Correlation between copy number variation genes (focal events) and molecular subtypes
Stomach Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
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/C1W958PD
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 88 focal events and 10 molecular subtypes across 441 patients, 607 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1p36.22 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_1q21.3 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'.

  • amp_1q42.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_3q26.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_5p13.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_6p21.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_6q12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_6q21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_7p22.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_7p11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_7q21.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_7q22.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_8p23.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • amp_9p24.1 cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CNMF'.

  • amp_9p13.2 cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • amp_9q34.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • amp_10p11.22 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_10q22.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_10q26.13 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

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

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

  • amp_11q13.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_12p12.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • amp_12q15 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CNMF'.

  • amp_13q12.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_13q22.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_14q21.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • amp_15q26.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • amp_19q13.32 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_20q13.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_xq27.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_1p36.11 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_1p13.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_1q44 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_2q32.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_2q33.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • del_2q37.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3p26.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3p21.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_3q26.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • del_4q35.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_5q23.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_6p25.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_6q14.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_6q24.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • del_7q36.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • del_9p21.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_9q21.11 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_10p15.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_10q22.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • del_11q23.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_12q12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_13q12.11 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_14q23.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_14q32.32 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_15q11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • del_17p12 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_17q24.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_18q12.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • del_19q13.11 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_21q11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_21q22.13 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_22q13.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_xp22.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_xp21.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_xq21.33 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 88 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 607 significant findings detected.

Clinical
Features
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
amp 1q21 3 160 (36%) 281 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.0334
(0.0501)
0.00467
(0.00858)
1e-05
(3.58e-05)
0.0002
(0.000515)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.00306
(0.00582)
1e-05
(3.58e-05)
amp 5p15 33 130 (29%) 311 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.0351
(0.0523)
0.0371
(0.0553)
1e-05
(3.58e-05)
7e-05
(0.000199)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.00241
(0.00464)
2e-05
(6.62e-05)
del 1p36 11 135 (31%) 306 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.00131
(0.00274)
8e-05
(0.000225)
1e-05
(3.58e-05)
0.00023
(0.000582)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.00569
(0.0103)
1e-05
(3.58e-05)
del 17p12 181 (41%) 260 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.0164
(0.0267)
0.00155
(0.00318)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.00174
(0.00355)
2e-05
(6.62e-05)
amp 6p21 1 124 (28%) 317 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.0333
(0.0501)
0.0558
(0.0796)
1e-05
(3.58e-05)
0.00135
(0.00282)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.0035
(0.00655)
2e-05
(6.62e-05)
amp 11p11 2 92 (21%) 349 1e-05
(3.58e-05)
4e-05
(0.000121)
0.717
(0.749)
0.0389
(0.0576)
0.00116
(0.00246)
0.00973
(0.0168)
5e-05
(0.000148)
1e-05
(3.58e-05)
0.0022
(0.00431)
2e-05
(6.62e-05)
amp 11q13 3 115 (26%) 326 1e-05
(3.58e-05)
0.00191
(0.00382)
0.0432
(0.063)
0.0633
(0.088)
0.00655
(0.0117)
0.0021
(0.00414)
0.00034
(0.000831)
0.00041
(0.000983)
0.00177
(0.00359)
0.00106
(0.00228)
amp 15q26 1 113 (26%) 328 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.146
(0.185)
0.0113
(0.019)
2e-05
(6.62e-05)
1e-05
(3.58e-05)
5e-05
(0.000148)
1e-05
(3.58e-05)
0.00012
(0.000321)
0.00079
(0.00175)
amp 17q12 147 (33%) 294 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.00726
(0.0129)
6e-05
(0.000174)
1e-05
(3.58e-05)
5e-05
(0.000148)
1e-05
(3.58e-05)
2e-05
(6.62e-05)
0.0736
(0.1)
0.00151
(0.0031)
amp 19q12 130 (29%) 311 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.00027
(0.000677)
0.00013
(0.000345)
1e-05
(3.58e-05)
4e-05
(0.000121)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.0583
(0.0824)
1e-05
(3.58e-05)
amp 20q13 2 293 (66%) 148 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.0276
(0.0425)
2e-05
(6.62e-05)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.0501
(0.0724)
1e-05
(3.58e-05)
del 1p13 2 93 (21%) 348 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.00265
(0.00508)
0.138
(0.177)
1e-05
(3.58e-05)
0.00023
(0.000582)
0.00223
(0.00435)
0.00244
(0.00469)
0.0207
(0.0329)
0.00054
(0.00125)
del 4q35 1 204 (46%) 237 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.831
(0.847)
0.00745
(0.0131)
1e-05
(3.58e-05)
0.00038
(0.000919)
0.00012
(0.000321)
1e-05
(3.58e-05)
0.00668
(0.0119)
2e-05
(6.62e-05)
del 5q12 1 170 (39%) 271 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.136
(0.175)
0.00026
(0.000654)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.00073
(0.00163)
1e-05
(3.58e-05)
del 5q23 2 158 (36%) 283 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.117
(0.153)
0.00079
(0.00175)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
del 9p23 195 (44%) 246 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.728
(0.756)
0.00019
(0.000492)
1e-05
(3.58e-05)
3e-05
(9.5e-05)
0.00116
(0.00246)
3e-05
(9.5e-05)
0.0391
(0.0578)
0.00118
(0.0025)
del 9p21 3 193 (44%) 248 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.438
(0.485)
0.00101
(0.00218)
1e-05
(3.58e-05)
3e-05
(9.5e-05)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.0336
(0.0503)
0.00016
(0.00042)
del 10q23 31 116 (26%) 325 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.0332
(0.05)
0.00797
(0.014)
1e-05
(3.58e-05)
4e-05
(0.000121)
0.00031
(0.000764)
1e-05
(3.58e-05)
0.0621
(0.0867)
0.00088
(0.00193)
del 15q11 2 120 (27%) 321 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.00068
(0.00152)
0.00234
(0.00455)
2e-05
(6.62e-05)
4e-05
(0.000121)
0.00038
(0.000919)
1e-05
(3.58e-05)
0.0504
(0.0726)
0.00058
(0.00133)
del 15q15 1 122 (28%) 319 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.0024
(0.00463)
0.0222
(0.0349)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.00041
(0.000983)
1e-05
(3.58e-05)
0.0868
(0.117)
2e-05
(6.62e-05)
del 19p13 3 162 (37%) 279 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.0547
(0.0783)
6e-05
(0.000174)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.00058
(0.00133)
1e-05
(3.58e-05)
amp 1q42 3 150 (34%) 291 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.351
(0.399)
0.00235
(0.00455)
1e-05
(3.58e-05)
0.012
(0.0201)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.0758
(0.103)
4e-05
(0.000121)
amp 7p22 1 229 (52%) 212 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.589
(0.629)
0.218
(0.259)
1e-05
(3.58e-05)
0.00194
(0.00387)
0.00185
(0.00373)
9e-05
(0.000251)
0.00949
(0.0164)
0.00068
(0.00152)
amp 7p11 2 214 (49%) 227 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.603
(0.643)
0.169
(0.208)
0.00088
(0.00193)
0.046
(0.0668)
0.0283
(0.0435)
0.00075
(0.00167)
0.0101
(0.0173)
0.00469
(0.0086)
amp 7q21 2 204 (46%) 237 1e-05
(3.58e-05)
6e-05
(0.000174)
0.146
(0.185)
0.119
(0.155)
0.0327
(0.0495)
0.0197
(0.0316)
0.0405
(0.0596)
0.00671
(0.012)
0.0239
(0.0374)
0.0147
(0.0243)
amp 19q13 32 111 (25%) 330 1e-05
(3.58e-05)
0.00226
(0.0044)
0.187
(0.228)
0.0114
(0.0192)
0.00038
(0.000919)
0.00335
(0.00633)
3e-05
(9.5e-05)
0.00149
(0.00307)
0.0533
(0.0764)
0.00039
(0.00094)
del 3p26 1 143 (32%) 298 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.609
(0.646)
0.0899
(0.12)
1e-05
(3.58e-05)
0.00107
(0.00229)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.0201
(0.0321)
1e-05
(3.58e-05)
del 3p21 1 153 (35%) 288 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.531
(0.574)
0.14
(0.179)
0.00044
(0.00105)
0.0018
(0.00364)
0.0124
(0.0206)
7e-05
(0.000199)
0.0135
(0.0223)
0.001
(0.00217)
del 3p14 2 157 (36%) 284 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.468
(0.513)
0.0708
(0.0972)
1e-05
(3.58e-05)
6e-05
(0.000174)
0.00014
(0.00037)
1e-05
(3.58e-05)
0.00058
(0.00133)
1e-05
(3.58e-05)
del 4p16 3 169 (38%) 272 1e-05
(3.58e-05)
2e-05
(6.62e-05)
0.498
(0.543)
0.471
(0.516)
4e-05
(0.000121)
0.014
(0.0232)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.00089
(0.00194)
1e-05
(3.58e-05)
del 6p25 3 115 (26%) 326 1e-05
(3.58e-05)
2e-05
(6.62e-05)
0.117
(0.153)
0.193
(0.233)
1e-05
(3.58e-05)
0.00029
(0.000717)
0.00044
(0.00105)
3e-05
(9.5e-05)
0.00195
(0.00388)
0.00371
(0.00692)
del 6q26 102 (23%) 339 1e-05
(3.58e-05)
0.00301
(0.00573)
0.395
(0.444)
0.297
(0.345)
5e-05
(0.000148)
1e-05
(3.58e-05)
0.00434
(0.00802)
0.00343
(0.00645)
0.0212
(0.0335)
0.00724
(0.0128)
del 9q21 11 113 (26%) 328 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.832
(0.848)
0.00609
(0.0109)
1e-05
(3.58e-05)
0.00235
(0.00455)
0.00018
(0.000467)
1e-05
(3.58e-05)
0.0594
(0.0835)
9e-05
(0.000251)
del 11p15 5 97 (22%) 344 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.0674
(0.093)
0.00212
(0.00417)
1e-05
(3.58e-05)
0.0001
(0.000274)
0.177
(0.216)
0.00088
(0.00193)
0.0413
(0.0606)
0.0168
(0.0273)
del 14q23 3 136 (31%) 305 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.677
(0.711)
0.355
(0.403)
1e-05
(3.58e-05)
3e-05
(9.5e-05)
4e-05
(0.000121)
1e-05
(3.58e-05)
0.00376
(0.007)
6e-05
(0.000174)
del 14q32 32 133 (30%) 308 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.768
(0.792)
0.638
(0.673)
0.00676
(0.012)
0.00047
(0.0011)
0.0134
(0.0222)
0.00412
(0.00765)
0.042
(0.0615)
0.0103
(0.0176)
del 16p13 3 98 (22%) 343 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.697
(0.728)
0.485
(0.53)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.00318
(0.00603)
1e-05
(3.58e-05)
del 16q23 1 182 (41%) 259 1e-05
(3.58e-05)
0.00124
(0.0026)
0.908
(0.916)
0.153
(0.193)
0.00536
(0.00977)
8e-05
(0.000225)
0.0058
(0.0105)
0.00355
(0.00663)
0.0281
(0.0433)
0.00095
(0.00207)
del 18q12 2 181 (41%) 260 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.343
(0.392)
0.0971
(0.129)
0.0001
(0.000274)
0.0001
(0.000274)
0.0014
(0.00291)
0.00028
(7e-04)
0.00445
(0.00819)
3e-05
(9.5e-05)
del 18q21 2 204 (46%) 237 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.533
(0.576)
0.0626
(0.0873)
2e-05
(6.62e-05)
0.00013
(0.000345)
0.002
(0.00396)
0.00042
(0.001)
0.00431
(0.00798)
0.00049
(0.00114)
del 19q13 11 75 (17%) 366 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.322
(0.371)
0.687
(0.719)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.0194
(0.0313)
2e-05
(6.62e-05)
del 21q11 2 182 (41%) 259 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.611
(0.648)
0.164
(0.203)
0.0001
(0.000274)
0.0027
(0.00517)
0.00187
(0.00376)
0.00058
(0.00133)
0.00087
(0.00192)
0.00057
(0.00132)
del 21q22 13 196 (44%) 245 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.158
(0.198)
0.161
(0.2)
0.00021
(0.000537)
0.00083
(0.00184)
0.00214
(0.0042)
5e-05
(0.000148)
0.00559
(0.0101)
0.00137
(0.00285)
del 22q13 31 161 (37%) 280 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.878
(0.889)
0.0102
(0.0175)
0.00105
(0.00226)
0.0012
(0.00253)
3e-05
(9.5e-05)
1e-05
(3.58e-05)
0.115
(0.151)
0.00012
(0.000321)
amp 1p36 22 66 (15%) 375 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.243
(0.286)
0.527
(0.571)
0.00017
(0.000444)
0.0109
(0.0184)
0.00335
(0.00633)
0.00046
(0.00109)
0.0567
(0.0805)
0.0289
(0.0441)
amp 5p13 1 126 (29%) 315 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.731
(0.759)
0.15
(0.19)
1e-05
(3.58e-05)
0.0002
(0.000515)
0.00011
(0.000297)
1e-05
(3.58e-05)
0.435
(0.481)
0.00011
(0.000297)
amp 6q12 88 (20%) 353 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.0752
(0.102)
0.573
(0.615)
1e-05
(3.58e-05)
0.00558
(0.0101)
1e-05
(3.58e-05)
3e-05
(9.5e-05)
0.086
(0.116)
0.00011
(0.000297)
amp 6q21 82 (19%) 359 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.467
(0.513)
0.468
(0.513)
1e-05
(3.58e-05)
5e-05
(0.000148)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.171
(0.21)
1e-05
(3.58e-05)
amp 8q24 21 309 (70%) 132 0.00742
(0.0131)
1e-05
(3.58e-05)
0.201
(0.241)
0.637
(0.673)
1e-05
(3.58e-05)
0.247
(0.291)
1e-05
(3.58e-05)
0.00017
(0.000444)
0.00897
(0.0156)
0.00064
(0.00145)
amp 10p11 22 119 (27%) 322 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.925
(0.93)
0.276
(0.322)
7e-05
(0.000199)
0.09
(0.12)
0.00191
(0.00382)
1e-05
(3.58e-05)
0.0104
(0.0178)
0.00011
(0.000297)
amp 13q12 3 170 (39%) 271 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.0589
(0.0832)
0.534
(0.577)
1e-05
(3.58e-05)
0.00119
(0.00251)
1e-05
(3.58e-05)
0.00011
(0.000297)
0.588
(0.628)
1e-05
(3.58e-05)
amp 13q22 1 181 (41%) 260 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.303
(0.351)
0.406
(0.455)
1e-05
(3.58e-05)
2e-05
(6.62e-05)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.072
(0.0984)
8e-05
(0.000225)
amp 18q11 2 140 (32%) 301 1e-05
(3.58e-05)
6e-05
(0.000174)
0.926
(0.931)
0.063
(0.0877)
1e-05
(3.58e-05)
0.00108
(0.0023)
0.0158
(0.0258)
0.00029
(0.000717)
0.117
(0.153)
0.0288
(0.044)
del 3q26 31 49 (11%) 392 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.575
(0.616)
0.483
(0.528)
1e-05
(3.58e-05)
2e-05
(6.62e-05)
1e-05
(3.58e-05)
0.00029
(0.000717)
0.0616
(0.0862)
0.0132
(0.022)
del 4q22 1 193 (44%) 248 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.958
(0.96)
0.0666
(0.092)
0.00067
(0.00151)
0.0224
(0.0351)
0.00959
(0.0165)
8e-05
(0.000225)
0.67
(0.706)
0.00344
(0.00645)
del 6q24 3 78 (18%) 363 1e-05
(3.58e-05)
0.00047
(0.0011)
0.562
(0.604)
0.606
(0.645)
0.00022
(0.000561)
0.00052
(0.00121)
0.0894
(0.12)
0.0289
(0.0441)
0.02
(0.0321)
0.0377
(0.0559)
del 7q31 1 71 (16%) 370 1e-05
(3.58e-05)
0.00122
(0.00256)
0.88
(0.89)
0.371
(0.42)
0.00997
(0.0171)
0.0298
(0.0452)
0.00198
(0.00393)
0.0329
(0.0497)
0.0728
(0.0991)
0.0243
(0.038)
del 7q36 3 98 (22%) 343 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.208
(0.249)
0.0653
(0.0905)
1e-05
(3.58e-05)
3e-05
(9.5e-05)
1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.0501
(0.0724)
4e-05
(0.000121)
del 8p23 2 122 (28%) 319 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.061
(0.0854)
0.145
(0.184)
1e-05
(3.58e-05)
0.00023
(0.000582)
0.0196
(0.0316)
7e-05
(0.000199)
0.0748
(0.102)
0.00021
(0.000537)
del 10q22 3 79 (18%) 362 1e-05
(3.58e-05)
0.00024
(0.000605)
0.809
(0.828)
0.106
(0.14)
2e-05
(6.62e-05)
0.00063
(0.00143)
0.0157
(0.0258)
4e-05
(0.000121)
0.383
(0.431)
0.0121
(0.0202)
del 11q23 2 99 (22%) 342 1e-05
(3.58e-05)
2e-05
(6.62e-05)
0.233
(0.277)
0.0294
(0.0447)
0.00747
(0.0131)
0.00837
(0.0146)
0.516
(0.56)
0.056
(0.0798)
0.0109
(0.0184)
0.021
(0.0332)
del 12p13 1 77 (17%) 364 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.769
(0.792)
0.19
(0.231)
1e-05
(3.58e-05)
3e-05
(9.5e-05)
0.00108
(0.0023)
0.00061
(0.00139)
0.375
(0.423)
0.00018
(0.000467)
del 20p12 1 39 (9%) 402 0.00221
(0.00432)
0.00167
(0.00342)
0.358
(0.406)
0.403
(0.451)
0.0146
(0.0241)
0.0283
(0.0435)
0.0202
(0.0323)
0.0285
(0.0436)
0.971
(0.972)
0.0205
(0.0327)
amp 3q26 2 164 (37%) 277 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.0594
(0.0835)
0.0641
(0.089)
0.0221
(0.0348)
1e-05
(3.58e-05)
0.0708
(0.0972)
0.00561
(0.0102)
0.0728
(0.0991)
0.00033
(0.000809)
amp 7q22 1 202 (46%) 239 1e-05
(3.58e-05)
0.00049
(0.00114)
0.181
(0.221)
0.274
(0.32)
0.0465
(0.0674)
0.137
(0.177)
0.11
(0.144)
0.0313
(0.0473)
0.041
(0.0602)
0.0275
(0.0425)
del 2q37 2 72 (16%) 369 1e-05
(3.58e-05)
2e-05
(6.62e-05)
0.18
(0.219)
0.304
(0.352)
0.0179
(0.029)
0.109
(0.143)
6e-05
(0.000174)
7e-05
(0.000199)
0.139
(0.179)
0.00935
(0.0162)
del 6q14 1 89 (20%) 352 1e-05
(3.58e-05)
0.00013
(0.000345)
0.185
(0.224)
0.197
(0.238)
5e-05
(0.000148)
0.00016
(0.00042)
0.133
(0.172)
0.012
(0.0202)
0.0116
(0.0195)
0.359
(0.408)
amp 11p13 88 (20%) 353 1e-05
(3.58e-05)
0.00147
(0.00304)
0.806
(0.827)
0.141
(0.179)
0.129
(0.167)
0.0821
(0.111)
0.0006
(0.00137)
4e-05
(0.000121)
0.265
(0.31)
0.00107
(0.00229)
del 2q32 1 64 (15%) 377 0.00046
(0.00109)
0.00037
(0.000902)
0.835
(0.849)
0.418
(0.468)
0.0217
(0.0342)
0.581
(0.622)
0.00481
(0.0088)
0.00029
(0.000717)
0.198
(0.238)
0.159
(0.199)
del 10p15 3 77 (17%) 364 1e-05
(3.58e-05)
0.00033
(0.000809)
0.727
(0.756)
0.16
(0.2)
0.0113
(0.0191)
0.0555
(0.0793)
0.035
(0.0523)
0.00338
(0.00637)
0.14
(0.179)
0.109
(0.143)
del xp22 2 85 (19%) 356 1e-05
(3.58e-05)
3e-05
(9.5e-05)
0.721
(0.751)
0.315
(0.364)
0.0422
(0.0616)
0.399
(0.448)
0.0255
(0.0398)
0.00147
(0.00304)
0.432
(0.48)
0.152
(0.191)
amp 9p13 2 91 (21%) 350 0.04
(0.0591)
0.327
(0.375)
0.47
(0.515)
0.0442
(0.0642)
0.0376
(0.0559)
0.0593
(0.0835)
0.00599
(0.0108)
0.158
(0.198)
0.162
(0.201)
0.316
(0.364)
amp 9q34 3 122 (28%) 319 0.00177
(0.00359)
0.0207
(0.0329)
0.8
(0.821)
0.292
(0.339)
0.00743
(0.0131)
0.1
(0.133)
0.0267
(0.0414)
0.215
(0.256)
0.435
(0.481)
0.499
(0.544)
amp 14q21 3 54 (12%) 387 4e-05
(0.000121)
0.00272
(0.00519)
0.919
(0.925)
0.263
(0.308)
0.029
(0.0441)
0.143
(0.182)
0.243
(0.286)
0.45
(0.497)
0.00912
(0.0158)
0.201
(0.242)
amp xq27 3 83 (19%) 358 0.0001
(0.000274)
0.0992
(0.132)
0.865
(0.878)
0.455
(0.501)
0.0205
(0.0327)
0.0081
(0.0142)
0.00066
(0.00149)
0.672
(0.706)
0.173
(0.212)
0.347
(0.396)
del 12q12 59 (13%) 382 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.762
(0.787)
0.91
(0.918)
0.0106
(0.018)
0.0693
(0.0955)
0.327
(0.375)
0.0192
(0.0311)
0.421
(0.47)
0.0567
(0.0805)
del 17q24 3 76 (17%) 365 1e-05
(3.58e-05)
0.0001
(0.000274)
0.868
(0.88)
0.427
(0.475)
0.00177
(0.00359)
0.0504
(0.0726)
0.86
(0.874)
0.0134
(0.0222)
0.362
(0.409)
0.537
(0.579)
amp 8p23 1 177 (40%) 264 0.00064
(0.00145)
4e-05
(0.000121)
0.151
(0.191)
0.817
(0.834)
0.169
(0.208)
0.0179
(0.0291)
0.0718
(0.0982)
0.164
(0.202)
0.755
(0.781)
0.202
(0.243)
amp 10q22 2 86 (20%) 355 1e-05
(3.58e-05)
0.00205
(0.00405)
0.807
(0.827)
0.385
(0.433)
0.182
(0.222)
0.0111
(0.0189)
0.259
(0.303)
0.333
(0.381)
0.152
(0.192)
0.349
(0.397)
amp 10q26 13 88 (20%) 353 1e-05
(3.58e-05)
0.00098
(0.00213)
0.632
(0.669)
0.323
(0.372)
0.0403
(0.0594)
0.0952
(0.127)
0.13
(0.169)
0.087
(0.117)
0.451
(0.497)
0.426
(0.475)
amp 12p12 1 128 (29%) 313 1e-05
(3.58e-05)
0.0157
(0.0257)
0.124
(0.162)
0.288
(0.336)
0.239
(0.282)
0.116
(0.153)
0.14
(0.179)
0.252
(0.296)
0.0257
(0.0399)
0.0527
(0.0757)
amp 12q15 109 (25%) 332 0.00047
(0.0011)
0.00652
(0.0117)
0.0176
(0.0286)
0.207
(0.247)
0.815
(0.833)
0.308
(0.356)
0.162
(0.202)
0.095
(0.127)
0.107
(0.141)
0.176
(0.216)
del 13q12 11 63 (14%) 378 1e-05
(3.58e-05)
0.0422
(0.0616)
0.541
(0.582)
0.236
(0.28)
0.337
(0.386)
0.0197
(0.0316)
0.898
(0.907)
0.2
(0.24)
0.68
(0.712)
0.672
(0.706)
del xq21 33 57 (13%) 384 1e-05
(3.58e-05)
1e-05
(3.58e-05)
0.737
(0.764)
0.0606
(0.0851)
0.0661
(0.0915)
0.258
(0.303)
0.263
(0.308)
0.0256
(0.0399)
0.215
(0.256)
0.153
(0.192)
amp 9p24 1 65 (15%) 376 0.933
(0.936)
0.163
(0.202)
0.503
(0.547)
0.725
(0.755)
0.125
(0.162)
0.0245
(0.0383)
0.052
(0.0747)
0.361
(0.409)
0.0329
(0.0496)
0.117
(0.153)
del 1q44 25 (6%) 416 0.00858
(0.015)
0.00185
(0.00373)
0.596
(0.636)
0.138
(0.178)
0.677
(0.711)
0.159
(0.199)
0.787
(0.809)
0.746
(0.772)
0.527
(0.571)
0.203
(0.243)
del 2q33 3 49 (11%) 392 2e-05
(6.62e-05)
0.165
(0.203)
0.0713
(0.0977)
0.427
(0.475)
0.219
(0.26)
0.17
(0.209)
0.0783
(0.106)
0.0044
(0.00812)
0.606
(0.645)
0.159
(0.199)
del xp21 1 76 (17%) 365 1e-05
(3.58e-05)
0.00529
(0.00966)
0.988
(0.988)
0.776
(0.799)
0.12
(0.157)
0.634
(0.671)
0.057
(0.0808)
0.191
(0.231)
0.427
(0.475)
0.561
(0.603)
'amp_1p36.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S1.  Gene #1: 'amp_1p36.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 1(1P36.22) MUTATED 59 2 5 0
AMP PEAK 1(1P36.22) WILD-TYPE 175 151 46 3

