Correlation between copy number variation genes (focal events) and molecular subtypes
Glioma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1CF9PGX
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1CF9PGX
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 75 focal events and 14 molecular subtypes across 1090 patients, 658 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1p36.21 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_1q22 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_1q32.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_1q44 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_2p24.3 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_3q26.33 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_4p16.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_4q12 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_5p15.33 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_7p11.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_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_7q11.21 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_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_7q21.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_7q31.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_7q32.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_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',  'MIR_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_9q34.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_10p15.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_11p13 cnv correlated to 'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_11q24.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_12p13.32 cnv correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_12q14.1 cnv correlated to 'MIR_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_12q15 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_13q34 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • amp_14q32.33 cnv correlated to 'MIR_CNMF',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_17p13.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'RPPA_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_17q25.1 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_19p13.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_19q12 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_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_19q13.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_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_xp11.21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_1p36.32 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_1p36.23 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'.

  • del_1p32.3 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_1p22.1 cnv correlated to 'MIR_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_1q42.11 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_1q44 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_2q22.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • del_2q37.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3p21.31 cnv correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3q13.31 cnv correlated to 'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_3q29 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • del_5p15.33 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_5q34 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_6p25.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_6q22.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_8p23.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_8q24.3 cnv correlated to 'MIR_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_9p21.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_10p15.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_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_10p13 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_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_10q23.31 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_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_10q26.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_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_11p15.5 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_11p15.1 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_11p11.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_12p13.1 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_12q12 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_12q15 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_13q22.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_14q24.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_14q31.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_15q14 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_16p12.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_16q23.1 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_17p13.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_17q11.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_18q23 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'METHLYATION_CNMF'.

  • del_19q13.41 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_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_19q13.43 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_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_22q13.32 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_xq21.1 cnv correlated to 'MRNA_CHIERARCHICAL',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  '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 75 focal events and 14 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 658 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		MIR
CNMF 		MIR
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 Fisher's exact test Fisher's exact test
amp 7p11 2 634 (58%) 456 1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.00046
(0.00122) 		0.00022
(0.000616) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.00017
(0.000484) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05)
amp 7q11 21 580 (53%) 510 2e-05
(6.84e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		4e-05
(0.000129) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.00874
(0.017) 		0.00096
(0.00238) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.00416
(0.00879) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05)
del 10p15 3 553 (51%) 537 1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.023
(0.0396) 		0.00334
(0.00729) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.00302
(0.00669) 		0.00074
(0.0019) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.00034
(0.000918) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05)
del 10p13 553 (51%) 537 1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.0049
(0.0101) 		0.00112
(0.00272) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.00104
(0.00255) 		2e-05
(6.84e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.00019
(0.000538) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05)
del 10q23 31 628 (58%) 462 3e-05
(9.91e-05) 		1e-05
(3.74e-05) 		0.0341
(0.0567) 		0.00304
(0.00672) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		9e-05
(0.000268) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05)
del 19q13 43 355 (33%) 735 2e-05
(6.84e-05) 		1e-05
(3.74e-05) 		0.00444
(0.00927) 		0.0432
(0.0699) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.0153
(0.0279) 		0.00757
(0.0149) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05)
amp 7q31 2 645 (59%) 445 0.0012
(0.00288) 		1e-05
(3.74e-05) 		0.0232
(0.04) 		0.00934
(0.018) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.105
(0.151) 		0.0284
(0.0481) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.0107
(0.0202) 		1e-05
(3.74e-05) 		0.00061
(0.00158) 		1e-05
(3.74e-05)
amp 19q12 247 (23%) 843 1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.374
(0.438) 		0.00488
(0.0101) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.0408
(0.0665) 		0.00087
(0.00217) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.00012
(0.00035) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05)
amp 19q13 2 231 (21%) 859 1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.14
(0.193) 		0.00609
(0.0122) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.0171
(0.0308) 		0.00102
(0.00251) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.00016
(0.000459) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05)
del 10q26 3 665 (61%) 425 1e-05
(3.74e-05) 		4e-05
(0.000129) 		0.0923
(0.136) 		0.00142
(0.00337) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.0001
(0.000297) 		2e-05
(6.84e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05)
del 19q13 41 364 (33%) 726 0.00209
(0.00482) 		5e-05
(0.000158) 		0.0641
(0.0989) 		0.0362
(0.06) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.00228
(0.00522) 		0.00066
(0.0017) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05)
amp 7q21 2 635 (58%) 455 0.00011
(0.000323) 		1e-05
(3.74e-05) 		0.0586
(0.0913) 		8e-05
(0.000243) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.072
(0.109) 		0.0144
(0.0264) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.00353
(0.00764) 		1e-05
(3.74e-05) 		0.00012
(0.00035) 		1e-05
(3.74e-05)
amp 7q32 3 658 (60%) 432 0.00076
(0.00194) 		7e-05
(0.000216) 		0.0952
(0.139) 		0.00476
(0.00986) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.125
(0.175) 		0.018
(0.0322) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.034
(0.0567) 		1e-05
(3.74e-05) 		0.00076
(0.00194) 		1e-05
(3.74e-05)
amp 19p13 3 375 (34%) 715 1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.0396
(0.0648) 		0.00246
(0.00562) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.0586
(0.0913) 		0.0277
(0.047) 		0.00522
(0.0107) 		1e-05
(3.74e-05) 		0.00054
(0.00142) 		0.155
(0.21) 		2e-05
(6.84e-05) 		5e-05
(0.000158)
del 9p21 3 595 (55%) 495 2e-05
(6.84e-05) 		2e-05
(6.84e-05) 		0.528
(0.585) 		0.03
(0.0504) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		8e-05
(0.000243) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.381
(0.443) 		1e-05
(3.74e-05) 		0.00086
(0.00216) 		1e-05
(3.74e-05)
amp 3q26 33 132 (12%) 958 0.00295
(0.00656) 		0.211
(0.274) 		0.317
(0.383) 		0.0565
(0.0886) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.00882
(0.0171) 		0.00635
(0.0127) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.00188
(0.00439) 		0.018
(0.0322) 		0.00339
(0.00737) 		0.00318
(0.007)
amp 8q24 21 169 (16%) 921 1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.0205
(0.0359) 		0.238
(0.302) 		2e-05
(6.84e-05) 		1e-05
(3.74e-05) 		0.505
(0.563) 		0.433
(0.493) 		0.00222
(0.0051) 		1e-05
(3.74e-05) 		0.0106
(0.0201) 		0.00093
(0.00231) 		0.016
(0.029) 		1e-05
(3.74e-05)
amp 10p15 1 88 (8%) 1002 0.00019
(0.000538) 		1e-05
(3.74e-05) 		0.00813
(0.0159) 		0.0567
(0.0888) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.001
(0.00247) 		0.144
(0.198) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		8e-05
(0.000243) 		0.218
(0.282) 		0.00224
(0.00514) 		1e-05
(3.74e-05)
del 1p36 23 347 (32%) 743 0.0201
(0.0354) 		0.225
(0.289) 		0.776
(0.81) 		0.627
(0.676) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.0301
(0.0504) 		0.00947
(0.0182) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05)
del 1p22 1 234 (21%) 856 0.975
(0.979) 		0.552
(0.606) 		0.957
(0.965) 		0.00436
(0.00916) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.00676
(0.0135) 		5e-05
(0.000158) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05)
del 2q37 1 121 (11%) 969 0.018
(0.0322) 		0.00546
(0.0111) 		0.545
(0.6) 		0.823
(0.848) 		0.0167
(0.0302) 		1e-05
(3.74e-05) 		0.0106
(0.0201) 		0.00549
(0.0112) 		0.148
(0.202) 		1e-05
(3.74e-05) 		0.00189
(0.0044) 		0.0226
(0.039) 		0.00065
(0.00168) 		9e-05
(0.000268)
del 5q34 133 (12%) 957 1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		3e-05
(9.91e-05) 		0.0053
(0.0108) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.35
(0.414) 		0.0864
(0.128) 		0.00397
(0.00847) 		1e-05
(3.74e-05) 		2e-05
(6.84e-05) 		0.0558
(0.0876) 		0.00159
(0.00376) 		1e-05
(3.74e-05)
del 11p15 5 234 (21%) 856 1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.198
(0.261) 		0.00175
(0.0041) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.0638
(0.0985) 		0.967
(0.974) 		0.0468
(0.0749) 		1e-05
(3.74e-05) 		2e-05
(6.84e-05) 		0.00559
(0.0114) 		0.00453
(0.00942) 		1e-05
(3.74e-05)
del 11p11 2 159 (15%) 931 1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.604
(0.655) 		0.0187
(0.0333) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.148
(0.202) 		0.471
(0.53) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.00051
(0.00135) 		1e-05
(3.74e-05) 		0.00692
(0.0138) 		2e-05
(6.84e-05)
del 15q14 215 (20%) 875 1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.00197
(0.00456) 		9e-05
(0.000268) 		2e-05
(6.84e-05) 		0.00025
(0.000698) 		0.0371
(0.0613) 		0.038
(0.0626) 		1e-05
(3.74e-05) 		0.00041
(0.0011) 		0.426
(0.49) 		0.783
(0.814) 		0.604
(0.655) 		0.0434
(0.0701)
amp 1p36 21 104 (10%) 986 0.326
(0.391) 		0.432
(0.493) 		0.356
(0.42) 		0.115
(0.164) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.00612
(0.0123) 		0.0207
(0.0362) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.0149
(0.0272) 		2e-05
(6.84e-05) 		0.00763
(0.015) 		0.00415
(0.00879)
amp 4q12 138 (13%) 952 0.00017
(0.000484) 		0.00363
(0.00784) 		0.589
(0.642) 		0.471
(0.53) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.0936
(0.137) 		0.0542
(0.0854) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.00337
(0.00734) 		8e-05
(0.000243) 		0.00254
(0.00577) 		0.00079
(0.002)
del 1p36 32 318 (29%) 772 0.729
(0.764) 		0.698
(0.738) 		0.69
(0.731) 		0.256
(0.32) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.00374
(0.00803) 		0.00059
(0.00154) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05)
del 1p32 3 257 (24%) 833 0.359
(0.423) 		0.361
(0.425) 		0.599
(0.651) 		0.157
(0.212) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.00573
(0.0116) 		3e-05
(9.91e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05)
del 11p15 1 176 (16%) 914 1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.719
(0.756) 		0.0777
(0.117) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.0904
(0.133) 		0.543
(0.6) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		3e-05
(9.91e-05) 		9e-05
(0.000268) 		0.0009
(0.00224) 		1e-05
(3.74e-05)
del 14q24 2 293 (27%) 797 1e-05
(3.74e-05) 		3e-05
(9.91e-05) 		0.082
(0.123) 		0.157
(0.212) 		0.00011
(0.000323) 		0.348
(0.412) 		0.0137
(0.0254) 		0.205
(0.268) 		4e-05
(0.000129) 		0.0002
(0.000565) 		0.0012
(0.00288) 		0.0049
(0.0101) 		0.00885
(0.0171) 		0.00258
(0.00584)
del 14q31 3 276 (25%) 814 1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.471
(0.53) 		0.165
(0.222) 		0.00013
(0.000377) 		0.232
(0.297) 		0.0442
(0.0713) 		0.354
(0.418) 		0.00017
(0.000484) 		0.00035
(0.000942) 		0.00104
(0.00255) 		0.00848
(0.0165) 		0.0128
(0.0237) 		0.00271
(0.00608)
del 22q13 32 289 (27%) 801 0.82
(0.847) 		0.971
(0.976) 		0.0845
(0.126) 		0.414
(0.48) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.00087
(0.00217) 		0.00256
(0.00581) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.0301
(0.0504) 		1e-05
(3.74e-05) 		2e-05
(6.84e-05) 		7e-05
(0.000216)
amp 1q22 144 (13%) 946 0.0142
(0.026) 		0.0266
(0.0456) 		0.0169
(0.0304) 		0.379
(0.442) 		1e-05
(3.74e-05) 		0.0008
(0.00202) 		0.0117
(0.022) 		0.205
(0.268) 		1e-05
(3.74e-05) 		7e-05
(0.000216) 		0.364
(0.427) 		0.0893
(0.132) 		0.00254
(0.00577) 		0.75
(0.785)
amp 12p13 32 152 (14%) 938 0.762
(0.796) 		0.384
(0.446) 		0.447
(0.509) 		0.43
(0.492) 		0.778
(0.812) 		1e-05
(3.74e-05) 		0.0006
(0.00156) 		0.0111
(0.0209) 		0.00619
(0.0124) 		1e-05
(3.74e-05) 		0.00444
(0.00927) 		0.00318
(0.007) 		0.00108
(0.00264) 		1e-05
(3.74e-05)
amp 12q14 1 171 (16%) 919 0.113
(0.161) 		0.149
(0.203) 		0.0104
(0.0198) 		0.0861
(0.128) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.127
(0.177) 		0.927
(0.939) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.00376
(0.00806) 		1e-05
(3.74e-05) 		2e-05
(6.84e-05) 		5e-05
(0.000158)
del 4q34 3 230 (21%) 860 0.00718
(0.0142) 		0.00033
(0.000895) 		0.0597
(0.0929) 		0.0988
(0.143) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.233
(0.298) 		0.802
(0.83) 		0.00991
(0.019) 		0.00026
(0.000718) 		0.0274
(0.0466) 		0.0459
(0.0738) 		0.682
(0.724) 		0.00014
(0.000405)
del 5p15 33 107 (10%) 983 2e-05
(6.84e-05) 		4e-05
(0.000129) 		0.0068
(0.0135) 		0.0531
(0.084) 		0.0001
(0.000297) 		1e-05
(3.74e-05) 		0.694
(0.733) 		0.636
(0.685) 		0.121
(0.17) 		0.00268
(0.00603) 		0.00441
(0.00924) 		0.205
(0.268) 		0.00409
(0.00871) 		2e-05
(6.84e-05)
del 6q26 261 (24%) 829 0.78
(0.812) 		0.757
(0.792) 		0.382
(0.444) 		0.546
(0.6) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.00963
(0.0185) 		5e-05
(0.000158) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.161
(0.216) 		0.0033
(0.00725) 		0.00034
(0.000918)
del 8q24 3 78 (7%) 1012 0.285
(0.35) 		0.867
(0.887) 		0.00756
(0.0149) 		0.466
(0.526) 		0.00144
(0.00341) 		2e-05
(6.84e-05) 		0.324
(0.389) 		0.109
(0.156) 		0.043
(0.0697) 		0.00391
(0.00836) 		0.0422
(0.0687) 		0.0012
(0.00288) 		0.0244
(0.0419) 		0.014
(0.0258)
del 13q14 2 383 (35%) 707 2e-05
(6.84e-05) 		3e-05
(9.91e-05) 		0.177
(0.236) 		0.143
(0.197) 		0.00079
(0.002) 		0.00021
(0.000591) 		0.284
(0.349) 		0.584
(0.637) 		6e-05
(0.000187) 		3e-05
(9.91e-05) 		0.0364
(0.0604) 		0.00601
(0.0121) 		0.287
(0.352) 		0.0112
(0.0211)
del 13q22 1 367 (34%) 723 1e-05
(3.74e-05) 		0.00016
(0.000459) 		0.39
(0.453) 		0.338
(0.403) 		0.00013
(0.000377) 		0.00175
(0.0041) 		0.196
(0.259) 		0.915
(0.93) 		6e-05
(0.000187) 		3e-05
(9.91e-05) 		0.0226
(0.039) 		0.00196
(0.00454) 		0.377
(0.441) 		0.0393
(0.0645)
del 17q11 2 93 (9%) 997 2e-05
(6.84e-05) 		2e-05
(6.84e-05) 		0.0041
(0.00871) 		0.0108
(0.0204) 		1e-05
(3.74e-05) 		0.00039
(0.00105) 		0.179
(0.238) 		0.00133
(0.00317) 		4e-05
(0.000129) 		1e-05
(3.74e-05) 		0.187
(0.247) 		0.137
(0.19) 		0.244
(0.309) 		0.0949
(0.139)
amp 1q32 1 205 (19%) 885 0.783
(0.814) 		0.0623
(0.0965) 		0.289
(0.354) 		0.149
(0.203) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.0474
(0.0757) 		0.228
(0.293) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.187
(0.247) 		1e-05
(3.74e-05) 		0.00169
(0.00399) 		1e-05
(3.74e-05)
del 6q22 31 240 (22%) 850 0.951
(0.961) 		1
(1.00) 		0.178
(0.237) 		0.379
(0.442) 		1e-05
(3.74e-05) 		2e-05
(6.84e-05) 		0.0611
(0.0948) 		0.00094
(0.00233) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.0007
(0.0018) 		0.121
(0.17) 		0.00263
(0.00593) 		0.00369
(0.00794)
del 14q13 1 246 (23%) 844 3e-05
(9.91e-05) 		0.0003
(0.000822) 		0.709
(0.747) 		0.663
(0.709) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.152
(0.207) 		0.313
(0.379) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.152
(0.207) 		0.00032
(0.000873) 		0.0656
(0.101) 		3e-05
(9.91e-05)
del xq21 1 183 (17%) 907 0.0726
(0.11) 		0.00081
(0.00204) 		0.0502
(0.08) 		0.107
(0.154) 		0.904
(0.921) 		0.00141
(0.00336) 		0.00081
(0.00204) 		0.0316
(0.0527) 		0.00059
(0.00154) 		0.319
(0.384) 		0.00051
(0.00135) 		0.36
(0.424) 		0.00011
(0.000323) 		0.00011
(0.000323)
amp 1q44 129 (12%) 961 0.129
(0.18) 		0.62
(0.669) 		0.355
(0.419) 		0.305
(0.371) 		1e-05
(3.74e-05) 		0.00044
(0.00117) 		0.0135
(0.0251) 		0.137
(0.19) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.484
(0.542) 		0.0208
(0.0364) 		0.00583
(0.0118) 		0.239
(0.303)
amp 5p15 33 76 (7%) 1014 0.0703
(0.107) 		0.0863
(0.128) 		0.0737
(0.111) 		0.234
(0.298) 		2e-05
(6.84e-05) 		0.0163
(0.0295) 		0.455
(0.516) 		0.2
(0.263) 		7e-05
(0.000216) 		0.00033
(0.000895) 		0.148
(0.202) 		0.00334
(0.00729) 		0.00108
(0.00264) 		0.0029
(0.00646)
amp 11q24 1 112 (10%) 978 0.00707
(0.014) 		0.00784
(0.0154) 		0.126
(0.176) 		0.0684
(0.104) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.32
(0.385) 		0.0835
(0.125) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.68
(0.723) 		0.114
(0.161) 		0.498
(0.557) 		0.00909
(0.0175)
del 3p21 31 109 (10%) 981 0.308
(0.374) 		0.168
(0.226) 		0.421
(0.486) 		0.216
(0.28) 		0.136
(0.19) 		0.00127
(0.00304) 		0.02
(0.0352) 		0.0425
(0.069) 		0.171
(0.228) 		0.0252
(0.0432) 		0.00342
(0.00742) 		0.0026
(0.00587) 		0.534
(0.592) 		0.0191
(0.0338)
del 8p23 2 88 (8%) 1002 0.256
(0.32) 		0.245
(0.309) 		0.176
(0.235) 		0.277
(0.343) 		7e-05
(0.000216) 		1e-05
(3.74e-05) 		0.297
(0.362) 		0.214
(0.278) 		1e-05
(3.74e-05) 		0.00026
(0.000718) 		0.295
(0.361) 		0.00782
(0.0153) 		0.00525
(0.0108) 		2e-05
(6.84e-05)
del 12q12 147 (13%) 943 0.0137
(0.0254) 		0.00056
(0.00147) 		0.422
(0.486) 		0.0839
(0.125) 		6e-05
(0.000187) 		1e-05
(3.74e-05) 		0.867
(0.887) 		0.944
(0.955) 		0.914
(0.93) 		5e-05
(0.000158) 		0.00282
(0.00631) 		0.467
(0.527) 		0.288
(0.352) 		0.00015
(0.000433)
del 12q15 142 (13%) 948 0.00111
(0.0027) 		0.00214
(0.00493) 		0.268
(0.334) 		0.427
(0.491) 		5e-05
(0.000158) 		1e-05
(3.74e-05) 		0.642
(0.69) 		0.916
(0.93) 		0.718
(0.755) 		1e-05
(3.74e-05) 		0.00026
(0.000718) 		0.313
(0.379) 		0.213
(0.277) 		1e-05
(3.74e-05)
del 16q23 1 129 (12%) 961 0.0102
(0.0195) 		0.489
(0.547) 		0.872
(0.891) 		0.539
(0.595) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.0511
(0.0812) 		0.00079
(0.002) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.27
(0.336) 		0.0145
(0.0266) 		0.139
(0.193) 		0.219
(0.282)
del 17p13 1 116 (11%) 974 0.00113
(0.00274) 		0.0019
(0.00441) 		0.65
(0.697) 		0.898
(0.916) 		1e-05
(3.74e-05) 		0.00026
(0.000718) 		0.327
(0.392) 		0.0636
(0.0983) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.202
(0.265) 		0.00428
(0.00901) 		0.239
(0.303) 		0.0662
(0.102)
amp 2p24 3 72 (7%) 1018 0.0674
(0.103) 		0.017
(0.0306) 		0.585
(0.638) 		0.978
(0.981) 		0.0186
(0.0331) 		0.14
(0.193) 		0.217
(0.28) 		0.501
(0.559) 		0.0122
(0.0227) 		0.0077
(0.0151) 		0.569
(0.622) 		0.0281
(0.0477) 		4e-05
(0.000129) 		0.0536
(0.0846)
amp 12q15 111 (10%) 979 0.676
(0.72) 		0.314
(0.38) 		0.478
(0.537) 		0.277
(0.343) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.556
(0.609) 		0.691
(0.731) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.42
(0.485) 		0.0554
(0.0872) 		0.022
(0.0382) 		0.0126
(0.0234)
amp xp11 21 104 (10%) 986 0.107
(0.154) 		0.785
(0.815) 		0.419
(0.485) 		0.971
(0.976) 		0.00022
(0.000616) 		1e-05
(3.74e-05) 		0.221
(0.285) 		0.0531
(0.084) 		0.103
(0.15) 		1e-05
(3.74e-05) 		8e-05
(0.000243) 		0.265
(0.331) 		4e-05
(0.000129) 		2e-05
(6.84e-05)
del 1q42 11 80 (7%) 1010 0.233
(0.298) 		0.822
(0.848) 		0.454
(0.516) 		0.283
(0.349) 		0.00445
(0.00927) 		0.0003
(0.000822) 		0.595
(0.647) 		0.0677
(0.104) 		0.245
(0.309) 		0.0296
(0.0497) 		0.0118
(0.022) 		0.117
(0.165) 		0.0386
(0.0634) 		0.0273
(0.0466)
del 12p13 1 110 (10%) 980 0.0558
(0.0876) 		0.0144
(0.0264) 		0.455
(0.516) 		0.232
(0.298) 		0.011
(0.0208) 		0.00411
(0.00872) 		0.527
(0.585) 		0.408
(0.473) 		0.121
(0.17) 		0.00172
(0.00405) 		0.0225
(0.039) 		0.0445
(0.0717) 		0.0929
(0.136) 		0.0984
(0.143)
del 16p12 2 114 (10%) 976 0.432
(0.493) 		0.233
(0.298) 		0.342
(0.407) 		0.867
(0.887) 		1e-05
(3.74e-05) 		3e-05
(9.91e-05) 		0.315
(0.382) 		0.0172
(0.0309) 		1e-05
(3.74e-05) 		1e-05
(3.74e-05) 		0.655
(0.701) 		0.021
(0.0366) 		0.328
(0.393) 		0.0978
(0.142)
amp 4p16 3 69 (6%) 1021 0.224
(0.288) 		0.728
(0.764) 		0.707
(0.746) 		0.0834
(0.125) 		2e-05
(6.84e-05) 		0.0107
(0.0203) 		0.853
(0.877) 		0.0938
(0.137) 		9e-05
(0.000268) 		9e-05
(0.000268) 		0.0991
(0.144) 		0.32
(0.385) 		0.0456
(0.0734) 		0.365
(0.428)
amp 9q34 3 141 (13%) 949 0.0376
(0.062) 		0.012
(0.0224) 		0.331
(0.396) 		0.0847
(0.126) 		0.00027
(0.000744) 		0.148
(0.202) 		0.0575
(0.0898) 		1
(1.00) 		0.00367
(0.00791) 		0.0183
(0.0326) 		0.207
(0.27) 		0.087
(0.129) 		0.927
(0.939) 		0.156
(0.212)
amp 17p13 2 74 (7%) 1016 0.00177
(0.00414) 		0.014
(0.0258) 		0.0396
(0.0648) 		0.112
(0.16) 		0.117
(0.166) 		0.0523
(0.083) 		0.00455
(0.00944) 		0.209
(0.272) 		0.508
(0.565) 		0.853
(0.877) 		0.255
(0.32) 		0.674
(0.719) 		0.338
(0.403) 		0.015
(0.0274)
del 6p25 3 138 (13%) 952 0.0647
(0.0995) 		0.0896
(0.132) 		0.303
(0.369) 		0.889
(0.907) 		0.0211
(0.0368) 		0.0216
(0.0376) 		0.963
(0.97) 		0.0138
(0.0254) 		0.00283
(0.00632) 		0.00121
(0.0029) 		0.458
(0.52) 		0.254
(0.319) 		0.284
(0.349) 		0.0847
(0.126)
amp 14q32 33 44 (4%) 1046 0.077
(0.116) 		0.657
(0.703) 		0.0398
(0.065) 		0.92
(0.933) 		0.00117
(0.00283) 		0.503
(0.561) 		0.546
(0.6) 		0.317
(0.383) 		0.0111
(0.0209) 		0.00828
(0.0161) 		1
(1.00) 		0.52
(0.578) 		0.0821
(0.123) 		0.0718
(0.109)
amp 17q25 1 128 (12%) 962 0.0284
(0.0481) 		0.258
(0.323) 		0.16
(0.215) 		0.731
(0.766) 		0.00596
(0.012) 		0.143
(0.197) 		0.428
(0.491) 		0.646
(0.693) 		0.0154
(0.0279) 		0.0351
(0.0583) 		0.166
(0.223) 		0.564
(0.617) 		0.0808
(0.122) 		0.341
(0.406)
del 2q22 1 68 (6%) 1022 0.0004
(0.00107) 		0.029
(0.0488) 		0.606
(0.656) 		0.549
(0.603) 		0.124
(0.174) 		0.0486
(0.0775) 		0.107
(0.154) 		0.546
(0.6) 		0.0287
(0.0484) 		0.0749
(0.113) 		0.108
(0.154) 		0.796
(0.825) 		0.293
(0.358) 		0.215
(0.279)
del 3q13 31 95 (9%) 995 0.422
(0.486) 		0.344
(0.409) 		0.953
(0.962) 		0.515
(0.573) 		0.429
(0.492) 		0.0042
(0.00886) 		0.18
(0.239) 		0.0197
(0.0347) 		0.602
(0.654) 		0.046
(0.0738) 		0.158
(0.213) 		0.00051
(0.00135) 		0.191
(0.253) 		0.121
(0.17)
amp 11p13 60 (6%) 1030 0.813
(0.84) 		0.347
(0.412) 		0.537
(0.594) 		0.245
(0.309) 		0.108
(0.154) 		4e-05
(0.000129) 		0.18
(0.239) 		0.157
(0.212) 		0.28
(0.346) 		0.0979
(0.142) 		0.0306
(0.0512) 		0.119
(0.168) 		0.141
(0.195) 		0.00333
(0.00729)
del 1q44 70 (6%) 1020 0.847
(0.872) 		0.474
(0.533) 		0.711
(0.749) 		0.245
(0.309) 		0.43
(0.492) 		0.00031
(0.000848) 		0.863
(0.885) 		0.0889
(0.131) 		0.269
(0.334) 		0.00807
(0.0158) 		0.0731
(0.111) 		0.681
(0.724) 		0.0378
(0.0623) 		0.137
(0.19)
del 3q29 107 (10%) 983 0.137
(0.19) 		0.172
(0.229) 		0.804
(0.832) 		0.855
(0.878) 		0.361
(0.425) 		0.003
(0.00666) 		0.326
(0.391) 		0.668
(0.714) 		0.0615
(0.0954) 		0.00543
(0.0111) 		0.245
(0.309) 		0.0423
(0.0687) 		0.282
(0.348) 		0.205
(0.268)
del 18q23 155 (14%) 935 0.0202
(0.0355) 		0.0192
(0.0339) 		0.266
(0.331) 		0.613
(0.663) 		0.266
(0.331) 		0.0276
(0.0469) 		0.566
(0.62) 		0.376
(0.44) 		0.677
(0.721) 		0.63
(0.679) 		0.136
(0.19) 		0.619
(0.669) 		0.463
(0.524) 		0.792
(0.821)
amp 13q34 54 (5%) 1036 0.234
(0.298) 		0.201
(0.264) 		0.0678
(0.104) 		0.482
(0.541) 		0.255
(0.32) 		0.00053
(0.00139) 		0.0517
(0.0822) 		0.462
(0.523) 		0.113
(0.16) 		0.0266
(0.0456) 		0.11
(0.158) 		0.69
(0.731) 		0.284
(0.349) 		0.109
(0.156)
'amp_1p36.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S1.  Gene #1: 'amp_1p36.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
AMP PEAK 1(1P36.21) MUTATED 85 3 16
AMP PEAK 1(1P36.21) WILD-TYPE 444 467 75

