Correlation between copy number variation genes (focal events) and molecular subtypes
Lung Squamous Cell Carcinoma (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/C1F18Z59
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 83 focal events and 12 molecular subtypes across 501 patients, 544 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1q21.2 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_2p16.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_2q31.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • amp_3q26.33 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_4q12 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_5p15.33 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_5p12 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_6p12.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

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

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

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

  • amp_8p11.23 cnv correlated to 'MRNA_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • amp_8q24.21 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_9p13.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • amp_12p13.33 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • amp_13q34 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • amp_14q13.3 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • amp_14q32.33 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • amp_18p11.32 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_19q12 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_19q13.2 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_20p12.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_20q11.21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • amp_22q11.21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_xq28 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

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

  • del_1p13.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_2p25.3 cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • del_3p25.3 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3p13 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3p12.3 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_3p12.3 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • del_4q32.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_4q35.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_5q31.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  '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', and 'MIRSEQ_CHIERARCHICAL'.

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

  • del_7q11.22 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

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

  • del_9p21.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • del_10p15.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • del_11p15.5 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • del_11q22.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_11q25 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

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

  • del_13q14.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • del_14q11.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_15q11.2 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • del_15q21.1 cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • del_16p13.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

  • del_17p11.2 cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • del_17q25.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_18q23 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

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

  • del_19q13.32 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

  • del_21q22.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_22q11.21 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

  • del_xp22.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_xp11.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_xq22.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 83 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 544 significant findings detected.

Clinical
Features
MRNA
CNMF
MRNA
CHIERARCHICAL
CN
CNMF
METHLYATION
CNMF
RPPA
CNMF
RPPA
CHIERARCHICAL
MRNASEQ
CNMF
MRNASEQ
CHIERARCHICAL
MIRSEQ
CNMF
MIRSEQ
CHIERARCHICAL
MIRSEQ
MATURE
CNMF
MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
amp 3q26 33 452 (90%) 49 0.00073
(0.00275)
0.00045
(0.00194)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
0.00072
(0.00273)
0.00847
(0.0207)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
0.00024
(0.00113)
del 1p36 11 228 (46%) 273 1e-05
(8.16e-05)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
0.00047
(0.00198)
0.0154
(0.0339)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
6e-05
(0.000349)
del 4q32 3 329 (66%) 172 0.00112
(0.00385)
0.018
(0.0385)
1e-05
(8.16e-05)
0.00685
(0.0174)
0.029
(0.0572)
0.0188
(0.0401)
2e-05
(0.000142)
0.00035
(0.00158)
3e-05
(0.000193)
0.00255
(0.00765)
0.00024
(0.00113)
0.00011
(0.000589)
amp 2p16 1 275 (55%) 226 0.00084
(0.00309)
0.00039
(0.00171)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
0.00797
(0.0196)
0.147
(0.217)
1e-05
(8.16e-05)
2e-05
(0.000142)
1e-05
(8.16e-05)
0.00071
(0.00271)
0.00037
(0.00163)
0.00061
(0.00243)
del 1p13 1 221 (44%) 280 0.00022
(0.00106)
5e-05
(3e-04)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
0.00048
(0.00202)
0.0503
(0.0919)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
0.00014
(0.000719)
0.00047
(0.00198)
del 2q37 1 159 (32%) 342 0.0016
(0.00516)
0.00071
(0.00271)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
0.00499
(0.0132)
0.357
(0.442)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
2e-05
(0.000142)
0.00028
(0.00129)
0.00037
(0.00163)
del 4p15 2 316 (63%) 185 0.00013
(0.000681)
3e-05
(0.000193)
1e-05
(8.16e-05)
0.00027
(0.00126)
0.0285
(0.0564)
0.0449
(0.0832)
7e-05
(0.000401)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
0.0562
(0.101)
0.0008
(0.00296)
0.00062
(0.00245)
del 9q21 11 251 (50%) 250 0.00061
(0.00243)
4e-05
(0.000247)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
0.138
(0.207)
0.0219
(0.0455)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
2e-05
(0.000142)
1e-05
(8.16e-05)
0.00317
(0.00907)
0.0151
(0.0336)
del 10q23 31 268 (53%) 233 0.00975
(0.0236)
0.00116
(0.00397)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
0.12
(0.183)
0.0425
(0.0798)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
0.00024
(0.00113)
1e-05
(8.16e-05)
5e-05
(3e-04)
0.0113
(0.0264)
amp 1q21 2 258 (51%) 243 0.0415
(0.0785)
0.0994
(0.158)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
0.0222
(0.046)
0.3
(0.387)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
3e-05
(0.000193)
0.00049
(0.00205)
0.0111
(0.026)
amp 17q25 1 236 (47%) 265 0.00399
(0.011)
0.134
(0.203)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
0.00052
(0.00216)
0.505
(0.582)
3e-05
(0.000193)
3e-05
(0.000193)
0.00064
(0.00252)
0.00473
(0.0126)
0.00065
(0.00255)
0.0251
(0.0508)
del 3p13 434 (87%) 67 0.0439
(0.0819)
0.355
(0.44)
1e-05
(8.16e-05)
2e-05
(0.000142)
0.258
(0.343)
0.0448
(0.0832)
0.0006
(0.00243)
0.0008
(0.00296)
2e-05
(0.000142)
1e-05
(8.16e-05)
2e-05
(0.000142)
0.00146
(0.00477)
del 3p12 3 421 (84%) 80 0.0357
(0.0689)
0.394
(0.48)
1e-05
(8.16e-05)
2e-05
(0.000142)
0.442
(0.522)
0.00751
(0.0187)
0.00216
(0.00665)
0.00757
(0.0188)
0.00159
(0.00514)
3e-05
(0.000193)
9e-05
(0.000501)
0.00369
(0.0104)
del 4q22 1 285 (57%) 216 0.00054
(0.00223)
0.00422
(0.0115)
1e-05
(8.16e-05)
0.0488
(0.0895)
0.0281
(0.0558)
0.15
(0.22)
3e-05
(0.000193)
0.0146
(0.0328)
1e-05
(8.16e-05)
0.00613
(0.0158)
0.00087
(0.00316)
0.322
(0.409)
del 9p23 332 (66%) 169 0.0149
(0.0332)
0.00163
(0.00524)
1e-05
(8.16e-05)
0.00217
(0.00665)
0.555
(0.624)
0.114
(0.176)
0.0001
(0.000544)
0.00099
(0.00348)
0.00089
(0.00321)
0.0002
(0.000981)
1e-05
(8.16e-05)
0.0205
(0.0432)
amp 2q31 2 172 (34%) 329 0.0389
(0.0744)
0.0228
(0.047)
1e-05
(8.16e-05)
0.00108
(0.00375)
0.00928
(0.0225)
0.0783
(0.133)
3e-05
(0.000193)
1e-05
(8.16e-05)
0.00078
(0.00292)
0.256
(0.342)
0.00397
(0.011)
0.0659
(0.115)
amp 7q21 2 264 (53%) 237 0.115
(0.177)
0.0151
(0.0336)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
0.13
(0.196)
0.976
(0.979)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
0.00098
(0.00346)
0.00269
(0.0079)
0.0419
(0.0788)
amp 11q13 3 185 (37%) 316 0.0416
(0.0785)
0.0341
(0.0662)
0.00165
(0.00525)
0.00017
(0.000847)
0.608
(0.669)
0.177
(0.252)
0.0211
(0.0443)
0.0647
(0.113)
0.0154
(0.0339)
0.00465
(0.0124)
0.00164
(0.00525)
0.0195
(0.0412)
amp 12p13 33 255 (51%) 246 0.00197
(0.00609)
0.0218
(0.0455)
1e-05
(8.16e-05)
0.00371
(0.0104)
0.244
(0.33)
0.745
(0.784)
1e-05
(8.16e-05)
0.0019
(0.0059)
0.0141
(0.0318)
0.00267
(0.00789)
0.00296
(0.00855)
0.0625
(0.11)
amp 18q11 2 151 (30%) 350 0.00069
(0.00267)
0.0157
(0.0342)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
0.0191
(0.0405)
0.473
(0.554)
1e-05
(8.16e-05)
8e-05
(0.000453)
0.0022
(0.00672)
0.00282
(0.00819)
0.0557
(0.1)
0.0586
(0.105)
del 2q22 1 131 (26%) 370 0.0511
(0.0929)
0.336
(0.423)
1e-05
(8.16e-05)
3e-05
(0.000193)
0.0477
(0.0878)
0.0998
(0.159)
0.00257
(0.00766)
0.00713
(0.0179)
0.00165
(0.00525)
0.00051
(0.00213)
0.00071
(0.00271)
0.0064
(0.0164)
del 3p25 3 398 (79%) 103 0.0402
(0.0766)
0.202
(0.28)
2e-05
(0.000142)
0.00023
(0.0011)
0.321
(0.408)
0.283
(0.369)
0.00271
(0.00794)
0.00032
(0.00146)
0.00444
(0.012)
0.00014
(0.000719)
0.0115
(0.0267)
0.024
(0.0492)
del 3p12 3 427 (85%) 74 0.0683
(0.118)
0.227
(0.31)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
0.532
(0.604)
0.00577
(0.015)
0.00061
(0.00243)
0.0046
(0.0123)
0.00145
(0.00475)
1e-05
(8.16e-05)
9e-05
(0.000501)
0.00236
(0.00712)
del 17q11 2 132 (26%) 369 0.00035
(0.00158)
0.00015
(0.000755)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
0.0052
(0.0137)
0.00672
(0.0172)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
0.126
(0.191)
0.00135
(0.0045)
0.256
(0.342)
0.0977
(0.156)
del xp11 3 149 (30%) 352 0.0794
(0.134)
0.401
(0.487)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
0.0132
(0.0301)
0.0959
(0.154)
6e-05
(0.000349)
0.00217
(0.00665)
0.00015
(0.000755)
0.00059
(0.0024)
0.00072
(0.00273)
0.00095
(0.00337)
del xq22 3 114 (23%) 387 0.00687
(0.0174)
0.0106
(0.0251)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
0.778
(0.814)
0.613
(0.673)
0.00178
(0.00557)
0.334
(0.42)
1e-05
(8.16e-05)
0.00011
(0.000589)
0.00028
(0.00129)
0.0165
(0.0357)
amp 7p11 2 256 (51%) 245 0.0905
(0.148)
0.0299
(0.0586)
1e-05
(8.16e-05)
0.0221
(0.0458)
0.556
(0.625)
0.213
(0.293)
0.00055
(0.00225)
4e-05
(0.000247)
0.0162
(0.0353)
0.0467
(0.0861)
0.0247
(0.0502)
0.433
(0.515)
amp 9p13 3 136 (27%) 365 0.198
(0.275)
0.716
(0.762)
1e-05
(8.16e-05)
0.00794
(0.0196)
0.0115
(0.0267)
0.00012
(0.000636)
0.00179
(0.00557)
0.00119
(0.00405)
0.00044
(0.00191)
0.00374
(0.0104)
0.413
(0.495)
0.805
(0.837)
amp 15q26 3 179 (36%) 322 0.247
(0.332)
0.0509
(0.0927)
2e-05
(0.000142)
0.00079
(0.00295)
0.309
(0.396)
0.246
(0.332)
2e-05
(0.000142)
0.00258
(0.00767)
0.00179
(0.00557)
0.00637
(0.0164)
0.00083
(0.00306)
0.0103
(0.0244)
amp 18p11 32 179 (36%) 322 0.0537
(0.0971)
0.0046
(0.0123)
1e-05
(8.16e-05)
5e-05
(3e-04)
0.0888
(0.146)
0.104
(0.163)
0.0206
(0.0433)
0.00143
(0.0047)
0.00275
(0.00801)
0.0948
(0.154)
0.0331
(0.0646)
0.026
(0.0523)
del 4q35 2 331 (66%) 170 0.0904
(0.148)
0.205
(0.283)
1e-05
(8.16e-05)
0.00993
(0.0238)
0.112
(0.173)
0.1
(0.159)
2e-05
(0.000142)
0.00325
(0.00925)
2e-05
(0.000142)
0.0079
(0.0196)
0.00108
(0.00375)
0.0011
(0.0038)
del 5q31 1 386 (77%) 115 0.275
(0.361)
0.276
(0.362)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
0.275
(0.361)
0.526
(0.598)
0.00723
(0.0181)
0.00649
(0.0166)
0.0156
(0.0341)
3e-05
(0.000193)
0.00015
(0.000755)
0.0211
(0.0443)
del 6q26 135 (27%) 366 0.0597
(0.106)
0.00525
(0.0138)
0.0043
(0.0117)
0.00175
(0.0055)
0.36
(0.444)
0.942
(0.95)
0.00111
(0.00383)
0.00814
(0.02)
0.0278
(0.0553)
0.0748
(0.128)
0.00069
(0.00267)
0.0439
(0.0819)
del 10p15 3 228 (46%) 273 0.514
(0.589)
0.448
(0.527)
2e-05
(0.000142)
4e-05
(0.000247)
0.0679
(0.118)
0.285
(0.371)
1e-05
(8.16e-05)
0.00026
(0.00122)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
4e-05
(0.000247)
0.0447
(0.0832)
del 11p15 5 245 (49%) 256 0.00223
(0.00679)
0.0108
(0.0256)
1e-05
(8.16e-05)
0.00014
(0.000719)
0.0531
(0.0963)
0.00855
(0.0209)
0.00795
(0.0196)
0.0822
(0.137)
0.00071
(0.00271)
0.088
(0.145)
0.00288
(0.00834)
0.193
(0.269)
del 14q11 2 175 (35%) 326 0.00524
(0.0138)
0.0335
(0.0652)
6e-05
(0.000349)
0.0692
(0.119)
0.104
(0.163)
0.118
(0.18)
8e-05
(0.000453)
0.00015
(0.000755)
0.069
(0.119)
0.00995
(0.0238)
0.00325
(0.00925)
0.0024
(0.00722)
del xp21 1 151 (30%) 350 0.316
(0.404)
0.478
(0.558)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
0.274
(0.361)
0.308
(0.394)
5e-05
(3e-04)
0.00062
(0.00245)
0.00143
(0.0047)
0.00119
(0.00405)
0.00037
(0.00163)
0.00108
(0.00375)
amp 14q32 33 158 (32%) 343 0.108
(0.168)
0.0156
(0.0341)
1e-05
(8.16e-05)
9e-05
(0.000501)
0.0241
(0.0494)
0.144
(0.214)
0.00037
(0.00163)
0.00041
(0.00178)
0.457
(0.536)
0.43
(0.514)
0.00328
(0.00928)
0.549
(0.62)
amp 19q12 225 (45%) 276 0.502
(0.58)
0.648
(0.703)
1e-05
(8.16e-05)
0.0549
(0.0989)
0.0256
(0.0516)
0.845
(0.874)
0.00124
(0.0042)
0.0386
(0.0739)
0.0109
(0.0256)
0.565
(0.632)
0.00978
(0.0236)
0.0112
(0.0263)
del 10p15 1 211 (42%) 290 0.253
(0.34)
0.434
(0.515)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
0.0817
(0.137)
0.404
(0.489)
1e-05
(8.16e-05)
7e-05
(0.000401)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
0.00037
(0.00163)
0.095
(0.154)
del 16q23 1 210 (42%) 291 0.987
(0.988)
0.114
(0.175)
0.0404
(0.0768)
0.205
(0.283)
0.007
(0.0177)
0.405
(0.489)
0.0456
(0.0843)
0.0376
(0.0723)
0.00463
(0.0124)
0.438
(0.519)
0.0131
(0.03)
0.0009
(0.00324)
del 22q13 32 127 (25%) 374 0.00047
(0.00198)
0.0105
(0.0248)
0.00013
(0.000681)
0.238
(0.322)
0.0433
(0.0811)
0.447
(0.526)
0.0001
(0.000544)
1e-05
(8.16e-05)
0.155
(0.226)
0.00055
(0.00225)
0.655
(0.71)
0.145
(0.215)
del xp22 2 155 (31%) 346 0.662
(0.716)
0.527
(0.599)
0.00014
(0.000719)
5e-05
(3e-04)
0.674
(0.726)
0.252
(0.338)
0.00461
(0.0123)
0.00982
(0.0236)
0.0246
(0.0502)
0.111
(0.172)
0.0003
(0.00138)
0.00598
(0.0155)
amp 20p12 2 280 (56%) 221 0.00143
(0.0047)
0.00235
(0.00711)
1e-05
(8.16e-05)
0.00274
(0.008)
0.147
(0.217)
0.551
(0.621)
0.00677
(0.0172)
0.0147
(0.033)
0.0821
(0.137)
0.648
(0.703)
0.0887
(0.146)
0.759
(0.798)
del 5q12 1 369 (74%) 132 0.349
(0.435)
0.433
(0.515)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
0.0631
(0.111)
0.434
(0.516)
0.00068
(0.00266)
0.00132
(0.00441)
0.139
(0.208)
6e-05
(0.000349)
0.00012
(0.000636)
0.0616
(0.109)
del 6p25 3 134 (27%) 367 0.541
(0.612)
0.281
(0.368)
7e-05
(0.000401)
3e-05
(0.000193)
0.942
(0.95)
0.478
(0.558)
1e-05
(8.16e-05)
1e-05
(8.16e-05)
0.039
(0.0744)
0.00086
(0.00314)
0.262
(0.347)
0.67
(0.722)
del 7q36 3 104 (21%) 397 0.302
(0.39)
0.0489
(0.0895)
0.00025
(0.00117)
0.0689
(0.119)
0.345
(0.432)
0.197
(0.274)
0.00018
(0.000892)
0.00127
(0.00427)
0.421
(0.505)
0.00442
(0.012)
0.175
(0.25)
0.00046
(0.00197)
del 9p21 3 388 (77%) 113 0.214
(0.295)
0.258
(0.343)
1e-05
(8.16e-05)
0.0958
(0.154)
0.635
(0.693)
0.275
(0.361)
0.00174
(0.0055)
0.0155
(0.0341)
0.352
(0.438)
0.0121
(0.0277)
0.00091
(0.00326)
0.0373
(0.0717)
del 17q25 3 102 (20%) 399 0.0275
(0.0548)
0.0113
(0.0264)
3e-05
(0.000193)
0.0826
(0.138)
0.776
(0.813)
0.574
(0.641)
0.00307
(0.00884)
0.00127
(0.00427)
0.405
(0.489)
0.0134
(0.0304)
0.0826
(0.138)
0.904
(0.924)
del 19p13 3 236 (47%) 265 0.39
(0.475)
0.234
(0.319)
1e-05
(8.16e-05)
0.102
(0.161)
0.152
(0.221)
0.116
(0.177)
0.0705
(0.121)
0.0219
(0.0455)
0.0273
(0.0547)
0.00086
(0.00314)
0.00384
(0.0107)
0.00426
(0.0116)
del 19q13 32 149 (30%) 352 0.79
(0.824)
0.589
(0.652)
1e-05
(8.16e-05)
0.0017
(0.00539)
0.0141
(0.0318)
0.442
(0.522)
0.018
(0.0385)
0.00713
(0.0179)
0.00435
(0.0118)
0.505
(0.582)
0.101
(0.159)
0.254
(0.34)
amp 6q12 152 (30%) 349 0.883
(0.907)
0.728
(0.77)
0.00016
(0.000801)
0.246
(0.332)
0.553
(0.622)
0.792
(0.825)
0.00095
(0.00337)
0.0055
(0.0143)
0.00315
(0.00904)
0.0229
(0.0472)
0.235
(0.319)
0.587
(0.651)
amp 19q13 2 234 (47%) 267 0.44
(0.521)
0.258
(0.343)
1e-05
(8.16e-05)
0.0931
(0.152)
0.0488
(0.0895)
0.518
(0.592)
0.00353
(0.00993)
0.0807
(0.136)
0.0363
(0.0699)
0.501
(0.58)
0.105
(0.164)
0.0137
(0.0311)
amp 22q11 21 256 (51%) 245 0.181
(0.256)
0.157
(0.228)
1e-05
(8.16e-05)
3e-05
(0.000193)
0.0639
(0.112)
0.641
(0.698)
6e-05
(0.000349)
0.00022
(0.00106)
0.38
(0.465)
0.0416
(0.0785)
0.0739
(0.127)
0.206
(0.283)
del 9p21 1 326 (65%) 175 0.329
(0.415)
0.285
(0.371)
1e-05
(8.16e-05)
0.0538
(0.0971)
0.348
(0.435)
0.506
(0.582)
0.00022
(0.00106)
0.00036
(0.00162)
0.0901
(0.148)
0.00918
(0.0224)
0.00138
(0.00458)
0.197
(0.274)
del 11q22 1 163 (33%) 338 0.483
(0.561)
0.177
(0.252)
0.00061
(0.00243)
0.00175
(0.0055)
0.279
(0.366)
0.277
(0.363)
0.0231
(0.0475)
0.0296
(0.0583)
0.162
(0.235)
0.0194
(0.041)
0.164
(0.236)
0.0955
(0.154)
del 21q11 2 244 (49%) 257 0.709
(0.755)
0.562
(0.629)
0.00089
(0.00321)
0.0181
(0.0387)
0.703
(0.751)
0.271
(0.358)
0.0624
(0.11)
0.436
(0.517)
3e-05
(0.000193)
4e-05
(0.000247)
0.00151
(0.00491)
0.0952
(0.154)
del 21q22 3 281 (56%) 220 0.896
(0.918)
0.128
(0.194)
2e-05
(0.000142)
0.00399
(0.011)
0.92
(0.935)
0.199
(0.276)
0.0651
(0.114)
0.0761
(0.13)
0.00055
(0.00225)
0.00047
(0.00198)
0.0273
(0.0547)
0.428
(0.511)
amp 5p15 33 387 (77%) 114 0.851
(0.88)
0.802
(0.834)
1e-05
(8.16e-05)
0.0001
(0.000544)
0.106
(0.166)
0.405
(0.489)
0.366
(0.45)
0.0656
(0.114)
0.0762
(0.13)
0.00544
(0.0142)
0.00348
(0.00982)
0.317
(0.404)
amp 12q15 178 (36%) 323 0.156
(0.227)
0.344
(0.432)
0.00041
(0.00178)
0.00538
(0.0141)
0.0741
(0.127)
0.368
(0.452)
0.00602
(0.0156)
0.0117
(0.0271)
0.128
(0.194)
0.643
(0.7)
0.153
(0.223)
0.136
(0.204)
amp 14q13 3 159 (32%) 342 0.41
(0.493)
0.0266
(0.0534)
1e-05
(8.16e-05)
0.409
(0.493)
0.259
(0.344)
0.356
(0.44)
0.0675
(0.117)
0.00261
(0.00774)
0.00405
(0.0111)
0.111
(0.172)
0.148
(0.217)
0.94
(0.95)
amp xq28 124 (25%) 377 0.913
(0.932)
0.87
(0.896)
0.00326
(0.00925)
0.00414
(0.0114)
0.413
(0.495)
0.863
(0.89)
0.0304
(0.0593)
0.308
(0.394)
0.0298
(0.0586)
0.164
(0.237)
0.558
(0.626)
0.303
(0.39)
del 2p25 3 50 (10%) 451 0.106
(0.166)
0.458
(0.536)
0.0119
(0.0274)
0.972
(0.977)
0.617
(0.678)
0.0418
(0.0788)
0.323
(0.41)
0.606
(0.668)
0.0113
(0.0264)
0.365
(0.45)
0.188
(0.264)
0.0282
(0.056)
del 8p23 2 341 (68%) 160 0.475
(0.555)
0.708
(0.755)
4e-05
(0.000247)
0.0249
(0.0506)
0.395
(0.481)
0.589
(0.652)
0.0846
(0.14)
0.0919
(0.15)
0.0152
(0.0338)
0.0656
(0.114)
0.12
(0.183)
0.0154
(0.0339)
del 16p13 3 187 (37%) 314 0.179
(0.253)
0.445
(0.524)
0.00021
(0.00103)
0.00979
(0.0236)
0.148
(0.217)
0.292
(0.378)
0.303
(0.391)
0.919
(0.935)
0.0179
(0.0384)
0.634
(0.693)
0.00232
(0.00704)
0.144
(0.215)
del 17p11 2 272 (54%) 229 0.205
(0.283)
0.113
(0.174)
1e-05
(8.16e-05)
0.0534
(0.0967)
0.576
(0.641)
0.0958
(0.154)
0.185
(0.261)
0.0161
(0.0349)
0.151
(0.22)
0.0256
(0.0517)
0.0134
(0.0304)
0.139
(0.207)
amp 6p12 1 166 (33%) 335 0.727
(0.769)
0.495
(0.574)
3e-05
(0.000193)
0.369
(0.453)
0.35
(0.435)
0.507
(0.583)
0.00092
(0.00328)
0.0641
(0.113)
0.0103
(0.0246)
0.118
(0.181)
0.451
(0.53)
0.1
(0.159)
amp 8p11 23 238 (48%) 263 0.0218
(0.0455)
0.0916
(0.15)
0.0601
(0.107)
0.0301
(0.0588)
0.326
(0.412)
0.229
(0.312)
0.0586
(0.105)
0.057
(0.102)
0.731
(0.771)
0.173
(0.248)
0.0215
(0.0449)
0.306
(0.393)
amp 20q11 21 306 (61%) 195 0.767
(0.804)
0.506
(0.582)
1e-05
(8.16e-05)
0.0119
(0.0274)
0.494
(0.573)
0.977
(0.979)
0.289
(0.375)
0.945
(0.953)
0.157
(0.227)
0.37
(0.453)
0.0149
(0.0332)
0.138
(0.207)
del 7q11 22 48 (10%) 453 0.839
(0.869)
0.698
(0.747)
0.00961
(0.0233)
0.73
(0.771)
0.215
(0.295)
0.576
(0.641)
0.00076
(0.00286)
0.00107
(0.00375)
0.401
(0.487)
0.375
(0.46)
0.726
(0.769)
0.32
(0.408)
del 11q25 184 (37%) 317 0.942
(0.95)
0.704
(0.752)
0.00011
(0.000589)
0.0169
(0.0364)
0.124
(0.189)
0.227
(0.31)
0.0352
(0.0681)
0.147
(0.217)
0.0952
(0.154)
0.148
(0.217)
0.218
(0.299)
0.151
(0.22)
del 13q12 11 331 (66%) 170 0.199
(0.276)
0.571
(0.638)
2e-05
(0.000142)
0.0409
(0.0776)
0.662
(0.716)
0.332
(0.419)
0.896
(0.918)
0.971
(0.977)
0.427
(0.511)
0.382
(0.466)
0.115
(0.177)
0.0123
(0.0281)
del 13q14 2 344 (69%) 157 0.123
(0.187)
0.0998
(0.159)
2e-05
(0.000142)
0.0254
(0.0515)
0.623
(0.683)
0.192
(0.269)
0.481
(0.56)
0.576
(0.641)
0.136
(0.205)
0.145
(0.216)
0.0147
(0.033)
0.0803
(0.136)
del 15q21 1 169 (34%) 332 0.511
(0.586)
0.762
(0.8)
2e-05
(0.000142)
0.0757
(0.129)
0.646
(0.703)
0.172
(0.247)
0.189
(0.266)
0.245
(0.331)
0.00128
(0.00429)
0.0975
(0.156)
0.0283
(0.056)
0.102
(0.161)
amp 4q12 119 (24%) 382 0.684
(0.735)
0.88
(0.904)
0.00256
(0.00766)
0.0989
(0.158)
0.905
(0.925)
0.0719
(0.124)
0.0506
(0.0923)
0.58
(0.644)
0.0815
(0.137)
0.35
(0.435)
0.196
(0.273)
0.0462
(0.0854)
amp 5p12 354 (71%) 147 0.938
(0.95)
0.759
(0.798)
1e-05
(8.16e-05)
0.0001
(0.000544)
0.19
(0.266)
0.81
(0.841)
0.356
(0.44)
0.9
(0.921)
0.596
(0.658)
0.0784
(0.133)
0.18
(0.255)
0.721
(0.766)
amp 8q24 21 352 (70%) 149 0.916
(0.934)
0.782
(0.817)
1e-05
(8.16e-05)
0.0165
(0.0357)
0.109
(0.169)
0.678
(0.728)
0.735
(0.775)
0.549
(0.62)
0.289
(0.375)
0.257
(0.343)
0.167
(0.241)
1
(1.00)
amp 13q34 91 (18%) 410 0.948
(0.954)
0.833
(0.863)
0.00268
(0.0079)
0.483
(0.561)
0.178
(0.252)
0.176
(0.251)
0.667
(0.72)
0.107
(0.166)
0.259
(0.344)
0.0336
(0.0652)
0.976
(0.979)
0.592
(0.654)
del 15q11 2 167 (33%) 334 0.635
(0.693)
0.523
(0.596)
1e-05
(8.16e-05)
0.522
(0.595)
0.346
(0.433)
0.181
(0.255)
0.14
(0.209)
0.0616
(0.109)
0.0171
(0.0368)
0.536
(0.607)
0.0966
(0.155)
0.261
(0.346)
del 18q23 234 (47%) 267 0.677
(0.728)
0.171
(0.246)
0.00154
(0.005)
0.132
(0.2)
0.618
(0.678)
0.318
(0.405)
0.935
(0.948)
0.484
(0.561)
0.284
(0.37)
0.538
(0.609)
0.00708
(0.0179)
0.52
(0.593)
del 22q11 21 95 (19%) 406 0.0868
(0.144)
0.0973
(0.156)
0.00776
(0.0193)
0.242
(0.328)
0.291
(0.376)
0.434
(0.515)
0.177
(0.252)
0.0002
(0.000981)
0.342
(0.43)
0.402
(0.488)
0.355
(0.44)
0.0836
(0.139)
del 3q11 1 79 (16%) 422 0.853
(0.88)
0.782
(0.817)
0.517
(0.591)
0.312
(0.399)
0.72
(0.766)
0.629
(0.688)
0.832
(0.863)
0.172
(0.247)
0.399
(0.485)
0.517
(0.591)
0.92
(0.935)
0.93
(0.945)
del 12q24 31 86 (17%) 415 0.667
(0.72)
0.598
(0.66)
0.566
(0.632)
0.692
(0.742)
0.866
(0.892)
0.151
(0.221)
0.723
(0.767)
0.695
(0.744)
0.0806
(0.136)
0.333
(0.419)
0.224
(0.307)
0.0873
(0.144)
'amp_1q21.2' versus 'MRNA_CNMF'

