) WILD-TYPE 184 56 131 58

Figure S366.  Get High-res Image Gene #40: 'amp_17q25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q25.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S367.  Gene #40: 'amp_17q25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 40(17Q25.1) MUTATED 53 21 7
AMP PEAK 40(17Q25.1) WILD-TYPE 119 75 123

Figure S367.  Get High-res Image Gene #40: 'amp_17q25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q25.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00011

Table S368.  Gene #40: 'amp_17q25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 40(17Q25.1) MUTATED 42 9 30
AMP PEAK 40(17Q25.1) WILD-TYPE 102 106 109

Figure S368.  Get High-res Image Gene #40: 'amp_17q25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18p11.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S369.  Gene #41: 'amp_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 41(18P11.31) MUTATED 87 5 3 0 1
AMP PEAK 41(18P11.31) WILD-TYPE 82 300 16 9 36

Figure S369.  Get High-res Image Gene #41: 'amp_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

'amp_18p11.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S370.  Gene #41: 'amp_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 41(18P11.31) MUTATED 62 16 7
AMP PEAK 41(18P11.31) WILD-TYPE 103 73 164

Figure S370.  Get High-res Image Gene #41: 'amp_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_18p11.31' versus 'RPPA_CNMF'

P value = 0.00528 (Fisher's exact test), Q value = 0.0076

Table S371.  Gene #41: 'amp_18p11.31' versus Molecular Subtype #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 41(18P11.31) MUTATED 7 4 0 0 1 5
AMP PEAK 41(18P11.31) WILD-TYPE 34 33 39 12 40 19

Figure S371.  Get High-res Image Gene #41: 'amp_18p11.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_18p11.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S372.  Gene #41: 'amp_18p11.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 41(18P11.31) MUTATED 85 3 8
AMP PEAK 41(18P11.31) WILD-TYPE 149 150 142

Figure S372.  Get High-res Image Gene #41: 'amp_18p11.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_18p11.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S373.  Gene #41: 'amp_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 41(18P11.31) MUTATED 61 1 17 1 9 4 3
AMP PEAK 41(18P11.31) WILD-TYPE 62 52 30 64 99 62 72

Figure S373.  Get High-res Image Gene #41: 'amp_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_18p11.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S374.  Gene #41: 'amp_18p11.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 41(18P11.31) MUTATED 79 9 7
AMP PEAK 41(18P11.31) WILD-TYPE 144 141 150

Figure S374.  Get High-res Image Gene #41: 'amp_18p11.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_18p11.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S375.  Gene #41: 'amp_18p11.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 41(18P11.31) MUTATED 28 1 6 60
AMP PEAK 41(18P11.31) WILD-TYPE 191 57 131 56

Figure S375.  Get High-res Image Gene #41: 'amp_18p11.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_18p11.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S376.  Gene #41: 'amp_18p11.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 41(18P11.31) MUTATED 52 23 7
AMP PEAK 41(18P11.31) WILD-TYPE 120 73 123

Figure S376.  Get High-res Image Gene #41: 'amp_18p11.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_18p11.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S377.  Gene #41: 'amp_18p11.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 41(18P11.31) MUTATED 46 6 30
AMP PEAK 41(18P11.31) WILD-TYPE 98 109 109

Figure S377.  Get High-res Image Gene #41: 'amp_18p11.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S378.  Gene #42: 'amp_18q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 42(18Q11.2) MUTATED 63 3 2 0 1
AMP PEAK 42(18Q11.2) WILD-TYPE 106 302 17 9 36

Figure S378.  Get High-res Image Gene #42: 'amp_18q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S379.  Gene #42: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 42(18Q11.2) MUTATED 47 11 3
AMP PEAK 42(18Q11.2) WILD-TYPE 118 78 168

Figure S379.  Get High-res Image Gene #42: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0226 (Fisher's exact test), Q value = 0.03

Table S380.  Gene #42: 'amp_18q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
AMP PEAK 42(18Q11.2) MUTATED 9 3 0 2
AMP PEAK 42(18Q11.2) WILD-TYPE 58 64 43 15

Figure S380.  Get High-res Image Gene #42: 'amp_18q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_18q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S381.  Gene #42: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 42(18Q11.2) MUTATED 63 3 3
AMP PEAK 42(18Q11.2) WILD-TYPE 171 150 147

Figure S381.  Get High-res Image Gene #42: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S382.  Gene #42: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 42(18Q11.2) MUTATED 49 1 9 1 6 2 1
AMP PEAK 42(18Q11.2) WILD-TYPE 74 52 38 64 102 64 74

Figure S382.  Get High-res Image Gene #42: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S383.  Gene #42: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 42(18Q11.2) MUTATED 57 9 2
AMP PEAK 42(18Q11.2) WILD-TYPE 166 141 155

Figure S383.  Get High-res Image Gene #42: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S384.  Gene #42: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 42(18Q11.2) MUTATED 24 1 1 42
AMP PEAK 42(18Q11.2) WILD-TYPE 195 57 136 74

Figure S384.  Get High-res Image Gene #42: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S385.  Gene #42: 'amp_18q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 42(18Q11.2) MUTATED 43 13 1
AMP PEAK 42(18Q11.2) WILD-TYPE 129 83 129

Figure S385.  Get High-res Image Gene #42: 'amp_18q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S386.  Gene #42: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 42(18Q11.2) MUTATED 35 1 21
AMP PEAK 42(18Q11.2) WILD-TYPE 109 114 118

Figure S386.  Get High-res Image Gene #42: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.2' versus 'MRNA_CNMF'

P value = 0.00359 (Fisher's exact test), Q value = 0.0052

Table S387.  Gene #43: 'amp_19p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
AMP PEAK 43(19P13.2) MUTATED 1 7 0 0
AMP PEAK 43(19P13.2) WILD-TYPE 13 10 12 10

Figure S387.  Get High-res Image Gene #43: 'amp_19p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19p13.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00021

Table S388.  Gene #43: 'amp_19p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
AMP PEAK 43(19P13.2) MUTATED 2 6 0 0 0
AMP PEAK 43(19P13.2) WILD-TYPE 12 3 7 7 16

Figure S388.  Get High-res Image Gene #43: 'amp_19p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S389.  Gene #43: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 43(19P13.2) MUTATED 95 0 1 0 3
AMP PEAK 43(19P13.2) WILD-TYPE 74 305 18 9 34

Figure S389.  Get High-res Image Gene #43: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S390.  Gene #43: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 43(19P13.2) MUTATED 65 15 7
AMP PEAK 43(19P13.2) WILD-TYPE 100 74 164

Figure S390.  Get High-res Image Gene #43: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'RPPA_CNMF'

P value = 0.0195 (Fisher's exact test), Q value = 0.026

Table S391.  Gene #43: 'amp_19p13.2' versus Molecular Subtype #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 43(19P13.2) MUTATED 4 9 2 0 1 4
AMP PEAK 43(19P13.2) WILD-TYPE 37 28 37 12 40 20

Figure S391.  Get High-res Image Gene #43: 'amp_19p13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19p13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.00063

Table S392.  Gene #43: 'amp_19p13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
AMP PEAK 43(19P13.2) MUTATED 13 3 0 4
AMP PEAK 43(19P13.2) WILD-TYPE 54 64 43 13

Figure S392.  Get High-res Image Gene #43: 'amp_19p13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_19p13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S393.  Gene #43: 'amp_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 43(19P13.2) MUTATED 90 2 6
AMP PEAK 43(19P13.2) WILD-TYPE 144 151 144

Figure S393.  Get High-res Image Gene #43: 'amp_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S394.  Gene #43: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 43(19P13.2) MUTATED 76 1 6 2 8 4 1
AMP PEAK 43(19P13.2) WILD-TYPE 47 52 41 63 100 62 74

Figure S394.  Get High-res Image Gene #43: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S395.  Gene #43: 'amp_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 43(19P13.2) MUTATED 82 9 6
AMP PEAK 43(19P13.2) WILD-TYPE 141 141 151

Figure S395.  Get High-res Image Gene #43: 'amp_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S396.  Gene #43: 'amp_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 43(19P13.2) MUTATED 29 1 6 61
AMP PEAK 43(19P13.2) WILD-TYPE 190 57 131 55

Figure S396.  Get High-res Image Gene #43: 'amp_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S397.  Gene #43: 'amp_19p13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 43(19P13.2) MUTATED 51 22 8
AMP PEAK 43(19P13.2) WILD-TYPE 121 74 122

Figure S397.  Get High-res Image Gene #43: 'amp_19p13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S398.  Gene #43: 'amp_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 43(19P13.2) MUTATED 47 8 26
AMP PEAK 43(19P13.2) WILD-TYPE 97 107 113

Figure S398.  Get High-res Image Gene #43: 'amp_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q12' versus 'MRNA_CNMF'

P value = 0.00485 (Fisher's exact test), Q value = 0.007

Table S399.  Gene #44: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
AMP PEAK 44(19Q12) MUTATED 1 8 1 0
AMP PEAK 44(19Q12) WILD-TYPE 13 9 11 10

Figure S399.  Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q12' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 7.1e-05

Table S400.  Gene #44: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
AMP PEAK 44(19Q12) MUTATED 2 7 1 0 0
AMP PEAK 44(19Q12) WILD-TYPE 12 2 6 7 16

Figure S400.  Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S401.  Gene #44: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 44(19Q12) MUTATED 113 2 2 0 4
AMP PEAK 44(19Q12) WILD-TYPE 56 303 17 9 33

Figure S401.  Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S402.  Gene #44: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 44(19Q12) MUTATED 80 18 9
AMP PEAK 44(19Q12) WILD-TYPE 85 71 162

Figure S402.  Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19q12' versus 'RPPA_CNMF'

P value = 0.00475 (Fisher's exact test), Q value = 0.0069

Table S403.  Gene #44: 'amp_19q12' versus Molecular Subtype #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 44(19Q12) MUTATED 5 6 1 0 1 7
AMP PEAK 44(19Q12) WILD-TYPE 36 31 38 12 40 17

Figure S403.  Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00145 (Fisher's exact test), Q value = 0.0022

Table S404.  Gene #44: 'amp_19q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
AMP PEAK 44(19Q12) MUTATED 12 4 0 4
AMP PEAK 44(19Q12) WILD-TYPE 55 63 43 13

Figure S404.  Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S405.  Gene #44: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 44(19Q12) MUTATED 111 3 7
AMP PEAK 44(19Q12) WILD-TYPE 123 150 143

Figure S405.  Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S406.  Gene #44: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 44(19Q12) MUTATED 81 1 19 3 11 5 1
AMP PEAK 44(19Q12) WILD-TYPE 42 52 28 62 97 61 74

Figure S406.  Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S407.  Gene #44: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 44(19Q12) MUTATED 99 10 8
AMP PEAK 44(19Q12) WILD-TYPE 124 140 149

Figure S407.  Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S408.  Gene #44: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 44(19Q12) MUTATED 37 1 7 72
AMP PEAK 44(19Q12) WILD-TYPE 182 57 130 44

Figure S408.  Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S409.  Gene #44: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 44(19Q12) MUTATED 66 27 8
AMP PEAK 44(19Q12) WILD-TYPE 106 69 122

Figure S409.  Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S410.  Gene #44: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 44(19Q12) MUTATED 56 10 35
AMP PEAK 44(19Q12) WILD-TYPE 88 105 104

Figure S410.  Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20p13' versus 'MRNA_CHIERARCHICAL'

P value = 0.049 (Fisher's exact test), Q value = 0.061

Table S411.  Gene #45: 'amp_20p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
AMP PEAK 45(20P13) MUTATED 2 3 0 0 0
AMP PEAK 45(20P13) WILD-TYPE 12 6 7 7 16

Figure S411.  Get High-res Image Gene #45: 'amp_20p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S412.  Gene #45: 'amp_20p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 45(20P13) MUTATED 87 8 12 2 8
AMP PEAK 45(20P13) WILD-TYPE 82 297 7 7 29

Figure S412.  Get High-res Image Gene #45: 'amp_20p13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S413.  Gene #45: 'amp_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 45(20P13) MUTATED 75 16 16
AMP PEAK 45(20P13) WILD-TYPE 90 73 155

Figure S413.  Get High-res Image Gene #45: 'amp_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20p13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S414.  Gene #45: 'amp_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 45(20P13) MUTATED 90 11 15
AMP PEAK 45(20P13) WILD-TYPE 144 142 135

Figure S414.  Get High-res Image Gene #45: 'amp_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S415.  Gene #45: 'amp_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 45(20P13) MUTATED 64 5 16 3 12 14 2
AMP PEAK 45(20P13) WILD-TYPE 59 48 31 62 96 52 73

Figure S415.  Get High-res Image Gene #45: 'amp_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20p13' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S416.  Gene #45: 'amp_20p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 45(20P13) MUTATED 84 17 15
AMP PEAK 45(20P13) WILD-TYPE 139 133 142

Figure S416.  Get High-res Image Gene #45: 'amp_20p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S417.  Gene #45: 'amp_20p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 45(20P13) MUTATED 43 5 12 56
AMP PEAK 45(20P13) WILD-TYPE 176 53 125 60

Figure S417.  Get High-res Image Gene #45: 'amp_20p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.00093

Table S418.  Gene #45: 'amp_20p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 45(20P13) MUTATED 57 23 18
AMP PEAK 45(20P13) WILD-TYPE 115 73 112

Figure S418.  Get High-res Image Gene #45: 'amp_20p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S419.  Gene #45: 'amp_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 45(20P13) MUTATED 56 13 29
AMP PEAK 45(20P13) WILD-TYPE 88 102 110

Figure S419.  Get High-res Image Gene #45: 'amp_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNA_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.00087

Table S420.  Gene #46: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
AMP PEAK 46(20Q11.21) MUTATED 2 9 0 0
AMP PEAK 46(20Q11.21) WILD-TYPE 12 8 12 10

Figure S420.  Get High-res Image Gene #46: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q11.21' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.7e-05

Table S421.  Gene #46: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
AMP PEAK 46(20Q11.21) MUTATED 4 7 0 0 0
AMP PEAK 46(20Q11.21) WILD-TYPE 10 2 7 7 16

Figure S421.  Get High-res Image Gene #46: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S422.  Gene #46: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 46(20Q11.21) MUTATED 120 8 13 3 8
AMP PEAK 46(20Q11.21) WILD-TYPE 49 297 6 6 29

Figure S422.  Get High-res Image Gene #46: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S423.  Gene #46: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 46(20Q11.21) MUTATED 89 20 24
AMP PEAK 46(20Q11.21) WILD-TYPE 76 69 147

Figure S423.  Get High-res Image Gene #46: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'RPPA_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.00072

Table S424.  Gene #46: 'amp_20q11.21' versus Molecular Subtype #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 46(20Q11.21) MUTATED 8 12 2 0 2 8
AMP PEAK 46(20Q11.21) WILD-TYPE 33 25 37 12 39 16

Figure S424.  Get High-res Image Gene #46: 'amp_20q11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S425.  Gene #46: 'amp_20q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 46(20Q11.21) MUTATED 119 11 21
AMP PEAK 46(20Q11.21) WILD-TYPE 115 142 129

Figure S425.  Get High-res Image Gene #46: 'amp_20q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S426.  Gene #46: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 46(20Q11.21) MUTATED 80 4 21 4 21 17 4
AMP PEAK 46(20Q11.21) WILD-TYPE 43 49 26 61 87 49 71

Figure S426.  Get High-res Image Gene #46: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S427.  Gene #46: 'amp_20q11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 46(20Q11.21) MUTATED 108 19 21
AMP PEAK 46(20Q11.21) WILD-TYPE 115 131 136

Figure S427.  Get High-res Image Gene #46: 'amp_20q11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S428.  Gene #46: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 46(20Q11.21) MUTATED 47 5 20 76
AMP PEAK 46(20Q11.21) WILD-TYPE 172 53 117 40

Figure S428.  Get High-res Image Gene #46: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S429.  Gene #46: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 46(20Q11.21) MUTATED 76 26 23
AMP PEAK 46(20Q11.21) WILD-TYPE 96 70 107

Figure S429.  Get High-res Image Gene #46: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S430.  Gene #46: 'amp_20q11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 46(20Q11.21) MUTATED 69 22 34
AMP PEAK 46(20Q11.21) WILD-TYPE 75 93 105

Figure S430.  Get High-res Image Gene #46: 'amp_20q11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.12' versus 'MRNA_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.018

Table S431.  Gene #47: 'amp_20q13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
AMP PEAK 47(20Q13.12) MUTATED 1 6 0 0
AMP PEAK 47(20Q13.12) WILD-TYPE 13 11 12 10

Figure S431.  Get High-res Image Gene #47: 'amp_20q13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q13.12' versus 'MRNA_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.014

Table S432.  Gene #47: 'amp_20q13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
AMP PEAK 47(20Q13.12) MUTATED 3 4 0 0 0
AMP PEAK 47(20Q13.12) WILD-TYPE 11 5 7 7 16

Figure S432.  Get High-res Image Gene #47: 'amp_20q13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q13.12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S433.  Gene #47: 'amp_20q13.12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 47(20Q13.12) MUTATED 118 10 14 3 7
AMP PEAK 47(20Q13.12) WILD-TYPE 51 295 5 6 30

Figure S433.  Get High-res Image Gene #47: 'amp_20q13.12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S434.  Gene #47: 'amp_20q13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 47(20Q13.12) MUTATED 94 20 24
AMP PEAK 47(20Q13.12) WILD-TYPE 71 69 147

Figure S434.  Get High-res Image Gene #47: 'amp_20q13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.12' versus 'RPPA_CNMF'

P value = 0.00531 (Fisher's exact test), Q value = 0.0076

Table S435.  Gene #47: 'amp_20q13.12' versus Molecular Subtype #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 47(20Q13.12) MUTATED 6 12 2 1 3 7
AMP PEAK 47(20Q13.12) WILD-TYPE 35 25 37 11 38 17

Figure S435.  Get High-res Image Gene #47: 'amp_20q13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q13.12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S436.  Gene #47: 'amp_20q13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 47(20Q13.12) MUTATED 119 12 20
AMP PEAK 47(20Q13.12) WILD-TYPE 115 141 130

Figure S436.  Get High-res Image Gene #47: 'amp_20q13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q13.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S437.  Gene #47: 'amp_20q13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 47(20Q13.12) MUTATED 82 4 21 4 21 15 4
AMP PEAK 47(20Q13.12) WILD-TYPE 41 49 26 61 87 51 71