Figure S1.  Get High-res Image Gene #1: 'amp_1p36.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_1p36.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S2.  Gene #1: 'amp_1p36.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
AMP PEAK 1(1P36.21) MUTATED 21 5 1 0
AMP PEAK 1(1P36.21) WILD-TYPE 156 220 87 160

Figure S2.  Get High-res Image Gene #1: 'amp_1p36.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_1p36.21' versus 'RPPA_CNMF'

P value = 0.00612 (Fisher's exact test), Q value = 0.012

Table S3.  Gene #1: 'amp_1p36.21' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
AMP PEAK 1(1P36.21) MUTATED 10 4 18 6
AMP PEAK 1(1P36.21) WILD-TYPE 203 164 138 103

Figure S3.  Get High-res Image Gene #1: 'amp_1p36.21' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_1p36.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.0207 (Fisher's exact test), Q value = 0.036

Table S4.  Gene #1: 'amp_1p36.21' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
AMP PEAK 1(1P36.21) MUTATED 14 21 3
AMP PEAK 1(1P36.21) WILD-TYPE 220 233 155

Figure S4.  Get High-res Image Gene #1: 'amp_1p36.21' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_1p36.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S5.  Gene #1: 'amp_1p36.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
AMP PEAK 1(1P36.21) MUTATED 39 0 1
AMP PEAK 1(1P36.21) WILD-TYPE 205 189 226

Figure S5.  Get High-res Image Gene #1: 'amp_1p36.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_1p36.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S6.  Gene #1: 'amp_1p36.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
AMP PEAK 1(1P36.21) MUTATED 35 5 0
AMP PEAK 1(1P36.21) WILD-TYPE 168 185 267

Figure S6.  Get High-res Image Gene #1: 'amp_1p36.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_1p36.21' versus 'MIRSEQ_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.027

Table S7.  Gene #1: 'amp_1p36.21' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
AMP PEAK 1(1P36.21) MUTATED 7 4 0 1
AMP PEAK 1(1P36.21) WILD-TYPE 133 103 82 179

Figure S7.  Get High-res Image Gene #1: 'amp_1p36.21' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_1p36.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.8e-05

Table S8.  Gene #1: 'amp_1p36.21' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 1(1P36.21) MUTATED 3 0 9
AMP PEAK 1(1P36.21) WILD-TYPE 219 184 94

Figure S8.  Get High-res Image Gene #1: 'amp_1p36.21' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_1p36.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00763 (Fisher's exact test), Q value = 0.015

Table S9.  Gene #1: 'amp_1p36.21' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 1(1P36.21) MUTATED 4 7 0 1
AMP PEAK 1(1P36.21) WILD-TYPE 123 112 105 153

Figure S9.  Get High-res Image Gene #1: 'amp_1p36.21' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_1p36.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00415 (Fisher's exact test), Q value = 0.0088

Table S10.  Gene #1: 'amp_1p36.21' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 1(1P36.21) MUTATED 1 4 0 0 5 2
AMP PEAK 1(1P36.21) WILD-TYPE 98 73 118 56 58 90

Figure S10.  Get High-res Image Gene #1: 'amp_1p36.21' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q22' versus 'MRNA_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.026

Table S11.  Gene #2: 'amp_1q22' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
AMP PEAK 2(1Q22) MUTATED 26 28 17 21
AMP PEAK 2(1Q22) WILD-TYPE 132 68 120 96

Figure S11.  Get High-res Image Gene #2: 'amp_1q22' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1q22' versus 'MRNA_CHIERARCHICAL'

P value = 0.0266 (Fisher's exact test), Q value = 0.046

Table S12.  Gene #2: 'amp_1q22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
AMP PEAK 2(1Q22) MUTATED 27 25 9 31
AMP PEAK 2(1Q22) WILD-TYPE 121 77 91 127

Figure S12.  Get High-res Image Gene #2: 'amp_1q22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_1q22' versus 'MIR_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.03

Table S13.  Gene #2: 'amp_1q22' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
AMP PEAK 2(1Q22) MUTATED 15 42 13 27
AMP PEAK 2(1Q22) WILD-TYPE 128 145 77 99

Figure S13.  Get High-res Image Gene #2: 'amp_1q22' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_1q22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S14.  Gene #2: 'amp_1q22' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
AMP PEAK 2(1Q22) MUTATED 88 35 21
AMP PEAK 2(1Q22) WILD-TYPE 441 435 70

Figure S14.  Get High-res Image Gene #2: 'amp_1q22' versus Molecular Subtype #5: 'CN_CNMF'

'amp_1q22' versus 'METHLYATION_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.002

Table S15.  Gene #2: 'amp_1q22' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
AMP PEAK 2(1Q22) MUTATED 29 19 3 8
AMP PEAK 2(1Q22) WILD-TYPE 148 206 85 152

Figure S15.  Get High-res Image Gene #2: 'amp_1q22' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_1q22' versus 'RPPA_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.022

Table S16.  Gene #2: 'amp_1q22' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
AMP PEAK 2(1Q22) MUTATED 16 14 28 11
AMP PEAK 2(1Q22) WILD-TYPE 197 154 128 98

Figure S16.  Get High-res Image Gene #2: 'amp_1q22' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_1q22' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S17.  Gene #2: 'amp_1q22' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
AMP PEAK 2(1Q22) MUTATED 46 11 13
AMP PEAK 2(1Q22) WILD-TYPE 198 178 214

Figure S17.  Get High-res Image Gene #2: 'amp_1q22' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_1q22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00022

Table S18.  Gene #2: 'amp_1q22' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
AMP PEAK 2(1Q22) MUTATED 37 19 14
AMP PEAK 2(1Q22) WILD-TYPE 166 171 253

Figure S18.  Get High-res Image Gene #2: 'amp_1q22' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_1q22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00254 (Fisher's exact test), Q value = 0.0058

Table S19.  Gene #2: 'amp_1q22' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 2(1Q22) MUTATED 11 16 1 14
AMP PEAK 2(1Q22) WILD-TYPE 116 103 104 140

Figure S19.  Get High-res Image Gene #2: 'amp_1q22' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_1q32.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S20.  Gene #3: 'amp_1q32.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
AMP PEAK 3(1Q32.1) MUTATED 158 26 21
AMP PEAK 3(1Q32.1) WILD-TYPE 371 444 70

Figure S20.  Get High-res Image Gene #3: 'amp_1q32.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_1q32.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S21.  Gene #3: 'amp_1q32.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
AMP PEAK 3(1Q32.1) MUTATED 50 11 10 6
AMP PEAK 3(1Q32.1) WILD-TYPE 127 214 78 154

Figure S21.  Get High-res Image Gene #3: 'amp_1q32.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_1q32.1' versus 'RPPA_CNMF'

P value = 0.0474 (Fisher's exact test), Q value = 0.076

Table S22.  Gene #3: 'amp_1q32.1' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
AMP PEAK 3(1Q32.1) MUTATED 23 22 33 17
AMP PEAK 3(1Q32.1) WILD-TYPE 190 146 123 92

Figure S22.  Get High-res Image Gene #3: 'amp_1q32.1' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_1q32.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S23.  Gene #3: 'amp_1q32.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
AMP PEAK 3(1Q32.1) MUTATED 64 16 4
AMP PEAK 3(1Q32.1) WILD-TYPE 180 173 223

Figure S23.  Get High-res Image Gene #3: 'amp_1q32.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_1q32.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S24.  Gene #3: 'amp_1q32.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
AMP PEAK 3(1Q32.1) MUTATED 58 8 18
AMP PEAK 3(1Q32.1) WILD-TYPE 145 182 249

Figure S24.  Get High-res Image Gene #3: 'amp_1q32.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_1q32.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S25.  Gene #3: 'amp_1q32.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 3(1Q32.1) MUTATED 8 14 23
AMP PEAK 3(1Q32.1) WILD-TYPE 214 170 80

Figure S25.  Get High-res Image Gene #3: 'amp_1q32.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_1q32.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00169 (Fisher's exact test), Q value = 0.004

Table S26.  Gene #3: 'amp_1q32.1' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 3(1Q32.1) MUTATED 9 19 2 15
AMP PEAK 3(1Q32.1) WILD-TYPE 118 100 103 139

Figure S26.  Get High-res Image Gene #3: 'amp_1q32.1' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_1q32.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S27.  Gene #3: 'amp_1q32.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 3(1Q32.1) MUTATED 5 3 11 1 19 6
AMP PEAK 3(1Q32.1) WILD-TYPE 94 74 107 55 44 86

Figure S27.  Get High-res Image Gene #3: 'amp_1q32.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q44' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S28.  Gene #4: 'amp_1q44' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
AMP PEAK 4(1Q44) MUTATED 91 22 16
AMP PEAK 4(1Q44) WILD-TYPE 438 448 75

Figure S28.  Get High-res Image Gene #4: 'amp_1q44' versus Molecular Subtype #5: 'CN_CNMF'

'amp_1q44' versus 'METHLYATION_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0012

Table S29.  Gene #4: 'amp_1q44' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
AMP PEAK 4(1Q44) MUTATED 25 12 3 5
AMP PEAK 4(1Q44) WILD-TYPE 152 213 85 155

Figure S29.  Get High-res Image Gene #4: 'amp_1q44' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_1q44' versus 'RPPA_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.025

Table S30.  Gene #4: 'amp_1q44' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
AMP PEAK 4(1Q44) MUTATED 11 13 23 7
AMP PEAK 4(1Q44) WILD-TYPE 202 155 133 102

Figure S30.  Get High-res Image Gene #4: 'amp_1q44' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_1q44' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S31.  Gene #4: 'amp_1q44' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
AMP PEAK 4(1Q44) MUTATED 41 10 5
AMP PEAK 4(1Q44) WILD-TYPE 203 179 222

Figure S31.  Get High-res Image Gene #4: 'amp_1q44' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_1q44' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S32.  Gene #4: 'amp_1q44' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
AMP PEAK 4(1Q44) MUTATED 35 9 12
AMP PEAK 4(1Q44) WILD-TYPE 168 181 255

Figure S32.  Get High-res Image Gene #4: 'amp_1q44' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_1q44' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0208 (Fisher's exact test), Q value = 0.036

Table S33.  Gene #4: 'amp_1q44' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 4(1Q44) MUTATED 8 10 12
AMP PEAK 4(1Q44) WILD-TYPE 214 174 91

Figure S33.  Get High-res Image Gene #4: 'amp_1q44' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_1q44' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00583 (Fisher's exact test), Q value = 0.012

Table S34.  Gene #4: 'amp_1q44' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 4(1Q44) MUTATED 3 13 2 12
AMP PEAK 4(1Q44) WILD-TYPE 124 106 103 142

Figure S34.  Get High-res Image Gene #4: 'amp_1q44' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_2p24.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.017 (Fisher's exact test), Q value = 0.031

Table S35.  Gene #5: 'amp_2p24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
AMP PEAK 5(2P24.3) MUTATED 11 17 4 13
AMP PEAK 5(2P24.3) WILD-TYPE 137 85 96 145

Figure S35.  Get High-res Image Gene #5: 'amp_2p24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_2p24.3' versus 'CN_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.033

Table S36.  Gene #5: 'amp_2p24.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
AMP PEAK 5(2P24.3) MUTATED 44 20 8
AMP PEAK 5(2P24.3) WILD-TYPE 485 450 83

Figure S36.  Get High-res Image Gene #5: 'amp_2p24.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_2p24.3' versus 'MRNASEQ_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.023

Table S37.  Gene #5: 'amp_2p24.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
AMP PEAK 5(2P24.3) MUTATED 23 7 8
AMP PEAK 5(2P24.3) WILD-TYPE 221 182 219

Figure S37.  Get High-res Image Gene #5: 'amp_2p24.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_2p24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0077 (Fisher's exact test), Q value = 0.015

Table S38.  Gene #5: 'amp_2p24.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
AMP PEAK 5(2P24.3) MUTATED 20 10 8
AMP PEAK 5(2P24.3) WILD-TYPE 183 180 259

Figure S38.  Get High-res Image Gene #5: 'amp_2p24.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_2p24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0281 (Fisher's exact test), Q value = 0.048

Table S39.  Gene #5: 'amp_2p24.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 5(2P24.3) MUTATED 8 5 10
AMP PEAK 5(2P24.3) WILD-TYPE 214 179 93

Figure S39.  Get High-res Image Gene #5: 'amp_2p24.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_2p24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00013

Table S40.  Gene #5: 'amp_2p24.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 5(2P24.3) MUTATED 3 15 0 5
AMP PEAK 5(2P24.3) WILD-TYPE 124 104 105 149

Figure S40.  Get High-res Image Gene #5: 'amp_2p24.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.33' versus 'MRNA_CNMF'

P value = 0.00295 (Fisher's exact test), Q value = 0.0066

Table S41.  Gene #6: 'amp_3q26.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
AMP PEAK 6(3Q26.33) MUTATED 30 28 15 28
AMP PEAK 6(3Q26.33) WILD-TYPE 128 68 122 89

Figure S41.  Get High-res Image Gene #6: 'amp_3q26.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S42.  Gene #6: 'amp_3q26.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
AMP PEAK 6(3Q26.33) MUTATED 102 19 11
AMP PEAK 6(3Q26.33) WILD-TYPE 427 451 80

Figure S42.  Get High-res Image Gene #6: 'amp_3q26.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_3q26.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S43.  Gene #6: 'amp_3q26.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
AMP PEAK 6(3Q26.33) MUTATED 31 9 2 3
AMP PEAK 6(3Q26.33) WILD-TYPE 146 216 86 157

Figure S43.  Get High-res Image Gene #6: 'amp_3q26.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_3q26.33' versus 'RPPA_CNMF'

P value = 0.00882 (Fisher's exact test), Q value = 0.017

Table S44.  Gene #6: 'amp_3q26.33' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
AMP PEAK 6(3Q26.33) MUTATED 18 5 20 9
AMP PEAK 6(3Q26.33) WILD-TYPE 195 163 136 100

Figure S44.  Get High-res Image Gene #6: 'amp_3q26.33' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_3q26.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.00635 (Fisher's exact test), Q value = 0.013

Table S45.  Gene #6: 'amp_3q26.33' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
AMP PEAK 6(3Q26.33) MUTATED 24 24 4
AMP PEAK 6(3Q26.33) WILD-TYPE 210 230 154

Figure S45.  Get High-res Image Gene #6: 'amp_3q26.33' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_3q26.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S46.  Gene #6: 'amp_3q26.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
AMP PEAK 6(3Q26.33) MUTATED 45 4 7
AMP PEAK 6(3Q26.33) WILD-TYPE 199 185 220

Figure S46.  Get High-res Image Gene #6: 'amp_3q26.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_3q26.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S47.  Gene #6: 'amp_3q26.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
AMP PEAK 6(3Q26.33) MUTATED 41 9 6
AMP PEAK 6(3Q26.33) WILD-TYPE 162 181 261

Figure S47.  Get High-res Image Gene #6: 'amp_3q26.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MIRSEQ_CNMF'

P value = 0.00188 (Fisher's exact test), Q value = 0.0044

Table S48.  Gene #6: 'amp_3q26.33' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
AMP PEAK 6(3Q26.33) MUTATED 10 8 2 1
AMP PEAK 6(3Q26.33) WILD-TYPE 130 99 80 179

Figure S48.  Get High-res Image Gene #6: 'amp_3q26.33' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_3q26.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.018 (Fisher's exact test), Q value = 0.032

Table S49.  Gene #6: 'amp_3q26.33' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 6(3Q26.33) MUTATED 9 3 9
AMP PEAK 6(3Q26.33) WILD-TYPE 213 181 94

Figure S49.  Get High-res Image Gene #6: 'amp_3q26.33' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00339 (Fisher's exact test), Q value = 0.0074

Table S50.  Gene #6: 'amp_3q26.33' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 6(3Q26.33) MUTATED 5 12 1 3
AMP PEAK 6(3Q26.33) WILD-TYPE 122 107 104 151

Figure S50.  Get High-res Image Gene #6: 'amp_3q26.33' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00318 (Fisher's exact test), Q value = 0.007

Table S51.  Gene #6: 'amp_3q26.33' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 6(3Q26.33) MUTATED 6 2 1 0 8 4
AMP PEAK 6(3Q26.33) WILD-TYPE 93 75 117 56 55 88

Figure S51.  Get High-res Image Gene #6: 'amp_3q26.33' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4p16.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.8e-05

Table S52.  Gene #7: 'amp_4p16.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
AMP PEAK 7(4P16.3) MUTATED 46 12 11
AMP PEAK 7(4P16.3) WILD-TYPE 483 458 80

Figure S52.  Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_4p16.3' versus 'METHLYATION_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.02

Table S53.  Gene #7: 'amp_4p16.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
AMP PEAK 7(4P16.3) MUTATED 13 12 4 1
AMP PEAK 7(4P16.3) WILD-TYPE 164 213 84 159

Figure S53.  Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_4p16.3' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00027

Table S54.  Gene #7: 'amp_4p16.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
AMP PEAK 7(4P16.3) MUTATED 26 3 8
AMP PEAK 7(4P16.3) WILD-TYPE 218 186 219

Figure S54.  Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00027

Table S55.  Gene #7: 'amp_4p16.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
AMP PEAK 7(4P16.3) MUTATED 22 11 4
AMP PEAK 7(4P16.3) WILD-TYPE 181 179 263

Figure S55.  Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0456 (Fisher's exact test), Q value = 0.073

Table S56.  Gene #7: 'amp_4p16.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 7(4P16.3) MUTATED 5 10 1 5
AMP PEAK 7(4P16.3) WILD-TYPE 122 109 104 149

Figure S56.  Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_4q12' versus 'MRNA_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00048

Table S57.  Gene #8: 'amp_4q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
AMP PEAK 8(4Q12) MUTATED 22 34 19 24
AMP PEAK 8(4Q12) WILD-TYPE 136 62 118 93

Figure S57.  Get High-res Image Gene #8: 'amp_4q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_4q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00363 (Fisher's exact test), Q value = 0.0078

Table S58.  Gene #8: 'amp_4q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
AMP PEAK 8(4Q12) MUTATED 18 31 16 34
AMP PEAK 8(4Q12) WILD-TYPE 130 71 84 124

Figure S58.  Get High-res Image Gene #8: 'amp_4q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_4q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S59.  Gene #8: 'amp_4q12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
AMP PEAK 8(4Q12) MUTATED 94 28 16
AMP PEAK 8(4Q12) WILD-TYPE 435 442 75

Figure S59.  Get High-res Image Gene #8: 'amp_4q12' versus Molecular Subtype #5: 'CN_CNMF'

'amp_4q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S60.  Gene #8: 'amp_4q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
AMP PEAK 8(4Q12) MUTATED 31 19 3 2
AMP PEAK 8(4Q12) WILD-TYPE 146 206 85 158

Figure S60.  Get High-res Image Gene #8: 'amp_4q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_4q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S61.  Gene #8: 'amp_4q12' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
AMP PEAK 8(4Q12) MUTATED 45 5 9
AMP PEAK 8(4Q12) WILD-TYPE 199 184 218

Figure S61.  Get High-res Image Gene #8: 'amp_4q12' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_4q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S62.  Gene #8: 'amp_4q12' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
AMP PEAK 8(4Q12) MUTATED 37 16 6
AMP PEAK 8(4Q12) WILD-TYPE 166 174 261

Figure S62.  Get High-res Image Gene #8: 'amp_4q12' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_4q12' versus 'MIRSEQ_CNMF'

P value = 0.00337 (Fisher's exact test), Q value = 0.0073

Table S63.  Gene #8: 'amp_4q12' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
AMP PEAK 8(4Q12) MUTATED 6 15 2 7
AMP PEAK 8(4Q12) WILD-TYPE 134 92 80 173

Figure S63.  Get High-res Image Gene #8: 'amp_4q12' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_4q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00024

Table S64.  Gene #8: 'amp_4q12' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 8(4Q12) MUTATED 7 7 16
AMP PEAK 8(4Q12) WILD-TYPE 215 177 87

Figure S64.  Get High-res Image Gene #8: 'amp_4q12' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_4q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00254 (Fisher's exact test), Q value = 0.0058

Table S65.  Gene #8: 'amp_4q12' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 8(4Q12) MUTATED 5 16 2 7
AMP PEAK 8(4Q12) WILD-TYPE 122 103 103 147

Figure S65.  Get High-res Image Gene #8: 'amp_4q12' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_4q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.002

Table S66.  Gene #8: 'amp_4q12' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 8(4Q12) MUTATED 3 12 5 0 7 3
AMP PEAK 8(4Q12) WILD-TYPE 96 65 113 56 56 89

Figure S66.  Get High-res Image Gene #8: 'amp_4q12' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.8e-05

Table S67.  Gene #9: 'amp_5p15.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
AMP PEAK 9(5P15.33) MUTATED 54 14 8
AMP PEAK 9(5P15.33) WILD-TYPE 475 456 83

Figure S67.  Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.029

Table S68.  Gene #9: 'amp_5p15.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
AMP PEAK 9(5P15.33) MUTATED 12 7 4 1
AMP PEAK 9(5P15.33) WILD-TYPE 165 218 84 159

Figure S68.  Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00022

Table S69.  Gene #9: 'amp_5p15.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
AMP PEAK 9(5P15.33) MUTATED 21 3 3
AMP PEAK 9(5P15.33) WILD-TYPE 223 186 224

Figure S69.  Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 9e-04

Table S70.  Gene #9: 'amp_5p15.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
AMP PEAK 9(5P15.33) MUTATED 18 5 4
AMP PEAK 9(5P15.33) WILD-TYPE 185 185 263

Figure S70.  Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00334 (Fisher's exact test), Q value = 0.0073

Table S71.  Gene #9: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 9(5P15.33) MUTATED 3 4 9
AMP PEAK 9(5P15.33) WILD-TYPE 219 180 94

Figure S71.  Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00108 (Fisher's exact test), Q value = 0.0026

Table S72.  Gene #9: 'amp_5p15.33' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 9(5P15.33) MUTATED 2 11 1 2
AMP PEAK 9(5P15.33) WILD-TYPE 125 108 104 152

Figure S72.  Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0029 (Fisher's exact test), Q value = 0.0065

Table S73.  Gene #9: 'amp_5p15.33' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 9(5P15.33) MUTATED 1 4 1 0 7 3
AMP PEAK 9(5P15.33) WILD-TYPE 98 73 117 56 56 89

Figure S73.  Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p11.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S74.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
AMP PEAK 10(7P11.2) MUTATED 150 69 132 92
AMP PEAK 10(7P11.2) WILD-TYPE 8 27 5 25

Figure S74.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_7p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S75.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
AMP PEAK 10(7P11.2) MUTATED 136 60 99 148
AMP PEAK 10(7P11.2) WILD-TYPE 12 42 1 10

Figure S75.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7p11.2' versus 'MIR_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S76.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
AMP PEAK 10(7P11.2) MUTATED 139 151 74 116
AMP PEAK 10(7P11.2) WILD-TYPE 4 36 16 10

Figure S76.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_7p11.2' versus 'MIR_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S77.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
AMP PEAK 10(7P11.2) MUTATED 234 120 126
AMP PEAK 10(7P11.2) WILD-TYPE 59 4 3

Figure S77.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S78.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
AMP PEAK 10(7P11.2) MUTATED 518 60 56
AMP PEAK 10(7P11.2) WILD-TYPE 11 410 35

Figure S78.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S79.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
AMP PEAK 10(7P11.2) MUTATED 162 40 33 14
AMP PEAK 10(7P11.2) WILD-TYPE 15 185 55 146

Figure S79.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'RPPA_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0012

Table S80.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
AMP PEAK 10(7P11.2) MUTATED 100 57 89 51
AMP PEAK 10(7P11.2) WILD-TYPE 113 111 67 58

Figure S80.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_7p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.00062

Table S81.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
AMP PEAK 10(7P11.2) MUTATED 119 128 50
AMP PEAK 10(7P11.2) WILD-TYPE 115 126 108

Figure S81.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S82.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
AMP PEAK 10(7P11.2) MUTATED 190 35 33
AMP PEAK 10(7P11.2) WILD-TYPE 54 154 194

Figure S82.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S83.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
AMP PEAK 10(7P11.2) MUTATED 183 30 45
AMP PEAK 10(7P11.2) WILD-TYPE 20 160 222

Figure S83.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00048

Table S84.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
AMP PEAK 10(7P11.2) MUTATED 45 37 11 32
AMP PEAK 10(7P11.2) WILD-TYPE 95 70 71 148

Figure S84.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S85.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 10(7P11.2) MUTATED 36 28 61
AMP PEAK 10(7P11.2) WILD-TYPE 186 156 42

Figure S85.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S86.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 10(7P11.2) MUTATED 33 50 9 32
AMP PEAK 10(7P11.2) WILD-TYPE 94 69 96 122

Figure S86.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S87.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 10(7P11.2) MUTATED 15 12 20 7 53 17
AMP PEAK 10(7P11.2) WILD-TYPE 84 65 98 49 10 75

Figure S87.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q11.21' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.8e-05

Table S88.  Gene #11: 'amp_7q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
AMP PEAK 11(7Q11.21) MUTATED 142 63 113 85
AMP PEAK 11(7Q11.21) WILD-TYPE 16 33 24 32

Figure S88.  Get High-res Image Gene #11: 'amp_7q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_7q11.21' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S89.  Gene #11: 'amp_7q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
AMP PEAK 11(7Q11.21) MUTATED 129 55 82 137
AMP PEAK 11(7Q11.21) WILD-TYPE 19 47 18 21

Figure S89.  Get High-res Image Gene #11: 'amp_7q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7q11.21' versus 'MIR_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S90.  Gene #11: 'amp_7q11.21' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
AMP PEAK 11(7Q11.21) MUTATED 131 138 63 108
AMP PEAK 11(7Q11.21) WILD-TYPE 12 49 27 18

Figure S90.  Get High-res Image Gene #11: 'amp_7q11.21' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_7q11.21' versus 'MIR_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00013

Table S91.  Gene #11: 'amp_7q11.21' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
AMP PEAK 11(7Q11.21) MUTATED 216 114 110
AMP PEAK 11(7Q11.21) WILD-TYPE 77 10 19

Figure S91.  Get High-res Image Gene #11: 'amp_7q11.21' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_7q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S92.  Gene #11: 'amp_7q11.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
AMP PEAK 11(7Q11.21) MUTATED 476 54 50
AMP PEAK 11(7Q11.21) WILD-TYPE 53 416 41

Figure S92.  Get High-res Image Gene #11: 'amp_7q11.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_7q11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S93.  Gene #11: 'amp_7q11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
AMP PEAK 11(7Q11.21) MUTATED 150 36 30 14
AMP PEAK 11(7Q11.21) WILD-TYPE 27 189 58 146

Figure S93.  Get High-res Image Gene #11: 'amp_7q11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_7q11.21' versus 'RPPA_CNMF'

P value = 0.00874 (Fisher's exact test), Q value = 0.017

Table S94.  Gene #11: 'amp_7q11.21' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
AMP PEAK 11(7Q11.21) MUTATED 92 54 79 47
AMP PEAK 11(7Q11.21) WILD-TYPE 121 114 77 62

Figure S94.  Get High-res Image Gene #11: 'amp_7q11.21' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_7q11.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.00096 (Fisher's exact test), Q value = 0.0024

Table S95.  Gene #11: 'amp_7q11.21' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
AMP PEAK 11(7Q11.21) MUTATED 110 115 47
AMP PEAK 11(7Q11.21) WILD-TYPE 124 139 111