Figure S1.  Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1p36.22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S2.  Gene #1: 'amp_1p36.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 1(1P36.22) MUTATED 11 16 0 25 6
AMP PEAK 1(1P36.22) WILD-TYPE 34 94 51 75 81

Figure S2.  Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1p36.22' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00044

Table S3.  Gene #1: 'amp_1p36.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 1(1P36.22) MUTATED 27 5 10 14 6
AMP PEAK 1(1P36.22) WILD-TYPE 67 89 83 68 44

Figure S3.  Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1p36.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.018

Table S4.  Gene #1: 'amp_1p36.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
AMP PEAK 1(1P36.22) MUTATED 22 4 24 12
AMP PEAK 1(1P36.22) WILD-TYPE 87 78 111 75

Figure S4.  Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1p36.22' versus 'MIRSEQ_CNMF'

P value = 0.00335 (Fisher's exact test), Q value = 0.0063

Table S5.  Gene #1: 'amp_1p36.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
AMP PEAK 1(1P36.22) MUTATED 15 8 7 9 9 17
AMP PEAK 1(1P36.22) WILD-TYPE 46 58 73 102 41 49

Figure S5.  Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1p36.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0011

Table S6.  Gene #1: 'amp_1p36.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
AMP PEAK 1(1P36.22) MUTATED 34 4 27
AMP PEAK 1(1P36.22) WILD-TYPE 209 78 82

Figure S6.  Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1p36.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0289 (Fisher's exact test), Q value = 0.044

Table S7.  Gene #1: 'amp_1p36.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
AMP PEAK 1(1P36.22) MUTATED 15 4 4 13 13
AMP PEAK 1(1P36.22) WILD-TYPE 88 68 40 49 47

Figure S7.  Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S8.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 2(1Q21.3) MUTATED 130 11 18 1
AMP PEAK 2(1Q21.3) WILD-TYPE 104 142 33 2

Figure S8.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S9.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 2(1Q21.3) MUTATED 23 42 5 61 12
AMP PEAK 2(1Q21.3) WILD-TYPE 22 68 46 39 75

Figure S9.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q21.3' versus 'RPPA_CNMF'

P value = 0.0334 (Fisher's exact test), Q value = 0.05

Table S10.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 92 82 93 59
AMP PEAK 2(1Q21.3) MUTATED 10 37 35 22 26
AMP PEAK 2(1Q21.3) WILD-TYPE 20 55 47 71 33

Figure S10.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_1q21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00467 (Fisher's exact test), Q value = 0.0086

Table S11.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 58 78 80
AMP PEAK 2(1Q21.3) MUTATED 65 20 27 18
AMP PEAK 2(1Q21.3) WILD-TYPE 75 38 51 62

Figure S11.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S12.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 2(1Q21.3) MUTATED 61 18 28 25 19
AMP PEAK 2(1Q21.3) WILD-TYPE 33 76 65 57 31

Figure S12.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00051

Table S13.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
AMP PEAK 2(1Q21.3) MUTATED 43 14 61 33
AMP PEAK 2(1Q21.3) WILD-TYPE 66 68 74 54

Figure S13.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S14.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
AMP PEAK 2(1Q21.3) MUTATED 31 14 28 25 13 46
AMP PEAK 2(1Q21.3) WILD-TYPE 30 52 52 86 37 20

Figure S14.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S15.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
AMP PEAK 2(1Q21.3) MUTATED 74 19 64
AMP PEAK 2(1Q21.3) WILD-TYPE 169 63 45

Figure S15.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00306 (Fisher's exact test), Q value = 0.0058

Table S16.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
AMP PEAK 2(1Q21.3) MUTATED 66 34 19
AMP PEAK 2(1Q21.3) WILD-TYPE 81 87 54

Figure S16.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S17.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
AMP PEAK 2(1Q21.3) MUTATED 32 11 10 38 28
AMP PEAK 2(1Q21.3) WILD-TYPE 71 61 34 24 32

Figure S17.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q42.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S18.  Gene #3: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 3(1Q42.3) MUTATED 116 15 18 1
AMP PEAK 3(1Q42.3) WILD-TYPE 118 138 33 2

Figure S18.  Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q42.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S19.  Gene #3: 'amp_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 3(1Q42.3) MUTATED 20 33 6 61 14
AMP PEAK 3(1Q42.3) WILD-TYPE 25 77 45 39 73

Figure S19.  Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q42.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00235 (Fisher's exact test), Q value = 0.0045

Table S20.  Gene #3: 'amp_1q42.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 58 78 80
AMP PEAK 3(1Q42.3) MUTATED 62 15 29 17
AMP PEAK 3(1Q42.3) WILD-TYPE 78 43 49 63

Figure S20.  Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_1q42.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S21.  Gene #3: 'amp_1q42.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 3(1Q42.3) MUTATED 57 22 27 19 15
AMP PEAK 3(1Q42.3) WILD-TYPE 37 72 66 63 35

Figure S21.  Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q42.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.02

Table S22.  Gene #3: 'amp_1q42.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
AMP PEAK 3(1Q42.3) MUTATED 32 19 59 30
AMP PEAK 3(1Q42.3) WILD-TYPE 77 63 76 57

Figure S22.  Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1q42.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S23.  Gene #3: 'amp_1q42.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
AMP PEAK 3(1Q42.3) MUTATED 25 9 28 30 10 46
AMP PEAK 3(1Q42.3) WILD-TYPE 36 57 52 81 40 20

Figure S23.  Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q42.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S24.  Gene #3: 'amp_1q42.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
AMP PEAK 3(1Q42.3) MUTATED 62 22 64
AMP PEAK 3(1Q42.3) WILD-TYPE 181 60 45

Figure S24.  Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q42.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S25.  Gene #3: 'amp_1q42.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
AMP PEAK 3(1Q42.3) MUTATED 28 18 10 38 20
AMP PEAK 3(1Q42.3) WILD-TYPE 75 54 34 24 40

Figure S25.  Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S26.  Gene #4: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 4(3Q26.2) MUTATED 121 25 16 2
AMP PEAK 4(3Q26.2) WILD-TYPE 113 128 35 1

Figure S26.  Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S27.  Gene #4: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 4(3Q26.2) MUTATED 23 33 21 52 17
AMP PEAK 4(3Q26.2) WILD-TYPE 22 77 30 48 70

Figure S27.  Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.035

Table S28.  Gene #4: 'amp_3q26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 4(3Q26.2) MUTATED 44 27 34 37 13
AMP PEAK 4(3Q26.2) WILD-TYPE 50 67 59 45 37

Figure S28.  Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S29.  Gene #4: 'amp_3q26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
AMP PEAK 4(3Q26.2) MUTATED 54 20 62 19
AMP PEAK 4(3Q26.2) WILD-TYPE 55 62 73 68

Figure S29.  Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00561 (Fisher's exact test), Q value = 0.01

Table S30.  Gene #4: 'amp_3q26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
AMP PEAK 4(3Q26.2) MUTATED 85 23 54
AMP PEAK 4(3Q26.2) WILD-TYPE 158 59 55

Figure S30.  Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.00081

Table S31.  Gene #4: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
AMP PEAK 4(3Q26.2) MUTATED 36 16 11 36 24
AMP PEAK 4(3Q26.2) WILD-TYPE 67 56 33 26 36

Figure S31.  Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S32.  Gene #5: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 5(5P15.33) MUTATED 100 11 17 2
AMP PEAK 5(5P15.33) WILD-TYPE 134 142 34 1

Figure S32.  Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S33.  Gene #5: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 5(5P15.33) MUTATED 13 23 8 60 13
AMP PEAK 5(5P15.33) WILD-TYPE 32 87 43 40 74

Figure S33.  Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'RPPA_CNMF'

P value = 0.0351 (Fisher's exact test), Q value = 0.052

Table S34.  Gene #5: 'amp_5p15.33' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 92 82 93 59
AMP PEAK 5(5P15.33) MUTATED 7 28 28 14 17
AMP PEAK 5(5P15.33) WILD-TYPE 23 64 54 79 42

Figure S34.  Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_5p15.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.0371 (Fisher's exact test), Q value = 0.055

Table S35.  Gene #5: 'amp_5p15.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 58 78 80
AMP PEAK 5(5P15.33) MUTATED 48 15 17 14
AMP PEAK 5(5P15.33) WILD-TYPE 92 43 61 66

Figure S35.  Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S36.  Gene #5: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 5(5P15.33) MUTATED 56 12 18 21 17
AMP PEAK 5(5P15.33) WILD-TYPE 38 82 75 61 33

Figure S36.  Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 2e-04

Table S37.  Gene #5: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
AMP PEAK 5(5P15.33) MUTATED 34 10 56 24
AMP PEAK 5(5P15.33) WILD-TYPE 75 72 79 63

Figure S37.  Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S38.  Gene #5: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
AMP PEAK 5(5P15.33) MUTATED 21 17 16 19 16 39
AMP PEAK 5(5P15.33) WILD-TYPE 40 49 64 92 34 27

Figure S38.  Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S39.  Gene #5: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
AMP PEAK 5(5P15.33) MUTATED 58 14 56
AMP PEAK 5(5P15.33) WILD-TYPE 185 68 53

Figure S39.  Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00241 (Fisher's exact test), Q value = 0.0046

Table S40.  Gene #5: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
AMP PEAK 5(5P15.33) MUTATED 56 23 23
AMP PEAK 5(5P15.33) WILD-TYPE 91 98 50

Figure S40.  Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S41.  Gene #5: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
AMP PEAK 5(5P15.33) MUTATED 29 9 12 33 19
AMP PEAK 5(5P15.33) WILD-TYPE 74 63 32 29 41

Figure S41.  Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S42.  Gene #6: 'amp_5p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 6(5P13.1) MUTATED 94 12 18 2
AMP PEAK 6(5P13.1) WILD-TYPE 140 141 33 1

Figure S42.  Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S43.  Gene #6: 'amp_5p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 6(5P13.1) MUTATED 11 25 8 53 14
AMP PEAK 6(5P13.1) WILD-TYPE 34 85 43 47 73

Figure S43.  Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S44.  Gene #6: 'amp_5p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 6(5P13.1) MUTATED 53 16 19 17 14
AMP PEAK 6(5P13.1) WILD-TYPE 41 78 74 65 36

Figure S44.  Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00051

Table S45.  Gene #6: 'amp_5p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
AMP PEAK 6(5P13.1) MUTATED 29 13 57 20
AMP PEAK 6(5P13.1) WILD-TYPE 80 69 78 67

Figure S45.  Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5p13.1' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 3e-04

Table S46.  Gene #6: 'amp_5p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
AMP PEAK 6(5P13.1) MUTATED 19 16 17 24 13 36
AMP PEAK 6(5P13.1) WILD-TYPE 42 50 63 87 37 30

Figure S46.  Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S47.  Gene #6: 'amp_5p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
AMP PEAK 6(5P13.1) MUTATED 53 17 55
AMP PEAK 6(5P13.1) WILD-TYPE 190 65 54

Figure S47.  Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 3e-04

Table S48.  Gene #6: 'amp_5p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
AMP PEAK 6(5P13.1) MUTATED 32 12 9 32 14
AMP PEAK 6(5P13.1) WILD-TYPE 71 60 35 30 46

Figure S48.  Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S49.  Gene #7: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 7(6P21.1) MUTATED 111 5 6 2
AMP PEAK 7(6P21.1) WILD-TYPE 123 148 45 1

Figure S49.  Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S50.  Gene #7: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 7(6P21.1) MUTATED 13 28 2 59 6
AMP PEAK 7(6P21.1) WILD-TYPE 32 82 49 41 81

Figure S50.  Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p21.1' versus 'RPPA_CNMF'

P value = 0.0333 (Fisher's exact test), Q value = 0.05

Table S51.  Gene #7: 'amp_6p21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 92 82 93 59
AMP PEAK 7(6P21.1) MUTATED 10 36 25 17 16
AMP PEAK 7(6P21.1) WILD-TYPE 20 56 57 76 43

Figure S51.  Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S52.  Gene #7: 'amp_6p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 7(6P21.1) MUTATED 47 14 19 19 19
AMP PEAK 7(6P21.1) WILD-TYPE 47 80 74 63 31

Figure S52.  Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00135 (Fisher's exact test), Q value = 0.0028

Table S53.  Gene #7: 'amp_6p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
AMP PEAK 7(6P21.1) MUTATED 33 10 47 28
AMP PEAK 7(6P21.1) WILD-TYPE 76 72 88 59

Figure S53.  Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S54.  Gene #7: 'amp_6p21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
AMP PEAK 7(6P21.1) MUTATED 24 15 19 13 13 38
AMP PEAK 7(6P21.1) WILD-TYPE 37 51 61 98 37 28

Figure S54.  Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6p21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S55.  Gene #7: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
AMP PEAK 7(6P21.1) MUTATED 58 11 53
AMP PEAK 7(6P21.1) WILD-TYPE 185 71 56

Figure S55.  Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0035 (Fisher's exact test), Q value = 0.0066

Table S56.  Gene #7: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
AMP PEAK 7(6P21.1) MUTATED 56 25 17
AMP PEAK 7(6P21.1) WILD-TYPE 91 96 56

Figure S56.  Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S57.  Gene #7: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
AMP PEAK 7(6P21.1) MUTATED 25 8 11 34 20
AMP PEAK 7(6P21.1) WILD-TYPE 78 64 33 28 40

Figure S57.  Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S58.  Gene #8: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 8(6Q12) MUTATED 78 6 4 0
AMP PEAK 8(6Q12) WILD-TYPE 156 147 47 3

Figure S58.  Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S59.  Gene #8: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 8(6Q12) MUTATED 8 17 1 44 4
AMP PEAK 8(6Q12) WILD-TYPE 37 93 50 56 83

Figure S59.  Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S60.  Gene #8: 'amp_6q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 8(6Q12) MUTATED 40 9 11 12 13
AMP PEAK 8(6Q12) WILD-TYPE 54 85 82 70 37

Figure S60.  Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00558 (Fisher's exact test), Q value = 0.01

Table S61.  Gene #8: 'amp_6q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
AMP PEAK 8(6Q12) MUTATED 19 8 39 19
AMP PEAK 8(6Q12) WILD-TYPE 90 74 96 68

Figure S61.  Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S62.  Gene #8: 'amp_6q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
AMP PEAK 8(6Q12) MUTATED 16 11 10 13 5 31
AMP PEAK 8(6Q12) WILD-TYPE 45 55 70 98 45 35

Figure S62.  Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.5e-05

Table S63.  Gene #8: 'amp_6q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
AMP PEAK 8(6Q12) MUTATED 39 9 38
AMP PEAK 8(6Q12) WILD-TYPE 204 73 71

Figure S63.  Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 3e-04

Table S64.  Gene #8: 'amp_6q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
AMP PEAK 8(6Q12) MUTATED 15 7 5 25 13
AMP PEAK 8(6Q12) WILD-TYPE 88 65 39 37 47

Figure S64.  Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S65.  Gene #9: 'amp_6q21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 9(6Q21) MUTATED 75 4 3 0
AMP PEAK 9(6Q21) WILD-TYPE 159 149 48 3

Figure S65.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S66.  Gene #9: 'amp_6q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 9(6Q21) MUTATED 7 17 1 38 6
AMP PEAK 9(6Q21) WILD-TYPE 38 93 50 62 81

Figure S66.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S67.  Gene #9: 'amp_6q21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 9(6Q21) MUTATED 39 9 12 7 11
AMP PEAK 9(6Q21) WILD-TYPE 55 85 81 75 39

Figure S67.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6q21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00015

Table S68.  Gene #9: 'amp_6q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
AMP PEAK 9(6Q21) MUTATED 12 8 42 16
AMP PEAK 9(6Q21) WILD-TYPE 97 74 93 71

Figure S68.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S69.  Gene #9: 'amp_6q21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
AMP PEAK 9(6Q21) MUTATED 13 12 12 12 4 28
AMP PEAK 9(6Q21) WILD-TYPE 48 54 68 99 46 38

Figure S69.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6q21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S70.  Gene #9: 'amp_6q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
AMP PEAK 9(6Q21) MUTATED 36 6 39
AMP PEAK 9(6Q21) WILD-TYPE 207 76 70

Figure S70.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S71.  Gene #9: 'amp_6q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
AMP PEAK 9(6Q21) MUTATED 13 5 4 24 15
AMP PEAK 9(6Q21) WILD-TYPE 90 67 40 38 45

Figure S71.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S72.  Gene #10: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 10(7P22.1) MUTATED 148 32 47 2
AMP PEAK 10(7P22.1) WILD-TYPE 86 121 4 1

Figure S72.  Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S73.  Gene #10: 'amp_7p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 10(7P22.1) MUTATED 25 62 22 70 25
AMP PEAK 10(7P22.1) WILD-TYPE 20 48 29 30 62

Figure S73.  Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S74.  Gene #10: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 10(7P22.1) MUTATED 67 36 43 35 32
AMP PEAK 10(7P22.1) WILD-TYPE 27 58 50 47 18

Figure S74.  Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00194 (Fisher's exact test), Q value = 0.0039

Table S75.  Gene #10: 'amp_7p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
AMP PEAK 10(7P22.1) MUTATED 52 29 81 51
AMP PEAK 10(7P22.1) WILD-TYPE 57 53 54 36

Figure S75.  Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7p22.1' versus 'MIRSEQ_CNMF'

P value = 0.00185 (Fisher's exact test), Q value = 0.0037

Table S76.  Gene #10: 'amp_7p22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
AMP PEAK 10(7P22.1) MUTATED 37 31 44 46 20 46
AMP PEAK 10(7P22.1) WILD-TYPE 24 35 36 65 30 20

Figure S76.  Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7p22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00025

Table S77.  Gene #10: 'amp_7p22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
AMP PEAK 10(7P22.1) MUTATED 122 29 73
AMP PEAK 10(7P22.1) WILD-TYPE 121 53 36

Figure S77.  Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7p22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00949 (Fisher's exact test), Q value = 0.016

Table S78.  Gene #10: 'amp_7p22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
AMP PEAK 10(7P22.1) MUTATED 87 49 38
AMP PEAK 10(7P22.1) WILD-TYPE 60 72 35

Figure S78.  Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7p22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00068 (Fisher's exact test), Q value = 0.0015

Table S79.  Gene #10: 'amp_7p22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
AMP PEAK 10(7P22.1) MUTATED 55 22 22 41 34
AMP PEAK 10(7P22.1) WILD-TYPE 48 50 22 21 26

Figure S79.  Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S80.  Gene #11: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 11(7P11.2) MUTATED 131 31 50 2
AMP PEAK 11(7P11.2) WILD-TYPE 103 122 1 1

Figure S80.  Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S81.  Gene #11: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 11(7P11.2) MUTATED 21 60 21 65 24
AMP PEAK 11(7P11.2) WILD-TYPE 24 50 30 35 63

Figure S81.  Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 0.00088 (Fisher's exact test), Q value = 0.0019

Table S82.  Gene #11: 'amp_7p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 11(7P11.2) MUTATED 60 34 41 36 30
AMP PEAK 11(7P11.2) WILD-TYPE 34 60 52 46 20

Figure S82.  Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.046 (Fisher's exact test), Q value = 0.067

Table S83.  Gene #11: 'amp_7p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
AMP PEAK 11(7P11.2) MUTATED 53 29 72 47
AMP PEAK 11(7P11.2) WILD-TYPE 56 53 63 40

Figure S83.  Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 0.0283 (Fisher's exact test), Q value = 0.043

Table S84.  Gene #11: 'amp_7p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
AMP PEAK 11(7P11.2) MUTATED 34 29 43 42 21 40
AMP PEAK 11(7P11.2) WILD-TYPE 27 37 37 69 29 26

Figure S84.  Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00075 (Fisher's exact test), Q value = 0.0017

Table S85.  Gene #11: 'amp_7p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
AMP PEAK 11(7P11.2) MUTATED 116 27 66
AMP PEAK 11(7P11.2) WILD-TYPE 127 55 43

Figure S85.  Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.017

Table S86.  Gene #11: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
AMP PEAK 11(7P11.2) MUTATED 82 45 34
AMP PEAK 11(7P11.2) WILD-TYPE 65 76 39