Figure S437.  Get High-res Image Gene #47: 'amp_20q13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S438.  Gene #47: 'amp_20q13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 47(20Q13.12) MUTATED 110 20 21
AMP PEAK 47(20Q13.12) WILD-TYPE 113 130 136

Figure S438.  Get High-res Image Gene #47: 'amp_20q13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q13.12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S439.  Gene #47: 'amp_20q13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 47(20Q13.12) MUTATED 52 5 19 75
AMP PEAK 47(20Q13.12) WILD-TYPE 167 53 118 41

Figure S439.  Get High-res Image Gene #47: 'amp_20q13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.12' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S440.  Gene #47: 'amp_20q13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 47(20Q13.12) MUTATED 77 28 24
AMP PEAK 47(20Q13.12) WILD-TYPE 95 68 106

Figure S440.  Get High-res Image Gene #47: 'amp_20q13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S441.  Gene #47: 'amp_20q13.12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 47(20Q13.12) MUTATED 74 21 34
AMP PEAK 47(20Q13.12) WILD-TYPE 70 94 105

Figure S441.  Get High-res Image Gene #47: 'amp_20q13.12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.33' versus 'MRNA_CNMF'

P value = 0.00883 (Fisher's exact test), Q value = 0.012

Table S442.  Gene #48: 'amp_20q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
AMP PEAK 48(20Q13.33) MUTATED 2 7 0 0
AMP PEAK 48(20Q13.33) WILD-TYPE 12 10 12 10

Figure S442.  Get High-res Image Gene #48: 'amp_20q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q13.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.00159 (Fisher's exact test), Q value = 0.0024

Table S443.  Gene #48: 'amp_20q13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
AMP PEAK 48(20Q13.33) MUTATED 4 5 0 0 0
AMP PEAK 48(20Q13.33) WILD-TYPE 10 4 7 7 16

Figure S443.  Get High-res Image Gene #48: 'amp_20q13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S444.  Gene #48: 'amp_20q13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 48(20Q13.33) MUTATED 117 11 15 3 7
AMP PEAK 48(20Q13.33) WILD-TYPE 52 294 4 6 30

Figure S444.  Get High-res Image Gene #48: 'amp_20q13.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S445.  Gene #48: 'amp_20q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 48(20Q13.33) MUTATED 91 21 24
AMP PEAK 48(20Q13.33) WILD-TYPE 74 68 147

Figure S445.  Get High-res Image Gene #48: 'amp_20q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.33' versus 'RPPA_CNMF'

P value = 0.0453 (Fisher's exact test), Q value = 0.057

Table S446.  Gene #48: 'amp_20q13.33' versus Molecular Subtype #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 48(20Q13.33) MUTATED 6 11 4 1 3 7
AMP PEAK 48(20Q13.33) WILD-TYPE 35 26 35 11 38 17

Figure S446.  Get High-res Image Gene #48: 'amp_20q13.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S447.  Gene #48: 'amp_20q13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 48(20Q13.33) MUTATED 118 14 21
AMP PEAK 48(20Q13.33) WILD-TYPE 116 139 129

Figure S447.  Get High-res Image Gene #48: 'amp_20q13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S448.  Gene #48: 'amp_20q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 48(20Q13.33) MUTATED 78 4 24 5 22 16 4
AMP PEAK 48(20Q13.33) WILD-TYPE 45 49 23 60 86 50 71

Figure S448.  Get High-res Image Gene #48: 'amp_20q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S449.  Gene #48: 'amp_20q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 48(20Q13.33) MUTATED 109 19 22
AMP PEAK 48(20Q13.33) WILD-TYPE 114 131 135

Figure S449.  Get High-res Image Gene #48: 'amp_20q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S450.  Gene #48: 'amp_20q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 48(20Q13.33) MUTATED 53 6 19 72
AMP PEAK 48(20Q13.33) WILD-TYPE 166 52 118 44

Figure S450.  Get High-res Image Gene #48: 'amp_20q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S451.  Gene #48: 'amp_20q13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 48(20Q13.33) MUTATED 76 28 23
AMP PEAK 48(20Q13.33) WILD-TYPE 96 68 107

Figure S451.  Get High-res Image Gene #48: 'amp_20q13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S452.  Gene #48: 'amp_20q13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 48(20Q13.33) MUTATED 71 21 35
AMP PEAK 48(20Q13.33) WILD-TYPE 73 94 104

Figure S452.  Get High-res Image Gene #48: 'amp_20q13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_22q12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S453.  Gene #49: 'amp_22q12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 49(22Q12.2) MUTATED 56 4 1 1 0
AMP PEAK 49(22Q12.2) WILD-TYPE 113 301 18 8 37

Figure S453.  Get High-res Image Gene #49: 'amp_22q12.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_22q12.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S454.  Gene #49: 'amp_22q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 49(22Q12.2) MUTATED 49 8 0
AMP PEAK 49(22Q12.2) WILD-TYPE 116 81 171

Figure S454.  Get High-res Image Gene #49: 'amp_22q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_22q12.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00493 (Fisher's exact test), Q value = 0.0071

Table S455.  Gene #49: 'amp_22q12.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
AMP PEAK 49(22Q12.2) MUTATED 6 0 0 2
AMP PEAK 49(22Q12.2) WILD-TYPE 61 67 43 15

Figure S455.  Get High-res Image Gene #49: 'amp_22q12.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_22q12.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S456.  Gene #49: 'amp_22q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 49(22Q12.2) MUTATED 60 1 0
AMP PEAK 49(22Q12.2) WILD-TYPE 174 152 150

Figure S456.  Get High-res Image Gene #49: 'amp_22q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_22q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S457.  Gene #49: 'amp_22q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 49(22Q12.2) MUTATED 43 1 15 0 2 0 0
AMP PEAK 49(22Q12.2) WILD-TYPE 80 52 32 65 106 66 75

Figure S457.  Get High-res Image Gene #49: 'amp_22q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_22q12.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S458.  Gene #49: 'amp_22q12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 49(22Q12.2) MUTATED 59 2 0
AMP PEAK 49(22Q12.2) WILD-TYPE 164 148 157

Figure S458.  Get High-res Image Gene #49: 'amp_22q12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_22q12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S459.  Gene #49: 'amp_22q12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 49(22Q12.2) MUTATED 16 1 0 44
AMP PEAK 49(22Q12.2) WILD-TYPE 203 57 137 72

Figure S459.  Get High-res Image Gene #49: 'amp_22q12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_22q12.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S460.  Gene #49: 'amp_22q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 49(22Q12.2) MUTATED 43 10 3
AMP PEAK 49(22Q12.2) WILD-TYPE 129 86 127

Figure S460.  Get High-res Image Gene #49: 'amp_22q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_22q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S461.  Gene #49: 'amp_22q12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 49(22Q12.2) MUTATED 40 1 15
AMP PEAK 49(22Q12.2) WILD-TYPE 104 114 124

Figure S461.  Get High-res Image Gene #49: 'amp_22q12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xp11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S462.  Gene #50: 'amp_xp11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 50(XP11.23) MUTATED 48 8 8 3 23
AMP PEAK 50(XP11.23) WILD-TYPE 121 297 11 6 14

Figure S462.  Get High-res Image Gene #50: 'amp_xp11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xp11.23' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00032

Table S463.  Gene #50: 'amp_xp11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 50(XP11.23) MUTATED 43 11 17
AMP PEAK 50(XP11.23) WILD-TYPE 122 78 154

Figure S463.  Get High-res Image Gene #50: 'amp_xp11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xp11.23' versus 'MRNASEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.00047

Table S464.  Gene #50: 'amp_xp11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 50(XP11.23) MUTATED 57 15 18
AMP PEAK 50(XP11.23) WILD-TYPE 177 138 132

Figure S464.  Get High-res Image Gene #50: 'amp_xp11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xp11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.00086

Table S465.  Gene #50: 'amp_xp11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 50(XP11.23) MUTATED 38 5 10 6 14 9 8
AMP PEAK 50(XP11.23) WILD-TYPE 85 48 37 59 94 57 67

Figure S465.  Get High-res Image Gene #50: 'amp_xp11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.23' versus 'MIRSEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00027

Table S466.  Gene #50: 'amp_xp11.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 50(XP11.23) MUTATED 55 18 16
AMP PEAK 50(XP11.23) WILD-TYPE 168 132 141

Figure S466.  Get High-res Image Gene #50: 'amp_xp11.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_xp11.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00228 (Fisher's exact test), Q value = 0.0034

Table S467.  Gene #50: 'amp_xp11.23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 50(XP11.23) MUTATED 34 6 16 33
AMP PEAK 50(XP11.23) WILD-TYPE 185 52 121 83

Figure S467.  Get High-res Image Gene #50: 'amp_xp11.23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_xp11.23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00839 (Fisher's exact test), Q value = 0.012

Table S468.  Gene #50: 'amp_xp11.23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 50(XP11.23) MUTATED 40 15 13
AMP PEAK 50(XP11.23) WILD-TYPE 132 81 117

Figure S468.  Get High-res Image Gene #50: 'amp_xp11.23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_xp11.23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00955 (Fisher's exact test), Q value = 0.013

Table S469.  Gene #50: 'amp_xp11.23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
AMP PEAK 50(XP11.23) MUTATED 32 10 26
AMP PEAK 50(XP11.23) WILD-TYPE 112 105 113

Figure S469.  Get High-res Image Gene #50: 'amp_xp11.23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xq28' versus 'MRNA_CHIERARCHICAL'

P value = 0.0264 (Fisher's exact test), Q value = 0.034

Table S470.  Gene #51: 'amp_xq28' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
AMP PEAK 51(XQ28) MUTATED 1 5 1 1 1
AMP PEAK 51(XQ28) WILD-TYPE 13 4 6 6 15

Figure S470.  Get High-res Image Gene #51: 'amp_xq28' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_xq28' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S471.  Gene #51: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
AMP PEAK 51(XQ28) MUTATED 49 10 8 3 23
AMP PEAK 51(XQ28) WILD-TYPE 120 295 11 6 14

Figure S471.  Get High-res Image Gene #51: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xq28' versus 'METHLYATION_CNMF'

P value = 0.0307 (Fisher's exact test), Q value = 0.04

Table S472.  Gene #51: 'amp_xq28' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
AMP PEAK 51(XQ28) MUTATED 37 14 20
AMP PEAK 51(XQ28) WILD-TYPE 128 75 151

Figure S472.  Get High-res Image Gene #51: 'amp_xq28' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xq28' versus 'MRNASEQ_CNMF'

P value = 0.00082 (Fisher's exact test), Q value = 0.0013

Table S473.  Gene #51: 'amp_xq28' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
AMP PEAK 51(XQ28) MUTATED 57 17 19
AMP PEAK 51(XQ28) WILD-TYPE 177 136 131

Figure S473.  Get High-res Image Gene #51: 'amp_xq28' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xq28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00252 (Fisher's exact test), Q value = 0.0038

Table S474.  Gene #51: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
AMP PEAK 51(XQ28) MUTATED 37 6 10 6 17 9 8
AMP PEAK 51(XQ28) WILD-TYPE 86 47 37 59 91 57 67

Figure S474.  Get High-res Image Gene #51: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_CNMF'

P value = 0.0024 (Fisher's exact test), Q value = 0.0036

Table S475.  Gene #51: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
AMP PEAK 51(XQ28) MUTATED 52 22 16
AMP PEAK 51(XQ28) WILD-TYPE 171 128 141

Figure S475.  Get High-res Image Gene #51: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_xq28' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0128 (Fisher's exact test), Q value = 0.018

Table S476.  Gene #51: 'amp_xq28' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
AMP PEAK 51(XQ28) MUTATED 36 7 16 31
AMP PEAK 51(XQ28) WILD-TYPE 183 51 121 85

Figure S476.  Get High-res Image Gene #51: 'amp_xq28' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.023

Table S477.  Gene #51: 'amp_xq28' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
AMP PEAK 51(XQ28) MUTATED 40 16 14
AMP PEAK 51(XQ28) WILD-TYPE 132 80 116

Figure S477.  Get High-res Image Gene #51: 'amp_xq28' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.21' versus 'MRNA_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.031

Table S478.  Gene #52: 'del_1p36.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 1(1P36.21) MUTATED 2 6 0 0
DEL PEAK 1(1P36.21) WILD-TYPE 12 11 12 10

Figure S478.  Get High-res Image Gene #52: 'del_1p36.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.00176 (Fisher's exact test), Q value = 0.0027

Table S479.  Gene #52: 'del_1p36.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 1(1P36.21) MUTATED 3 5 0 0 0
DEL PEAK 1(1P36.21) WILD-TYPE 11 4 7 7 16

Figure S479.  Get High-res Image Gene #52: 'del_1p36.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S480.  Gene #52: 'del_1p36.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 1(1P36.21) MUTATED 60 3 3 5 0
DEL PEAK 1(1P36.21) WILD-TYPE 109 302 16 4 37

Figure S480.  Get High-res Image Gene #52: 'del_1p36.21' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S481.  Gene #52: 'del_1p36.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 1(1P36.21) MUTATED 39 15 6
DEL PEAK 1(1P36.21) WILD-TYPE 126 74 165

Figure S481.  Get High-res Image Gene #52: 'del_1p36.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.21' versus 'RPPA_CNMF'

P value = 0.00492 (Fisher's exact test), Q value = 0.0071

Table S482.  Gene #52: 'del_1p36.21' versus Molecular Subtype #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 1(1P36.21) MUTATED 3 8 0 0 1 3
DEL PEAK 1(1P36.21) WILD-TYPE 38 29 39 12 40 21

Figure S482.  Get High-res Image Gene #52: 'del_1p36.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p36.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S483.  Gene #52: 'del_1p36.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 1(1P36.21) MUTATED 61 6 4
DEL PEAK 1(1P36.21) WILD-TYPE 173 147 146

Figure S483.  Get High-res Image Gene #52: 'del_1p36.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S484.  Gene #52: 'del_1p36.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 1(1P36.21) MUTATED 42 1 9 4 12 3 0
DEL PEAK 1(1P36.21) WILD-TYPE 81 52 38 61 96 63 75

Figure S484.  Get High-res Image Gene #52: 'del_1p36.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S485.  Gene #52: 'del_1p36.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 1(1P36.21) MUTATED 53 9 6
DEL PEAK 1(1P36.21) WILD-TYPE 170 141 151

Figure S485.  Get High-res Image Gene #52: 'del_1p36.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S486.  Gene #52: 'del_1p36.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 1(1P36.21) MUTATED 27 0 3 38
DEL PEAK 1(1P36.21) WILD-TYPE 192 58 134 78

Figure S486.  Get High-res Image Gene #52: 'del_1p36.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00119 (Fisher's exact test), Q value = 0.0018

Table S487.  Gene #52: 'del_1p36.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 1(1P36.21) MUTATED 24 25 11
DEL PEAK 1(1P36.21) WILD-TYPE 148 71 119

Figure S487.  Get High-res Image Gene #52: 'del_1p36.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00027

Table S488.  Gene #52: 'del_1p36.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 1(1P36.21) MUTATED 27 5 28
DEL PEAK 1(1P36.21) WILD-TYPE 117 110 111

Figure S488.  Get High-res Image Gene #52: 'del_1p36.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.11' versus 'MRNA_CHIERARCHICAL'

P value = 0.00719 (Fisher's exact test), Q value = 0.01

Table S489.  Gene #53: 'del_1p36.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 2(1P36.11) MUTATED 2 4 0 0 0
DEL PEAK 2(1P36.11) WILD-TYPE 12 5 7 7 16

Figure S489.  Get High-res Image Gene #53: 'del_1p36.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S490.  Gene #53: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 2(1P36.11) MUTATED 72 2 4 5 0
DEL PEAK 2(1P36.11) WILD-TYPE 97 303 15 4 37

Figure S490.  Get High-res Image Gene #53: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S491.  Gene #53: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 2(1P36.11) MUTATED 56 12 6
DEL PEAK 2(1P36.11) WILD-TYPE 109 77 165

Figure S491.  Get High-res Image Gene #53: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.11' versus 'RPPA_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.03

Table S492.  Gene #53: 'del_1p36.11' versus Molecular Subtype #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 2(1P36.11) MUTATED 3 7 0 1 1 2
DEL PEAK 2(1P36.11) WILD-TYPE 38 30 39 11 40 22

Figure S492.  Get High-res Image Gene #53: 'del_1p36.11' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S493.  Gene #53: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 2(1P36.11) MUTATED 73 6 4
DEL PEAK 2(1P36.11) WILD-TYPE 161 147 146

Figure S493.  Get High-res Image Gene #53: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S494.  Gene #53: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 2(1P36.11) MUTATED 51 1 10 4 14 3 0
DEL PEAK 2(1P36.11) WILD-TYPE 72 52 37 61 94 63 75

Figure S494.  Get High-res Image Gene #53: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S495.  Gene #53: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 2(1P36.11) MUTATED 64 9 7
DEL PEAK 2(1P36.11) WILD-TYPE 159 141 150

Figure S495.  Get High-res Image Gene #53: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S496.  Gene #53: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 2(1P36.11) MUTATED 33 0 3 44
DEL PEAK 2(1P36.11) WILD-TYPE 186 58 134 72

Figure S496.  Get High-res Image Gene #53: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.0016

Table S497.  Gene #53: 'del_1p36.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 2(1P36.11) MUTATED 40 22 11
DEL PEAK 2(1P36.11) WILD-TYPE 132 74 119

Figure S497.  Get High-res Image Gene #53: 'del_1p36.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S498.  Gene #53: 'del_1p36.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 2(1P36.11) MUTATED 42 6 25
DEL PEAK 2(1P36.11) WILD-TYPE 102 109 114

Figure S498.  Get High-res Image Gene #53: 'del_1p36.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2p25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S499.  Gene #54: 'del_2p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 3(2P25.3) MUTATED 24 2 0 0 0
DEL PEAK 3(2P25.3) WILD-TYPE 145 303 19 9 37

Figure S499.  Get High-res Image Gene #54: 'del_2p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_2p25.3' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00024

Table S500.  Gene #54: 'del_2p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 3(2P25.3) MUTATED 19 4 2
DEL PEAK 3(2P25.3) WILD-TYPE 146 85 169

Figure S500.  Get High-res Image Gene #54: 'del_2p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2p25.3' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 8.9e-05

Table S501.  Gene #54: 'del_2p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 3(2P25.3) MUTATED 22 1 3
DEL PEAK 3(2P25.3) WILD-TYPE 212 152 147

Figure S501.  Get High-res Image Gene #54: 'del_2p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00027