P value = 0.0415 (Fisher's exact test), Q value = 0.078

Table S1.  Gene #1: 'amp_1q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
AMP PEAK 1(1Q21.2) MUTATED 18 36 17 16
AMP PEAK 1(1Q21.2) WILD-TYPE 23 14 17 13

Figure S1.  Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S2.  Gene #1: 'amp_1q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
AMP PEAK 1(1Q21.2) MUTATED 21 43 11 29 120 34
AMP PEAK 1(1Q21.2) WILD-TYPE 22 72 18 58 49 24

Figure S2.  Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S3.  Gene #1: 'amp_1q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
AMP PEAK 1(1Q21.2) MUTATED 40 55 43 46
AMP PEAK 1(1Q21.2) WILD-TYPE 50 40 14 79

Figure S3.  Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q21.2' versus 'RPPA_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 0.046

Table S4.  Gene #1: 'amp_1q21.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
AMP PEAK 1(1Q21.2) MUTATED 51 55 56 9
AMP PEAK 1(1Q21.2) WILD-TYPE 54 54 30 17

Figure S4.  Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_1q21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S5.  Gene #1: 'amp_1q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
AMP PEAK 1(1Q21.2) MUTATED 41 104 83 29
AMP PEAK 1(1Q21.2) WILD-TYPE 65 46 76 54

Figure S5.  Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S6.  Gene #1: 'amp_1q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 1(1Q21.2) MUTATED 63 123 71
AMP PEAK 1(1Q21.2) WILD-TYPE 115 66 60

Figure S6.  Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S7.  Gene #1: 'amp_1q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
AMP PEAK 1(1Q21.2) MUTATED 109 38 43 54
AMP PEAK 1(1Q21.2) WILD-TYPE 75 49 81 26

Figure S7.  Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S8.  Gene #1: 'amp_1q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 1(1Q21.2) MUTATED 64 67 89 24
AMP PEAK 1(1Q21.2) WILD-TYPE 25 51 110 45

Figure S8.  Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0021

Table S9.  Gene #1: 'amp_1q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
AMP PEAK 1(1Q21.2) MUTATED 23 65 22 56
AMP PEAK 1(1Q21.2) WILD-TYPE 38 50 44 36

Figure S9.  Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0111 (Fisher's exact test), Q value = 0.026

Table S10.  Gene #1: 'amp_1q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
AMP PEAK 1(1Q21.2) MUTATED 14 107 45
AMP PEAK 1(1Q21.2) WILD-TYPE 23 81 64

Figure S10.  Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_2p16.1' versus 'MRNA_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.0031

Table S11.  Gene #2: 'amp_2p16.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
AMP PEAK 2(2P16.1) MUTATED 17 39 16 13
AMP PEAK 2(2P16.1) WILD-TYPE 24 11 18 16

Figure S11.  Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_2p16.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0017

Table S12.  Gene #2: 'amp_2p16.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
AMP PEAK 2(2P16.1) MUTATED 24 42 19
AMP PEAK 2(2P16.1) WILD-TYPE 23 14 32

Figure S12.  Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_2p16.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S13.  Gene #2: 'amp_2p16.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
AMP PEAK 2(2P16.1) MUTATED 18 38 18 28 126 47
AMP PEAK 2(2P16.1) WILD-TYPE 25 77 11 59 43 11

Figure S13.  Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2p16.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S14.  Gene #2: 'amp_2p16.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
AMP PEAK 2(2P16.1) MUTATED 40 71 41 52
AMP PEAK 2(2P16.1) WILD-TYPE 50 24 16 73

Figure S14.  Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2p16.1' versus 'RPPA_CNMF'

P value = 0.00797 (Fisher's exact test), Q value = 0.02

Table S15.  Gene #2: 'amp_2p16.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
AMP PEAK 2(2P16.1) MUTATED 52 56 61 12
AMP PEAK 2(2P16.1) WILD-TYPE 53 53 25 14

Figure S15.  Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_2p16.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S16.  Gene #2: 'amp_2p16.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
AMP PEAK 2(2P16.1) MUTATED 42 112 92 27
AMP PEAK 2(2P16.1) WILD-TYPE 64 38 67 56

Figure S16.  Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2p16.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S17.  Gene #2: 'amp_2p16.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 2(2P16.1) MUTATED 82 131 60
AMP PEAK 2(2P16.1) WILD-TYPE 96 58 71

Figure S17.  Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_2p16.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S18.  Gene #2: 'amp_2p16.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
AMP PEAK 2(2P16.1) MUTATED 107 61 47 48
AMP PEAK 2(2P16.1) WILD-TYPE 77 26 77 32

Figure S18.  Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_2p16.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00071 (Fisher's exact test), Q value = 0.0027

Table S19.  Gene #2: 'amp_2p16.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 2(2P16.1) MUTATED 54 64 122 23
AMP PEAK 2(2P16.1) WILD-TYPE 35 54 77 46

Figure S19.  Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_2p16.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0016

Table S20.  Gene #2: 'amp_2p16.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
AMP PEAK 2(2P16.1) MUTATED 33 71 22 60
AMP PEAK 2(2P16.1) WILD-TYPE 28 44 44 32

Figure S20.  Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_2p16.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.0024

Table S21.  Gene #2: 'amp_2p16.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
AMP PEAK 2(2P16.1) MUTATED 20 121 45
AMP PEAK 2(2P16.1) WILD-TYPE 17 67 64

Figure S21.  Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_2q31.2' versus 'MRNA_CNMF'

P value = 0.0389 (Fisher's exact test), Q value = 0.074

Table S22.  Gene #3: 'amp_2q31.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
AMP PEAK 3(2Q31.2) MUTATED 11 26 9 9
AMP PEAK 3(2Q31.2) WILD-TYPE 30 24 25 20

Figure S22.  Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_2q31.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0228 (Fisher's exact test), Q value = 0.047

Table S23.  Gene #3: 'amp_2q31.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
AMP PEAK 3(2Q31.2) MUTATED 13 28 14
AMP PEAK 3(2Q31.2) WILD-TYPE 34 28 37

Figure S23.  Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_2q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S24.  Gene #3: 'amp_2q31.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
AMP PEAK 3(2Q31.2) MUTATED 9 20 8 22 86 27
AMP PEAK 3(2Q31.2) WILD-TYPE 34 95 21 65 83 31

Figure S24.  Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2q31.2' versus 'METHLYATION_CNMF'

P value = 0.00108 (Fisher's exact test), Q value = 0.0037

Table S25.  Gene #3: 'amp_2q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
AMP PEAK 3(2Q31.2) MUTATED 26 47 25 33
AMP PEAK 3(2Q31.2) WILD-TYPE 64 48 32 92

Figure S25.  Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2q31.2' versus 'RPPA_CNMF'

P value = 0.00928 (Fisher's exact test), Q value = 0.023

Table S26.  Gene #3: 'amp_2q31.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
AMP PEAK 3(2Q31.2) MUTATED 28 36 43 9
AMP PEAK 3(2Q31.2) WILD-TYPE 77 73 43 17

Figure S26.  Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_2q31.2' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S27.  Gene #3: 'amp_2q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
AMP PEAK 3(2Q31.2) MUTATED 26 77 50 18
AMP PEAK 3(2Q31.2) WILD-TYPE 80 73 109 65

Figure S27.  Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S28.  Gene #3: 'amp_2q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 3(2Q31.2) MUTATED 42 91 38
AMP PEAK 3(2Q31.2) WILD-TYPE 136 98 93

Figure S28.  Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_2q31.2' versus 'MIRSEQ_CNMF'

P value = 0.00078 (Fisher's exact test), Q value = 0.0029

Table S29.  Gene #3: 'amp_2q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
AMP PEAK 3(2Q31.2) MUTATED 77 32 25 30
AMP PEAK 3(2Q31.2) WILD-TYPE 107 55 99 50

Figure S29.  Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_2q31.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00397 (Fisher's exact test), Q value = 0.011

Table S30.  Gene #3: 'amp_2q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
AMP PEAK 3(2Q31.2) MUTATED 15 47 13 38
AMP PEAK 3(2Q31.2) WILD-TYPE 46 68 53 54

Figure S30.  Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.33' versus 'MRNA_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.0028

Table S31.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
AMP PEAK 4(3Q26.33) MUTATED 39 50 27 24
AMP PEAK 4(3Q26.33) WILD-TYPE 2 0 7 5

Figure S31.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0019

Table S32.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
AMP PEAK 4(3Q26.33) MUTATED 43 56 41
AMP PEAK 4(3Q26.33) WILD-TYPE 4 0 10

Figure S32.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_3q26.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S33.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
AMP PEAK 4(3Q26.33) MUTATED 42 77 28 81 169 55
AMP PEAK 4(3Q26.33) WILD-TYPE 1 38 1 6 0 3

Figure S33.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S34.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
AMP PEAK 4(3Q26.33) MUTATED 85 95 55 95
AMP PEAK 4(3Q26.33) WILD-TYPE 5 0 2 30

Figure S34.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.33' versus 'RPPA_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.0027

Table S35.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
AMP PEAK 4(3Q26.33) MUTATED 84 99 84 23
AMP PEAK 4(3Q26.33) WILD-TYPE 21 10 2 3

Figure S35.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_3q26.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.00847 (Fisher's exact test), Q value = 0.021

Table S36.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 79 67 62 60 30 28
AMP PEAK 4(3Q26.33) MUTATED 68 59 58 59 25 21
AMP PEAK 4(3Q26.33) WILD-TYPE 11 8 4 1 5 7