Figure S86.  Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00469 (Fisher's exact test), Q value = 0.0086

Table S87.  Gene #11: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
AMP PEAK 11(7P11.2) MUTATED 50 21 20 36 34
AMP PEAK 11(7P11.2) WILD-TYPE 53 51 24 26 26

Figure S87.  Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S88.  Gene #12: 'amp_7q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 12(7Q21.2) MUTATED 122 31 50 1
AMP PEAK 12(7Q21.2) WILD-TYPE 112 122 1 2

Figure S88.  Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q21.2' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00017

Table S89.  Gene #12: 'amp_7q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 12(7Q21.2) MUTATED 21 50 21 63 24
AMP PEAK 12(7Q21.2) WILD-TYPE 24 60 30 37 63

Figure S89.  Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q21.2' versus 'MRNASEQ_CNMF'

P value = 0.0327 (Fisher's exact test), Q value = 0.05

Table S90.  Gene #12: 'amp_7q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 12(7Q21.2) MUTATED 49 34 40 38 31
AMP PEAK 12(7Q21.2) WILD-TYPE 45 60 53 44 19

Figure S90.  Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0197 (Fisher's exact test), Q value = 0.032

Table S91.  Gene #12: 'amp_7q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
AMP PEAK 12(7Q21.2) MUTATED 50 27 66 49
AMP PEAK 12(7Q21.2) WILD-TYPE 59 55 69 38

Figure S91.  Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'MIRSEQ_CNMF'

P value = 0.0405 (Fisher's exact test), Q value = 0.06

Table S92.  Gene #12: 'amp_7q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
AMP PEAK 12(7Q21.2) MUTATED 35 32 42 40 18 33
AMP PEAK 12(7Q21.2) WILD-TYPE 26 34 38 71 32 33

Figure S92.  Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00671 (Fisher's exact test), Q value = 0.012

Table S93.  Gene #12: 'amp_7q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
AMP PEAK 12(7Q21.2) MUTATED 115 26 59
AMP PEAK 12(7Q21.2) WILD-TYPE 128 56 50

Figure S93.  Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0239 (Fisher's exact test), Q value = 0.037

Table S94.  Gene #12: 'amp_7q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
AMP PEAK 12(7Q21.2) MUTATED 75 42 35
AMP PEAK 12(7Q21.2) WILD-TYPE 72 79 38

Figure S94.  Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0147 (Fisher's exact test), Q value = 0.024

Table S95.  Gene #12: 'amp_7q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
AMP PEAK 12(7Q21.2) MUTATED 46 20 22 34 30
AMP PEAK 12(7Q21.2) WILD-TYPE 57 52 22 28 30

Figure S95.  Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S96.  Gene #13: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 13(7Q22.1) MUTATED 119 31 50 2
AMP PEAK 13(7Q22.1) WILD-TYPE 115 122 1 1

Figure S96.  Get High-res Image Gene #13: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q22.1' versus 'METHLYATION_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0011

Table S97.  Gene #13: 'amp_7q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 13(7Q22.1) MUTATED 20 49 21 62 26
AMP PEAK 13(7Q22.1) WILD-TYPE 25 61 30 38 61

Figure S97.  Get High-res Image Gene #13: 'amp_7q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q22.1' versus 'MRNASEQ_CNMF'

P value = 0.0465 (Fisher's exact test), Q value = 0.067

Table S98.  Gene #13: 'amp_7q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 13(7Q22.1) MUTATED 48 35 39 37 31
AMP PEAK 13(7Q22.1) WILD-TYPE 46 59 54 45 19

Figure S98.  Get High-res Image Gene #13: 'amp_7q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0313 (Fisher's exact test), Q value = 0.047

Table S99.  Gene #13: 'amp_7q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
AMP PEAK 13(7Q22.1) MUTATED 112 28 58
AMP PEAK 13(7Q22.1) WILD-TYPE 131 54 51

Figure S99.  Get High-res Image Gene #13: 'amp_7q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.041 (Fisher's exact test), Q value = 0.06

Table S100.  Gene #13: 'amp_7q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
AMP PEAK 13(7Q22.1) MUTATED 76 44 33
AMP PEAK 13(7Q22.1) WILD-TYPE 71 77 40

Figure S100.  Get High-res Image Gene #13: 'amp_7q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0275 (Fisher's exact test), Q value = 0.043

Table S101.  Gene #13: 'amp_7q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
AMP PEAK 13(7Q22.1) MUTATED 47 21 20 33 32
AMP PEAK 13(7Q22.1) WILD-TYPE 56 51 24 29 28

Figure S101.  Get High-res Image Gene #13: 'amp_7q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p23.1' versus 'CN_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.0014

Table S102.  Gene #14: 'amp_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 14(8P23.1) MUTATED 79 78 17 3
AMP PEAK 14(8P23.1) WILD-TYPE 155 75 34 0

Figure S102.  Get High-res Image Gene #14: 'amp_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p23.1' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S103.  Gene #14: 'amp_8p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 14(8P23.1) MUTATED 12 66 18 31 27
AMP PEAK 14(8P23.1) WILD-TYPE 33 44 33 69 60

Figure S103.  Get High-res Image Gene #14: 'amp_8p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8p23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0179 (Fisher's exact test), Q value = 0.029

Table S104.  Gene #14: 'amp_8p23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
AMP PEAK 14(8P23.1) MUTATED 51 37 40 39
AMP PEAK 14(8P23.1) WILD-TYPE 58 45 95 48

Figure S104.  Get High-res Image Gene #14: 'amp_8p23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 0.00742 (Fisher's exact test), Q value = 0.013

Table S105.  Gene #15: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 15(8Q24.21) MUTATED 177 92 37 3
AMP PEAK 15(8Q24.21) WILD-TYPE 57 61 14 0

Figure S105.  Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S106.  Gene #15: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 15(8Q24.21) MUTATED 25 89 23 87 48
AMP PEAK 15(8Q24.21) WILD-TYPE 20 21 28 13 39

Figure S106.  Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S107.  Gene #15: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 15(8Q24.21) MUTATED 85 55 64 50 36
AMP PEAK 15(8Q24.21) WILD-TYPE 9 39 29 32 14

Figure S107.  Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S108.  Gene #15: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
AMP PEAK 15(8Q24.21) MUTATED 51 46 53 60 36 59
AMP PEAK 15(8Q24.21) WILD-TYPE 10 20 27 51 14 7

Figure S108.  Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00044

Table S109.  Gene #15: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
AMP PEAK 15(8Q24.21) MUTATED 165 48 92
AMP PEAK 15(8Q24.21) WILD-TYPE 78 34 17

Figure S109.  Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00897 (Fisher's exact test), Q value = 0.016

Table S110.  Gene #15: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
AMP PEAK 15(8Q24.21) MUTATED 113 72 52
AMP PEAK 15(8Q24.21) WILD-TYPE 34 49 21

Figure S110.  Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00064 (Fisher's exact test), Q value = 0.0014

Table S111.  Gene #15: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
AMP PEAK 15(8Q24.21) MUTATED 74 37 30 53 43
AMP PEAK 15(8Q24.21) WILD-TYPE 29 35 14 9 17

Figure S111.  Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9p24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0245 (Fisher's exact test), Q value = 0.038

Table S112.  Gene #16: 'amp_9p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
AMP PEAK 16(9P24.1) MUTATED 16 6 30 11
AMP PEAK 16(9P24.1) WILD-TYPE 93 76 105 76

Figure S112.  Get High-res Image Gene #16: 'amp_9p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_9p24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 0.05

Table S113.  Gene #16: 'amp_9p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
AMP PEAK 16(9P24.1) MUTATED 23 9 14
AMP PEAK 16(9P24.1) WILD-TYPE 124 112 59

Figure S113.  Get High-res Image Gene #16: 'amp_9p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_9p13.2' versus 'CN_CNMF'

P value = 0.04 (Fisher's exact test), Q value = 0.059

Table S114.  Gene #17: 'amp_9p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 17(9P13.2) MUTATED 59 21 11 0
AMP PEAK 17(9P13.2) WILD-TYPE 175 132 40 3

Figure S114.  Get High-res Image Gene #17: 'amp_9p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0442 (Fisher's exact test), Q value = 0.064

Table S115.  Gene #17: 'amp_9p13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 58 78 80
AMP PEAK 17(9P13.2) MUTATED 37 8 18 10
AMP PEAK 17(9P13.2) WILD-TYPE 103 50 60 70

Figure S115.  Get High-res Image Gene #17: 'amp_9p13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_9p13.2' versus 'MRNASEQ_CNMF'

P value = 0.0376 (Fisher's exact test), Q value = 0.056

Table S116.  Gene #17: 'amp_9p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 17(9P13.2) MUTATED 25 10 19 18 14
AMP PEAK 17(9P13.2) WILD-TYPE 69 84 74 64 36

Figure S116.  Get High-res Image Gene #17: 'amp_9p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_9p13.2' versus 'MIRSEQ_CNMF'

P value = 0.00599 (Fisher's exact test), Q value = 0.011

Table S117.  Gene #17: 'amp_9p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
AMP PEAK 17(9P13.2) MUTATED 16 13 18 10 12 20
AMP PEAK 17(9P13.2) WILD-TYPE 45 53 62 101 38 46

Figure S117.  Get High-res Image Gene #17: 'amp_9p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_9q34.3' versus 'CN_CNMF'

P value = 0.00177 (Fisher's exact test), Q value = 0.0036

Table S118.  Gene #18: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 18(9Q34.3) MUTATED 78 26 17 1
AMP PEAK 18(9Q34.3) WILD-TYPE 156 127 34 2

Figure S118.  Get High-res Image Gene #18: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9q34.3' versus 'METHLYATION_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.033

Table S119.  Gene #18: 'amp_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 18(9Q34.3) MUTATED 16 31 7 36 19
AMP PEAK 18(9Q34.3) WILD-TYPE 29 79 44 64 68

Figure S119.  Get High-res Image Gene #18: 'amp_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9q34.3' versus 'MRNASEQ_CNMF'

P value = 0.00743 (Fisher's exact test), Q value = 0.013

Table S120.  Gene #18: 'amp_9q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 18(9Q34.3) MUTATED 32 14 29 20 19
AMP PEAK 18(9Q34.3) WILD-TYPE 62 80 64 62 31

Figure S120.  Get High-res Image Gene #18: 'amp_9q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_9q34.3' versus 'MIRSEQ_CNMF'

P value = 0.0267 (Fisher's exact test), Q value = 0.041

Table S121.  Gene #18: 'amp_9q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
AMP PEAK 18(9Q34.3) MUTATED 24 12 26 22 14 22
AMP PEAK 18(9Q34.3) WILD-TYPE 37 54 54 89 36 44

Figure S121.  Get High-res Image Gene #18: 'amp_9q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_10p11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S122.  Gene #19: 'amp_10p11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 19(10P11.22) MUTATED 95 8 16 0
AMP PEAK 19(10P11.22) WILD-TYPE 139 145 35 3

Figure S122.  Get High-res Image Gene #19: 'amp_10p11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10p11.22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S123.  Gene #19: 'amp_10p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 19(10P11.22) MUTATED 10 29 4 50 14
AMP PEAK 19(10P11.22) WILD-TYPE 35 81 47 50 73

Figure S123.  Get High-res Image Gene #19: 'amp_10p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_10p11.22' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 2e-04

Table S124.  Gene #19: 'amp_10p11.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 19(10P11.22) MUTATED 44 16 21 19 14
AMP PEAK 19(10P11.22) WILD-TYPE 50 78 72 63 36

Figure S124.  Get High-res Image Gene #19: 'amp_10p11.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_10p11.22' versus 'MIRSEQ_CNMF'

P value = 0.00191 (Fisher's exact test), Q value = 0.0038

Table S125.  Gene #19: 'amp_10p11.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
AMP PEAK 19(10P11.22) MUTATED 22 11 18 22 14 29
AMP PEAK 19(10P11.22) WILD-TYPE 39 55 62 89 36 37

Figure S125.  Get High-res Image Gene #19: 'amp_10p11.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_10p11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S126.  Gene #19: 'amp_10p11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
AMP PEAK 19(10P11.22) MUTATED 50 17 49
AMP PEAK 19(10P11.22) WILD-TYPE 193 65 60

Figure S126.  Get High-res Image Gene #19: 'amp_10p11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_10p11.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.018

Table S127.  Gene #19: 'amp_10p11.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
AMP PEAK 19(10P11.22) MUTATED 52 26 14
AMP PEAK 19(10P11.22) WILD-TYPE 95 95 59

Figure S127.  Get High-res Image Gene #19: 'amp_10p11.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_10p11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 3e-04

Table S128.  Gene #19: 'amp_10p11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
AMP PEAK 19(10P11.22) MUTATED 22 10 8 29 23
AMP PEAK 19(10P11.22) WILD-TYPE 81 62 36 33 37

Figure S128.  Get High-res Image Gene #19: 'amp_10p11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10q22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S129.  Gene #20: 'amp_10q22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 20(10Q22.2) MUTATED 71 9 6 0
AMP PEAK 20(10Q22.2) WILD-TYPE 163 144 45 3

Figure S129.  Get High-res Image Gene #20: 'amp_10q22.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10q22.2' versus 'METHLYATION_CNMF'

P value = 0.00205 (Fisher's exact test), Q value = 0.0041

Table S130.  Gene #20: 'amp_10q22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 20(10Q22.2) MUTATED 15 26 5 23 8
AMP PEAK 20(10Q22.2) WILD-TYPE 30 84 46 77 79

Figure S130.  Get High-res Image Gene #20: 'amp_10q22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_10q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0111 (Fisher's exact test), Q value = 0.019

Table S131.  Gene #20: 'amp_10q22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
AMP PEAK 20(10Q22.2) MUTATED 27 13 33 8
AMP PEAK 20(10Q22.2) WILD-TYPE 82 69 102 79

Figure S131.  Get High-res Image Gene #20: 'amp_10q22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_10q26.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S132.  Gene #21: 'amp_10q26.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 21(10Q26.13) MUTATED 72 11 5 0
AMP PEAK 21(10Q26.13) WILD-TYPE 162 142 46 3

Figure S132.  Get High-res Image Gene #21: 'amp_10q26.13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10q26.13' versus 'METHLYATION_CNMF'

P value = 0.00098 (Fisher's exact test), Q value = 0.0021

Table S133.  Gene #21: 'amp_10q26.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 21(10Q26.13) MUTATED 12 18 4 31 10
AMP PEAK 21(10Q26.13) WILD-TYPE 33 92 47 69 77

Figure S133.  Get High-res Image Gene #21: 'amp_10q26.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_10q26.13' versus 'MRNASEQ_CNMF'

P value = 0.0403 (Fisher's exact test), Q value = 0.059

Table S134.  Gene #21: 'amp_10q26.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 21(10Q26.13) MUTATED 29 18 15 13 6
AMP PEAK 21(10Q26.13) WILD-TYPE 65 76 78 69 44

Figure S134.  Get High-res Image Gene #21: 'amp_10q26.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_11p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S135.  Gene #22: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 22(11P13) MUTATED 69 11 8 0
AMP PEAK 22(11P13) WILD-TYPE 165 142 43 3

Figure S135.  Get High-res Image Gene #22: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11p13' versus 'METHLYATION_CNMF'

P value = 0.00147 (Fisher's exact test), Q value = 0.003

Table S136.  Gene #22: 'amp_11p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 22(11P13) MUTATED 10 13 8 34 14
AMP PEAK 22(11P13) WILD-TYPE 35 97 43 66 73

Figure S136.  Get High-res Image Gene #22: 'amp_11p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11p13' versus 'MIRSEQ_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0014

Table S137.  Gene #22: 'amp_11p13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
AMP PEAK 22(11P13) MUTATED 14 9 13 17 6 27
AMP PEAK 22(11P13) WILD-TYPE 47 57 67 94 44 39

Figure S137.  Get High-res Image Gene #22: 'amp_11p13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_11p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S138.  Gene #22: 'amp_11p13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
AMP PEAK 22(11P13) MUTATED 35 12 39
AMP PEAK 22(11P13) WILD-TYPE 208 70 70

Figure S138.  Get High-res Image Gene #22: 'amp_11p13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00107 (Fisher's exact test), Q value = 0.0023

Table S139.  Gene #22: 'amp_11p13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
AMP PEAK 22(11P13) MUTATED 16 10 6 25 10
AMP PEAK 22(11P13) WILD-TYPE 87 62 38 37 50

Figure S139.  Get High-res Image Gene #22: 'amp_11p13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S140.  Gene #23: 'amp_11p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 23(11P11.2) MUTATED 78 7 7 0
AMP PEAK 23(11P11.2) WILD-TYPE 156 146 44 3

Figure S140.  Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11p11.2' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S141.  Gene #23: 'amp_11p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 23(11P11.2) MUTATED 11 15 8 38 9
AMP PEAK 23(11P11.2) WILD-TYPE 34 95 43 62 78

Figure S141.  Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0389 (Fisher's exact test), Q value = 0.058

Table S142.  Gene #23: 'amp_11p11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 58 78 80
AMP PEAK 23(11P11.2) MUTATED 35 6 20 12
AMP PEAK 23(11P11.2) WILD-TYPE 105 52 58 68

Figure S142.  Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_11p11.2' versus 'MRNASEQ_CNMF'

P value = 0.00116 (Fisher's exact test), Q value = 0.0025

Table S143.  Gene #23: 'amp_11p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 23(11P11.2) MUTATED 35 14 14 14 10
AMP PEAK 23(11P11.2) WILD-TYPE 59 80 79 68 40

Figure S143.  Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_11p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00973 (Fisher's exact test), Q value = 0.017

Table S144.  Gene #23: 'amp_11p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
AMP PEAK 23(11P11.2) MUTATED 22 9 40 16
AMP PEAK 23(11P11.2) WILD-TYPE 87 73 95 71

Figure S144.  Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11p11.2' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00015

Table S145.  Gene #23: 'amp_11p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
AMP PEAK 23(11P11.2) MUTATED 18 10 13 12 9 27
AMP PEAK 23(11P11.2) WILD-TYPE 43 56 67 99 41 39

Figure S145.  Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_11p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S146.  Gene #23: 'amp_11p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
AMP PEAK 23(11P11.2) MUTATED 41 6 42
AMP PEAK 23(11P11.2) WILD-TYPE 202 76 67

Figure S146.  Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0022 (Fisher's exact test), Q value = 0.0043

Table S147.  Gene #23: 'amp_11p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
AMP PEAK 23(11P11.2) MUTATED 42 18 8
AMP PEAK 23(11P11.2) WILD-TYPE 105 103 65

Figure S147.  Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_11p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S148.  Gene #23: 'amp_11p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
AMP PEAK 23(11P11.2) MUTATED 19 4 6 25 14
AMP PEAK 23(11P11.2) WILD-TYPE 84 68 38 37 46

Figure S148.  Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S149.  Gene #24: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 24(11Q13.3) MUTATED 95 11 7 2
AMP PEAK 24(11Q13.3) WILD-TYPE 139 142 44 1

Figure S149.  Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 0.00191 (Fisher's exact test), Q value = 0.0038

Table S150.  Gene #24: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 24(11Q13.3) MUTATED 16 28 7 37 14
AMP PEAK 24(11Q13.3) WILD-TYPE 29 82 44 63 73

Figure S150.  Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'RPPA_CNMF'

P value = 0.0432 (Fisher's exact test), Q value = 0.063

Table S151.  Gene #24: 'amp_11q13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 92 82 93 59
AMP PEAK 24(11Q13.3) MUTATED 3 32 23 20 12
AMP PEAK 24(11Q13.3) WILD-TYPE 27 60 59 73 47

Figure S151.  Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 0.00655 (Fisher's exact test), Q value = 0.012

Table S152.  Gene #24: 'amp_11q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 24(11Q13.3) MUTATED 35 13 24 24 13
AMP PEAK 24(11Q13.3) WILD-TYPE 59 81 69 58 37

Figure S152.  Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0021 (Fisher's exact test), Q value = 0.0041

Table S153.  Gene #24: 'amp_11q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
AMP PEAK 24(11Q13.3) MUTATED 35 10 44 20
AMP PEAK 24(11Q13.3) WILD-TYPE 74 72 91 67

Figure S153.  Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.00083

Table S154.  Gene #24: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
AMP PEAK 24(11Q13.3) MUTATED 21 11 23 16 13 28
AMP PEAK 24(11Q13.3) WILD-TYPE 40 55 57 95 37 38

Figure S154.  Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.00098

Table S155.  Gene #24: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
AMP PEAK 24(11Q13.3) MUTATED 64 9 39
AMP PEAK 24(11Q13.3) WILD-TYPE 179 73 70

Figure S155.  Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00177 (Fisher's exact test), Q value = 0.0036

Table S156.  Gene #24: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
AMP PEAK 24(11Q13.3) MUTATED 52 26 11
AMP PEAK 24(11Q13.3) WILD-TYPE 95 95 62

Figure S156.  Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00106 (Fisher's exact test), Q value = 0.0023

Table S157.  Gene #24: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
AMP PEAK 24(11Q13.3) MUTATED 32 8 7 23 19
AMP PEAK 24(11Q13.3) WILD-TYPE 71 64 37 39 41

Figure S157.  Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S158.  Gene #25: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 25(12P12.1) MUTATED 86 19 22 1
AMP PEAK 25(12P12.1) WILD-TYPE 148 134 29 2

Figure S158.  Get High-res Image Gene #25: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p12.1' versus 'METHLYATION_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.026

Table S159.  Gene #25: 'amp_12p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 25(12P12.1) MUTATED 22 34 12 33 18
AMP PEAK 25(12P12.1) WILD-TYPE 23 76 39 67 69

Figure S159.  Get High-res Image Gene #25: 'amp_12p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0257 (Fisher's exact test), Q value = 0.04

Table S160.  Gene #25: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
AMP PEAK 25(12P12.1) MUTATED 55 29 17
AMP PEAK 25(12P12.1) WILD-TYPE 92 92 56

Figure S160.  Get High-res Image Gene #25: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_12q15' versus 'CN_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0011

Table S161.  Gene #26: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 26(12Q15) MUTATED 73 21 14 1
AMP PEAK 26(12Q15) WILD-TYPE 161 132 37 2

Figure S161.  Get High-res Image Gene #26: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 0.00652 (Fisher's exact test), Q value = 0.012

Table S162.  Gene #26: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 26(12Q15) MUTATED 18 21 16 29 13
AMP PEAK 26(12Q15) WILD-TYPE 27 89 35 71 74

Figure S162.  Get High-res Image Gene #26: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12q15' versus 'RPPA_CNMF'

P value = 0.0176 (Fisher's exact test), Q value = 0.029

Table S163.  Gene #26: 'amp_12q15' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 92 82 93 59
AMP PEAK 26(12Q15) MUTATED 12 15 23 15 17
AMP PEAK 26(12Q15) WILD-TYPE 18 77 59 78 42