Table S502.  Gene #54: 'del_2p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 3(2P25.3) MUTATED 16 1 3 0 3 3 0
DEL PEAK 3(2P25.3) WILD-TYPE 107 52 44 65 105 63 75

Figure S502.  Get High-res Image Gene #54: 'del_2p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2p25.3' versus 'MIRSEQ_CNMF'

P value = 0.00149 (Fisher's exact test), Q value = 0.0023

Table S503.  Gene #54: 'del_2p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 3(2P25.3) MUTATED 20 3 3
DEL PEAK 3(2P25.3) WILD-TYPE 203 147 154

Figure S503.  Get High-res Image Gene #54: 'del_2p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.00079

Table S504.  Gene #54: 'del_2p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 3(2P25.3) MUTATED 7 1 3 15
DEL PEAK 3(2P25.3) WILD-TYPE 212 57 134 101

Figure S504.  Get High-res Image Gene #54: 'del_2p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MRNA_CNMF'

P value = 0.0385 (Fisher's exact test), Q value = 0.049

Table S505.  Gene #55: 'del_2q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 4(2Q22.1) MUTATED 0 4 0 0
DEL PEAK 4(2Q22.1) WILD-TYPE 14 13 12 10

Figure S505.  Get High-res Image Gene #55: 'del_2q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_2q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00067 (Fisher's exact test), Q value = 0.0011

Table S506.  Gene #55: 'del_2q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 4(2Q22.1) MUTATED 0 4 0 0 0
DEL PEAK 4(2Q22.1) WILD-TYPE 14 5 7 7 16

Figure S506.  Get High-res Image Gene #55: 'del_2q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_2q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S507.  Gene #55: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 4(2Q22.1) MUTATED 46 0 2 0 0
DEL PEAK 4(2Q22.1) WILD-TYPE 123 305 17 9 37

Figure S507.  Get High-res Image Gene #55: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S508.  Gene #55: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 4(2Q22.1) MUTATED 30 8 4
DEL PEAK 4(2Q22.1) WILD-TYPE 135 81 167

Figure S508.  Get High-res Image Gene #55: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q22.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0114 (Fisher's exact test), Q value = 0.016

Table S509.  Gene #55: 'del_2q22.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
DEL PEAK 4(2Q22.1) MUTATED 4 1 0 3
DEL PEAK 4(2Q22.1) WILD-TYPE 63 66 43 14

Figure S509.  Get High-res Image Gene #55: 'del_2q22.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S510.  Gene #55: 'del_2q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 4(2Q22.1) MUTATED 43 0 5
DEL PEAK 4(2Q22.1) WILD-TYPE 191 153 145

Figure S510.  Get High-res Image Gene #55: 'del_2q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S511.  Gene #55: 'del_2q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 4(2Q22.1) MUTATED 31 0 3 0 9 5 0
DEL PEAK 4(2Q22.1) WILD-TYPE 92 53 44 65 99 61 75

Figure S511.  Get High-res Image Gene #55: 'del_2q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S512.  Gene #55: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 4(2Q22.1) MUTATED 37 5 4
DEL PEAK 4(2Q22.1) WILD-TYPE 186 145 153

Figure S512.  Get High-res Image Gene #55: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S513.  Gene #55: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 4(2Q22.1) MUTATED 19 0 4 23
DEL PEAK 4(2Q22.1) WILD-TYPE 200 58 133 93

Figure S513.  Get High-res Image Gene #55: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00099 (Fisher's exact test), Q value = 0.0016

Table S514.  Gene #55: 'del_2q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 4(2Q22.1) MUTATED 29 5 7
DEL PEAK 4(2Q22.1) WILD-TYPE 143 91 123

Figure S514.  Get High-res Image Gene #55: 'del_2q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_2q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00103 (Fisher's exact test), Q value = 0.0016

Table S515.  Gene #55: 'del_2q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 4(2Q22.1) MUTATED 26 7 8
DEL PEAK 4(2Q22.1) WILD-TYPE 118 108 131

Figure S515.  Get High-res Image Gene #55: 'del_2q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S516.  Gene #56: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 5(2Q37.3) MUTATED 49 1 2 0 1
DEL PEAK 5(2Q37.3) WILD-TYPE 120 304 17 9 36

Figure S516.  Get High-res Image Gene #56: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S517.  Gene #56: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 5(2Q37.3) MUTATED 35 6 8
DEL PEAK 5(2Q37.3) WILD-TYPE 130 83 163

Figure S517.  Get High-res Image Gene #56: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S518.  Gene #56: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 5(2Q37.3) MUTATED 42 3 7
DEL PEAK 5(2Q37.3) WILD-TYPE 192 150 143

Figure S518.  Get High-res Image Gene #56: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.7e-05

Table S519.  Gene #56: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 5(2Q37.3) MUTATED 24 0 9 3 10 6 0
DEL PEAK 5(2Q37.3) WILD-TYPE 99 53 38 62 98 60 75

Figure S519.  Get High-res Image Gene #56: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S520.  Gene #56: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 5(2Q37.3) MUTATED 39 5 8
DEL PEAK 5(2Q37.3) WILD-TYPE 184 145 149

Figure S520.  Get High-res Image Gene #56: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00071 (Fisher's exact test), Q value = 0.0011

Table S521.  Gene #56: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 5(2Q37.3) MUTATED 21 1 8 22
DEL PEAK 5(2Q37.3) WILD-TYPE 198 57 129 94

Figure S521.  Get High-res Image Gene #56: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00747 (Fisher's exact test), Q value = 0.011

Table S522.  Gene #57: 'del_3p14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 6(3P14.2) MUTATED 2 4 0 0 0
DEL PEAK 6(3P14.2) WILD-TYPE 12 5 7 7 16

Figure S522.  Get High-res Image Gene #57: 'del_3p14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S523.  Gene #57: 'del_3p14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 6(3P14.2) MUTATED 72 0 4 2 1
DEL PEAK 6(3P14.2) WILD-TYPE 97 305 15 7 36

Figure S523.  Get High-res Image Gene #57: 'del_3p14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S524.  Gene #57: 'del_3p14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 6(3P14.2) MUTATED 51 12 5
DEL PEAK 6(3P14.2) WILD-TYPE 114 77 166

Figure S524.  Get High-res Image Gene #57: 'del_3p14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p14.2' versus 'RPPA_CNMF'

P value = 0.00322 (Fisher's exact test), Q value = 0.0047

Table S525.  Gene #57: 'del_3p14.2' versus Molecular Subtype #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 6(3P14.2) MUTATED 3 10 1 0 1 2
DEL PEAK 6(3P14.2) WILD-TYPE 38 27 38 12 40 22

Figure S525.  Get High-res Image Gene #57: 'del_3p14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S526.  Gene #57: 'del_3p14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 6(3P14.2) MUTATED 73 1 4
DEL PEAK 6(3P14.2) WILD-TYPE 161 152 146

Figure S526.  Get High-res Image Gene #57: 'del_3p14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S527.  Gene #57: 'del_3p14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 6(3P14.2) MUTATED 49 0 12 0 12 5 0
DEL PEAK 6(3P14.2) WILD-TYPE 74 53 35 65 96 61 75

Figure S527.  Get High-res Image Gene #57: 'del_3p14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S528.  Gene #57: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 6(3P14.2) MUTATED 62 11 4
DEL PEAK 6(3P14.2) WILD-TYPE 161 139 153

Figure S528.  Get High-res Image Gene #57: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S529.  Gene #57: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 6(3P14.2) MUTATED 34 1 3 39
DEL PEAK 6(3P14.2) WILD-TYPE 185 57 134 77

Figure S529.  Get High-res Image Gene #57: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.00056

Table S530.  Gene #57: 'del_3p14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 6(3P14.2) MUTATED 41 16 9
DEL PEAK 6(3P14.2) WILD-TYPE 131 80 121

Figure S530.  Get High-res Image Gene #57: 'del_3p14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S531.  Gene #57: 'del_3p14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 6(3P14.2) MUTATED 42 4 20
DEL PEAK 6(3P14.2) WILD-TYPE 102 111 119

Figure S531.  Get High-res Image Gene #57: 'del_3p14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q13.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S532.  Gene #58: 'del_3q13.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 7(3Q13.31) MUTATED 36 4 0 2 1
DEL PEAK 7(3Q13.31) WILD-TYPE 133 301 19 7 36

Figure S532.  Get High-res Image Gene #58: 'del_3q13.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q13.31' versus 'METHLYATION_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.00089

Table S533.  Gene #58: 'del_3q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 7(3Q13.31) MUTATED 24 7 5
DEL PEAK 7(3Q13.31) WILD-TYPE 141 82 166

Figure S533.  Get High-res Image Gene #58: 'del_3q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3q13.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S534.  Gene #58: 'del_3q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 7(3Q13.31) MUTATED 35 2 6
DEL PEAK 7(3Q13.31) WILD-TYPE 199 151 144

Figure S534.  Get High-res Image Gene #58: 'del_3q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S535.  Gene #58: 'del_3q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 7(3Q13.31) MUTATED 28 2 4 0 3 5 1
DEL PEAK 7(3Q13.31) WILD-TYPE 95 51 43 65 105 61 74

Figure S535.  Get High-res Image Gene #58: 'del_3q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3q13.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S536.  Gene #58: 'del_3q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 7(3Q13.31) MUTATED 32 4 5
DEL PEAK 7(3Q13.31) WILD-TYPE 191 146 152

Figure S536.  Get High-res Image Gene #58: 'del_3q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 5.4e-05

Table S537.  Gene #58: 'del_3q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 7(3Q13.31) MUTATED 13 2 4 22
DEL PEAK 7(3Q13.31) WILD-TYPE 206 56 133 94

Figure S537.  Get High-res Image Gene #58: 'del_3q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3q13.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.021

Table S538.  Gene #58: 'del_3q13.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 7(3Q13.31) MUTATED 19 11 4
DEL PEAK 7(3Q13.31) WILD-TYPE 153 85 126

Figure S538.  Get High-res Image Gene #58: 'del_3q13.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4p16.3' versus 'MRNA_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.018

Table S539.  Gene #59: 'del_4p16.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 8(4P16.3) MUTATED 1 6 0 0
DEL PEAK 8(4P16.3) WILD-TYPE 13 11 12 10

Figure S539.  Get High-res Image Gene #59: 'del_4p16.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4p16.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00114 (Fisher's exact test), Q value = 0.0018

Table S540.  Gene #59: 'del_4p16.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 8(4P16.3) MUTATED 2 5 0 0 0
DEL PEAK 8(4P16.3) WILD-TYPE 12 4 7 7 16

Figure S540.  Get High-res Image Gene #59: 'del_4p16.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4p16.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S541.  Gene #59: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 8(4P16.3) MUTATED 79 4 5 4 2
DEL PEAK 8(4P16.3) WILD-TYPE 90 301 14 5 35

Figure S541.  Get High-res Image Gene #59: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S542.  Gene #59: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 8(4P16.3) MUTATED 62 13 7
DEL PEAK 8(4P16.3) WILD-TYPE 103 76 164

Figure S542.  Get High-res Image Gene #59: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p16.3' versus 'RPPA_CNMF'

P value = 0.00421 (Fisher's exact test), Q value = 0.0061

Table S543.  Gene #59: 'del_4p16.3' versus Molecular Subtype #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 8(4P16.3) MUTATED 5 9 0 1 2 5
DEL PEAK 8(4P16.3) WILD-TYPE 36 28 39 11 39 19

Figure S543.  Get High-res Image Gene #59: 'del_4p16.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4p16.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S544.  Gene #59: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 8(4P16.3) MUTATED 79 6 9
DEL PEAK 8(4P16.3) WILD-TYPE 155 147 141

Figure S544.  Get High-res Image Gene #59: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S545.  Gene #59: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 8(4P16.3) MUTATED 55 1 15 2 14 6 1
DEL PEAK 8(4P16.3) WILD-TYPE 68 52 32 63 94 60 74

Figure S545.  Get High-res Image Gene #59: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S546.  Gene #59: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 8(4P16.3) MUTATED 70 12 9
DEL PEAK 8(4P16.3) WILD-TYPE 153 138 148

Figure S546.  Get High-res Image Gene #59: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S547.  Gene #59: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 8(4P16.3) MUTATED 32 1 6 52
DEL PEAK 8(4P16.3) WILD-TYPE 187 57 131 64

Figure S547.  Get High-res Image Gene #59: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00014

Table S548.  Gene #59: 'del_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 8(4P16.3) MUTATED 46 24 10
DEL PEAK 8(4P16.3) WILD-TYPE 126 72 120

Figure S548.  Get High-res Image Gene #59: 'del_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 5.4e-05

Table S549.  Gene #59: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 8(4P16.3) MUTATED 45 8 27
DEL PEAK 8(4P16.3) WILD-TYPE 99 107 112

Figure S549.  Get High-res Image Gene #59: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p15.2' versus 'MRNA_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.018

Table S550.  Gene #60: 'del_4p15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 9(4P15.2) MUTATED 1 6 0 0
DEL PEAK 9(4P15.2) WILD-TYPE 13 11 12 10

Figure S550.  Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4p15.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0095 (Fisher's exact test), Q value = 0.013

Table S551.  Gene #60: 'del_4p15.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 9(4P15.2) MUTATED 3 4 0 0 0
DEL PEAK 9(4P15.2) WILD-TYPE 11 5 7 7 16

Figure S551.  Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4p15.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S552.  Gene #60: 'del_4p15.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 9(4P15.2) MUTATED 84 3 5 4 2
DEL PEAK 9(4P15.2) WILD-TYPE 85 302 14 5 35

Figure S552.  Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p15.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S553.  Gene #60: 'del_4p15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 9(4P15.2) MUTATED 67 14 6
DEL PEAK 9(4P15.2) WILD-TYPE 98 75 165

Figure S553.  Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p15.2' versus 'RPPA_CNMF'

P value = 0.00789 (Fisher's exact test), Q value = 0.011

Table S554.  Gene #60: 'del_4p15.2' versus Molecular Subtype #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 9(4P15.2) MUTATED 5 8 0 1 2 5
DEL PEAK 9(4P15.2) WILD-TYPE 36 29 39 11 39 19

Figure S554.  Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4p15.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S555.  Gene #60: 'del_4p15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 9(4P15.2) MUTATED 84 6 8
DEL PEAK 9(4P15.2) WILD-TYPE 150 147 142

Figure S555.  Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p15.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S556.  Gene #60: 'del_4p15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 9(4P15.2) MUTATED 57 1 15 2 17 5 1
DEL PEAK 9(4P15.2) WILD-TYPE 66 52 32 63 91 61 74

Figure S556.  Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p15.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S557.  Gene #60: 'del_4p15.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 9(4P15.2) MUTATED 76 12 8
DEL PEAK 9(4P15.2) WILD-TYPE 147 138 149

Figure S557.  Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4p15.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S558.  Gene #60: 'del_4p15.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 9(4P15.2) MUTATED 36 1 5 54
DEL PEAK 9(4P15.2) WILD-TYPE 183 57 132 62

Figure S558.  Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4p15.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S559.  Gene #60: 'del_4p15.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 9(4P15.2) MUTATED 52 24 10
DEL PEAK 9(4P15.2) WILD-TYPE 120 72 120

Figure S559.  Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4p15.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S560.  Gene #60: 'del_4p15.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 9(4P15.2) MUTATED 49 7 30
DEL PEAK 9(4P15.2) WILD-TYPE 95 108 109

Figure S560.  Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.1' versus 'MRNA_CNMF'

P value = 0.00365 (Fisher's exact test), Q value = 0.0053

Table S561.  Gene #61: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 10(4Q22.1) MUTATED 1 7 0 0
DEL PEAK 10(4Q22.1) WILD-TYPE 13 10 12 10

Figure S561.  Get High-res Image Gene #61: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00029

Table S562.  Gene #61: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 10(4Q22.1) MUTATED 2 6 0 0 0
DEL PEAK 10(4Q22.1) WILD-TYPE 12 3 7 7 16

Figure S562.  Get High-res Image Gene #61: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S563.  Gene #61: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 10(4Q22.1) MUTATED 94 2 4 4 2
DEL PEAK 10(4Q22.1) WILD-TYPE 75 303 15 5 35

Figure S563.  Get High-res Image Gene #61: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S564.  Gene #61: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 10(4Q22.1) MUTATED 71 16 5
DEL PEAK 10(4Q22.1) WILD-TYPE 94 73 166

Figure S564.  Get High-res Image Gene #61: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q22.1' versus 'RPPA_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.02

Table S565.  Gene #61: 'del_4q22.1' versus Molecular Subtype #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 10(4Q22.1) MUTATED 6 8 1 1 1 5
DEL PEAK 10(4Q22.1) WILD-TYPE 35 29 38 11 40 19

Figure S565.  Get High-res Image Gene #61: 'del_4q22.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S566.  Gene #61: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 10(4Q22.1) MUTATED 94 5 7
DEL PEAK 10(4Q22.1) WILD-TYPE 140 148 143

Figure S566.  Get High-res Image Gene #61: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S567.  Gene #61: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 10(4Q22.1) MUTATED 68 1 12 2 18 5 0
DEL PEAK 10(4Q22.1) WILD-TYPE 55 52 35 63 90 61 75

Figure S567.  Get High-res Image Gene #61: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S568.  Gene #61: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 10(4Q22.1) MUTATED 86 10 7
DEL PEAK 10(4Q22.1) WILD-TYPE 137 140 150

Figure S568.  Get High-res Image Gene #61: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S569.  Gene #61: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 10(4Q22.1) MUTATED 38 0 3 62
DEL PEAK 10(4Q22.1) WILD-TYPE 181 58 134 54

Figure S569.  Get High-res Image Gene #61: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S570.  Gene #61: 'del_4q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 10(4Q22.1) MUTATED 56 26 8
DEL PEAK 10(4Q22.1) WILD-TYPE 116 70 122

Figure S570.  Get High-res Image Gene #61: 'del_4q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S571.  Gene #61: 'del_4q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 10(4Q22.1) MUTATED 48 5 37
DEL PEAK 10(4Q22.1) WILD-TYPE 96 110 102

Figure S571.  Get High-res Image Gene #61: 'del_4q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'MRNA_CNMF'

P value = 0.00396 (Fisher's exact test), Q value = 0.0058

Table S572.  Gene #62: 'del_4q34.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 11(4Q34.3) MUTATED 1 7 0 0
DEL PEAK 11(4Q34.3) WILD-TYPE 13 10 12 10

Figure S572.  Get High-res Image Gene #62: 'del_4q34.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q34.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00022