Figure S36.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_3q26.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S37.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
AMP PEAK 4(3Q26.33) MUTATED 101 150 137 61
AMP PEAK 4(3Q26.33) WILD-TYPE 5 0 22 22

Figure S37.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S38.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 4(3Q26.33) MUTATED 163 188 98
AMP PEAK 4(3Q26.33) WILD-TYPE 15 1 33

Figure S38.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S39.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
AMP PEAK 4(3Q26.33) MUTATED 172 85 95 77
AMP PEAK 4(3Q26.33) WILD-TYPE 12 2 29 3

Figure S39.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S40.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 4(3Q26.33) MUTATED 89 108 189 43
AMP PEAK 4(3Q26.33) WILD-TYPE 0 10 10 26

Figure S40.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S41.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
AMP PEAK 4(3Q26.33) MUTATED 56 109 47 88
AMP PEAK 4(3Q26.33) WILD-TYPE 5 6 19 4

Figure S41.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0011

Table S42.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
AMP PEAK 4(3Q26.33) MUTATED 34 179 87
AMP PEAK 4(3Q26.33) WILD-TYPE 3 9 22

Figure S42.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q12' versus 'CN_CNMF'

P value = 0.00256 (Fisher's exact test), Q value = 0.0077

Table S43.  Gene #5: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
AMP PEAK 5(4Q12) MUTATED 12 15 10 16 44 22
AMP PEAK 5(4Q12) WILD-TYPE 31 100 19 71 125 36

Figure S43.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_4q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0462 (Fisher's exact test), Q value = 0.085

Table S44.  Gene #5: 'amp_4q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
AMP PEAK 5(4Q12) MUTATED 13 41 17
AMP PEAK 5(4Q12) WILD-TYPE 24 147 92

Figure S44.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S45.  Gene #6: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
AMP PEAK 6(5P15.33) MUTATED 37 76 26 67 123 58
AMP PEAK 6(5P15.33) WILD-TYPE 6 39 3 20 46 0

Figure S45.  Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00054

Table S46.  Gene #6: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
AMP PEAK 6(5P15.33) MUTATED 84 71 40 88
AMP PEAK 6(5P15.33) WILD-TYPE 6 24 17 37

Figure S46.  Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00544 (Fisher's exact test), Q value = 0.014

Table S47.  Gene #6: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 6(5P15.33) MUTATED 66 88 168 45
AMP PEAK 6(5P15.33) WILD-TYPE 23 30 31 24

Figure S47.  Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00348 (Fisher's exact test), Q value = 0.0098

Table S48.  Gene #6: 'amp_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
AMP PEAK 6(5P15.33) MUTATED 54 93 41 70
AMP PEAK 6(5P15.33) WILD-TYPE 7 22 25 22

Figure S48.  Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_5p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S49.  Gene #7: 'amp_5p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
AMP PEAK 7(5P12) MUTATED 32 63 26 56 120 57
AMP PEAK 7(5P12) WILD-TYPE 11 52 3 31 49 1

Figure S49.  Get High-res Image Gene #7: 'amp_5p12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p12' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00054

Table S50.  Gene #7: 'amp_5p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
AMP PEAK 7(5P12) MUTATED 78 67 37 75
AMP PEAK 7(5P12) WILD-TYPE 12 28 20 50

Figure S50.  Get High-res Image Gene #7: 'amp_5p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6p12.1' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S51.  Gene #8: 'amp_6p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
AMP PEAK 8(6P12.1) MUTATED 15 23 8 20 71 29
AMP PEAK 8(6P12.1) WILD-TYPE 28 92 21 67 98 29

Figure S51.  Get High-res Image Gene #8: 'amp_6p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p12.1' versus 'MRNASEQ_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.0033

Table S52.  Gene #8: 'amp_6p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
AMP PEAK 8(6P12.1) MUTATED 19 60 59 26
AMP PEAK 8(6P12.1) WILD-TYPE 87 90 100 57

Figure S52.  Get High-res Image Gene #8: 'amp_6p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6p12.1' versus 'MIRSEQ_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.025

Table S53.  Gene #8: 'amp_6p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
AMP PEAK 8(6P12.1) MUTATED 72 28 27 30
AMP PEAK 8(6P12.1) WILD-TYPE 112 59 97 50

Figure S53.  Get High-res Image Gene #8: 'amp_6p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_6q12' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 8e-04

Table S54.  Gene #9: 'amp_6q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
AMP PEAK 9(6Q12) MUTATED 10 19 7 24 66 26
AMP PEAK 9(6Q12) WILD-TYPE 33 96 22 63 103 32

Figure S54.  Get High-res Image Gene #9: 'amp_6q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6q12' versus 'MRNASEQ_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0034

Table S55.  Gene #9: 'amp_6q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
AMP PEAK 9(6Q12) MUTATED 17 56 55 22
AMP PEAK 9(6Q12) WILD-TYPE 89 94 104 61

Figure S55.  Get High-res Image Gene #9: 'amp_6q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0055 (Fisher's exact test), Q value = 0.014

Table S56.  Gene #9: 'amp_6q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 9(6Q12) MUTATED 38 66 46
AMP PEAK 9(6Q12) WILD-TYPE 140 123 85

Figure S56.  Get High-res Image Gene #9: 'amp_6q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6q12' versus 'MIRSEQ_CNMF'

P value = 0.00315 (Fisher's exact test), Q value = 0.009

Table S57.  Gene #9: 'amp_6q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
AMP PEAK 9(6Q12) MUTATED 70 22 25 29
AMP PEAK 9(6Q12) WILD-TYPE 114 65 99 51

Figure S57.  Get High-res Image Gene #9: 'amp_6q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_6q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0229 (Fisher's exact test), Q value = 0.047

Table S58.  Gene #9: 'amp_6q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 9(6Q12) MUTATED 36 30 66 14
AMP PEAK 9(6Q12) WILD-TYPE 53 88 133 55

Figure S58.  Get High-res Image Gene #9: 'amp_6q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0299 (Fisher's exact test), Q value = 0.059

Table S59.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
AMP PEAK 10(7P11.2) MUTATED 23 37 21
AMP PEAK 10(7P11.2) WILD-TYPE 24 19 30

Figure S59.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S60.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
AMP PEAK 10(7P11.2) MUTATED 33 44 16 22 107 34
AMP PEAK 10(7P11.2) WILD-TYPE 10 71 13 65 62 24

Figure S60.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.046

Table S61.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
AMP PEAK 10(7P11.2) MUTATED 43 61 26 56
AMP PEAK 10(7P11.2) WILD-TYPE 47 34 31 69

Figure S61.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0022

Table S62.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
AMP PEAK 10(7P11.2) MUTATED 51 96 76 31
AMP PEAK 10(7P11.2) WILD-TYPE 55 54 83 52

Figure S62.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00025

Table S63.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 10(7P11.2) MUTATED 78 122 54
AMP PEAK 10(7P11.2) WILD-TYPE 100 67 77

Figure S63.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.035

Table S64.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
AMP PEAK 10(7P11.2) MUTATED 99 53 50 45
AMP PEAK 10(7P11.2) WILD-TYPE 85 34 74 35

Figure S64.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0467 (Fisher's exact test), Q value = 0.086

Table S65.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 10(7P11.2) MUTATED 58 56 100 33
AMP PEAK 10(7P11.2) WILD-TYPE 31 62 99 36

Figure S65.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.05

Table S66.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
AMP PEAK 10(7P11.2) MUTATED 29 60 25 57
AMP PEAK 10(7P11.2) WILD-TYPE 32 55 41 35

Figure S66.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7q21.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0151 (Fisher's exact test), Q value = 0.034

Table S67.  Gene #11: 'amp_7q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
AMP PEAK 11(7Q21.2) MUTATED 30 39 22
AMP PEAK 11(7Q21.2) WILD-TYPE 17 17 29

Figure S67.  Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S68.  Gene #11: 'amp_7q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
AMP PEAK 11(7Q21.2) MUTATED 35 34 17 17 119 42
AMP PEAK 11(7Q21.2) WILD-TYPE 8 81 12 70 50 16

Figure S68.  Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S69.  Gene #11: 'amp_7q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
AMP PEAK 11(7Q21.2) MUTATED 43 67 31 45
AMP PEAK 11(7Q21.2) WILD-TYPE 47 28 26 80

Figure S69.  Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7q21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S70.  Gene #11: 'amp_7q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
AMP PEAK 11(7Q21.2) MUTATED 49 107 74 32
AMP PEAK 11(7Q21.2) WILD-TYPE 57 43 85 51

Figure S70.  Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S71.  Gene #11: 'amp_7q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 11(7Q21.2) MUTATED 74 130 58
AMP PEAK 11(7Q21.2) WILD-TYPE 104 59 73

Figure S71.  Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S72.  Gene #11: 'amp_7q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
AMP PEAK 11(7Q21.2) MUTATED 111 48 41 54
AMP PEAK 11(7Q21.2) WILD-TYPE 73 39 83 26

Figure S72.  Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00098 (Fisher's exact test), Q value = 0.0035

Table S73.  Gene #11: 'amp_7q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 11(7Q21.2) MUTATED 63 63 100 28
AMP PEAK 11(7Q21.2) WILD-TYPE 26 55 99 41

Figure S73.  Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00269 (Fisher's exact test), Q value = 0.0079

Table S74.  Gene #11: 'amp_7q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
AMP PEAK 11(7Q21.2) MUTATED 26 61 23 58
AMP PEAK 11(7Q21.2) WILD-TYPE 35 54 43 34

Figure S74.  Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0419 (Fisher's exact test), Q value = 0.079

Table S75.  Gene #11: 'amp_7q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
AMP PEAK 11(7Q21.2) MUTATED 15 106 47
AMP PEAK 11(7Q21.2) WILD-TYPE 22 82 62

Figure S75.  Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p11.23' versus 'MRNA_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.045

Table S76.  Gene #12: 'amp_8p11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
AMP PEAK 12(8P11.23) MUTATED 29 23 13 13
AMP PEAK 12(8P11.23) WILD-TYPE 12 27 21 16

Figure S76.  Get High-res Image Gene #12: 'amp_8p11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8p11.23' versus 'METHLYATION_CNMF'

P value = 0.0301 (Fisher's exact test), Q value = 0.059

Table S77.  Gene #12: 'amp_8p11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
AMP PEAK 12(8P11.23) MUTATED 46 53 21 49
AMP PEAK 12(8P11.23) WILD-TYPE 44 42 36 76

Figure S77.  Get High-res Image Gene #12: 'amp_8p11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8p11.23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.045

Table S78.  Gene #12: 'amp_8p11.23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
AMP PEAK 12(8P11.23) MUTATED 28 50 21 52
AMP PEAK 12(8P11.23) WILD-TYPE 33 65 45 40

Figure S78.  Get High-res Image Gene #12: 'amp_8p11.23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S79.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
AMP PEAK 13(8Q24.21) MUTATED 39 69 24 52 115 53
AMP PEAK 13(8Q24.21) WILD-TYPE 4 46 5 35 54 5

Figure S79.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.036

Table S80.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
AMP PEAK 13(8Q24.21) MUTATED 71 74 36 79
AMP PEAK 13(8Q24.21) WILD-TYPE 19 21 21 46

Figure S80.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_9p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S81.  Gene #14: 'amp_9p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
AMP PEAK 14(9P13.3) MUTATED 16 20 8 10 66 16
AMP PEAK 14(9P13.3) WILD-TYPE 27 95 21 77 103 42

Figure S81.  Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_9p13.3' versus 'METHLYATION_CNMF'

P value = 0.00794 (Fisher's exact test), Q value = 0.02

Table S82.  Gene #14: 'amp_9p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
AMP PEAK 14(9P13.3) MUTATED 25 38 18 24
AMP PEAK 14(9P13.3) WILD-TYPE 65 57 39 101

Figure S82.  Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_9p13.3' versus 'RPPA_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.027

Table S83.  Gene #14: 'amp_9p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
AMP PEAK 14(9P13.3) MUTATED 23 23 35 6
AMP PEAK 14(9P13.3) WILD-TYPE 82 86 51 20

Figure S83.  Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_9p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00064

Table S84.  Gene #14: 'amp_9p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 79 67 62 60 30 28
AMP PEAK 14(9P13.3) MUTATED 29 16 17 22 0 3
AMP PEAK 14(9P13.3) WILD-TYPE 50 51 45 38 30 25

Figure S84.  Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_9p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00179 (Fisher's exact test), Q value = 0.0056

Table S85.  Gene #14: 'amp_9p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
AMP PEAK 14(9P13.3) MUTATED 21 57 43 15
AMP PEAK 14(9P13.3) WILD-TYPE 85 93 116 68

Figure S85.  Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_9p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00119 (Fisher's exact test), Q value = 0.004

Table S86.  Gene #14: 'amp_9p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 14(9P13.3) MUTATED 34 68 34
AMP PEAK 14(9P13.3) WILD-TYPE 144 121 97

Figure S86.  Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_9p13.3' versus 'MIRSEQ_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0019

Table S87.  Gene #14: 'amp_9p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
AMP PEAK 14(9P13.3) MUTATED 59 23 18 31
AMP PEAK 14(9P13.3) WILD-TYPE 125 64 106 49

Figure S87.  Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_9p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00374 (Fisher's exact test), Q value = 0.01

Table S88.  Gene #14: 'amp_9p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 14(9P13.3) MUTATED 32 41 48 10
AMP PEAK 14(9P13.3) WILD-TYPE 57 77 151 59

Figure S88.  Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MRNA_CNMF'

P value = 0.0416 (Fisher's exact test), Q value = 0.078

Table S89.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
AMP PEAK 15(11Q13.3) MUTATED 17 10 12 14
AMP PEAK 15(11Q13.3) WILD-TYPE 24 40 22 15

Figure S89.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11q13.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0341 (Fisher's exact test), Q value = 0.066

Table S90.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
AMP PEAK 15(11Q13.3) MUTATED 19 12 22
AMP PEAK 15(11Q13.3) WILD-TYPE 28 44 29

Figure S90.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

P value = 0.00165 (Fisher's exact test), Q value = 0.0053

Table S91.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
AMP PEAK 15(11Q13.3) MUTATED 26 30 14 35 56 24
AMP PEAK 15(11Q13.3) WILD-TYPE 17 85 15 52 113 34

Figure S91.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00085

Table S92.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
AMP PEAK 15(11Q13.3) MUTATED 50 37 20 32
AMP PEAK 15(11Q13.3) WILD-TYPE 40 58 37 93

Figure S92.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 0.0211 (Fisher's exact test), Q value = 0.044

Table S93.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
AMP PEAK 15(11Q13.3) MUTATED 44 42 70 29
AMP PEAK 15(11Q13.3) WILD-TYPE 62 108 89 54

Figure S93.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.034

Table S94.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
AMP PEAK 15(11Q13.3) MUTATED 78 39 41 20
AMP PEAK 15(11Q13.3) WILD-TYPE 106 48 83 60

Figure S94.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00465 (Fisher's exact test), Q value = 0.012

Table S95.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 15(11Q13.3) MUTATED 24 47 89 18
AMP PEAK 15(11Q13.3) WILD-TYPE 65 71 110 51

Figure S95.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00164 (Fisher's exact test), Q value = 0.0053

Table S96.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
AMP PEAK 15(11Q13.3) MUTATED 25 57 14 32
AMP PEAK 15(11Q13.3) WILD-TYPE 36 58 52 60

Figure S96.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0195 (Fisher's exact test), Q value = 0.041

Table S97.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
AMP PEAK 15(11Q13.3) MUTATED 20 76 32
AMP PEAK 15(11Q13.3) WILD-TYPE 17 112 77

Figure S97.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p13.33' versus 'MRNA_CNMF'

P value = 0.00197 (Fisher's exact test), Q value = 0.0061

Table S98.  Gene #16: 'amp_12p13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
AMP PEAK 16(12P13.33) MUTATED 11 33 14 13
AMP PEAK 16(12P13.33) WILD-TYPE 30 17 20 16

Figure S98.  Get High-res Image Gene #16: 'amp_12p13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_12p13.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.045

Table S99.  Gene #16: 'amp_12p13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
AMP PEAK 16(12P13.33) MUTATED 17 34 20
AMP PEAK 16(12P13.33) WILD-TYPE 30 22 31

Figure S99.  Get High-res Image Gene #16: 'amp_12p13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_12p13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S100.  Gene #16: 'amp_12p13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
AMP PEAK 16(12P13.33) MUTATED 24 40 12 32 108 39
AMP PEAK 16(12P13.33) WILD-TYPE 19 75 17 55 61 19

Figure S100.  Get High-res Image Gene #16: 'amp_12p13.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p13.33' versus 'METHLYATION_CNMF'

P value = 0.00371 (Fisher's exact test), Q value = 0.01

Table S101.  Gene #16: 'amp_12p13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
AMP PEAK 16(12P13.33) MUTATED 51 58 38 52
AMP PEAK 16(12P13.33) WILD-TYPE 39 37 19 73

Figure S101.  Get High-res Image Gene #16: 'amp_12p13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12p13.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S102.  Gene #16: 'amp_12p13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
AMP PEAK 16(12P13.33) MUTATED 35 98 92 28
AMP PEAK 16(12P13.33) WILD-TYPE 71 52 67 55

Figure S102.  Get High-res Image Gene #16: 'amp_12p13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12p13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0019 (Fisher's exact test), Q value = 0.0059

Table S103.  Gene #16: 'amp_12p13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 16(12P13.33) MUTATED 72 111 70
AMP PEAK 16(12P13.33) WILD-TYPE 106 78 61

Figure S103.  Get High-res Image Gene #16: 'amp_12p13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12p13.33' versus 'MIRSEQ_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.032

Table S104.  Gene #16: 'amp_12p13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
AMP PEAK 16(12P13.33) MUTATED 104 48 49 46
AMP PEAK 16(12P13.33) WILD-TYPE 80 39 75 34

Figure S104.  Get High-res Image Gene #16: 'amp_12p13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12p13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00267 (Fisher's exact test), Q value = 0.0079

Table S105.  Gene #16: 'amp_12p13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 16(12P13.33) MUTATED 57 58 108 24
AMP PEAK 16(12P13.33) WILD-TYPE 32 60 91 45

Figure S105.  Get High-res Image Gene #16: 'amp_12p13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p13.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00296 (Fisher's exact test), Q value = 0.0085

Table S106.  Gene #16: 'amp_12p13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
AMP PEAK 16(12P13.33) MUTATED 34 69 22 54
AMP PEAK 16(12P13.33) WILD-TYPE 27 46 44 38

Figure S106.  Get High-res Image Gene #16: 'amp_12p13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12q15' versus 'CN_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0018

Table S107.  Gene #17: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
AMP PEAK 17(12Q15) MUTATED 16 30 8 20 80 24
AMP PEAK 17(12Q15) WILD-TYPE 27 85 21 67 89 34

Figure S107.  Get High-res Image Gene #17: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 0.00538 (Fisher's exact test), Q value = 0.014

Table S108.  Gene #17: 'amp_12q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
AMP PEAK 17(12Q15) MUTATED 29 45 24 32
AMP PEAK 17(12Q15) WILD-TYPE 61 50 33 93

Figure S108.  Get High-res Image Gene #17: 'amp_12q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q15' versus 'MRNASEQ_CNMF'

P value = 0.00602 (Fisher's exact test), Q value = 0.016

Table S109.  Gene #17: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
AMP PEAK 17(12Q15) MUTATED 27 69 54 26
AMP PEAK 17(12Q15) WILD-TYPE 79 81 105 57

Figure S109.  Get High-res Image Gene #17: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0117 (Fisher's exact test), Q value = 0.027

Table S110.  Gene #17: 'amp_12q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 17(12Q15) MUTATED 48 73 55
AMP PEAK 17(12Q15) WILD-TYPE 130 116 76

Figure S110.  Get High-res Image Gene #17: 'amp_12q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q34' versus 'CN_CNMF'