Figure S95.  Get High-res Image Gene #11: 'amp_7q11.21' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_7q11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S96.  Gene #11: 'amp_7q11.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
AMP PEAK 11(7Q11.21) MUTATED 168 35 31
AMP PEAK 11(7Q11.21) WILD-TYPE 76 154 196

Figure S96.  Get High-res Image Gene #11: 'amp_7q11.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_7q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S97.  Gene #11: 'amp_7q11.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
AMP PEAK 11(7Q11.21) MUTATED 163 26 45
AMP PEAK 11(7Q11.21) WILD-TYPE 40 164 222

Figure S97.  Get High-res Image Gene #11: 'amp_7q11.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_7q11.21' versus 'MIRSEQ_CNMF'

P value = 0.00416 (Fisher's exact test), Q value = 0.0088

Table S98.  Gene #11: 'amp_7q11.21' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
AMP PEAK 11(7Q11.21) MUTATED 40 32 11 31
AMP PEAK 11(7Q11.21) WILD-TYPE 100 75 71 149

Figure S98.  Get High-res Image Gene #11: 'amp_7q11.21' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_7q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S99.  Gene #11: 'amp_7q11.21' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 11(7Q11.21) MUTATED 33 27 54
AMP PEAK 11(7Q11.21) WILD-TYPE 189 157 49

Figure S99.  Get High-res Image Gene #11: 'amp_7q11.21' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_7q11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S100.  Gene #11: 'amp_7q11.21' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 11(7Q11.21) MUTATED 30 43 8 32
AMP PEAK 11(7Q11.21) WILD-TYPE 97 76 97 122

Figure S100.  Get High-res Image Gene #11: 'amp_7q11.21' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_7q11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S101.  Gene #11: 'amp_7q11.21' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 11(7Q11.21) MUTATED 13 10 20 7 46 17
AMP PEAK 11(7Q11.21) WILD-TYPE 86 67 98 49 17 75

Figure S101.  Get High-res Image Gene #11: 'amp_7q11.21' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q21.2' versus 'MRNA_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00032

Table S102.  Gene #12: 'amp_7q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
AMP PEAK 12(7Q21.2) MUTATED 141 66 120 91
AMP PEAK 12(7Q21.2) WILD-TYPE 17 30 17 26

Figure S102.  Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_7q21.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S103.  Gene #12: 'amp_7q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
AMP PEAK 12(7Q21.2) MUTATED 126 62 89 141
AMP PEAK 12(7Q21.2) WILD-TYPE 22 40 11 17

Figure S103.  Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7q21.2' versus 'MIR_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00024

Table S104.  Gene #12: 'amp_7q21.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
AMP PEAK 12(7Q21.2) MUTATED 224 111 117
AMP PEAK 12(7Q21.2) WILD-TYPE 69 13 12

Figure S104.  Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_7q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S105.  Gene #12: 'amp_7q21.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
AMP PEAK 12(7Q21.2) MUTATED 487 93 55
AMP PEAK 12(7Q21.2) WILD-TYPE 42 377 36

Figure S105.  Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_7q21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S106.  Gene #12: 'amp_7q21.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
AMP PEAK 12(7Q21.2) MUTATED 153 65 33 24
AMP PEAK 12(7Q21.2) WILD-TYPE 24 160 55 136

Figure S106.  Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_7q21.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.026

Table S107.  Gene #12: 'amp_7q21.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
AMP PEAK 12(7Q21.2) MUTATED 123 125 60
AMP PEAK 12(7Q21.2) WILD-TYPE 111 129 98

Figure S107.  Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_7q21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S108.  Gene #12: 'amp_7q21.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
AMP PEAK 12(7Q21.2) MUTATED 180 48 53
AMP PEAK 12(7Q21.2) WILD-TYPE 64 141 174

Figure S108.  Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_7q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S109.  Gene #12: 'amp_7q21.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
AMP PEAK 12(7Q21.2) MUTATED 171 48 62
AMP PEAK 12(7Q21.2) WILD-TYPE 32 142 205

Figure S109.  Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'MIRSEQ_CNMF'

P value = 0.00353 (Fisher's exact test), Q value = 0.0076

Table S110.  Gene #12: 'amp_7q21.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
AMP PEAK 12(7Q21.2) MUTATED 51 41 15 46
AMP PEAK 12(7Q21.2) WILD-TYPE 89 66 67 134

Figure S110.  Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_7q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S111.  Gene #12: 'amp_7q21.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 12(7Q21.2) MUTATED 51 43 59
AMP PEAK 12(7Q21.2) WILD-TYPE 171 141 44

Figure S111.  Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00035

Table S112.  Gene #12: 'amp_7q21.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 12(7Q21.2) MUTATED 40 51 16 45
AMP PEAK 12(7Q21.2) WILD-TYPE 87 68 89 109

Figure S112.  Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_7q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S113.  Gene #12: 'amp_7q21.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 12(7Q21.2) MUTATED 22 15 29 7 49 30
AMP PEAK 12(7Q21.2) WILD-TYPE 77 62 89 49 14 62

Figure S113.  Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q31.2' versus 'MRNA_CNMF'

P value = 0.0012 (Fisher's exact test), Q value = 0.0029

Table S114.  Gene #13: 'amp_7q31.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
AMP PEAK 13(7Q31.2) MUTATED 141 67 113 91
AMP PEAK 13(7Q31.2) WILD-TYPE 17 29 24 26

Figure S114.  Get High-res Image Gene #13: 'amp_7q31.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_7q31.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S115.  Gene #13: 'amp_7q31.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
AMP PEAK 13(7Q31.2) MUTATED 130 63 83 136
AMP PEAK 13(7Q31.2) WILD-TYPE 18 39 17 22

Figure S115.  Get High-res Image Gene #13: 'amp_7q31.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7q31.2' versus 'MIR_CNMF'

P value = 0.0232 (Fisher's exact test), Q value = 0.04

Table S116.  Gene #13: 'amp_7q31.2' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
AMP PEAK 13(7Q31.2) MUTATED 126 141 72 106
AMP PEAK 13(7Q31.2) WILD-TYPE 17 46 18 20

Figure S116.  Get High-res Image Gene #13: 'amp_7q31.2' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_7q31.2' versus 'MIR_CHIERARCHICAL'

P value = 0.00934 (Fisher's exact test), Q value = 0.018

Table S117.  Gene #13: 'amp_7q31.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
AMP PEAK 13(7Q31.2) MUTATED 225 109 111
AMP PEAK 13(7Q31.2) WILD-TYPE 68 15 18

Figure S117.  Get High-res Image Gene #13: 'amp_7q31.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_7q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S118.  Gene #13: 'amp_7q31.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
AMP PEAK 13(7Q31.2) MUTATED 478 111 56
AMP PEAK 13(7Q31.2) WILD-TYPE 51 359 35

Figure S118.  Get High-res Image Gene #13: 'amp_7q31.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_7q31.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S119.  Gene #13: 'amp_7q31.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
AMP PEAK 13(7Q31.2) MUTATED 152 78 34 28
AMP PEAK 13(7Q31.2) WILD-TYPE 25 147 54 132

Figure S119.  Get High-res Image Gene #13: 'amp_7q31.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_7q31.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0284 (Fisher's exact test), Q value = 0.048

Table S120.  Gene #13: 'amp_7q31.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
AMP PEAK 13(7Q31.2) MUTATED 126 129 64
AMP PEAK 13(7Q31.2) WILD-TYPE 108 125 94

Figure S120.  Get High-res Image Gene #13: 'amp_7q31.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_7q31.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S121.  Gene #13: 'amp_7q31.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
AMP PEAK 13(7Q31.2) MUTATED 176 54 65
AMP PEAK 13(7Q31.2) WILD-TYPE 68 135 162

Figure S121.  Get High-res Image Gene #13: 'amp_7q31.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S122.  Gene #13: 'amp_7q31.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
AMP PEAK 13(7Q31.2) MUTATED 168 57 70
AMP PEAK 13(7Q31.2) WILD-TYPE 35 133 197

Figure S122.  Get High-res Image Gene #13: 'amp_7q31.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.02

Table S123.  Gene #13: 'amp_7q31.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
AMP PEAK 13(7Q31.2) MUTATED 56 44 19 52
AMP PEAK 13(7Q31.2) WILD-TYPE 84 63 63 128

Figure S123.  Get High-res Image Gene #13: 'amp_7q31.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_7q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S124.  Gene #13: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 13(7Q31.2) MUTATED 64 48 59
AMP PEAK 13(7Q31.2) WILD-TYPE 158 136 44

Figure S124.  Get High-res Image Gene #13: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0016

Table S125.  Gene #13: 'amp_7q31.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 13(7Q31.2) MUTATED 43 55 21 51
AMP PEAK 13(7Q31.2) WILD-TYPE 84 64 84 103

Figure S125.  Get High-res Image Gene #13: 'amp_7q31.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S126.  Gene #13: 'amp_7q31.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 13(7Q31.2) MUTATED 27 18 32 9 49 35
AMP PEAK 13(7Q31.2) WILD-TYPE 72 59 86 47 14 57

Figure S126.  Get High-res Image Gene #13: 'amp_7q31.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q32.3' versus 'MRNA_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0019

Table S127.  Gene #14: 'amp_7q32.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
AMP PEAK 14(7Q32.3) MUTATED 141 66 115 94
AMP PEAK 14(7Q32.3) WILD-TYPE 17 30 22 23

Figure S127.  Get High-res Image Gene #14: 'amp_7q32.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_7q32.3' versus 'MRNA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00022

Table S128.  Gene #14: 'amp_7q32.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
AMP PEAK 14(7Q32.3) MUTATED 127 66 86 137
AMP PEAK 14(7Q32.3) WILD-TYPE 21 36 14 21

Figure S128.  Get High-res Image Gene #14: 'amp_7q32.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7q32.3' versus 'MIR_CHIERARCHICAL'

P value = 0.00476 (Fisher's exact test), Q value = 0.0099

Table S129.  Gene #14: 'amp_7q32.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
AMP PEAK 14(7Q32.3) MUTATED 227 110 113
AMP PEAK 14(7Q32.3) WILD-TYPE 66 14 16

Figure S129.  Get High-res Image Gene #14: 'amp_7q32.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_7q32.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S130.  Gene #14: 'amp_7q32.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
AMP PEAK 14(7Q32.3) MUTATED 481 122 55
AMP PEAK 14(7Q32.3) WILD-TYPE 48 348 36

Figure S130.  Get High-res Image Gene #14: 'amp_7q32.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_7q32.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S131.  Gene #14: 'amp_7q32.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
AMP PEAK 14(7Q32.3) MUTATED 152 83 35 29
AMP PEAK 14(7Q32.3) WILD-TYPE 25 142 53 131

Figure S131.  Get High-res Image Gene #14: 'amp_7q32.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_7q32.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.018 (Fisher's exact test), Q value = 0.032

Table S132.  Gene #14: 'amp_7q32.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
AMP PEAK 14(7Q32.3) MUTATED 131 134 66
AMP PEAK 14(7Q32.3) WILD-TYPE 103 120 92

Figure S132.  Get High-res Image Gene #14: 'amp_7q32.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_7q32.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S133.  Gene #14: 'amp_7q32.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
AMP PEAK 14(7Q32.3) MUTATED 176 58 69
AMP PEAK 14(7Q32.3) WILD-TYPE 68 131 158

Figure S133.  Get High-res Image Gene #14: 'amp_7q32.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_7q32.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S134.  Gene #14: 'amp_7q32.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
AMP PEAK 14(7Q32.3) MUTATED 168 60 75
AMP PEAK 14(7Q32.3) WILD-TYPE 35 130 192

Figure S134.  Get High-res Image Gene #14: 'amp_7q32.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_7q32.3' versus 'MIRSEQ_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.057

Table S135.  Gene #14: 'amp_7q32.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
AMP PEAK 14(7Q32.3) MUTATED 58 44 21 56
AMP PEAK 14(7Q32.3) WILD-TYPE 82 63 61 124

Figure S135.  Get High-res Image Gene #14: 'amp_7q32.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_7q32.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S136.  Gene #14: 'amp_7q32.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 14(7Q32.3) MUTATED 67 52 60
AMP PEAK 14(7Q32.3) WILD-TYPE 155 132 43

Figure S136.  Get High-res Image Gene #14: 'amp_7q32.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_7q32.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0019

Table S137.  Gene #14: 'amp_7q32.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 14(7Q32.3) MUTATED 45 57 23 53
AMP PEAK 14(7Q32.3) WILD-TYPE 82 62 82 101

Figure S137.  Get High-res Image Gene #14: 'amp_7q32.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_7q32.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S138.  Gene #14: 'amp_7q32.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 14(7Q32.3) MUTATED 31 19 34 10 49 35
AMP PEAK 14(7Q32.3) WILD-TYPE 68 58 84 46 14 57

Figure S138.  Get High-res Image Gene #14: 'amp_7q32.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S139.  Gene #15: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
AMP PEAK 15(8Q24.21) MUTATED 8 25 6 22
AMP PEAK 15(8Q24.21) WILD-TYPE 150 71 131 95

Figure S139.  Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8q24.21' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S140.  Gene #15: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
AMP PEAK 15(8Q24.21) MUTATED 10 29 6 16
AMP PEAK 15(8Q24.21) WILD-TYPE 138 73 94 142

Figure S140.  Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8q24.21' versus 'MIR_CNMF'

P value = 0.0205 (Fisher's exact test), Q value = 0.036

Table S141.  Gene #15: 'amp_8q24.21' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
AMP PEAK 15(8Q24.21) MUTATED 10 31 13 10
AMP PEAK 15(8Q24.21) WILD-TYPE 133 156 77 116

Figure S141.  Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.8e-05

Table S142.  Gene #15: 'amp_8q24.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
AMP PEAK 15(8Q24.21) MUTATED 51 94 24
AMP PEAK 15(8Q24.21) WILD-TYPE 478 376 67

Figure S142.  Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S143.  Gene #15: 'amp_8q24.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
AMP PEAK 15(8Q24.21) MUTATED 13 83 7 11
AMP PEAK 15(8Q24.21) WILD-TYPE 164 142 81 149

Figure S143.  Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 0.00222 (Fisher's exact test), Q value = 0.0051

Table S144.  Gene #15: 'amp_8q24.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
AMP PEAK 15(8Q24.21) MUTATED 32 31 58
AMP PEAK 15(8Q24.21) WILD-TYPE 212 158 169

Figure S144.  Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S145.  Gene #15: 'amp_8q24.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
AMP PEAK 15(8Q24.21) MUTATED 21 63 37
AMP PEAK 15(8Q24.21) WILD-TYPE 182 127 230

Figure S145.  Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.02

Table S146.  Gene #15: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
AMP PEAK 15(8Q24.21) MUTATED 34 22 6 36
AMP PEAK 15(8Q24.21) WILD-TYPE 106 85 76 144

Figure S146.  Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00093 (Fisher's exact test), Q value = 0.0023

Table S147.  Gene #15: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 15(8Q24.21) MUTATED 58 30 10
AMP PEAK 15(8Q24.21) WILD-TYPE 164 154 93

Figure S147.  Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.029

Table S148.  Gene #15: 'amp_8q24.21' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 15(8Q24.21) MUTATED 37 22 15 24
AMP PEAK 15(8Q24.21) WILD-TYPE 90 97 90 130

Figure S148.  Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S149.  Gene #15: 'amp_8q24.21' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 15(8Q24.21) MUTATED 33 16 14 2 3 30
AMP PEAK 15(8Q24.21) WILD-TYPE 66 61 104 54 60 62

Figure S149.  Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9q34.3' versus 'MRNA_CNMF'

P value = 0.0376 (Fisher's exact test), Q value = 0.062

Table S150.  Gene #16: 'amp_9q34.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
AMP PEAK 16(9Q34.3) MUTATED 26 26 17 19
AMP PEAK 16(9Q34.3) WILD-TYPE 132 70 120 98

Figure S150.  Get High-res Image Gene #16: 'amp_9q34.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_9q34.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.022

Table S151.  Gene #16: 'amp_9q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
AMP PEAK 16(9Q34.3) MUTATED 23 28 10 27
AMP PEAK 16(9Q34.3) WILD-TYPE 125 74 90 131

Figure S151.  Get High-res Image Gene #16: 'amp_9q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_9q34.3' versus 'CN_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.00074

Table S152.  Gene #16: 'amp_9q34.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
AMP PEAK 16(9Q34.3) MUTATED 79 41 21
AMP PEAK 16(9Q34.3) WILD-TYPE 450 429 70

Figure S152.  Get High-res Image Gene #16: 'amp_9q34.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_9q34.3' versus 'MRNASEQ_CNMF'

P value = 0.00367 (Fisher's exact test), Q value = 0.0079

Table S153.  Gene #16: 'amp_9q34.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
AMP PEAK 16(9Q34.3) MUTATED 40 14 18
AMP PEAK 16(9Q34.3) WILD-TYPE 204 175 209

Figure S153.  Get High-res Image Gene #16: 'amp_9q34.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_9q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0183 (Fisher's exact test), Q value = 0.033

Table S154.  Gene #16: 'amp_9q34.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
AMP PEAK 16(9Q34.3) MUTATED 31 22 19
AMP PEAK 16(9Q34.3) WILD-TYPE 172 168 248

Figure S154.  Get High-res Image Gene #16: 'amp_9q34.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_10p15.1' versus 'MRNA_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00054

Table S155.  Gene #17: 'amp_10p15.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
AMP PEAK 17(10P15.1) MUTATED 1 8 1 8
AMP PEAK 17(10P15.1) WILD-TYPE 157 88 136 109

Figure S155.  Get High-res Image Gene #17: 'amp_10p15.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_10p15.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S156.  Gene #17: 'amp_10p15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
AMP PEAK 17(10P15.1) MUTATED 2 13 1 2
AMP PEAK 17(10P15.1) WILD-TYPE 146 89 99 156

Figure S156.  Get High-res Image Gene #17: 'amp_10p15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_10p15.1' versus 'MIR_CNMF'

P value = 0.00813 (Fisher's exact test), Q value = 0.016

Table S157.  Gene #17: 'amp_10p15.1' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
AMP PEAK 17(10P15.1) MUTATED 1 12 3 1
AMP PEAK 17(10P15.1) WILD-TYPE 142 175 87 125

Figure S157.  Get High-res Image Gene #17: 'amp_10p15.1' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_10p15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S158.  Gene #17: 'amp_10p15.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
AMP PEAK 17(10P15.1) MUTATED 6 76 6
AMP PEAK 17(10P15.1) WILD-TYPE 523 394 85

Figure S158.  Get High-res Image Gene #17: 'amp_10p15.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_10p15.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S159.  Gene #17: 'amp_10p15.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
AMP PEAK 17(10P15.1) MUTATED 2 64 5 0
AMP PEAK 17(10P15.1) WILD-TYPE 175 161 83 160

Figure S159.  Get High-res Image Gene #17: 'amp_10p15.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_10p15.1' versus 'RPPA_CNMF'

P value = 0.001 (Fisher's exact test), Q value = 0.0025

Table S160.  Gene #17: 'amp_10p15.1' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
AMP PEAK 17(10P15.1) MUTATED 22 9 11 22
AMP PEAK 17(10P15.1) WILD-TYPE 191 159 145 87

Figure S160.  Get High-res Image Gene #17: 'amp_10p15.1' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_10p15.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S161.  Gene #17: 'amp_10p15.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
AMP PEAK 17(10P15.1) MUTATED 12 17 43
AMP PEAK 17(10P15.1) WILD-TYPE 232 172 184

Figure S161.  Get High-res Image Gene #17: 'amp_10p15.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_10p15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S162.  Gene #17: 'amp_10p15.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
AMP PEAK 17(10P15.1) MUTATED 3 50 19
AMP PEAK 17(10P15.1) WILD-TYPE 200 140 248

Figure S162.  Get High-res Image Gene #17: 'amp_10p15.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_10p15.1' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00024

Table S163.  Gene #17: 'amp_10p15.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
AMP PEAK 17(10P15.1) MUTATED 18 27 3 20
AMP PEAK 17(10P15.1) WILD-TYPE 122 80 79 160

Figure S163.  Get High-res Image Gene #17: 'amp_10p15.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_10p15.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00224 (Fisher's exact test), Q value = 0.0051

Table S164.  Gene #17: 'amp_10p15.1' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 17(10P15.1) MUTATED 24 22 5 17
AMP PEAK 17(10P15.1) WILD-TYPE 103 97 100 137

Figure S164.  Get High-res Image Gene #17: 'amp_10p15.1' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_10p15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S165.  Gene #17: 'amp_10p15.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 17(10P15.1) MUTATED 26 15 10 0 1 16
AMP PEAK 17(10P15.1) WILD-TYPE 73 62 108 56 62 76

Figure S165.  Get High-res Image Gene #17: 'amp_10p15.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11p13' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00013

Table S166.  Gene #18: 'amp_11p13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
AMP PEAK 18(11P13) MUTATED 5 9 0 20
AMP PEAK 18(11P13) WILD-TYPE 172 216 88 140

Figure S166.  Get High-res Image Gene #18: 'amp_11p13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_11p13' versus 'MIRSEQ_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 0.051

Table S167.  Gene #18: 'amp_11p13' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
AMP PEAK 18(11P13) MUTATED 6 4 11 8
AMP PEAK 18(11P13) WILD-TYPE 134 103 71 172

Figure S167.  Get High-res Image Gene #18: 'amp_11p13' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_11p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00333 (Fisher's exact test), Q value = 0.0073

Table S168.  Gene #18: 'amp_11p13' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 18(11P13) MUTATED 5 1 6 8 0 9
AMP PEAK 18(11P13) WILD-TYPE 94 76 112 48 63 83

Figure S168.  Get High-res Image Gene #18: 'amp_11p13' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q24.1' versus 'MRNA_CNMF'

P value = 0.00707 (Fisher's exact test), Q value = 0.014

Table S169.  Gene #19: 'amp_11q24.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
AMP PEAK 19(11Q24.1) MUTATED 4 7 2 11
AMP PEAK 19(11Q24.1) WILD-TYPE 154 89 135 106

Figure S169.  Get High-res Image Gene #19: 'amp_11q24.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11q24.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00784 (Fisher's exact test), Q value = 0.015

Table S170.  Gene #19: 'amp_11q24.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
AMP PEAK 19(11Q24.1) MUTATED 4 11 1 8
AMP PEAK 19(11Q24.1) WILD-TYPE 144 91 99 150

Figure S170.  Get High-res Image Gene #19: 'amp_11q24.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11q24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S171.  Gene #19: 'amp_11q24.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
AMP PEAK 19(11Q24.1) MUTATED 22 78 12
AMP PEAK 19(11Q24.1) WILD-TYPE 507 392 79

Figure S171.  Get High-res Image Gene #19: 'amp_11q24.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_11q24.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S172.  Gene #19: 'amp_11q24.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
AMP PEAK 19(11Q24.1) MUTATED 9 51 5 28
AMP PEAK 19(11Q24.1) WILD-TYPE 168 174 83 132

Figure S172.  Get High-res Image Gene #19: 'amp_11q24.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_11q24.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S173.  Gene #19: 'amp_11q24.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
AMP PEAK 19(11Q24.1) MUTATED 16 27 50
AMP PEAK 19(11Q24.1) WILD-TYPE 228 162 177

Figure S173.  Get High-res Image Gene #19: 'amp_11q24.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_11q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S174.  Gene #19: 'amp_11q24.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
AMP PEAK 19(11Q24.1) MUTATED 8 39 46
AMP PEAK 19(11Q24.1) WILD-TYPE 195 151 221

Figure S174.  Get High-res Image Gene #19: 'amp_11q24.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_11q24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00909 (Fisher's exact test), Q value = 0.018

Table S175.  Gene #19: 'amp_11q24.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 19(11Q24.1) MUTATED 22 14 18 10 2 21
AMP PEAK 19(11Q24.1) WILD-TYPE 77 63 100 46 61 71

Figure S175.  Get High-res Image Gene #19: 'amp_11q24.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p13.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S176.  Gene #20: 'amp_12p13.32' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
AMP PEAK 20(12P13.32) MUTATED 23 56 4 4
AMP PEAK 20(12P13.32) WILD-TYPE 154 169 84 156

Figure S176.  Get High-res Image Gene #20: 'amp_12p13.32' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_12p13.32' versus 'RPPA_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0016

Table S177.  Gene #20: 'amp_12p13.32' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
AMP PEAK 20(12P13.32) MUTATED 19 15 35 16
AMP PEAK 20(12P13.32) WILD-TYPE 194 153 121 93

Figure S177.  Get High-res Image Gene #20: 'amp_12p13.32' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_12p13.32' versus 'RPPA_CHIERARCHICAL'

P value = 0.0111 (Fisher's exact test), Q value = 0.021

Table S178.  Gene #20: 'amp_12p13.32' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
AMP PEAK 20(12P13.32) MUTATED 31 43 11
AMP PEAK 20(12P13.32) WILD-TYPE 203 211 147

Figure S178.  Get High-res Image Gene #20: 'amp_12p13.32' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_12p13.32' versus 'MRNASEQ_CNMF'

P value = 0.00619 (Fisher's exact test), Q value = 0.012

Table S179.  Gene #20: 'amp_12p13.32' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
AMP PEAK 20(12P13.32) MUTATED 38 14 39
AMP PEAK 20(12P13.32) WILD-TYPE 206 175 188

Figure S179.  Get High-res Image Gene #20: 'amp_12p13.32' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_12p13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S180.  Gene #20: 'amp_12p13.32' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
AMP PEAK 20(12P13.32) MUTATED 29 43 19
AMP PEAK 20(12P13.32) WILD-TYPE 174 147 248

Figure S180.  Get High-res Image Gene #20: 'amp_12p13.32' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_12p13.32' versus 'MIRSEQ_CNMF'

P value = 0.00444 (Fisher's exact test), Q value = 0.0093

Table S181.  Gene #20: 'amp_12p13.32' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
AMP PEAK 20(12P13.32) MUTATED 17 26 9 16
AMP PEAK 20(12P13.32) WILD-TYPE 123 81 73 164

Figure S181.  Get High-res Image Gene #20: 'amp_12p13.32' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_12p13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00318 (Fisher's exact test), Q value = 0.007

Table S182.  Gene #20: 'amp_12p13.32' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 20(12P13.32) MUTATED 35 13 20
AMP PEAK 20(12P13.32) WILD-TYPE 187 171 83

Figure S182.  Get High-res Image Gene #20: 'amp_12p13.32' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_12p13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00108 (Fisher's exact test), Q value = 0.0026

Table S183.  Gene #20: 'amp_12p13.32' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 20(12P13.32) MUTATED 22 26 7 13
AMP PEAK 20(12P13.32) WILD-TYPE 105 93 98 141

Figure S183.  Get High-res Image Gene #20: 'amp_12p13.32' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_12p13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S184.  Gene #20: 'amp_12p13.32' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 20(12P13.32) MUTATED 19 21 4 3 7 14
AMP PEAK 20(12P13.32) WILD-TYPE 80 56 114 53 56 78

Figure S184.  Get High-res Image Gene #20: 'amp_12p13.32' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q14.1' versus 'MIR_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.02

Table S185.  Gene #21: 'amp_12q14.1' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
AMP PEAK 21(12Q14.1) MUTATED 25 60 18 26
AMP PEAK 21(12Q14.1) WILD-TYPE 118 127 72 100

Figure S185.  Get High-res Image Gene #21: 'amp_12q14.1' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_12q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S186.  Gene #21: 'amp_12q14.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
AMP PEAK 21(12Q14.1) MUTATED 135 28 8
AMP PEAK 21(12Q14.1) WILD-TYPE 394 442 83

Figure S186.  Get High-res Image Gene #21: 'amp_12q14.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_12q14.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S187.  Gene #21: 'amp_12q14.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
AMP PEAK 21(12Q14.1) MUTATED 42 16 3 5
AMP PEAK 21(12Q14.1) WILD-TYPE 135 209 85 155

Figure S187.  Get High-res Image Gene #21: 'amp_12q14.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S188.  Gene #21: 'amp_12q14.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
AMP PEAK 21(12Q14.1) MUTATED 67 4 8
AMP PEAK 21(12Q14.1) WILD-TYPE 177 185 219

Figure S188.  Get High-res Image Gene #21: 'amp_12q14.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S189.  Gene #21: 'amp_12q14.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
AMP PEAK 21(12Q14.1) MUTATED 58 13 8
AMP PEAK 21(12Q14.1) WILD-TYPE 145 177 259

Figure S189.  Get High-res Image Gene #21: 'amp_12q14.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'MIRSEQ_CNMF'