Figure S163.  Get High-res Image Gene #26: 'amp_12q15' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_13q12.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S164.  Gene #27: 'amp_13q12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 27(13Q12.3) MUTATED 113 22 34 1
AMP PEAK 27(13Q12.3) WILD-TYPE 121 131 17 2

Figure S164.  Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q12.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S165.  Gene #27: 'amp_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 27(13Q12.3) MUTATED 16 39 9 62 25
AMP PEAK 27(13Q12.3) WILD-TYPE 29 71 42 38 62

Figure S165.  Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q12.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S166.  Gene #27: 'amp_13q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 27(13Q12.3) MUTATED 56 25 33 17 30
AMP PEAK 27(13Q12.3) WILD-TYPE 38 69 60 65 20

Figure S166.  Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q12.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00119 (Fisher's exact test), Q value = 0.0025

Table S167.  Gene #27: 'amp_13q12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
AMP PEAK 27(13Q12.3) MUTATED 36 21 58 46
AMP PEAK 27(13Q12.3) WILD-TYPE 73 61 77 41

Figure S167.  Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_13q12.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S168.  Gene #27: 'amp_13q12.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
AMP PEAK 27(13Q12.3) MUTATED 34 22 31 29 8 43
AMP PEAK 27(13Q12.3) WILD-TYPE 27 44 49 82 42 23

Figure S168.  Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_13q12.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 3e-04

Table S169.  Gene #27: 'amp_13q12.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
AMP PEAK 27(13Q12.3) MUTATED 80 26 61
AMP PEAK 27(13Q12.3) WILD-TYPE 163 56 48

Figure S169.  Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_13q12.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S170.  Gene #27: 'amp_13q12.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
AMP PEAK 27(13Q12.3) MUTATED 34 21 17 41 16
AMP PEAK 27(13Q12.3) WILD-TYPE 69 51 27 21 44

Figure S170.  Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S171.  Gene #28: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 28(13Q22.1) MUTATED 124 26 31 0
AMP PEAK 28(13Q22.1) WILD-TYPE 110 127 20 3

Figure S171.  Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S172.  Gene #28: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 28(13Q22.1) MUTATED 17 38 10 69 25
AMP PEAK 28(13Q22.1) WILD-TYPE 28 72 41 31 62

Figure S172.  Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S173.  Gene #28: 'amp_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 28(13Q22.1) MUTATED 64 22 36 19 28
AMP PEAK 28(13Q22.1) WILD-TYPE 30 72 57 63 22

Figure S173.  Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S174.  Gene #28: 'amp_13q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
AMP PEAK 28(13Q22.1) MUTATED 36 19 69 45
AMP PEAK 28(13Q22.1) WILD-TYPE 73 63 66 42

Figure S174.  Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S175.  Gene #28: 'amp_13q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
AMP PEAK 28(13Q22.1) MUTATED 35 23 27 30 13 49
AMP PEAK 28(13Q22.1) WILD-TYPE 26 43 53 81 37 17

Figure S175.  Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_13q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S176.  Gene #28: 'amp_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
AMP PEAK 28(13Q22.1) MUTATED 82 26 69
AMP PEAK 28(13Q22.1) WILD-TYPE 161 56 40

Figure S176.  Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00022

Table S177.  Gene #28: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
AMP PEAK 28(13Q22.1) MUTATED 38 20 17 42 21
AMP PEAK 28(13Q22.1) WILD-TYPE 65 52 27 20 39

Figure S177.  Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_14q21.3' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S178.  Gene #29: 'amp_14q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 29(14Q21.3) MUTATED 41 5 8 0
AMP PEAK 29(14Q21.3) WILD-TYPE 193 148 43 3

Figure S178.  Get High-res Image Gene #29: 'amp_14q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_14q21.3' versus 'METHLYATION_CNMF'

P value = 0.00272 (Fisher's exact test), Q value = 0.0052

Table S179.  Gene #29: 'amp_14q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 29(14Q21.3) MUTATED 10 14 0 16 8
AMP PEAK 29(14Q21.3) WILD-TYPE 35 96 51 84 79

Figure S179.  Get High-res Image Gene #29: 'amp_14q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_14q21.3' versus 'MRNASEQ_CNMF'

P value = 0.029 (Fisher's exact test), Q value = 0.044

Table S180.  Gene #29: 'amp_14q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 29(14Q21.3) MUTATED 18 6 7 9 9
AMP PEAK 29(14Q21.3) WILD-TYPE 76 88 86 73 41

Figure S180.  Get High-res Image Gene #29: 'amp_14q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_14q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00912 (Fisher's exact test), Q value = 0.016

Table S181.  Gene #29: 'amp_14q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
AMP PEAK 29(14Q21.3) MUTATED 27 9 5
AMP PEAK 29(14Q21.3) WILD-TYPE 120 112 68

Figure S181.  Get High-res Image Gene #29: 'amp_14q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_15q26.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S182.  Gene #30: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 30(15Q26.1) MUTATED 97 9 7 0
AMP PEAK 30(15Q26.1) WILD-TYPE 137 144 44 3

Figure S182.  Get High-res Image Gene #30: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_15q26.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S183.  Gene #30: 'amp_15q26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 30(15Q26.1) MUTATED 21 27 2 41 11
AMP PEAK 30(15Q26.1) WILD-TYPE 24 83 49 59 76

Figure S183.  Get High-res Image Gene #30: 'amp_15q26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_15q26.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.019

Table S184.  Gene #30: 'amp_15q26.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 58 78 80
AMP PEAK 30(15Q26.1) MUTATED 46 12 22 11
AMP PEAK 30(15Q26.1) WILD-TYPE 94 46 56 69

Figure S184.  Get High-res Image Gene #30: 'amp_15q26.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_15q26.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S185.  Gene #30: 'amp_15q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 30(15Q26.1) MUTATED 39 8 24 20 14
AMP PEAK 30(15Q26.1) WILD-TYPE 55 86 69 62 36

Figure S185.  Get High-res Image Gene #30: 'amp_15q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_15q26.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S186.  Gene #30: 'amp_15q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
AMP PEAK 30(15Q26.1) MUTATED 25 6 51 23
AMP PEAK 30(15Q26.1) WILD-TYPE 84 76 84 64

Figure S186.  Get High-res Image Gene #30: 'amp_15q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.1' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00015

Table S187.  Gene #30: 'amp_15q26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
AMP PEAK 30(15Q26.1) MUTATED 19 17 18 13 12 32
AMP PEAK 30(15Q26.1) WILD-TYPE 42 49 62 98 38 34

Figure S187.  Get High-res Image Gene #30: 'amp_15q26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_15q26.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S188.  Gene #30: 'amp_15q26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
AMP PEAK 30(15Q26.1) MUTATED 61 8 42
AMP PEAK 30(15Q26.1) WILD-TYPE 182 74 67

Figure S188.  Get High-res Image Gene #30: 'amp_15q26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_15q26.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00032

Table S189.  Gene #30: 'amp_15q26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
AMP PEAK 30(15Q26.1) MUTATED 51 17 25
AMP PEAK 30(15Q26.1) WILD-TYPE 96 104 48

Figure S189.  Get High-res Image Gene #30: 'amp_15q26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_15q26.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.0018

Table S190.  Gene #30: 'amp_15q26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
AMP PEAK 30(15Q26.1) MUTATED 29 7 15 24 18
AMP PEAK 30(15Q26.1) WILD-TYPE 74 65 29 38 42

Figure S190.  Get High-res Image Gene #30: 'amp_15q26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S191.  Gene #31: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 31(17Q12) MUTATED 121 11 13 2
AMP PEAK 31(17Q12) WILD-TYPE 113 142 38 1

Figure S191.  Get High-res Image Gene #31: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S192.  Gene #31: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 31(17Q12) MUTATED 16 30 16 59 12
AMP PEAK 31(17Q12) WILD-TYPE 29 80 35 41 75

Figure S192.  Get High-res Image Gene #31: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q12' versus 'RPPA_CNMF'

P value = 0.00726 (Fisher's exact test), Q value = 0.013

Table S193.  Gene #31: 'amp_17q12' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 92 82 93 59
AMP PEAK 31(17Q12) MUTATED 16 37 24 22 14
AMP PEAK 31(17Q12) WILD-TYPE 14 55 58 71 45

Figure S193.  Get High-res Image Gene #31: 'amp_17q12' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_17q12' versus 'RPPA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00017

Table S194.  Gene #31: 'amp_17q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 58 78 80
AMP PEAK 31(17Q12) MUTATED 55 7 33 18
AMP PEAK 31(17Q12) WILD-TYPE 85 51 45 62

Figure S194.  Get High-res Image Gene #31: 'amp_17q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S195.  Gene #31: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 31(17Q12) MUTATED 54 12 27 28 16
AMP PEAK 31(17Q12) WILD-TYPE 40 82 66 54 34

Figure S195.  Get High-res Image Gene #31: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00015

Table S196.  Gene #31: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
AMP PEAK 31(17Q12) MUTATED 39 12 61 25
AMP PEAK 31(17Q12) WILD-TYPE 70 70 74 62

Figure S196.  Get High-res Image Gene #31: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S197.  Gene #31: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
AMP PEAK 31(17Q12) MUTATED 21 17 26 20 20 40
AMP PEAK 31(17Q12) WILD-TYPE 40 49 54 91 30 26

Figure S197.  Get High-res Image Gene #31: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S198.  Gene #31: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
AMP PEAK 31(17Q12) MUTATED 71 16 57
AMP PEAK 31(17Q12) WILD-TYPE 172 66 52

Figure S198.  Get High-res Image Gene #31: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00151 (Fisher's exact test), Q value = 0.0031

Table S199.  Gene #31: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
AMP PEAK 31(17Q12) MUTATED 34 13 16 32 18
AMP PEAK 31(17Q12) WILD-TYPE 69 59 28 30 42

Figure S199.  Get High-res Image Gene #31: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S200.  Gene #32: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 32(18Q11.2) MUTATED 109 16 15 0
AMP PEAK 32(18Q11.2) WILD-TYPE 125 137 36 3

Figure S200.  Get High-res Image Gene #32: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00017

Table S201.  Gene #32: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 32(18Q11.2) MUTATED 19 32 6 46 20
AMP PEAK 32(18Q11.2) WILD-TYPE 26 78 45 54 67

Figure S201.  Get High-res Image Gene #32: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S202.  Gene #32: 'amp_18q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 32(18Q11.2) MUTATED 47 17 22 33 10
AMP PEAK 32(18Q11.2) WILD-TYPE 47 77 71 49 40

Figure S202.  Get High-res Image Gene #32: 'amp_18q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00108 (Fisher's exact test), Q value = 0.0023

Table S203.  Gene #32: 'amp_18q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
AMP PEAK 32(18Q11.2) MUTATED 46 16 48 19
AMP PEAK 32(18Q11.2) WILD-TYPE 63 66 87 68

Figure S203.  Get High-res Image Gene #32: 'amp_18q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.026

Table S204.  Gene #32: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
AMP PEAK 32(18Q11.2) MUTATED 20 17 22 28 18 33
AMP PEAK 32(18Q11.2) WILD-TYPE 41 49 58 83 32 33

Figure S204.  Get High-res Image Gene #32: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.00072

Table S205.  Gene #32: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
AMP PEAK 32(18Q11.2) MUTATED 66 20 52
AMP PEAK 32(18Q11.2) WILD-TYPE 177 62 57

Figure S205.  Get High-res Image Gene #32: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0288 (Fisher's exact test), Q value = 0.044

Table S206.  Gene #32: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
AMP PEAK 32(18Q11.2) MUTATED 26 16 11 27 23
AMP PEAK 32(18Q11.2) WILD-TYPE 77 56 33 35 37

Figure S206.  Get High-res Image Gene #32: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S207.  Gene #33: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 33(19Q12) MUTATED 104 12 14 0
AMP PEAK 33(19Q12) WILD-TYPE 130 141 37 3

Figure S207.  Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S208.  Gene #33: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 33(19Q12) MUTATED 11 20 9 62 16
AMP PEAK 33(19Q12) WILD-TYPE 34 90 42 38 71

Figure S208.  Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q12' versus 'RPPA_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.00068

Table S209.  Gene #33: 'amp_19q12' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 92 82 93 59
AMP PEAK 33(19Q12) MUTATED 9 20 37 15 21
AMP PEAK 33(19Q12) WILD-TYPE 21 72 45 78 38

Figure S209.  Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_19q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00034

Table S210.  Gene #33: 'amp_19q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 58 78 80
AMP PEAK 33(19Q12) MUTATED 59 11 17 15
AMP PEAK 33(19Q12) WILD-TYPE 81 47 61 65

Figure S210.  Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S211.  Gene #33: 'amp_19q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 33(19Q12) MUTATED 57 15 18 18 13
AMP PEAK 33(19Q12) WILD-TYPE 37 79 75 64 37

Figure S211.  Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S212.  Gene #33: 'amp_19q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
AMP PEAK 33(19Q12) MUTATED 26 13 60 22
AMP PEAK 33(19Q12) WILD-TYPE 83 69 75 65

Figure S212.  Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S213.  Gene #33: 'amp_19q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
AMP PEAK 33(19Q12) MUTATED 18 13 18 26 7 47
AMP PEAK 33(19Q12) WILD-TYPE 43 53 62 85 43 19

Figure S213.  Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S214.  Gene #33: 'amp_19q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
AMP PEAK 33(19Q12) MUTATED 46 15 68
AMP PEAK 33(19Q12) WILD-TYPE 197 67 41

Figure S214.  Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S215.  Gene #33: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
AMP PEAK 33(19Q12) MUTATED 20 13 10 43 18
AMP PEAK 33(19Q12) WILD-TYPE 83 59 34 19 42

Figure S215.  Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S216.  Gene #34: 'amp_19q13.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 34(19Q13.32) MUTATED 79 13 19 0
AMP PEAK 34(19Q13.32) WILD-TYPE 155 140 32 3

Figure S216.  Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q13.32' versus 'METHLYATION_CNMF'

P value = 0.00226 (Fisher's exact test), Q value = 0.0044

Table S217.  Gene #34: 'amp_19q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 34(19Q13.32) MUTATED 10 22 12 40 14
AMP PEAK 34(19Q13.32) WILD-TYPE 35 88 39 60 73

Figure S217.  Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q13.32' versus 'RPPA_CHIERARCHICAL'

P value = 0.0114 (Fisher's exact test), Q value = 0.019

Table S218.  Gene #34: 'amp_19q13.32' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 58 78 80
AMP PEAK 34(19Q13.32) MUTATED 45 9 17 12
AMP PEAK 34(19Q13.32) WILD-TYPE 95 49 61 68

Figure S218.  Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_19q13.32' versus 'MRNASEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.00092

Table S219.  Gene #34: 'amp_19q13.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 34(19Q13.32) MUTATED 40 14 21 20 10
AMP PEAK 34(19Q13.32) WILD-TYPE 54 80 72 62 40

Figure S219.  Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00335 (Fisher's exact test), Q value = 0.0063

Table S220.  Gene #34: 'amp_19q13.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
AMP PEAK 34(19Q13.32) MUTATED 22 13 49 21
AMP PEAK 34(19Q13.32) WILD-TYPE 87 69 86 66

Figure S220.  Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19q13.32' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.5e-05

Table S221.  Gene #34: 'amp_19q13.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
AMP PEAK 34(19Q13.32) MUTATED 13 12 22 19 10 34
AMP PEAK 34(19Q13.32) WILD-TYPE 48 54 58 92 40 32

Figure S221.  Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_19q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00149 (Fisher's exact test), Q value = 0.0031

Table S222.  Gene #34: 'amp_19q13.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
AMP PEAK 34(19Q13.32) MUTATED 53 15 42
AMP PEAK 34(19Q13.32) WILD-TYPE 190 67 67

Figure S222.  Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_19q13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.00094

Table S223.  Gene #34: 'amp_19q13.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
AMP PEAK 34(19Q13.32) MUTATED 27 10 7 28 11
AMP PEAK 34(19Q13.32) WILD-TYPE 76 62 37 34 49

Figure S223.  Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S224.  Gene #35: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 35(20Q13.2) MUTATED 205 46 39 3
AMP PEAK 35(20Q13.2) WILD-TYPE 29 107 12 0

Figure S224.  Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S225.  Gene #35: 'amp_20q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
AMP PEAK 35(20Q13.2) MUTATED 35 56 36 97 37
AMP PEAK 35(20Q13.2) WILD-TYPE 10 54 15 3 50

Figure S225.  Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q13.2' versus 'RPPA_CNMF'

P value = 0.0276 (Fisher's exact test), Q value = 0.043

Table S226.  Gene #35: 'amp_20q13.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 92 82 93 59
AMP PEAK 35(20Q13.2) MUTATED 24 64 57 49 41
AMP PEAK 35(20Q13.2) WILD-TYPE 6 28 25 44 18

Figure S226.  Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_20q13.2' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S227.  Gene #35: 'amp_20q13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 58 78 80
AMP PEAK 35(20Q13.2) MUTATED 112 27 54 42
AMP PEAK 35(20Q13.2) WILD-TYPE 28 31 24 38

Figure S227.  Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_20q13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S228.  Gene #35: 'amp_20q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 35(20Q13.2) MUTATED 92 46 48 56 35
AMP PEAK 35(20Q13.2) WILD-TYPE 2 48 45 26 15

Figure S228.  Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_20q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S229.  Gene #35: 'amp_20q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
AMP PEAK 35(20Q13.2) MUTATED 74 38 115 50
AMP PEAK 35(20Q13.2) WILD-TYPE 35 44 20 37

Figure S229.  Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S230.  Gene #35: 'amp_20q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
AMP PEAK 35(20Q13.2) MUTATED 36 39 54 62 32 65
AMP PEAK 35(20Q13.2) WILD-TYPE 25 27 26 49 18 1

Figure S230.  Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_20q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S231.  Gene #35: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
AMP PEAK 35(20Q13.2) MUTATED 144 42 102
AMP PEAK 35(20Q13.2) WILD-TYPE 99 40 7

Figure S231.  Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S232.  Gene #35: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
AMP PEAK 35(20Q13.2) MUTATED 54 38 30 60 39
AMP PEAK 35(20Q13.2) WILD-TYPE 49 34 14 2 21

Figure S232.  Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xq27.3' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00027

Table S233.  Gene #36: 'amp_xq27.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
AMP PEAK 36(XQ27.3) MUTATED 51 14 18 0
AMP PEAK 36(XQ27.3) WILD-TYPE 183 139 33 3

Figure S233.  Get High-res Image Gene #36: 'amp_xq27.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq27.3' versus 'MRNASEQ_CNMF'

P value = 0.0205 (Fisher's exact test), Q value = 0.033

Table S234.  Gene #36: 'amp_xq27.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
AMP PEAK 36(XQ27.3) MUTATED 15 10 17 14 17
AMP PEAK 36(XQ27.3) WILD-TYPE 79 84 76 68 33

Figure S234.  Get High-res Image Gene #36: 'amp_xq27.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_xq27.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0081 (Fisher's exact test), Q value = 0.014

Table S235.  Gene #36: 'amp_xq27.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
AMP PEAK 36(XQ27.3) MUTATED 19 9 19 26
AMP PEAK 36(XQ27.3) WILD-TYPE 90 73 116 61

Figure S235.  Get High-res Image Gene #36: 'amp_xq27.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_xq27.3' versus 'MIRSEQ_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0015

Table S236.  Gene #36: 'amp_xq27.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
AMP PEAK 36(XQ27.3) MUTATED 24 13 14 12 6 12
AMP PEAK 36(XQ27.3) WILD-TYPE 37 53 66 99 44 54

Figure S236.  Get High-res Image Gene #36: 'amp_xq27.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p36.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S237.  Gene #37: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 1(1P36.11) MUTATED 123 5 7 0
DEL PEAK 1(1P36.11) WILD-TYPE 111 148 44 3

Figure S237.  Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S238.  Gene #37: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 1(1P36.11) MUTATED 27 23 5 52 10
DEL PEAK 1(1P36.11) WILD-TYPE 18 87 46 48 77

Figure S238.  Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.11' versus 'RPPA_CNMF'

P value = 0.00131 (Fisher's exact test), Q value = 0.0027

Table S239.  Gene #37: 'del_1p36.11' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 92 82 93 59
DEL PEAK 1(1P36.11) MUTATED 12 40 22 16 18
DEL PEAK 1(1P36.11) WILD-TYPE 18 52 60 77 41

Figure S239.  Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_1p36.11' versus 'RPPA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00022

Table S240.  Gene #37: 'del_1p36.11' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 58 78 80
DEL PEAK 1(1P36.11) MUTATED 50 13 34 11
DEL PEAK 1(1P36.11) WILD-TYPE 90 45 44 69

Figure S240.  Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S241.  Gene #37: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 1(1P36.11) MUTATED 47 12 25 28 16
DEL PEAK 1(1P36.11) WILD-TYPE 47 82 68 54 34

Figure S241.  Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.00058

Table S242.  Gene #37: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 1(1P36.11) MUTATED 38 11 54 25
DEL PEAK 1(1P36.11) WILD-TYPE 71 71 81 62

Figure S242.  Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S243.  Gene #37: 'del_1p36.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 1(1P36.11) MUTATED 15 19 25 18 15 40
DEL PEAK 1(1P36.11) WILD-TYPE 46 47 55 93 35 26

Figure S243.  Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p36.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S244.  Gene #37: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 1(1P36.11) MUTATED 63 14 55
DEL PEAK 1(1P36.11) WILD-TYPE 180 68 54

Figure S244.  Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00569 (Fisher's exact test), Q value = 0.01

Table S245.  Gene #37: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
DEL PEAK 1(1P36.11) MUTATED 55 24 24
DEL PEAK 1(1P36.11) WILD-TYPE 92 97 49

Figure S245.  Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S246.  Gene #37: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 1(1P36.11) MUTATED 31 7 12 33 20
DEL PEAK 1(1P36.11) WILD-TYPE 72 65 32 29 40

Figure S246.  Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S247.  Gene #38: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 2(1P13.2) MUTATED 80 4 9 0
DEL PEAK 2(1P13.2) WILD-TYPE 154 149 42 3

Figure S247.  Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S248.  Gene #38: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 2(1P13.2) MUTATED 15 20 6 38 5
DEL PEAK 2(1P13.2) WILD-TYPE 30 90 45 62 82

Figure S248.  Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p13.2' versus 'RPPA_CNMF'

P value = 0.00265 (Fisher's exact test), Q value = 0.0051

Table S249.  Gene #38: 'del_1p13.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 92 82 93 59
DEL PEAK 2(1P13.2) MUTATED 6 16 24 10 20
DEL PEAK 2(1P13.2) WILD-TYPE 24 76 58 83 39

Figure S249.  Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_1p13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S250.  Gene #38: 'del_1p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 2(1P13.2) MUTATED 36 6 18 13 14
DEL PEAK 2(1P13.2) WILD-TYPE 58 88 75 69 36