P value = 0.00268 (Fisher's exact test), Q value = 0.0079

Table S111.  Gene #18: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
AMP PEAK 18(13Q34) MUTATED 10 14 11 8 33 15
AMP PEAK 18(13Q34) WILD-TYPE 33 101 18 79 136 43

Figure S111.  Get High-res Image Gene #18: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0336 (Fisher's exact test), Q value = 0.065

Table S112.  Gene #18: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 18(13Q34) MUTATED 8 27 41 10
AMP PEAK 18(13Q34) WILD-TYPE 81 91 158 59

Figure S112.  Get High-res Image Gene #18: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_14q13.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0266 (Fisher's exact test), Q value = 0.053

Table S113.  Gene #19: 'amp_14q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
AMP PEAK 19(14Q13.3) MUTATED 23 15 13
AMP PEAK 19(14Q13.3) WILD-TYPE 24 41 38

Figure S113.  Get High-res Image Gene #19: 'amp_14q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_14q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S114.  Gene #19: 'amp_14q13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
AMP PEAK 19(14Q13.3) MUTATED 35 33 12 14 50 15
AMP PEAK 19(14Q13.3) WILD-TYPE 8 82 17 73 119 43

Figure S114.  Get High-res Image Gene #19: 'amp_14q13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_14q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00261 (Fisher's exact test), Q value = 0.0077

Table S115.  Gene #19: 'amp_14q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 19(14Q13.3) MUTATED 73 56 30
AMP PEAK 19(14Q13.3) WILD-TYPE 105 133 101

Figure S115.  Get High-res Image Gene #19: 'amp_14q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_14q13.3' versus 'MIRSEQ_CNMF'

P value = 0.00405 (Fisher's exact test), Q value = 0.011

Table S116.  Gene #19: 'amp_14q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
AMP PEAK 19(14Q13.3) MUTATED 75 26 38 15
AMP PEAK 19(14Q13.3) WILD-TYPE 109 61 86 65

Figure S116.  Get High-res Image Gene #19: 'amp_14q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_14q32.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.0156 (Fisher's exact test), Q value = 0.034

Table S117.  Gene #20: 'amp_14q32.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
AMP PEAK 20(14Q32.33) MUTATED 22 17 10
AMP PEAK 20(14Q32.33) WILD-TYPE 25 39 41

Figure S117.  Get High-res Image Gene #20: 'amp_14q32.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_14q32.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S118.  Gene #20: 'amp_14q32.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
AMP PEAK 20(14Q32.33) MUTATED 33 28 13 11 59 14
AMP PEAK 20(14Q32.33) WILD-TYPE 10 87 16 76 110 44

Figure S118.  Get High-res Image Gene #20: 'amp_14q32.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_14q32.33' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 5e-04

Table S119.  Gene #20: 'amp_14q32.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
AMP PEAK 20(14Q32.33) MUTATED 32 47 13 27
AMP PEAK 20(14Q32.33) WILD-TYPE 58 48 44 98

Figure S119.  Get High-res Image Gene #20: 'amp_14q32.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_14q32.33' versus 'RPPA_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.049

Table S120.  Gene #20: 'amp_14q32.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
AMP PEAK 20(14Q32.33) MUTATED 25 44 25 12
AMP PEAK 20(14Q32.33) WILD-TYPE 80 65 61 14

Figure S120.  Get High-res Image Gene #20: 'amp_14q32.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_14q32.33' versus 'MRNASEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0016

Table S121.  Gene #20: 'amp_14q32.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
AMP PEAK 20(14Q32.33) MUTATED 45 58 38 17
AMP PEAK 20(14Q32.33) WILD-TYPE 61 92 121 66

Figure S121.  Get High-res Image Gene #20: 'amp_14q32.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_14q32.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0018

Table S122.  Gene #20: 'amp_14q32.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 20(14Q32.33) MUTATED 66 68 24
AMP PEAK 20(14Q32.33) WILD-TYPE 112 121 107

Figure S122.  Get High-res Image Gene #20: 'amp_14q32.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_14q32.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00328 (Fisher's exact test), Q value = 0.0093

Table S123.  Gene #20: 'amp_14q32.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
AMP PEAK 20(14Q32.33) MUTATED 22 35 10 38
AMP PEAK 20(14Q32.33) WILD-TYPE 39 80 56 54

Figure S123.  Get High-res Image Gene #20: 'amp_14q32.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_15q26.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S124.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
AMP PEAK 21(15Q26.3) MUTATED 8 23 15 32 83 18
AMP PEAK 21(15Q26.3) WILD-TYPE 35 92 14 55 86 40

Figure S124.  Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_15q26.3' versus 'METHLYATION_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.0029

Table S125.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
AMP PEAK 21(15Q26.3) MUTATED 33 43 25 27
AMP PEAK 21(15Q26.3) WILD-TYPE 57 52 32 98

Figure S125.  Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S126.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
AMP PEAK 21(15Q26.3) MUTATED 24 76 52 24
AMP PEAK 21(15Q26.3) WILD-TYPE 82 74 107 59

Figure S126.  Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00258 (Fisher's exact test), Q value = 0.0077

Table S127.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 21(15Q26.3) MUTATED 57 84 35
AMP PEAK 21(15Q26.3) WILD-TYPE 121 105 96

Figure S127.  Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'MIRSEQ_CNMF'

P value = 0.00179 (Fisher's exact test), Q value = 0.0056

Table S128.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
AMP PEAK 21(15Q26.3) MUTATED 65 37 31 40
AMP PEAK 21(15Q26.3) WILD-TYPE 119 50 93 40

Figure S128.  Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_15q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00637 (Fisher's exact test), Q value = 0.016

Table S129.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 21(15Q26.3) MUTATED 44 39 74 16
AMP PEAK 21(15Q26.3) WILD-TYPE 45 79 125 53

Figure S129.  Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.0031

Table S130.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
AMP PEAK 21(15Q26.3) MUTATED 15 47 12 41
AMP PEAK 21(15Q26.3) WILD-TYPE 46 68 54 51

Figure S130.  Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_15q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.024

Table S131.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
AMP PEAK 21(15Q26.3) MUTATED 12 77 26
AMP PEAK 21(15Q26.3) WILD-TYPE 25 111 83

Figure S131.  Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q25.1' versus 'MRNA_CNMF'

P value = 0.00399 (Fisher's exact test), Q value = 0.011

Table S132.  Gene #22: 'amp_17q25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
AMP PEAK 22(17Q25.1) MUTATED 18 31 10 20
AMP PEAK 22(17Q25.1) WILD-TYPE 23 19 24 9

Figure S132.  Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q25.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S133.  Gene #22: 'amp_17q25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
AMP PEAK 22(17Q25.1) MUTATED 22 27 8 33 113 33
AMP PEAK 22(17Q25.1) WILD-TYPE 21 88 21 54 56 25

Figure S133.  Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q25.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S134.  Gene #22: 'amp_17q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
AMP PEAK 22(17Q25.1) MUTATED 41 61 28 37
AMP PEAK 22(17Q25.1) WILD-TYPE 49 34 29 88

Figure S134.  Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q25.1' versus 'RPPA_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0022

Table S135.  Gene #22: 'amp_17q25.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
AMP PEAK 22(17Q25.1) MUTATED 41 47 56 8
AMP PEAK 22(17Q25.1) WILD-TYPE 64 62 30 18

Figure S135.  Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_17q25.1' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S136.  Gene #22: 'amp_17q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
AMP PEAK 22(17Q25.1) MUTATED 40 95 71 28
AMP PEAK 22(17Q25.1) WILD-TYPE 66 55 88 55

Figure S136.  Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S137.  Gene #22: 'amp_17q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 22(17Q25.1) MUTATED 67 115 52
AMP PEAK 22(17Q25.1) WILD-TYPE 111 74 79

Figure S137.  Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q25.1' versus 'MIRSEQ_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.0025

Table S138.  Gene #22: 'amp_17q25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
AMP PEAK 22(17Q25.1) MUTATED 99 45 39 40
AMP PEAK 22(17Q25.1) WILD-TYPE 85 42 85 40

Figure S138.  Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00473 (Fisher's exact test), Q value = 0.013

Table S139.  Gene #22: 'amp_17q25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 22(17Q25.1) MUTATED 53 51 97 22
AMP PEAK 22(17Q25.1) WILD-TYPE 36 67 102 47

Figure S139.  Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q25.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.0025

Table S140.  Gene #22: 'amp_17q25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
AMP PEAK 22(17Q25.1) MUTATED 25 62 17 50
AMP PEAK 22(17Q25.1) WILD-TYPE 36 53 49 42

Figure S140.  Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q25.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0251 (Fisher's exact test), Q value = 0.051

Table S141.  Gene #22: 'amp_17q25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
AMP PEAK 22(17Q25.1) MUTATED 14 99 41
AMP PEAK 22(17Q25.1) WILD-TYPE 23 89 68

Figure S141.  Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18p11.32' versus 'MRNA_CHIERARCHICAL'

P value = 0.0046 (Fisher's exact test), Q value = 0.012

Table S142.  Gene #23: 'amp_18p11.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
AMP PEAK 23(18P11.32) MUTATED 13 30 13
AMP PEAK 23(18P11.32) WILD-TYPE 34 26 38

Figure S142.  Get High-res Image Gene #23: 'amp_18p11.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_18p11.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S143.  Gene #23: 'amp_18p11.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
AMP PEAK 23(18P11.32) MUTATED 19 23 10 20 86 21
AMP PEAK 23(18P11.32) WILD-TYPE 24 92 19 67 83 37

Figure S143.  Get High-res Image Gene #23: 'amp_18p11.32' versus Molecular Subtype #3: 'CN_CNMF'

'amp_18p11.32' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 3e-04

Table S144.  Gene #23: 'amp_18p11.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
AMP PEAK 23(18P11.32) MUTATED 39 48 19 26
AMP PEAK 23(18P11.32) WILD-TYPE 51 47 38 99

Figure S144.  Get High-res Image Gene #23: 'amp_18p11.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_18p11.32' versus 'MRNASEQ_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.043

Table S145.  Gene #23: 'amp_18p11.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
AMP PEAK 23(18P11.32) MUTATED 34 68 54 22
AMP PEAK 23(18P11.32) WILD-TYPE 72 82 105 61

Figure S145.  Get High-res Image Gene #23: 'amp_18p11.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_18p11.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00143 (Fisher's exact test), Q value = 0.0047

Table S146.  Gene #23: 'amp_18p11.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 23(18P11.32) MUTATED 50 86 42
AMP PEAK 23(18P11.32) WILD-TYPE 128 103 89

Figure S146.  Get High-res Image Gene #23: 'amp_18p11.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_18p11.32' versus 'MIRSEQ_CNMF'

P value = 0.00275 (Fisher's exact test), Q value = 0.008

Table S147.  Gene #23: 'amp_18p11.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
AMP PEAK 23(18P11.32) MUTATED 72 38 28 33
AMP PEAK 23(18P11.32) WILD-TYPE 112 49 96 47

Figure S147.  Get High-res Image Gene #23: 'amp_18p11.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_18p11.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0331 (Fisher's exact test), Q value = 0.065

Table S148.  Gene #23: 'amp_18p11.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
AMP PEAK 23(18P11.32) MUTATED 18 46 15 39
AMP PEAK 23(18P11.32) WILD-TYPE 43 69 51 53

Figure S148.  Get High-res Image Gene #23: 'amp_18p11.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_18p11.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.026 (Fisher's exact test), Q value = 0.052

Table S149.  Gene #23: 'amp_18p11.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
AMP PEAK 23(18P11.32) MUTATED 9 78 31
AMP PEAK 23(18P11.32) WILD-TYPE 28 110 78

Figure S149.  Get High-res Image Gene #23: 'amp_18p11.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18q11.2' versus 'MRNA_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0027

Table S150.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
AMP PEAK 24(18Q11.2) MUTATED 9 24 5 15
AMP PEAK 24(18Q11.2) WILD-TYPE 32 26 29 14

Figure S150.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_18q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0157 (Fisher's exact test), Q value = 0.034

Table S151.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
AMP PEAK 24(18Q11.2) MUTATED 10 27 16
AMP PEAK 24(18Q11.2) WILD-TYPE 37 29 35

Figure S151.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_18q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S152.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
AMP PEAK 24(18Q11.2) MUTATED 16 15 7 16 78 19
AMP PEAK 24(18Q11.2) WILD-TYPE 27 100 22 71 91 39

Figure S152.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S153.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
AMP PEAK 24(18Q11.2) MUTATED 24 49 16 18
AMP PEAK 24(18Q11.2) WILD-TYPE 66 46 41 107

Figure S153.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'RPPA_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.041

Table S154.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
AMP PEAK 24(18Q11.2) MUTATED 31 26 37 5
AMP PEAK 24(18Q11.2) WILD-TYPE 74 83 49 21

Figure S154.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S155.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
AMP PEAK 24(18Q11.2) MUTATED 25 64 52 9
AMP PEAK 24(18Q11.2) WILD-TYPE 81 86 107 74

Figure S155.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00045

Table S156.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 24(18Q11.2) MUTATED 35 77 38
AMP PEAK 24(18Q11.2) WILD-TYPE 143 112 93

Figure S156.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_CNMF'

P value = 0.0022 (Fisher's exact test), Q value = 0.0067

Table S157.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
AMP PEAK 24(18Q11.2) MUTATED 64 26 22 31
AMP PEAK 24(18Q11.2) WILD-TYPE 120 61 102 49

Figure S157.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00282 (Fisher's exact test), Q value = 0.0082

Table S158.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 24(18Q11.2) MUTATED 38 32 62 11
AMP PEAK 24(18Q11.2) WILD-TYPE 51 86 137 58

Figure S158.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S159.  Gene #25: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
AMP PEAK 25(19Q12) MUTATED 19 40 9 19 100 38
AMP PEAK 25(19Q12) WILD-TYPE 24 75 20 68 69 20

Figure S159.  Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q12' versus 'RPPA_CNMF'

P value = 0.0256 (Fisher's exact test), Q value = 0.052

Table S160.  Gene #25: 'amp_19q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
AMP PEAK 25(19Q12) MUTATED 46 44 52 10
AMP PEAK 25(19Q12) WILD-TYPE 59 65 34 16

Figure S160.  Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 0.00124 (Fisher's exact test), Q value = 0.0042

Table S161.  Gene #25: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
AMP PEAK 25(19Q12) MUTATED 34 82 76 31
AMP PEAK 25(19Q12) WILD-TYPE 72 68 83 52

Figure S161.  Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0386 (Fisher's exact test), Q value = 0.074

Table S162.  Gene #25: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 25(19Q12) MUTATED 67 96 60
AMP PEAK 25(19Q12) WILD-TYPE 111 93 71

Figure S162.  Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.026

Table S163.  Gene #25: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
AMP PEAK 25(19Q12) MUTATED 93 45 41 38
AMP PEAK 25(19Q12) WILD-TYPE 91 42 83 42

Figure S163.  Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00978 (Fisher's exact test), Q value = 0.024

Table S164.  Gene #25: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
AMP PEAK 25(19Q12) MUTATED 29 53 19 51
AMP PEAK 25(19Q12) WILD-TYPE 32 62 47 41

Figure S164.  Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.026

Table S165.  Gene #25: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
AMP PEAK 25(19Q12) MUTATED 18 97 37
AMP PEAK 25(19Q12) WILD-TYPE 19 91 72

Figure S165.  Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S166.  Gene #26: 'amp_19q13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
AMP PEAK 26(19Q13.2) MUTATED 21 41 10 20 100 42
AMP PEAK 26(19Q13.2) WILD-TYPE 22 74 19 67 69 16

Figure S166.  Get High-res Image Gene #26: 'amp_19q13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q13.2' versus 'RPPA_CNMF'

P value = 0.0488 (Fisher's exact test), Q value = 0.089

Table S167.  Gene #26: 'amp_19q13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
AMP PEAK 26(19Q13.2) MUTATED 50 44 51 10
AMP PEAK 26(19Q13.2) WILD-TYPE 55 65 35 16

Figure S167.  Get High-res Image Gene #26: 'amp_19q13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19q13.2' versus 'MRNASEQ_CNMF'

P value = 0.00353 (Fisher's exact test), Q value = 0.0099

Table S168.  Gene #26: 'amp_19q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
AMP PEAK 26(19Q13.2) MUTATED 37 85 76 33
AMP PEAK 26(19Q13.2) WILD-TYPE 69 65 83 50

Figure S168.  Get High-res Image Gene #26: 'amp_19q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q13.2' versus 'MIRSEQ_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.07

Table S169.  Gene #26: 'amp_19q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
AMP PEAK 26(19Q13.2) MUTATED 91 48 46 42
AMP PEAK 26(19Q13.2) WILD-TYPE 93 39 78 38

Figure S169.  Get High-res Image Gene #26: 'amp_19q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 0.031

Table S170.  Gene #26: 'amp_19q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
AMP PEAK 26(19Q13.2) MUTATED 19 100 39
AMP PEAK 26(19Q13.2) WILD-TYPE 18 88 70

Figure S170.  Get High-res Image Gene #26: 'amp_19q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20p12.2' versus 'MRNA_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.0047

Table S171.  Gene #27: 'amp_20p12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
AMP PEAK 27(20P12.2) MUTATED 24 35 10 12
AMP PEAK 27(20P12.2) WILD-TYPE 17 15 24 17

Figure S171.  Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20p12.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00235 (Fisher's exact test), Q value = 0.0071

Table S172.  Gene #27: 'amp_20p12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
AMP PEAK 27(20P12.2) MUTATED 27 37 17
AMP PEAK 27(20P12.2) WILD-TYPE 20 19 34

Figure S172.  Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20p12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S173.  Gene #27: 'amp_20p12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
AMP PEAK 27(20P12.2) MUTATED 32 45 21 25 118 39
AMP PEAK 27(20P12.2) WILD-TYPE 11 70 8 62 51 19

Figure S173.  Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p12.2' versus 'METHLYATION_CNMF'

P value = 0.00274 (Fisher's exact test), Q value = 0.008

Table S174.  Gene #27: 'amp_20p12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
AMP PEAK 27(20P12.2) MUTATED 50 66 37 57
AMP PEAK 27(20P12.2) WILD-TYPE 40 29 20 68

Figure S174.  Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20p12.2' versus 'MRNASEQ_CNMF'

P value = 0.00677 (Fisher's exact test), Q value = 0.017

Table S175.  Gene #27: 'amp_20p12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
AMP PEAK 27(20P12.2) MUTATED 52 101 86 40
AMP PEAK 27(20P12.2) WILD-TYPE 54 49 73 43

Figure S175.  Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20p12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0147 (Fisher's exact test), Q value = 0.033

Table S176.  Gene #27: 'amp_20p12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 27(20P12.2) MUTATED 94 121 64
AMP PEAK 27(20P12.2) WILD-TYPE 84 68 67

Figure S176.  Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S177.  Gene #28: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
AMP PEAK 28(20Q11.21) MUTATED 40 56 24 27 113 46
AMP PEAK 28(20Q11.21) WILD-TYPE 3 59 5 60 56 12

Figure S177.  Get High-res Image Gene #28: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q11.21' versus 'METHLYATION_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.027

Table S178.  Gene #28: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
AMP PEAK 28(20Q11.21) MUTATED 56 65 41 63
AMP PEAK 28(20Q11.21) WILD-TYPE 34 30 16 62

Figure S178.  Get High-res Image Gene #28: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.033

Table S179.  Gene #28: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
AMP PEAK 28(20Q11.21) MUTATED 39 72 30 65
AMP PEAK 28(20Q11.21) WILD-TYPE 22 43 36 27

Figure S179.  Get High-res Image Gene #28: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_22q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S180.  Gene #29: 'amp_22q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
AMP PEAK 29(22Q11.21) MUTATED 23 40 28 21 105 39
AMP PEAK 29(22Q11.21) WILD-TYPE 20 75 1 66 64 19

Figure S180.  Get High-res Image Gene #29: 'amp_22q11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_22q11.21' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S181.  Gene #29: 'amp_22q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
AMP PEAK 29(22Q11.21) MUTATED 49 66 32 45
AMP PEAK 29(22Q11.21) WILD-TYPE 41 29 25 80