P value = 0.00376 (Fisher's exact test), Q value = 0.0081

Table S190.  Gene #21: 'amp_12q14.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
AMP PEAK 21(12Q14.1) MUTATED 13 15 3 6
AMP PEAK 21(12Q14.1) WILD-TYPE 127 92 79 174

Figure S190.  Get High-res Image Gene #21: 'amp_12q14.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_12q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S191.  Gene #21: 'amp_12q14.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 21(12Q14.1) MUTATED 10 5 22
AMP PEAK 21(12Q14.1) WILD-TYPE 212 179 81

Figure S191.  Get High-res Image Gene #21: 'amp_12q14.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.8e-05

Table S192.  Gene #21: 'amp_12q14.1' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 21(12Q14.1) MUTATED 9 21 1 6
AMP PEAK 21(12Q14.1) WILD-TYPE 118 98 104 148

Figure S192.  Get High-res Image Gene #21: 'amp_12q14.1' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_12q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00016

Table S193.  Gene #21: 'amp_12q14.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 21(12Q14.1) MUTATED 6 6 2 2 15 6
AMP PEAK 21(12Q14.1) WILD-TYPE 93 71 116 54 48 86

Figure S193.  Get High-res Image Gene #21: 'amp_12q14.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S194.  Gene #22: 'amp_12q15' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
AMP PEAK 22(12Q15) MUTATED 97 11 3
AMP PEAK 22(12Q15) WILD-TYPE 432 459 88

Figure S194.  Get High-res Image Gene #22: 'amp_12q15' versus Molecular Subtype #5: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S195.  Gene #22: 'amp_12q15' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
AMP PEAK 22(12Q15) MUTATED 28 4 2 4
AMP PEAK 22(12Q15) WILD-TYPE 149 221 86 156

Figure S195.  Get High-res Image Gene #22: 'amp_12q15' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_12q15' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S196.  Gene #22: 'amp_12q15' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
AMP PEAK 22(12Q15) MUTATED 34 4 4
AMP PEAK 22(12Q15) WILD-TYPE 210 185 223

Figure S196.  Get High-res Image Gene #22: 'amp_12q15' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S197.  Gene #22: 'amp_12q15' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
AMP PEAK 22(12Q15) MUTATED 34 1 7
AMP PEAK 22(12Q15) WILD-TYPE 169 189 260

Figure S197.  Get High-res Image Gene #22: 'amp_12q15' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.022 (Fisher's exact test), Q value = 0.038

Table S198.  Gene #22: 'amp_12q15' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 22(12Q15) MUTATED 3 10 1 4
AMP PEAK 22(12Q15) WILD-TYPE 124 109 104 150

Figure S198.  Get High-res Image Gene #22: 'amp_12q15' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_12q15' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0126 (Fisher's exact test), Q value = 0.023

Table S199.  Gene #22: 'amp_12q15' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 22(12Q15) MUTATED 2 1 2 2 8 3
AMP PEAK 22(12Q15) WILD-TYPE 97 76 116 54 55 89

Figure S199.  Get High-res Image Gene #22: 'amp_12q15' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q34' versus 'METHLYATION_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.0014

Table S200.  Gene #23: 'amp_13q34' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
AMP PEAK 23(13Q34) MUTATED 6 19 1 1
AMP PEAK 23(13Q34) WILD-TYPE 171 206 87 159

Figure S200.  Get High-res Image Gene #23: 'amp_13q34' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0266 (Fisher's exact test), Q value = 0.046

Table S201.  Gene #23: 'amp_13q34' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
AMP PEAK 23(13Q34) MUTATED 13 13 6
AMP PEAK 23(13Q34) WILD-TYPE 190 177 261

Figure S201.  Get High-res Image Gene #23: 'amp_13q34' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_14q32.33' versus 'MIR_CNMF'

P value = 0.0398 (Fisher's exact test), Q value = 0.065

Table S202.  Gene #24: 'amp_14q32.33' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
AMP PEAK 24(14Q32.33) MUTATED 12 10 10 3
AMP PEAK 24(14Q32.33) WILD-TYPE 131 177 80 123

Figure S202.  Get High-res Image Gene #24: 'amp_14q32.33' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_14q32.33' versus 'CN_CNMF'

P value = 0.00117 (Fisher's exact test), Q value = 0.0028

Table S203.  Gene #24: 'amp_14q32.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
AMP PEAK 24(14Q32.33) MUTATED 32 8 4
AMP PEAK 24(14Q32.33) WILD-TYPE 497 462 87

Figure S203.  Get High-res Image Gene #24: 'amp_14q32.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_14q32.33' versus 'MRNASEQ_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.021

Table S204.  Gene #24: 'amp_14q32.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
AMP PEAK 24(14Q32.33) MUTATED 13 2 3
AMP PEAK 24(14Q32.33) WILD-TYPE 231 187 224

Figure S204.  Get High-res Image Gene #24: 'amp_14q32.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_14q32.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00828 (Fisher's exact test), Q value = 0.016

Table S205.  Gene #24: 'amp_14q32.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
AMP PEAK 24(14Q32.33) MUTATED 11 5 2
AMP PEAK 24(14Q32.33) WILD-TYPE 192 185 265

Figure S205.  Get High-res Image Gene #24: 'amp_14q32.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_17p13.2' versus 'MRNA_CNMF'

P value = 0.00177 (Fisher's exact test), Q value = 0.0041

Table S206.  Gene #25: 'amp_17p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
AMP PEAK 25(17P13.2) MUTATED 9 13 6 19
AMP PEAK 25(17P13.2) WILD-TYPE 149 83 131 98

Figure S206.  Get High-res Image Gene #25: 'amp_17p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17p13.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.026

Table S207.  Gene #25: 'amp_17p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
AMP PEAK 25(17P13.2) MUTATED 10 18 5 14
AMP PEAK 25(17P13.2) WILD-TYPE 138 84 95 144

Figure S207.  Get High-res Image Gene #25: 'amp_17p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17p13.2' versus 'MIR_CNMF'

P value = 0.0396 (Fisher's exact test), Q value = 0.065

Table S208.  Gene #25: 'amp_17p13.2' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
AMP PEAK 25(17P13.2) MUTATED 5 22 8 13
AMP PEAK 25(17P13.2) WILD-TYPE 138 165 82 113

Figure S208.  Get High-res Image Gene #25: 'amp_17p13.2' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_17p13.2' versus 'RPPA_CNMF'

P value = 0.00455 (Fisher's exact test), Q value = 0.0094

Table S209.  Gene #25: 'amp_17p13.2' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
AMP PEAK 25(17P13.2) MUTATED 17 2 14 6
AMP PEAK 25(17P13.2) WILD-TYPE 196 166 142 103

Figure S209.  Get High-res Image Gene #25: 'amp_17p13.2' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_17p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 0.027

Table S210.  Gene #25: 'amp_17p13.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 25(17P13.2) MUTATED 3 4 2 8 1 5
AMP PEAK 25(17P13.2) WILD-TYPE 96 73 116 48 62 87

Figure S210.  Get High-res Image Gene #25: 'amp_17p13.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q25.1' versus 'MRNA_CNMF'

P value = 0.0284 (Fisher's exact test), Q value = 0.048

Table S211.  Gene #26: 'amp_17q25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
AMP PEAK 26(17Q25.1) MUTATED 19 22 13 19
AMP PEAK 26(17Q25.1) WILD-TYPE 139 74 124 98

Figure S211.  Get High-res Image Gene #26: 'amp_17q25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q25.1' versus 'CN_CNMF'

P value = 0.00596 (Fisher's exact test), Q value = 0.012

Table S212.  Gene #26: 'amp_17q25.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
AMP PEAK 26(17Q25.1) MUTATED 79 40 9
AMP PEAK 26(17Q25.1) WILD-TYPE 450 430 82

Figure S212.  Get High-res Image Gene #26: 'amp_17q25.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_17q25.1' versus 'MRNASEQ_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.028

Table S213.  Gene #26: 'amp_17q25.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
AMP PEAK 26(17Q25.1) MUTATED 33 10 21
AMP PEAK 26(17Q25.1) WILD-TYPE 211 179 206

Figure S213.  Get High-res Image Gene #26: 'amp_17q25.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_17q25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0351 (Fisher's exact test), Q value = 0.058

Table S214.  Gene #26: 'amp_17q25.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
AMP PEAK 26(17Q25.1) MUTATED 27 20 17
AMP PEAK 26(17Q25.1) WILD-TYPE 176 170 250

Figure S214.  Get High-res Image Gene #26: 'amp_17q25.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S215.  Gene #27: 'amp_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
AMP PEAK 27(19P13.3) MUTATED 63 35 90 29
AMP PEAK 27(19P13.3) WILD-TYPE 95 61 47 88

Figure S215.  Get High-res Image Gene #27: 'amp_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19p13.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S216.  Gene #27: 'amp_19p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
AMP PEAK 27(19P13.3) MUTATED 67 31 62 57
AMP PEAK 27(19P13.3) WILD-TYPE 81 71 38 101

Figure S216.  Get High-res Image Gene #27: 'amp_19p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19p13.3' versus 'MIR_CNMF'

P value = 0.0396 (Fisher's exact test), Q value = 0.065

Table S217.  Gene #27: 'amp_19p13.3' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
AMP PEAK 27(19P13.3) MUTATED 59 89 27 57
AMP PEAK 27(19P13.3) WILD-TYPE 84 98 63 69

Figure S217.  Get High-res Image Gene #27: 'amp_19p13.3' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_19p13.3' versus 'MIR_CHIERARCHICAL'

P value = 0.00246 (Fisher's exact test), Q value = 0.0056

Table S218.  Gene #27: 'amp_19p13.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
AMP PEAK 27(19P13.3) MUTATED 108 53 71
AMP PEAK 27(19P13.3) WILD-TYPE 185 71 58

Figure S218.  Get High-res Image Gene #27: 'amp_19p13.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S219.  Gene #27: 'amp_19p13.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
AMP PEAK 27(19P13.3) MUTATED 245 109 21
AMP PEAK 27(19P13.3) WILD-TYPE 284 361 70

Figure S219.  Get High-res Image Gene #27: 'amp_19p13.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S220.  Gene #27: 'amp_19p13.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
AMP PEAK 27(19P13.3) MUTATED 76 21 6 80
AMP PEAK 27(19P13.3) WILD-TYPE 101 204 82 80

Figure S220.  Get High-res Image Gene #27: 'amp_19p13.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_19p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0277 (Fisher's exact test), Q value = 0.047

Table S221.  Gene #27: 'amp_19p13.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
AMP PEAK 27(19P13.3) MUTATED 69 91 37
AMP PEAK 27(19P13.3) WILD-TYPE 165 163 121

Figure S221.  Get High-res Image Gene #27: 'amp_19p13.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_19p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00522 (Fisher's exact test), Q value = 0.011

Table S222.  Gene #27: 'amp_19p13.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
AMP PEAK 27(19P13.3) MUTATED 84 53 48
AMP PEAK 27(19P13.3) WILD-TYPE 160 136 179

Figure S222.  Get High-res Image Gene #27: 'amp_19p13.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S223.  Gene #27: 'amp_19p13.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
AMP PEAK 27(19P13.3) MUTATED 77 19 89
AMP PEAK 27(19P13.3) WILD-TYPE 126 171 178

Figure S223.  Get High-res Image Gene #27: 'amp_19p13.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.3' versus 'MIRSEQ_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.0014

Table S224.  Gene #27: 'amp_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
AMP PEAK 27(19P13.3) MUTATED 26 23 36 44
AMP PEAK 27(19P13.3) WILD-TYPE 114 84 46 136

Figure S224.  Get High-res Image Gene #27: 'amp_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.8e-05

Table S225.  Gene #27: 'amp_19p13.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 27(19P13.3) MUTATED 19 27 46 37
AMP PEAK 27(19P13.3) WILD-TYPE 108 92 59 117

Figure S225.  Get High-res Image Gene #27: 'amp_19p13.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00016

Table S226.  Gene #27: 'amp_19p13.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 27(19P13.3) MUTATED 12 15 30 27 23 22
AMP PEAK 27(19P13.3) WILD-TYPE 87 62 88 29 40 70

Figure S226.  Get High-res Image Gene #27: 'amp_19p13.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S227.  Gene #28: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
AMP PEAK 28(19Q12) MUTATED 60 31 79 18
AMP PEAK 28(19Q12) WILD-TYPE 98 65 58 99

Figure S227.  Get High-res Image Gene #28: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S228.  Gene #28: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
AMP PEAK 28(19Q12) MUTATED 62 21 54 51
AMP PEAK 28(19Q12) WILD-TYPE 86 81 46 107

Figure S228.  Get High-res Image Gene #28: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q12' versus 'MIR_CHIERARCHICAL'

P value = 0.00488 (Fisher's exact test), Q value = 0.01

Table S229.  Gene #28: 'amp_19q12' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
AMP PEAK 28(19Q12) MUTATED 91 49 61
AMP PEAK 28(19Q12) WILD-TYPE 202 75 68

Figure S229.  Get High-res Image Gene #28: 'amp_19q12' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S230.  Gene #28: 'amp_19q12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
AMP PEAK 28(19Q12) MUTATED 212 14 21
AMP PEAK 28(19Q12) WILD-TYPE 317 456 70

Figure S230.  Get High-res Image Gene #28: 'amp_19q12' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S231.  Gene #28: 'amp_19q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
AMP PEAK 28(19Q12) MUTATED 62 8 6 0
AMP PEAK 28(19Q12) WILD-TYPE 115 217 82 160

Figure S231.  Get High-res Image Gene #28: 'amp_19q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_19q12' versus 'RPPA_CNMF'

P value = 0.0408 (Fisher's exact test), Q value = 0.067

Table S232.  Gene #28: 'amp_19q12' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
AMP PEAK 28(19Q12) MUTATED 39 16 30 20
AMP PEAK 28(19Q12) WILD-TYPE 174 152 126 89

Figure S232.  Get High-res Image Gene #28: 'amp_19q12' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_19q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00087 (Fisher's exact test), Q value = 0.0022

Table S233.  Gene #28: 'amp_19q12' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
AMP PEAK 28(19Q12) MUTATED 40 53 12
AMP PEAK 28(19Q12) WILD-TYPE 194 201 146

Figure S233.  Get High-res Image Gene #28: 'amp_19q12' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S234.  Gene #28: 'amp_19q12' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
AMP PEAK 28(19Q12) MUTATED 74 5 2
AMP PEAK 28(19Q12) WILD-TYPE 170 184 225

Figure S234.  Get High-res Image Gene #28: 'amp_19q12' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S235.  Gene #28: 'amp_19q12' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
AMP PEAK 28(19Q12) MUTATED 69 7 5
AMP PEAK 28(19Q12) WILD-TYPE 134 183 262

Figure S235.  Get High-res Image Gene #28: 'amp_19q12' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00035

Table S236.  Gene #28: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
AMP PEAK 28(19Q12) MUTATED 10 15 0 6
AMP PEAK 28(19Q12) WILD-TYPE 130 92 82 174

Figure S236.  Get High-res Image Gene #28: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S237.  Gene #28: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 28(19Q12) MUTATED 6 2 23
AMP PEAK 28(19Q12) WILD-TYPE 216 182 80

Figure S237.  Get High-res Image Gene #28: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S238.  Gene #28: 'amp_19q12' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 28(19Q12) MUTATED 9 18 0 4
AMP PEAK 28(19Q12) WILD-TYPE 118 101 105 150

Figure S238.  Get High-res Image Gene #28: 'amp_19q12' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S239.  Gene #28: 'amp_19q12' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 28(19Q12) MUTATED 3 4 4 0 20 0
AMP PEAK 28(19Q12) WILD-TYPE 96 73 114 56 43 92

Figure S239.  Get High-res Image Gene #28: 'amp_19q12' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q13.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S240.  Gene #29: 'amp_19q13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
AMP PEAK 29(19Q13.2) MUTATED 57 28 72 14
AMP PEAK 29(19Q13.2) WILD-TYPE 101 68 65 103

Figure S240.  Get High-res Image Gene #29: 'amp_19q13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q13.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S241.  Gene #29: 'amp_19q13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
AMP PEAK 29(19Q13.2) MUTATED 62 18 49 42
AMP PEAK 29(19Q13.2) WILD-TYPE 86 84 51 116

Figure S241.  Get High-res Image Gene #29: 'amp_19q13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q13.2' versus 'MIR_CHIERARCHICAL'

P value = 0.00609 (Fisher's exact test), Q value = 0.012

Table S242.  Gene #29: 'amp_19q13.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
AMP PEAK 29(19Q13.2) MUTATED 83 47 56
AMP PEAK 29(19Q13.2) WILD-TYPE 210 77 73

Figure S242.  Get High-res Image Gene #29: 'amp_19q13.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_19q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S243.  Gene #29: 'amp_19q13.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
AMP PEAK 29(19Q13.2) MUTATED 199 10 22
AMP PEAK 29(19Q13.2) WILD-TYPE 330 460 69

Figure S243.  Get High-res Image Gene #29: 'amp_19q13.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19q13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S244.  Gene #29: 'amp_19q13.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
AMP PEAK 29(19Q13.2) MUTATED 62 5 8 0
AMP PEAK 29(19Q13.2) WILD-TYPE 115 220 80 160

Figure S244.  Get High-res Image Gene #29: 'amp_19q13.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_19q13.2' versus 'RPPA_CNMF'

P value = 0.0171 (Fisher's exact test), Q value = 0.031

Table S245.  Gene #29: 'amp_19q13.2' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
AMP PEAK 29(19Q13.2) MUTATED 33 12 25 20
AMP PEAK 29(19Q13.2) WILD-TYPE 180 156 131 89

Figure S245.  Get High-res Image Gene #29: 'amp_19q13.2' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_19q13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00102 (Fisher's exact test), Q value = 0.0025

Table S246.  Gene #29: 'amp_19q13.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
AMP PEAK 29(19Q13.2) MUTATED 32 48 10
AMP PEAK 29(19Q13.2) WILD-TYPE 202 206 148

Figure S246.  Get High-res Image Gene #29: 'amp_19q13.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_19q13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S247.  Gene #29: 'amp_19q13.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
AMP PEAK 29(19Q13.2) MUTATED 67 5 3
AMP PEAK 29(19Q13.2) WILD-TYPE 177 184 224

Figure S247.  Get High-res Image Gene #29: 'amp_19q13.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_19q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S248.  Gene #29: 'amp_19q13.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
AMP PEAK 29(19Q13.2) MUTATED 63 7 5
AMP PEAK 29(19Q13.2) WILD-TYPE 140 183 262

Figure S248.  Get High-res Image Gene #29: 'amp_19q13.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_19q13.2' versus 'MIRSEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00046

Table S249.  Gene #29: 'amp_19q13.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
AMP PEAK 29(19Q13.2) MUTATED 13 13 0 5
AMP PEAK 29(19Q13.2) WILD-TYPE 127 94 82 175

Figure S249.  Get High-res Image Gene #29: 'amp_19q13.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_19q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S250.  Gene #29: 'amp_19q13.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
AMP PEAK 29(19Q13.2) MUTATED 7 1 23
AMP PEAK 29(19Q13.2) WILD-TYPE 215 183 80

Figure S250.  Get High-res Image Gene #29: 'amp_19q13.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_19q13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S251.  Gene #29: 'amp_19q13.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 29(19Q13.2) MUTATED 10 18 0 3
AMP PEAK 29(19Q13.2) WILD-TYPE 117 101 105 151

Figure S251.  Get High-res Image Gene #29: 'amp_19q13.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_19q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S252.  Gene #29: 'amp_19q13.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 29(19Q13.2) MUTATED 5 2 4 0 20 0
AMP PEAK 29(19Q13.2) WILD-TYPE 94 75 114 56 43 92

Figure S252.  Get High-res Image Gene #29: 'amp_19q13.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xp11.21' versus 'CN_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00062

Table S253.  Gene #30: 'amp_xp11.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
AMP PEAK 30(XP11.21) MUTATED 31 61 12
AMP PEAK 30(XP11.21) WILD-TYPE 498 409 79

Figure S253.  Get High-res Image Gene #30: 'amp_xp11.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_xp11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S254.  Gene #30: 'amp_xp11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
AMP PEAK 30(XP11.21) MUTATED 6 62 6 2
AMP PEAK 30(XP11.21) WILD-TYPE 171 163 82 158

Figure S254.  Get High-res Image Gene #30: 'amp_xp11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_xp11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S255.  Gene #30: 'amp_xp11.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
AMP PEAK 30(XP11.21) MUTATED 9 49 19
AMP PEAK 30(XP11.21) WILD-TYPE 194 141 248

Figure S255.  Get High-res Image Gene #30: 'amp_xp11.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.21' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00024

Table S256.  Gene #30: 'amp_xp11.21' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
AMP PEAK 30(XP11.21) MUTATED 26 21 1 21
AMP PEAK 30(XP11.21) WILD-TYPE 114 86 81 159

Figure S256.  Get High-res Image Gene #30: 'amp_xp11.21' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_xp11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00013

Table S257.  Gene #30: 'amp_xp11.21' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
AMP PEAK 30(XP11.21) MUTATED 27 23 3 16
AMP PEAK 30(XP11.21) WILD-TYPE 100 96 102 138

Figure S257.  Get High-res Image Gene #30: 'amp_xp11.21' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_xp11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.8e-05

Table S258.  Gene #30: 'amp_xp11.21' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
AMP PEAK 30(XP11.21) MUTATED 25 16 11 0 4 13
AMP PEAK 30(XP11.21) WILD-TYPE 74 61 107 56 59 79

Figure S258.  Get High-res Image Gene #30: 'amp_xp11.21' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S259.  Gene #31: 'del_1p36.32' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 1(1P36.32) MUTATED 113 201 4
DEL PEAK 1(1P36.32) WILD-TYPE 416 269 87

Figure S259.  Get High-res Image Gene #31: 'del_1p36.32' versus Molecular Subtype #5: 'CN_CNMF'

'del_1p36.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S260.  Gene #31: 'del_1p36.32' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 1(1P36.32) MUTATED 36 10 27 158
DEL PEAK 1(1P36.32) WILD-TYPE 141 215 61 2

Figure S260.  Get High-res Image Gene #31: 'del_1p36.32' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_1p36.32' versus 'RPPA_CNMF'

P value = 0.00374 (Fisher's exact test), Q value = 0.008

Table S261.  Gene #31: 'del_1p36.32' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
DEL PEAK 1(1P36.32) MUTATED 63 74 55 27
DEL PEAK 1(1P36.32) WILD-TYPE 150 94 101 82

Figure S261.  Get High-res Image Gene #31: 'del_1p36.32' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_1p36.32' versus 'RPPA_CHIERARCHICAL'

P value = 0.00059 (Fisher's exact test), Q value = 0.0015

Table S262.  Gene #31: 'del_1p36.32' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
DEL PEAK 1(1P36.32) MUTATED 69 76 74
DEL PEAK 1(1P36.32) WILD-TYPE 165 178 84

Figure S262.  Get High-res Image Gene #31: 'del_1p36.32' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_1p36.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S263.  Gene #31: 'del_1p36.32' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 1(1P36.32) MUTATED 39 103 86
DEL PEAK 1(1P36.32) WILD-TYPE 205 86 141

Figure S263.  Get High-res Image Gene #31: 'del_1p36.32' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_1p36.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S264.  Gene #31: 'del_1p36.32' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 1(1P36.32) MUTATED 34 16 178
DEL PEAK 1(1P36.32) WILD-TYPE 169 174 89

Figure S264.  Get High-res Image Gene #31: 'del_1p36.32' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S265.  Gene #31: 'del_1p36.32' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 1(1P36.32) MUTATED 35 12 69 90
DEL PEAK 1(1P36.32) WILD-TYPE 105 95 13 90

Figure S265.  Get High-res Image Gene #31: 'del_1p36.32' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_1p36.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S266.  Gene #31: 'del_1p36.32' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 1(1P36.32) MUTATED 84 101 21
DEL PEAK 1(1P36.32) WILD-TYPE 138 83 82

Figure S266.  Get High-res Image Gene #31: 'del_1p36.32' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S267.  Gene #31: 'del_1p36.32' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 1(1P36.32) MUTATED 23 23 84 76
DEL PEAK 1(1P36.32) WILD-TYPE 104 96 21 78

Figure S267.  Get High-res Image Gene #31: 'del_1p36.32' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_1p36.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S268.  Gene #31: 'del_1p36.32' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 1(1P36.32) MUTATED 7 26 63 55 16 39
DEL PEAK 1(1P36.32) WILD-TYPE 92 51 55 1 47 53

Figure S268.  Get High-res Image Gene #31: 'del_1p36.32' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.23' versus 'MRNA_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.035

Table S269.  Gene #32: 'del_1p36.23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
DEL PEAK 2(1P36.23) MUTATED 36 14 44 27
DEL PEAK 2(1P36.23) WILD-TYPE 122 82 93 90

Figure S269.  Get High-res Image Gene #32: 'del_1p36.23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S270.  Gene #32: 'del_1p36.23' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 2(1P36.23) MUTATED 149 195 3
DEL PEAK 2(1P36.23) WILD-TYPE 380 275 88

Figure S270.  Get High-res Image Gene #32: 'del_1p36.23' versus Molecular Subtype #5: 'CN_CNMF'

'del_1p36.23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S271.  Gene #32: 'del_1p36.23' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 2(1P36.23) MUTATED 50 11 27 158
DEL PEAK 2(1P36.23) WILD-TYPE 127 214 61 2

Figure S271.  Get High-res Image Gene #32: 'del_1p36.23' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_1p36.23' versus 'RPPA_CNMF'

P value = 0.0301 (Fisher's exact test), Q value = 0.05

Table S272.  Gene #32: 'del_1p36.23' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
DEL PEAK 2(1P36.23) MUTATED 73 77 58 32
DEL PEAK 2(1P36.23) WILD-TYPE 140 91 98 77

Figure S272.  Get High-res Image Gene #32: 'del_1p36.23' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_1p36.23' versus 'RPPA_CHIERARCHICAL'

P value = 0.00947 (Fisher's exact test), Q value = 0.018

Table S273.  Gene #32: 'del_1p36.23' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
DEL PEAK 2(1P36.23) MUTATED 80 85 75
DEL PEAK 2(1P36.23) WILD-TYPE 154 169 83

Figure S273.  Get High-res Image Gene #32: 'del_1p36.23' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_1p36.23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S274.  Gene #32: 'del_1p36.23' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 2(1P36.23) MUTATED 54 106 87
DEL PEAK 2(1P36.23) WILD-TYPE 190 83 140

Figure S274.  Get High-res Image Gene #32: 'del_1p36.23' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_1p36.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S275.  Gene #32: 'del_1p36.23' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 2(1P36.23) MUTATED 49 17 181
DEL PEAK 2(1P36.23) WILD-TYPE 154 173 86

Figure S275.  Get High-res Image Gene #32: 'del_1p36.23' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S276.  Gene #32: 'del_1p36.23' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 2(1P36.23) MUTATED 37 14 69 92
DEL PEAK 2(1P36.23) WILD-TYPE 103 93 13 88

Figure S276.  Get High-res Image Gene #32: 'del_1p36.23' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_1p36.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S277.  Gene #32: 'del_1p36.23' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 2(1P36.23) MUTATED 85 103 24
DEL PEAK 2(1P36.23) WILD-TYPE 137 81 79

Figure S277.  Get High-res Image Gene #32: 'del_1p36.23' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.23' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S278.  Gene #32: 'del_1p36.23' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 2(1P36.23) MUTATED 24 26 84 78
DEL PEAK 2(1P36.23) WILD-TYPE 103 93 21 76

Figure S278.  Get High-res Image Gene #32: 'del_1p36.23' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_1p36.23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S279.  Gene #32: 'del_1p36.23' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 2(1P36.23) MUTATED 7 27 65 55 19 39
DEL PEAK 2(1P36.23) WILD-TYPE 92 50 53 1 44 53

Figure S279.  Get High-res Image Gene #32: 'del_1p36.23' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p32.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S280.  Gene #33: 'del_1p32.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 3(1P32.3) MUTATED 64 187 6
DEL PEAK 3(1P32.3) WILD-TYPE 465 283 85

Figure S280.  Get High-res Image Gene #33: 'del_1p32.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_1p32.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S281.  Gene #33: 'del_1p32.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 3(1P32.3) MUTATED 22 4 24 158
DEL PEAK 3(1P32.3) WILD-TYPE 155 221 64 2

Figure S281.  Get High-res Image Gene #33: 'del_1p32.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_1p32.3' versus 'RPPA_CNMF'