Figure S250.  Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.00058

Table S251.  Gene #38: 'del_1p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 2(1P13.2) MUTATED 21 5 40 21
DEL PEAK 2(1P13.2) WILD-TYPE 88 77 95 66

Figure S251.  Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.2' versus 'MIRSEQ_CNMF'

P value = 0.00223 (Fisher's exact test), Q value = 0.0044

Table S252.  Gene #38: 'del_1p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 2(1P13.2) MUTATED 11 11 20 14 9 26
DEL PEAK 2(1P13.2) WILD-TYPE 50 55 60 97 41 40

Figure S252.  Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00244 (Fisher's exact test), Q value = 0.0047

Table S253.  Gene #38: 'del_1p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 2(1P13.2) MUTATED 48 9 34
DEL PEAK 2(1P13.2) WILD-TYPE 195 73 75

Figure S253.  Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.033

Table S254.  Gene #38: 'del_1p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
DEL PEAK 2(1P13.2) MUTATED 41 17 14
DEL PEAK 2(1P13.2) WILD-TYPE 106 104 59

Figure S254.  Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.0013

Table S255.  Gene #38: 'del_1p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 2(1P13.2) MUTATED 24 5 9 23 11
DEL PEAK 2(1P13.2) WILD-TYPE 79 67 35 39 49

Figure S255.  Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1q44' versus 'CN_CNMF'

P value = 0.00858 (Fisher's exact test), Q value = 0.015

Table S256.  Gene #39: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 3(1Q44) MUTATED 21 2 2 0
DEL PEAK 3(1Q44) WILD-TYPE 213 151 49 3

Figure S256.  Get High-res Image Gene #39: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q44' versus 'METHLYATION_CNMF'

P value = 0.00185 (Fisher's exact test), Q value = 0.0037

Table S257.  Gene #39: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 3(1Q44) MUTATED 5 5 2 12 0
DEL PEAK 3(1Q44) WILD-TYPE 40 105 49 88 87

Figure S257.  Get High-res Image Gene #39: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q32.1' versus 'CN_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0011

Table S258.  Gene #40: 'del_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 4(2Q32.1) MUTATED 49 10 5 0
DEL PEAK 4(2Q32.1) WILD-TYPE 185 143 46 3

Figure S258.  Get High-res Image Gene #40: 'del_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q32.1' versus 'METHLYATION_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 9e-04

Table S259.  Gene #40: 'del_2q32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 4(2Q32.1) MUTATED 9 16 1 24 6
DEL PEAK 4(2Q32.1) WILD-TYPE 36 94 50 76 81

Figure S259.  Get High-res Image Gene #40: 'del_2q32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q32.1' versus 'MRNASEQ_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.034

Table S260.  Gene #40: 'del_2q32.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 4(2Q32.1) MUTATED 22 12 7 13 4
DEL PEAK 4(2Q32.1) WILD-TYPE 72 82 86 69 46

Figure S260.  Get High-res Image Gene #40: 'del_2q32.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q32.1' versus 'MIRSEQ_CNMF'

P value = 0.00481 (Fisher's exact test), Q value = 0.0088

Table S261.  Gene #40: 'del_2q32.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 4(2Q32.1) MUTATED 7 5 7 18 6 20
DEL PEAK 4(2Q32.1) WILD-TYPE 54 61 73 93 44 46

Figure S261.  Get High-res Image Gene #40: 'del_2q32.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q32.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.00072

Table S262.  Gene #40: 'del_2q32.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 4(2Q32.1) MUTATED 24 10 29
DEL PEAK 4(2Q32.1) WILD-TYPE 219 72 80

Figure S262.  Get High-res Image Gene #40: 'del_2q32.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q33.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S263.  Gene #41: 'del_2q33.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 5(2Q33.3) MUTATED 43 4 2 0
DEL PEAK 5(2Q33.3) WILD-TYPE 191 149 49 3

Figure S263.  Get High-res Image Gene #41: 'del_2q33.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q33.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0044 (Fisher's exact test), Q value = 0.0081

Table S264.  Gene #41: 'del_2q33.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 5(2Q33.3) MUTATED 25 3 20
DEL PEAK 5(2Q33.3) WILD-TYPE 218 79 89

Figure S264.  Get High-res Image Gene #41: 'del_2q33.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S265.  Gene #42: 'del_2q37.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 6(2Q37.2) MUTATED 66 3 3 0
DEL PEAK 6(2Q37.2) WILD-TYPE 168 150 48 3

Figure S265.  Get High-res Image Gene #42: 'del_2q37.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S266.  Gene #42: 'del_2q37.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 6(2Q37.2) MUTATED 12 13 2 32 8
DEL PEAK 6(2Q37.2) WILD-TYPE 33 97 49 68 79

Figure S266.  Get High-res Image Gene #42: 'del_2q37.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.2' versus 'MRNASEQ_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.029

Table S267.  Gene #42: 'del_2q37.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 6(2Q37.2) MUTATED 23 10 11 20 6
DEL PEAK 6(2Q37.2) WILD-TYPE 71 84 82 62 44

Figure S267.  Get High-res Image Gene #42: 'del_2q37.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q37.2' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00017

Table S268.  Gene #42: 'del_2q37.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 6(2Q37.2) MUTATED 7 6 9 13 11 25
DEL PEAK 6(2Q37.2) WILD-TYPE 54 60 71 98 39 41

Figure S268.  Get High-res Image Gene #42: 'del_2q37.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q37.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 2e-04

Table S269.  Gene #42: 'del_2q37.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 6(2Q37.2) MUTATED 32 6 33
DEL PEAK 6(2Q37.2) WILD-TYPE 211 76 76

Figure S269.  Get High-res Image Gene #42: 'del_2q37.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00935 (Fisher's exact test), Q value = 0.016

Table S270.  Gene #42: 'del_2q37.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 6(2Q37.2) MUTATED 15 5 9 18 13
DEL PEAK 6(2Q37.2) WILD-TYPE 88 67 35 44 47

Figure S270.  Get High-res Image Gene #42: 'del_2q37.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p26.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S271.  Gene #43: 'del_3p26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 7(3P26.1) MUTATED 114 6 20 3
DEL PEAK 7(3P26.1) WILD-TYPE 120 147 31 0

Figure S271.  Get High-res Image Gene #43: 'del_3p26.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p26.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S272.  Gene #43: 'del_3p26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 7(3P26.1) MUTATED 13 30 10 58 18
DEL PEAK 7(3P26.1) WILD-TYPE 32 80 41 42 69

Figure S272.  Get High-res Image Gene #43: 'del_3p26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p26.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S273.  Gene #43: 'del_3p26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 7(3P26.1) MUTATED 53 17 22 21 20
DEL PEAK 7(3P26.1) WILD-TYPE 41 77 71 61 30

Figure S273.  Get High-res Image Gene #43: 'del_3p26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p26.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00107 (Fisher's exact test), Q value = 0.0023

Table S274.  Gene #43: 'del_3p26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 7(3P26.1) MUTATED 31 14 56 32
DEL PEAK 7(3P26.1) WILD-TYPE 78 68 79 55

Figure S274.  Get High-res Image Gene #43: 'del_3p26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S275.  Gene #43: 'del_3p26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 7(3P26.1) MUTATED 21 18 24 25 12 40
DEL PEAK 7(3P26.1) WILD-TYPE 40 48 56 86 38 26

Figure S275.  Get High-res Image Gene #43: 'del_3p26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p26.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S276.  Gene #43: 'del_3p26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 7(3P26.1) MUTATED 66 16 58
DEL PEAK 7(3P26.1) WILD-TYPE 177 66 51

Figure S276.  Get High-res Image Gene #43: 'del_3p26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.032

Table S277.  Gene #43: 'del_3p26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
DEL PEAK 7(3P26.1) MUTATED 60 31 20
DEL PEAK 7(3P26.1) WILD-TYPE 87 90 53

Figure S277.  Get High-res Image Gene #43: 'del_3p26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p26.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S278.  Gene #43: 'del_3p26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 7(3P26.1) MUTATED 30 13 15 38 15
DEL PEAK 7(3P26.1) WILD-TYPE 73 59 29 24 45

Figure S278.  Get High-res Image Gene #43: 'del_3p26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S279.  Gene #44: 'del_3p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 8(3P21.1) MUTATED 119 9 22 3
DEL PEAK 8(3P21.1) WILD-TYPE 115 144 29 0

Figure S279.  Get High-res Image Gene #44: 'del_3p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S280.  Gene #44: 'del_3p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 8(3P21.1) MUTATED 23 34 11 53 18
DEL PEAK 8(3P21.1) WILD-TYPE 22 76 40 47 69

Figure S280.  Get High-res Image Gene #44: 'del_3p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p21.1' versus 'MRNASEQ_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.001

Table S281.  Gene #44: 'del_3p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 8(3P21.1) MUTATED 48 21 25 27 19
DEL PEAK 8(3P21.1) WILD-TYPE 46 73 68 55 31

Figure S281.  Get High-res Image Gene #44: 'del_3p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0018 (Fisher's exact test), Q value = 0.0036

Table S282.  Gene #44: 'del_3p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 8(3P21.1) MUTATED 35 15 58 32
DEL PEAK 8(3P21.1) WILD-TYPE 74 67 77 55

Figure S282.  Get High-res Image Gene #44: 'del_3p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.1' versus 'MIRSEQ_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.021

Table S283.  Gene #44: 'del_3p21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 8(3P21.1) MUTATED 23 19 29 30 14 35
DEL PEAK 8(3P21.1) WILD-TYPE 38 47 51 81 36 31

Figure S283.  Get High-res Image Gene #44: 'del_3p21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 2e-04

Table S284.  Gene #44: 'del_3p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 8(3P21.1) MUTATED 78 17 55
DEL PEAK 8(3P21.1) WILD-TYPE 165 65 54

Figure S284.  Get High-res Image Gene #44: 'del_3p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.022

Table S285.  Gene #44: 'del_3p21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
DEL PEAK 8(3P21.1) MUTATED 64 33 22
DEL PEAK 8(3P21.1) WILD-TYPE 83 88 51

Figure S285.  Get High-res Image Gene #44: 'del_3p21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.001 (Fisher's exact test), Q value = 0.0022

Table S286.  Gene #44: 'del_3p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 8(3P21.1) MUTATED 34 15 18 34 18
DEL PEAK 8(3P21.1) WILD-TYPE 69 57 26 28 42

Figure S286.  Get High-res Image Gene #44: 'del_3p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S287.  Gene #45: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 9(3P14.2) MUTATED 118 16 20 3
DEL PEAK 9(3P14.2) WILD-TYPE 116 137 31 0

Figure S287.  Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S288.  Gene #45: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 9(3P14.2) MUTATED 18 38 16 58 14
DEL PEAK 9(3P14.2) WILD-TYPE 27 72 35 42 73

Figure S288.  Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S289.  Gene #45: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 9(3P14.2) MUTATED 52 15 30 28 21
DEL PEAK 9(3P14.2) WILD-TYPE 42 79 63 54 29

Figure S289.  Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00017

Table S290.  Gene #45: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 9(3P14.2) MUTATED 34 14 62 36
DEL PEAK 9(3P14.2) WILD-TYPE 75 68 73 51

Figure S290.  Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00037

Table S291.  Gene #45: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 9(3P14.2) MUTATED 21 23 27 26 17 40
DEL PEAK 9(3P14.2) WILD-TYPE 40 43 53 85 33 26

Figure S291.  Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S292.  Gene #45: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 9(3P14.2) MUTATED 78 16 60
DEL PEAK 9(3P14.2) WILD-TYPE 165 66 49

Figure S292.  Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.0013

Table S293.  Gene #45: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
DEL PEAK 9(3P14.2) MUTATED 66 28 28
DEL PEAK 9(3P14.2) WILD-TYPE 81 93 45

Figure S293.  Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S294.  Gene #45: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 9(3P14.2) MUTATED 32 11 20 36 23
DEL PEAK 9(3P14.2) WILD-TYPE 71 61 24 26 37

Figure S294.  Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q26.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S295.  Gene #46: 'del_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 10(3Q26.31) MUTATED 40 1 8 0
DEL PEAK 10(3Q26.31) WILD-TYPE 194 152 43 3

Figure S295.  Get High-res Image Gene #46: 'del_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q26.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S296.  Gene #46: 'del_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 10(3Q26.31) MUTATED 2 11 2 28 2
DEL PEAK 10(3Q26.31) WILD-TYPE 43 99 49 72 85

Figure S296.  Get High-res Image Gene #46: 'del_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q26.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S297.  Gene #46: 'del_3q26.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 10(3Q26.31) MUTATED 25 4 6 2 11
DEL PEAK 10(3Q26.31) WILD-TYPE 69 90 87 80 39

Figure S297.  Get High-res Image Gene #46: 'del_3q26.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3q26.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S298.  Gene #46: 'del_3q26.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 10(3Q26.31) MUTATED 2 6 24 16
DEL PEAK 10(3Q26.31) WILD-TYPE 107 76 111 71

Figure S298.  Get High-res Image Gene #46: 'del_3q26.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3q26.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S299.  Gene #46: 'del_3q26.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 10(3Q26.31) MUTATED 8 1 11 6 3 19
DEL PEAK 10(3Q26.31) WILD-TYPE 53 65 69 105 47 47

Figure S299.  Get High-res Image Gene #46: 'del_3q26.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3q26.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.00072

Table S300.  Gene #46: 'del_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 10(3Q26.31) MUTATED 20 4 24
DEL PEAK 10(3Q26.31) WILD-TYPE 223 78 85

Figure S300.  Get High-res Image Gene #46: 'del_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3q26.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0132 (Fisher's exact test), Q value = 0.022

Table S301.  Gene #46: 'del_3q26.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 10(3Q26.31) MUTATED 10 4 5 15 4
DEL PEAK 10(3Q26.31) WILD-TYPE 93 68 39 47 56

Figure S301.  Get High-res Image Gene #46: 'del_3q26.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p16.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S302.  Gene #47: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 11(4P16.3) MUTATED 143 11 14 1
DEL PEAK 11(4P16.3) WILD-TYPE 91 142 37 2

Figure S302.  Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S303.  Gene #47: 'del_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 11(4P16.3) MUTATED 20 34 9 58 29
DEL PEAK 11(4P16.3) WILD-TYPE 25 76 42 42 58

Figure S303.  Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4p16.3' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S304.  Gene #47: 'del_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 11(4P16.3) MUTATED 59 29 30 24 17
DEL PEAK 11(4P16.3) WILD-TYPE 35 65 63 58 33

Figure S304.  Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.023

Table S305.  Gene #47: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 11(4P16.3) MUTATED 34 28 67 30
DEL PEAK 11(4P16.3) WILD-TYPE 75 54 68 57

Figure S305.  Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S306.  Gene #47: 'del_4p16.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 11(4P16.3) MUTATED 26 12 25 45 14 46
DEL PEAK 11(4P16.3) WILD-TYPE 35 54 55 66 36 20

Figure S306.  Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S307.  Gene #47: 'del_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 11(4P16.3) MUTATED 71 27 70
DEL PEAK 11(4P16.3) WILD-TYPE 172 55 39

Figure S307.  Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.0019

Table S308.  Gene #47: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
DEL PEAK 11(4P16.3) MUTATED 65 54 15
DEL PEAK 11(4P16.3) WILD-TYPE 82 67 58

Figure S308.  Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S309.  Gene #47: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 11(4P16.3) MUTATED 39 25 7 45 18
DEL PEAK 11(4P16.3) WILD-TYPE 64 47 37 17 42

Figure S309.  Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S310.  Gene #48: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 12(4Q22.1) MUTATED 166 12 14 1
DEL PEAK 12(4Q22.1) WILD-TYPE 68 141 37 2

Figure S310.  Get High-res Image Gene #48: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S311.  Gene #48: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 12(4Q22.1) MUTATED 26 48 9 64 25
DEL PEAK 12(4Q22.1) WILD-TYPE 19 62 42 36 62

Figure S311.  Get High-res Image Gene #48: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0015

Table S312.  Gene #48: 'del_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 12(4Q22.1) MUTATED 58 29 37 33 22
DEL PEAK 12(4Q22.1) WILD-TYPE 36 65 56 49 28

Figure S312.  Get High-res Image Gene #48: 'del_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0224 (Fisher's exact test), Q value = 0.035

Table S313.  Gene #48: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 12(4Q22.1) MUTATED 46 25 70 38
DEL PEAK 12(4Q22.1) WILD-TYPE 63 57 65 49

Figure S313.  Get High-res Image Gene #48: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_CNMF'

P value = 0.00959 (Fisher's exact test), Q value = 0.017

Table S314.  Gene #48: 'del_4q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 12(4Q22.1) MUTATED 28 22 34 42 21 42
DEL PEAK 12(4Q22.1) WILD-TYPE 33 44 46 69 29 24

Figure S314.  Get High-res Image Gene #48: 'del_4q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00022

Table S315.  Gene #48: 'del_4q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 12(4Q22.1) MUTATED 94 28 67
DEL PEAK 12(4Q22.1) WILD-TYPE 149 54 42

Figure S315.  Get High-res Image Gene #48: 'del_4q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00344 (Fisher's exact test), Q value = 0.0065

Table S316.  Gene #48: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 12(4Q22.1) MUTATED 39 24 18 40 25
DEL PEAK 12(4Q22.1) WILD-TYPE 64 48 26 22 35

Figure S316.  Get High-res Image Gene #48: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q35.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S317.  Gene #49: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 13(4Q35.1) MUTATED 176 12 15 1
DEL PEAK 13(4Q35.1) WILD-TYPE 58 141 36 2

Figure S317.  Get High-res Image Gene #49: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q35.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S318.  Gene #49: 'del_4q35.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 13(4Q35.1) MUTATED 30 45 10 69 30
DEL PEAK 13(4Q35.1) WILD-TYPE 15 65 41 31 57

Figure S318.  Get High-res Image Gene #49: 'del_4q35.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q35.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00745 (Fisher's exact test), Q value = 0.013

Table S319.  Gene #49: 'del_4q35.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 58 78 80
DEL PEAK 13(4Q35.1) MUTATED 77 18 39 31
DEL PEAK 13(4Q35.1) WILD-TYPE 63 40 39 49

Figure S319.  Get High-res Image Gene #49: 'del_4q35.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_4q35.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S320.  Gene #49: 'del_4q35.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 13(4Q35.1) MUTATED 68 29 35 42 19
DEL PEAK 13(4Q35.1) WILD-TYPE 26 65 58 40 31

Figure S320.  Get High-res Image Gene #49: 'del_4q35.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.00092

Table S321.  Gene #49: 'del_4q35.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 13(4Q35.1) MUTATED 52 27 81 33
DEL PEAK 13(4Q35.1) WILD-TYPE 57 55 54 54

Figure S321.  Get High-res Image Gene #49: 'del_4q35.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00032

Table S322.  Gene #49: 'del_4q35.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 13(4Q35.1) MUTATED 29 22 35 42 27 47
DEL PEAK 13(4Q35.1) WILD-TYPE 32 44 45 69 23 19

Figure S322.  Get High-res Image Gene #49: 'del_4q35.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q35.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S323.  Gene #49: 'del_4q35.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 13(4Q35.1) MUTATED 101 26 75
DEL PEAK 13(4Q35.1) WILD-TYPE 142 56 34

Figure S323.  Get High-res Image Gene #49: 'del_4q35.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00668 (Fisher's exact test), Q value = 0.012

Table S324.  Gene #49: 'del_4q35.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
DEL PEAK 13(4Q35.1) MUTATED 84 51 27
DEL PEAK 13(4Q35.1) WILD-TYPE 63 70 46

Figure S324.  Get High-res Image Gene #49: 'del_4q35.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q35.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S325.  Gene #49: 'del_4q35.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 13(4Q35.1) MUTATED 49 22 16 48 27
DEL PEAK 13(4Q35.1) WILD-TYPE 54 50 28 14 33

Figure S325.  Get High-res Image Gene #49: 'del_4q35.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S326.  Gene #50: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 14(5Q12.1) MUTATED 150 3 15 2
DEL PEAK 14(5Q12.1) WILD-TYPE 84 150 36 1

Figure S326.  Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S327.  Gene #50: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 14(5Q12.1) MUTATED 19 38 5 75 19
DEL PEAK 14(5Q12.1) WILD-TYPE 26 72 46 25 68

Figure S327.  Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q12.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.00065

Table S328.  Gene #50: 'del_5q12.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 58 78 80
DEL PEAK 14(5Q12.1) MUTATED 65 14 32 17
DEL PEAK 14(5Q12.1) WILD-TYPE 75 44 46 63

Figure S328.  Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_5q12.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S329.  Gene #50: 'del_5q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 14(5Q12.1) MUTATED 74 12 25 28 21
DEL PEAK 14(5Q12.1) WILD-TYPE 20 82 68 54 29

Figure S329.  Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S330.  Gene #50: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 14(5Q12.1) MUTATED 46 7 78 29
DEL PEAK 14(5Q12.1) WILD-TYPE 63 75 57 58

Figure S330.  Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S331.  Gene #50: 'del_5q12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 14(5Q12.1) MUTATED 27 19 26 20 23 52
DEL PEAK 14(5Q12.1) WILD-TYPE 34 47 54 91 27 14

Figure S331.  Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S332.  Gene #50: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 14(5Q12.1) MUTATED 77 11 79
DEL PEAK 14(5Q12.1) WILD-TYPE 166 71 30

Figure S332.  Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.0016

Table S333.  Gene #50: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
DEL PEAK 14(5Q12.1) MUTATED 76 35 28
DEL PEAK 14(5Q12.1) WILD-TYPE 71 86 45

Figure S333.  Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S334.  Gene #50: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 14(5Q12.1) MUTATED 38 9 17 53 22
DEL PEAK 14(5Q12.1) WILD-TYPE 65 63 27 9 38

Figure S334.  Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S335.  Gene #51: 'del_5q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 15(5Q23.2) MUTATED 140 3 14 1
DEL PEAK 15(5Q23.2) WILD-TYPE 94 150 37 2

Figure S335.  Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S336.  Gene #51: 'del_5q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 15(5Q23.2) MUTATED 17 34 7 72 15
DEL PEAK 15(5Q23.2) WILD-TYPE 28 76 44 28 72

Figure S336.  Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q23.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.0018

Table S337.  Gene #51: 'del_5q23.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 58 78 80
DEL PEAK 15(5Q23.2) MUTATED 62 12 31 18
DEL PEAK 15(5Q23.2) WILD-TYPE 78 46 47 62

Figure S337.  Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_5q23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S338.  Gene #51: 'del_5q23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 15(5Q23.2) MUTATED 71 10 22 28 19
DEL PEAK 15(5Q23.2) WILD-TYPE 23 84 71 54 31

Figure S338.  Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S339.  Gene #51: 'del_5q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 15(5Q23.2) MUTATED 41 6 75 28
DEL PEAK 15(5Q23.2) WILD-TYPE 68 76 60 59