Table S573.  Gene #62: 'del_4q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 11(4Q34.3) MUTATED 2 6 0 0 0
DEL PEAK 11(4Q34.3) WILD-TYPE 12 3 7 7 16

Figure S573.  Get High-res Image Gene #62: 'del_4q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S574.  Gene #62: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 11(4Q34.3) MUTATED 111 6 6 4 3
DEL PEAK 11(4Q34.3) WILD-TYPE 58 299 13 5 34

Figure S574.  Get High-res Image Gene #62: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S575.  Gene #62: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 11(4Q34.3) MUTATED 81 22 11
DEL PEAK 11(4Q34.3) WILD-TYPE 84 67 160

Figure S575.  Get High-res Image Gene #62: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S576.  Gene #62: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 11(4Q34.3) MUTATED 114 8 8
DEL PEAK 11(4Q34.3) WILD-TYPE 120 145 142

Figure S576.  Get High-res Image Gene #62: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S577.  Gene #62: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 11(4Q34.3) MUTATED 81 1 16 3 23 6 0
DEL PEAK 11(4Q34.3) WILD-TYPE 42 52 31 62 85 60 75

Figure S577.  Get High-res Image Gene #62: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S578.  Gene #62: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 11(4Q34.3) MUTATED 99 20 8
DEL PEAK 11(4Q34.3) WILD-TYPE 124 130 149

Figure S578.  Get High-res Image Gene #62: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S579.  Gene #62: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 11(4Q34.3) MUTATED 51 1 5 70
DEL PEAK 11(4Q34.3) WILD-TYPE 168 57 132 46

Figure S579.  Get High-res Image Gene #62: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S580.  Gene #62: 'del_4q34.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 11(4Q34.3) MUTATED 66 33 13
DEL PEAK 11(4Q34.3) WILD-TYPE 106 63 117

Figure S580.  Get High-res Image Gene #62: 'del_4q34.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S581.  Gene #62: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 11(4Q34.3) MUTATED 59 7 46
DEL PEAK 11(4Q34.3) WILD-TYPE 85 108 93

Figure S581.  Get High-res Image Gene #62: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q12.1' versus 'MRNA_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.018

Table S582.  Gene #63: 'del_5q12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 12(5Q12.1) MUTATED 1 6 0 0
DEL PEAK 12(5Q12.1) WILD-TYPE 13 11 12 10

Figure S582.  Get High-res Image Gene #63: 'del_5q12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q12.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0092 (Fisher's exact test), Q value = 0.013

Table S583.  Gene #63: 'del_5q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 12(5Q12.1) MUTATED 3 4 0 0 0
DEL PEAK 12(5Q12.1) WILD-TYPE 11 5 7 7 16

Figure S583.  Get High-res Image Gene #63: 'del_5q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S584.  Gene #63: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 12(5Q12.1) MUTATED 103 0 2 2 4
DEL PEAK 12(5Q12.1) WILD-TYPE 66 305 17 7 33

Figure S584.  Get High-res Image Gene #63: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S585.  Gene #63: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 12(5Q12.1) MUTATED 75 14 8
DEL PEAK 12(5Q12.1) WILD-TYPE 90 75 163

Figure S585.  Get High-res Image Gene #63: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q12.1' versus 'RPPA_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.00045

Table S586.  Gene #63: 'del_5q12.1' versus Molecular Subtype #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 12(5Q12.1) MUTATED 6 9 1 0 0 6
DEL PEAK 12(5Q12.1) WILD-TYPE 35 28 38 12 41 18

Figure S586.  Get High-res Image Gene #63: 'del_5q12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_5q12.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.019

Table S587.  Gene #63: 'del_5q12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
DEL PEAK 12(5Q12.1) MUTATED 12 5 1 4
DEL PEAK 12(5Q12.1) WILD-TYPE 55 62 42 13

Figure S587.  Get High-res Image Gene #63: 'del_5q12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_5q12.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S588.  Gene #63: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 12(5Q12.1) MUTATED 96 4 10
DEL PEAK 12(5Q12.1) WILD-TYPE 138 149 140

Figure S588.  Get High-res Image Gene #63: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S589.  Gene #63: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 12(5Q12.1) MUTATED 69 0 11 2 18 10 0
DEL PEAK 12(5Q12.1) WILD-TYPE 54 53 36 63 90 56 75

Figure S589.  Get High-res Image Gene #63: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S590.  Gene #63: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 12(5Q12.1) MUTATED 88 12 10
DEL PEAK 12(5Q12.1) WILD-TYPE 135 138 147

Figure S590.  Get High-res Image Gene #63: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S591.  Gene #63: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 12(5Q12.1) MUTATED 44 0 8 58
DEL PEAK 12(5Q12.1) WILD-TYPE 175 58 129 58

Figure S591.  Get High-res Image Gene #63: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S592.  Gene #63: 'del_5q12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 12(5Q12.1) MUTATED 61 22 12
DEL PEAK 12(5Q12.1) WILD-TYPE 111 74 118

Figure S592.  Get High-res Image Gene #63: 'del_5q12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S593.  Gene #63: 'del_5q12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 12(5Q12.1) MUTATED 54 10 31
DEL PEAK 12(5Q12.1) WILD-TYPE 90 105 108

Figure S593.  Get High-res Image Gene #63: 'del_5q12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q26' versus 'MRNA_CHIERARCHICAL'

P value = 0.0291 (Fisher's exact test), Q value = 0.038

Table S594.  Gene #64: 'del_6q26' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 13(6Q26) MUTATED 1 3 0 0 0
DEL PEAK 13(6Q26) WILD-TYPE 13 6 7 7 16

Figure S594.  Get High-res Image Gene #64: 'del_6q26' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S595.  Gene #64: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 13(6Q26) MUTATED 39 4 2 1 0
DEL PEAK 13(6Q26) WILD-TYPE 130 301 17 8 37

Figure S595.  Get High-res Image Gene #64: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S596.  Gene #64: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 13(6Q26) MUTATED 31 8 1
DEL PEAK 13(6Q26) WILD-TYPE 134 81 170

Figure S596.  Get High-res Image Gene #64: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S597.  Gene #64: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 13(6Q26) MUTATED 42 2 2
DEL PEAK 13(6Q26) WILD-TYPE 192 151 148

Figure S597.  Get High-res Image Gene #64: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S598.  Gene #64: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 13(6Q26) MUTATED 36 1 3 0 5 0 1
DEL PEAK 13(6Q26) WILD-TYPE 87 52 44 65 103 66 74

Figure S598.  Get High-res Image Gene #64: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S599.  Gene #64: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 13(6Q26) MUTATED 37 6 2
DEL PEAK 13(6Q26) WILD-TYPE 186 144 155

Figure S599.  Get High-res Image Gene #64: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S600.  Gene #64: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 13(6Q26) MUTATED 16 0 1 28
DEL PEAK 13(6Q26) WILD-TYPE 203 58 136 88

Figure S600.  Get High-res Image Gene #64: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00078 (Fisher's exact test), Q value = 0.0012

Table S601.  Gene #64: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 13(6Q26) MUTATED 23 13 3
DEL PEAK 13(6Q26) WILD-TYPE 149 83 127

Figure S601.  Get High-res Image Gene #64: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00011

Table S602.  Gene #64: 'del_6q26' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 13(6Q26) MUTATED 19 1 19
DEL PEAK 13(6Q26) WILD-TYPE 125 114 120

Figure S602.  Get High-res Image Gene #64: 'del_6q26' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7p22.3' versus 'MRNA_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00024

Table S603.  Gene #65: 'del_7p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 14(7P22.3) MUTATED 0 8 0 0
DEL PEAK 14(7P22.3) WILD-TYPE 14 9 12 10

Figure S603.  Get High-res Image Gene #65: 'del_7p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_7p22.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00162 (Fisher's exact test), Q value = 0.0025

Table S604.  Gene #65: 'del_7p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 14(7P22.3) MUTATED 3 5 0 0 0
DEL PEAK 14(7P22.3) WILD-TYPE 11 4 7 7 16

Figure S604.  Get High-res Image Gene #65: 'del_7p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_7p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S605.  Gene #65: 'del_7p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 14(7P22.3) MUTATED 65 4 1 1 1
DEL PEAK 14(7P22.3) WILD-TYPE 104 301 18 8 36

Figure S605.  Get High-res Image Gene #65: 'del_7p22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_7p22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S606.  Gene #65: 'del_7p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 14(7P22.3) MUTATED 45 13 4
DEL PEAK 14(7P22.3) WILD-TYPE 120 76 167

Figure S606.  Get High-res Image Gene #65: 'del_7p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_7p22.3' versus 'RPPA_CNMF'

P value = 0.00744 (Fisher's exact test), Q value = 0.011

Table S607.  Gene #65: 'del_7p22.3' versus Molecular Subtype #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 14(7P22.3) MUTATED 6 5 0 1 0 3
DEL PEAK 14(7P22.3) WILD-TYPE 35 32 39 11 41 21

Figure S607.  Get High-res Image Gene #65: 'del_7p22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_7p22.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0217 (Fisher's exact test), Q value = 0.029

Table S608.  Gene #65: 'del_7p22.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
DEL PEAK 14(7P22.3) MUTATED 9 2 1 3
DEL PEAK 14(7P22.3) WILD-TYPE 58 65 42 14

Figure S608.  Get High-res Image Gene #65: 'del_7p22.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_7p22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S609.  Gene #65: 'del_7p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 14(7P22.3) MUTATED 66 2 4
DEL PEAK 14(7P22.3) WILD-TYPE 168 151 146

Figure S609.  Get High-res Image Gene #65: 'del_7p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7p22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S610.  Gene #65: 'del_7p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 14(7P22.3) MUTATED 51 0 9 0 8 4 0
DEL PEAK 14(7P22.3) WILD-TYPE 72 53 38 65 100 62 75

Figure S610.  Get High-res Image Gene #65: 'del_7p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7p22.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S611.  Gene #65: 'del_7p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 14(7P22.3) MUTATED 57 8 5
DEL PEAK 14(7P22.3) WILD-TYPE 166 142 152

Figure S611.  Get High-res Image Gene #65: 'del_7p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_7p22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S612.  Gene #65: 'del_7p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 14(7P22.3) MUTATED 23 0 2 45
DEL PEAK 14(7P22.3) WILD-TYPE 196 58 135 71

Figure S612.  Get High-res Image Gene #65: 'del_7p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7p22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00017

Table S613.  Gene #65: 'del_7p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 14(7P22.3) MUTATED 34 18 6
DEL PEAK 14(7P22.3) WILD-TYPE 138 78 124

Figure S613.  Get High-res Image Gene #65: 'del_7p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 5.4e-05

Table S614.  Gene #65: 'del_7p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 14(7P22.3) MUTATED 33 4 21
DEL PEAK 14(7P22.3) WILD-TYPE 111 111 118

Figure S614.  Get High-res Image Gene #65: 'del_7p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S615.  Gene #66: 'del_7q11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 15(7Q11.22) MUTATED 39 0 0 1 1
DEL PEAK 15(7Q11.22) WILD-TYPE 130 305 19 8 36

Figure S615.  Get High-res Image Gene #66: 'del_7q11.22' versus Molecular Subtype #3: 'CN_CNMF'

'del_7q11.22' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.7e-05

Table S616.  Gene #66: 'del_7q11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 15(7Q11.22) MUTATED 27 8 3
DEL PEAK 15(7Q11.22) WILD-TYPE 138 81 168

Figure S616.  Get High-res Image Gene #66: 'del_7q11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_7q11.22' versus 'RPPA_CNMF'

P value = 0.0383 (Fisher's exact test), Q value = 0.049

Table S617.  Gene #66: 'del_7q11.22' versus Molecular Subtype #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 15(7Q11.22) MUTATED 5 3 0 0 0 2
DEL PEAK 15(7Q11.22) WILD-TYPE 36 34 39 12 41 22

Figure S617.  Get High-res Image Gene #66: 'del_7q11.22' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_7q11.22' versus 'RPPA_CHIERARCHICAL'

P value = 0.0156 (Fisher's exact test), Q value = 0.021

Table S618.  Gene #66: 'del_7q11.22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
DEL PEAK 15(7Q11.22) MUTATED 7 1 0 2
DEL PEAK 15(7Q11.22) WILD-TYPE 60 66 43 15

Figure S618.  Get High-res Image Gene #66: 'del_7q11.22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_7q11.22' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S619.  Gene #66: 'del_7q11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 15(7Q11.22) MUTATED 39 0 2
DEL PEAK 15(7Q11.22) WILD-TYPE 195 153 148

Figure S619.  Get High-res Image Gene #66: 'del_7q11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7q11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S620.  Gene #66: 'del_7q11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 15(7Q11.22) MUTATED 27 0 4 0 7 3 0
DEL PEAK 15(7Q11.22) WILD-TYPE 96 53 43 65 101 63 75

Figure S620.  Get High-res Image Gene #66: 'del_7q11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7q11.22' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S621.  Gene #66: 'del_7q11.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 15(7Q11.22) MUTATED 33 4 3
DEL PEAK 15(7Q11.22) WILD-TYPE 190 146 154

Figure S621.  Get High-res Image Gene #66: 'del_7q11.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_7q11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S622.  Gene #66: 'del_7q11.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 15(7Q11.22) MUTATED 15 0 2 23
DEL PEAK 15(7Q11.22) WILD-TYPE 204 58 135 93

Figure S622.  Get High-res Image Gene #66: 'del_7q11.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7q11.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0074 (Fisher's exact test), Q value = 0.011

Table S623.  Gene #66: 'del_7q11.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 15(7Q11.22) MUTATED 24 7 5
DEL PEAK 15(7Q11.22) WILD-TYPE 148 89 125

Figure S623.  Get High-res Image Gene #66: 'del_7q11.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7q11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00129 (Fisher's exact test), Q value = 0.002

Table S624.  Gene #66: 'del_7q11.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 15(7Q11.22) MUTATED 22 3 11
DEL PEAK 15(7Q11.22) WILD-TYPE 122 112 128

Figure S624.  Get High-res Image Gene #66: 'del_7q11.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S625.  Gene #67: 'del_7q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 16(7Q31.1) MUTATED 54 0 0 1 0
DEL PEAK 16(7Q31.1) WILD-TYPE 115 305 19 8 37

Figure S625.  Get High-res Image Gene #67: 'del_7q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_7q31.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S626.  Gene #67: 'del_7q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 16(7Q31.1) MUTATED 38 11 1
DEL PEAK 16(7Q31.1) WILD-TYPE 127 78 170

Figure S626.  Get High-res Image Gene #67: 'del_7q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_7q31.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0118 (Fisher's exact test), Q value = 0.016

Table S627.  Gene #67: 'del_7q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
DEL PEAK 16(7Q31.1) MUTATED 9 2 0 2
DEL PEAK 16(7Q31.1) WILD-TYPE 58 65 43 15

Figure S627.  Get High-res Image Gene #67: 'del_7q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_7q31.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S628.  Gene #67: 'del_7q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 16(7Q31.1) MUTATED 54 0 1
DEL PEAK 16(7Q31.1) WILD-TYPE 180 153 149

Figure S628.  Get High-res Image Gene #67: 'del_7q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S629.  Gene #67: 'del_7q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 16(7Q31.1) MUTATED 44 0 4 0 5 2 0
DEL PEAK 16(7Q31.1) WILD-TYPE 79 53 43 65 103 64 75

Figure S629.  Get High-res Image Gene #67: 'del_7q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7q31.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S630.  Gene #67: 'del_7q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 16(7Q31.1) MUTATED 48 3 3
DEL PEAK 16(7Q31.1) WILD-TYPE 175 147 154

Figure S630.  Get High-res Image Gene #67: 'del_7q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_7q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S631.  Gene #67: 'del_7q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 16(7Q31.1) MUTATED 14 0 2 38
DEL PEAK 16(7Q31.1) WILD-TYPE 205 58 135 78

Figure S631.  Get High-res Image Gene #67: 'del_7q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7q31.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00037

Table S632.  Gene #67: 'del_7q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 16(7Q31.1) MUTATED 32 10 5
DEL PEAK 16(7Q31.1) WILD-TYPE 140 86 125

Figure S632.  Get High-res Image Gene #67: 'del_7q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.00079

Table S633.  Gene #67: 'del_7q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 16(7Q31.1) MUTATED 27 4 16
DEL PEAK 16(7Q31.1) WILD-TYPE 117 111 123

Figure S633.  Get High-res Image Gene #67: 'del_7q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q36.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S634.  Gene #68: 'del_7q36.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 17(7Q36.1) MUTATED 60 1 0 1 1
DEL PEAK 17(7Q36.1) WILD-TYPE 109 304 19 8 36

Figure S634.  Get High-res Image Gene #68: 'del_7q36.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_7q36.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S635.  Gene #68: 'del_7q36.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 17(7Q36.1) MUTATED 41 12 1
DEL PEAK 17(7Q36.1) WILD-TYPE 124 77 170

Figure S635.  Get High-res Image Gene #68: 'del_7q36.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_7q36.1' versus 'RPPA_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.016

Table S636.  Gene #68: 'del_7q36.1' versus Molecular Subtype #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 17(7Q36.1) MUTATED 5 7 1 0 0 3
DEL PEAK 17(7Q36.1) WILD-TYPE 36 30 38 12 41 21

Figure S636.  Get High-res Image Gene #68: 'del_7q36.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_7q36.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00349 (Fisher's exact test), Q value = 0.0051

Table S637.  Gene #68: 'del_7q36.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
DEL PEAK 17(7Q36.1) MUTATED 12 3 0 1
DEL PEAK 17(7Q36.1) WILD-TYPE 55 64 43 16

Figure S637.  Get High-res Image Gene #68: 'del_7q36.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_7q36.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S638.  Gene #68: 'del_7q36.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 17(7Q36.1) MUTATED 62 0 1
DEL PEAK 17(7Q36.1) WILD-TYPE 172 153 149

Figure S638.  Get High-res Image Gene #68: 'del_7q36.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7q36.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S639.  Gene #68: 'del_7q36.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 17(7Q36.1) MUTATED 50 0 7 0 4 2 0
DEL PEAK 17(7Q36.1) WILD-TYPE 73 53 40 65 104 64 75

Figure S639.  Get High-res Image Gene #68: 'del_7q36.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7q36.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S640.  Gene #68: 'del_7q36.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 17(7Q36.1) MUTATED 55 4 3
DEL PEAK 17(7Q36.1) WILD-TYPE 168 146 154