P value = 0.00573 (Fisher's exact test), Q value = 0.012

Table S282.  Gene #33: 'del_1p32.3' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
DEL PEAK 3(1P32.3) MUTATED 56 67 39 26
DEL PEAK 3(1P32.3) WILD-TYPE 157 101 117 83

Figure S282.  Get High-res Image Gene #33: 'del_1p32.3' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_1p32.3' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.9e-05

Table S283.  Gene #33: 'del_1p32.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
DEL PEAK 3(1P32.3) MUTATED 59 60 69
DEL PEAK 3(1P32.3) WILD-TYPE 175 194 89

Figure S283.  Get High-res Image Gene #33: 'del_1p32.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_1p32.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S284.  Gene #33: 'del_1p32.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 3(1P32.3) MUTATED 37 98 84
DEL PEAK 3(1P32.3) WILD-TYPE 207 91 143

Figure S284.  Get High-res Image Gene #33: 'del_1p32.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_1p32.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S285.  Gene #33: 'del_1p32.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 3(1P32.3) MUTATED 33 13 173
DEL PEAK 3(1P32.3) WILD-TYPE 170 177 94

Figure S285.  Get High-res Image Gene #33: 'del_1p32.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_1p32.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S286.  Gene #33: 'del_1p32.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 3(1P32.3) MUTATED 35 9 68 84
DEL PEAK 3(1P32.3) WILD-TYPE 105 98 14 96

Figure S286.  Get High-res Image Gene #33: 'del_1p32.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_1p32.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S287.  Gene #33: 'del_1p32.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 3(1P32.3) MUTATED 82 96 18
DEL PEAK 3(1P32.3) WILD-TYPE 140 88 85

Figure S287.  Get High-res Image Gene #33: 'del_1p32.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_1p32.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S288.  Gene #33: 'del_1p32.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 3(1P32.3) MUTATED 20 22 83 71
DEL PEAK 3(1P32.3) WILD-TYPE 107 97 22 83

Figure S288.  Get High-res Image Gene #33: 'del_1p32.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_1p32.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S289.  Gene #33: 'del_1p32.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 3(1P32.3) MUTATED 7 25 61 55 12 36
DEL PEAK 3(1P32.3) WILD-TYPE 92 52 57 1 51 56

Figure S289.  Get High-res Image Gene #33: 'del_1p32.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p22.1' versus 'MIR_CHIERARCHICAL'

P value = 0.00436 (Fisher's exact test), Q value = 0.0092

Table S290.  Gene #34: 'del_1p22.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
DEL PEAK 4(1P22.1) MUTATED 25 3 17
DEL PEAK 4(1P22.1) WILD-TYPE 268 121 112

Figure S290.  Get High-res Image Gene #34: 'del_1p22.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_1p22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S291.  Gene #34: 'del_1p22.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 4(1P22.1) MUTATED 47 187 0
DEL PEAK 4(1P22.1) WILD-TYPE 482 283 91

Figure S291.  Get High-res Image Gene #34: 'del_1p22.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_1p22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S292.  Gene #34: 'del_1p22.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 4(1P22.1) MUTATED 12 6 20 158
DEL PEAK 4(1P22.1) WILD-TYPE 165 219 68 2

Figure S292.  Get High-res Image Gene #34: 'del_1p22.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_1p22.1' versus 'RPPA_CNMF'

P value = 0.00676 (Fisher's exact test), Q value = 0.013

Table S293.  Gene #34: 'del_1p22.1' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
DEL PEAK 4(1P22.1) MUTATED 57 63 39 21
DEL PEAK 4(1P22.1) WILD-TYPE 156 105 117 88

Figure S293.  Get High-res Image Gene #34: 'del_1p22.1' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_1p22.1' versus 'RPPA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00016

Table S294.  Gene #34: 'del_1p22.1' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
DEL PEAK 4(1P22.1) MUTATED 56 58 66
DEL PEAK 4(1P22.1) WILD-TYPE 178 196 92

Figure S294.  Get High-res Image Gene #34: 'del_1p22.1' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_1p22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S295.  Gene #34: 'del_1p22.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 4(1P22.1) MUTATED 15 98 83
DEL PEAK 4(1P22.1) WILD-TYPE 229 91 144

Figure S295.  Get High-res Image Gene #34: 'del_1p22.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_1p22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S296.  Gene #34: 'del_1p22.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 4(1P22.1) MUTATED 11 11 174
DEL PEAK 4(1P22.1) WILD-TYPE 192 179 93

Figure S296.  Get High-res Image Gene #34: 'del_1p22.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_1p22.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S297.  Gene #34: 'del_1p22.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 4(1P22.1) MUTATED 27 8 68 83
DEL PEAK 4(1P22.1) WILD-TYPE 113 99 14 97

Figure S297.  Get High-res Image Gene #34: 'del_1p22.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_1p22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S298.  Gene #34: 'del_1p22.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 4(1P22.1) MUTATED 81 98 7
DEL PEAK 4(1P22.1) WILD-TYPE 141 86 96

Figure S298.  Get High-res Image Gene #34: 'del_1p22.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_1p22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S299.  Gene #34: 'del_1p22.1' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 4(1P22.1) MUTATED 16 18 83 69
DEL PEAK 4(1P22.1) WILD-TYPE 111 101 22 85

Figure S299.  Get High-res Image Gene #34: 'del_1p22.1' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_1p22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S300.  Gene #34: 'del_1p22.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 4(1P22.1) MUTATED 7 26 60 55 3 35
DEL PEAK 4(1P22.1) WILD-TYPE 92 51 58 1 60 57

Figure S300.  Get High-res Image Gene #34: 'del_1p22.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1q42.11' versus 'CN_CNMF'

P value = 0.00445 (Fisher's exact test), Q value = 0.0093

Table S301.  Gene #35: 'del_1q42.11' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 5(1Q42.11) MUTATED 52 21 7
DEL PEAK 5(1Q42.11) WILD-TYPE 477 449 84

Figure S301.  Get High-res Image Gene #35: 'del_1q42.11' versus Molecular Subtype #5: 'CN_CNMF'

'del_1q42.11' versus 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.00082

Table S302.  Gene #35: 'del_1q42.11' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 5(1Q42.11) MUTATED 18 18 8 1
DEL PEAK 5(1Q42.11) WILD-TYPE 159 207 80 159

Figure S302.  Get High-res Image Gene #35: 'del_1q42.11' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_1q42.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0296 (Fisher's exact test), Q value = 0.05

Table S303.  Gene #35: 'del_1q42.11' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 5(1Q42.11) MUTATED 15 17 9
DEL PEAK 5(1Q42.11) WILD-TYPE 188 173 258

Figure S303.  Get High-res Image Gene #35: 'del_1q42.11' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_1q42.11' versus 'MIRSEQ_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.022

Table S304.  Gene #35: 'del_1q42.11' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 5(1Q42.11) MUTATED 6 13 1 9
DEL PEAK 5(1Q42.11) WILD-TYPE 134 94 81 171

Figure S304.  Get High-res Image Gene #35: 'del_1q42.11' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_1q42.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0386 (Fisher's exact test), Q value = 0.063

Table S305.  Gene #35: 'del_1q42.11' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 5(1Q42.11) MUTATED 9 12 2 6
DEL PEAK 5(1Q42.11) WILD-TYPE 118 107 103 148

Figure S305.  Get High-res Image Gene #35: 'del_1q42.11' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_1q42.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0273 (Fisher's exact test), Q value = 0.047

Table S306.  Gene #35: 'del_1q42.11' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 5(1Q42.11) MUTATED 6 9 6 1 6 1
DEL PEAK 5(1Q42.11) WILD-TYPE 93 68 112 55 57 91

Figure S306.  Get High-res Image Gene #35: 'del_1q42.11' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1q44' versus 'METHLYATION_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.00085

Table S307.  Gene #36: 'del_1q44' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 6(1Q44) MUTATED 11 27 7 2
DEL PEAK 6(1Q44) WILD-TYPE 166 198 81 158

Figure S307.  Get High-res Image Gene #36: 'del_1q44' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_1q44' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00807 (Fisher's exact test), Q value = 0.016

Table S308.  Gene #36: 'del_1q44' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 6(1Q44) MUTATED 12 22 11
DEL PEAK 6(1Q44) WILD-TYPE 191 168 256

Figure S308.  Get High-res Image Gene #36: 'del_1q44' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_1q44' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0378 (Fisher's exact test), Q value = 0.062

Table S309.  Gene #36: 'del_1q44' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 6(1Q44) MUTATED 15 8 3 7
DEL PEAK 6(1Q44) WILD-TYPE 112 111 102 147

Figure S309.  Get High-res Image Gene #36: 'del_1q44' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_2q22.1' versus 'MRNA_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0011

Table S310.  Gene #37: 'del_2q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
DEL PEAK 7(2Q22.1) MUTATED 9 19 6 7
DEL PEAK 7(2Q22.1) WILD-TYPE 149 77 131 110

Figure S310.  Get High-res Image Gene #37: 'del_2q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_2q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.029 (Fisher's exact test), Q value = 0.049

Table S311.  Gene #37: 'del_2q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 7(2Q22.1) MUTATED 9 16 5 11
DEL PEAK 7(2Q22.1) WILD-TYPE 139 86 95 147

Figure S311.  Get High-res Image Gene #37: 'del_2q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 0.0486 (Fisher's exact test), Q value = 0.078

Table S312.  Gene #37: 'del_2q22.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 7(2Q22.1) MUTATED 15 14 4 3
DEL PEAK 7(2Q22.1) WILD-TYPE 162 211 84 157

Figure S312.  Get High-res Image Gene #37: 'del_2q22.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 0.0287 (Fisher's exact test), Q value = 0.048

Table S313.  Gene #37: 'del_2q22.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 7(2Q22.1) MUTATED 19 7 6
DEL PEAK 7(2Q22.1) WILD-TYPE 225 182 221

Figure S313.  Get High-res Image Gene #37: 'del_2q22.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_2q37.1' versus 'MRNA_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.032

Table S314.  Gene #38: 'del_2q37.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
DEL PEAK 8(2Q37.1) MUTATED 12 18 9 10
DEL PEAK 8(2Q37.1) WILD-TYPE 146 78 128 107

Figure S314.  Get High-res Image Gene #38: 'del_2q37.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_2q37.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00546 (Fisher's exact test), Q value = 0.011

Table S315.  Gene #38: 'del_2q37.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 8(2Q37.1) MUTATED 10 20 7 12
DEL PEAK 8(2Q37.1) WILD-TYPE 138 82 93 146

Figure S315.  Get High-res Image Gene #38: 'del_2q37.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_2q37.1' versus 'CN_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.03

Table S316.  Gene #38: 'del_2q37.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 8(2Q37.1) MUTATED 45 61 15
DEL PEAK 8(2Q37.1) WILD-TYPE 484 409 76

Figure S316.  Get High-res Image Gene #38: 'del_2q37.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_2q37.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S317.  Gene #38: 'del_2q37.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 8(2Q37.1) MUTATED 17 55 5 4
DEL PEAK 8(2Q37.1) WILD-TYPE 160 170 83 156

Figure S317.  Get High-res Image Gene #38: 'del_2q37.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_2q37.1' versus 'RPPA_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.02

Table S318.  Gene #38: 'del_2q37.1' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
DEL PEAK 8(2Q37.1) MUTATED 26 9 26 13
DEL PEAK 8(2Q37.1) WILD-TYPE 187 159 130 96

Figure S318.  Get High-res Image Gene #38: 'del_2q37.1' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_2q37.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00549 (Fisher's exact test), Q value = 0.011

Table S319.  Gene #38: 'del_2q37.1' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
DEL PEAK 8(2Q37.1) MUTATED 35 31 8
DEL PEAK 8(2Q37.1) WILD-TYPE 199 223 150

Figure S319.  Get High-res Image Gene #38: 'del_2q37.1' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_2q37.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S320.  Gene #38: 'del_2q37.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 8(2Q37.1) MUTATED 15 46 16
DEL PEAK 8(2Q37.1) WILD-TYPE 188 144 251

Figure S320.  Get High-res Image Gene #38: 'del_2q37.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.1' versus 'MIRSEQ_CNMF'

P value = 0.00189 (Fisher's exact test), Q value = 0.0044

Table S321.  Gene #38: 'del_2q37.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 8(2Q37.1) MUTATED 25 21 6 13
DEL PEAK 8(2Q37.1) WILD-TYPE 115 86 76 167

Figure S321.  Get High-res Image Gene #38: 'del_2q37.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_2q37.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0226 (Fisher's exact test), Q value = 0.039

Table S322.  Gene #38: 'del_2q37.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 8(2Q37.1) MUTATED 33 14 18
DEL PEAK 8(2Q37.1) WILD-TYPE 189 170 85

Figure S322.  Get High-res Image Gene #38: 'del_2q37.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.0017

Table S323.  Gene #38: 'del_2q37.1' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 8(2Q37.1) MUTATED 26 20 6 12
DEL PEAK 8(2Q37.1) WILD-TYPE 101 99 99 142

Figure S323.  Get High-res Image Gene #38: 'del_2q37.1' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_2q37.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00027

Table S324.  Gene #38: 'del_2q37.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 8(2Q37.1) MUTATED 19 19 6 2 5 13
DEL PEAK 8(2Q37.1) WILD-TYPE 80 58 112 54 58 79

Figure S324.  Get High-res Image Gene #38: 'del_2q37.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p21.31' versus 'METHLYATION_CNMF'

P value = 0.00127 (Fisher's exact test), Q value = 0.003

Table S325.  Gene #39: 'del_3p21.31' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 9(3P21.31) MUTATED 15 35 8 6
DEL PEAK 9(3P21.31) WILD-TYPE 162 190 80 154

Figure S325.  Get High-res Image Gene #39: 'del_3p21.31' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_3p21.31' versus 'RPPA_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.035

Table S326.  Gene #39: 'del_3p21.31' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
DEL PEAK 9(3P21.31) MUTATED 18 10 23 16
DEL PEAK 9(3P21.31) WILD-TYPE 195 158 133 93

Figure S326.  Get High-res Image Gene #39: 'del_3p21.31' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_3p21.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0425 (Fisher's exact test), Q value = 0.069

Table S327.  Gene #39: 'del_3p21.31' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
DEL PEAK 9(3P21.31) MUTATED 33 24 10
DEL PEAK 9(3P21.31) WILD-TYPE 201 230 148

Figure S327.  Get High-res Image Gene #39: 'del_3p21.31' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_3p21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0252 (Fisher's exact test), Q value = 0.043

Table S328.  Gene #39: 'del_3p21.31' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 9(3P21.31) MUTATED 23 26 17
DEL PEAK 9(3P21.31) WILD-TYPE 180 164 250

Figure S328.  Get High-res Image Gene #39: 'del_3p21.31' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_CNMF'

P value = 0.00342 (Fisher's exact test), Q value = 0.0074

Table S329.  Gene #39: 'del_3p21.31' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 9(3P21.31) MUTATED 14 20 8 9
DEL PEAK 9(3P21.31) WILD-TYPE 126 87 74 171

Figure S329.  Get High-res Image Gene #39: 'del_3p21.31' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_3p21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0026 (Fisher's exact test), Q value = 0.0059

Table S330.  Gene #39: 'del_3p21.31' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 9(3P21.31) MUTATED 24 9 18
DEL PEAK 9(3P21.31) WILD-TYPE 198 175 85

Figure S330.  Get High-res Image Gene #39: 'del_3p21.31' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0191 (Fisher's exact test), Q value = 0.034

Table S331.  Gene #39: 'del_3p21.31' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 9(3P21.31) MUTATED 12 15 6 2 6 9
DEL PEAK 9(3P21.31) WILD-TYPE 87 62 112 54 57 83

Figure S331.  Get High-res Image Gene #39: 'del_3p21.31' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q13.31' versus 'METHLYATION_CNMF'

P value = 0.0042 (Fisher's exact test), Q value = 0.0089

Table S332.  Gene #40: 'del_3q13.31' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 10(3Q13.31) MUTATED 12 27 7 4
DEL PEAK 10(3Q13.31) WILD-TYPE 165 198 81 156

Figure S332.  Get High-res Image Gene #40: 'del_3q13.31' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_3q13.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0197 (Fisher's exact test), Q value = 0.035

Table S333.  Gene #40: 'del_3q13.31' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
DEL PEAK 10(3Q13.31) MUTATED 31 16 11
DEL PEAK 10(3Q13.31) WILD-TYPE 203 238 147

Figure S333.  Get High-res Image Gene #40: 'del_3q13.31' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_3q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.046 (Fisher's exact test), Q value = 0.074

Table S334.  Gene #40: 'del_3q13.31' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 10(3Q13.31) MUTATED 15 21 13
DEL PEAK 10(3Q13.31) WILD-TYPE 188 169 254

Figure S334.  Get High-res Image Gene #40: 'del_3q13.31' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_3q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.0013

Table S335.  Gene #40: 'del_3q13.31' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 10(3Q13.31) MUTATED 16 6 17
DEL PEAK 10(3Q13.31) WILD-TYPE 206 178 86

Figure S335.  Get High-res Image Gene #40: 'del_3q13.31' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_3q29' versus 'METHLYATION_CNMF'

P value = 0.003 (Fisher's exact test), Q value = 0.0067

Table S336.  Gene #41: 'del_3q29' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 11(3Q29) MUTATED 16 31 8 5
DEL PEAK 11(3Q29) WILD-TYPE 161 194 80 155

Figure S336.  Get High-res Image Gene #41: 'del_3q29' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_3q29' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00543 (Fisher's exact test), Q value = 0.011

Table S337.  Gene #41: 'del_3q29' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 11(3Q29) MUTATED 25 26 15
DEL PEAK 11(3Q29) WILD-TYPE 178 164 252

Figure S337.  Get High-res Image Gene #41: 'del_3q29' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_3q29' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0423 (Fisher's exact test), Q value = 0.069

Table S338.  Gene #41: 'del_3q29' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 11(3Q29) MUTATED 18 12 16
DEL PEAK 11(3Q29) WILD-TYPE 204 172 87

Figure S338.  Get High-res Image Gene #41: 'del_3q29' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MRNA_CNMF'

P value = 0.00718 (Fisher's exact test), Q value = 0.014

Table S339.  Gene #42: 'del_4q34.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
DEL PEAK 12(4Q34.3) MUTATED 18 23 15 25
DEL PEAK 12(4Q34.3) WILD-TYPE 140 73 122 92

Figure S339.  Get High-res Image Gene #42: 'del_4q34.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q34.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 9e-04

Table S340.  Gene #42: 'del_4q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 12(4Q34.3) MUTATED 17 31 10 23
DEL PEAK 12(4Q34.3) WILD-TYPE 131 71 90 135

Figure S340.  Get High-res Image Gene #42: '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 = 3.7e-05

Table S341.  Gene #42: 'del_4q34.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 12(4Q34.3) MUTATED 77 139 14
DEL PEAK 12(4Q34.3) WILD-TYPE 452 331 77

Figure S341.  Get High-res Image Gene #42: 'del_4q34.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S342.  Gene #42: 'del_4q34.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 12(4Q34.3) MUTATED 25 77 8 51
DEL PEAK 12(4Q34.3) WILD-TYPE 152 148 80 109

Figure S342.  Get High-res Image Gene #42: 'del_4q34.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 0.00991 (Fisher's exact test), Q value = 0.019

Table S343.  Gene #42: 'del_4q34.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 12(4Q34.3) MUTATED 46 52 69
DEL PEAK 12(4Q34.3) WILD-TYPE 198 137 158

Figure S343.  Get High-res Image Gene #42: 'del_4q34.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.00072

Table S344.  Gene #42: 'del_4q34.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 12(4Q34.3) MUTATED 31 56 80
DEL PEAK 12(4Q34.3) WILD-TYPE 172 134 187

Figure S344.  Get High-res Image Gene #42: 'del_4q34.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CNMF'

P value = 0.0274 (Fisher's exact test), Q value = 0.047

Table S345.  Gene #42: 'del_4q34.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 12(4Q34.3) MUTATED 26 30 30 50
DEL PEAK 12(4Q34.3) WILD-TYPE 114 77 52 130

Figure S345.  Get High-res Image Gene #42: 'del_4q34.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0459 (Fisher's exact test), Q value = 0.074

Table S346.  Gene #42: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 12(4Q34.3) MUTATED 62 56 18
DEL PEAK 12(4Q34.3) WILD-TYPE 160 128 85

Figure S346.  Get High-res Image Gene #42: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 4e-04

Table S347.  Gene #42: 'del_4q34.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 12(4Q34.3) MUTATED 22 30 31 18 4 31
DEL PEAK 12(4Q34.3) WILD-TYPE 77 47 87 38 59 61

Figure S347.  Get High-res Image Gene #42: 'del_4q34.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5p15.33' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.8e-05

Table S348.  Gene #43: 'del_5p15.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
DEL PEAK 13(5P15.33) MUTATED 6 22 9 14
DEL PEAK 13(5P15.33) WILD-TYPE 152 74 128 103

Figure S348.  Get High-res Image Gene #43: 'del_5p15.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5p15.33' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00013

Table S349.  Gene #43: 'del_5p15.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 13(5P15.33) MUTATED 7 24 8 12
DEL PEAK 13(5P15.33) WILD-TYPE 141 78 92 146

Figure S349.  Get High-res Image Gene #43: 'del_5p15.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5p15.33' versus 'MIR_CNMF'

P value = 0.0068 (Fisher's exact test), Q value = 0.014

Table S350.  Gene #43: 'del_5p15.33' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
DEL PEAK 13(5P15.33) MUTATED 7 28 9 7
DEL PEAK 13(5P15.33) WILD-TYPE 136 159 81 119

Figure S350.  Get High-res Image Gene #43: 'del_5p15.33' versus Molecular Subtype #3: 'MIR_CNMF'

'del_5p15.33' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 3e-04

Table S351.  Gene #43: 'del_5p15.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 13(5P15.33) MUTATED 35 53 19
DEL PEAK 13(5P15.33) WILD-TYPE 494 417 72

Figure S351.  Get High-res Image Gene #43: 'del_5p15.33' versus Molecular Subtype #5: 'CN_CNMF'

'del_5p15.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S352.  Gene #43: 'del_5p15.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 13(5P15.33) MUTATED 16 40 4 3
DEL PEAK 13(5P15.33) WILD-TYPE 161 185 84 157

Figure S352.  Get High-res Image Gene #43: 'del_5p15.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00268 (Fisher's exact test), Q value = 0.006

Table S353.  Gene #43: 'del_5p15.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 13(5P15.33) MUTATED 20 31 17
DEL PEAK 13(5P15.33) WILD-TYPE 183 159 250

Figure S353.  Get High-res Image Gene #43: 'del_5p15.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_5p15.33' versus 'MIRSEQ_CNMF'

P value = 0.00441 (Fisher's exact test), Q value = 0.0092

Table S354.  Gene #43: 'del_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 13(5P15.33) MUTATED 10 20 3 17
DEL PEAK 13(5P15.33) WILD-TYPE 130 87 79 163

Figure S354.  Get High-res Image Gene #43: 'del_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00409 (Fisher's exact test), Q value = 0.0087

Table S355.  Gene #43: 'del_5p15.33' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 13(5P15.33) MUTATED 14 20 3 13
DEL PEAK 13(5P15.33) WILD-TYPE 113 99 102 141

Figure S355.  Get High-res Image Gene #43: 'del_5p15.33' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.8e-05

Table S356.  Gene #43: 'del_5p15.33' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 13(5P15.33) MUTATED 7 20 9 0 4 10
DEL PEAK 13(5P15.33) WILD-TYPE 92 57 109 56 59 82

Figure S356.  Get High-res Image Gene #43: 'del_5p15.33' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q34' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S357.  Gene #44: 'del_5q34' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
DEL PEAK 14(5Q34) MUTATED 8 26 12 17
DEL PEAK 14(5Q34) WILD-TYPE 150 70 125 100

Figure S357.  Get High-res Image Gene #44: 'del_5q34' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q34' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S358.  Gene #44: 'del_5q34' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 14(5Q34) MUTATED 10 31 11 11
DEL PEAK 14(5Q34) WILD-TYPE 138 71 89 147

Figure S358.  Get High-res Image Gene #44: 'del_5q34' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q34' versus 'MIR_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.9e-05

Table S359.  Gene #44: 'del_5q34' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
DEL PEAK 14(5Q34) MUTATED 5 37 9 11
DEL PEAK 14(5Q34) WILD-TYPE 138 150 81 115

Figure S359.  Get High-res Image Gene #44: 'del_5q34' versus Molecular Subtype #3: 'MIR_CNMF'

'del_5q34' versus 'MIR_CHIERARCHICAL'

P value = 0.0053 (Fisher's exact test), Q value = 0.011

Table S360.  Gene #44: 'del_5q34' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
DEL PEAK 14(5Q34) MUTATED 42 5 15
DEL PEAK 14(5Q34) WILD-TYPE 251 119 114

Figure S360.  Get High-res Image Gene #44: 'del_5q34' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_5q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S361.  Gene #44: 'del_5q34' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 14(5Q34) MUTATED 39 72 22
DEL PEAK 14(5Q34) WILD-TYPE 490 398 69

Figure S361.  Get High-res Image Gene #44: 'del_5q34' versus Molecular Subtype #5: 'CN_CNMF'

'del_5q34' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S362.  Gene #44: 'del_5q34' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 14(5Q34) MUTATED 19 54 4 3
DEL PEAK 14(5Q34) WILD-TYPE 158 171 84 157

Figure S362.  Get High-res Image Gene #44: 'del_5q34' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_5q34' versus 'MRNASEQ_CNMF'

P value = 0.00397 (Fisher's exact test), Q value = 0.0085

Table S363.  Gene #44: 'del_5q34' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 14(5Q34) MUTATED 47 19 22
DEL PEAK 14(5Q34) WILD-TYPE 197 170 205

Figure S363.  Get High-res Image Gene #44: 'del_5q34' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_5q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S364.  Gene #44: 'del_5q34' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 14(5Q34) MUTATED 24 46 18
DEL PEAK 14(5Q34) WILD-TYPE 179 144 249

Figure S364.  Get High-res Image Gene #44: 'del_5q34' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_5q34' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.8e-05

Table S365.  Gene #44: 'del_5q34' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 14(5Q34) MUTATED 14 28 4 17
DEL PEAK 14(5Q34) WILD-TYPE 126 79 78 163

Figure S365.  Get High-res Image Gene #44: 'del_5q34' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_5q34' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00159 (Fisher's exact test), Q value = 0.0038

Table S366.  Gene #44: 'del_5q34' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 14(5Q34) MUTATED 20 24 5 14
DEL PEAK 14(5Q34) WILD-TYPE 107 95 100 140

Figure S366.  Get High-res Image Gene #44: 'del_5q34' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_5q34' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S367.  Gene #44: 'del_5q34' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 14(5Q34) MUTATED 14 23 10 0 4 12
DEL PEAK 14(5Q34) WILD-TYPE 85 54 108 56 59 80

Figure S367.  Get High-res Image Gene #44: 'del_5q34' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

P value = 0.0211 (Fisher's exact test), Q value = 0.037

Table S368.  Gene #45: 'del_6p25.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 15(6P25.3) MUTATED 81 45 12
DEL PEAK 15(6P25.3) WILD-TYPE 448 425 79

Figure S368.  Get High-res Image Gene #45: 'del_6p25.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 0.038

Table S369.  Gene #45: 'del_6p25.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 15(6P25.3) MUTATED 21 28 14 8
DEL PEAK 15(6P25.3) WILD-TYPE 156 197 74 152

Figure S369.  Get High-res Image Gene #45: 'del_6p25.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_6p25.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0138 (Fisher's exact test), Q value = 0.025

Table S370.  Gene #45: 'del_6p25.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
DEL PEAK 15(6P25.3) MUTATED 42 23 19
DEL PEAK 15(6P25.3) WILD-TYPE 192 231 139

Figure S370.  Get High-res Image Gene #45: 'del_6p25.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 0.00283 (Fisher's exact test), Q value = 0.0063

Table S371.  Gene #45: 'del_6p25.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 15(6P25.3) MUTATED 43 14 22
DEL PEAK 15(6P25.3) WILD-TYPE 201 175 205

Figure S371.  Get High-res Image Gene #45: 'del_6p25.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_6p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00121 (Fisher's exact test), Q value = 0.0029

Table S372.  Gene #45: 'del_6p25.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 15(6P25.3) MUTATED 37 23 19
DEL PEAK 15(6P25.3) WILD-TYPE 166 167 248