Figure S339.  Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q23.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S340.  Gene #51: 'del_5q23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 15(5Q23.2) MUTATED 26 13 28 17 20 51
DEL PEAK 15(5Q23.2) WILD-TYPE 35 53 52 94 30 15

Figure S340.  Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S341.  Gene #51: 'del_5q23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 15(5Q23.2) MUTATED 75 9 71
DEL PEAK 15(5Q23.2) WILD-TYPE 168 73 38

Figure S341.  Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S342.  Gene #51: 'del_5q23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
DEL PEAK 15(5Q23.2) MUTATED 78 30 20
DEL PEAK 15(5Q23.2) WILD-TYPE 69 91 53

Figure S342.  Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S343.  Gene #51: 'del_5q23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 15(5Q23.2) MUTATED 40 8 13 46 21
DEL PEAK 15(5Q23.2) WILD-TYPE 63 64 31 16 39

Figure S343.  Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S344.  Gene #52: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 16(6P25.3) MUTATED 94 11 10 0
DEL PEAK 16(6P25.3) WILD-TYPE 140 142 41 3

Figure S344.  Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S345.  Gene #52: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 16(6P25.3) MUTATED 18 31 5 41 13
DEL PEAK 16(6P25.3) WILD-TYPE 27 79 46 59 74

Figure S345.  Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S346.  Gene #52: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 16(6P25.3) MUTATED 37 9 22 30 7
DEL PEAK 16(6P25.3) WILD-TYPE 57 85 71 52 43

Figure S346.  Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.00072

Table S347.  Gene #52: 'del_6p25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 16(6P25.3) MUTATED 33 10 47 15
DEL PEAK 16(6P25.3) WILD-TYPE 76 72 88 72

Figure S347.  Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6p25.3' versus 'MIRSEQ_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.001

Table S348.  Gene #52: 'del_6p25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 16(6P25.3) MUTATED 13 12 23 18 17 30
DEL PEAK 16(6P25.3) WILD-TYPE 48 54 57 93 33 36

Figure S348.  Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.5e-05

Table S349.  Gene #52: 'del_6p25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 16(6P25.3) MUTATED 55 11 47
DEL PEAK 16(6P25.3) WILD-TYPE 188 71 62

Figure S349.  Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6p25.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00195 (Fisher's exact test), Q value = 0.0039

Table S350.  Gene #52: 'del_6p25.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
DEL PEAK 16(6P25.3) MUTATED 52 20 21
DEL PEAK 16(6P25.3) WILD-TYPE 95 101 52

Figure S350.  Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6p25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00371 (Fisher's exact test), Q value = 0.0069

Table S351.  Gene #52: 'del_6p25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 16(6P25.3) MUTATED 25 9 16 24 19
DEL PEAK 16(6P25.3) WILD-TYPE 78 63 28 38 41

Figure S351.  Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S352.  Gene #53: 'del_6q14.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 17(6Q14.1) MUTATED 67 8 12 2
DEL PEAK 17(6Q14.1) WILD-TYPE 167 145 39 1

Figure S352.  Get High-res Image Gene #53: 'del_6q14.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q14.1' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00034

Table S353.  Gene #53: 'del_6q14.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 17(6Q14.1) MUTATED 18 19 5 28 9
DEL PEAK 17(6Q14.1) WILD-TYPE 27 91 46 72 78

Figure S353.  Get High-res Image Gene #53: 'del_6q14.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q14.1' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00015

Table S354.  Gene #53: 'del_6q14.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 17(6Q14.1) MUTATED 25 7 16 30 6
DEL PEAK 17(6Q14.1) WILD-TYPE 69 87 77 52 44

Figure S354.  Get High-res Image Gene #53: 'del_6q14.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00042

Table S355.  Gene #53: 'del_6q14.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 17(6Q14.1) MUTATED 35 6 30 13
DEL PEAK 17(6Q14.1) WILD-TYPE 74 76 105 74

Figure S355.  Get High-res Image Gene #53: 'del_6q14.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.02

Table S356.  Gene #53: 'del_6q14.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 17(6Q14.1) MUTATED 50 8 29
DEL PEAK 17(6Q14.1) WILD-TYPE 193 74 80

Figure S356.  Get High-res Image Gene #53: 'del_6q14.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.02

Table S357.  Gene #53: 'del_6q14.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
DEL PEAK 17(6Q14.1) MUTATED 38 14 13
DEL PEAK 17(6Q14.1) WILD-TYPE 109 107 60

Figure S357.  Get High-res Image Gene #53: 'del_6q14.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S358.  Gene #54: 'del_6q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 18(6Q24.3) MUTATED 61 5 11 1
DEL PEAK 18(6Q24.3) WILD-TYPE 173 148 40 2

Figure S358.  Get High-res Image Gene #54: 'del_6q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q24.3' versus 'METHLYATION_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0011

Table S359.  Gene #54: 'del_6q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 18(6Q24.3) MUTATED 14 14 3 27 10
DEL PEAK 18(6Q24.3) WILD-TYPE 31 96 48 73 77

Figure S359.  Get High-res Image Gene #54: 'del_6q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q24.3' versus 'MRNASEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00056

Table S360.  Gene #54: 'del_6q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 18(6Q24.3) MUTATED 26 6 12 22 7
DEL PEAK 18(6Q24.3) WILD-TYPE 68 88 81 60 43

Figure S360.  Get High-res Image Gene #54: 'del_6q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0012

Table S361.  Gene #54: 'del_6q24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 18(6Q24.3) MUTATED 26 4 31 12
DEL PEAK 18(6Q24.3) WILD-TYPE 83 78 104 75

Figure S361.  Get High-res Image Gene #54: 'del_6q24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0289 (Fisher's exact test), Q value = 0.044

Table S362.  Gene #54: 'del_6q24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 18(6Q24.3) MUTATED 42 7 25
DEL PEAK 18(6Q24.3) WILD-TYPE 201 75 84

Figure S362.  Get High-res Image Gene #54: 'del_6q24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.032

Table S363.  Gene #54: 'del_6q24.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
DEL PEAK 18(6Q24.3) MUTATED 34 13 10
DEL PEAK 18(6Q24.3) WILD-TYPE 113 108 63

Figure S363.  Get High-res Image Gene #54: 'del_6q24.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0377 (Fisher's exact test), Q value = 0.056

Table S364.  Gene #54: 'del_6q24.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 18(6Q24.3) MUTATED 19 5 5 15 13
DEL PEAK 18(6Q24.3) WILD-TYPE 84 67 39 47 47

Figure S364.  Get High-res Image Gene #54: 'del_6q24.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S365.  Gene #55: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 19(6Q26) MUTATED 77 7 17 1
DEL PEAK 19(6Q26) WILD-TYPE 157 146 34 2

Figure S365.  Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 0.00301 (Fisher's exact test), Q value = 0.0057

Table S366.  Gene #55: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 19(6Q26) MUTATED 18 21 7 31 14
DEL PEAK 19(6Q26) WILD-TYPE 27 89 44 69 73

Figure S366.  Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00015

Table S367.  Gene #55: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 19(6Q26) MUTATED 30 10 23 28 5
DEL PEAK 19(6Q26) WILD-TYPE 64 84 70 54 45

Figure S367.  Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S368.  Gene #55: 'del_6q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 19(6Q26) MUTATED 32 8 45 11
DEL PEAK 19(6Q26) WILD-TYPE 77 74 90 76

Figure S368.  Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 0.00434 (Fisher's exact test), Q value = 0.008

Table S369.  Gene #55: 'del_6q26' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 19(6Q26) MUTATED 8 13 24 17 14 24
DEL PEAK 19(6Q26) WILD-TYPE 53 53 56 94 36 42

Figure S369.  Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00343 (Fisher's exact test), Q value = 0.0064

Table S370.  Gene #55: 'del_6q26' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 19(6Q26) MUTATED 57 9 34
DEL PEAK 19(6Q26) WILD-TYPE 186 73 75

Figure S370.  Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.034

Table S371.  Gene #55: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
DEL PEAK 19(6Q26) MUTATED 40 17 19
DEL PEAK 19(6Q26) WILD-TYPE 107 104 54

Figure S371.  Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00724 (Fisher's exact test), Q value = 0.013

Table S372.  Gene #55: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 19(6Q26) MUTATED 24 7 13 21 11
DEL PEAK 19(6Q26) WILD-TYPE 79 65 31 41 49

Figure S372.  Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S373.  Gene #56: 'del_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 20(7Q31.1) MUTATED 62 7 1 1
DEL PEAK 20(7Q31.1) WILD-TYPE 172 146 50 2

Figure S373.  Get High-res Image Gene #56: 'del_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q31.1' versus 'METHLYATION_CNMF'

P value = 0.00122 (Fisher's exact test), Q value = 0.0026

Table S374.  Gene #56: 'del_7q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 20(7Q31.1) MUTATED 11 20 5 23 4
DEL PEAK 20(7Q31.1) WILD-TYPE 34 90 46 77 83

Figure S374.  Get High-res Image Gene #56: 'del_7q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q31.1' versus 'MRNASEQ_CNMF'

P value = 0.00997 (Fisher's exact test), Q value = 0.017

Table S375.  Gene #56: 'del_7q31.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 20(7Q31.1) MUTATED 27 10 13 13 5
DEL PEAK 20(7Q31.1) WILD-TYPE 67 84 80 69 45

Figure S375.  Get High-res Image Gene #56: 'del_7q31.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_7q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0298 (Fisher's exact test), Q value = 0.045

Table S376.  Gene #56: 'del_7q31.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 20(7Q31.1) MUTATED 18 9 32 9
DEL PEAK 20(7Q31.1) WILD-TYPE 91 73 103 78

Figure S376.  Get High-res Image Gene #56: 'del_7q31.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_7q31.1' versus 'MIRSEQ_CNMF'

P value = 0.00198 (Fisher's exact test), Q value = 0.0039

Table S377.  Gene #56: 'del_7q31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 20(7Q31.1) MUTATED 7 5 12 12 11 21
DEL PEAK 20(7Q31.1) WILD-TYPE 54 61 68 99 39 45

Figure S377.  Get High-res Image Gene #56: 'del_7q31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_7q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0329 (Fisher's exact test), Q value = 0.05

Table S378.  Gene #56: 'del_7q31.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 20(7Q31.1) MUTATED 32 10 26
DEL PEAK 20(7Q31.1) WILD-TYPE 211 72 83

Figure S378.  Get High-res Image Gene #56: 'del_7q31.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_7q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0243 (Fisher's exact test), Q value = 0.038

Table S379.  Gene #56: 'del_7q31.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 20(7Q31.1) MUTATED 16 6 4 15 15
DEL PEAK 20(7Q31.1) WILD-TYPE 87 66 40 47 45

Figure S379.  Get High-res Image Gene #56: 'del_7q31.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q36.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S380.  Gene #57: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 21(7Q36.3) MUTATED 92 3 2 1
DEL PEAK 21(7Q36.3) WILD-TYPE 142 150 49 2

Figure S380.  Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q36.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S381.  Gene #57: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 21(7Q36.3) MUTATED 15 25 3 37 9
DEL PEAK 21(7Q36.3) WILD-TYPE 30 85 48 63 78

Figure S381.  Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q36.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S382.  Gene #57: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 21(7Q36.3) MUTATED 39 13 21 18 3
DEL PEAK 21(7Q36.3) WILD-TYPE 55 81 72 64 47

Figure S382.  Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_7q36.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.5e-05

Table S383.  Gene #57: 'del_7q36.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 21(7Q36.3) MUTATED 27 11 47 9
DEL PEAK 21(7Q36.3) WILD-TYPE 82 71 88 78

Figure S383.  Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_7q36.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S384.  Gene #57: 'del_7q36.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 21(7Q36.3) MUTATED 13 10 13 13 14 33
DEL PEAK 21(7Q36.3) WILD-TYPE 48 56 67 98 36 33

Figure S384.  Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_7q36.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S385.  Gene #57: 'del_7q36.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 21(7Q36.3) MUTATED 44 8 44
DEL PEAK 21(7Q36.3) WILD-TYPE 199 74 65

Figure S385.  Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_7q36.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S386.  Gene #57: 'del_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 21(7Q36.3) MUTATED 21 5 11 28 16
DEL PEAK 21(7Q36.3) WILD-TYPE 82 67 33 34 44

Figure S386.  Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S387.  Gene #58: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 22(8P23.2) MUTATED 96 5 21 0
DEL PEAK 22(8P23.2) WILD-TYPE 138 148 30 3

Figure S387.  Get High-res Image Gene #58: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S388.  Gene #58: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 22(8P23.2) MUTATED 18 23 4 45 20
DEL PEAK 22(8P23.2) WILD-TYPE 27 87 47 55 67

Figure S388.  Get High-res Image Gene #58: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S389.  Gene #58: 'del_8p23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 22(8P23.2) MUTATED 46 12 18 22 16
DEL PEAK 22(8P23.2) WILD-TYPE 48 82 75 60 34

Figure S389.  Get High-res Image Gene #58: 'del_8p23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.00058

Table S390.  Gene #58: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 22(8P23.2) MUTATED 31 9 51 23
DEL PEAK 22(8P23.2) WILD-TYPE 78 73 84 64

Figure S390.  Get High-res Image Gene #58: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.032

Table S391.  Gene #58: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 22(8P23.2) MUTATED 19 14 22 22 14 29
DEL PEAK 22(8P23.2) WILD-TYPE 42 52 58 89 36 37

Figure S391.  Get High-res Image Gene #58: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 2e-04

Table S392.  Gene #58: 'del_8p23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 22(8P23.2) MUTATED 59 13 48
DEL PEAK 22(8P23.2) WILD-TYPE 184 69 61

Figure S392.  Get High-res Image Gene #58: 'del_8p23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00054

Table S393.  Gene #58: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 22(8P23.2) MUTATED 34 9 12 29 13
DEL PEAK 22(8P23.2) WILD-TYPE 69 63 32 33 47

Figure S393.  Get High-res Image Gene #58: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S394.  Gene #59: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 23(9P23) MUTATED 162 9 22 2
DEL PEAK 23(9P23) WILD-TYPE 72 144 29 1

Figure S394.  Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S395.  Gene #59: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 23(9P23) MUTATED 28 40 11 69 28
DEL PEAK 23(9P23) WILD-TYPE 17 70 40 31 59

Figure S395.  Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p23' versus 'RPPA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00049

Table S396.  Gene #59: 'del_9p23' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 58 78 80
DEL PEAK 23(9P23) MUTATED 78 13 33 37
DEL PEAK 23(9P23) WILD-TYPE 62 45 45 43

Figure S396.  Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S397.  Gene #59: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 23(9P23) MUTATED 65 28 29 43 21
DEL PEAK 23(9P23) WILD-TYPE 29 66 64 39 29

Figure S397.  Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.5e-05

Table S398.  Gene #59: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 23(9P23) MUTATED 53 24 79 30
DEL PEAK 23(9P23) WILD-TYPE 56 58 56 57

Figure S398.  Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 0.00116 (Fisher's exact test), Q value = 0.0025

Table S399.  Gene #59: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 23(9P23) MUTATED 25 23 31 44 24 45
DEL PEAK 23(9P23) WILD-TYPE 36 43 49 67 26 21

Figure S399.  Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.5e-05

Table S400.  Gene #59: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 23(9P23) MUTATED 97 27 68
DEL PEAK 23(9P23) WILD-TYPE 146 55 41

Figure S400.  Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0391 (Fisher's exact test), Q value = 0.058

Table S401.  Gene #59: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
DEL PEAK 23(9P23) MUTATED 78 48 28
DEL PEAK 23(9P23) WILD-TYPE 69 73 45

Figure S401.  Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00118 (Fisher's exact test), Q value = 0.0025

Table S402.  Gene #59: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 23(9P23) MUTATED 44 22 22 41 25
DEL PEAK 23(9P23) WILD-TYPE 59 50 22 21 35

Figure S402.  Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S403.  Gene #60: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 24(9P21.3) MUTATED 166 9 16 2
DEL PEAK 24(9P21.3) WILD-TYPE 68 144 35 1

Figure S403.  Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S404.  Gene #60: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 24(9P21.3) MUTATED 31 42 2 73 27
DEL PEAK 24(9P21.3) WILD-TYPE 14 68 49 27 60

Figure S404.  Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00101 (Fisher's exact test), Q value = 0.0022

Table S405.  Gene #60: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 58 78 80
DEL PEAK 24(9P21.3) MUTATED 76 14 31 36
DEL PEAK 24(9P21.3) WILD-TYPE 64 44 47 44

Figure S405.  Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S406.  Gene #60: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 24(9P21.3) MUTATED 68 28 27 40 22
DEL PEAK 24(9P21.3) WILD-TYPE 26 66 66 42 28

Figure S406.  Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.5e-05

Table S407.  Gene #60: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 24(9P21.3) MUTATED 54 24 78 29
DEL PEAK 24(9P21.3) WILD-TYPE 55 58 57 58

Figure S407.  Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S408.  Gene #60: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 24(9P21.3) MUTATED 25 21 27 43 26 48
DEL PEAK 24(9P21.3) WILD-TYPE 36 45 53 68 24 18

Figure S408.  Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S409.  Gene #60: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 24(9P21.3) MUTATED 94 26 70
DEL PEAK 24(9P21.3) WILD-TYPE 149 56 39

Figure S409.  Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0336 (Fisher's exact test), Q value = 0.05

Table S410.  Gene #60: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
DEL PEAK 24(9P21.3) MUTATED 77 52 25
DEL PEAK 24(9P21.3) WILD-TYPE 70 69 48

Figure S410.  Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00042

Table S411.  Gene #60: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 24(9P21.3) MUTATED 43 23 19 44 25
DEL PEAK 24(9P21.3) WILD-TYPE 60 49 25 18 35

Figure S411.  Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q21.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S412.  Gene #61: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 25(9Q21.11) MUTATED 102 1 9 1
DEL PEAK 25(9Q21.11) WILD-TYPE 132 152 42 2

Figure S412.  Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q21.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S413.  Gene #61: 'del_9q21.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 25(9Q21.11) MUTATED 16 23 2 44 19
DEL PEAK 25(9Q21.11) WILD-TYPE 29 87 49 56 68

Figure S413.  Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9q21.11' versus 'RPPA_CHIERARCHICAL'

P value = 0.00609 (Fisher's exact test), Q value = 0.011

Table S414.  Gene #61: 'del_9q21.11' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 58 78 80
DEL PEAK 25(9Q21.11) MUTATED 46 6 17 19
DEL PEAK 25(9Q21.11) WILD-TYPE 94 52 61 61

Figure S414.  Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9q21.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S415.  Gene #61: 'del_9q21.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 25(9Q21.11) MUTATED 46 18 16 17 9
DEL PEAK 25(9Q21.11) WILD-TYPE 48 76 77 65 41

Figure S415.  Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9q21.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00235 (Fisher's exact test), Q value = 0.0045

Table S416.  Gene #61: 'del_9q21.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 25(9Q21.11) MUTATED 28 15 49 14
DEL PEAK 25(9Q21.11) WILD-TYPE 81 67 86 73

Figure S416.  Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00047

Table S417.  Gene #61: 'del_9q21.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 25(9Q21.11) MUTATED 16 10 17 25 10 33
DEL PEAK 25(9Q21.11) WILD-TYPE 45 56 63 86 40 33

Figure S417.  Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9q21.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S418.  Gene #61: 'del_9q21.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 25(9Q21.11) MUTATED 46 15 50
DEL PEAK 25(9Q21.11) WILD-TYPE 197 67 59

Figure S418.  Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00025

Table S419.  Gene #61: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 25(9Q21.11) MUTATED 20 13 10 32 16
DEL PEAK 25(9Q21.11) WILD-TYPE 83 59 34 30 44

Figure S419.  Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S420.  Gene #62: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 26(10P15.3) MUTATED 61 4 11 1
DEL PEAK 26(10P15.3) WILD-TYPE 173 149 40 2

Figure S420.  Get High-res Image Gene #62: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.00081

Table S421.  Gene #62: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 26(10P15.3) MUTATED 14 17 2 26 9
DEL PEAK 26(10P15.3) WILD-TYPE 31 93 49 74 78

Figure S421.  Get High-res Image Gene #62: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.019

Table S422.  Gene #62: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 26(10P15.3) MUTATED 24 8 14 20 7
DEL PEAK 26(10P15.3) WILD-TYPE 70 86 79 62 43

Figure S422.  Get High-res Image Gene #62: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MIRSEQ_CNMF'

P value = 0.035 (Fisher's exact test), Q value = 0.052

Table S423.  Gene #62: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 26(10P15.3) MUTATED 11 8 18 11 10 18
DEL PEAK 26(10P15.3) WILD-TYPE 50 58 62 100 40 48

Figure S423.  Get High-res Image Gene #62: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10p15.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00338 (Fisher's exact test), Q value = 0.0064

Table S424.  Gene #62: 'del_10p15.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 26(10P15.3) MUTATED 42 6 28
DEL PEAK 26(10P15.3) WILD-TYPE 201 76 81

Figure S424.  Get High-res Image Gene #62: 'del_10p15.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S425.  Gene #63: 'del_10q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 27(10Q22.3) MUTATED 61 2 15 1
DEL PEAK 27(10Q22.3) WILD-TYPE 173 151 36 2

Figure S425.  Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q22.3' versus 'METHLYATION_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00061

Table S426.  Gene #63: 'del_10q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 27(10Q22.3) MUTATED 7 14 3 33 13
DEL PEAK 27(10Q22.3) WILD-TYPE 38 96 48 67 74

Figure S426.  Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q22.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S427.  Gene #63: 'del_10q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 27(10Q22.3) MUTATED 34 5 13 12 11
DEL PEAK 27(10Q22.3) WILD-TYPE 60 89 80 70 39

Figure S427.  Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00063 (Fisher's exact test), Q value = 0.0014

Table S428.  Gene #63: 'del_10q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 27(10Q22.3) MUTATED 18 4 33 20
DEL PEAK 27(10Q22.3) WILD-TYPE 91 78 102 67

Figure S428.  Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q22.3' versus 'MIRSEQ_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.026

Table S429.  Gene #63: 'del_10q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 27(10Q22.3) MUTATED 15 10 15 10 9 19
DEL PEAK 27(10Q22.3) WILD-TYPE 46 56 65 101 41 47

Figure S429.  Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S430.  Gene #63: 'del_10q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 27(10Q22.3) MUTATED 37 6 35
DEL PEAK 27(10Q22.3) WILD-TYPE 206 76 74

Figure S430.  Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0121 (Fisher's exact test), Q value = 0.02

Table S431.  Gene #63: 'del_10q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 27(10Q22.3) MUTATED 13 5 8 17 13
DEL PEAK 27(10Q22.3) WILD-TYPE 90 67 36 45 47

Figure S431.  Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S432.  Gene #64: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 28(10Q23.31) MUTATED 95 6 14 1
DEL PEAK 28(10Q23.31) WILD-TYPE 139 147 37 2