Figure S640.  Get High-res Image Gene #68: 'del_7q36.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_7q36.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S641.  Gene #68: 'del_7q36.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 17(7Q36.1) MUTATED 15 0 2 45
DEL PEAK 17(7Q36.1) WILD-TYPE 204 58 135 71

Figure S641.  Get High-res Image Gene #68: 'del_7q36.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7q36.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00017

Table S642.  Gene #68: 'del_7q36.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 17(7Q36.1) MUTATED 34 11 5
DEL PEAK 17(7Q36.1) WILD-TYPE 138 85 125

Figure S642.  Get High-res Image Gene #68: 'del_7q36.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7q36.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.7e-05

Table S643.  Gene #68: 'del_7q36.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 17(7Q36.1) MUTATED 31 3 16
DEL PEAK 17(7Q36.1) WILD-TYPE 113 112 123

Figure S643.  Get High-res Image Gene #68: 'del_7q36.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'MRNA_CNMF'

P value = 0.002 (Fisher's exact test), Q value = 0.003

Table S644.  Gene #69: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 18(8P23.2) MUTATED 0 6 0 0
DEL PEAK 18(8P23.2) WILD-TYPE 14 11 12 10

Figure S644.  Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p23.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S645.  Gene #69: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 18(8P23.2) MUTATED 0 6 0 0 0
DEL PEAK 18(8P23.2) WILD-TYPE 14 3 7 7 16

Figure S645.  Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S646.  Gene #69: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 18(8P23.2) MUTATED 107 7 4 1 0
DEL PEAK 18(8P23.2) WILD-TYPE 62 298 15 8 37

Figure S646.  Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S647.  Gene #69: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 18(8P23.2) MUTATED 84 16 5
DEL PEAK 18(8P23.2) WILD-TYPE 81 73 166

Figure S647.  Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.2' versus 'RPPA_CNMF'

P value = 0.0444 (Fisher's exact test), Q value = 0.056

Table S648.  Gene #69: 'del_8p23.2' versus Molecular Subtype #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 18(8P23.2) MUTATED 7 4 4 1 1 7
DEL PEAK 18(8P23.2) WILD-TYPE 34 33 35 11 40 17

Figure S648.  Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_8p23.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0163 (Fisher's exact test), Q value = 0.022

Table S649.  Gene #69: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
DEL PEAK 18(8P23.2) MUTATED 12 5 2 5
DEL PEAK 18(8P23.2) WILD-TYPE 55 62 41 12

Figure S649.  Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S650.  Gene #69: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 18(8P23.2) MUTATED 108 5 5
DEL PEAK 18(8P23.2) WILD-TYPE 126 148 145

Figure S650.  Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S651.  Gene #69: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 18(8P23.2) MUTATED 77 0 20 1 14 5 1
DEL PEAK 18(8P23.2) WILD-TYPE 46 53 27 64 94 61 74

Figure S651.  Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S652.  Gene #69: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 18(8P23.2) MUTATED 102 7 7
DEL PEAK 18(8P23.2) WILD-TYPE 121 143 150

Figure S652.  Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S653.  Gene #69: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 18(8P23.2) MUTATED 36 1 5 74
DEL PEAK 18(8P23.2) WILD-TYPE 183 57 132 42

Figure S653.  Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S654.  Gene #69: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 18(8P23.2) MUTATED 68 22 9
DEL PEAK 18(8P23.2) WILD-TYPE 104 74 121

Figure S654.  Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S655.  Gene #69: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 18(8P23.2) MUTATED 61 4 34
DEL PEAK 18(8P23.2) WILD-TYPE 83 111 105

Figure S655.  Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p21.2' versus 'MRNA_CNMF'

P value = 0.00218 (Fisher's exact test), Q value = 0.0033

Table S656.  Gene #70: 'del_8p21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 19(8P21.2) MUTATED 0 6 0 0
DEL PEAK 19(8P21.2) WILD-TYPE 14 11 12 10

Figure S656.  Get High-res Image Gene #70: 'del_8p21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p21.2' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.7e-05

Table S657.  Gene #70: 'del_8p21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 19(8P21.2) MUTATED 0 6 0 0 0
DEL PEAK 19(8P21.2) WILD-TYPE 14 3 7 7 16

Figure S657.  Get High-res Image Gene #70: 'del_8p21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S658.  Gene #70: 'del_8p21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 19(8P21.2) MUTATED 109 4 3 1 0
DEL PEAK 19(8P21.2) WILD-TYPE 60 301 16 8 37

Figure S658.  Get High-res Image Gene #70: 'del_8p21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S659.  Gene #70: 'del_8p21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 19(8P21.2) MUTATED 86 15 2
DEL PEAK 19(8P21.2) WILD-TYPE 79 74 169

Figure S659.  Get High-res Image Gene #70: 'del_8p21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p21.2' versus 'RPPA_CNMF'

P value = 0.0203 (Fisher's exact test), Q value = 0.027

Table S660.  Gene #70: 'del_8p21.2' versus Molecular Subtype #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 19(8P21.2) MUTATED 7 5 3 0 1 7
DEL PEAK 19(8P21.2) WILD-TYPE 34 32 36 12 40 17

Figure S660.  Get High-res Image Gene #70: 'del_8p21.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_8p21.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00174 (Fisher's exact test), Q value = 0.0026

Table S661.  Gene #70: 'del_8p21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
DEL PEAK 19(8P21.2) MUTATED 13 4 1 5
DEL PEAK 19(8P21.2) WILD-TYPE 54 63 42 12

Figure S661.  Get High-res Image Gene #70: 'del_8p21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_8p21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S662.  Gene #70: 'del_8p21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 19(8P21.2) MUTATED 110 4 2
DEL PEAK 19(8P21.2) WILD-TYPE 124 149 148

Figure S662.  Get High-res Image Gene #70: 'del_8p21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S663.  Gene #70: 'del_8p21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 19(8P21.2) MUTATED 80 0 20 1 12 3 0
DEL PEAK 19(8P21.2) WILD-TYPE 43 53 27 64 96 63 75

Figure S663.  Get High-res Image Gene #70: 'del_8p21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p21.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S664.  Gene #70: 'del_8p21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 19(8P21.2) MUTATED 104 7 3
DEL PEAK 19(8P21.2) WILD-TYPE 119 143 154

Figure S664.  Get High-res Image Gene #70: 'del_8p21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S665.  Gene #70: 'del_8p21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 19(8P21.2) MUTATED 32 1 2 79
DEL PEAK 19(8P21.2) WILD-TYPE 187 57 135 37

Figure S665.  Get High-res Image Gene #70: 'del_8p21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S666.  Gene #70: 'del_8p21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 19(8P21.2) MUTATED 68 23 7
DEL PEAK 19(8P21.2) WILD-TYPE 104 73 123

Figure S666.  Get High-res Image Gene #70: 'del_8p21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S667.  Gene #70: 'del_8p21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 19(8P21.2) MUTATED 62 2 34
DEL PEAK 19(8P21.2) WILD-TYPE 82 113 105

Figure S667.  Get High-res Image Gene #70: 'del_8p21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'MRNA_CHIERARCHICAL'

P value = 0.0304 (Fisher's exact test), Q value = 0.039

Table S668.  Gene #71: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 20(9P23) MUTATED 1 3 0 0 0
DEL PEAK 20(9P23) WILD-TYPE 13 6 7 7 16

Figure S668.  Get High-res Image Gene #71: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S669.  Gene #71: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 20(9P23) MUTATED 67 2 5 1 4
DEL PEAK 20(9P23) WILD-TYPE 102 303 14 8 33

Figure S669.  Get High-res Image Gene #71: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S670.  Gene #71: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 20(9P23) MUTATED 44 18 8
DEL PEAK 20(9P23) WILD-TYPE 121 71 163

Figure S670.  Get High-res Image Gene #71: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p23' versus 'RPPA_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 0.023

Table S671.  Gene #71: 'del_9p23' versus Molecular Subtype #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 20(9P23) MUTATED 4 5 1 1 0 5
DEL PEAK 20(9P23) WILD-TYPE 37 32 38 11 41 19

Figure S671.  Get High-res Image Gene #71: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S672.  Gene #71: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 20(9P23) MUTATED 63 5 11
DEL PEAK 20(9P23) WILD-TYPE 171 148 139

Figure S672.  Get High-res Image Gene #71: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S673.  Gene #71: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 20(9P23) MUTATED 41 0 14 2 12 9 1
DEL PEAK 20(9P23) WILD-TYPE 82 53 33 63 96 57 74

Figure S673.  Get High-res Image Gene #71: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S674.  Gene #71: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 20(9P23) MUTATED 56 8 14
DEL PEAK 20(9P23) WILD-TYPE 167 142 143

Figure S674.  Get High-res Image Gene #71: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S675.  Gene #71: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 20(9P23) MUTATED 25 0 10 43
DEL PEAK 20(9P23) WILD-TYPE 194 58 127 73

Figure S675.  Get High-res Image Gene #71: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.029

Table S676.  Gene #71: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 20(9P23) MUTATED 37 18 13
DEL PEAK 20(9P23) WILD-TYPE 135 78 117

Figure S676.  Get High-res Image Gene #71: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00654 (Fisher's exact test), Q value = 0.0093

Table S677.  Gene #71: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 20(9P23) MUTATED 35 11 22
DEL PEAK 20(9P23) WILD-TYPE 109 104 117

Figure S677.  Get High-res Image Gene #71: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q21.2' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 7.1e-05

Table S678.  Gene #72: 'del_9q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 21(9Q21.2) MUTATED 0 9 0 0
DEL PEAK 21(9Q21.2) WILD-TYPE 14 8 12 10

Figure S678.  Get High-res Image Gene #72: 'del_9q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9q21.2' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.7e-05

Table S679.  Gene #72: 'del_9q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 21(9Q21.2) MUTATED 2 7 0 0 0
DEL PEAK 21(9Q21.2) WILD-TYPE 12 2 7 7 16

Figure S679.  Get High-res Image Gene #72: 'del_9q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S680.  Gene #72: 'del_9q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 21(9Q21.2) MUTATED 112 3 7 2 5
DEL PEAK 21(9Q21.2) WILD-TYPE 57 302 12 7 32

Figure S680.  Get High-res Image Gene #72: 'del_9q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S681.  Gene #72: 'del_9q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 21(9Q21.2) MUTATED 78 20 15
DEL PEAK 21(9Q21.2) WILD-TYPE 87 69 156

Figure S681.  Get High-res Image Gene #72: 'del_9q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q21.2' versus 'RPPA_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.00048

Table S682.  Gene #72: 'del_9q21.2' versus Molecular Subtype #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(9Q21.2) MUTATED 6 12 1 2 1 6
DEL PEAK 21(9Q21.2) WILD-TYPE 35 25 38 10 40 18

Figure S682.  Get High-res Image Gene #72: 'del_9q21.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9q21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S683.  Gene #72: 'del_9q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 21(9Q21.2) MUTATED 105 8 16
DEL PEAK 21(9Q21.2) WILD-TYPE 129 145 134

Figure S683.  Get High-res Image Gene #72: 'del_9q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S684.  Gene #72: 'del_9q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 21(9Q21.2) MUTATED 77 0 16 3 19 13 1
DEL PEAK 21(9Q21.2) WILD-TYPE 46 53 31 62 89 53 74

Figure S684.  Get High-res Image Gene #72: 'del_9q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S685.  Gene #72: 'del_9q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 21(9Q21.2) MUTATED 93 16 17
DEL PEAK 21(9Q21.2) WILD-TYPE 130 134 140

Figure S685.  Get High-res Image Gene #72: 'del_9q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S686.  Gene #72: 'del_9q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 21(9Q21.2) MUTATED 47 1 13 65
DEL PEAK 21(9Q21.2) WILD-TYPE 172 57 124 51

Figure S686.  Get High-res Image Gene #72: 'del_9q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.00056

Table S687.  Gene #72: 'del_9q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 21(9Q21.2) MUTATED 61 29 20
DEL PEAK 21(9Q21.2) WILD-TYPE 111 67 110

Figure S687.  Get High-res Image Gene #72: 'del_9q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.7e-05

Table S688.  Gene #72: 'del_9q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 21(9Q21.2) MUTATED 61 16 33
DEL PEAK 21(9Q21.2) WILD-TYPE 83 99 106

Figure S688.  Get High-res Image Gene #72: 'del_9q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q34.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S689.  Gene #73: 'del_9q34.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 22(9Q34.2) MUTATED 0 9 0 0
DEL PEAK 22(9Q34.2) WILD-TYPE 14 8 12 10

Figure S689.  Get High-res Image Gene #73: 'del_9q34.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9q34.2' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 7.1e-05

Table S690.  Gene #73: 'del_9q34.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 22(9Q34.2) MUTATED 2 7 0 0 0
DEL PEAK 22(9Q34.2) WILD-TYPE 12 2 7 7 16

Figure S690.  Get High-res Image Gene #73: 'del_9q34.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9q34.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S691.  Gene #73: 'del_9q34.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 22(9Q34.2) MUTATED 117 4 6 1 4
DEL PEAK 22(9Q34.2) WILD-TYPE 52 301 13 8 33

Figure S691.  Get High-res Image Gene #73: 'del_9q34.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q34.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S692.  Gene #73: 'del_9q34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 22(9Q34.2) MUTATED 78 23 13
DEL PEAK 22(9Q34.2) WILD-TYPE 87 66 158

Figure S692.  Get High-res Image Gene #73: 'del_9q34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q34.2' versus 'RPPA_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.00078

Table S693.  Gene #73: 'del_9q34.2' versus Molecular Subtype #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 22(9Q34.2) MUTATED 7 13 2 2 1 6
DEL PEAK 22(9Q34.2) WILD-TYPE 34 24 37 10 40 18

Figure S693.  Get High-res Image Gene #73: 'del_9q34.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9q34.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S694.  Gene #73: 'del_9q34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 22(9Q34.2) MUTATED 106 8 17
DEL PEAK 22(9Q34.2) WILD-TYPE 128 145 133

Figure S694.  Get High-res Image Gene #73: 'del_9q34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9q34.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S695.  Gene #73: 'del_9q34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 22(9Q34.2) MUTATED 75 0 16 3 22 14 1
DEL PEAK 22(9Q34.2) WILD-TYPE 48 53 31 62 86 52 74

Figure S695.  Get High-res Image Gene #73: 'del_9q34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q34.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S696.  Gene #73: 'del_9q34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 22(9Q34.2) MUTATED 96 15 18
DEL PEAK 22(9Q34.2) WILD-TYPE 127 135 139

Figure S696.  Get High-res Image Gene #73: 'del_9q34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9q34.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S697.  Gene #73: 'del_9q34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 22(9Q34.2) MUTATED 48 1 13 67
DEL PEAK 22(9Q34.2) WILD-TYPE 171 57 124 49

Figure S697.  Get High-res Image Gene #73: 'del_9q34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q34.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00021

Table S698.  Gene #73: 'del_9q34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 22(9Q34.2) MUTATED 64 27 20
DEL PEAK 22(9Q34.2) WILD-TYPE 108 69 110

Figure S698.  Get High-res Image Gene #73: 'del_9q34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9q34.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S699.  Gene #73: 'del_9q34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 22(9Q34.2) MUTATED 65 17 29
DEL PEAK 22(9Q34.2) WILD-TYPE 79 98 110

Figure S699.  Get High-res Image Gene #73: 'del_9q34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S700.  Gene #74: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 23(10Q23.31) MUTATED 70 5 2 0 0
DEL PEAK 23(10Q23.31) WILD-TYPE 99 300 17 9 37

Figure S700.  Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S701.  Gene #74: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 23(10Q23.31) MUTATED 49 13 6
DEL PEAK 23(10Q23.31) WILD-TYPE 116 76 165

Figure S701.  Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S702.  Gene #74: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 23(10Q23.31) MUTATED 64 4 8
DEL PEAK 23(10Q23.31) WILD-TYPE 170 149 142

Figure S702.  Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S703.  Gene #74: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 23(10Q23.31) MUTATED 47 0 7 3 12 5 2
DEL PEAK 23(10Q23.31) WILD-TYPE 76 53 40 62 96 61 73

Figure S703.  Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S704.  Gene #74: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 23(10Q23.31) MUTATED 61 7 8
DEL PEAK 23(10Q23.31) WILD-TYPE 162 143 149

Figure S704.  Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S705.  Gene #74: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 23(10Q23.31) MUTATED 30 0 7 39
DEL PEAK 23(10Q23.31) WILD-TYPE 189 58 130 77

Figure S705.  Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.00098

Table S706.  Gene #74: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 23(10Q23.31) MUTATED 43 12 12
DEL PEAK 23(10Q23.31) WILD-TYPE 129 84 118

Figure S706.  Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.7e-05

Table S707.  Gene #74: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 23(10Q23.31) MUTATED 41 7 19
DEL PEAK 23(10Q23.31) WILD-TYPE 103 108 120

Figure S707.  Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S708.  Gene #75: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 24(11P15.5) MUTATED 94 1 6 4 1
DEL PEAK 24(11P15.5) WILD-TYPE 75 304 13 5 36

Figure S708.  Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S709.  Gene #75: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 24(11P15.5) MUTATED 74 17 6
DEL PEAK 24(11P15.5) WILD-TYPE 91 72 165

Figure S709.  Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S710.  Gene #75: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 24(11P15.5) MUTATED 90 3 12
DEL PEAK 24(11P15.5) WILD-TYPE 144 150 138

Figure S710.  Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S711.  Gene #75: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 24(11P15.5) MUTATED 61 1 18 0 14 9 2
DEL PEAK 24(11P15.5) WILD-TYPE 62 52 29 65 94 57 73

Figure S711.  Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S712.  Gene #75: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 24(11P15.5) MUTATED 83 9 13
DEL PEAK 24(11P15.5) WILD-TYPE 140 141 144

Figure S712.  Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S713.  Gene #75: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 24(11P15.5) MUTATED 33 1 11 60
DEL PEAK 24(11P15.5) WILD-TYPE 186 57 126 56

Figure S713.  Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S714.  Gene #75: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 24(11P15.5) MUTATED 66 18 13
DEL PEAK 24(11P15.5) WILD-TYPE 106 78 117

Figure S714.  Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S715.  Gene #75: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 24(11P15.5) MUTATED 62 12 23
DEL PEAK 24(11P15.5) WILD-TYPE 82 103 116

Figure S715.  Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S716.  Gene #76: 'del_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 25(11Q14.1) MUTATED 61 0 4 4 1
DEL PEAK 25(11Q14.1) WILD-TYPE 108 305 15 5 36