Figure S372.  Get High-res Image Gene #45: 'del_6p25.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_6q22.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S373.  Gene #46: 'del_6q22.31' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 16(6Q22.31) MUTATED 156 71 13
DEL PEAK 16(6Q22.31) WILD-TYPE 373 399 78

Figure S373.  Get High-res Image Gene #46: 'del_6q22.31' versus Molecular Subtype #5: 'CN_CNMF'

'del_6q22.31' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.8e-05

Table S374.  Gene #46: 'del_6q22.31' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 16(6Q22.31) MUTATED 43 48 17 9
DEL PEAK 16(6Q22.31) WILD-TYPE 134 177 71 151

Figure S374.  Get High-res Image Gene #46: 'del_6q22.31' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_6q22.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.0023

Table S375.  Gene #46: 'del_6q22.31' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
DEL PEAK 16(6Q22.31) MUTATED 60 49 17
DEL PEAK 16(6Q22.31) WILD-TYPE 174 205 141

Figure S375.  Get High-res Image Gene #46: 'del_6q22.31' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_6q22.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S376.  Gene #46: 'del_6q22.31' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 16(6Q22.31) MUTATED 75 21 35
DEL PEAK 16(6Q22.31) WILD-TYPE 169 168 192

Figure S376.  Get High-res Image Gene #46: 'del_6q22.31' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_6q22.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S377.  Gene #46: 'del_6q22.31' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 16(6Q22.31) MUTATED 66 39 26
DEL PEAK 16(6Q22.31) WILD-TYPE 137 151 241

Figure S377.  Get High-res Image Gene #46: 'del_6q22.31' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_6q22.31' versus 'MIRSEQ_CNMF'

P value = 7e-04 (Fisher's exact test), Q value = 0.0018

Table S378.  Gene #46: 'del_6q22.31' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 16(6Q22.31) MUTATED 35 17 6 19
DEL PEAK 16(6Q22.31) WILD-TYPE 105 90 76 161

Figure S378.  Get High-res Image Gene #46: 'del_6q22.31' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_6q22.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00263 (Fisher's exact test), Q value = 0.0059

Table S379.  Gene #46: 'del_6q22.31' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 16(6Q22.31) MUTATED 29 21 7 18
DEL PEAK 16(6Q22.31) WILD-TYPE 98 98 98 136

Figure S379.  Get High-res Image Gene #46: 'del_6q22.31' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_6q22.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00369 (Fisher's exact test), Q value = 0.0079

Table S380.  Gene #46: 'del_6q22.31' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 16(6Q22.31) MUTATED 24 9 13 5 16 8
DEL PEAK 16(6Q22.31) WILD-TYPE 75 68 105 51 47 84

Figure S380.  Get High-res Image Gene #46: 'del_6q22.31' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S381.  Gene #47: 'del_6q26' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 17(6Q26) MUTATED 173 74 14
DEL PEAK 17(6Q26) WILD-TYPE 356 396 77

Figure S381.  Get High-res Image Gene #47: 'del_6q26' versus Molecular Subtype #5: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S382.  Gene #47: 'del_6q26' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 17(6Q26) MUTATED 50 50 16 9
DEL PEAK 17(6Q26) WILD-TYPE 127 175 72 151

Figure S382.  Get High-res Image Gene #47: 'del_6q26' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_6q26' versus 'RPPA_CNMF'

P value = 0.00963 (Fisher's exact test), Q value = 0.018

Table S383.  Gene #47: 'del_6q26' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
DEL PEAK 17(6Q26) MUTATED 58 23 39 23
DEL PEAK 17(6Q26) WILD-TYPE 155 145 117 86

Figure S383.  Get High-res Image Gene #47: 'del_6q26' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_6q26' versus 'RPPA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00016

Table S384.  Gene #47: 'del_6q26' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
DEL PEAK 17(6Q26) MUTATED 66 61 16
DEL PEAK 17(6Q26) WILD-TYPE 168 193 142

Figure S384.  Get High-res Image Gene #47: 'del_6q26' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S385.  Gene #47: 'del_6q26' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 17(6Q26) MUTATED 77 21 40
DEL PEAK 17(6Q26) WILD-TYPE 167 168 187

Figure S385.  Get High-res Image Gene #47: 'del_6q26' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S386.  Gene #47: 'del_6q26' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 17(6Q26) MUTATED 69 43 26
DEL PEAK 17(6Q26) WILD-TYPE 134 147 241

Figure S386.  Get High-res Image Gene #47: 'del_6q26' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S387.  Gene #47: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 17(6Q26) MUTATED 40 16 5 20
DEL PEAK 17(6Q26) WILD-TYPE 100 91 77 160

Figure S387.  Get High-res Image Gene #47: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0033 (Fisher's exact test), Q value = 0.0072

Table S388.  Gene #47: 'del_6q26' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 17(6Q26) MUTATED 29 22 7 20
DEL PEAK 17(6Q26) WILD-TYPE 98 97 98 134

Figure S388.  Get High-res Image Gene #47: 'del_6q26' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.00092

Table S389.  Gene #47: 'del_6q26' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 17(6Q26) MUTATED 27 7 13 5 17 9
DEL PEAK 17(6Q26) WILD-TYPE 72 70 105 51 46 83

Figure S389.  Get High-res Image Gene #47: 'del_6q26' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00022

Table S390.  Gene #48: 'del_8p23.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 18(8P23.2) MUTATED 60 19 9
DEL PEAK 18(8P23.2) WILD-TYPE 469 451 82

Figure S390.  Get High-res Image Gene #48: 'del_8p23.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S391.  Gene #48: 'del_8p23.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 18(8P23.2) MUTATED 23 11 1 0
DEL PEAK 18(8P23.2) WILD-TYPE 154 214 87 160

Figure S391.  Get High-res Image Gene #48: 'del_8p23.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S392.  Gene #48: 'del_8p23.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 18(8P23.2) MUTATED 27 6 3
DEL PEAK 18(8P23.2) WILD-TYPE 217 183 224

Figure S392.  Get High-res Image Gene #48: 'del_8p23.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.00072

Table S393.  Gene #48: 'del_8p23.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 18(8P23.2) MUTATED 22 8 6
DEL PEAK 18(8P23.2) WILD-TYPE 181 182 261

Figure S393.  Get High-res Image Gene #48: 'del_8p23.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00782 (Fisher's exact test), Q value = 0.015

Table S394.  Gene #48: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 18(8P23.2) MUTATED 9 3 10
DEL PEAK 18(8P23.2) WILD-TYPE 213 181 93

Figure S394.  Get High-res Image Gene #48: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00525 (Fisher's exact test), Q value = 0.011

Table S395.  Gene #48: 'del_8p23.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 18(8P23.2) MUTATED 3 12 1 5
DEL PEAK 18(8P23.2) WILD-TYPE 124 107 104 149

Figure S395.  Get High-res Image Gene #48: 'del_8p23.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.8e-05

Table S396.  Gene #48: 'del_8p23.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 18(8P23.2) MUTATED 1 8 3 0 9 0
DEL PEAK 18(8P23.2) WILD-TYPE 98 69 115 56 54 92

Figure S396.  Get High-res Image Gene #48: 'del_8p23.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8q24.3' versus 'MIR_CNMF'

P value = 0.00756 (Fisher's exact test), Q value = 0.015

Table S397.  Gene #49: 'del_8q24.3' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
DEL PEAK 19(8Q24.3) MUTATED 23 15 8 5
DEL PEAK 19(8Q24.3) WILD-TYPE 120 172 82 121

Figure S397.  Get High-res Image Gene #49: 'del_8q24.3' versus Molecular Subtype #3: 'MIR_CNMF'

'del_8q24.3' versus 'CN_CNMF'

P value = 0.00144 (Fisher's exact test), Q value = 0.0034

Table S398.  Gene #49: 'del_8q24.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 19(8Q24.3) MUTATED 52 19 7
DEL PEAK 19(8Q24.3) WILD-TYPE 477 451 84

Figure S398.  Get High-res Image Gene #49: 'del_8q24.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_8q24.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.8e-05

Table S399.  Gene #49: 'del_8q24.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 19(8Q24.3) MUTATED 20 16 2 0
DEL PEAK 19(8Q24.3) WILD-TYPE 157 209 86 160

Figure S399.  Get High-res Image Gene #49: 'del_8q24.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_8q24.3' versus 'MRNASEQ_CNMF'

P value = 0.043 (Fisher's exact test), Q value = 0.07

Table S400.  Gene #49: 'del_8q24.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 19(8Q24.3) MUTATED 22 7 10
DEL PEAK 19(8Q24.3) WILD-TYPE 222 182 217

Figure S400.  Get High-res Image Gene #49: 'del_8q24.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_8q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00391 (Fisher's exact test), Q value = 0.0084

Table S401.  Gene #49: 'del_8q24.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 19(8Q24.3) MUTATED 20 12 7
DEL PEAK 19(8Q24.3) WILD-TYPE 183 178 260

Figure S401.  Get High-res Image Gene #49: 'del_8q24.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_8q24.3' versus 'MIRSEQ_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.069

Table S402.  Gene #49: 'del_8q24.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 19(8Q24.3) MUTATED 11 9 1 6
DEL PEAK 19(8Q24.3) WILD-TYPE 129 98 81 174

Figure S402.  Get High-res Image Gene #49: 'del_8q24.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_8q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0012 (Fisher's exact test), Q value = 0.0029

Table S403.  Gene #49: 'del_8q24.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 19(8Q24.3) MUTATED 10 4 13
DEL PEAK 19(8Q24.3) WILD-TYPE 212 180 90

Figure S403.  Get High-res Image Gene #49: 'del_8q24.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_8q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 0.042

Table S404.  Gene #49: 'del_8q24.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 19(8Q24.3) MUTATED 9 11 2 4
DEL PEAK 19(8Q24.3) WILD-TYPE 118 108 103 150

Figure S404.  Get High-res Image Gene #49: 'del_8q24.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_8q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.026

Table S405.  Gene #49: 'del_8q24.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 19(8Q24.3) MUTATED 6 5 2 0 8 5
DEL PEAK 19(8Q24.3) WILD-TYPE 93 72 116 56 55 87

Figure S405.  Get High-res Image Gene #49: 'del_8q24.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.8e-05

Table S406.  Gene #50: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
DEL PEAK 20(9P21.3) MUTATED 107 62 121 78
DEL PEAK 20(9P21.3) WILD-TYPE 51 34 16 39

Figure S406.  Get High-res Image Gene #50: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p21.3' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.8e-05

Table S407.  Gene #50: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 20(9P21.3) MUTATED 102 60 91 115
DEL PEAK 20(9P21.3) WILD-TYPE 46 42 9 43

Figure S407.  Get High-res Image Gene #50: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p21.3' versus 'MIR_CHIERARCHICAL'

P value = 0.03 (Fisher's exact test), Q value = 0.05

Table S408.  Gene #50: 'del_9p21.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
DEL PEAK 20(9P21.3) MUTATED 198 96 101
DEL PEAK 20(9P21.3) WILD-TYPE 95 28 28

Figure S408.  Get High-res Image Gene #50: 'del_9p21.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S409.  Gene #50: 'del_9p21.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 20(9P21.3) MUTATED 406 147 42
DEL PEAK 20(9P21.3) WILD-TYPE 123 323 49

Figure S409.  Get High-res Image Gene #50: 'del_9p21.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S410.  Gene #50: 'del_9p21.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 20(9P21.3) MUTATED 138 91 25 29
DEL PEAK 20(9P21.3) WILD-TYPE 39 134 63 131

Figure S410.  Get High-res Image Gene #50: 'del_9p21.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00024

Table S411.  Gene #50: 'del_9p21.3' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
DEL PEAK 20(9P21.3) MUTATED 112 63 98 49
DEL PEAK 20(9P21.3) WILD-TYPE 101 105 58 60

Figure S411.  Get High-res Image Gene #50: 'del_9p21.3' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S412.  Gene #50: 'del_9p21.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
DEL PEAK 20(9P21.3) MUTATED 143 127 52
DEL PEAK 20(9P21.3) WILD-TYPE 91 127 106

Figure S412.  Get High-res Image Gene #50: 'del_9p21.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S413.  Gene #50: 'del_9p21.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 20(9P21.3) MUTATED 163 57 58
DEL PEAK 20(9P21.3) WILD-TYPE 81 132 169

Figure S413.  Get High-res Image Gene #50: 'del_9p21.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S414.  Gene #50: 'del_9p21.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 20(9P21.3) MUTATED 144 65 69
DEL PEAK 20(9P21.3) WILD-TYPE 59 125 198

Figure S414.  Get High-res Image Gene #50: 'del_9p21.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S415.  Gene #50: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 20(9P21.3) MUTATED 59 56 59
DEL PEAK 20(9P21.3) WILD-TYPE 163 128 44

Figure S415.  Get High-res Image Gene #50: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00086 (Fisher's exact test), Q value = 0.0022

Table S416.  Gene #50: 'del_9p21.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 20(9P21.3) MUTATED 48 55 23 47
DEL PEAK 20(9P21.3) WILD-TYPE 79 64 82 107

Figure S416.  Get High-res Image Gene #50: 'del_9p21.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S417.  Gene #50: 'del_9p21.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 20(9P21.3) MUTATED 32 26 36 8 44 27
DEL PEAK 20(9P21.3) WILD-TYPE 67 51 82 48 19 65

Figure S417.  Get High-res Image Gene #50: 'del_9p21.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p15.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S418.  Gene #51: 'del_10p15.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
DEL PEAK 21(10P15.3) MUTATED 136 61 125 86
DEL PEAK 21(10P15.3) WILD-TYPE 22 35 12 31

Figure S418.  Get High-res Image Gene #51: 'del_10p15.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10p15.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S419.  Gene #51: 'del_10p15.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 21(10P15.3) MUTATED 125 59 89 135
DEL PEAK 21(10P15.3) WILD-TYPE 23 43 11 23

Figure S419.  Get High-res Image Gene #51: 'del_10p15.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10p15.3' versus 'MIR_CNMF'

P value = 0.023 (Fisher's exact test), Q value = 0.04

Table S420.  Gene #51: 'del_10p15.3' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
DEL PEAK 21(10P15.3) MUTATED 127 142 71 103
DEL PEAK 21(10P15.3) WILD-TYPE 16 45 19 23

Figure S420.  Get High-res Image Gene #51: 'del_10p15.3' versus Molecular Subtype #3: 'MIR_CNMF'

'del_10p15.3' versus 'MIR_CHIERARCHICAL'

P value = 0.00334 (Fisher's exact test), Q value = 0.0073

Table S421.  Gene #51: 'del_10p15.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
DEL PEAK 21(10P15.3) MUTATED 223 105 115
DEL PEAK 21(10P15.3) WILD-TYPE 70 19 14

Figure S421.  Get High-res Image Gene #51: 'del_10p15.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S422.  Gene #51: 'del_10p15.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 21(10P15.3) MUTATED 468 25 60
DEL PEAK 21(10P15.3) WILD-TYPE 61 445 31

Figure S422.  Get High-res Image Gene #51: 'del_10p15.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S423.  Gene #51: 'del_10p15.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 21(10P15.3) MUTATED 162 8 27 7
DEL PEAK 21(10P15.3) WILD-TYPE 15 217 61 153

Figure S423.  Get High-res Image Gene #51: 'del_10p15.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_10p15.3' versus 'RPPA_CNMF'

P value = 0.00302 (Fisher's exact test), Q value = 0.0067

Table S424.  Gene #51: 'del_10p15.3' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
DEL PEAK 21(10P15.3) MUTATED 86 49 75 36
DEL PEAK 21(10P15.3) WILD-TYPE 127 119 81 73

Figure S424.  Get High-res Image Gene #51: 'del_10p15.3' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_10p15.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00074 (Fisher's exact test), Q value = 0.0019

Table S425.  Gene #51: 'del_10p15.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
DEL PEAK 21(10P15.3) MUTATED 98 108 40
DEL PEAK 21(10P15.3) WILD-TYPE 136 146 118

Figure S425.  Get High-res Image Gene #51: 'del_10p15.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S426.  Gene #51: 'del_10p15.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 21(10P15.3) MUTATED 186 21 3
DEL PEAK 21(10P15.3) WILD-TYPE 58 168 224

Figure S426.  Get High-res Image Gene #51: 'del_10p15.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S427.  Gene #51: 'del_10p15.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 21(10P15.3) MUTATED 178 9 23
DEL PEAK 21(10P15.3) WILD-TYPE 25 181 244

Figure S427.  Get High-res Image Gene #51: 'del_10p15.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.00092

Table S428.  Gene #51: 'del_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 21(10P15.3) MUTATED 32 26 6 19
DEL PEAK 21(10P15.3) WILD-TYPE 108 81 76 161

Figure S428.  Get High-res Image Gene #51: 'del_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_10p15.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S429.  Gene #51: 'del_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 21(10P15.3) MUTATED 11 13 59
DEL PEAK 21(10P15.3) WILD-TYPE 211 171 44

Figure S429.  Get High-res Image Gene #51: 'del_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S430.  Gene #51: 'del_10p15.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 21(10P15.3) MUTATED 26 37 3 17
DEL PEAK 21(10P15.3) WILD-TYPE 101 82 102 137

Figure S430.  Get High-res Image Gene #51: 'del_10p15.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_10p15.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S431.  Gene #51: 'del_10p15.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 21(10P15.3) MUTATED 4 8 12 1 54 4
DEL PEAK 21(10P15.3) WILD-TYPE 95 69 106 55 9 88

Figure S431.  Get High-res Image Gene #51: 'del_10p15.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p13' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S432.  Gene #52: 'del_10p13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
DEL PEAK 22(10P13) MUTATED 139 63 125 83
DEL PEAK 22(10P13) WILD-TYPE 19 33 12 34

Figure S432.  Get High-res Image Gene #52: 'del_10p13' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10p13' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S433.  Gene #52: 'del_10p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 22(10P13) MUTATED 129 58 89 134
DEL PEAK 22(10P13) WILD-TYPE 19 44 11 24

Figure S433.  Get High-res Image Gene #52: 'del_10p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10p13' versus 'MIR_CNMF'

P value = 0.0049 (Fisher's exact test), Q value = 0.01

Table S434.  Gene #52: 'del_10p13' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
DEL PEAK 22(10P13) MUTATED 129 143 69 105
DEL PEAK 22(10P13) WILD-TYPE 14 44 21 21

Figure S434.  Get High-res Image Gene #52: 'del_10p13' versus Molecular Subtype #3: 'MIR_CNMF'

'del_10p13' versus 'MIR_CHIERARCHICAL'

P value = 0.00112 (Fisher's exact test), Q value = 0.0027

Table S435.  Gene #52: 'del_10p13' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
DEL PEAK 22(10P13) MUTATED 223 108 115
DEL PEAK 22(10P13) WILD-TYPE 70 16 14

Figure S435.  Get High-res Image Gene #52: 'del_10p13' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_10p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S436.  Gene #52: 'del_10p13' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 22(10P13) MUTATED 471 23 59
DEL PEAK 22(10P13) WILD-TYPE 58 447 32

Figure S436.  Get High-res Image Gene #52: 'del_10p13' versus Molecular Subtype #5: 'CN_CNMF'

'del_10p13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S437.  Gene #52: 'del_10p13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 22(10P13) MUTATED 162 6 27 7
DEL PEAK 22(10P13) WILD-TYPE 15 219 61 153

Figure S437.  Get High-res Image Gene #52: 'del_10p13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_10p13' versus 'RPPA_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.0026

Table S438.  Gene #52: 'del_10p13' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
DEL PEAK 22(10P13) MUTATED 88 45 73 37
DEL PEAK 22(10P13) WILD-TYPE 125 123 83 72

Figure S438.  Get High-res Image Gene #52: 'del_10p13' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_10p13' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.8e-05

Table S439.  Gene #52: 'del_10p13' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
DEL PEAK 22(10P13) MUTATED 99 108 36
DEL PEAK 22(10P13) WILD-TYPE 135 146 122

Figure S439.  Get High-res Image Gene #52: 'del_10p13' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_10p13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S440.  Gene #52: 'del_10p13' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 22(10P13) MUTATED 186 20 3
DEL PEAK 22(10P13) WILD-TYPE 58 169 224

Figure S440.  Get High-res Image Gene #52: 'del_10p13' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_10p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S441.  Gene #52: 'del_10p13' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 22(10P13) MUTATED 178 9 22
DEL PEAK 22(10P13) WILD-TYPE 25 181 245

Figure S441.  Get High-res Image Gene #52: 'del_10p13' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_10p13' versus 'MIRSEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00054

Table S442.  Gene #52: 'del_10p13' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 22(10P13) MUTATED 32 26 6 18
DEL PEAK 22(10P13) WILD-TYPE 108 81 76 162

Figure S442.  Get High-res Image Gene #52: 'del_10p13' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_10p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S443.  Gene #52: 'del_10p13' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 22(10P13) MUTATED 11 11 60
DEL PEAK 22(10P13) WILD-TYPE 211 173 43

Figure S443.  Get High-res Image Gene #52: 'del_10p13' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_10p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S444.  Gene #52: 'del_10p13' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 22(10P13) MUTATED 26 37 3 16
DEL PEAK 22(10P13) WILD-TYPE 101 82 102 138

Figure S444.  Get High-res Image Gene #52: 'del_10p13' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_10p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S445.  Gene #52: 'del_10p13' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 22(10P13) MUTATED 4 7 11 1 55 4
DEL PEAK 22(10P13) WILD-TYPE 95 70 107 55 8 88

Figure S445.  Get High-res Image Gene #52: 'del_10p13' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.9e-05

Table S446.  Gene #53: 'del_10q23.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
DEL PEAK 23(10Q23.31) MUTATED 146 76 132 95
DEL PEAK 23(10Q23.31) WILD-TYPE 12 20 5 22

Figure S446.  Get High-res Image Gene #53: 'del_10q23.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q23.31' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S447.  Gene #53: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 23(10Q23.31) MUTATED 132 75 98 144
DEL PEAK 23(10Q23.31) WILD-TYPE 16 27 2 14

Figure S447.  Get High-res Image Gene #53: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q23.31' versus 'MIR_CNMF'

P value = 0.0341 (Fisher's exact test), Q value = 0.057

Table S448.  Gene #53: 'del_10q23.31' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
DEL PEAK 23(10Q23.31) MUTATED 135 162 75 113
DEL PEAK 23(10Q23.31) WILD-TYPE 8 25 15 13

Figure S448.  Get High-res Image Gene #53: 'del_10q23.31' versus Molecular Subtype #3: 'MIR_CNMF'

'del_10q23.31' versus 'MIR_CHIERARCHICAL'

P value = 0.00304 (Fisher's exact test), Q value = 0.0067

Table S449.  Gene #53: 'del_10q23.31' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
DEL PEAK 23(10Q23.31) MUTATED 248 115 122
DEL PEAK 23(10Q23.31) WILD-TYPE 45 9 7

Figure S449.  Get High-res Image Gene #53: 'del_10q23.31' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S450.  Gene #53: 'del_10q23.31' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 23(10Q23.31) MUTATED 496 63 69
DEL PEAK 23(10Q23.31) WILD-TYPE 33 407 22

Figure S450.  Get High-res Image Gene #53: 'del_10q23.31' versus Molecular Subtype #5: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S451.  Gene #53: 'del_10q23.31' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 23(10Q23.31) MUTATED 169 37 27 8
DEL PEAK 23(10Q23.31) WILD-TYPE 8 188 61 152

Figure S451.  Get High-res Image Gene #53: 'del_10q23.31' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S452.  Gene #53: 'del_10q23.31' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
DEL PEAK 23(10Q23.31) MUTATED 105 51 91 41
DEL PEAK 23(10Q23.31) WILD-TYPE 108 117 65 68

Figure S452.  Get High-res Image Gene #53: 'del_10q23.31' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_10q23.31' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S453.  Gene #53: 'del_10q23.31' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
DEL PEAK 23(10Q23.31) MUTATED 123 123 42
DEL PEAK 23(10Q23.31) WILD-TYPE 111 131 116

Figure S453.  Get High-res Image Gene #53: 'del_10q23.31' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S454.  Gene #53: 'del_10q23.31' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 23(10Q23.31) MUTATED 202 26 20
DEL PEAK 23(10Q23.31) WILD-TYPE 42 163 207

Figure S454.  Get High-res Image Gene #53: 'del_10q23.31' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S455.  Gene #53: 'del_10q23.31' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 23(10Q23.31) MUTATED 186 32 30
DEL PEAK 23(10Q23.31) WILD-TYPE 17 158 237

Figure S455.  Get High-res Image Gene #53: 'del_10q23.31' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00027

Table S456.  Gene #53: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 23(10Q23.31) MUTATED 39 37 9 29
DEL PEAK 23(10Q23.31) WILD-TYPE 101 70 73 151

Figure S456.  Get High-res Image Gene #53: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S457.  Gene #53: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 23(10Q23.31) MUTATED 24 18 72
DEL PEAK 23(10Q23.31) WILD-TYPE 198 166 31

Figure S457.  Get High-res Image Gene #53: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S458.  Gene #53: 'del_10q23.31' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 23(10Q23.31) MUTATED 36 46 10 22
DEL PEAK 23(10Q23.31) WILD-TYPE 91 73 95 132

Figure S458.  Get High-res Image Gene #53: 'del_10q23.31' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S459.  Gene #53: 'del_10q23.31' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 23(10Q23.31) MUTATED 11 16 14 2 56 15
DEL PEAK 23(10Q23.31) WILD-TYPE 88 61 104 54 7 77

Figure S459.  Get High-res Image Gene #53: 'del_10q23.31' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q26.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S460.  Gene #54: 'del_10q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
DEL PEAK 24(10Q26.3) MUTATED 145 75 135 95
DEL PEAK 24(10Q26.3) WILD-TYPE 13 21 2 22

Figure S460.  Get High-res Image Gene #54: 'del_10q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q26.3' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00013

Table S461.  Gene #54: 'del_10q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 24(10Q26.3) MUTATED 132 77 97 144
DEL PEAK 24(10Q26.3) WILD-TYPE 16 25 3 14

Figure S461.  Get High-res Image Gene #54: 'del_10q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q26.3' versus 'MIR_CHIERARCHICAL'

P value = 0.00142 (Fisher's exact test), Q value = 0.0034

Table S462.  Gene #54: 'del_10q26.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
DEL PEAK 24(10Q26.3) MUTATED 252 109 125
DEL PEAK 24(10Q26.3) WILD-TYPE 41 15 4

Figure S462.  Get High-res Image Gene #54: 'del_10q26.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_10q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S463.  Gene #54: 'del_10q26.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 24(10Q26.3) MUTATED 499 98 68
DEL PEAK 24(10Q26.3) WILD-TYPE 30 372 23

Figure S463.  Get High-res Image Gene #54: 'del_10q26.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_10q26.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S464.  Gene #54: 'del_10q26.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 24(10Q26.3) MUTATED 169 70 30 9
DEL PEAK 24(10Q26.3) WILD-TYPE 8 155 58 151

Figure S464.  Get High-res Image Gene #54: 'del_10q26.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_10q26.3' versus 'RPPA_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 3e-04

Table S465.  Gene #54: 'del_10q26.3' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
DEL PEAK 24(10Q26.3) MUTATED 114 61 94 48
DEL PEAK 24(10Q26.3) WILD-TYPE 99 107 62 61

Figure S465.  Get High-res Image Gene #54: 'del_10q26.3' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_10q26.3' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.8e-05

Table S466.  Gene #54: 'del_10q26.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
DEL PEAK 24(10Q26.3) MUTATED 133 133 51
DEL PEAK 24(10Q26.3) WILD-TYPE 101 121 107

Figure S466.  Get High-res Image Gene #54: 'del_10q26.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S467.  Gene #54: 'del_10q26.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 24(10Q26.3) MUTATED 207 36 41
DEL PEAK 24(10Q26.3) WILD-TYPE 37 153 186

Figure S467.  Get High-res Image Gene #54: 'del_10q26.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S468.  Gene #54: 'del_10q26.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 24(10Q26.3) MUTATED 185 59 40
DEL PEAK 24(10Q26.3) WILD-TYPE 18 131 227

Figure S468.  Get High-res Image Gene #54: 'del_10q26.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S469.  Gene #54: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 24(10Q26.3) MUTATED 55 46 11 38
DEL PEAK 24(10Q26.3) WILD-TYPE 85 61 71 142

Figure S469.  Get High-res Image Gene #54: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_10q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S470.  Gene #54: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 24(10Q26.3) MUTATED 49 28 73
DEL PEAK 24(10Q26.3) WILD-TYPE 173 156 30