Figure S181.  Get High-res Image Gene #29: 'amp_22q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_22q11.21' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00035

Table S182.  Gene #29: 'amp_22q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
AMP PEAK 29(22Q11.21) MUTATED 50 100 72 32
AMP PEAK 29(22Q11.21) WILD-TYPE 56 50 87 51

Figure S182.  Get High-res Image Gene #29: 'amp_22q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_22q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.0011

Table S183.  Gene #29: 'amp_22q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 29(22Q11.21) MUTATED 97 110 47
AMP PEAK 29(22Q11.21) WILD-TYPE 81 79 84

Figure S183.  Get High-res Image Gene #29: 'amp_22q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_22q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0416 (Fisher's exact test), Q value = 0.078

Table S184.  Gene #29: 'amp_22q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 29(22Q11.21) MUTATED 48 55 114 27
AMP PEAK 29(22Q11.21) WILD-TYPE 41 63 85 42

Figure S184.  Get High-res Image Gene #29: 'amp_22q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_xq28' versus 'CN_CNMF'

P value = 0.00326 (Fisher's exact test), Q value = 0.0093

Table S185.  Gene #30: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
AMP PEAK 30(XQ28) MUTATED 12 22 5 12 50 23
AMP PEAK 30(XQ28) WILD-TYPE 31 93 24 75 119 35

Figure S185.  Get High-res Image Gene #30: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xq28' versus 'METHLYATION_CNMF'

P value = 0.00414 (Fisher's exact test), Q value = 0.011

Table S186.  Gene #30: 'amp_xq28' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
AMP PEAK 30(XQ28) MUTATED 22 36 10 22
AMP PEAK 30(XQ28) WILD-TYPE 68 59 47 103

Figure S186.  Get High-res Image Gene #30: 'amp_xq28' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xq28' versus 'MRNASEQ_CNMF'

P value = 0.0304 (Fisher's exact test), Q value = 0.059

Table S187.  Gene #30: 'amp_xq28' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
AMP PEAK 30(XQ28) MUTATED 17 48 37 19
AMP PEAK 30(XQ28) WILD-TYPE 89 102 122 64

Figure S187.  Get High-res Image Gene #30: 'amp_xq28' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xq28' versus 'MIRSEQ_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.059

Table S188.  Gene #30: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
AMP PEAK 30(XQ28) MUTATED 47 27 20 25
AMP PEAK 30(XQ28) WILD-TYPE 137 60 104 55

Figure S188.  Get High-res Image Gene #30: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.11' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S189.  Gene #31: 'del_1p36.11' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
DEL PEAK 1(1P36.11) MUTATED 12 39 13 10
DEL PEAK 1(1P36.11) WILD-TYPE 29 11 21 19

Figure S189.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.11' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S190.  Gene #31: 'del_1p36.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 1(1P36.11) MUTATED 14 43 17
DEL PEAK 1(1P36.11) WILD-TYPE 33 13 34

Figure S190.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S191.  Gene #31: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 1(1P36.11) MUTATED 26 24 16 9 140 13
DEL PEAK 1(1P36.11) WILD-TYPE 17 91 13 78 29 45

Figure S191.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S192.  Gene #31: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 1(1P36.11) MUTATED 28 70 37 26
DEL PEAK 1(1P36.11) WILD-TYPE 62 25 20 99

Figure S192.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.11' versus 'RPPA_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.002

Table S193.  Gene #31: 'del_1p36.11' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
DEL PEAK 1(1P36.11) MUTATED 45 40 57 12
DEL PEAK 1(1P36.11) WILD-TYPE 60 69 29 14

Figure S193.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p36.11' versus 'RPPA_CHIERARCHICAL'

P value = 0.0154 (Fisher's exact test), Q value = 0.034

Table S194.  Gene #31: 'del_1p36.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 79 67 62 60 30 28
DEL PEAK 1(1P36.11) MUTATED 41 36 21 36 11 9
DEL PEAK 1(1P36.11) WILD-TYPE 38 31 41 24 19 19

Figure S194.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S195.  Gene #31: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 1(1P36.11) MUTATED 29 119 55 24
DEL PEAK 1(1P36.11) WILD-TYPE 77 31 104 59

Figure S195.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S196.  Gene #31: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 1(1P36.11) MUTATED 46 140 41
DEL PEAK 1(1P36.11) WILD-TYPE 132 49 90

Figure S196.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S197.  Gene #31: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 1(1P36.11) MUTATED 94 33 32 57
DEL PEAK 1(1P36.11) WILD-TYPE 90 54 92 23

Figure S197.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S198.  Gene #31: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 1(1P36.11) MUTATED 66 52 83 15
DEL PEAK 1(1P36.11) WILD-TYPE 23 66 116 54

Figure S198.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S199.  Gene #31: 'del_1p36.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 1(1P36.11) MUTATED 17 59 13 55
DEL PEAK 1(1P36.11) WILD-TYPE 44 56 53 37

Figure S199.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00035

Table S200.  Gene #31: 'del_1p36.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
DEL PEAK 1(1P36.11) MUTATED 8 100 36
DEL PEAK 1(1P36.11) WILD-TYPE 29 88 73

Figure S200.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p13.1' versus 'MRNA_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0011

Table S201.  Gene #32: 'del_1p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
DEL PEAK 2(1P13.1) MUTATED 17 36 10 9
DEL PEAK 2(1P13.1) WILD-TYPE 24 14 24 20

Figure S201.  Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p13.1' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 3e-04

Table S202.  Gene #32: 'del_1p13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 2(1P13.1) MUTATED 19 39 14
DEL PEAK 2(1P13.1) WILD-TYPE 28 17 37

Figure S202.  Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S203.  Gene #32: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 2(1P13.1) MUTATED 24 24 13 17 123 20
DEL PEAK 2(1P13.1) WILD-TYPE 19 91 16 70 46 38

Figure S203.  Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S204.  Gene #32: 'del_1p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 2(1P13.1) MUTATED 31 60 37 29
DEL PEAK 2(1P13.1) WILD-TYPE 59 35 20 96

Figure S204.  Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p13.1' versus 'RPPA_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.002

Table S205.  Gene #32: 'del_1p13.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
DEL PEAK 2(1P13.1) MUTATED 39 41 55 10
DEL PEAK 2(1P13.1) WILD-TYPE 66 68 31 16

Figure S205.  Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S206.  Gene #32: 'del_1p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 2(1P13.1) MUTATED 32 106 57 25
DEL PEAK 2(1P13.1) WILD-TYPE 74 44 102 58

Figure S206.  Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S207.  Gene #32: 'del_1p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 2(1P13.1) MUTATED 48 125 47
DEL PEAK 2(1P13.1) WILD-TYPE 130 64 84

Figure S207.  Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S208.  Gene #32: 'del_1p13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 2(1P13.1) MUTATED 90 36 29 55
DEL PEAK 2(1P13.1) WILD-TYPE 94 51 95 25

Figure S208.  Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S209.  Gene #32: 'del_1p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 2(1P13.1) MUTATED 62 53 79 16
DEL PEAK 2(1P13.1) WILD-TYPE 27 65 120 53

Figure S209.  Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00072

Table S210.  Gene #32: 'del_1p13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 2(1P13.1) MUTATED 20 58 15 49
DEL PEAK 2(1P13.1) WILD-TYPE 41 57 51 43

Figure S210.  Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.002

Table S211.  Gene #32: 'del_1p13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
DEL PEAK 2(1P13.1) MUTATED 9 97 36
DEL PEAK 2(1P13.1) WILD-TYPE 28 91 73

Figure S211.  Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2p25.3' versus 'CN_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.027

Table S212.  Gene #33: 'del_2p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 3(2P25.3) MUTATED 10 7 3 5 15 10
DEL PEAK 3(2P25.3) WILD-TYPE 33 108 26 82 154 48

Figure S212.  Get High-res Image Gene #33: 'del_2p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_2p25.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0418 (Fisher's exact test), Q value = 0.079

Table S213.  Gene #33: 'del_2p25.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 79 67 62 60 30 28
DEL PEAK 3(2P25.3) MUTATED 10 3 5 11 2 0
DEL PEAK 3(2P25.3) WILD-TYPE 69 64 57 49 28 28

Figure S213.  Get High-res Image Gene #33: 'del_2p25.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_2p25.3' versus 'MIRSEQ_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.026

Table S214.  Gene #33: 'del_2p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 3(2P25.3) MUTATED 28 9 5 6
DEL PEAK 3(2P25.3) WILD-TYPE 156 78 119 74

Figure S214.  Get High-res Image Gene #33: 'del_2p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2p25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0282 (Fisher's exact test), Q value = 0.056

Table S215.  Gene #33: 'del_2p25.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
DEL PEAK 3(2P25.3) MUTATED 2 23 4
DEL PEAK 3(2P25.3) WILD-TYPE 35 165 105

Figure S215.  Get High-res Image Gene #33: 'del_2p25.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S216.  Gene #34: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 4(2Q22.1) MUTATED 10 14 4 16 63 24
DEL PEAK 4(2Q22.1) WILD-TYPE 33 101 25 71 106 34

Figure S216.  Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S217.  Gene #34: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 4(2Q22.1) MUTATED 25 25 26 16
DEL PEAK 4(2Q22.1) WILD-TYPE 65 70 31 109

Figure S217.  Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q22.1' versus 'RPPA_CNMF'

P value = 0.0477 (Fisher's exact test), Q value = 0.088

Table S218.  Gene #34: 'del_2q22.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
DEL PEAK 4(2Q22.1) MUTATED 17 29 26 3
DEL PEAK 4(2Q22.1) WILD-TYPE 88 80 60 23

Figure S218.  Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00257 (Fisher's exact test), Q value = 0.0077

Table S219.  Gene #34: 'del_2q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 4(2Q22.1) MUTATED 22 49 49 11
DEL PEAK 4(2Q22.1) WILD-TYPE 84 101 110 72

Figure S219.  Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00713 (Fisher's exact test), Q value = 0.018

Table S220.  Gene #34: 'del_2q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 4(2Q22.1) MUTATED 33 62 36
DEL PEAK 4(2Q22.1) WILD-TYPE 145 127 95

Figure S220.  Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_CNMF'

P value = 0.00165 (Fisher's exact test), Q value = 0.0053

Table S221.  Gene #34: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 4(2Q22.1) MUTATED 60 20 19 28
DEL PEAK 4(2Q22.1) WILD-TYPE 124 67 105 52

Figure S221.  Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.0021

Table S222.  Gene #34: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 4(2Q22.1) MUTATED 35 38 45 9
DEL PEAK 4(2Q22.1) WILD-TYPE 54 80 154 60

Figure S222.  Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0027

Table S223.  Gene #34: 'del_2q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 4(2Q22.1) MUTATED 14 41 6 24
DEL PEAK 4(2Q22.1) WILD-TYPE 47 74 60 68

Figure S223.  Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_2q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0064 (Fisher's exact test), Q value = 0.016

Table S224.  Gene #34: 'del_2q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
DEL PEAK 4(2Q22.1) MUTATED 8 60 17
DEL PEAK 4(2Q22.1) WILD-TYPE 29 128 92

Figure S224.  Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q37.1' versus 'MRNA_CNMF'

P value = 0.0016 (Fisher's exact test), Q value = 0.0052

Table S225.  Gene #35: 'del_2q37.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
DEL PEAK 5(2Q37.1) MUTATED 7 26 7 10
DEL PEAK 5(2Q37.1) WILD-TYPE 34 24 27 19

Figure S225.  Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_2q37.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00071 (Fisher's exact test), Q value = 0.0027

Table S226.  Gene #35: 'del_2q37.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 5(2Q37.1) MUTATED 11 29 10
DEL PEAK 5(2Q37.1) WILD-TYPE 36 27 41

Figure S226.  Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_2q37.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S227.  Gene #35: 'del_2q37.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 5(2Q37.1) MUTATED 12 18 5 15 86 23
DEL PEAK 5(2Q37.1) WILD-TYPE 31 97 24 72 83 35

Figure S227.  Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q37.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S228.  Gene #35: 'del_2q37.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 5(2Q37.1) MUTATED 28 49 23 20
DEL PEAK 5(2Q37.1) WILD-TYPE 62 46 34 105

Figure S228.  Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q37.1' versus 'RPPA_CNMF'

P value = 0.00499 (Fisher's exact test), Q value = 0.013

Table S229.  Gene #35: 'del_2q37.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
DEL PEAK 5(2Q37.1) MUTATED 26 29 40 6
DEL PEAK 5(2Q37.1) WILD-TYPE 79 80 46 20

Figure S229.  Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_2q37.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S230.  Gene #35: 'del_2q37.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 5(2Q37.1) MUTATED 32 71 44 11
DEL PEAK 5(2Q37.1) WILD-TYPE 74 79 115 72

Figure S230.  Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q37.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S231.  Gene #35: 'del_2q37.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 5(2Q37.1) MUTATED 38 88 32
DEL PEAK 5(2Q37.1) WILD-TYPE 140 101 99

Figure S231.  Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S232.  Gene #35: 'del_2q37.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 5(2Q37.1) MUTATED 75 31 16 31
DEL PEAK 5(2Q37.1) WILD-TYPE 109 56 108 49

Figure S232.  Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q37.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S233.  Gene #35: 'del_2q37.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 5(2Q37.1) MUTATED 34 54 56 9
DEL PEAK 5(2Q37.1) WILD-TYPE 55 64 143 60

Figure S233.  Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0013

Table S234.  Gene #35: 'del_2q37.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 5(2Q37.1) MUTATED 17 46 8 35
DEL PEAK 5(2Q37.1) WILD-TYPE 44 69 58 57

Figure S234.  Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_2q37.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.0016

Table S235.  Gene #35: 'del_2q37.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
DEL PEAK 5(2Q37.1) MUTATED 3 72 31
DEL PEAK 5(2Q37.1) WILD-TYPE 34 116 78

Figure S235.  Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p25.3' versus 'MRNA_CNMF'

P value = 0.0402 (Fisher's exact test), Q value = 0.077

Table S236.  Gene #36: 'del_3p25.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
DEL PEAK 6(3P25.3) MUTATED 30 45 23 25
DEL PEAK 6(3P25.3) WILD-TYPE 11 5 11 4

Figure S236.  Get High-res Image Gene #36: 'del_3p25.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p25.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S237.  Gene #36: 'del_3p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 6(3P25.3) MUTATED 37 70 25 72 150 44
DEL PEAK 6(3P25.3) WILD-TYPE 6 45 4 15 19 14

Figure S237.  Get High-res Image Gene #36: 'del_3p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p25.3' versus 'METHLYATION_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0011

Table S238.  Gene #36: 'del_3p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 6(3P25.3) MUTATED 76 84 49 83
DEL PEAK 6(3P25.3) WILD-TYPE 14 11 8 42

Figure S238.  Get High-res Image Gene #36: 'del_3p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p25.3' versus 'MRNASEQ_CNMF'

P value = 0.00271 (Fisher's exact test), Q value = 0.0079

Table S239.  Gene #36: 'del_3p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 6(3P25.3) MUTATED 83 131 127 55
DEL PEAK 6(3P25.3) WILD-TYPE 23 19 32 28

Figure S239.  Get High-res Image Gene #36: 'del_3p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.0015

Table S240.  Gene #36: 'del_3p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 6(3P25.3) MUTATED 141 165 90
DEL PEAK 6(3P25.3) WILD-TYPE 37 24 41

Figure S240.  Get High-res Image Gene #36: 'del_3p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p25.3' versus 'MIRSEQ_CNMF'

P value = 0.00444 (Fisher's exact test), Q value = 0.012

Table S241.  Gene #36: 'del_3p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 6(3P25.3) MUTATED 147 76 85 68
DEL PEAK 6(3P25.3) WILD-TYPE 37 11 39 12

Figure S241.  Get High-res Image Gene #36: 'del_3p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00072

Table S242.  Gene #36: 'del_3p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 6(3P25.3) MUTATED 76 94 166 40
DEL PEAK 6(3P25.3) WILD-TYPE 13 24 33 29

Figure S242.  Get High-res Image Gene #36: 'del_3p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p25.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.027

Table S243.  Gene #36: 'del_3p25.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 6(3P25.3) MUTATED 47 97 43 78
DEL PEAK 6(3P25.3) WILD-TYPE 14 18 23 14

Figure S243.  Get High-res Image Gene #36: 'del_3p25.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.024 (Fisher's exact test), Q value = 0.049

Table S244.  Gene #36: 'del_3p25.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
DEL PEAK 6(3P25.3) MUTATED 30 158 77
DEL PEAK 6(3P25.3) WILD-TYPE 7 30 32

Figure S244.  Get High-res Image Gene #36: 'del_3p25.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p13' versus 'MRNA_CNMF'

P value = 0.0439 (Fisher's exact test), Q value = 0.082

Table S245.  Gene #37: 'del_3p13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
DEL PEAK 7(3P13) MUTATED 37 45 24 27
DEL PEAK 7(3P13) WILD-TYPE 4 5 10 2

Figure S245.  Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S246.  Gene #37: 'del_3p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 7(3P13) MUTATED 41 70 28 81 161 53
DEL PEAK 7(3P13) WILD-TYPE 2 45 1 6 8 5

Figure S246.  Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p13' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S247.  Gene #37: 'del_3p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 7(3P13) MUTATED 82 88 56 92
DEL PEAK 7(3P13) WILD-TYPE 8 7 1 33

Figure S247.  Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p13' versus 'RPPA_CHIERARCHICAL'

P value = 0.0448 (Fisher's exact test), Q value = 0.083

Table S248.  Gene #37: 'del_3p13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 79 67 62 60 30 28
DEL PEAK 7(3P13) MUTATED 68 59 57 55 24 19
DEL PEAK 7(3P13) WILD-TYPE 11 8 5 5 6 9

Figure S248.  Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p13' versus 'MRNASEQ_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0024

Table S249.  Gene #37: 'del_3p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 7(3P13) MUTATED 95 138 138 60
DEL PEAK 7(3P13) WILD-TYPE 11 12 21 23

Figure S249.  Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-04 (Fisher's exact test), Q value = 0.003

Table S250.  Gene #37: 'del_3p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 7(3P13) MUTATED 154 175 102
DEL PEAK 7(3P13) WILD-TYPE 24 14 29

Figure S250.  Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p13' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S251.  Gene #37: 'del_3p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 7(3P13) MUTATED 168 82 91 70
DEL PEAK 7(3P13) WILD-TYPE 16 5 33 10

Figure S251.  Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S252.  Gene #37: 'del_3p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 7(3P13) MUTATED 79 104 185 43
DEL PEAK 7(3P13) WILD-TYPE 10 14 14 26

Figure S252.  Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S253.  Gene #37: 'del_3p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 7(3P13) MUTATED 54 108 44 85
DEL PEAK 7(3P13) WILD-TYPE 7 7 22 7

Figure S253.  Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00146 (Fisher's exact test), Q value = 0.0048

Table S254.  Gene #37: 'del_3p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
DEL PEAK 7(3P13) MUTATED 32 174 85
DEL PEAK 7(3P13) WILD-TYPE 5 14 24

Figure S254.  Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p12.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S255.  Gene #38: 'del_3p12.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 8(3P12.3) MUTATED 41 67 28 81 158 52
DEL PEAK 8(3P12.3) WILD-TYPE 2 48 1 6 11 6

Figure S255.  Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p12.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S256.  Gene #38: 'del_3p12.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 8(3P12.3) MUTATED 83 84 56 89
DEL PEAK 8(3P12.3) WILD-TYPE 7 11 1 36

Figure S256.  Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p12.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00577 (Fisher's exact test), Q value = 0.015

Table S257.  Gene #38: 'del_3p12.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 79 67 62 60 30 28
DEL PEAK 8(3P12.3) MUTATED 65 58 57 55 24 17
DEL PEAK 8(3P12.3) WILD-TYPE 14 9 5 5 6 11

Figure S257.  Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p12.3' versus 'MRNASEQ_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0024

Table S258.  Gene #38: 'del_3p12.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 8(3P12.3) MUTATED 94 136 136 58
DEL PEAK 8(3P12.3) WILD-TYPE 12 14 23 25