Figure S716.  Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q14.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S717.  Gene #76: 'del_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 25(11Q14.1) MUTATED 51 10 5
DEL PEAK 25(11Q14.1) WILD-TYPE 114 79 166

Figure S717.  Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S718.  Gene #76: 'del_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 25(11Q14.1) MUTATED 60 2 7
DEL PEAK 25(11Q14.1) WILD-TYPE 174 151 143

Figure S718.  Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S719.  Gene #76: 'del_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 25(11Q14.1) MUTATED 43 1 12 1 8 4 0
DEL PEAK 25(11Q14.1) WILD-TYPE 80 52 35 64 100 62 75

Figure S719.  Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q14.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S720.  Gene #76: 'del_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 25(11Q14.1) MUTATED 55 7 8
DEL PEAK 25(11Q14.1) WILD-TYPE 168 143 149

Figure S720.  Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S721.  Gene #76: 'del_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 25(11Q14.1) MUTATED 22 0 6 42
DEL PEAK 25(11Q14.1) WILD-TYPE 197 58 131 74

Figure S721.  Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S722.  Gene #76: 'del_11q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 25(11Q14.1) MUTATED 46 12 7
DEL PEAK 25(11Q14.1) WILD-TYPE 126 84 123

Figure S722.  Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.7e-05

Table S723.  Gene #76: 'del_11q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 25(11Q14.1) MUTATED 42 6 17
DEL PEAK 25(11Q14.1) WILD-TYPE 102 109 122

Figure S723.  Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q25' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S724.  Gene #77: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 26(11Q25) MUTATED 77 3 6 4 3
DEL PEAK 26(11Q25) WILD-TYPE 92 302 13 5 34

Figure S724.  Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q25' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S725.  Gene #77: 'del_11q25' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 26(11Q25) MUTATED 66 11 7
DEL PEAK 26(11Q25) WILD-TYPE 99 78 164

Figure S725.  Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q25' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S726.  Gene #77: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 26(11Q25) MUTATED 76 6 10
DEL PEAK 26(11Q25) WILD-TYPE 158 147 140

Figure S726.  Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q25' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S727.  Gene #77: 'del_11q25' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 26(11Q25) MUTATED 52 1 14 2 16 6 1
DEL PEAK 26(11Q25) WILD-TYPE 71 52 33 63 92 60 74

Figure S727.  Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q25' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S728.  Gene #77: 'del_11q25' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 26(11Q25) MUTATED 67 12 12
DEL PEAK 26(11Q25) WILD-TYPE 156 138 145

Figure S728.  Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11q25' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S729.  Gene #77: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 26(11Q25) MUTATED 37 0 7 47
DEL PEAK 26(11Q25) WILD-TYPE 182 58 130 69

Figure S729.  Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11q25' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S730.  Gene #77: 'del_11q25' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 26(11Q25) MUTATED 53 18 11
DEL PEAK 26(11Q25) WILD-TYPE 119 78 119

Figure S730.  Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11q25' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S731.  Gene #77: 'del_11q25' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 26(11Q25) MUTATED 49 8 25
DEL PEAK 26(11Q25) WILD-TYPE 95 107 114

Figure S731.  Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S732.  Gene #78: 'del_12q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 27(12Q23.1) MUTATED 54 0 1 0 1
DEL PEAK 27(12Q23.1) WILD-TYPE 115 305 18 9 36

Figure S732.  Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S733.  Gene #78: 'del_12q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 27(12Q23.1) MUTATED 42 6 0
DEL PEAK 27(12Q23.1) WILD-TYPE 123 83 171

Figure S733.  Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12q23.1' versus 'RPPA_CNMF'

P value = 0.0362 (Fisher's exact test), Q value = 0.046

Table S734.  Gene #78: 'del_12q23.1' versus Molecular Subtype #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 27(12Q23.1) MUTATED 3 7 2 0 0 2
DEL PEAK 27(12Q23.1) WILD-TYPE 38 30 37 12 41 22

Figure S734.  Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_12q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0221 (Fisher's exact test), Q value = 0.029

Table S735.  Gene #78: 'del_12q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
DEL PEAK 27(12Q23.1) MUTATED 9 3 0 2
DEL PEAK 27(12Q23.1) WILD-TYPE 58 64 43 15

Figure S735.  Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_12q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S736.  Gene #78: 'del_12q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 27(12Q23.1) MUTATED 51 1 4
DEL PEAK 27(12Q23.1) WILD-TYPE 183 152 146

Figure S736.  Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S737.  Gene #78: 'del_12q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 27(12Q23.1) MUTATED 39 0 9 0 3 5 0
DEL PEAK 27(12Q23.1) WILD-TYPE 84 53 38 65 105 61 75

Figure S737.  Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q23.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S738.  Gene #78: 'del_12q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 27(12Q23.1) MUTATED 46 6 2
DEL PEAK 27(12Q23.1) WILD-TYPE 177 144 155

Figure S738.  Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_12q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S739.  Gene #78: 'del_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 27(12Q23.1) MUTATED 19 0 0 35
DEL PEAK 27(12Q23.1) WILD-TYPE 200 58 137 81

Figure S739.  Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00017

Table S740.  Gene #78: 'del_12q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 27(12Q23.1) MUTATED 32 11 4
DEL PEAK 27(12Q23.1) WILD-TYPE 140 85 126

Figure S740.  Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_12q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S741.  Gene #78: 'del_12q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 27(12Q23.1) MUTATED 30 2 15
DEL PEAK 27(12Q23.1) WILD-TYPE 114 113 124

Figure S741.  Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q24.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S742.  Gene #79: 'del_12q24.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 28(12Q24.33) MUTATED 63 1 1 0 1
DEL PEAK 28(12Q24.33) WILD-TYPE 106 304 18 9 36

Figure S742.  Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q24.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S743.  Gene #79: 'del_12q24.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 28(12Q24.33) MUTATED 50 8 3
DEL PEAK 28(12Q24.33) WILD-TYPE 115 81 168

Figure S743.  Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12q24.33' versus 'RPPA_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.053

Table S744.  Gene #79: 'del_12q24.33' versus Molecular Subtype #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 28(12Q24.33) MUTATED 2 6 1 0 0 2
DEL PEAK 28(12Q24.33) WILD-TYPE 39 31 38 12 41 22

Figure S744.  Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_12q24.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.0388 (Fisher's exact test), Q value = 0.049

Table S745.  Gene #79: 'del_12q24.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
DEL PEAK 28(12Q24.33) MUTATED 7 2 0 2
DEL PEAK 28(12Q24.33) WILD-TYPE 60 65 43 15

Figure S745.  Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_12q24.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S746.  Gene #79: 'del_12q24.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 28(12Q24.33) MUTATED 62 1 3
DEL PEAK 28(12Q24.33) WILD-TYPE 172 152 147

Figure S746.  Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q24.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S747.  Gene #79: 'del_12q24.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 28(12Q24.33) MUTATED 45 0 8 0 9 4 0
DEL PEAK 28(12Q24.33) WILD-TYPE 78 53 39 65 99 62 75

Figure S747.  Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q24.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S748.  Gene #79: 'del_12q24.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 28(12Q24.33) MUTATED 55 6 3
DEL PEAK 28(12Q24.33) WILD-TYPE 168 144 154

Figure S748.  Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_12q24.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S749.  Gene #79: 'del_12q24.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 28(12Q24.33) MUTATED 23 0 2 39
DEL PEAK 28(12Q24.33) WILD-TYPE 196 58 135 77

Figure S749.  Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q24.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 7.1e-05

Table S750.  Gene #79: 'del_12q24.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 28(12Q24.33) MUTATED 40 12 7
DEL PEAK 28(12Q24.33) WILD-TYPE 132 84 123

Figure S750.  Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_12q24.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S751.  Gene #79: 'del_12q24.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 28(12Q24.33) MUTATED 37 4 18
DEL PEAK 28(12Q24.33) WILD-TYPE 107 111 121

Figure S751.  Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q11' versus 'MRNA_CHIERARCHICAL'

P value = 0.0399 (Fisher's exact test), Q value = 0.051

Table S752.  Gene #80: 'del_13q11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 29(13Q11) MUTATED 3 3 0 0 0
DEL PEAK 29(13Q11) WILD-TYPE 11 6 7 7 16

Figure S752.  Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S753.  Gene #80: 'del_13q11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 29(13Q11) MUTATED 80 3 6 3 6
DEL PEAK 29(13Q11) WILD-TYPE 89 302 13 6 31

Figure S753.  Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S754.  Gene #80: 'del_13q11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 29(13Q11) MUTATED 57 17 10
DEL PEAK 29(13Q11) WILD-TYPE 108 72 161

Figure S754.  Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S755.  Gene #80: 'del_13q11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 29(13Q11) MUTATED 76 6 16
DEL PEAK 29(13Q11) WILD-TYPE 158 147 134

Figure S755.  Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S756.  Gene #80: 'del_13q11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 29(13Q11) MUTATED 52 1 11 0 21 12 1
DEL PEAK 29(13Q11) WILD-TYPE 71 52 36 65 87 54 74

Figure S756.  Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q11' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S757.  Gene #80: 'del_13q11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 29(13Q11) MUTATED 71 13 13
DEL PEAK 29(13Q11) WILD-TYPE 152 137 144

Figure S757.  Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S758.  Gene #80: 'del_13q11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 29(13Q11) MUTATED 41 1 10 45
DEL PEAK 29(13Q11) WILD-TYPE 178 57 127 71

Figure S758.  Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0256 (Fisher's exact test), Q value = 0.033

Table S759.  Gene #80: 'del_13q11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 29(13Q11) MUTATED 42 24 17
DEL PEAK 29(13Q11) WILD-TYPE 130 72 113

Figure S759.  Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_13q11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00688 (Fisher's exact test), Q value = 0.0098

Table S760.  Gene #80: 'del_13q11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 29(13Q11) MUTATED 38 13 32
DEL PEAK 29(13Q11) WILD-TYPE 106 102 107

Figure S760.  Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S761.  Gene #81: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 30(13Q14.2) MUTATED 86 5 8 3 5
DEL PEAK 30(13Q14.2) WILD-TYPE 83 300 11 6 32

Figure S761.  Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S762.  Gene #81: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 30(13Q14.2) MUTATED 60 20 14
DEL PEAK 30(13Q14.2) WILD-TYPE 105 69 157

Figure S762.  Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S763.  Gene #81: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 30(13Q14.2) MUTATED 80 8 19
DEL PEAK 30(13Q14.2) WILD-TYPE 154 145 131

Figure S763.  Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S764.  Gene #81: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 30(13Q14.2) MUTATED 48 3 15 0 25 14 2
DEL PEAK 30(13Q14.2) WILD-TYPE 75 50 32 65 83 52 73

Figure S764.  Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S765.  Gene #81: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 30(13Q14.2) MUTATED 71 18 17
DEL PEAK 30(13Q14.2) WILD-TYPE 152 132 140

Figure S765.  Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S766.  Gene #81: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 30(13Q14.2) MUTATED 48 2 13 43
DEL PEAK 30(13Q14.2) WILD-TYPE 171 56 124 73

Figure S766.  Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.029

Table S767.  Gene #81: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 30(13Q14.2) MUTATED 49 25 20
DEL PEAK 30(13Q14.2) WILD-TYPE 123 71 110

Figure S767.  Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00291 (Fisher's exact test), Q value = 0.0043

Table S768.  Gene #81: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 30(13Q14.2) MUTATED 47 17 30
DEL PEAK 30(13Q14.2) WILD-TYPE 97 98 109

Figure S768.  Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q13.1' versus 'MRNA_CNMF'

P value = 0.00832 (Fisher's exact test), Q value = 0.012

Table S769.  Gene #82: 'del_14q13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 31(14Q13.1) MUTATED 0 5 0 0
DEL PEAK 31(14Q13.1) WILD-TYPE 14 12 12 10

Figure S769.  Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q13.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00505 (Fisher's exact test), Q value = 0.0073

Table S770.  Gene #82: 'del_14q13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 31(14Q13.1) MUTATED 1 4 0 0 0
DEL PEAK 31(14Q13.1) WILD-TYPE 13 5 7 7 16

Figure S770.  Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S771.  Gene #82: 'del_14q13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 31(14Q13.1) MUTATED 63 2 2 3 3
DEL PEAK 31(14Q13.1) WILD-TYPE 106 303 17 6 34

Figure S771.  Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S772.  Gene #82: 'del_14q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 31(14Q13.1) MUTATED 51 8 5
DEL PEAK 31(14Q13.1) WILD-TYPE 114 81 166

Figure S772.  Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S773.  Gene #82: 'del_14q13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 31(14Q13.1) MUTATED 62 4 6
DEL PEAK 31(14Q13.1) WILD-TYPE 172 149 144

Figure S773.  Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S774.  Gene #82: 'del_14q13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 31(14Q13.1) MUTATED 50 1 5 1 9 5 1
DEL PEAK 31(14Q13.1) WILD-TYPE 73 52 42 64 99 61 74

Figure S774.  Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q13.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S775.  Gene #82: 'del_14q13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 31(14Q13.1) MUTATED 58 10 4
DEL PEAK 31(14Q13.1) WILD-TYPE 165 140 153

Figure S775.  Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_14q13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S776.  Gene #82: 'del_14q13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 31(14Q13.1) MUTATED 27 0 4 41
DEL PEAK 31(14Q13.1) WILD-TYPE 192 58 133 75

Figure S776.  Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 9e-04 (Fisher's exact test), Q value = 0.0014

Table S777.  Gene #82: 'del_14q13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 31(14Q13.1) MUTATED 37 18 9
DEL PEAK 31(14Q13.1) WILD-TYPE 135 78 121

Figure S777.  Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_14q13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S778.  Gene #82: 'del_14q13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 31(14Q13.1) MUTATED 38 5 21
DEL PEAK 31(14Q13.1) WILD-TYPE 106 110 118

Figure S778.  Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q15.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.015

Table S779.  Gene #83: 'del_15q15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 32(15Q15.1) MUTATED 1 4 0 1 0
DEL PEAK 32(15Q15.1) WILD-TYPE 13 5 7 6 16

Figure S779.  Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S780.  Gene #83: 'del_15q15.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 32(15Q15.1) MUTATED 119 5 8 5 3
DEL PEAK 32(15Q15.1) WILD-TYPE 50 300 11 4 34

Figure S780.  Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q15.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S781.  Gene #83: 'del_15q15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 32(15Q15.1) MUTATED 90 23 12
DEL PEAK 32(15Q15.1) WILD-TYPE 75 66 159

Figure S781.  Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q15.1' versus 'RPPA_CNMF'

P value = 0.00273 (Fisher's exact test), Q value = 0.0041

Table S782.  Gene #83: 'del_15q15.1' versus Molecular Subtype #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 32(15Q15.1) MUTATED 4 12 2 2 2 6
DEL PEAK 32(15Q15.1) WILD-TYPE 37 25 37 10 39 18

Figure S782.  Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_15q15.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S783.  Gene #83: 'del_15q15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 32(15Q15.1) MUTATED 119 9 12
DEL PEAK 32(15Q15.1) WILD-TYPE 115 144 138

Figure S783.  Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S784.  Gene #83: 'del_15q15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 32(15Q15.1) MUTATED 86 1 14 4 25 9 1
DEL PEAK 32(15Q15.1) WILD-TYPE 37 52 33 61 83 57 74

Figure S784.  Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S785.  Gene #83: 'del_15q15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 32(15Q15.1) MUTATED 108 18 12
DEL PEAK 32(15Q15.1) WILD-TYPE 115 132 145

Figure S785.  Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S786.  Gene #83: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 32(15Q15.1) MUTATED 51 1 9 77
DEL PEAK 32(15Q15.1) WILD-TYPE 168 57 128 39

Figure S786.  Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S787.  Gene #83: 'del_15q15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 32(15Q15.1) MUTATED 70 34 18
DEL PEAK 32(15Q15.1) WILD-TYPE 102 62 112

Figure S787.  Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S788.  Gene #83: 'del_15q15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 32(15Q15.1) MUTATED 67 12 43
DEL PEAK 32(15Q15.1) WILD-TYPE 77 103 96

Figure S788.  Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q23' versus 'MRNA_CNMF'

P value = 0.00199 (Fisher's exact test), Q value = 0.003

Table S789.  Gene #84: 'del_15q23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 33(15Q23) MUTATED 0 6 0 0
DEL PEAK 33(15Q23) WILD-TYPE 14 11 12 10

Figure S789.  Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q23' versus 'MRNA_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 7e-04

Table S790.  Gene #84: 'del_15q23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 33(15Q23) MUTATED 1 5 0 0 0
DEL PEAK 33(15Q23) WILD-TYPE 13 4 7 7 16

Figure S790.  Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S791.  Gene #84: 'del_15q23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 33(15Q23) MUTATED 95 4 7 6 3
DEL PEAK 33(15Q23) WILD-TYPE 74 301 12 3 34

Figure S791.  Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S792.  Gene #84: 'del_15q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 33(15Q23) MUTATED 77 16 8
DEL PEAK 33(15Q23) WILD-TYPE 88 73 163

Figure S792.  Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S793.  Gene #84: 'del_15q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 33(15Q23) MUTATED 98 8 9
DEL PEAK 33(15Q23) WILD-TYPE 136 145 141

Figure S793.  Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S794.  Gene #84: 'del_15q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 33(15Q23) MUTATED 75 1 12 2 17 7 1
DEL PEAK 33(15Q23) WILD-TYPE 48 52 35 63 91 59 74

Figure S794.  Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S795.  Gene #84: 'del_15q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 33(15Q23) MUTATED 88 16 9
DEL PEAK 33(15Q23) WILD-TYPE 135 134 148

Figure S795.  Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S796.  Gene #84: 'del_15q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 33(15Q23) MUTATED 41 1 6 65
DEL PEAK 33(15Q23) WILD-TYPE 178 57 131 51

Figure S796.  Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_15q23' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S797.  Gene #84: 'del_15q23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 33(15Q23) MUTATED 64 22 12
DEL PEAK 33(15Q23) WILD-TYPE 108 74 118

Figure S797.  Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S798.  Gene #84: 'del_15q23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 33(15Q23) MUTATED 59 7 32
DEL PEAK 33(15Q23) WILD-TYPE 85 108 107

Figure S798.  Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16p13.3' versus 'MRNA_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.017

Table S799.  Gene #85: 'del_16p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 34(16P13.3) MUTATED 1 6 0 0
DEL PEAK 34(16P13.3) WILD-TYPE 13 11 12 10

Figure S799.  Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_16p13.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.014

Table S800.  Gene #85: 'del_16p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 34(16P13.3) MUTATED 3 4 0 0 0
DEL PEAK 34(16P13.3) WILD-TYPE 11 5 7 7 16