Figure S432.  Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S433.  Gene #64: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 28(10Q23.31) MUTATED 13 23 4 48 14
DEL PEAK 28(10Q23.31) WILD-TYPE 32 87 47 52 73

Figure S433.  Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CNMF'

P value = 0.0332 (Fisher's exact test), Q value = 0.05

Table S434.  Gene #64: 'del_10q23.31' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 92 82 93 59
DEL PEAK 28(10Q23.31) MUTATED 13 23 25 15 14
DEL PEAK 28(10Q23.31) WILD-TYPE 17 69 57 78 45

Figure S434.  Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_10q23.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00797 (Fisher's exact test), Q value = 0.014

Table S435.  Gene #64: 'del_10q23.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 58 78 80
DEL PEAK 28(10Q23.31) MUTATED 49 9 17 15
DEL PEAK 28(10Q23.31) WILD-TYPE 91 49 61 65

Figure S435.  Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S436.  Gene #64: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 28(10Q23.31) MUTATED 49 9 15 20 15
DEL PEAK 28(10Q23.31) WILD-TYPE 45 85 78 62 35

Figure S436.  Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S437.  Gene #64: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 28(10Q23.31) MUTATED 31 6 47 24
DEL PEAK 28(10Q23.31) WILD-TYPE 78 76 88 63

Figure S437.  Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.00076

Table S438.  Gene #64: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 28(10Q23.31) MUTATED 20 17 18 15 14 30
DEL PEAK 28(10Q23.31) WILD-TYPE 41 49 62 96 36 36

Figure S438.  Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S439.  Gene #64: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 28(10Q23.31) MUTATED 55 10 49
DEL PEAK 28(10Q23.31) WILD-TYPE 188 72 60

Figure S439.  Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00088 (Fisher's exact test), Q value = 0.0019

Table S440.  Gene #64: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 28(10Q23.31) MUTATED 23 8 12 26 18
DEL PEAK 28(10Q23.31) WILD-TYPE 80 64 32 36 42

Figure S440.  Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S441.  Gene #65: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 29(11P15.5) MUTATED 81 10 6 0
DEL PEAK 29(11P15.5) WILD-TYPE 153 143 45 3

Figure S441.  Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S442.  Gene #65: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 29(11P15.5) MUTATED 18 20 3 33 9
DEL PEAK 29(11P15.5) WILD-TYPE 27 90 48 67 78

Figure S442.  Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.5' versus 'RPPA_CHIERARCHICAL'

P value = 0.00212 (Fisher's exact test), Q value = 0.0042

Table S443.  Gene #65: 'del_11p15.5' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 58 78 80
DEL PEAK 29(11P15.5) MUTATED 46 11 10 13
DEL PEAK 29(11P15.5) WILD-TYPE 94 47 68 67

Figure S443.  Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S444.  Gene #65: 'del_11p15.5' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 29(11P15.5) MUTATED 40 10 14 15 8
DEL PEAK 29(11P15.5) WILD-TYPE 54 84 79 67 42

Figure S444.  Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00027

Table S445.  Gene #65: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 29(11P15.5) MUTATED 23 9 45 10
DEL PEAK 29(11P15.5) WILD-TYPE 86 73 90 77

Figure S445.  Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00088 (Fisher's exact test), Q value = 0.0019

Table S446.  Gene #65: 'del_11p15.5' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 29(11P15.5) MUTATED 47 10 37
DEL PEAK 29(11P15.5) WILD-TYPE 196 72 72

Figure S446.  Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0413 (Fisher's exact test), Q value = 0.061

Table S447.  Gene #65: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
DEL PEAK 29(11P15.5) MUTATED 36 16 18
DEL PEAK 29(11P15.5) WILD-TYPE 111 105 55

Figure S447.  Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.027

Table S448.  Gene #65: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 29(11P15.5) MUTATED 16 9 12 21 12
DEL PEAK 29(11P15.5) WILD-TYPE 87 63 32 41 48

Figure S448.  Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S449.  Gene #66: 'del_11q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 30(11Q23.2) MUTATED 73 10 14 2
DEL PEAK 30(11Q23.2) WILD-TYPE 161 143 37 1

Figure S449.  Get High-res Image Gene #66: 'del_11q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S450.  Gene #66: 'del_11q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 30(11Q23.2) MUTATED 23 18 5 29 14
DEL PEAK 30(11Q23.2) WILD-TYPE 22 92 46 71 73

Figure S450.  Get High-res Image Gene #66: 'del_11q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q23.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0294 (Fisher's exact test), Q value = 0.045

Table S451.  Gene #66: 'del_11q23.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 58 78 80
DEL PEAK 30(11Q23.2) MUTATED 37 6 19 12
DEL PEAK 30(11Q23.2) WILD-TYPE 103 52 59 68

Figure S451.  Get High-res Image Gene #66: 'del_11q23.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_11q23.2' versus 'MRNASEQ_CNMF'

P value = 0.00747 (Fisher's exact test), Q value = 0.013

Table S452.  Gene #66: 'del_11q23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 30(11Q23.2) MUTATED 30 11 16 22 11
DEL PEAK 30(11Q23.2) WILD-TYPE 64 83 77 60 39

Figure S452.  Get High-res Image Gene #66: 'del_11q23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00837 (Fisher's exact test), Q value = 0.015

Table S453.  Gene #66: 'del_11q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 30(11Q23.2) MUTATED 32 9 34 15
DEL PEAK 30(11Q23.2) WILD-TYPE 77 73 101 72

Figure S453.  Get High-res Image Gene #66: 'del_11q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.018

Table S454.  Gene #66: 'del_11q23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
DEL PEAK 30(11Q23.2) MUTATED 43 17 16
DEL PEAK 30(11Q23.2) WILD-TYPE 104 104 57

Figure S454.  Get High-res Image Gene #66: 'del_11q23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.021 (Fisher's exact test), Q value = 0.033

Table S455.  Gene #66: 'del_11q23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 30(11Q23.2) MUTATED 22 10 11 23 10
DEL PEAK 30(11Q23.2) WILD-TYPE 81 62 33 39 50

Figure S455.  Get High-res Image Gene #66: 'del_11q23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S456.  Gene #67: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 31(12P13.1) MUTATED 72 3 2 0
DEL PEAK 31(12P13.1) WILD-TYPE 162 150 49 3

Figure S456.  Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S457.  Gene #67: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 31(12P13.1) MUTATED 11 15 1 38 4
DEL PEAK 31(12P13.1) WILD-TYPE 34 95 50 62 83

Figure S457.  Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12p13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S458.  Gene #67: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 31(12P13.1) MUTATED 35 10 9 12 6
DEL PEAK 31(12P13.1) WILD-TYPE 59 84 84 70 44

Figure S458.  Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.5e-05

Table S459.  Gene #67: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 31(12P13.1) MUTATED 16 6 41 9
DEL PEAK 31(12P13.1) WILD-TYPE 93 76 94 78

Figure S459.  Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_CNMF'

P value = 0.00108 (Fisher's exact test), Q value = 0.0023

Table S460.  Gene #67: 'del_12p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 31(12P13.1) MUTATED 13 9 10 12 8 24
DEL PEAK 31(12P13.1) WILD-TYPE 48 57 70 99 42 42

Figure S460.  Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_12p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.0014

Table S461.  Gene #67: 'del_12p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 31(12P13.1) MUTATED 33 10 33
DEL PEAK 31(12P13.1) WILD-TYPE 210 72 76

Figure S461.  Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00047

Table S462.  Gene #67: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 31(12P13.1) MUTATED 15 5 8 24 13
DEL PEAK 31(12P13.1) WILD-TYPE 88 67 36 38 47

Figure S462.  Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S463.  Gene #68: 'del_12q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 32(12Q12) MUTATED 52 5 2 0
DEL PEAK 32(12Q12) WILD-TYPE 182 148 49 3

Figure S463.  Get High-res Image Gene #68: 'del_12q12' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S464.  Gene #68: 'del_12q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 32(12Q12) MUTATED 14 12 0 23 5
DEL PEAK 32(12Q12) WILD-TYPE 31 98 51 77 82

Figure S464.  Get High-res Image Gene #68: 'del_12q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12q12' versus 'MRNASEQ_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.018

Table S465.  Gene #68: 'del_12q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 32(12Q12) MUTATED 22 6 9 10 8
DEL PEAK 32(12Q12) WILD-TYPE 72 88 84 72 42

Figure S465.  Get High-res Image Gene #68: 'del_12q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_12q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0192 (Fisher's exact test), Q value = 0.031

Table S466.  Gene #68: 'del_12q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 32(12Q12) MUTATED 24 10 23
DEL PEAK 32(12Q12) WILD-TYPE 219 72 86

Figure S466.  Get High-res Image Gene #68: 'del_12q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q12.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S467.  Gene #69: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 33(13Q12.11) MUTATED 53 4 5 1
DEL PEAK 33(13Q12.11) WILD-TYPE 181 149 46 2

Figure S467.  Get High-res Image Gene #69: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q12.11' versus 'METHLYATION_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.062

Table S468.  Gene #69: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 33(13Q12.11) MUTATED 10 15 3 20 8
DEL PEAK 33(13Q12.11) WILD-TYPE 35 95 48 80 79

Figure S468.  Get High-res Image Gene #69: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q12.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0197 (Fisher's exact test), Q value = 0.032

Table S469.  Gene #69: 'del_13q12.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 33(13Q12.11) MUTATED 18 7 28 7
DEL PEAK 33(13Q12.11) WILD-TYPE 91 75 107 80

Figure S469.  Get High-res Image Gene #69: 'del_13q12.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S470.  Gene #70: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 34(14Q23.3) MUTATED 122 7 6 1
DEL PEAK 34(14Q23.3) WILD-TYPE 112 146 45 2

Figure S470.  Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q23.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S471.  Gene #70: 'del_14q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 34(14Q23.3) MUTATED 20 27 9 56 11
DEL PEAK 34(14Q23.3) WILD-TYPE 25 83 42 44 76

Figure S471.  Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q23.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S472.  Gene #70: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 34(14Q23.3) MUTATED 52 19 21 24 10
DEL PEAK 34(14Q23.3) WILD-TYPE 42 75 72 58 40

Figure S472.  Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.5e-05

Table S473.  Gene #70: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 34(14Q23.3) MUTATED 35 15 59 17
DEL PEAK 34(14Q23.3) WILD-TYPE 74 67 76 70

Figure S473.  Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S474.  Gene #70: 'del_14q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 34(14Q23.3) MUTATED 19 11 24 25 15 38
DEL PEAK 34(14Q23.3) WILD-TYPE 42 55 56 86 35 28

Figure S474.  Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_14q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S475.  Gene #70: 'del_14q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 34(14Q23.3) MUTATED 60 15 57
DEL PEAK 34(14Q23.3) WILD-TYPE 183 67 52

Figure S475.  Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00376 (Fisher's exact test), Q value = 0.007

Table S476.  Gene #70: 'del_14q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
DEL PEAK 34(14Q23.3) MUTATED 58 31 14
DEL PEAK 34(14Q23.3) WILD-TYPE 89 90 59

Figure S476.  Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_14q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00017

Table S477.  Gene #70: 'del_14q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 34(14Q23.3) MUTATED 34 12 11 33 13
DEL PEAK 34(14Q23.3) WILD-TYPE 69 60 33 29 47

Figure S477.  Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q32.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S478.  Gene #71: 'del_14q32.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 35(14Q32.32) MUTATED 117 8 8 0
DEL PEAK 35(14Q32.32) WILD-TYPE 117 145 43 3

Figure S478.  Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S479.  Gene #71: 'del_14q32.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 35(14Q32.32) MUTATED 24 26 9 47 13
DEL PEAK 35(14Q32.32) WILD-TYPE 21 84 42 53 74

Figure S479.  Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q32.32' versus 'MRNASEQ_CNMF'

P value = 0.00676 (Fisher's exact test), Q value = 0.012

Table S480.  Gene #71: 'del_14q32.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 35(14Q32.32) MUTATED 43 23 26 24 10
DEL PEAK 35(14Q32.32) WILD-TYPE 51 71 67 58 40

Figure S480.  Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q32.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.0011

Table S481.  Gene #71: 'del_14q32.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 35(14Q32.32) MUTATED 32 16 59 19
DEL PEAK 35(14Q32.32) WILD-TYPE 77 66 76 68

Figure S481.  Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.32' versus 'MIRSEQ_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.022

Table S482.  Gene #71: 'del_14q32.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 35(14Q32.32) MUTATED 17 13 25 30 13 32
DEL PEAK 35(14Q32.32) WILD-TYPE 44 53 55 81 37 34

Figure S482.  Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_14q32.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00412 (Fisher's exact test), Q value = 0.0076

Table S483.  Gene #71: 'del_14q32.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 35(14Q32.32) MUTATED 66 18 46
DEL PEAK 35(14Q32.32) WILD-TYPE 177 64 63

Figure S483.  Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_14q32.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.042 (Fisher's exact test), Q value = 0.062

Table S484.  Gene #71: 'del_14q32.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
DEL PEAK 35(14Q32.32) MUTATED 53 32 15
DEL PEAK 35(14Q32.32) WILD-TYPE 94 89 58

Figure S484.  Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_14q32.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.018

Table S485.  Gene #71: 'del_14q32.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 35(14Q32.32) MUTATED 32 15 11 29 13
DEL PEAK 35(14Q32.32) WILD-TYPE 71 57 33 33 47

Figure S485.  Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S486.  Gene #72: 'del_15q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 36(15Q11.2) MUTATED 102 4 13 1
DEL PEAK 36(15Q11.2) WILD-TYPE 132 149 38 2

Figure S486.  Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S487.  Gene #72: 'del_15q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 36(15Q11.2) MUTATED 17 26 5 49 13
DEL PEAK 36(15Q11.2) WILD-TYPE 28 84 46 51 74

Figure S487.  Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q11.2' versus 'RPPA_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.0015

Table S488.  Gene #72: 'del_15q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 92 82 93 59
DEL PEAK 36(15Q11.2) MUTATED 10 20 31 12 21
DEL PEAK 36(15Q11.2) WILD-TYPE 20 72 51 81 38

Figure S488.  Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_15q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00234 (Fisher's exact test), Q value = 0.0045

Table S489.  Gene #72: 'del_15q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 58 78 80
DEL PEAK 36(15Q11.2) MUTATED 52 14 15 13
DEL PEAK 36(15Q11.2) WILD-TYPE 88 44 63 67

Figure S489.  Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_15q11.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S490.  Gene #72: 'del_15q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 36(15Q11.2) MUTATED 44 10 20 23 17
DEL PEAK 36(15Q11.2) WILD-TYPE 50 84 73 59 33

Figure S490.  Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S491.  Gene #72: 'del_15q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 36(15Q11.2) MUTATED 30 7 50 27
DEL PEAK 36(15Q11.2) WILD-TYPE 79 75 85 60

Figure S491.  Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.00092

Table S492.  Gene #72: 'del_15q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 36(15Q11.2) MUTATED 23 11 22 18 15 29
DEL PEAK 36(15Q11.2) WILD-TYPE 38 55 58 93 35 37

Figure S492.  Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_15q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S493.  Gene #72: 'del_15q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 36(15Q11.2) MUTATED 58 11 49
DEL PEAK 36(15Q11.2) WILD-TYPE 185 71 60

Figure S493.  Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.0013

Table S494.  Gene #72: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 36(15Q11.2) MUTATED 30 7 13 26 18
DEL PEAK 36(15Q11.2) WILD-TYPE 73 65 31 36 42

Figure S494.  Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S495.  Gene #73: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 37(15Q15.1) MUTATED 109 3 10 0
DEL PEAK 37(15Q15.1) WILD-TYPE 125 150 41 3

Figure S495.  Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q15.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S496.  Gene #73: 'del_15q15.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 37(15Q15.1) MUTATED 21 24 6 47 11
DEL PEAK 37(15Q15.1) WILD-TYPE 24 86 45 53 76

Figure S496.  Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q15.1' versus 'RPPA_CNMF'

P value = 0.0024 (Fisher's exact test), Q value = 0.0046

Table S497.  Gene #73: 'del_15q15.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 92 82 93 59
DEL PEAK 37(15Q15.1) MUTATED 9 26 27 11 21
DEL PEAK 37(15Q15.1) WILD-TYPE 21 66 55 82 38

Figure S497.  Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_15q15.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0222 (Fisher's exact test), Q value = 0.035

Table S498.  Gene #73: 'del_15q15.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 58 78 80
DEL PEAK 37(15Q15.1) MUTATED 48 16 17 13
DEL PEAK 37(15Q15.1) WILD-TYPE 92 42 61 67

Figure S498.  Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_15q15.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S499.  Gene #73: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 37(15Q15.1) MUTATED 48 9 22 24 13
DEL PEAK 37(15Q15.1) WILD-TYPE 46 85 71 58 37

Figure S499.  Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S500.  Gene #73: 'del_15q15.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 37(15Q15.1) MUTATED 32 5 54 25
DEL PEAK 37(15Q15.1) WILD-TYPE 77 77 81 62

Figure S500.  Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.00098

Table S501.  Gene #73: 'del_15q15.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 37(15Q15.1) MUTATED 20 13 23 18 15 31
DEL PEAK 37(15Q15.1) WILD-TYPE 41 53 57 93 35 35

Figure S501.  Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_15q15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S502.  Gene #73: 'del_15q15.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 37(15Q15.1) MUTATED 60 10 50
DEL PEAK 37(15Q15.1) WILD-TYPE 183 72 59

Figure S502.  Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S503.  Gene #73: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 37(15Q15.1) MUTATED 30 5 13 27 17
DEL PEAK 37(15Q15.1) WILD-TYPE 73 67 31 35 43

Figure S503.  Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S504.  Gene #74: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 38(16P13.3) MUTATED 91 3 2 2
DEL PEAK 38(16P13.3) WILD-TYPE 143 150 49 1

Figure S504.  Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S505.  Gene #74: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 38(16P13.3) MUTATED 10 22 1 43 13
DEL PEAK 38(16P13.3) WILD-TYPE 35 88 50 57 74

Figure S505.  Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S506.  Gene #74: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 38(16P13.3) MUTATED 51 8 12 14 5
DEL PEAK 38(16P13.3) WILD-TYPE 43 86 81 68 45

Figure S506.  Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S507.  Gene #74: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 38(16P13.3) MUTATED 21 8 53 8
DEL PEAK 38(16P13.3) WILD-TYPE 88 74 82 79

Figure S507.  Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S508.  Gene #74: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 38(16P13.3) MUTATED 12 6 16 16 12 35
DEL PEAK 38(16P13.3) WILD-TYPE 49 60 64 95 38 31

Figure S508.  Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S509.  Gene #74: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 38(16P13.3) MUTATED 39 9 49
DEL PEAK 38(16P13.3) WILD-TYPE 204 73 60

Figure S509.  Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00318 (Fisher's exact test), Q value = 0.006

Table S510.  Gene #74: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
DEL PEAK 38(16P13.3) MUTATED 46 23 9
DEL PEAK 38(16P13.3) WILD-TYPE 101 98 64

Figure S510.  Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S511.  Gene #74: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 38(16P13.3) MUTATED 19 8 3 31 17
DEL PEAK 38(16P13.3) WILD-TYPE 84 64 41 31 43

Figure S511.  Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S512.  Gene #75: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 39(16Q23.1) MUTATED 134 27 20 1
DEL PEAK 39(16Q23.1) WILD-TYPE 100 126 31 2

Figure S512.  Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 0.00124 (Fisher's exact test), Q value = 0.0026

Table S513.  Gene #75: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 39(16Q23.1) MUTATED 16 50 16 55 24
DEL PEAK 39(16Q23.1) WILD-TYPE 29 60 35 45 63

Figure S513.  Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 0.00536 (Fisher's exact test), Q value = 0.0098

Table S514.  Gene #75: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 39(16Q23.1) MUTATED 54 30 35 32 18
DEL PEAK 39(16Q23.1) WILD-TYPE 40 64 58 50 32

Figure S514.  Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00022

Table S515.  Gene #75: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 39(16Q23.1) MUTATED 43 22 76 28
DEL PEAK 39(16Q23.1) WILD-TYPE 66 60 59 59

Figure S515.  Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 0.0058 (Fisher's exact test), Q value = 0.01

Table S516.  Gene #75: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 39(16Q23.1) MUTATED 27 23 31 35 23 40
DEL PEAK 39(16Q23.1) WILD-TYPE 34 43 49 76 27 26

Figure S516.  Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00355 (Fisher's exact test), Q value = 0.0066

Table S517.  Gene #75: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 39(16Q23.1) MUTATED 99 23 57
DEL PEAK 39(16Q23.1) WILD-TYPE 144 59 52

Figure S517.  Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0281 (Fisher's exact test), Q value = 0.043

Table S518.  Gene #75: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
DEL PEAK 39(16Q23.1) MUTATED 71 42 24
DEL PEAK 39(16Q23.1) WILD-TYPE 76 79 49

Figure S518.  Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00095 (Fisher's exact test), Q value = 0.0021

Table S519.  Gene #75: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 39(16Q23.1) MUTATED 45 17 14 36 25
DEL PEAK 39(16Q23.1) WILD-TYPE 58 55 30 26 35

Figure S519.  Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S520.  Gene #76: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 40(17P12) MUTATED 160 5 15 1
DEL PEAK 40(17P12) WILD-TYPE 74 148 36 2

Figure S520.  Get High-res Image Gene #76: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S521.  Gene #76: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 40(17P12) MUTATED 28 42 7 72 16
DEL PEAK 40(17P12) WILD-TYPE 17 68 44 28 71

Figure S521.  Get High-res Image Gene #76: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p12' versus 'RPPA_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.027

Table S522.  Gene #76: 'del_17p12' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 92 82 93 59
DEL PEAK 40(17P12) MUTATED 17 45 29 27 25
DEL PEAK 40(17P12) WILD-TYPE 13 47 53 66 34

Figure S522.  Get High-res Image Gene #76: 'del_17p12' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_17p12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00155 (Fisher's exact test), Q value = 0.0032

Table S523.  Gene #76: 'del_17p12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 58 78 80
DEL PEAK 40(17P12) MUTATED 69 16 36 22
DEL PEAK 40(17P12) WILD-TYPE 71 42 42 58

Figure S523.  Get High-res Image Gene #76: 'del_17p12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S524.  Gene #76: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 40(17P12) MUTATED 64 17 30 37 20
DEL PEAK 40(17P12) WILD-TYPE 30 77 63 45 30

Figure S524.  Get High-res Image Gene #76: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S525.  Gene #76: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 40(17P12) MUTATED 52 14 69 33
DEL PEAK 40(17P12) WILD-TYPE 57 68 66 54

Figure S525.  Get High-res Image Gene #76: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S526.  Gene #76: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 40(17P12) MUTATED 25 23 31 28 24 45
DEL PEAK 40(17P12) WILD-TYPE 36 43 49 83 26 21

Figure S526.  Get High-res Image Gene #76: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S527.  Gene #76: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 40(17P12) MUTATED 90 16 70
DEL PEAK 40(17P12) WILD-TYPE 153 66 39