Figure S258.  Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p12.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0046 (Fisher's exact test), Q value = 0.012

Table S259.  Gene #38: 'del_3p12.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 8(3P12.3) MUTATED 152 171 101
DEL PEAK 8(3P12.3) WILD-TYPE 26 18 30

Figure S259.  Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p12.3' versus 'MIRSEQ_CNMF'

P value = 0.00145 (Fisher's exact test), Q value = 0.0048

Table S260.  Gene #38: 'del_3p12.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 8(3P12.3) MUTATED 163 80 92 69
DEL PEAK 8(3P12.3) WILD-TYPE 21 7 32 11

Figure S260.  Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p12.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S261.  Gene #38: 'del_3p12.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 8(3P12.3) MUTATED 79 103 180 42
DEL PEAK 8(3P12.3) WILD-TYPE 10 15 19 27

Figure S261.  Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p12.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 5e-04

Table S262.  Gene #38: 'del_3p12.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 8(3P12.3) MUTATED 53 106 44 83
DEL PEAK 8(3P12.3) WILD-TYPE 8 9 22 9

Figure S262.  Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p12.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00236 (Fisher's exact test), Q value = 0.0071

Table S263.  Gene #38: 'del_3p12.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
DEL PEAK 8(3P12.3) MUTATED 32 171 83
DEL PEAK 8(3P12.3) WILD-TYPE 5 17 26

Figure S263.  Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p12.3' versus 'MRNA_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 0.069

Table S264.  Gene #39: 'del_3p12.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
DEL PEAK 9(3P12.3) MUTATED 36 44 23 27
DEL PEAK 9(3P12.3) WILD-TYPE 5 6 11 2

Figure S264.  Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p12.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S265.  Gene #39: 'del_3p12.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 9(3P12.3) MUTATED 41 66 27 79 157 51
DEL PEAK 9(3P12.3) WILD-TYPE 2 49 2 8 12 7

Figure S265.  Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p12.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S266.  Gene #39: 'del_3p12.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 9(3P12.3) MUTATED 81 83 56 88
DEL PEAK 9(3P12.3) WILD-TYPE 9 12 1 37

Figure S266.  Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p12.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00751 (Fisher's exact test), Q value = 0.019

Table S267.  Gene #39: 'del_3p12.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 79 67 62 60 30 28
DEL PEAK 9(3P12.3) MUTATED 64 57 57 54 23 17
DEL PEAK 9(3P12.3) WILD-TYPE 15 10 5 6 7 11

Figure S267.  Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p12.3' versus 'MRNASEQ_CNMF'

P value = 0.00216 (Fisher's exact test), Q value = 0.0067

Table S268.  Gene #39: 'del_3p12.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 9(3P12.3) MUTATED 92 134 134 58
DEL PEAK 9(3P12.3) WILD-TYPE 14 16 25 25

Figure S268.  Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p12.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00757 (Fisher's exact test), Q value = 0.019

Table S269.  Gene #39: 'del_3p12.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 9(3P12.3) MUTATED 149 169 100
DEL PEAK 9(3P12.3) WILD-TYPE 29 20 31

Figure S269.  Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p12.3' versus 'MIRSEQ_CNMF'

P value = 0.00159 (Fisher's exact test), Q value = 0.0051

Table S270.  Gene #39: 'del_3p12.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 9(3P12.3) MUTATED 160 79 90 69
DEL PEAK 9(3P12.3) WILD-TYPE 24 8 34 11

Figure S270.  Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p12.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S271.  Gene #39: 'del_3p12.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 9(3P12.3) MUTATED 79 101 176 42
DEL PEAK 9(3P12.3) WILD-TYPE 10 17 23 27

Figure S271.  Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p12.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 5e-04

Table S272.  Gene #39: 'del_3p12.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 9(3P12.3) MUTATED 53 105 43 82
DEL PEAK 9(3P12.3) WILD-TYPE 8 10 23 10

Figure S272.  Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p12.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00369 (Fisher's exact test), Q value = 0.01

Table S273.  Gene #39: 'del_3p12.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
DEL PEAK 9(3P12.3) MUTATED 32 169 82
DEL PEAK 9(3P12.3) WILD-TYPE 5 19 27

Figure S273.  Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p15.2' versus 'MRNA_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00068

Table S274.  Gene #41: 'del_4p15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
DEL PEAK 11(4P15.2) MUTATED 31 39 12 15
DEL PEAK 11(4P15.2) WILD-TYPE 10 11 22 14

Figure S274.  Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4p15.2' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S275.  Gene #41: 'del_4p15.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 11(4P15.2) MUTATED 34 44 19
DEL PEAK 11(4P15.2) WILD-TYPE 13 12 32

Figure S275.  Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4p15.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S276.  Gene #41: 'del_4p15.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 11(4P15.2) MUTATED 31 46 15 50 138 36
DEL PEAK 11(4P15.2) WILD-TYPE 12 69 14 37 31 22

Figure S276.  Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p15.2' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0013

Table S277.  Gene #41: 'del_4p15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 11(4P15.2) MUTATED 58 71 42 60
DEL PEAK 11(4P15.2) WILD-TYPE 32 24 15 65

Figure S277.  Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p15.2' versus 'RPPA_CNMF'

P value = 0.0285 (Fisher's exact test), Q value = 0.056

Table S278.  Gene #41: 'del_4p15.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
DEL PEAK 11(4P15.2) MUTATED 62 72 68 18
DEL PEAK 11(4P15.2) WILD-TYPE 43 37 18 8

Figure S278.  Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4p15.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0449 (Fisher's exact test), Q value = 0.083

Table S279.  Gene #41: 'del_4p15.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 79 67 62 60 30 28
DEL PEAK 11(4P15.2) MUTATED 52 49 45 45 16 13
DEL PEAK 11(4P15.2) WILD-TYPE 27 18 17 15 14 15

Figure S279.  Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4p15.2' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 4e-04

Table S280.  Gene #41: 'del_4p15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 11(4P15.2) MUTATED 69 115 86 45
DEL PEAK 11(4P15.2) WILD-TYPE 37 35 73 38

Figure S280.  Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p15.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S281.  Gene #41: 'del_4p15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 11(4P15.2) MUTATED 105 147 63
DEL PEAK 11(4P15.2) WILD-TYPE 73 42 68

Figure S281.  Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p15.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S282.  Gene #41: 'del_4p15.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 11(4P15.2) MUTATED 134 60 56 53
DEL PEAK 11(4P15.2) WILD-TYPE 50 27 68 27

Figure S282.  Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4p15.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.003

Table S283.  Gene #41: 'del_4p15.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 11(4P15.2) MUTATED 37 79 28 67
DEL PEAK 11(4P15.2) WILD-TYPE 24 36 38 25

Figure S283.  Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4p15.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0025

Table S284.  Gene #41: 'del_4p15.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
DEL PEAK 11(4P15.2) MUTATED 17 135 59
DEL PEAK 11(4P15.2) WILD-TYPE 20 53 50

Figure S284.  Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.1' versus 'MRNA_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.0022

Table S285.  Gene #42: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
DEL PEAK 12(4Q22.1) MUTATED 29 37 11 17
DEL PEAK 12(4Q22.1) WILD-TYPE 12 13 23 12

Figure S285.  Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00422 (Fisher's exact test), Q value = 0.012

Table S286.  Gene #42: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 12(4Q22.1) MUTATED 31 41 22
DEL PEAK 12(4Q22.1) WILD-TYPE 16 15 29

Figure S286.  Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S287.  Gene #42: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 12(4Q22.1) MUTATED 31 44 8 45 128 29
DEL PEAK 12(4Q22.1) WILD-TYPE 12 71 21 42 41 29

Figure S287.  Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 0.0488 (Fisher's exact test), Q value = 0.089

Table S288.  Gene #42: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 12(4Q22.1) MUTATED 47 62 34 59
DEL PEAK 12(4Q22.1) WILD-TYPE 43 33 23 66

Figure S288.  Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q22.1' versus 'RPPA_CNMF'

P value = 0.0281 (Fisher's exact test), Q value = 0.056

Table S289.  Gene #42: 'del_4q22.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
DEL PEAK 12(4Q22.1) MUTATED 63 54 60 13
DEL PEAK 12(4Q22.1) WILD-TYPE 42 55 26 13

Figure S289.  Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S290.  Gene #42: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 12(4Q22.1) MUTATED 58 107 85 33
DEL PEAK 12(4Q22.1) WILD-TYPE 48 43 74 50

Figure S290.  Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0146 (Fisher's exact test), Q value = 0.033

Table S291.  Gene #42: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 12(4Q22.1) MUTATED 97 122 64
DEL PEAK 12(4Q22.1) WILD-TYPE 81 67 67

Figure S291.  Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S292.  Gene #42: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 12(4Q22.1) MUTATED 119 47 49 57
DEL PEAK 12(4Q22.1) WILD-TYPE 65 40 75 23

Figure S292.  Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00613 (Fisher's exact test), Q value = 0.016

Table S293.  Gene #42: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 12(4Q22.1) MUTATED 61 67 116 28
DEL PEAK 12(4Q22.1) WILD-TYPE 28 51 83 41

Figure S293.  Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0032

Table S294.  Gene #42: 'del_4q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 12(4Q22.1) MUTATED 34 69 22 59
DEL PEAK 12(4Q22.1) WILD-TYPE 27 46 44 33

Figure S294.  Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q32.3' versus 'MRNA_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.0038

Table S295.  Gene #43: 'del_4q32.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
DEL PEAK 13(4Q32.3) MUTATED 28 41 14 22
DEL PEAK 13(4Q32.3) WILD-TYPE 13 9 20 7

Figure S295.  Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q32.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.018 (Fisher's exact test), Q value = 0.038

Table S296.  Gene #43: 'del_4q32.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 13(4Q32.3) MUTATED 32 45 28
DEL PEAK 13(4Q32.3) WILD-TYPE 15 11 23

Figure S296.  Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q32.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S297.  Gene #43: 'del_4q32.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 13(4Q32.3) MUTATED 30 52 11 49 146 41
DEL PEAK 13(4Q32.3) WILD-TYPE 13 63 18 38 23 17

Figure S297.  Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q32.3' versus 'METHLYATION_CNMF'

P value = 0.00685 (Fisher's exact test), Q value = 0.017

Table S298.  Gene #43: 'del_4q32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 13(4Q32.3) MUTATED 60 71 41 67
DEL PEAK 13(4Q32.3) WILD-TYPE 30 24 16 58

Figure S298.  Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q32.3' versus 'RPPA_CNMF'

P value = 0.029 (Fisher's exact test), Q value = 0.057

Table S299.  Gene #43: 'del_4q32.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
DEL PEAK 13(4Q32.3) MUTATED 65 67 68 16
DEL PEAK 13(4Q32.3) WILD-TYPE 40 42 18 10

Figure S299.  Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4q32.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0188 (Fisher's exact test), Q value = 0.04

Table S300.  Gene #43: 'del_4q32.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 79 67 62 60 30 28
DEL PEAK 13(4Q32.3) MUTATED 56 44 41 47 13 15
DEL PEAK 13(4Q32.3) WILD-TYPE 23 23 21 13 17 13

Figure S300.  Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4q32.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S301.  Gene #43: 'del_4q32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 13(4Q32.3) MUTATED 69 121 97 40
DEL PEAK 13(4Q32.3) WILD-TYPE 37 29 62 43

Figure S301.  Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q32.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.0016

Table S302.  Gene #43: 'del_4q32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 13(4Q32.3) MUTATED 110 144 73
DEL PEAK 13(4Q32.3) WILD-TYPE 68 45 58

Figure S302.  Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q32.3' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S303.  Gene #43: 'del_4q32.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 13(4Q32.3) MUTATED 130 65 57 62
DEL PEAK 13(4Q32.3) WILD-TYPE 54 22 67 18

Figure S303.  Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q32.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00255 (Fisher's exact test), Q value = 0.0076

Table S304.  Gene #43: 'del_4q32.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 13(4Q32.3) MUTATED 66 75 140 33
DEL PEAK 13(4Q32.3) WILD-TYPE 23 43 59 36

Figure S304.  Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q32.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0011

Table S305.  Gene #43: 'del_4q32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 13(4Q32.3) MUTATED 38 80 29 71
DEL PEAK 13(4Q32.3) WILD-TYPE 23 35 37 21

Figure S305.  Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q32.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00059

Table S306.  Gene #43: 'del_4q32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
DEL PEAK 13(4Q32.3) MUTATED 25 139 54
DEL PEAK 13(4Q32.3) WILD-TYPE 12 49 55

Figure S306.  Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q35.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S307.  Gene #44: 'del_4q35.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 14(4Q35.2) MUTATED 30 56 10 51 146 38
DEL PEAK 14(4Q35.2) WILD-TYPE 13 59 19 36 23 20

Figure S307.  Get High-res Image Gene #44: 'del_4q35.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q35.2' versus 'METHLYATION_CNMF'

P value = 0.00993 (Fisher's exact test), Q value = 0.024

Table S308.  Gene #44: 'del_4q35.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 14(4Q35.2) MUTATED 60 72 39 68
DEL PEAK 14(4Q35.2) WILD-TYPE 30 23 18 57

Figure S308.  Get High-res Image Gene #44: 'del_4q35.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q35.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S309.  Gene #44: 'del_4q35.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 14(4Q35.2) MUTATED 66 121 101 41
DEL PEAK 14(4Q35.2) WILD-TYPE 40 29 58 42

Figure S309.  Get High-res Image Gene #44: 'del_4q35.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q35.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00325 (Fisher's exact test), Q value = 0.0092

Table S310.  Gene #44: 'del_4q35.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 14(4Q35.2) MUTATED 113 141 75
DEL PEAK 14(4Q35.2) WILD-TYPE 65 48 56

Figure S310.  Get High-res Image Gene #44: 'del_4q35.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.2' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S311.  Gene #44: 'del_4q35.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 14(4Q35.2) MUTATED 130 63 57 64
DEL PEAK 14(4Q35.2) WILD-TYPE 54 24 67 16

Figure S311.  Get High-res Image Gene #44: 'del_4q35.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q35.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0079 (Fisher's exact test), Q value = 0.02

Table S312.  Gene #44: 'del_4q35.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 14(4Q35.2) MUTATED 67 74 138 35
DEL PEAK 14(4Q35.2) WILD-TYPE 22 44 61 34

Figure S312.  Get High-res Image Gene #44: 'del_4q35.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q35.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00108 (Fisher's exact test), Q value = 0.0037

Table S313.  Gene #44: 'del_4q35.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 14(4Q35.2) MUTATED 41 81 29 67
DEL PEAK 14(4Q35.2) WILD-TYPE 20 34 37 25

Figure S313.  Get High-res Image Gene #44: 'del_4q35.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q35.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0011 (Fisher's exact test), Q value = 0.0038

Table S314.  Gene #44: 'del_4q35.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
DEL PEAK 14(4Q35.2) MUTATED 26 136 56
DEL PEAK 14(4Q35.2) WILD-TYPE 11 52 53

Figure S314.  Get High-res Image Gene #44: 'del_4q35.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S315.  Gene #45: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 15(5Q12.1) MUTATED 30 52 28 71 143 45
DEL PEAK 15(5Q12.1) WILD-TYPE 13 63 1 16 26 13

Figure S315.  Get High-res Image Gene #45: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S316.  Gene #45: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 15(5Q12.1) MUTATED 78 78 41 71
DEL PEAK 15(5Q12.1) WILD-TYPE 12 17 16 54

Figure S316.  Get High-res Image Gene #45: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q12.1' versus 'MRNASEQ_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.0027

Table S317.  Gene #45: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 15(5Q12.1) MUTATED 72 125 119 50
DEL PEAK 15(5Q12.1) WILD-TYPE 34 25 40 33

Figure S317.  Get High-res Image Gene #45: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00132 (Fisher's exact test), Q value = 0.0044

Table S318.  Gene #45: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 15(5Q12.1) MUTATED 131 153 82
DEL PEAK 15(5Q12.1) WILD-TYPE 47 36 49

Figure S318.  Get High-res Image Gene #45: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00035

Table S319.  Gene #45: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 15(5Q12.1) MUTATED 66 82 167 38
DEL PEAK 15(5Q12.1) WILD-TYPE 23 36 32 31

Figure S319.  Get High-res Image Gene #45: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00064

Table S320.  Gene #45: 'del_5q12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 15(5Q12.1) MUTATED 47 97 35 66
DEL PEAK 15(5Q12.1) WILD-TYPE 14 18 31 26

Figure S320.  Get High-res Image Gene #45: 'del_5q12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S321.  Gene #46: 'del_5q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 16(5Q31.1) MUTATED 35 56 29 75 142 49
DEL PEAK 16(5Q31.1) WILD-TYPE 8 59 0 12 27 9

Figure S321.  Get High-res Image Gene #46: 'del_5q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q31.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S322.  Gene #46: 'del_5q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 16(5Q31.1) MUTATED 85 81 43 75
DEL PEAK 16(5Q31.1) WILD-TYPE 5 14 14 50

Figure S322.  Get High-res Image Gene #46: 'del_5q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q31.1' versus 'MRNASEQ_CNMF'

P value = 0.00723 (Fisher's exact test), Q value = 0.018

Table S323.  Gene #46: 'del_5q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 16(5Q31.1) MUTATED 79 128 121 55
DEL PEAK 16(5Q31.1) WILD-TYPE 27 22 38 28

Figure S323.  Get High-res Image Gene #46: 'del_5q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00649 (Fisher's exact test), Q value = 0.017

Table S324.  Gene #46: 'del_5q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 16(5Q31.1) MUTATED 137 157 89
DEL PEAK 16(5Q31.1) WILD-TYPE 41 32 42

Figure S324.  Get High-res Image Gene #46: 'del_5q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q31.1' versus 'MIRSEQ_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.034

Table S325.  Gene #46: 'del_5q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 16(5Q31.1) MUTATED 146 76 86 60
DEL PEAK 16(5Q31.1) WILD-TYPE 38 11 38 20

Figure S325.  Get High-res Image Gene #46: 'del_5q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S326.  Gene #46: 'del_5q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 16(5Q31.1) MUTATED 69 90 171 38
DEL PEAK 16(5Q31.1) WILD-TYPE 20 28 28 31

Figure S326.  Get High-res Image Gene #46: 'del_5q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q31.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00075

Table S327.  Gene #46: 'del_5q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 16(5Q31.1) MUTATED 50 100 38 70
DEL PEAK 16(5Q31.1) WILD-TYPE 11 15 28 22

Figure S327.  Get High-res Image Gene #46: 'del_5q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0211 (Fisher's exact test), Q value = 0.044

Table S328.  Gene #46: 'del_5q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
DEL PEAK 16(5Q31.1) MUTATED 31 153 74
DEL PEAK 16(5Q31.1) WILD-TYPE 6 35 35

Figure S328.  Get High-res Image Gene #46: 'del_5q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 4e-04

Table S329.  Gene #47: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 17(6P25.3) MUTATED 14 24 13 14 62 7
DEL PEAK 17(6P25.3) WILD-TYPE 29 91 16 73 107 51

Figure S329.  Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S330.  Gene #47: 'del_6p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 17(6P25.3) MUTATED 17 45 18 24
DEL PEAK 17(6P25.3) WILD-TYPE 73 50 39 101

Figure S330.  Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S331.  Gene #47: 'del_6p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 17(6P25.3) MUTATED 28 63 23 19
DEL PEAK 17(6P25.3) WILD-TYPE 78 87 136 64

Figure S331.  Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S332.  Gene #47: 'del_6p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 17(6P25.3) MUTATED 37 78 18
DEL PEAK 17(6P25.3) WILD-TYPE 141 111 113

Figure S332.  Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6p25.3' versus 'MIRSEQ_CNMF'

P value = 0.039 (Fisher's exact test), Q value = 0.074

Table S333.  Gene #47: 'del_6p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 17(6P25.3) MUTATED 42 23 31 32
DEL PEAK 17(6P25.3) WILD-TYPE 142 64 93 48