Figure S800.  Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_16p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S801.  Gene #85: 'del_16p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 34(16P13.3) MUTATED 84 2 3 1 2
DEL PEAK 34(16P13.3) WILD-TYPE 85 303 16 8 35

Figure S801.  Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_16p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S802.  Gene #85: 'del_16p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 34(16P13.3) MUTATED 62 17 4
DEL PEAK 34(16P13.3) WILD-TYPE 103 72 167

Figure S802.  Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0474 (Fisher's exact test), Q value = 0.059

Table S803.  Gene #85: 'del_16p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
DEL PEAK 34(16P13.3) MUTATED 9 2 2 3
DEL PEAK 34(16P13.3) WILD-TYPE 58 65 41 14

Figure S803.  Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_16p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S804.  Gene #85: 'del_16p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 34(16P13.3) MUTATED 83 2 7
DEL PEAK 34(16P13.3) WILD-TYPE 151 151 143

Figure S804.  Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S805.  Gene #85: 'del_16p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 34(16P13.3) MUTATED 63 1 9 1 11 6 1
DEL PEAK 34(16P13.3) WILD-TYPE 60 52 38 64 97 60 74

Figure S805.  Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S806.  Gene #85: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 34(16P13.3) MUTATED 74 9 7
DEL PEAK 34(16P13.3) WILD-TYPE 149 141 150

Figure S806.  Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S807.  Gene #85: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 34(16P13.3) MUTATED 31 0 5 54
DEL PEAK 34(16P13.3) WILD-TYPE 188 58 132 62

Figure S807.  Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S808.  Gene #85: 'del_16p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 34(16P13.3) MUTATED 51 21 10
DEL PEAK 34(16P13.3) WILD-TYPE 121 75 120

Figure S808.  Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S809.  Gene #85: 'del_16p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 34(16P13.3) MUTATED 49 6 27
DEL PEAK 34(16P13.3) WILD-TYPE 95 109 112

Figure S809.  Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q21' versus 'MRNA_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.0013

Table S810.  Gene #86: 'del_16q21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 35(16Q21) MUTATED 0 8 1 0
DEL PEAK 35(16Q21) WILD-TYPE 14 9 11 10

Figure S810.  Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_16q21' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 5.4e-05

Table S811.  Gene #86: 'del_16q21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 35(16Q21) MUTATED 1 7 0 0 1
DEL PEAK 35(16Q21) WILD-TYPE 13 2 7 7 15

Figure S811.  Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_16q21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S812.  Gene #86: 'del_16q21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 35(16Q21) MUTATED 128 14 7 1 4
DEL PEAK 35(16Q21) WILD-TYPE 41 291 12 8 33

Figure S812.  Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S813.  Gene #86: 'del_16q21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 35(16Q21) MUTATED 93 26 16
DEL PEAK 35(16Q21) WILD-TYPE 72 63 155

Figure S813.  Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S814.  Gene #86: 'del_16q21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 35(16Q21) MUTATED 123 14 16
DEL PEAK 35(16Q21) WILD-TYPE 111 139 134

Figure S814.  Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16q21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S815.  Gene #86: 'del_16q21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 35(16Q21) MUTATED 89 7 17 3 22 11 4
DEL PEAK 35(16Q21) WILD-TYPE 34 46 30 62 86 55 71

Figure S815.  Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16q21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S816.  Gene #86: 'del_16q21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 35(16Q21) MUTATED 108 25 17
DEL PEAK 35(16Q21) WILD-TYPE 115 125 140

Figure S816.  Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16q21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S817.  Gene #86: 'del_16q21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 35(16Q21) MUTATED 54 6 14 76
DEL PEAK 35(16Q21) WILD-TYPE 165 52 123 40

Figure S817.  Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16q21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S818.  Gene #86: 'del_16q21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 35(16Q21) MUTATED 78 31 22
DEL PEAK 35(16Q21) WILD-TYPE 94 65 108

Figure S818.  Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16q21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S819.  Gene #86: 'del_16q21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 35(16Q21) MUTATED 72 16 43
DEL PEAK 35(16Q21) WILD-TYPE 72 99 96

Figure S819.  Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q22.3' versus 'MRNA_CNMF'

P value = 0.033 (Fisher's exact test), Q value = 0.043

Table S820.  Gene #87: 'del_16q22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 36(16Q22.3) MUTATED 1 7 2 0
DEL PEAK 36(16Q22.3) WILD-TYPE 13 10 10 10

Figure S820.  Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_16q22.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.014

Table S821.  Gene #87: 'del_16q22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 36(16Q22.3) MUTATED 4 5 0 0 1
DEL PEAK 36(16Q22.3) WILD-TYPE 10 4 7 7 15

Figure S821.  Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_16q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S822.  Gene #87: 'del_16q22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 36(16Q22.3) MUTATED 129 17 7 1 4
DEL PEAK 36(16Q22.3) WILD-TYPE 40 288 12 8 33

Figure S822.  Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S823.  Gene #87: 'del_16q22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 36(16Q22.3) MUTATED 91 28 19
DEL PEAK 36(16Q22.3) WILD-TYPE 74 61 152

Figure S823.  Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S824.  Gene #87: 'del_16q22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 36(16Q22.3) MUTATED 125 15 18
DEL PEAK 36(16Q22.3) WILD-TYPE 109 138 132

Figure S824.  Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S825.  Gene #87: 'del_16q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 36(16Q22.3) MUTATED 88 8 18 3 24 12 5
DEL PEAK 36(16Q22.3) WILD-TYPE 35 45 29 62 84 54 70

Figure S825.  Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16q22.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S826.  Gene #87: 'del_16q22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 36(16Q22.3) MUTATED 110 25 19
DEL PEAK 36(16Q22.3) WILD-TYPE 113 125 138

Figure S826.  Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S827.  Gene #87: 'del_16q22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 36(16Q22.3) MUTATED 55 6 16 77
DEL PEAK 36(16Q22.3) WILD-TYPE 164 52 121 39

Figure S827.  Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 7.1e-05

Table S828.  Gene #87: 'del_16q22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 36(16Q22.3) MUTATED 75 34 25
DEL PEAK 36(16Q22.3) WILD-TYPE 97 62 105

Figure S828.  Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S829.  Gene #87: 'del_16q22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 36(16Q22.3) MUTATED 68 16 50
DEL PEAK 36(16Q22.3) WILD-TYPE 76 99 89

Figure S829.  Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'MRNA_CNMF'

P value = 0.00267 (Fisher's exact test), Q value = 0.004

Table S830.  Gene #88: 'del_16q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 37(16Q23.1) MUTATED 1 9 2 0
DEL PEAK 37(16Q23.1) WILD-TYPE 13 8 10 10

Figure S830.  Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_16q23.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.00042

Table S831.  Gene #88: 'del_16q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 37(16Q23.1) MUTATED 4 7 0 0 1
DEL PEAK 37(16Q23.1) WILD-TYPE 10 2 7 7 15

Figure S831.  Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S832.  Gene #88: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 37(16Q23.1) MUTATED 134 19 8 1 4
DEL PEAK 37(16Q23.1) WILD-TYPE 35 286 11 8 33

Figure S832.  Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S833.  Gene #88: 'del_16q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 37(16Q23.1) MUTATED 96 27 19
DEL PEAK 37(16Q23.1) WILD-TYPE 69 62 152

Figure S833.  Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q23.1' versus 'RPPA_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.046

Table S834.  Gene #88: 'del_16q23.1' versus Molecular Subtype #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 37(16Q23.1) MUTATED 8 15 4 2 6 6
DEL PEAK 37(16Q23.1) WILD-TYPE 33 22 35 10 35 18

Figure S834.  Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S835.  Gene #88: 'del_16q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 37(16Q23.1) MUTATED 133 16 17
DEL PEAK 37(16Q23.1) WILD-TYPE 101 137 133

Figure S835.  Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S836.  Gene #88: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 37(16Q23.1) MUTATED 93 8 20 4 25 11 5
DEL PEAK 37(16Q23.1) WILD-TYPE 30 45 27 61 83 55 70

Figure S836.  Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S837.  Gene #88: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 37(16Q23.1) MUTATED 118 25 18
DEL PEAK 37(16Q23.1) WILD-TYPE 105 125 139

Figure S837.  Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S838.  Gene #88: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 37(16Q23.1) MUTATED 55 6 15 85
DEL PEAK 37(16Q23.1) WILD-TYPE 164 52 122 31

Figure S838.  Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S839.  Gene #88: 'del_16q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 37(16Q23.1) MUTATED 80 35 23
DEL PEAK 37(16Q23.1) WILD-TYPE 92 61 107

Figure S839.  Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S840.  Gene #88: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 37(16Q23.1) MUTATED 72 15 51
DEL PEAK 37(16Q23.1) WILD-TYPE 72 100 88

Figure S840.  Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p13.3' versus 'MRNA_CNMF'

P value = 0.00078 (Fisher's exact test), Q value = 0.0012

Table S841.  Gene #89: 'del_17p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 38(17P13.3) MUTATED 0 8 1 0
DEL PEAK 38(17P13.3) WILD-TYPE 14 9 11 10

Figure S841.  Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p13.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S842.  Gene #89: 'del_17p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 38(17P13.3) MUTATED 1 7 1 0 0
DEL PEAK 38(17P13.3) WILD-TYPE 13 2 6 7 16

Figure S842.  Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S843.  Gene #89: 'del_17p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 38(17P13.3) MUTATED 109 4 5 1 3
DEL PEAK 38(17P13.3) WILD-TYPE 60 301 14 8 34

Figure S843.  Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S844.  Gene #89: 'del_17p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 38(17P13.3) MUTATED 71 20 13
DEL PEAK 38(17P13.3) WILD-TYPE 94 69 158

Figure S844.  Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p13.3' versus 'RPPA_CNMF'

P value = 0.00127 (Fisher's exact test), Q value = 0.002

Table S845.  Gene #89: 'del_17p13.3' versus Molecular Subtype #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 38(17P13.3) MUTATED 3 10 3 0 2 8
DEL PEAK 38(17P13.3) WILD-TYPE 38 27 36 12 39 16

Figure S845.  Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_17p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S846.  Gene #89: 'del_17p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 38(17P13.3) MUTATED 100 6 15
DEL PEAK 38(17P13.3) WILD-TYPE 134 147 135

Figure S846.  Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S847.  Gene #89: 'del_17p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 38(17P13.3) MUTATED 79 1 8 3 16 13 1
DEL PEAK 38(17P13.3) WILD-TYPE 44 52 39 62 92 53 74

Figure S847.  Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S848.  Gene #89: 'del_17p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 38(17P13.3) MUTATED 88 16 15
DEL PEAK 38(17P13.3) WILD-TYPE 135 134 142

Figure S848.  Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S849.  Gene #89: 'del_17p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 38(17P13.3) MUTATED 46 1 12 60
DEL PEAK 38(17P13.3) WILD-TYPE 173 57 125 56

Figure S849.  Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 5.4e-05

Table S850.  Gene #89: 'del_17p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 38(17P13.3) MUTATED 60 26 14
DEL PEAK 38(17P13.3) WILD-TYPE 112 70 116

Figure S850.  Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 7.1e-05

Table S851.  Gene #89: 'del_17p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 38(17P13.3) MUTATED 53 15 32
DEL PEAK 38(17P13.3) WILD-TYPE 91 100 107

Figure S851.  Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p11.2' versus 'MRNA_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.0013

Table S852.  Gene #90: 'del_17p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 39(17P11.2) MUTATED 0 8 1 0
DEL PEAK 39(17P11.2) WILD-TYPE 14 9 11 10

Figure S852.  Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S853.  Gene #90: 'del_17p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 39(17P11.2) MUTATED 0 8 1 0 0
DEL PEAK 39(17P11.2) WILD-TYPE 14 1 6 7 16

Figure S853.  Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S854.  Gene #90: 'del_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 39(17P11.2) MUTATED 116 4 4 1 3
DEL PEAK 39(17P11.2) WILD-TYPE 53 301 15 8 34

Figure S854.  Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S855.  Gene #90: 'del_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 39(17P11.2) MUTATED 79 21 12
DEL PEAK 39(17P11.2) WILD-TYPE 86 68 159

Figure S855.  Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p11.2' versus 'RPPA_CNMF'

P value = 0.00349 (Fisher's exact test), Q value = 0.0051

Table S856.  Gene #90: 'del_17p11.2' versus Molecular Subtype #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 39(17P11.2) MUTATED 6 8 3 0 1 8
DEL PEAK 39(17P11.2) WILD-TYPE 35 29 36 12 40 16

Figure S856.  Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_17p11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S857.  Gene #90: 'del_17p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 39(17P11.2) MUTATED 110 4 14
DEL PEAK 39(17P11.2) WILD-TYPE 124 149 136

Figure S857.  Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S858.  Gene #90: 'del_17p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 39(17P11.2) MUTATED 85 1 10 2 17 12 1
DEL PEAK 39(17P11.2) WILD-TYPE 38 52 37 63 91 54 74

Figure S858.  Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S859.  Gene #90: 'del_17p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 39(17P11.2) MUTATED 94 14 16
DEL PEAK 39(17P11.2) WILD-TYPE 129 136 141

Figure S859.  Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S860.  Gene #90: 'del_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 39(17P11.2) MUTATED 45 0 13 66
DEL PEAK 39(17P11.2) WILD-TYPE 174 58 124 50

Figure S860.  Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.7e-05

Table S861.  Gene #90: 'del_17p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 39(17P11.2) MUTATED 63 29 15
DEL PEAK 39(17P11.2) WILD-TYPE 109 67 115

Figure S861.  Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S862.  Gene #90: 'del_17p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 39(17P11.2) MUTATED 57 15 35
DEL PEAK 39(17P11.2) WILD-TYPE 87 100 104

Figure S862.  Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q11.2' versus 'MRNA_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.00092

Table S863.  Gene #91: 'del_17q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 40(17Q11.2) MUTATED 0 7 0 0
DEL PEAK 40(17Q11.2) WILD-TYPE 14 10 12 10

Figure S863.  Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S864.  Gene #91: 'del_17q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 40(17Q11.2) MUTATED 0 7 0 0 0
DEL PEAK 40(17Q11.2) WILD-TYPE 14 2 7 7 16

Figure S864.  Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S865.  Gene #91: 'del_17q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 40(17Q11.2) MUTATED 93 2 5 1 4
DEL PEAK 40(17Q11.2) WILD-TYPE 76 303 14 8 33

Figure S865.  Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_17q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S866.  Gene #91: 'del_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 40(17Q11.2) MUTATED 58 18 14
DEL PEAK 40(17Q11.2) WILD-TYPE 107 71 157

Figure S866.  Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17q11.2' versus 'RPPA_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.026

Table S867.  Gene #91: 'del_17q11.2' versus Molecular Subtype #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 40(17Q11.2) MUTATED 3 9 3 0 2 6
DEL PEAK 40(17Q11.2) WILD-TYPE 38 28 36 12 39 18

Figure S867.  Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_17q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S868.  Gene #91: 'del_17q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 40(17Q11.2) MUTATED 84 6 14
DEL PEAK 40(17Q11.2) WILD-TYPE 150 147 136

Figure S868.  Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S869.  Gene #91: 'del_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 40(17Q11.2) MUTATED 62 1 6 3 19 11 2
DEL PEAK 40(17Q11.2) WILD-TYPE 61 52 41 62 89 55 73

Figure S869.  Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17q11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S870.  Gene #91: 'del_17q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 40(17Q11.2) MUTATED 75 10 16
DEL PEAK 40(17Q11.2) WILD-TYPE 148 140 141

Figure S870.  Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S871.  Gene #91: 'del_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 40(17Q11.2) MUTATED 40 1 13 47
DEL PEAK 40(17Q11.2) WILD-TYPE 179 57 124 69

Figure S871.  Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00336 (Fisher's exact test), Q value = 0.0049

Table S872.  Gene #91: 'del_17q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 40(17Q11.2) MUTATED 50 21 17
DEL PEAK 40(17Q11.2) WILD-TYPE 122 75 113

Figure S872.  Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00315 (Fisher's exact test), Q value = 0.0046

Table S873.  Gene #91: 'del_17q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 40(17Q11.2) MUTATED 44 15 29
DEL PEAK 40(17Q11.2) WILD-TYPE 100 100 110

Figure S873.  Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q21.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S874.  Gene #92: 'del_17q21.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 41(17Q21.31) MUTATED 0 9 0 0
DEL PEAK 41(17Q21.31) WILD-TYPE 14 8 12 10

Figure S874.  Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17q21.31' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S875.  Gene #92: 'del_17q21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 41(17Q21.31) MUTATED 1 8 0 0 0
DEL PEAK 41(17Q21.31) WILD-TYPE 13 1 7 7 16

Figure S875.  Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17q21.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S876.  Gene #92: 'del_17q21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 41(17Q21.31) MUTATED 104 1 4 1 4
DEL PEAK 41(17Q21.31) WILD-TYPE 65 304 15 8 33

Figure S876.  Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_17q21.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S877.  Gene #92: 'del_17q21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 41(17Q21.31) MUTATED 64 22 13
DEL PEAK 41(17Q21.31) WILD-TYPE 101 67 158

Figure S877.  Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17q21.31' versus 'RPPA_CNMF'

P value = 0.0046 (Fisher's exact test), Q value = 0.0067

Table S878.  Gene #92: 'del_17q21.31' versus Molecular Subtype #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 41(17Q21.31) MUTATED 4 10 3 0 1 6
DEL PEAK 41(17Q21.31) WILD-TYPE 37 27 36 12 40 18

Figure S878.  Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_17q21.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S879.  Gene #92: 'del_17q21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 41(17Q21.31) MUTATED 93 5 15
DEL PEAK 41(17Q21.31) WILD-TYPE 141 148 135

Figure S879.  Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17q21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S880.  Gene #92: 'del_17q21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 41(17Q21.31) MUTATED 72 1 6 3 18 12 1
DEL PEAK 41(17Q21.31) WILD-TYPE 51 52 41 62 90 54 74

Figure S880.  Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17q21.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S881.  Gene #92: 'del_17q21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 41(17Q21.31) MUTATED 78 14 17
DEL PEAK 41(17Q21.31) WILD-TYPE 145 136 140

Figure S881.  Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17q21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S882.  Gene #92: 'del_17q21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 41(17Q21.31) MUTATED 41 0 14 54
DEL PEAK 41(17Q21.31) WILD-TYPE 178 58 123 62

Figure S882.  Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17q21.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00024

Table S883.  Gene #92: 'del_17q21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 41(17Q21.31) MUTATED 58 21 17
DEL PEAK 41(17Q21.31) WILD-TYPE 114 75 113