Figure S527.  Get High-res Image Gene #76: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00174 (Fisher's exact test), Q value = 0.0036

Table S528.  Gene #76: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
DEL PEAK 40(17P12) MUTATED 75 36 29
DEL PEAK 40(17P12) WILD-TYPE 72 85 44

Figure S528.  Get High-res Image Gene #76: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S529.  Gene #76: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 40(17P12) MUTATED 45 14 18 40 23
DEL PEAK 40(17P12) WILD-TYPE 58 58 26 22 37

Figure S529.  Get High-res Image Gene #76: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S530.  Gene #77: 'del_17q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 41(17Q24.3) MUTATED 67 2 7 0
DEL PEAK 41(17Q24.3) WILD-TYPE 167 151 44 3

Figure S530.  Get High-res Image Gene #77: 'del_17q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q24.3' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00027

Table S531.  Gene #77: 'del_17q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 41(17Q24.3) MUTATED 10 18 0 26 10
DEL PEAK 41(17Q24.3) WILD-TYPE 35 92 51 74 77

Figure S531.  Get High-res Image Gene #77: 'del_17q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q24.3' versus 'MRNASEQ_CNMF'

P value = 0.00177 (Fisher's exact test), Q value = 0.0036

Table S532.  Gene #77: 'del_17q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 41(17Q24.3) MUTATED 26 12 8 12 14
DEL PEAK 41(17Q24.3) WILD-TYPE 68 82 85 70 36

Figure S532.  Get High-res Image Gene #77: 'del_17q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.022

Table S533.  Gene #77: 'del_17q24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 41(17Q24.3) MUTATED 34 11 29
DEL PEAK 41(17Q24.3) WILD-TYPE 209 71 80

Figure S533.  Get High-res Image Gene #77: 'del_17q24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S534.  Gene #78: 'del_18q12.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 42(18Q12.2) MUTATED 142 15 24 0
DEL PEAK 42(18Q12.2) WILD-TYPE 92 138 27 3

Figure S534.  Get High-res Image Gene #78: 'del_18q12.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q12.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S535.  Gene #78: 'del_18q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 42(18Q12.2) MUTATED 34 32 22 50 21
DEL PEAK 42(18Q12.2) WILD-TYPE 11 78 29 50 66

Figure S535.  Get High-res Image Gene #78: 'del_18q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q12.2' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00027

Table S536.  Gene #78: 'del_18q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 42(18Q12.2) MUTATED 57 26 38 35 15
DEL PEAK 42(18Q12.2) WILD-TYPE 37 68 55 47 35

Figure S536.  Get High-res Image Gene #78: 'del_18q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00027

Table S537.  Gene #78: 'del_18q12.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 42(18Q12.2) MUTATED 46 23 75 27
DEL PEAK 42(18Q12.2) WILD-TYPE 63 59 60 60

Figure S537.  Get High-res Image Gene #78: 'del_18q12.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q12.2' versus 'MIRSEQ_CNMF'

P value = 0.0014 (Fisher's exact test), Q value = 0.0029

Table S538.  Gene #78: 'del_18q12.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 42(18Q12.2) MUTATED 28 21 37 38 14 40
DEL PEAK 42(18Q12.2) WILD-TYPE 33 45 43 73 36 26

Figure S538.  Get High-res Image Gene #78: 'del_18q12.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 7e-04

Table S539.  Gene #78: 'del_18q12.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 42(18Q12.2) MUTATED 91 25 62
DEL PEAK 42(18Q12.2) WILD-TYPE 152 57 47

Figure S539.  Get High-res Image Gene #78: 'del_18q12.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q12.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00445 (Fisher's exact test), Q value = 0.0082

Table S540.  Gene #78: 'del_18q12.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
DEL PEAK 42(18Q12.2) MUTATED 73 39 23
DEL PEAK 42(18Q12.2) WILD-TYPE 74 82 50

Figure S540.  Get High-res Image Gene #78: 'del_18q12.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.5e-05

Table S541.  Gene #78: 'del_18q12.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 42(18Q12.2) MUTATED 40 17 17 41 20
DEL PEAK 42(18Q12.2) WILD-TYPE 63 55 27 21 40

Figure S541.  Get High-res Image Gene #78: 'del_18q12.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S542.  Gene #79: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 43(18Q21.2) MUTATED 157 19 28 0
DEL PEAK 43(18Q21.2) WILD-TYPE 77 134 23 3

Figure S542.  Get High-res Image Gene #79: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S543.  Gene #79: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 43(18Q21.2) MUTATED 36 41 23 58 24
DEL PEAK 43(18Q21.2) WILD-TYPE 9 69 28 42 63

Figure S543.  Get High-res Image Gene #79: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S544.  Gene #79: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 43(18Q21.2) MUTATED 64 29 43 39 18
DEL PEAK 43(18Q21.2) WILD-TYPE 30 65 50 43 32

Figure S544.  Get High-res Image Gene #79: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00034

Table S545.  Gene #79: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 43(18Q21.2) MUTATED 51 25 82 35
DEL PEAK 43(18Q21.2) WILD-TYPE 58 57 53 52

Figure S545.  Get High-res Image Gene #79: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CNMF'

P value = 0.002 (Fisher's exact test), Q value = 0.004

Table S546.  Gene #79: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 43(18Q21.2) MUTATED 35 24 41 44 16 41
DEL PEAK 43(18Q21.2) WILD-TYPE 26 42 39 67 34 25

Figure S546.  Get High-res Image Gene #79: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.001

Table S547.  Gene #79: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 43(18Q21.2) MUTATED 106 28 67
DEL PEAK 43(18Q21.2) WILD-TYPE 137 54 42

Figure S547.  Get High-res Image Gene #79: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00431 (Fisher's exact test), Q value = 0.008

Table S548.  Gene #79: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
DEL PEAK 43(18Q21.2) MUTATED 81 45 27
DEL PEAK 43(18Q21.2) WILD-TYPE 66 76 46

Figure S548.  Get High-res Image Gene #79: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.0011

Table S549.  Gene #79: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 43(18Q21.2) MUTATED 47 20 20 41 25
DEL PEAK 43(18Q21.2) WILD-TYPE 56 52 24 21 35

Figure S549.  Get High-res Image Gene #79: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S550.  Gene #80: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 44(19P13.3) MUTATED 146 2 13 1
DEL PEAK 44(19P13.3) WILD-TYPE 88 151 38 2

Figure S550.  Get High-res Image Gene #80: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S551.  Gene #80: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 44(19P13.3) MUTATED 15 31 5 81 14
DEL PEAK 44(19P13.3) WILD-TYPE 30 79 46 19 73

Figure S551.  Get High-res Image Gene #80: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00017

Table S552.  Gene #80: 'del_19p13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 58 78 80
DEL PEAK 44(19P13.3) MUTATED 73 14 26 21
DEL PEAK 44(19P13.3) WILD-TYPE 67 44 52 59

Figure S552.  Get High-res Image Gene #80: 'del_19p13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S553.  Gene #80: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 44(19P13.3) MUTATED 77 12 22 28 15
DEL PEAK 44(19P13.3) WILD-TYPE 17 82 71 54 35

Figure S553.  Get High-res Image Gene #80: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S554.  Gene #80: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 44(19P13.3) MUTATED 44 7 82 21
DEL PEAK 44(19P13.3) WILD-TYPE 65 75 53 66

Figure S554.  Get High-res Image Gene #80: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S555.  Gene #80: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 44(19P13.3) MUTATED 22 14 23 22 19 59
DEL PEAK 44(19P13.3) WILD-TYPE 39 52 57 89 31 7

Figure S555.  Get High-res Image Gene #80: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S556.  Gene #80: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 44(19P13.3) MUTATED 66 8 85
DEL PEAK 44(19P13.3) WILD-TYPE 177 74 24

Figure S556.  Get High-res Image Gene #80: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.0013

Table S557.  Gene #80: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
DEL PEAK 44(19P13.3) MUTATED 71 31 25
DEL PEAK 44(19P13.3) WILD-TYPE 76 90 48

Figure S557.  Get High-res Image Gene #80: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S558.  Gene #80: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 44(19P13.3) MUTATED 28 8 18 50 23
DEL PEAK 44(19P13.3) WILD-TYPE 75 64 26 12 37

Figure S558.  Get High-res Image Gene #80: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S559.  Gene #81: 'del_19q13.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 45(19Q13.11) MUTATED 70 3 1 1
DEL PEAK 45(19Q13.11) WILD-TYPE 164 150 50 2

Figure S559.  Get High-res Image Gene #81: 'del_19q13.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S560.  Gene #81: 'del_19q13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 45(19Q13.11) MUTATED 7 16 1 40 4
DEL PEAK 45(19Q13.11) WILD-TYPE 38 94 50 60 83

Figure S560.  Get High-res Image Gene #81: 'del_19q13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S561.  Gene #81: 'del_19q13.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 45(19Q13.11) MUTATED 40 3 11 11 7
DEL PEAK 45(19Q13.11) WILD-TYPE 54 91 82 71 43

Figure S561.  Get High-res Image Gene #81: 'del_19q13.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19q13.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S562.  Gene #81: 'del_19q13.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 45(19Q13.11) MUTATED 20 2 38 12
DEL PEAK 45(19Q13.11) WILD-TYPE 89 80 97 75

Figure S562.  Get High-res Image Gene #81: 'del_19q13.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.11' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S563.  Gene #81: 'del_19q13.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 45(19Q13.11) MUTATED 9 8 11 6 11 29
DEL PEAK 45(19Q13.11) WILD-TYPE 52 58 69 105 39 37

Figure S563.  Get High-res Image Gene #81: 'del_19q13.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19q13.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S564.  Gene #81: 'del_19q13.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 45(19Q13.11) MUTATED 28 4 42
DEL PEAK 45(19Q13.11) WILD-TYPE 215 78 67

Figure S564.  Get High-res Image Gene #81: 'del_19q13.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0194 (Fisher's exact test), Q value = 0.031

Table S565.  Gene #81: 'del_19q13.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
DEL PEAK 45(19Q13.11) MUTATED 35 13 12
DEL PEAK 45(19Q13.11) WILD-TYPE 112 108 61

Figure S565.  Get High-res Image Gene #81: 'del_19q13.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19q13.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S566.  Gene #81: 'del_19q13.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 45(19Q13.11) MUTATED 12 3 5 24 16
DEL PEAK 45(19Q13.11) WILD-TYPE 91 69 39 38 44

Figure S566.  Get High-res Image Gene #81: 'del_19q13.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p12.1' versus 'CN_CNMF'

P value = 0.00221 (Fisher's exact test), Q value = 0.0043

Table S567.  Gene #82: 'del_20p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 46(20P12.1) MUTATED 32 5 2 0
DEL PEAK 46(20P12.1) WILD-TYPE 202 148 49 3

Figure S567.  Get High-res Image Gene #82: 'del_20p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_20p12.1' versus 'METHLYATION_CNMF'

P value = 0.00167 (Fisher's exact test), Q value = 0.0034

Table S568.  Gene #82: 'del_20p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 46(20P12.1) MUTATED 9 6 1 16 5
DEL PEAK 46(20P12.1) WILD-TYPE 36 104 50 84 82

Figure S568.  Get High-res Image Gene #82: 'del_20p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_20p12.1' versus 'MRNASEQ_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 0.024

Table S569.  Gene #82: 'del_20p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 46(20P12.1) MUTATED 11 2 9 13 3
DEL PEAK 46(20P12.1) WILD-TYPE 83 92 84 69 47

Figure S569.  Get High-res Image Gene #82: 'del_20p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0283 (Fisher's exact test), Q value = 0.043

Table S570.  Gene #82: 'del_20p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 46(20P12.1) MUTATED 15 2 15 6
DEL PEAK 46(20P12.1) WILD-TYPE 94 80 120 81

Figure S570.  Get High-res Image Gene #82: 'del_20p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_CNMF'

P value = 0.0202 (Fisher's exact test), Q value = 0.032

Table S571.  Gene #82: 'del_20p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 46(20P12.1) MUTATED 3 2 10 6 8 10
DEL PEAK 46(20P12.1) WILD-TYPE 58 64 70 105 42 56

Figure S571.  Get High-res Image Gene #82: 'del_20p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_20p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0285 (Fisher's exact test), Q value = 0.044

Table S572.  Gene #82: 'del_20p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 46(20P12.1) MUTATED 20 3 16
DEL PEAK 46(20P12.1) WILD-TYPE 223 79 93

Figure S572.  Get High-res Image Gene #82: 'del_20p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0205 (Fisher's exact test), Q value = 0.033

Table S573.  Gene #82: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 46(20P12.1) MUTATED 10 1 4 8 10
DEL PEAK 46(20P12.1) WILD-TYPE 93 71 40 54 50

Figure S573.  Get High-res Image Gene #82: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S574.  Gene #83: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 47(21Q11.2) MUTATED 142 16 22 2
DEL PEAK 47(21Q11.2) WILD-TYPE 92 137 29 1

Figure S574.  Get High-res Image Gene #83: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S575.  Gene #83: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 47(21Q11.2) MUTATED 23 47 7 61 29
DEL PEAK 47(21Q11.2) WILD-TYPE 22 63 44 39 58

Figure S575.  Get High-res Image Gene #83: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00027

Table S576.  Gene #83: 'del_21q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 47(21Q11.2) MUTATED 58 27 36 33 17
DEL PEAK 47(21Q11.2) WILD-TYPE 36 67 57 49 33

Figure S576.  Get High-res Image Gene #83: 'del_21q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_21q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0027 (Fisher's exact test), Q value = 0.0052

Table S577.  Gene #83: 'del_21q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 47(21Q11.2) MUTATED 47 22 70 32
DEL PEAK 47(21Q11.2) WILD-TYPE 62 60 65 55

Figure S577.  Get High-res Image Gene #83: 'del_21q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00187 (Fisher's exact test), Q value = 0.0038

Table S578.  Gene #83: 'del_21q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 47(21Q11.2) MUTATED 25 20 30 39 23 42
DEL PEAK 47(21Q11.2) WILD-TYPE 36 46 50 72 27 24

Figure S578.  Get High-res Image Gene #83: 'del_21q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_21q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.0013

Table S579.  Gene #83: 'del_21q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 47(21Q11.2) MUTATED 91 26 62
DEL PEAK 47(21Q11.2) WILD-TYPE 152 56 47

Figure S579.  Get High-res Image Gene #83: 'del_21q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0019

Table S580.  Gene #83: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
DEL PEAK 47(21Q11.2) MUTATED 79 44 22
DEL PEAK 47(21Q11.2) WILD-TYPE 68 77 51

Figure S580.  Get High-res Image Gene #83: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_21q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00057 (Fisher's exact test), Q value = 0.0013

Table S581.  Gene #83: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 47(21Q11.2) MUTATED 47 22 14 40 22
DEL PEAK 47(21Q11.2) WILD-TYPE 56 50 30 22 38

Figure S581.  Get High-res Image Gene #83: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q22.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S582.  Gene #84: 'del_21q22.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 48(21Q22.13) MUTATED 153 17 24 2
DEL PEAK 48(21Q22.13) WILD-TYPE 81 136 27 1

Figure S582.  Get High-res Image Gene #84: 'del_21q22.13' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q22.13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S583.  Gene #84: 'del_21q22.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 48(21Q22.13) MUTATED 26 52 8 60 31
DEL PEAK 48(21Q22.13) WILD-TYPE 19 58 43 40 56

Figure S583.  Get High-res Image Gene #84: 'del_21q22.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q22.13' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00054

Table S584.  Gene #84: 'del_21q22.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 48(21Q22.13) MUTATED 59 29 42 38 17
DEL PEAK 48(21Q22.13) WILD-TYPE 35 65 51 44 33

Figure S584.  Get High-res Image Gene #84: 'del_21q22.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_21q22.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00083 (Fisher's exact test), Q value = 0.0018

Table S585.  Gene #84: 'del_21q22.13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 48(21Q22.13) MUTATED 53 24 75 33
DEL PEAK 48(21Q22.13) WILD-TYPE 56 58 60 54

Figure S585.  Get High-res Image Gene #84: 'del_21q22.13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_21q22.13' versus 'MIRSEQ_CNMF'

P value = 0.00214 (Fisher's exact test), Q value = 0.0042

Table S586.  Gene #84: 'del_21q22.13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 48(21Q22.13) MUTATED 29 22 33 40 27 42
DEL PEAK 48(21Q22.13) WILD-TYPE 32 44 47 71 23 24

Figure S586.  Get High-res Image Gene #84: 'del_21q22.13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_21q22.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00015

Table S587.  Gene #84: 'del_21q22.13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 48(21Q22.13) MUTATED 100 26 67
DEL PEAK 48(21Q22.13) WILD-TYPE 143 56 42

Figure S587.  Get High-res Image Gene #84: 'del_21q22.13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_21q22.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00559 (Fisher's exact test), Q value = 0.01

Table S588.  Gene #84: 'del_21q22.13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 121 73
DEL PEAK 48(21Q22.13) MUTATED 82 46 28
DEL PEAK 48(21Q22.13) WILD-TYPE 65 75 45

Figure S588.  Get High-res Image Gene #84: 'del_21q22.13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_21q22.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00137 (Fisher's exact test), Q value = 0.0029

Table S589.  Gene #84: 'del_21q22.13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 48(21Q22.13) MUTATED 51 23 15 40 27
DEL PEAK 48(21Q22.13) WILD-TYPE 52 49 29 22 33

Figure S589.  Get High-res Image Gene #84: 'del_21q22.13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S590.  Gene #85: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 49(22Q13.31) MUTATED 143 6 12 0
DEL PEAK 49(22Q13.31) WILD-TYPE 91 147 39 3

Figure S590.  Get High-res Image Gene #85: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S591.  Gene #85: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 49(22Q13.31) MUTATED 22 36 6 59 21
DEL PEAK 49(22Q13.31) WILD-TYPE 23 74 45 41 66

Figure S591.  Get High-res Image Gene #85: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.018

Table S592.  Gene #85: 'del_22q13.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 58 78 80
DEL PEAK 49(22Q13.31) MUTATED 62 13 29 22
DEL PEAK 49(22Q13.31) WILD-TYPE 78 45 49 58

Figure S592.  Get High-res Image Gene #85: 'del_22q13.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_22q13.31' versus 'MRNASEQ_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.0023

Table S593.  Gene #85: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 49(22Q13.31) MUTATED 50 23 30 33 16
DEL PEAK 49(22Q13.31) WILD-TYPE 44 71 63 49 34

Figure S593.  Get High-res Image Gene #85: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0012 (Fisher's exact test), Q value = 0.0025

Table S594.  Gene #85: 'del_22q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 109 82 135 87
DEL PEAK 49(22Q13.31) MUTATED 48 18 60 26
DEL PEAK 49(22Q13.31) WILD-TYPE 61 64 75 61

Figure S594.  Get High-res Image Gene #85: 'del_22q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.5e-05

Table S595.  Gene #85: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 49(22Q13.31) MUTATED 20 16 28 30 22 42
DEL PEAK 49(22Q13.31) WILD-TYPE 41 50 52 81 28 24

Figure S595.  Get High-res Image Gene #85: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S596.  Gene #85: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 49(22Q13.31) MUTATED 77 17 64
DEL PEAK 49(22Q13.31) WILD-TYPE 166 65 45

Figure S596.  Get High-res Image Gene #85: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00032

Table S597.  Gene #85: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 103 72 44 62 60
DEL PEAK 49(22Q13.31) MUTATED 37 14 16 37 24
DEL PEAK 49(22Q13.31) WILD-TYPE 66 58 28 25 36

Figure S597.  Get High-res Image Gene #85: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S598.  Gene #86: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 50(XP22.2) MUTATED 70 8 7 0
DEL PEAK 50(XP22.2) WILD-TYPE 164 145 44 3

Figure S598.  Get High-res Image Gene #86: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp22.2' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.5e-05

Table S599.  Gene #86: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 50(XP22.2) MUTATED 16 21 3 31 8
DEL PEAK 50(XP22.2) WILD-TYPE 29 89 48 69 79

Figure S599.  Get High-res Image Gene #86: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp22.2' versus 'MRNASEQ_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.062

Table S600.  Gene #86: 'del_xp22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 94 94 93 82 50
DEL PEAK 50(XP22.2) MUTATED 25 13 12 15 14
DEL PEAK 50(XP22.2) WILD-TYPE 69 81 81 67 36

Figure S600.  Get High-res Image Gene #86: 'del_xp22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp22.2' versus 'MIRSEQ_CNMF'

P value = 0.0255 (Fisher's exact test), Q value = 0.04

Table S601.  Gene #86: 'del_xp22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 66 80 111 50 66
DEL PEAK 50(XP22.2) MUTATED 16 10 8 19 11 20
DEL PEAK 50(XP22.2) WILD-TYPE 45 56 72 92 39 46

Figure S601.  Get High-res Image Gene #86: 'del_xp22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xp22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00147 (Fisher's exact test), Q value = 0.003

Table S602.  Gene #86: 'del_xp22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 50(XP22.2) MUTATED 40 10 34
DEL PEAK 50(XP22.2) WILD-TYPE 203 72 75

Figure S602.  Get High-res Image Gene #86: 'del_xp22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xp21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S603.  Gene #87: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 51(XP21.1) MUTATED 63 4 9 0
DEL PEAK 51(XP21.1) WILD-TYPE 171 149 42 3

Figure S603.  Get High-res Image Gene #87: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 0.00529 (Fisher's exact test), Q value = 0.0097

Table S604.  Gene #87: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 51(XP21.1) MUTATED 15 19 4 21 9
DEL PEAK 51(XP21.1) WILD-TYPE 30 91 47 79 78

Figure S604.  Get High-res Image Gene #87: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq21.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S605.  Gene #88: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 234 153 51 3
DEL PEAK 52(XQ21.33) MUTATED 48 2 7 0
DEL PEAK 52(XQ21.33) WILD-TYPE 186 151 44 3

Figure S605.  Get High-res Image Gene #88: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq21.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S606.  Gene #88: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 110 51 100 87
DEL PEAK 52(XQ21.33) MUTATED 17 10 2 15 5
DEL PEAK 52(XQ21.33) WILD-TYPE 28 100 49 85 82

Figure S606.  Get High-res Image Gene #88: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq21.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0256 (Fisher's exact test), Q value = 0.04

Table S607.  Gene #88: 'del_xq21.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 243 82 109
DEL PEAK 52(XQ21.33) MUTATED 33 4 19
DEL PEAK 52(XQ21.33) WILD-TYPE 210 78 90

Figure S607.  Get High-res Image Gene #88: 'del_xq21.33' versus Molecular Subtype #8: 'MIRSEQ_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/STAD-TP/22533932/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/STAD-TP/22552605/STAD-TP.transferedmergedcluster.txt

  • Number of patients = 441

  • Number of significantly focal cnvs = 88

  • Number of molecular subtypes = 10

  • 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)