Figure S470.  Get High-res Image Gene #54: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S471.  Gene #54: 'del_10q26.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 24(10Q26.3) MUTATED 56 51 12 31
DEL PEAK 24(10Q26.3) WILD-TYPE 71 68 93 123

Figure S471.  Get High-res Image Gene #54: 'del_10q26.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_10q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S472.  Gene #54: 'del_10q26.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 24(10Q26.3) MUTATED 28 23 20 3 55 21
DEL PEAK 24(10Q26.3) WILD-TYPE 71 54 98 53 8 71

Figure S472.  Get High-res Image Gene #54: 'del_10q26.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S473.  Gene #55: 'del_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
DEL PEAK 25(11P15.5) MUTATED 32 42 12 32
DEL PEAK 25(11P15.5) WILD-TYPE 126 54 125 85

Figure S473.  Get High-res Image Gene #55: 'del_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11p15.5' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S474.  Gene #55: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 25(11P15.5) MUTATED 30 48 9 31
DEL PEAK 25(11P15.5) WILD-TYPE 118 54 91 127

Figure S474.  Get High-res Image Gene #55: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11p15.5' versus 'MIR_CHIERARCHICAL'

P value = 0.00175 (Fisher's exact test), Q value = 0.0041

Table S475.  Gene #55: 'del_11p15.5' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
DEL PEAK 25(11P15.5) MUTATED 84 23 18
DEL PEAK 25(11P15.5) WILD-TYPE 209 101 111

Figure S475.  Get High-res Image Gene #55: 'del_11p15.5' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S476.  Gene #55: 'del_11p15.5' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 25(11P15.5) MUTATED 89 104 41
DEL PEAK 25(11P15.5) WILD-TYPE 440 366 50

Figure S476.  Get High-res Image Gene #55: 'del_11p15.5' versus Molecular Subtype #5: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S477.  Gene #55: 'del_11p15.5' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 25(11P15.5) MUTATED 23 89 11 1
DEL PEAK 25(11P15.5) WILD-TYPE 154 136 77 159

Figure S477.  Get High-res Image Gene #55: 'del_11p15.5' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 0.0468 (Fisher's exact test), Q value = 0.075

Table S478.  Gene #55: 'del_11p15.5' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 25(11P15.5) MUTATED 63 31 44
DEL PEAK 25(11P15.5) WILD-TYPE 181 158 183

Figure S478.  Get High-res Image Gene #55: 'del_11p15.5' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S479.  Gene #55: 'del_11p15.5' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 25(11P15.5) MUTATED 35 72 31
DEL PEAK 25(11P15.5) WILD-TYPE 168 118 236

Figure S479.  Get High-res Image Gene #55: 'del_11p15.5' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.8e-05

Table S480.  Gene #55: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 25(11P15.5) MUTATED 24 40 7 34
DEL PEAK 25(11P15.5) WILD-TYPE 116 67 75 146

Figure S480.  Get High-res Image Gene #55: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00559 (Fisher's exact test), Q value = 0.011

Table S481.  Gene #55: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 25(11P15.5) MUTATED 43 29 33
DEL PEAK 25(11P15.5) WILD-TYPE 179 155 70

Figure S481.  Get High-res Image Gene #55: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00453 (Fisher's exact test), Q value = 0.0094

Table S482.  Gene #55: 'del_11p15.5' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 25(11P15.5) MUTATED 35 30 11 28
DEL PEAK 25(11P15.5) WILD-TYPE 92 89 94 126

Figure S482.  Get High-res Image Gene #55: 'del_11p15.5' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S483.  Gene #55: 'del_11p15.5' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 25(11P15.5) MUTATED 22 32 19 0 9 22
DEL PEAK 25(11P15.5) WILD-TYPE 77 45 99 56 54 70

Figure S483.  Get High-res Image Gene #55: 'del_11p15.5' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S484.  Gene #56: 'del_11p15.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
DEL PEAK 26(11P15.1) MUTATED 28 35 7 24
DEL PEAK 26(11P15.1) WILD-TYPE 130 61 130 93

Figure S484.  Get High-res Image Gene #56: 'del_11p15.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11p15.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S485.  Gene #56: 'del_11p15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 26(11P15.1) MUTATED 27 37 4 26
DEL PEAK 26(11P15.1) WILD-TYPE 121 65 96 132

Figure S485.  Get High-res Image Gene #56: 'del_11p15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11p15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S486.  Gene #56: 'del_11p15.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 26(11P15.1) MUTATED 73 65 38
DEL PEAK 26(11P15.1) WILD-TYPE 456 405 53

Figure S486.  Get High-res Image Gene #56: 'del_11p15.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_11p15.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S487.  Gene #56: 'del_11p15.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 26(11P15.1) MUTATED 21 57 9 1
DEL PEAK 26(11P15.1) WILD-TYPE 156 168 79 159

Figure S487.  Get High-res Image Gene #56: 'del_11p15.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_11p15.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S488.  Gene #56: 'del_11p15.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 26(11P15.1) MUTATED 58 18 24
DEL PEAK 26(11P15.1) WILD-TYPE 186 171 203

Figure S488.  Get High-res Image Gene #56: 'del_11p15.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_11p15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S489.  Gene #56: 'del_11p15.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 26(11P15.1) MUTATED 34 49 17
DEL PEAK 26(11P15.1) WILD-TYPE 169 141 250

Figure S489.  Get High-res Image Gene #56: 'del_11p15.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.1' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.9e-05

Table S490.  Gene #56: 'del_11p15.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 26(11P15.1) MUTATED 16 32 5 19
DEL PEAK 26(11P15.1) WILD-TYPE 124 75 77 161

Figure S490.  Get High-res Image Gene #56: 'del_11p15.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_11p15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00027

Table S491.  Gene #56: 'del_11p15.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 26(11P15.1) MUTATED 27 16 29
DEL PEAK 26(11P15.1) WILD-TYPE 195 168 74

Figure S491.  Get High-res Image Gene #56: 'del_11p15.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 9e-04 (Fisher's exact test), Q value = 0.0022

Table S492.  Gene #56: 'del_11p15.1' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 26(11P15.1) MUTATED 22 27 6 16
DEL PEAK 26(11P15.1) WILD-TYPE 105 92 99 138

Figure S492.  Get High-res Image Gene #56: 'del_11p15.1' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_11p15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S493.  Gene #56: 'del_11p15.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 26(11P15.1) MUTATED 13 29 11 0 9 9
DEL PEAK 26(11P15.1) WILD-TYPE 86 48 107 56 54 83

Figure S493.  Get High-res Image Gene #56: 'del_11p15.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p11.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S494.  Gene #57: 'del_11p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
DEL PEAK 27(11P11.2) MUTATED 27 35 9 24
DEL PEAK 27(11P11.2) WILD-TYPE 131 61 128 93

Figure S494.  Get High-res Image Gene #57: 'del_11p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S495.  Gene #57: 'del_11p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 27(11P11.2) MUTATED 27 36 5 27
DEL PEAK 27(11P11.2) WILD-TYPE 121 66 95 131

Figure S495.  Get High-res Image Gene #57: 'del_11p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11p11.2' versus 'MIR_CHIERARCHICAL'

P value = 0.0187 (Fisher's exact test), Q value = 0.033

Table S496.  Gene #57: 'del_11p11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
DEL PEAK 27(11P11.2) MUTATED 65 22 14
DEL PEAK 27(11P11.2) WILD-TYPE 228 102 115

Figure S496.  Get High-res Image Gene #57: 'del_11p11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_11p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S497.  Gene #57: 'del_11p11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 27(11P11.2) MUTATED 78 42 39
DEL PEAK 27(11P11.2) WILD-TYPE 451 428 52

Figure S497.  Get High-res Image Gene #57: 'del_11p11.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_11p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S498.  Gene #57: 'del_11p11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 27(11P11.2) MUTATED 24 39 7 0
DEL PEAK 27(11P11.2) WILD-TYPE 153 186 81 160

Figure S498.  Get High-res Image Gene #57: 'del_11p11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_11p11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S499.  Gene #57: 'del_11p11.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 27(11P11.2) MUTATED 53 12 15
DEL PEAK 27(11P11.2) WILD-TYPE 191 177 212

Figure S499.  Get High-res Image Gene #57: 'del_11p11.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_11p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S500.  Gene #57: 'del_11p11.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 27(11P11.2) MUTATED 34 35 11
DEL PEAK 27(11P11.2) WILD-TYPE 169 155 256

Figure S500.  Get High-res Image Gene #57: 'del_11p11.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_11p11.2' versus 'MIRSEQ_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0013

Table S501.  Gene #57: 'del_11p11.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 27(11P11.2) MUTATED 11 24 4 15
DEL PEAK 27(11P11.2) WILD-TYPE 129 83 78 165

Figure S501.  Get High-res Image Gene #57: 'del_11p11.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_11p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S502.  Gene #57: 'del_11p11.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 27(11P11.2) MUTATED 18 10 26
DEL PEAK 27(11P11.2) WILD-TYPE 204 174 77

Figure S502.  Get High-res Image Gene #57: 'del_11p11.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_11p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00692 (Fisher's exact test), Q value = 0.014

Table S503.  Gene #57: 'del_11p11.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 27(11P11.2) MUTATED 19 18 4 12
DEL PEAK 27(11P11.2) WILD-TYPE 108 101 101 142

Figure S503.  Get High-res Image Gene #57: 'del_11p11.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_11p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.8e-05

Table S504.  Gene #57: 'del_11p11.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 27(11P11.2) MUTATED 8 20 9 0 11 5
DEL PEAK 27(11P11.2) WILD-TYPE 91 57 109 56 52 87

Figure S504.  Get High-res Image Gene #57: 'del_11p11.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12p13.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.026

Table S505.  Gene #58: 'del_12p13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 28(12P13.1) MUTATED 17 20 5 22
DEL PEAK 28(12P13.1) WILD-TYPE 131 82 95 136

Figure S505.  Get High-res Image Gene #58: 'del_12p13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12p13.1' versus 'CN_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.021

Table S506.  Gene #58: 'del_12p13.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 28(12P13.1) MUTATED 50 42 18
DEL PEAK 28(12P13.1) WILD-TYPE 479 428 73

Figure S506.  Get High-res Image Gene #58: 'del_12p13.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 0.00411 (Fisher's exact test), Q value = 0.0087

Table S507.  Gene #58: 'del_12p13.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 28(12P13.1) MUTATED 15 29 5 5
DEL PEAK 28(12P13.1) WILD-TYPE 162 196 83 155

Figure S507.  Get High-res Image Gene #58: 'del_12p13.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00172 (Fisher's exact test), Q value = 0.004

Table S508.  Gene #58: 'del_12p13.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 28(12P13.1) MUTATED 18 25 11
DEL PEAK 28(12P13.1) WILD-TYPE 185 165 256

Figure S508.  Get High-res Image Gene #58: 'del_12p13.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.039

Table S509.  Gene #58: 'del_12p13.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 28(12P13.1) MUTATED 7 16 5 10
DEL PEAK 28(12P13.1) WILD-TYPE 133 91 77 170

Figure S509.  Get High-res Image Gene #58: 'del_12p13.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_12p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0445 (Fisher's exact test), Q value = 0.072

Table S510.  Gene #58: 'del_12p13.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 28(12P13.1) MUTATED 13 11 14
DEL PEAK 28(12P13.1) WILD-TYPE 209 173 89

Figure S510.  Get High-res Image Gene #58: 'del_12p13.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_12q12' versus 'MRNA_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.025

Table S511.  Gene #59: 'del_12q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
DEL PEAK 29(12Q12) MUTATED 18 19 10 21
DEL PEAK 29(12Q12) WILD-TYPE 140 77 127 96

Figure S511.  Get High-res Image Gene #59: 'del_12q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0015

Table S512.  Gene #59: 'del_12q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 29(12Q12) MUTATED 19 26 6 17
DEL PEAK 29(12Q12) WILD-TYPE 129 76 94 141

Figure S512.  Get High-res Image Gene #59: 'del_12q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12q12' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00019

Table S513.  Gene #59: 'del_12q12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 29(12Q12) MUTATED 53 69 25
DEL PEAK 29(12Q12) WILD-TYPE 476 401 66

Figure S513.  Get High-res Image Gene #59: 'del_12q12' versus Molecular Subtype #5: 'CN_CNMF'

'del_12q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S514.  Gene #59: 'del_12q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 29(12Q12) MUTATED 17 56 8 7
DEL PEAK 29(12Q12) WILD-TYPE 160 169 80 153

Figure S514.  Get High-res Image Gene #59: 'del_12q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_12q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00016

Table S515.  Gene #59: 'del_12q12' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 29(12Q12) MUTATED 17 42 25
DEL PEAK 29(12Q12) WILD-TYPE 186 148 242

Figure S515.  Get High-res Image Gene #59: 'del_12q12' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_12q12' versus 'MIRSEQ_CNMF'

P value = 0.00282 (Fisher's exact test), Q value = 0.0063

Table S516.  Gene #59: 'del_12q12' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 29(12Q12) MUTATED 13 27 8 22
DEL PEAK 29(12Q12) WILD-TYPE 127 80 74 158

Figure S516.  Get High-res Image Gene #59: 'del_12q12' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_12q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00043

Table S517.  Gene #59: 'del_12q12' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 29(12Q12) MUTATED 15 22 13 3 2 15
DEL PEAK 29(12Q12) WILD-TYPE 84 55 105 53 61 77

Figure S517.  Get High-res Image Gene #59: 'del_12q12' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q15' versus 'MRNA_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0027

Table S518.  Gene #60: 'del_12q15' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
DEL PEAK 30(12Q15) MUTATED 22 21 7 19
DEL PEAK 30(12Q15) WILD-TYPE 136 75 130 98

Figure S518.  Get High-res Image Gene #60: 'del_12q15' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12q15' versus 'MRNA_CHIERARCHICAL'

P value = 0.00214 (Fisher's exact test), Q value = 0.0049

Table S519.  Gene #60: 'del_12q15' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 30(12Q15) MUTATED 20 22 4 23
DEL PEAK 30(12Q15) WILD-TYPE 128 80 96 135

Figure S519.  Get High-res Image Gene #60: 'del_12q15' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12q15' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00016

Table S520.  Gene #60: 'del_12q15' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 30(12Q15) MUTATED 57 58 27
DEL PEAK 30(12Q15) WILD-TYPE 472 412 64

Figure S520.  Get High-res Image Gene #60: 'del_12q15' versus Molecular Subtype #5: 'CN_CNMF'

'del_12q15' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S521.  Gene #60: 'del_12q15' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 30(12Q15) MUTATED 16 54 7 5
DEL PEAK 30(12Q15) WILD-TYPE 161 171 81 155

Figure S521.  Get High-res Image Gene #60: 'del_12q15' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S522.  Gene #60: 'del_12q15' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 30(12Q15) MUTATED 18 42 20
DEL PEAK 30(12Q15) WILD-TYPE 185 148 247

Figure S522.  Get High-res Image Gene #60: 'del_12q15' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_12q15' versus 'MIRSEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.00072

Table S523.  Gene #60: 'del_12q15' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 30(12Q15) MUTATED 11 27 6 19
DEL PEAK 30(12Q15) WILD-TYPE 129 80 76 161

Figure S523.  Get High-res Image Gene #60: 'del_12q15' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_12q15' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S524.  Gene #60: 'del_12q15' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 30(12Q15) MUTATED 16 23 12 1 0 11
DEL PEAK 30(12Q15) WILD-TYPE 83 54 106 55 63 81

Figure S524.  Get High-res Image Gene #60: 'del_12q15' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q14.2' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.8e-05

Table S525.  Gene #61: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
DEL PEAK 31(13Q14.2) MUTATED 82 45 32 56
DEL PEAK 31(13Q14.2) WILD-TYPE 76 51 105 61

Figure S525.  Get High-res Image Gene #61: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.9e-05

Table S526.  Gene #61: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 31(13Q14.2) MUTATED 68 50 21 76
DEL PEAK 31(13Q14.2) WILD-TYPE 80 52 79 82

Figure S526.  Get High-res Image Gene #61: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.002

Table S527.  Gene #61: 'del_13q14.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 31(13Q14.2) MUTATED 208 136 39
DEL PEAK 31(13Q14.2) WILD-TYPE 321 334 52

Figure S527.  Get High-res Image Gene #61: 'del_13q14.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00059

Table S528.  Gene #61: 'del_13q14.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 31(13Q14.2) MUTATED 61 81 19 29
DEL PEAK 31(13Q14.2) WILD-TYPE 116 144 69 131

Figure S528.  Get High-res Image Gene #61: 'del_13q14.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00019

Table S529.  Gene #61: 'del_13q14.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 31(13Q14.2) MUTATED 99 40 62
DEL PEAK 31(13Q14.2) WILD-TYPE 145 149 165

Figure S529.  Get High-res Image Gene #61: 'del_13q14.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.9e-05

Table S530.  Gene #61: 'del_13q14.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 31(13Q14.2) MUTATED 73 74 54
DEL PEAK 31(13Q14.2) WILD-TYPE 130 116 213

Figure S530.  Get High-res Image Gene #61: 'del_13q14.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 0.0364 (Fisher's exact test), Q value = 0.06

Table S531.  Gene #61: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 31(13Q14.2) MUTATED 38 41 22 40
DEL PEAK 31(13Q14.2) WILD-TYPE 102 66 60 140

Figure S531.  Get High-res Image Gene #61: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00601 (Fisher's exact test), Q value = 0.012

Table S532.  Gene #61: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 31(13Q14.2) MUTATED 66 37 38
DEL PEAK 31(13Q14.2) WILD-TYPE 156 147 65

Figure S532.  Get High-res Image Gene #61: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.021

Table S533.  Gene #61: 'del_13q14.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 31(13Q14.2) MUTATED 23 31 25 10 20 32
DEL PEAK 31(13Q14.2) WILD-TYPE 76 46 93 46 43 60

Figure S533.  Get High-res Image Gene #61: 'del_13q14.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q22.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S534.  Gene #62: 'del_13q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
DEL PEAK 32(13Q22.1) MUTATED 82 40 30 53
DEL PEAK 32(13Q22.1) WILD-TYPE 76 56 107 64

Figure S534.  Get High-res Image Gene #62: 'del_13q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00046

Table S535.  Gene #62: 'del_13q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 32(13Q22.1) MUTATED 68 45 21 71
DEL PEAK 32(13Q22.1) WILD-TYPE 80 57 79 87

Figure S535.  Get High-res Image Gene #62: 'del_13q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q22.1' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00038

Table S536.  Gene #62: 'del_13q22.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 32(13Q22.1) MUTATED 198 127 42
DEL PEAK 32(13Q22.1) WILD-TYPE 331 343 49

Figure S536.  Get High-res Image Gene #62: 'del_13q22.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_13q22.1' versus 'METHLYATION_CNMF'

P value = 0.00175 (Fisher's exact test), Q value = 0.0041

Table S537.  Gene #62: 'del_13q22.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 32(13Q22.1) MUTATED 61 73 18 30
DEL PEAK 32(13Q22.1) WILD-TYPE 116 152 70 130

Figure S537.  Get High-res Image Gene #62: 'del_13q22.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_13q22.1' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00019

Table S538.  Gene #62: 'del_13q22.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 32(13Q22.1) MUTATED 93 37 61
DEL PEAK 32(13Q22.1) WILD-TYPE 151 152 166

Figure S538.  Get High-res Image Gene #62: 'del_13q22.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_13q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.9e-05

Table S539.  Gene #62: 'del_13q22.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 32(13Q22.1) MUTATED 71 69 51
DEL PEAK 32(13Q22.1) WILD-TYPE 132 121 216

Figure S539.  Get High-res Image Gene #62: 'del_13q22.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_13q22.1' versus 'MIRSEQ_CNMF'

P value = 0.0226 (Fisher's exact test), Q value = 0.039

Table S540.  Gene #62: 'del_13q22.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 32(13Q22.1) MUTATED 38 40 21 37
DEL PEAK 32(13Q22.1) WILD-TYPE 102 67 61 143

Figure S540.  Get High-res Image Gene #62: 'del_13q22.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_13q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00196 (Fisher's exact test), Q value = 0.0045

Table S541.  Gene #62: 'del_13q22.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 32(13Q22.1) MUTATED 64 34 38
DEL PEAK 32(13Q22.1) WILD-TYPE 158 150 65

Figure S541.  Get High-res Image Gene #62: 'del_13q22.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_13q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0393 (Fisher's exact test), Q value = 0.065

Table S542.  Gene #62: 'del_13q22.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 32(13Q22.1) MUTATED 22 28 25 10 21 30
DEL PEAK 32(13Q22.1) WILD-TYPE 77 49 93 46 42 62

Figure S542.  Get High-res Image Gene #62: 'del_13q22.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q13.1' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.9e-05

Table S543.  Gene #63: 'del_14q13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
DEL PEAK 33(14Q13.1) MUTATED 56 39 21 45
DEL PEAK 33(14Q13.1) WILD-TYPE 102 57 116 72

Figure S543.  Get High-res Image Gene #63: 'del_14q13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q13.1' versus 'MRNA_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.00082

Table S544.  Gene #63: 'del_14q13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 33(14Q13.1) MUTATED 49 42 15 55
DEL PEAK 33(14Q13.1) WILD-TYPE 99 60 85 103

Figure S544.  Get High-res Image Gene #63: '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 = 3.7e-05

Table S545.  Gene #63: 'del_14q13.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 33(14Q13.1) MUTATED 164 47 35
DEL PEAK 33(14Q13.1) WILD-TYPE 365 423 56

Figure S545.  Get High-res Image Gene #63: 'del_14q13.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_14q13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S546.  Gene #63: 'del_14q13.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 33(14Q13.1) MUTATED 60 21 17 17
DEL PEAK 33(14Q13.1) WILD-TYPE 117 204 71 143

Figure S546.  Get High-res Image Gene #63: 'del_14q13.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_14q13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S547.  Gene #63: 'del_14q13.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 33(14Q13.1) MUTATED 87 24 16
DEL PEAK 33(14Q13.1) WILD-TYPE 157 165 211

Figure S547.  Get High-res Image Gene #63: 'del_14q13.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_14q13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S548.  Gene #63: 'del_14q13.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 33(14Q13.1) MUTATED 78 21 28
DEL PEAK 33(14Q13.1) WILD-TYPE 125 169 239

Figure S548.  Get High-res Image Gene #63: 'del_14q13.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_14q13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.00087

Table S549.  Gene #63: 'del_14q13.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 33(14Q13.1) MUTATED 22 18 27
DEL PEAK 33(14Q13.1) WILD-TYPE 200 166 76

Figure S549.  Get High-res Image Gene #63: 'del_14q13.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_14q13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.9e-05

Table S550.  Gene #63: 'del_14q13.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 33(14Q13.1) MUTATED 8 11 11 6 23 8
DEL PEAK 33(14Q13.1) WILD-TYPE 91 66 107 50 40 84

Figure S550.  Get High-res Image Gene #63: 'del_14q13.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q24.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S551.  Gene #64: 'del_14q24.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
DEL PEAK 34(14Q24.2) MUTATED 53 43 18 47
DEL PEAK 34(14Q24.2) WILD-TYPE 105 53 119 70

Figure S551.  Get High-res Image Gene #64: 'del_14q24.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q24.2' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.9e-05

Table S552.  Gene #64: 'del_14q24.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 34(14Q24.2) MUTATED 48 46 14 53
DEL PEAK 34(14Q24.2) WILD-TYPE 100 56 86 105

Figure S552.  Get High-res Image Gene #64: 'del_14q24.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q24.2' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00032

Table S553.  Gene #64: 'del_14q24.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 34(14Q24.2) MUTATED 150 103 40
DEL PEAK 34(14Q24.2) WILD-TYPE 379 367 51

Figure S553.  Get High-res Image Gene #64: 'del_14q24.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_14q24.2' versus 'RPPA_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.025

Table S554.  Gene #64: 'del_14q24.2' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
DEL PEAK 34(14Q24.2) MUTATED 55 35 54 21
DEL PEAK 34(14Q24.2) WILD-TYPE 158 133 102 88

Figure S554.  Get High-res Image Gene #64: 'del_14q24.2' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_14q24.2' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00013

Table S555.  Gene #64: 'del_14q24.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 34(14Q24.2) MUTATED 89 38 47
DEL PEAK 34(14Q24.2) WILD-TYPE 155 151 180

Figure S555.  Get High-res Image Gene #64: 'del_14q24.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_14q24.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00056

Table S556.  Gene #64: 'del_14q24.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 34(14Q24.2) MUTATED 73 51 50
DEL PEAK 34(14Q24.2) WILD-TYPE 130 139 217

Figure S556.  Get High-res Image Gene #64: 'del_14q24.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_14q24.2' versus 'MIRSEQ_CNMF'

P value = 0.0012 (Fisher's exact test), Q value = 0.0029

Table S557.  Gene #64: 'del_14q24.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 34(14Q24.2) MUTATED 50 20 17 32
DEL PEAK 34(14Q24.2) WILD-TYPE 90 87 65 148

Figure S557.  Get High-res Image Gene #64: 'del_14q24.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_14q24.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0049 (Fisher's exact test), Q value = 0.01

Table S558.  Gene #64: 'del_14q24.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 34(14Q24.2) MUTATED 53 31 35
DEL PEAK 34(14Q24.2) WILD-TYPE 169 153 68

Figure S558.  Get High-res Image Gene #64: 'del_14q24.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_14q24.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00885 (Fisher's exact test), Q value = 0.017

Table S559.  Gene #64: 'del_14q24.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 34(14Q24.2) MUTATED 35 37 24 23
DEL PEAK 34(14Q24.2) WILD-TYPE 92 82 81 131

Figure S559.  Get High-res Image Gene #64: 'del_14q24.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_14q24.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00258 (Fisher's exact test), Q value = 0.0058

Table S560.  Gene #64: 'del_14q24.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 34(14Q24.2) MUTATED 26 24 18 13 24 14
DEL PEAK 34(14Q24.2) WILD-TYPE 73 53 100 43 39 78

Figure S560.  Get High-res Image Gene #64: 'del_14q24.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q31.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S561.  Gene #65: 'del_14q31.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
DEL PEAK 35(14Q31.3) MUTATED 53 39 12 43
DEL PEAK 35(14Q31.3) WILD-TYPE 105 57 125 74

Figure S561.  Get High-res Image Gene #65: 'del_14q31.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q31.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S562.  Gene #65: 'del_14q31.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 35(14Q31.3) MUTATED 47 41 10 49
DEL PEAK 35(14Q31.3) WILD-TYPE 101 61 90 109

Figure S562.  Get High-res Image Gene #65: 'del_14q31.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q31.3' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00038

Table S563.  Gene #65: 'del_14q31.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 35(14Q31.3) MUTATED 142 96 38
DEL PEAK 35(14Q31.3) WILD-TYPE 387 374 53

Figure S563.  Get High-res Image Gene #65: 'del_14q31.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_14q31.3' versus 'RPPA_CNMF'

P value = 0.0442 (Fisher's exact test), Q value = 0.071

Table S564.  Gene #65: 'del_14q31.3' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
DEL PEAK 35(14Q31.3) MUTATED 52 35 51 21
DEL PEAK 35(14Q31.3) WILD-TYPE 161 133 105 88

Figure S564.  Get High-res Image Gene #65: 'del_14q31.3' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_14q31.3' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00048

Table S565.  Gene #65: 'del_14q31.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 35(14Q31.3) MUTATED 84 38 44
DEL PEAK 35(14Q31.3) WILD-TYPE 160 151 183

Figure S565.  Get High-res Image Gene #65: 'del_14q31.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_14q31.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.00094

Table S566.  Gene #65: 'del_14q31.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 35(14Q31.3) MUTATED 69 49 48
DEL PEAK 35(14Q31.3) WILD-TYPE 134 141 219

Figure S566.  Get High-res Image Gene #65: 'del_14q31.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_14q31.3' versus 'MIRSEQ_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.0026

Table S567.  Gene #65: 'del_14q31.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 35(14Q31.3) MUTATED 49 18 16 32
DEL PEAK 35(14Q31.3) WILD-TYPE 91 89 66 148

Figure S567.  Get High-res Image Gene #65: 'del_14q31.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_14q31.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00848 (Fisher's exact test), Q value = 0.016

Table S568.  Gene #65: 'del_14q31.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 35(14Q31.3) MUTATED 50 31 34
DEL PEAK 35(14Q31.3) WILD-TYPE 172 153 69

Figure S568.  Get High-res Image Gene #65: 'del_14q31.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_14q31.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.024