Figure S883.  Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17q21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.001 (Fisher's exact test), Q value = 0.0016

Table S884.  Gene #92: 'del_17q21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 41(17Q21.31) MUTATED 49 17 30
DEL PEAK 41(17Q21.31) WILD-TYPE 95 98 109

Figure S884.  Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S885.  Gene #93: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 42(18Q21.2) MUTATED 74 2 8 4 3
DEL PEAK 42(18Q21.2) WILD-TYPE 95 303 11 5 34

Figure S885.  Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S886.  Gene #93: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 42(18Q21.2) MUTATED 57 14 10
DEL PEAK 42(18Q21.2) WILD-TYPE 108 75 161

Figure S886.  Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q21.2' versus 'RPPA_CNMF'

P value = 0.0427 (Fisher's exact test), Q value = 0.054

Table S887.  Gene #93: 'del_18q21.2' versus Molecular Subtype #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(18Q21.2) MUTATED 6 7 1 1 1 4
DEL PEAK 42(18Q21.2) WILD-TYPE 35 30 38 11 40 20

Figure S887.  Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S888.  Gene #93: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 42(18Q21.2) MUTATED 75 5 11
DEL PEAK 42(18Q21.2) WILD-TYPE 159 148 139

Figure S888.  Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S889.  Gene #93: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 42(18Q21.2) MUTATED 41 1 15 1 24 9 0
DEL PEAK 42(18Q21.2) WILD-TYPE 82 52 32 64 84 57 75

Figure S889.  Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S890.  Gene #93: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 42(18Q21.2) MUTATED 71 8 11
DEL PEAK 42(18Q21.2) WILD-TYPE 152 142 146

Figure S890.  Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S891.  Gene #93: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 42(18Q21.2) MUTATED 35 0 8 47
DEL PEAK 42(18Q21.2) WILD-TYPE 184 58 129 69

Figure S891.  Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00202 (Fisher's exact test), Q value = 0.0031

Table S892.  Gene #93: 'del_18q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 42(18Q21.2) MUTATED 46 19 14
DEL PEAK 42(18Q21.2) WILD-TYPE 126 77 116

Figure S892.  Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 5.4e-05

Table S893.  Gene #93: 'del_18q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 42(18Q21.2) MUTATED 44 10 25
DEL PEAK 42(18Q21.2) WILD-TYPE 100 105 114

Figure S893.  Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S894.  Gene #94: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 43(18Q23) MUTATED 80 2 9 3 4
DEL PEAK 43(18Q23) WILD-TYPE 89 303 10 6 33

Figure S894.  Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S895.  Gene #94: 'del_18q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 43(18Q23) MUTATED 62 14 10
DEL PEAK 43(18Q23) WILD-TYPE 103 75 161

Figure S895.  Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q23' versus 'RPPA_CNMF'

P value = 0.0401 (Fisher's exact test), Q value = 0.051

Table S896.  Gene #94: 'del_18q23' versus Molecular Subtype #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 43(18Q23) MUTATED 6 9 1 1 2 3
DEL PEAK 43(18Q23) WILD-TYPE 35 28 38 11 39 21

Figure S896.  Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_18q23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S897.  Gene #94: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 43(18Q23) MUTATED 82 5 11
DEL PEAK 43(18Q23) WILD-TYPE 152 148 139

Figure S897.  Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S898.  Gene #94: 'del_18q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 43(18Q23) MUTATED 46 1 19 1 22 8 1
DEL PEAK 43(18Q23) WILD-TYPE 77 52 28 64 86 58 74

Figure S898.  Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S899.  Gene #94: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 43(18Q23) MUTATED 74 10 12
DEL PEAK 43(18Q23) WILD-TYPE 149 140 145

Figure S899.  Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18q23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S900.  Gene #94: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 43(18Q23) MUTATED 33 1 9 53
DEL PEAK 43(18Q23) WILD-TYPE 186 57 128 63

Figure S900.  Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.00055

Table S901.  Gene #94: 'del_18q23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 43(18Q23) MUTATED 49 22 13
DEL PEAK 43(18Q23) WILD-TYPE 123 74 117

Figure S901.  Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00029

Table S902.  Gene #94: 'del_18q23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 43(18Q23) MUTATED 44 11 29
DEL PEAK 43(18Q23) WILD-TYPE 100 104 110

Figure S902.  Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S903.  Gene #95: 'del_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 44(19P13.3) MUTATED 0 11 0 0
DEL PEAK 44(19P13.3) WILD-TYPE 14 6 12 10

Figure S903.  Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19p13.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S904.  Gene #95: 'del_19p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 44(19P13.3) MUTATED 2 9 0 0 0
DEL PEAK 44(19P13.3) WILD-TYPE 12 0 7 7 16

Figure S904.  Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S905.  Gene #95: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 44(19P13.3) MUTATED 145 0 5 3 1
DEL PEAK 44(19P13.3) WILD-TYPE 24 305 14 6 36

Figure S905.  Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S906.  Gene #95: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 44(19P13.3) MUTATED 108 23 5
DEL PEAK 44(19P13.3) WILD-TYPE 57 66 166

Figure S906.  Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p13.3' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 7.1e-05

Table S907.  Gene #95: 'del_19p13.3' versus Molecular Subtype #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 44(19P13.3) MUTATED 7 14 2 0 1 7
DEL PEAK 44(19P13.3) WILD-TYPE 34 23 37 12 40 17

Figure S907.  Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0117 (Fisher's exact test), Q value = 0.016

Table S908.  Gene #95: 'del_19p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
DEL PEAK 44(19P13.3) MUTATED 16 8 2 5
DEL PEAK 44(19P13.3) WILD-TYPE 51 59 41 12

Figure S908.  Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S909.  Gene #95: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 44(19P13.3) MUTATED 140 4 9
DEL PEAK 44(19P13.3) WILD-TYPE 94 149 141

Figure S909.  Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S910.  Gene #95: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 44(19P13.3) MUTATED 102 1 20 2 21 7 0
DEL PEAK 44(19P13.3) WILD-TYPE 21 52 27 63 87 59 75

Figure S910.  Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S911.  Gene #95: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 44(19P13.3) MUTATED 127 12 10
DEL PEAK 44(19P13.3) WILD-TYPE 96 138 147

Figure S911.  Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S912.  Gene #95: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 44(19P13.3) MUTATED 45 0 10 94
DEL PEAK 44(19P13.3) WILD-TYPE 174 58 127 22

Figure S912.  Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S913.  Gene #95: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 44(19P13.3) MUTATED 83 31 18
DEL PEAK 44(19P13.3) WILD-TYPE 89 65 112

Figure S913.  Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S914.  Gene #95: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 44(19P13.3) MUTATED 78 11 43
DEL PEAK 44(19P13.3) WILD-TYPE 66 104 96

Figure S914.  Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S915.  Gene #96: 'del_19p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 45(19P12) MUTATED 50 1 5 1 1
DEL PEAK 45(19P12) WILD-TYPE 119 304 14 8 36

Figure S915.  Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S916.  Gene #96: 'del_19p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 45(19P12) MUTATED 38 10 4
DEL PEAK 45(19P12) WILD-TYPE 127 79 167

Figure S916.  Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S917.  Gene #96: 'del_19p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 45(19P12) MUTATED 47 5 6
DEL PEAK 45(19P12) WILD-TYPE 187 148 144

Figure S917.  Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S918.  Gene #96: 'del_19p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 45(19P12) MUTATED 32 1 9 1 11 4 0
DEL PEAK 45(19P12) WILD-TYPE 91 52 38 64 97 62 75

Figure S918.  Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S919.  Gene #96: 'del_19p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 45(19P12) MUTATED 43 9 5
DEL PEAK 45(19P12) WILD-TYPE 180 141 152

Figure S919.  Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S920.  Gene #96: 'del_19p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 45(19P12) MUTATED 24 1 4 28
DEL PEAK 45(19P12) WILD-TYPE 195 57 133 88

Figure S920.  Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.033 (Fisher's exact test), Q value = 0.043

Table S921.  Gene #96: 'del_19p12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 45(19P12) MUTATED 30 10 10
DEL PEAK 45(19P12) WILD-TYPE 142 86 120

Figure S921.  Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 5.4e-05

Table S922.  Gene #96: 'del_19p12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 45(19P12) MUTATED 32 5 13
DEL PEAK 45(19P12) WILD-TYPE 112 110 126

Figure S922.  Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.43' versus 'MRNA_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0011

Table S923.  Gene #97: 'del_19q13.43' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 46(19Q13.43) MUTATED 0 8 1 0
DEL PEAK 46(19Q13.43) WILD-TYPE 14 9 11 10

Figure S923.  Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19q13.43' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 5.4e-05

Table S924.  Gene #97: 'del_19q13.43' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 46(19Q13.43) MUTATED 1 7 1 0 0
DEL PEAK 46(19Q13.43) WILD-TYPE 13 2 6 7 16

Figure S924.  Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19q13.43' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S925.  Gene #97: 'del_19q13.43' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 46(19Q13.43) MUTATED 61 1 3 1 1
DEL PEAK 46(19Q13.43) WILD-TYPE 108 304 16 8 36

Figure S925.  Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.43' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S926.  Gene #97: 'del_19q13.43' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 46(19Q13.43) MUTATED 43 11 2
DEL PEAK 46(19Q13.43) WILD-TYPE 122 78 169

Figure S926.  Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.43' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S927.  Gene #97: 'del_19q13.43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 46(19Q13.43) MUTATED 59 3 4
DEL PEAK 46(19Q13.43) WILD-TYPE 175 150 146

Figure S927.  Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19q13.43' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S928.  Gene #97: 'del_19q13.43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 46(19Q13.43) MUTATED 44 1 8 0 11 2 0
DEL PEAK 46(19Q13.43) WILD-TYPE 79 52 39 65 97 64 75

Figure S928.  Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.43' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S929.  Gene #97: 'del_19q13.43' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 46(19Q13.43) MUTATED 55 4 4
DEL PEAK 46(19Q13.43) WILD-TYPE 168 146 153

Figure S929.  Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19q13.43' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S930.  Gene #97: 'del_19q13.43' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 46(19Q13.43) MUTATED 27 0 2 34
DEL PEAK 46(19Q13.43) WILD-TYPE 192 58 135 82

Figure S930.  Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.43' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.015

Table S931.  Gene #97: 'del_19q13.43' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 46(19Q13.43) MUTATED 32 15 9
DEL PEAK 46(19Q13.43) WILD-TYPE 140 81 121

Figure S931.  Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19q13.43' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S932.  Gene #97: 'del_19q13.43' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 46(19Q13.43) MUTATED 29 2 25
DEL PEAK 46(19Q13.43) WILD-TYPE 115 113 114

Figure S932.  Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S933.  Gene #98: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 47(20P12.1) MUTATED 25 6 2 1 2
DEL PEAK 47(20P12.1) WILD-TYPE 144 299 17 8 35

Figure S933.  Get High-res Image Gene #98: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_20p12.1' versus 'METHLYATION_CNMF'

P value = 0.0441 (Fisher's exact test), Q value = 0.056

Table S934.  Gene #98: 'del_20p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 47(20P12.1) MUTATED 17 5 6
DEL PEAK 47(20P12.1) WILD-TYPE 148 84 165

Figure S934.  Get High-res Image Gene #98: 'del_20p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_20p12.1' versus 'MRNASEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00039

Table S935.  Gene #98: 'del_20p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 47(20P12.1) MUTATED 27 3 6
DEL PEAK 47(20P12.1) WILD-TYPE 207 150 144

Figure S935.  Get High-res Image Gene #98: 'del_20p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00136 (Fisher's exact test), Q value = 0.0021

Table S936.  Gene #98: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 47(20P12.1) MUTATED 17 3 6 0 6 2 2
DEL PEAK 47(20P12.1) WILD-TYPE 106 50 41 65 102 64 73

Figure S936.  Get High-res Image Gene #98: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.00064

Table S937.  Gene #98: 'del_20p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 47(20P12.1) MUTATED 26 5 4
DEL PEAK 47(20P12.1) WILD-TYPE 197 145 153

Figure S937.  Get High-res Image Gene #98: 'del_20p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_20p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00098 (Fisher's exact test), Q value = 0.0015

Table S938.  Gene #98: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 47(20P12.1) MUTATED 10 1 6 18
DEL PEAK 47(20P12.1) WILD-TYPE 209 57 131 98

Figure S938.  Get High-res Image Gene #98: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 5.4e-05

Table S939.  Gene #99: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 48(22Q13.32) MUTATED 0 9 0 0
DEL PEAK 48(22Q13.32) WILD-TYPE 14 8 12 10

Figure S939.  Get High-res Image Gene #99: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_22q13.32' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 5.4e-05

Table S940.  Gene #99: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 48(22Q13.32) MUTATED 2 7 0 0 0
DEL PEAK 48(22Q13.32) WILD-TYPE 12 2 7 7 16

Figure S940.  Get High-res Image Gene #99: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S941.  Gene #99: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 48(22Q13.32) MUTATED 122 7 4 5 3
DEL PEAK 48(22Q13.32) WILD-TYPE 47 298 15 4 34

Figure S941.  Get High-res Image Gene #99: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S942.  Gene #99: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 48(22Q13.32) MUTATED 84 23 18
DEL PEAK 48(22Q13.32) WILD-TYPE 81 66 153

Figure S942.  Get High-res Image Gene #99: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q13.32' versus 'RPPA_CNMF'

P value = 0.00126 (Fisher's exact test), Q value = 0.0019

Table S943.  Gene #99: 'del_22q13.32' versus Molecular Subtype #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 48(22Q13.32) MUTATED 9 13 3 1 1 5
DEL PEAK 48(22Q13.32) WILD-TYPE 32 24 36 11 40 19

Figure S943.  Get High-res Image Gene #99: 'del_22q13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S944.  Gene #99: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 48(22Q13.32) MUTATED 113 8 19
DEL PEAK 48(22Q13.32) WILD-TYPE 121 145 131

Figure S944.  Get High-res Image Gene #99: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S945.  Gene #99: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 48(22Q13.32) MUTATED 83 1 10 2 26 14 4
DEL PEAK 48(22Q13.32) WILD-TYPE 40 52 37 63 82 52 71

Figure S945.  Get High-res Image Gene #99: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S946.  Gene #99: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 48(22Q13.32) MUTATED 103 14 20
DEL PEAK 48(22Q13.32) WILD-TYPE 120 136 137

Figure S946.  Get High-res Image Gene #99: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_22q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S947.  Gene #99: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 48(22Q13.32) MUTATED 52 0 17 68
DEL PEAK 48(22Q13.32) WILD-TYPE 167 58 120 48

Figure S947.  Get High-res Image Gene #99: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.7e-05

Table S948.  Gene #99: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 48(22Q13.32) MUTATED 69 28 22
DEL PEAK 48(22Q13.32) WILD-TYPE 103 68 108

Figure S948.  Get High-res Image Gene #99: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_22q13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S949.  Gene #99: 'del_22q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 48(22Q13.32) MUTATED 64 19 36
DEL PEAK 48(22Q13.32) WILD-TYPE 80 96 103

Figure S949.  Get High-res Image Gene #99: 'del_22q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp21.1' versus 'MRNA_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.00099

Table S950.  Gene #100: 'del_xp21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 49(XP21.1) MUTATED 0 7 0 0
DEL PEAK 49(XP21.1) WILD-TYPE 14 10 12 10

Figure S950.  Get High-res Image Gene #100: 'del_xp21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_xp21.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00112 (Fisher's exact test), Q value = 0.0017

Table S951.  Gene #100: 'del_xp21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
DEL PEAK 49(XP21.1) MUTATED 2 5 0 0 0
DEL PEAK 49(XP21.1) WILD-TYPE 12 4 7 7 16

Figure S951.  Get High-res Image Gene #100: 'del_xp21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_xp21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S952.  Gene #100: 'del_xp21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
DEL PEAK 49(XP21.1) MUTATED 78 2 3 2 3
DEL PEAK 49(XP21.1) WILD-TYPE 91 303 16 7 34

Figure S952.  Get High-res Image Gene #100: 'del_xp21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S953.  Gene #100: 'del_xp21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
DEL PEAK 49(XP21.1) MUTATED 54 12 9
DEL PEAK 49(XP21.1) WILD-TYPE 111 77 162

Figure S953.  Get High-res Image Gene #100: 'del_xp21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xp21.1' versus 'RPPA_CNMF'

P value = 0.00245 (Fisher's exact test), Q value = 0.0037

Table S954.  Gene #100: 'del_xp21.1' versus Molecular Subtype #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 49(XP21.1) MUTATED 4 10 0 1 2 4
DEL PEAK 49(XP21.1) WILD-TYPE 37 27 39 11 39 20

Figure S954.  Get High-res Image Gene #100: 'del_xp21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_xp21.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S955.  Gene #100: 'del_xp21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
DEL PEAK 49(XP21.1) MUTATED 76 5 6
DEL PEAK 49(XP21.1) WILD-TYPE 158 148 144

Figure S955.  Get High-res Image Gene #100: 'del_xp21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_xp21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S956.  Gene #100: 'del_xp21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
DEL PEAK 49(XP21.1) MUTATED 55 2 10 1 15 4 0
DEL PEAK 49(XP21.1) WILD-TYPE 68 51 37 64 93 62 75

Figure S956.  Get High-res Image Gene #100: 'del_xp21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S957.  Gene #100: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
DEL PEAK 49(XP21.1) MUTATED 65 11 9
DEL PEAK 49(XP21.1) WILD-TYPE 158 139 148

Figure S957.  Get High-res Image Gene #100: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_xp21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S958.  Gene #100: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
DEL PEAK 49(XP21.1) MUTATED 34 0 5 46
DEL PEAK 49(XP21.1) WILD-TYPE 185 58 132 70

Figure S958.  Get High-res Image Gene #100: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00026

Table S959.  Gene #100: 'del_xp21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
DEL PEAK 49(XP21.1) MUTATED 47 17 11
DEL PEAK 49(XP21.1) WILD-TYPE 125 79 119

Figure S959.  Get High-res Image Gene #100: 'del_xp21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_xp21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.9e-05

Table S960.  Gene #100: 'del_xp21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
DEL PEAK 49(XP21.1) MUTATED 44 6 25
DEL PEAK 49(XP21.1) WILD-TYPE 100 109 114

Figure S960.  Get High-res Image Gene #100: 'del_xp21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = all_lesions.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UCEC-TP/15106279/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UCEC-TP/15120652/UCEC-TP.transferedmergedcluster.txt

  • Number of patients = 539

  • Number of significantly focal cnvs = 100

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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