Figure S333.  Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00086 (Fisher's exact test), Q value = 0.0031

Table S334.  Gene #47: 'del_6p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 17(6P25.3) MUTATED 39 32 45 12
DEL PEAK 17(6P25.3) WILD-TYPE 50 86 154 57

Figure S334.  Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'MRNA_CHIERARCHICAL'

P value = 0.00525 (Fisher's exact test), Q value = 0.014

Table S335.  Gene #48: 'del_6q26' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 18(6Q26) MUTATED 11 23 7
DEL PEAK 18(6Q26) WILD-TYPE 36 33 44

Figure S335.  Get High-res Image Gene #48: 'del_6q26' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

P value = 0.0043 (Fisher's exact test), Q value = 0.012

Table S336.  Gene #48: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 18(6Q26) MUTATED 13 21 6 19 64 12
DEL PEAK 18(6Q26) WILD-TYPE 30 94 23 68 105 46

Figure S336.  Get High-res Image Gene #48: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 0.00175 (Fisher's exact test), Q value = 0.0055

Table S337.  Gene #48: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 18(6Q26) MUTATED 21 34 24 23
DEL PEAK 18(6Q26) WILD-TYPE 69 61 33 102

Figure S337.  Get High-res Image Gene #48: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0038

Table S338.  Gene #48: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 18(6Q26) MUTATED 23 59 35 17
DEL PEAK 18(6Q26) WILD-TYPE 83 91 124 66

Figure S338.  Get High-res Image Gene #48: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00814 (Fisher's exact test), Q value = 0.02

Table S339.  Gene #48: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 18(6Q26) MUTATED 39 66 29
DEL PEAK 18(6Q26) WILD-TYPE 139 123 102

Figure S339.  Get High-res Image Gene #48: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 0.0278 (Fisher's exact test), Q value = 0.055

Table S340.  Gene #48: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 18(6Q26) MUTATED 57 22 22 27
DEL PEAK 18(6Q26) WILD-TYPE 127 65 102 53

Figure S340.  Get High-res Image Gene #48: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0027

Table S341.  Gene #48: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 18(6Q26) MUTATED 13 33 7 35
DEL PEAK 18(6Q26) WILD-TYPE 48 82 59 57

Figure S341.  Get High-res Image Gene #48: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0439 (Fisher's exact test), Q value = 0.082

Table S342.  Gene #48: 'del_6q26' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
DEL PEAK 18(6Q26) MUTATED 9 59 20
DEL PEAK 18(6Q26) WILD-TYPE 28 129 89

Figure S342.  Get High-res Image Gene #48: 'del_6q26' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q11.22' versus 'CN_CNMF'

P value = 0.00961 (Fisher's exact test), Q value = 0.023

Table S343.  Gene #49: 'del_7q11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 19(7Q11.22) MUTATED 4 6 2 9 13 14
DEL PEAK 19(7Q11.22) WILD-TYPE 39 109 27 78 156 44

Figure S343.  Get High-res Image Gene #49: 'del_7q11.22' versus Molecular Subtype #3: 'CN_CNMF'

'del_7q11.22' versus 'MRNASEQ_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0029

Table S344.  Gene #49: 'del_7q11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 19(7Q11.22) MUTATED 6 7 28 7
DEL PEAK 19(7Q11.22) WILD-TYPE 100 143 131 76

Figure S344.  Get High-res Image Gene #49: 'del_7q11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7q11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00107 (Fisher's exact test), Q value = 0.0037

Table S345.  Gene #49: 'del_7q11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 19(7Q11.22) MUTATED 12 12 24
DEL PEAK 19(7Q11.22) WILD-TYPE 166 177 107

Figure S345.  Get High-res Image Gene #49: 'del_7q11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7q36.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0489 (Fisher's exact test), Q value = 0.089

Table S346.  Gene #50: 'del_7q36.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 20(7Q36.3) MUTATED 14 6 11
DEL PEAK 20(7Q36.3) WILD-TYPE 33 50 40

Figure S346.  Get High-res Image Gene #50: 'del_7q36.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_7q36.3' versus 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0012

Table S347.  Gene #50: 'del_7q36.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 20(7Q36.3) MUTATED 14 26 8 13 21 22
DEL PEAK 20(7Q36.3) WILD-TYPE 29 89 21 74 148 36

Figure S347.  Get High-res Image Gene #50: 'del_7q36.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_7q36.3' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00089

Table S348.  Gene #50: 'del_7q36.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 20(7Q36.3) MUTATED 25 18 49 12
DEL PEAK 20(7Q36.3) WILD-TYPE 81 132 110 71

Figure S348.  Get High-res Image Gene #50: 'del_7q36.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7q36.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00127 (Fisher's exact test), Q value = 0.0043

Table S349.  Gene #50: 'del_7q36.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 20(7Q36.3) MUTATED 44 24 36
DEL PEAK 20(7Q36.3) WILD-TYPE 134 165 95

Figure S349.  Get High-res Image Gene #50: 'del_7q36.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7q36.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00442 (Fisher's exact test), Q value = 0.012

Table S350.  Gene #50: 'del_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 20(7Q36.3) MUTATED 14 29 49 5
DEL PEAK 20(7Q36.3) WILD-TYPE 75 89 150 64

Figure S350.  Get High-res Image Gene #50: 'del_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7q36.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.002

Table S351.  Gene #50: 'del_7q36.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
DEL PEAK 20(7Q36.3) MUTATED 14 45 11
DEL PEAK 20(7Q36.3) WILD-TYPE 23 143 98

Figure S351.  Get High-res Image Gene #50: 'del_7q36.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00025

Table S352.  Gene #51: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 21(8P23.2) MUTATED 36 57 19 57 127 45
DEL PEAK 21(8P23.2) WILD-TYPE 7 58 10 30 42 13

Figure S352.  Get High-res Image Gene #51: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 0.051

Table S353.  Gene #51: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 21(8P23.2) MUTATED 62 71 43 72
DEL PEAK 21(8P23.2) WILD-TYPE 28 24 14 53

Figure S353.  Get High-res Image Gene #51: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.034

Table S354.  Gene #51: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 21(8P23.2) MUTATED 132 64 70 58
DEL PEAK 21(8P23.2) WILD-TYPE 52 23 54 22

Figure S354.  Get High-res Image Gene #51: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0154 (Fisher's exact test), Q value = 0.034

Table S355.  Gene #51: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
DEL PEAK 21(8P23.2) MUTATED 29 133 62
DEL PEAK 21(8P23.2) WILD-TYPE 8 55 47

Figure S355.  Get High-res Image Gene #51: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'MRNA_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.033

Table S356.  Gene #52: 'del_9p23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
DEL PEAK 22(9P23) MUTATED 35 29 20 17
DEL PEAK 22(9P23) WILD-TYPE 6 21 14 12

Figure S356.  Get High-res Image Gene #52: 'del_9p23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p23' versus 'MRNA_CHIERARCHICAL'

P value = 0.00163 (Fisher's exact test), Q value = 0.0052

Table S357.  Gene #52: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 22(9P23) MUTATED 40 30 31
DEL PEAK 22(9P23) WILD-TYPE 7 26 20

Figure S357.  Get High-res Image Gene #52: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S358.  Gene #52: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 22(9P23) MUTATED 33 54 25 75 105 40
DEL PEAK 22(9P23) WILD-TYPE 10 61 4 12 64 18

Figure S358.  Get High-res Image Gene #52: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 0.00217 (Fisher's exact test), Q value = 0.0067

Table S359.  Gene #52: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 22(9P23) MUTATED 74 58 37 75
DEL PEAK 22(9P23) WILD-TYPE 16 37 20 50

Figure S359.  Get High-res Image Gene #52: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00054

Table S360.  Gene #52: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 22(9P23) MUTATED 83 87 115 44
DEL PEAK 22(9P23) WILD-TYPE 23 63 44 39

Figure S360.  Get High-res Image Gene #52: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00099 (Fisher's exact test), Q value = 0.0035

Table S361.  Gene #52: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 22(9P23) MUTATED 136 112 81
DEL PEAK 22(9P23) WILD-TYPE 42 77 50

Figure S361.  Get High-res Image Gene #52: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.0032

Table S362.  Gene #52: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 22(9P23) MUTATED 132 68 74 43
DEL PEAK 22(9P23) WILD-TYPE 52 19 50 37

Figure S362.  Get High-res Image Gene #52: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00098

Table S363.  Gene #52: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 22(9P23) MUTATED 50 81 151 35
DEL PEAK 22(9P23) WILD-TYPE 39 37 48 34

Figure S363.  Get High-res Image Gene #52: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S364.  Gene #52: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 22(9P23) MUTATED 45 90 28 60
DEL PEAK 22(9P23) WILD-TYPE 16 25 38 32

Figure S364.  Get High-res Image Gene #52: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0205 (Fisher's exact test), Q value = 0.043

Table S365.  Gene #52: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
DEL PEAK 22(9P23) MUTATED 30 130 63
DEL PEAK 22(9P23) WILD-TYPE 7 58 46

Figure S365.  Get High-res Image Gene #52: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S366.  Gene #53: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 23(9P21.3) MUTATED 37 63 27 81 135 45
DEL PEAK 23(9P21.3) WILD-TYPE 6 52 2 6 34 13

Figure S366.  Get High-res Image Gene #53: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 0.00174 (Fisher's exact test), Q value = 0.0055

Table S367.  Gene #53: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 23(9P21.3) MUTATED 93 111 127 54
DEL PEAK 23(9P21.3) WILD-TYPE 13 39 32 29

Figure S367.  Get High-res Image Gene #53: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0155 (Fisher's exact test), Q value = 0.034

Table S368.  Gene #53: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 23(9P21.3) MUTATED 150 141 94
DEL PEAK 23(9P21.3) WILD-TYPE 28 48 37

Figure S368.  Get High-res Image Gene #53: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0121 (Fisher's exact test), Q value = 0.028

Table S369.  Gene #53: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 23(9P21.3) MUTATED 68 95 165 44
DEL PEAK 23(9P21.3) WILD-TYPE 21 23 34 25

Figure S369.  Get High-res Image Gene #53: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.0033

Table S370.  Gene #53: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 23(9P21.3) MUTATED 53 99 41 69
DEL PEAK 23(9P21.3) WILD-TYPE 8 16 25 23

Figure S370.  Get High-res Image Gene #53: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0373 (Fisher's exact test), Q value = 0.072

Table S371.  Gene #53: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
DEL PEAK 23(9P21.3) MUTATED 34 149 79
DEL PEAK 23(9P21.3) WILD-TYPE 3 39 30

Figure S371.  Get High-res Image Gene #53: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S372.  Gene #54: 'del_9p21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 24(9P21.1) MUTATED 28 55 25 77 102 39
DEL PEAK 24(9P21.1) WILD-TYPE 15 60 4 10 67 19

Figure S372.  Get High-res Image Gene #54: 'del_9p21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.1' versus 'MRNASEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0011

Table S373.  Gene #54: 'del_9p21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 24(9P21.1) MUTATED 83 85 111 44
DEL PEAK 24(9P21.1) WILD-TYPE 23 65 48 39

Figure S373.  Get High-res Image Gene #54: 'del_9p21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.0016

Table S374.  Gene #54: 'del_9p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 24(9P21.1) MUTATED 135 106 82
DEL PEAK 24(9P21.1) WILD-TYPE 43 83 49

Figure S374.  Get High-res Image Gene #54: 'del_9p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00918 (Fisher's exact test), Q value = 0.022

Table S375.  Gene #54: 'del_9p21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 24(9P21.1) MUTATED 51 84 140 36
DEL PEAK 24(9P21.1) WILD-TYPE 38 34 59 33

Figure S375.  Get High-res Image Gene #54: 'del_9p21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00138 (Fisher's exact test), Q value = 0.0046

Table S376.  Gene #54: 'del_9p21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 24(9P21.1) MUTATED 45 88 33 56
DEL PEAK 24(9P21.1) WILD-TYPE 16 27 33 36

Figure S376.  Get High-res Image Gene #54: 'del_9p21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9q21.11' versus 'MRNA_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0024

Table S377.  Gene #55: 'del_9q21.11' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
DEL PEAK 25(9Q21.11) MUTATED 27 13 20 15
DEL PEAK 25(9Q21.11) WILD-TYPE 14 37 14 14

Figure S377.  Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9q21.11' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00025

Table S378.  Gene #55: 'del_9q21.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 25(9Q21.11) MUTATED 31 14 30
DEL PEAK 25(9Q21.11) WILD-TYPE 16 42 21

Figure S378.  Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9q21.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S379.  Gene #55: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 25(9Q21.11) MUTATED 27 50 20 60 52 42
DEL PEAK 25(9Q21.11) WILD-TYPE 16 65 9 27 117 16

Figure S379.  Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q21.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S380.  Gene #55: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 25(9Q21.11) MUTATED 66 23 27 68
DEL PEAK 25(9Q21.11) WILD-TYPE 24 72 30 57

Figure S380.  Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q21.11' versus 'RPPA_CHIERARCHICAL'

P value = 0.0219 (Fisher's exact test), Q value = 0.045

Table S381.  Gene #55: 'del_9q21.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 79 67 62 60 30 28
DEL PEAK 25(9Q21.11) MUTATED 31 29 41 35 16 15
DEL PEAK 25(9Q21.11) WILD-TYPE 48 38 21 25 14 13

Figure S381.  Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9q21.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S382.  Gene #55: 'del_9q21.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 25(9Q21.11) MUTATED 68 36 104 41
DEL PEAK 25(9Q21.11) WILD-TYPE 38 114 55 42

Figure S382.  Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9q21.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S383.  Gene #55: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 25(9Q21.11) MUTATED 125 46 78
DEL PEAK 25(9Q21.11) WILD-TYPE 53 143 53

Figure S383.  Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S384.  Gene #55: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 25(9Q21.11) MUTATED 85 60 69 23
DEL PEAK 25(9Q21.11) WILD-TYPE 99 27 55 57

Figure S384.  Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9q21.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S385.  Gene #55: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 25(9Q21.11) MUTATED 23 54 129 31
DEL PEAK 25(9Q21.11) WILD-TYPE 66 64 70 38

Figure S385.  Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00317 (Fisher's exact test), Q value = 0.0091

Table S386.  Gene #55: 'del_9q21.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 25(9Q21.11) MUTATED 42 61 24 46
DEL PEAK 25(9Q21.11) WILD-TYPE 19 54 42 46

Figure S386.  Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9q21.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0151 (Fisher's exact test), Q value = 0.034

Table S387.  Gene #55: 'del_9q21.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
DEL PEAK 25(9Q21.11) MUTATED 27 96 50
DEL PEAK 25(9Q21.11) WILD-TYPE 10 92 59

Figure S387.  Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S388.  Gene #56: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 26(10P15.3) MUTATED 21 34 17 27 103 26
DEL PEAK 26(10P15.3) WILD-TYPE 22 81 12 60 66 32

Figure S388.  Get High-res Image Gene #56: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00025

Table S389.  Gene #56: 'del_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 26(10P15.3) MUTATED 34 60 35 42
DEL PEAK 26(10P15.3) WILD-TYPE 56 35 22 83

Figure S389.  Get High-res Image Gene #56: 'del_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S390.  Gene #56: 'del_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 26(10P15.3) MUTATED 37 95 69 26
DEL PEAK 26(10P15.3) WILD-TYPE 69 55 90 57

Figure S390.  Get High-res Image Gene #56: 'del_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.0012

Table S391.  Gene #56: 'del_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 26(10P15.3) MUTATED 71 108 48
DEL PEAK 26(10P15.3) WILD-TYPE 107 81 83

Figure S391.  Get High-res Image Gene #56: 'del_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S392.  Gene #56: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 26(10P15.3) MUTATED 96 40 35 50
DEL PEAK 26(10P15.3) WILD-TYPE 88 47 89 30

Figure S392.  Get High-res Image Gene #56: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10p15.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S393.  Gene #56: 'del_10p15.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 26(10P15.3) MUTATED 63 45 97 16
DEL PEAK 26(10P15.3) WILD-TYPE 26 73 102 53

Figure S393.  Get High-res Image Gene #56: 'del_10p15.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00025

Table S394.  Gene #56: 'del_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 26(10P15.3) MUTATED 26 63 14 49
DEL PEAK 26(10P15.3) WILD-TYPE 35 52 52 43

Figure S394.  Get High-res Image Gene #56: 'del_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10p15.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0447 (Fisher's exact test), Q value = 0.083

Table S395.  Gene #56: 'del_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
DEL PEAK 26(10P15.3) MUTATED 18 95 39
DEL PEAK 26(10P15.3) WILD-TYPE 19 93 70

Figure S395.  Get High-res Image Gene #56: 'del_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S396.  Gene #57: 'del_10p15.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 27(10P15.1) MUTATED 17 29 16 27 99 23
DEL PEAK 27(10P15.1) WILD-TYPE 26 86 13 60 70 35

Figure S396.  Get High-res Image Gene #57: 'del_10p15.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_10p15.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S397.  Gene #57: 'del_10p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 27(10P15.1) MUTATED 31 57 34 35
DEL PEAK 27(10P15.1) WILD-TYPE 59 38 23 90

Figure S397.  Get High-res Image Gene #57: 'del_10p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10p15.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S398.  Gene #57: 'del_10p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 27(10P15.1) MUTATED 34 92 63 21
DEL PEAK 27(10P15.1) WILD-TYPE 72 58 96 62

Figure S398.  Get High-res Image Gene #57: 'del_10p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10p15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 4e-04

Table S399.  Gene #57: 'del_10p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 27(10P15.1) MUTATED 62 103 45
DEL PEAK 27(10P15.1) WILD-TYPE 116 86 86

Figure S399.  Get High-res Image Gene #57: 'del_10p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S400.  Gene #57: 'del_10p15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 27(10P15.1) MUTATED 85 36 31 52
DEL PEAK 27(10P15.1) WILD-TYPE 99 51 93 28

Figure S400.  Get High-res Image Gene #57: 'del_10p15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10p15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S401.  Gene #57: 'del_10p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 27(10P15.1) MUTATED 62 39 89 14
DEL PEAK 27(10P15.1) WILD-TYPE 27 79 110 55

Figure S401.  Get High-res Image Gene #57: 'del_10p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0016

Table S402.  Gene #57: 'del_10p15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 27(10P15.1) MUTATED 23 56 13 45
DEL PEAK 27(10P15.1) WILD-TYPE 38 59 53 47

Figure S402.  Get High-res Image Gene #57: 'del_10p15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MRNA_CNMF'

P value = 0.00975 (Fisher's exact test), Q value = 0.024

Table S403.  Gene #58: 'del_10q23.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
DEL PEAK 28(10Q23.31) MUTATED 17 36 15 13
DEL PEAK 28(10Q23.31) WILD-TYPE 24 14 19 16

Figure S403.  Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q23.31' versus 'MRNA_CHIERARCHICAL'

P value = 0.00116 (Fisher's exact test), Q value = 0.004

Table S404.  Gene #58: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 28(10Q23.31) MUTATED 17 40 24
DEL PEAK 28(10Q23.31) WILD-TYPE 30 16 27

Figure S404.  Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S405.  Gene #58: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 28(10Q23.31) MUTATED 26 39 13 41 127 22
DEL PEAK 28(10Q23.31) WILD-TYPE 17 76 16 46 42 36

Figure S405.  Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S406.  Gene #58: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 28(10Q23.31) MUTATED 43 69 38 48
DEL PEAK 28(10Q23.31) WILD-TYPE 47 26 19 77

Figure S406.  Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0425 (Fisher's exact test), Q value = 0.08

Table S407.  Gene #58: 'del_10q23.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 79 67 62 60 30 28
DEL PEAK 28(10Q23.31) MUTATED 39 34 36 40 10 12
DEL PEAK 28(10Q23.31) WILD-TYPE 40 33 26 20 20 16

Figure S407.  Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S408.  Gene #58: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 28(10Q23.31) MUTATED 46 114 72 35
DEL PEAK 28(10Q23.31) WILD-TYPE 60 36 87 48