Table S569.  Gene #65: 'del_14q31.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 35(14Q31.3) MUTATED 34 36 22 23
DEL PEAK 35(14Q31.3) WILD-TYPE 93 83 83 131

Figure S569.  Get High-res Image Gene #65: 'del_14q31.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_14q31.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00271 (Fisher's exact test), Q value = 0.0061

Table S570.  Gene #65: 'del_14q31.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 35(14Q31.3) MUTATED 25 25 18 10 23 14
DEL PEAK 35(14Q31.3) WILD-TYPE 74 52 100 46 40 78

Figure S570.  Get High-res Image Gene #65: 'del_14q31.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q14' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S571.  Gene #66: 'del_15q14' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
DEL PEAK 36(15Q14) MUTATED 37 36 20 45
DEL PEAK 36(15Q14) WILD-TYPE 121 60 117 72

Figure S571.  Get High-res Image Gene #66: 'del_15q14' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q14' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S572.  Gene #66: 'del_15q14' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 36(15Q14) MUTATED 34 47 12 45
DEL PEAK 36(15Q14) WILD-TYPE 114 55 88 113

Figure S572.  Get High-res Image Gene #66: 'del_15q14' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q14' versus 'MIR_CNMF'

P value = 0.00197 (Fisher's exact test), Q value = 0.0046

Table S573.  Gene #66: 'del_15q14' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
DEL PEAK 36(15Q14) MUTATED 30 66 25 22
DEL PEAK 36(15Q14) WILD-TYPE 113 121 65 104

Figure S573.  Get High-res Image Gene #66: 'del_15q14' versus Molecular Subtype #3: 'MIR_CNMF'

'del_15q14' versus 'MIR_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00027

Table S574.  Gene #66: 'del_15q14' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
DEL PEAK 36(15Q14) MUTATED 95 15 33
DEL PEAK 36(15Q14) WILD-TYPE 198 109 96

Figure S574.  Get High-res Image Gene #66: 'del_15q14' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_15q14' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.8e-05

Table S575.  Gene #66: 'del_15q14' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 36(15Q14) MUTATED 131 61 23
DEL PEAK 36(15Q14) WILD-TYPE 398 409 68

Figure S575.  Get High-res Image Gene #66: 'del_15q14' versus Molecular Subtype #5: 'CN_CNMF'

'del_15q14' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 7e-04

Table S576.  Gene #66: 'del_15q14' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 36(15Q14) MUTATED 37 23 4 28
DEL PEAK 36(15Q14) WILD-TYPE 140 202 84 132

Figure S576.  Get High-res Image Gene #66: 'del_15q14' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_15q14' versus 'RPPA_CNMF'

P value = 0.0371 (Fisher's exact test), Q value = 0.061

Table S577.  Gene #66: 'del_15q14' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
DEL PEAK 36(15Q14) MUTATED 39 18 34 15
DEL PEAK 36(15Q14) WILD-TYPE 174 150 122 94

Figure S577.  Get High-res Image Gene #66: 'del_15q14' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_15q14' versus 'RPPA_CHIERARCHICAL'

P value = 0.038 (Fisher's exact test), Q value = 0.063

Table S578.  Gene #66: 'del_15q14' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
DEL PEAK 36(15Q14) MUTATED 49 39 18
DEL PEAK 36(15Q14) WILD-TYPE 185 215 140

Figure S578.  Get High-res Image Gene #66: 'del_15q14' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_15q14' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S579.  Gene #66: 'del_15q14' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 36(15Q14) MUTATED 62 18 25
DEL PEAK 36(15Q14) WILD-TYPE 182 171 202

Figure S579.  Get High-res Image Gene #66: 'del_15q14' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_15q14' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0011

Table S580.  Gene #66: 'del_15q14' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 36(15Q14) MUTATED 50 21 34
DEL PEAK 36(15Q14) WILD-TYPE 153 169 233

Figure S580.  Get High-res Image Gene #66: 'del_15q14' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_15q14' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0434 (Fisher's exact test), Q value = 0.07

Table S581.  Gene #66: 'del_15q14' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 36(15Q14) MUTATED 10 12 9 14 6 10
DEL PEAK 36(15Q14) WILD-TYPE 89 65 109 42 57 82

Figure S581.  Get High-res Image Gene #66: 'del_15q14' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16p12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S582.  Gene #67: 'del_16p12.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 37(16P12.2) MUTATED 82 13 19
DEL PEAK 37(16P12.2) WILD-TYPE 447 457 72

Figure S582.  Get High-res Image Gene #67: 'del_16p12.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_16p12.2' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.9e-05

Table S583.  Gene #67: 'del_16p12.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 37(16P12.2) MUTATED 26 11 5 3
DEL PEAK 37(16P12.2) WILD-TYPE 151 214 83 157

Figure S583.  Get High-res Image Gene #67: 'del_16p12.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_16p12.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0172 (Fisher's exact test), Q value = 0.031

Table S584.  Gene #67: 'del_16p12.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
DEL PEAK 37(16P12.2) MUTATED 31 20 8
DEL PEAK 37(16P12.2) WILD-TYPE 203 234 150

Figure S584.  Get High-res Image Gene #67: 'del_16p12.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_16p12.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S585.  Gene #67: 'del_16p12.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 37(16P12.2) MUTATED 37 7 7
DEL PEAK 37(16P12.2) WILD-TYPE 207 182 220

Figure S585.  Get High-res Image Gene #67: 'del_16p12.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_16p12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S586.  Gene #67: 'del_16p12.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 37(16P12.2) MUTATED 32 8 11
DEL PEAK 37(16P12.2) WILD-TYPE 171 182 256

Figure S586.  Get High-res Image Gene #67: 'del_16p12.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_16p12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.021 (Fisher's exact test), Q value = 0.037

Table S587.  Gene #67: 'del_16p12.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 37(16P12.2) MUTATED 7 5 10
DEL PEAK 37(16P12.2) WILD-TYPE 215 179 93

Figure S587.  Get High-res Image Gene #67: 'del_16p12.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MRNA_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.019

Table S588.  Gene #68: 'del_16q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
DEL PEAK 38(16Q23.1) MUTATED 32 24 13 21
DEL PEAK 38(16Q23.1) WILD-TYPE 126 72 124 96

Figure S588.  Get High-res Image Gene #68: 'del_16q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S589.  Gene #68: 'del_16q23.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 38(16Q23.1) MUTATED 89 23 17
DEL PEAK 38(16Q23.1) WILD-TYPE 440 447 74

Figure S589.  Get High-res Image Gene #68: 'del_16q23.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S590.  Gene #68: 'del_16q23.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 38(16Q23.1) MUTATED 32 15 4 4
DEL PEAK 38(16Q23.1) WILD-TYPE 145 210 84 156

Figure S590.  Get High-res Image Gene #68: 'del_16q23.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_16q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.002

Table S591.  Gene #68: 'del_16q23.1' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
DEL PEAK 38(16Q23.1) MUTATED 37 22 7
DEL PEAK 38(16Q23.1) WILD-TYPE 197 232 151

Figure S591.  Get High-res Image Gene #68: 'del_16q23.1' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S592.  Gene #68: 'del_16q23.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 38(16Q23.1) MUTATED 42 9 11
DEL PEAK 38(16Q23.1) WILD-TYPE 202 180 216

Figure S592.  Get High-res Image Gene #68: 'del_16q23.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S593.  Gene #68: 'del_16q23.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 38(16Q23.1) MUTATED 39 9 14
DEL PEAK 38(16Q23.1) WILD-TYPE 164 181 253

Figure S593.  Get High-res Image Gene #68: 'del_16q23.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0145 (Fisher's exact test), Q value = 0.027

Table S594.  Gene #68: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 38(16Q23.1) MUTATED 10 6 12
DEL PEAK 38(16Q23.1) WILD-TYPE 212 178 91

Figure S594.  Get High-res Image Gene #68: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_17p13.1' versus 'MRNA_CNMF'

P value = 0.00113 (Fisher's exact test), Q value = 0.0027

Table S595.  Gene #69: 'del_17p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
DEL PEAK 39(17P13.1) MUTATED 33 26 12 17
DEL PEAK 39(17P13.1) WILD-TYPE 125 70 125 100

Figure S595.  Get High-res Image Gene #69: 'del_17p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p13.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0019 (Fisher's exact test), Q value = 0.0044

Table S596.  Gene #69: 'del_17p13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 39(17P13.1) MUTATED 32 27 9 20
DEL PEAK 39(17P13.1) WILD-TYPE 116 75 91 138

Figure S596.  Get High-res Image Gene #69: 'del_17p13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S597.  Gene #69: 'del_17p13.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 39(17P13.1) MUTATED 76 21 19
DEL PEAK 39(17P13.1) WILD-TYPE 453 449 72

Figure S597.  Get High-res Image Gene #69: 'del_17p13.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_17p13.1' versus 'METHLYATION_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.00072

Table S598.  Gene #69: 'del_17p13.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 39(17P13.1) MUTATED 21 10 3 2
DEL PEAK 39(17P13.1) WILD-TYPE 156 215 85 158

Figure S598.  Get High-res Image Gene #69: 'del_17p13.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_17p13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S599.  Gene #69: 'del_17p13.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 39(17P13.1) MUTATED 36 3 8
DEL PEAK 39(17P13.1) WILD-TYPE 208 186 219

Figure S599.  Get High-res Image Gene #69: 'del_17p13.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_17p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S600.  Gene #69: 'del_17p13.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 39(17P13.1) MUTATED 30 13 4
DEL PEAK 39(17P13.1) WILD-TYPE 173 177 263

Figure S600.  Get High-res Image Gene #69: 'del_17p13.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00428 (Fisher's exact test), Q value = 0.009

Table S601.  Gene #69: 'del_17p13.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 39(17P13.1) MUTATED 7 2 9
DEL PEAK 39(17P13.1) WILD-TYPE 215 182 94

Figure S601.  Get High-res Image Gene #69: 'del_17p13.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_17q11.2' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.8e-05

Table S602.  Gene #70: 'del_17q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
DEL PEAK 40(17Q11.2) MUTATED 36 9 11 5
DEL PEAK 40(17Q11.2) WILD-TYPE 122 87 126 112

Figure S602.  Get High-res Image Gene #70: 'del_17q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.8e-05

Table S603.  Gene #70: 'del_17q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 40(17Q11.2) MUTATED 35 7 9 10
DEL PEAK 40(17Q11.2) WILD-TYPE 113 95 91 148

Figure S603.  Get High-res Image Gene #70: 'del_17q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17q11.2' versus 'MIR_CNMF'

P value = 0.0041 (Fisher's exact test), Q value = 0.0087

Table S604.  Gene #70: 'del_17q11.2' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
DEL PEAK 40(17Q11.2) MUTATED 27 18 4 19
DEL PEAK 40(17Q11.2) WILD-TYPE 116 169 86 107

Figure S604.  Get High-res Image Gene #70: 'del_17q11.2' versus Molecular Subtype #3: 'MIR_CNMF'

'del_17q11.2' versus 'MIR_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.02

Table S605.  Gene #70: 'del_17q11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
DEL PEAK 40(17Q11.2) MUTATED 26 24 18
DEL PEAK 40(17Q11.2) WILD-TYPE 267 100 111

Figure S605.  Get High-res Image Gene #70: 'del_17q11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_17q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S606.  Gene #70: 'del_17q11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 40(17Q11.2) MUTATED 60 14 19
DEL PEAK 40(17Q11.2) WILD-TYPE 469 456 72

Figure S606.  Get High-res Image Gene #70: 'del_17q11.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_17q11.2' versus 'METHLYATION_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.001

Table S607.  Gene #70: 'del_17q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 40(17Q11.2) MUTATED 19 9 8 2
DEL PEAK 40(17Q11.2) WILD-TYPE 158 216 80 158

Figure S607.  Get High-res Image Gene #70: 'del_17q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_17q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00133 (Fisher's exact test), Q value = 0.0032

Table S608.  Gene #70: 'del_17q11.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
DEL PEAK 40(17Q11.2) MUTATED 29 11 7
DEL PEAK 40(17Q11.2) WILD-TYPE 205 243 151

Figure S608.  Get High-res Image Gene #70: 'del_17q11.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_17q11.2' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00013

Table S609.  Gene #70: 'del_17q11.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 40(17Q11.2) MUTATED 29 4 7
DEL PEAK 40(17Q11.2) WILD-TYPE 215 185 220

Figure S609.  Get High-res Image Gene #70: 'del_17q11.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_17q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S610.  Gene #70: 'del_17q11.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 40(17Q11.2) MUTATED 25 11 4
DEL PEAK 40(17Q11.2) WILD-TYPE 178 179 263

Figure S610.  Get High-res Image Gene #70: 'del_17q11.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_18q23' versus 'MRNA_CNMF'

P value = 0.0202 (Fisher's exact test), Q value = 0.036

Table S611.  Gene #71: 'del_18q23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
DEL PEAK 41(18Q23) MUTATED 21 17 8 18
DEL PEAK 41(18Q23) WILD-TYPE 137 79 129 99

Figure S611.  Get High-res Image Gene #71: 'del_18q23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q23' versus 'MRNA_CHIERARCHICAL'

P value = 0.0192 (Fisher's exact test), Q value = 0.034

Table S612.  Gene #71: 'del_18q23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 41(18Q23) MUTATED 22 15 4 23
DEL PEAK 41(18Q23) WILD-TYPE 126 87 96 135

Figure S612.  Get High-res Image Gene #71: 'del_18q23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18q23' versus 'METHLYATION_CNMF'

P value = 0.0276 (Fisher's exact test), Q value = 0.047

Table S613.  Gene #71: 'del_18q23' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 41(18Q23) MUTATED 28 28 8 35
DEL PEAK 41(18Q23) WILD-TYPE 149 197 80 125

Figure S613.  Get High-res Image Gene #71: 'del_18q23' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_19q13.41' versus 'MRNA_CNMF'

P value = 0.00209 (Fisher's exact test), Q value = 0.0048

Table S614.  Gene #72: 'del_19q13.41' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
DEL PEAK 42(19Q13.41) MUTATED 23 23 13 29
DEL PEAK 42(19Q13.41) WILD-TYPE 135 73 124 88

Figure S614.  Get High-res Image Gene #72: 'del_19q13.41' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19q13.41' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00016

Table S615.  Gene #72: 'del_19q13.41' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 42(19Q13.41) MUTATED 24 33 6 25
DEL PEAK 42(19Q13.41) WILD-TYPE 124 69 94 133

Figure S615.  Get High-res Image Gene #72: 'del_19q13.41' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19q13.41' versus 'MIR_CHIERARCHICAL'

P value = 0.0362 (Fisher's exact test), Q value = 0.06

Table S616.  Gene #72: 'del_19q13.41' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
DEL PEAK 42(19Q13.41) MUTATED 61 19 14
DEL PEAK 42(19Q13.41) WILD-TYPE 232 105 115

Figure S616.  Get High-res Image Gene #72: 'del_19q13.41' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_19q13.41' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S617.  Gene #72: 'del_19q13.41' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 42(19Q13.41) MUTATED 73 283 8
DEL PEAK 42(19Q13.41) WILD-TYPE 456 187 83

Figure S617.  Get High-res Image Gene #72: 'del_19q13.41' versus Molecular Subtype #5: 'CN_CNMF'

'del_19q13.41' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S618.  Gene #72: 'del_19q13.41' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 42(19Q13.41) MUTATED 24 80 24 159
DEL PEAK 42(19Q13.41) WILD-TYPE 153 145 64 1

Figure S618.  Get High-res Image Gene #72: 'del_19q13.41' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_19q13.41' versus 'RPPA_CNMF'

P value = 0.00228 (Fisher's exact test), Q value = 0.0052

Table S619.  Gene #72: 'del_19q13.41' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
DEL PEAK 42(19Q13.41) MUTATED 78 84 70 32
DEL PEAK 42(19Q13.41) WILD-TYPE 135 84 86 77

Figure S619.  Get High-res Image Gene #72: 'del_19q13.41' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_19q13.41' versus 'RPPA_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.0017

Table S620.  Gene #72: 'del_19q13.41' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
DEL PEAK 42(19Q13.41) MUTATED 86 93 85
DEL PEAK 42(19Q13.41) WILD-TYPE 148 161 73

Figure S620.  Get High-res Image Gene #72: 'del_19q13.41' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_19q13.41' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S621.  Gene #72: 'del_19q13.41' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 42(19Q13.41) MUTATED 46 119 126
DEL PEAK 42(19Q13.41) WILD-TYPE 198 70 101

Figure S621.  Get High-res Image Gene #72: 'del_19q13.41' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_19q13.41' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S622.  Gene #72: 'del_19q13.41' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 42(19Q13.41) MUTATED 23 70 198
DEL PEAK 42(19Q13.41) WILD-TYPE 180 120 69

Figure S622.  Get High-res Image Gene #72: 'del_19q13.41' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.41' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S623.  Gene #72: 'del_19q13.41' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 42(19Q13.41) MUTATED 52 35 76 104
DEL PEAK 42(19Q13.41) WILD-TYPE 88 72 6 76

Figure S623.  Get High-res Image Gene #72: 'del_19q13.41' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_19q13.41' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S624.  Gene #72: 'del_19q13.41' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 42(19Q13.41) MUTATED 130 117 20
DEL PEAK 42(19Q13.41) WILD-TYPE 92 67 83

Figure S624.  Get High-res Image Gene #72: 'del_19q13.41' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.41' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S625.  Gene #72: 'del_19q13.41' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 42(19Q13.41) MUTATED 41 43 95 87
DEL PEAK 42(19Q13.41) WILD-TYPE 86 76 10 67

Figure S625.  Get High-res Image Gene #72: 'del_19q13.41' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_19q13.41' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S626.  Gene #72: 'del_19q13.41' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 42(19Q13.41) MUTATED 34 51 74 56 2 49
DEL PEAK 42(19Q13.41) WILD-TYPE 65 26 44 0 61 43

Figure S626.  Get High-res Image Gene #72: 'del_19q13.41' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.43' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.8e-05

Table S627.  Gene #73: 'del_19q13.43' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
DEL PEAK 43(19Q13.43) MUTATED 17 23 7 29
DEL PEAK 43(19Q13.43) WILD-TYPE 141 73 130 88

Figure S627.  Get High-res Image Gene #73: 'del_19q13.43' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19q13.43' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S628.  Gene #73: 'del_19q13.43' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 43(19Q13.43) MUTATED 18 32 3 23
DEL PEAK 43(19Q13.43) WILD-TYPE 130 70 97 135

Figure S628.  Get High-res Image Gene #73: 'del_19q13.43' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19q13.43' versus 'MIR_CNMF'

P value = 0.00444 (Fisher's exact test), Q value = 0.0093

Table S629.  Gene #73: 'del_19q13.43' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
DEL PEAK 43(19Q13.43) MUTATED 13 42 10 16
DEL PEAK 43(19Q13.43) WILD-TYPE 130 145 80 110

Figure S629.  Get High-res Image Gene #73: 'del_19q13.43' versus Molecular Subtype #3: 'MIR_CNMF'

'del_19q13.43' versus 'MIR_CHIERARCHICAL'

P value = 0.0432 (Fisher's exact test), Q value = 0.07

Table S630.  Gene #73: 'del_19q13.43' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
DEL PEAK 43(19Q13.43) MUTATED 54 13 14
DEL PEAK 43(19Q13.43) WILD-TYPE 239 111 115

Figure S630.  Get High-res Image Gene #73: 'del_19q13.43' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_19q13.43' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S631.  Gene #73: 'del_19q13.43' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 43(19Q13.43) MUTATED 57 290 8
DEL PEAK 43(19Q13.43) WILD-TYPE 472 180 83

Figure S631.  Get High-res Image Gene #73: 'del_19q13.43' versus Molecular Subtype #5: 'CN_CNMF'

'del_19q13.43' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S632.  Gene #73: 'del_19q13.43' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 43(19Q13.43) MUTATED 20 87 23 158
DEL PEAK 43(19Q13.43) WILD-TYPE 157 138 65 2

Figure S632.  Get High-res Image Gene #73: 'del_19q13.43' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_19q13.43' versus 'RPPA_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.028

Table S633.  Gene #73: 'del_19q13.43' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
DEL PEAK 43(19Q13.43) MUTATED 78 80 71 34
DEL PEAK 43(19Q13.43) WILD-TYPE 135 88 85 75

Figure S633.  Get High-res Image Gene #73: 'del_19q13.43' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_19q13.43' versus 'RPPA_CHIERARCHICAL'

P value = 0.00757 (Fisher's exact test), Q value = 0.015

Table S634.  Gene #73: 'del_19q13.43' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
DEL PEAK 43(19Q13.43) MUTATED 90 92 81
DEL PEAK 43(19Q13.43) WILD-TYPE 144 162 77

Figure S634.  Get High-res Image Gene #73: 'del_19q13.43' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_19q13.43' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S635.  Gene #73: 'del_19q13.43' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 43(19Q13.43) MUTATED 43 118 132
DEL PEAK 43(19Q13.43) WILD-TYPE 201 71 95

Figure S635.  Get High-res Image Gene #73: 'del_19q13.43' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_19q13.43' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S636.  Gene #73: 'del_19q13.43' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 43(19Q13.43) MUTATED 19 76 198
DEL PEAK 43(19Q13.43) WILD-TYPE 184 114 69

Figure S636.  Get High-res Image Gene #73: 'del_19q13.43' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.43' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S637.  Gene #73: 'del_19q13.43' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 43(19Q13.43) MUTATED 58 35 77 100
DEL PEAK 43(19Q13.43) WILD-TYPE 82 72 5 80

Figure S637.  Get High-res Image Gene #73: 'del_19q13.43' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_19q13.43' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S638.  Gene #73: 'del_19q13.43' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 43(19Q13.43) MUTATED 136 115 19
DEL PEAK 43(19Q13.43) WILD-TYPE 86 69 84

Figure S638.  Get High-res Image Gene #73: 'del_19q13.43' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.43' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S639.  Gene #73: 'del_19q13.43' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 43(19Q13.43) MUTATED 47 42 95 85
DEL PEAK 43(19Q13.43) WILD-TYPE 80 77 10 69

Figure S639.  Get High-res Image Gene #73: 'del_19q13.43' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_19q13.43' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S640.  Gene #73: 'del_19q13.43' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 43(19Q13.43) MUTATED 39 50 70 56 2 52
DEL PEAK 43(19Q13.43) WILD-TYPE 60 27 48 0 61 40

Figure S640.  Get High-res Image Gene #73: 'del_19q13.43' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S641.  Gene #74: 'del_22q13.32' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
DEL PEAK 44(22Q13.32) MUTATED 194 57 38
DEL PEAK 44(22Q13.32) WILD-TYPE 335 413 53

Figure S641.  Get High-res Image Gene #74: 'del_22q13.32' versus Molecular Subtype #5: 'CN_CNMF'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S642.  Gene #74: 'del_22q13.32' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 44(22Q13.32) MUTATED 60 45 20 5
DEL PEAK 44(22Q13.32) WILD-TYPE 117 180 68 155

Figure S642.  Get High-res Image Gene #74: 'del_22q13.32' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_22q13.32' versus 'RPPA_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0022

Table S643.  Gene #74: 'del_22q13.32' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
DEL PEAK 44(22Q13.32) MUTATED 41 26 53 24
DEL PEAK 44(22Q13.32) WILD-TYPE 172 142 103 85

Figure S643.  Get High-res Image Gene #74: 'del_22q13.32' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_22q13.32' versus 'RPPA_CHIERARCHICAL'

P value = 0.00256 (Fisher's exact test), Q value = 0.0058

Table S644.  Gene #74: 'del_22q13.32' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
DEL PEAK 44(22Q13.32) MUTATED 60 64 20
DEL PEAK 44(22Q13.32) WILD-TYPE 174 190 138

Figure S644.  Get High-res Image Gene #74: 'del_22q13.32' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S645.  Gene #74: 'del_22q13.32' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 44(22Q13.32) MUTATED 95 23 23
DEL PEAK 44(22Q13.32) WILD-TYPE 149 166 204

Figure S645.  Get High-res Image Gene #74: 'del_22q13.32' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S646.  Gene #74: 'del_22q13.32' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
DEL PEAK 44(22Q13.32) MUTATED 80 36 25
DEL PEAK 44(22Q13.32) WILD-TYPE 123 154 242

Figure S646.  Get High-res Image Gene #74: 'del_22q13.32' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CNMF'

P value = 0.0301 (Fisher's exact test), Q value = 0.05

Table S647.  Gene #74: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 44(22Q13.32) MUTATED 27 22 7 21
DEL PEAK 44(22Q13.32) WILD-TYPE 113 85 75 159

Figure S647.  Get High-res Image Gene #74: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_22q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.7e-05

Table S648.  Gene #74: 'del_22q13.32' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
DEL PEAK 44(22Q13.32) MUTATED 27 18 32
DEL PEAK 44(22Q13.32) WILD-TYPE 195 166 71

Figure S648.  Get High-res Image Gene #74: 'del_22q13.32' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.8e-05

Table S649.  Gene #74: 'del_22q13.32' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 44(22Q13.32) MUTATED 24 32 6 14
DEL PEAK 44(22Q13.32) WILD-TYPE 103 87 99 140

Figure S649.  Get High-res Image Gene #74: 'del_22q13.32' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_22q13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00022

Table S650.  Gene #74: 'del_22q13.32' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 44(22Q13.32) MUTATED 11 20 13 3 20 9
DEL PEAK 44(22Q13.32) WILD-TYPE 88 57 105 53 43 83

Figure S650.  Get High-res Image Gene #74: 'del_22q13.32' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xq21.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00081 (Fisher's exact test), Q value = 0.002

Table S651.  Gene #75: 'del_xq21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 45(XQ21.1) MUTATED 16 32 16 28
DEL PEAK 45(XQ21.1) WILD-TYPE 132 70 84 130

Figure S651.  Get High-res Image Gene #75: 'del_xq21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_xq21.1' versus 'METHLYATION_CNMF'

P value = 0.00141 (Fisher's exact test), Q value = 0.0034

Table S652.  Gene #75: 'del_xq21.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
DEL PEAK 45(XQ21.1) MUTATED 39 39 4 30
DEL PEAK 45(XQ21.1) WILD-TYPE 138 186 84 130

Figure S652.  Get High-res Image Gene #75: 'del_xq21.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_xq21.1' versus 'RPPA_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.002

Table S653.  Gene #75: 'del_xq21.1' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
DEL PEAK 45(XQ21.1) MUTATED 40 19 42 13
DEL PEAK 45(XQ21.1) WILD-TYPE 173 149 114 96

Figure S653.  Get High-res Image Gene #75: 'del_xq21.1' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_xq21.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0316 (Fisher's exact test), Q value = 0.053

Table S654.  Gene #75: 'del_xq21.1' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
DEL PEAK 45(XQ21.1) MUTATED 52 43 19
DEL PEAK 45(XQ21.1) WILD-TYPE 182 211 139

Figure S654.  Get High-res Image Gene #75: 'del_xq21.1' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_xq21.1' versus 'MRNASEQ_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.0015

Table S655.  Gene #75: 'del_xq21.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
DEL PEAK 45(XQ21.1) MUTATED 60 21 34
DEL PEAK 45(XQ21.1) WILD-TYPE 184 168 193

Figure S655.  Get High-res Image Gene #75: 'del_xq21.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_xq21.1' versus 'MIRSEQ_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0013

Table S656.  Gene #75: 'del_xq21.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
DEL PEAK 45(XQ21.1) MUTATED 14 18 25 21
DEL PEAK 45(XQ21.1) WILD-TYPE 126 89 57 159

Figure S656.  Get High-res Image Gene #75: 'del_xq21.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_xq21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00032

Table S657.  Gene #75: 'del_xq21.1' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
DEL PEAK 45(XQ21.1) MUTATED 20 15 30 12
DEL PEAK 45(XQ21.1) WILD-TYPE 107 104 75 142

Figure S657.  Get High-res Image Gene #75: 'del_xq21.1' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_xq21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00032

Table S658.  Gene #75: 'del_xq21.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
DEL PEAK 45(XQ21.1) MUTATED 12 18 6 13 6 22
DEL PEAK 45(XQ21.1) WILD-TYPE 87 59 112 43 57 70

Figure S658.  Get High-res Image Gene #75: 'del_xq21.1' versus Molecular Subtype #14: '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/GBMLGG-TP/22534381/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/GBMLGG-TP/22573865/GBMLGG-TP.transferedmergedcluster.txt

  • Number of patients = 1090

  • Number of significantly focal cnvs = 75

  • Number of molecular subtypes = 14

  • 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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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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