Figure S408.  Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S409.  Gene #58: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 28(10Q23.31) MUTATED 78 135 54
DEL PEAK 28(10Q23.31) WILD-TYPE 100 54 77

Figure S409.  Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0011

Table S410.  Gene #58: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 28(10Q23.31) MUTATED 100 49 49 56
DEL PEAK 28(10Q23.31) WILD-TYPE 84 38 75 24

Figure S410.  Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S411.  Gene #58: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 28(10Q23.31) MUTATED 64 51 112 27
DEL PEAK 28(10Q23.31) WILD-TYPE 25 67 87 42

Figure S411.  Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 3e-04

Table S412.  Gene #58: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 28(10Q23.31) MUTATED 28 73 20 58
DEL PEAK 28(10Q23.31) WILD-TYPE 33 42 46 34

Figure S412.  Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.026

Table S413.  Gene #58: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
DEL PEAK 28(10Q23.31) MUTATED 20 113 46
DEL PEAK 28(10Q23.31) WILD-TYPE 17 75 63

Figure S413.  Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'MRNA_CNMF'

P value = 0.00223 (Fisher's exact test), Q value = 0.0068

Table S414.  Gene #59: 'del_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
DEL PEAK 29(11P15.5) MUTATED 29 19 12 18
DEL PEAK 29(11P15.5) WILD-TYPE 12 31 22 11

Figure S414.  Get High-res Image Gene #59: 'del_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11p15.5' versus 'MRNA_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.026

Table S415.  Gene #59: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 29(11P15.5) MUTATED 32 22 24
DEL PEAK 29(11P15.5) WILD-TYPE 15 34 27

Figure S415.  Get High-res Image Gene #59: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S416.  Gene #59: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 29(11P15.5) MUTATED 31 30 13 53 79 39
DEL PEAK 29(11P15.5) WILD-TYPE 12 85 16 34 90 19

Figure S416.  Get High-res Image Gene #59: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00072

Table S417.  Gene #59: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 29(11P15.5) MUTATED 60 43 27 46
DEL PEAK 29(11P15.5) WILD-TYPE 30 52 30 79

Figure S417.  Get High-res Image Gene #59: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11p15.5' versus 'RPPA_CHIERARCHICAL'

P value = 0.00855 (Fisher's exact test), Q value = 0.021

Table S418.  Gene #59: 'del_11p15.5' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 79 67 62 60 30 28
DEL PEAK 29(11P15.5) MUTATED 35 28 41 34 15 8
DEL PEAK 29(11P15.5) WILD-TYPE 44 39 21 26 15 20

Figure S418.  Get High-res Image Gene #59: 'del_11p15.5' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 0.00795 (Fisher's exact test), Q value = 0.02

Table S419.  Gene #59: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 29(11P15.5) MUTATED 59 66 89 30
DEL PEAK 29(11P15.5) WILD-TYPE 47 84 70 53

Figure S419.  Get High-res Image Gene #59: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0027

Table S420.  Gene #59: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 29(11P15.5) MUTATED 110 45 53 28
DEL PEAK 29(11P15.5) WILD-TYPE 74 42 71 52

Figure S420.  Get High-res Image Gene #59: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00288 (Fisher's exact test), Q value = 0.0083

Table S421.  Gene #59: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 29(11P15.5) MUTATED 35 62 19 48
DEL PEAK 29(11P15.5) WILD-TYPE 26 53 47 44

Figure S421.  Get High-res Image Gene #59: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11q22.1' versus 'CN_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0024

Table S422.  Gene #60: 'del_11q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 30(11Q22.1) MUTATED 10 27 11 19 68 28
DEL PEAK 30(11Q22.1) WILD-TYPE 33 88 18 68 101 30

Figure S422.  Get High-res Image Gene #60: 'del_11q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q22.1' versus 'METHLYATION_CNMF'

P value = 0.00175 (Fisher's exact test), Q value = 0.0055

Table S423.  Gene #60: 'del_11q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 30(11Q22.1) MUTATED 36 39 25 27
DEL PEAK 30(11Q22.1) WILD-TYPE 54 56 32 98

Figure S423.  Get High-res Image Gene #60: 'del_11q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q22.1' versus 'MRNASEQ_CNMF'

P value = 0.0231 (Fisher's exact test), Q value = 0.047

Table S424.  Gene #60: 'del_11q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 30(11Q22.1) MUTATED 31 61 52 18
DEL PEAK 30(11Q22.1) WILD-TYPE 75 89 107 65

Figure S424.  Get High-res Image Gene #60: 'del_11q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0296 (Fisher's exact test), Q value = 0.058

Table S425.  Gene #60: 'del_11q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 30(11Q22.1) MUTATED 49 75 38
DEL PEAK 30(11Q22.1) WILD-TYPE 129 114 93

Figure S425.  Get High-res Image Gene #60: 'del_11q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0194 (Fisher's exact test), Q value = 0.041

Table S426.  Gene #60: 'del_11q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 30(11Q22.1) MUTATED 39 40 64 14
DEL PEAK 30(11Q22.1) WILD-TYPE 50 78 135 55

Figure S426.  Get High-res Image Gene #60: 'del_11q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11q25' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00059

Table S427.  Gene #61: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 31(11Q25) MUTATED 8 33 13 23 80 27
DEL PEAK 31(11Q25) WILD-TYPE 35 82 16 64 89 31

Figure S427.  Get High-res Image Gene #61: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q25' versus 'METHLYATION_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.036

Table S428.  Gene #61: 'del_11q25' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 31(11Q25) MUTATED 32 39 30 36
DEL PEAK 31(11Q25) WILD-TYPE 58 56 27 89

Figure S428.  Get High-res Image Gene #61: 'del_11q25' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q25' versus 'MRNASEQ_CNMF'

P value = 0.0352 (Fisher's exact test), Q value = 0.068

Table S429.  Gene #61: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 31(11Q25) MUTATED 33 65 63 22
DEL PEAK 31(11Q25) WILD-TYPE 73 85 96 61

Figure S429.  Get High-res Image Gene #61: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q12.11' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S430.  Gene #63: 'del_13q12.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 33(13Q12.11) MUTATED 34 57 14 71 111 44
DEL PEAK 33(13Q12.11) WILD-TYPE 9 58 15 16 58 14

Figure S430.  Get High-res Image Gene #63: 'del_13q12.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q12.11' versus 'METHLYATION_CNMF'

P value = 0.0409 (Fisher's exact test), Q value = 0.078

Table S431.  Gene #63: 'del_13q12.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 33(13Q12.11) MUTATED 64 69 37 70
DEL PEAK 33(13Q12.11) WILD-TYPE 26 26 20 55

Figure S431.  Get High-res Image Gene #63: 'del_13q12.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q12.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0123 (Fisher's exact test), Q value = 0.028

Table S432.  Gene #63: 'del_13q12.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
DEL PEAK 33(13Q12.11) MUTATED 21 138 64
DEL PEAK 33(13Q12.11) WILD-TYPE 16 50 45

Figure S432.  Get High-res Image Gene #63: 'del_13q12.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S433.  Gene #64: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 34(13Q14.2) MUTATED 34 62 13 73 118 44
DEL PEAK 34(13Q14.2) WILD-TYPE 9 53 16 14 51 14

Figure S433.  Get High-res Image Gene #64: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 0.0254 (Fisher's exact test), Q value = 0.051

Table S434.  Gene #64: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 34(13Q14.2) MUTATED 65 72 39 72
DEL PEAK 34(13Q14.2) WILD-TYPE 25 23 18 53

Figure S434.  Get High-res Image Gene #64: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.033

Table S435.  Gene #64: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 34(13Q14.2) MUTATED 42 87 35 67
DEL PEAK 34(13Q14.2) WILD-TYPE 19 28 31 25

Figure S435.  Get High-res Image Gene #64: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_14q11.2' versus 'MRNA_CNMF'

P value = 0.00524 (Fisher's exact test), Q value = 0.014

Table S436.  Gene #65: 'del_14q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
DEL PEAK 35(14Q11.2) MUTATED 5 21 14 12
DEL PEAK 35(14Q11.2) WILD-TYPE 36 29 20 17

Figure S436.  Get High-res Image Gene #65: 'del_14q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0335 (Fisher's exact test), Q value = 0.065

Table S437.  Gene #65: 'del_14q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 35(14Q11.2) MUTATED 9 22 21
DEL PEAK 35(14Q11.2) WILD-TYPE 38 34 30

Figure S437.  Get High-res Image Gene #65: 'del_14q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q11.2' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00035

Table S438.  Gene #65: 'del_14q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 35(14Q11.2) MUTATED 5 29 8 37 67 29
DEL PEAK 35(14Q11.2) WILD-TYPE 38 86 21 50 102 29

Figure S438.  Get High-res Image Gene #65: 'del_14q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q11.2' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00045

Table S439.  Gene #65: 'del_14q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 35(14Q11.2) MUTATED 22 56 73 22
DEL PEAK 35(14Q11.2) WILD-TYPE 84 94 86 61

Figure S439.  Get High-res Image Gene #65: 'del_14q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00075

Table S440.  Gene #65: 'del_14q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 35(14Q11.2) MUTATED 43 69 61
DEL PEAK 35(14Q11.2) WILD-TYPE 135 120 70

Figure S440.  Get High-res Image Gene #65: 'del_14q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00995 (Fisher's exact test), Q value = 0.024

Table S441.  Gene #65: 'del_14q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 35(14Q11.2) MUTATED 42 42 67 15
DEL PEAK 35(14Q11.2) WILD-TYPE 47 76 132 54

Figure S441.  Get High-res Image Gene #65: 'del_14q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00325 (Fisher's exact test), Q value = 0.0092

Table S442.  Gene #65: 'del_14q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 35(14Q11.2) MUTATED 11 52 22 35
DEL PEAK 35(14Q11.2) WILD-TYPE 50 63 44 57

Figure S442.  Get High-res Image Gene #65: 'del_14q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_14q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0024 (Fisher's exact test), Q value = 0.0072

Table S443.  Gene #65: 'del_14q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
DEL PEAK 35(14Q11.2) MUTATED 6 81 33
DEL PEAK 35(14Q11.2) WILD-TYPE 31 107 76

Figure S443.  Get High-res Image Gene #65: 'del_14q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S444.  Gene #66: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 36(15Q11.2) MUTATED 27 39 6 16 52 27
DEL PEAK 36(15Q11.2) WILD-TYPE 16 76 23 71 117 31

Figure S444.  Get High-res Image Gene #66: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q11.2' versus 'MIRSEQ_CNMF'

P value = 0.0171 (Fisher's exact test), Q value = 0.037

Table S445.  Gene #66: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 36(15Q11.2) MUTATED 76 30 32 21
DEL PEAK 36(15Q11.2) WILD-TYPE 108 57 92 59

Figure S445.  Get High-res Image Gene #66: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q21.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S446.  Gene #67: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 37(15Q21.1) MUTATED 26 35 8 15 55 30
DEL PEAK 37(15Q21.1) WILD-TYPE 17 80 21 72 114 28

Figure S446.  Get High-res Image Gene #67: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q21.1' versus 'MIRSEQ_CNMF'

P value = 0.00128 (Fisher's exact test), Q value = 0.0043

Table S447.  Gene #67: 'del_15q21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 37(15Q21.1) MUTATED 77 34 28 21
DEL PEAK 37(15Q21.1) WILD-TYPE 107 53 96 59

Figure S447.  Get High-res Image Gene #67: 'del_15q21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0283 (Fisher's exact test), Q value = 0.056

Table S448.  Gene #67: 'del_15q21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 37(15Q21.1) MUTATED 19 41 12 36
DEL PEAK 37(15Q21.1) WILD-TYPE 42 74 54 56

Figure S448.  Get High-res Image Gene #67: 'del_15q21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16p13.3' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.001

Table S449.  Gene #68: 'del_16p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 38(16P13.3) MUTATED 14 26 11 32 70 34
DEL PEAK 38(16P13.3) WILD-TYPE 29 89 18 55 99 24

Figure S449.  Get High-res Image Gene #68: 'del_16p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_16p13.3' versus 'METHLYATION_CNMF'

P value = 0.00979 (Fisher's exact test), Q value = 0.024

Table S450.  Gene #68: 'del_16p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 38(16P13.3) MUTATED 43 34 28 36
DEL PEAK 38(16P13.3) WILD-TYPE 47 61 29 89

Figure S450.  Get High-res Image Gene #68: 'del_16p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16p13.3' versus 'MIRSEQ_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.038

Table S451.  Gene #68: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 38(16P13.3) MUTATED 76 38 32 31
DEL PEAK 38(16P13.3) WILD-TYPE 108 49 92 49

Figure S451.  Get High-res Image Gene #68: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00232 (Fisher's exact test), Q value = 0.007

Table S452.  Gene #68: 'del_16p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 38(16P13.3) MUTATED 25 51 12 38
DEL PEAK 38(16P13.3) WILD-TYPE 36 64 54 54

Figure S452.  Get High-res Image Gene #68: 'del_16p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 0.0404 (Fisher's exact test), Q value = 0.077

Table S453.  Gene #69: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 39(16Q23.1) MUTATED 16 34 12 40 82 26
DEL PEAK 39(16Q23.1) WILD-TYPE 27 81 17 47 87 32

Figure S453.  Get High-res Image Gene #69: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q23.1' versus 'RPPA_CNMF'

P value = 0.007 (Fisher's exact test), Q value = 0.018

Table S454.  Gene #69: 'del_16q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
DEL PEAK 39(16Q23.1) MUTATED 43 41 50 7
DEL PEAK 39(16Q23.1) WILD-TYPE 62 68 36 19

Figure S454.  Get High-res Image Gene #69: 'del_16q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 0.0456 (Fisher's exact test), Q value = 0.084

Table S455.  Gene #69: 'del_16q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 39(16Q23.1) MUTATED 37 70 74 27
DEL PEAK 39(16Q23.1) WILD-TYPE 69 80 85 56

Figure S455.  Get High-res Image Gene #69: 'del_16q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0376 (Fisher's exact test), Q value = 0.072

Table S456.  Gene #69: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 39(16Q23.1) MUTATED 61 88 59
DEL PEAK 39(16Q23.1) WILD-TYPE 117 101 72

Figure S456.  Get High-res Image Gene #69: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 0.00463 (Fisher's exact test), Q value = 0.012

Table S457.  Gene #69: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 39(16Q23.1) MUTATED 80 46 37 38
DEL PEAK 39(16Q23.1) WILD-TYPE 104 41 87 42

Figure S457.  Get High-res Image Gene #69: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.03

Table S458.  Gene #69: 'del_16q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 39(16Q23.1) MUTATED 21 59 19 42
DEL PEAK 39(16Q23.1) WILD-TYPE 40 56 47 50

Figure S458.  Get High-res Image Gene #69: 'del_16q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-04 (Fisher's exact test), Q value = 0.0032

Table S459.  Gene #69: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
DEL PEAK 39(16Q23.1) MUTATED 10 96 35
DEL PEAK 39(16Q23.1) WILD-TYPE 27 92 74

Figure S459.  Get High-res Image Gene #69: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S460.  Gene #70: 'del_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 40(17P11.2) MUTATED 31 38 14 63 93 33
DEL PEAK 40(17P11.2) WILD-TYPE 12 77 15 24 76 25

Figure S460.  Get High-res Image Gene #70: 'del_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0161 (Fisher's exact test), Q value = 0.035

Table S461.  Gene #70: 'del_17p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 40(17P11.2) MUTATED 112 92 67
DEL PEAK 40(17P11.2) WILD-TYPE 66 97 64

Figure S461.  Get High-res Image Gene #70: 'del_17p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0256 (Fisher's exact test), Q value = 0.052

Table S462.  Gene #70: 'del_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 40(17P11.2) MUTATED 42 67 122 30
DEL PEAK 40(17P11.2) WILD-TYPE 47 51 77 39

Figure S462.  Get High-res Image Gene #70: 'del_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.03

Table S463.  Gene #70: 'del_17p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 40(17P11.2) MUTATED 31 60 28 62
DEL PEAK 40(17P11.2) WILD-TYPE 30 55 38 30

Figure S463.  Get High-res Image Gene #70: 'del_17p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17q11.2' versus 'MRNA_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0016

Table S464.  Gene #71: 'del_17q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
DEL PEAK 41(17Q11.2) MUTATED 20 5 11 7
DEL PEAK 41(17Q11.2) WILD-TYPE 21 45 23 22

Figure S464.  Get High-res Image Gene #71: 'del_17q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00075

Table S465.  Gene #71: 'del_17q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 41(17Q11.2) MUTATED 21 5 17
DEL PEAK 41(17Q11.2) WILD-TYPE 26 51 34

Figure S465.  Get High-res Image Gene #71: 'del_17q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S466.  Gene #71: 'del_17q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 41(17Q11.2) MUTATED 22 28 11 34 17 20
DEL PEAK 41(17Q11.2) WILD-TYPE 21 87 18 53 152 38

Figure S466.  Get High-res Image Gene #71: 'del_17q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_17q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S467.  Gene #71: 'del_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 41(17Q11.2) MUTATED 34 9 11 38
DEL PEAK 41(17Q11.2) WILD-TYPE 56 86 46 87

Figure S467.  Get High-res Image Gene #71: 'del_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17q11.2' versus 'RPPA_CNMF'

P value = 0.0052 (Fisher's exact test), Q value = 0.014

Table S468.  Gene #71: 'del_17q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
DEL PEAK 41(17Q11.2) MUTATED 29 36 11 9
DEL PEAK 41(17Q11.2) WILD-TYPE 76 73 75 17

Figure S468.  Get High-res Image Gene #71: 'del_17q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_17q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00672 (Fisher's exact test), Q value = 0.017

Table S469.  Gene #71: 'del_17q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 79 67 62 60 30 28
DEL PEAK 41(17Q11.2) MUTATED 21 11 28 11 7 7
DEL PEAK 41(17Q11.2) WILD-TYPE 58 56 34 49 23 21

Figure S469.  Get High-res Image Gene #71: 'del_17q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_17q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S470.  Gene #71: 'del_17q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 41(17Q11.2) MUTATED 40 13 52 26
DEL PEAK 41(17Q11.2) WILD-TYPE 66 137 107 57

Figure S470.  Get High-res Image Gene #71: 'del_17q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S471.  Gene #71: 'del_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 41(17Q11.2) MUTATED 74 19 38
DEL PEAK 41(17Q11.2) WILD-TYPE 104 170 93

Figure S471.  Get High-res Image Gene #71: 'del_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00135 (Fisher's exact test), Q value = 0.0045

Table S472.  Gene #71: 'del_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 41(17Q11.2) MUTATED 12 27 64 25
DEL PEAK 41(17Q11.2) WILD-TYPE 77 91 135 44

Figure S472.  Get High-res Image Gene #71: 'del_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17q25.3' versus 'MRNA_CNMF'

P value = 0.0275 (Fisher's exact test), Q value = 0.055

Table S473.  Gene #72: 'del_17q25.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
DEL PEAK 42(17Q25.3) MUTATED 14 5 8 4
DEL PEAK 42(17Q25.3) WILD-TYPE 27 45 26 25

Figure S473.  Get High-res Image Gene #72: 'del_17q25.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17q25.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.026

Table S474.  Gene #72: 'del_17q25.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 42(17Q25.3) MUTATED 15 5 11
DEL PEAK 42(17Q25.3) WILD-TYPE 32 51 40

Figure S474.  Get High-res Image Gene #72: 'del_17q25.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17q25.3' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S475.  Gene #72: 'del_17q25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 42(17Q25.3) MUTATED 14 20 7 32 16 13
DEL PEAK 42(17Q25.3) WILD-TYPE 29 95 22 55 153 45

Figure S475.  Get High-res Image Gene #72: 'del_17q25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_17q25.3' versus 'MRNASEQ_CNMF'

P value = 0.00307 (Fisher's exact test), Q value = 0.0088

Table S476.  Gene #72: 'del_17q25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 42(17Q25.3) MUTATED 32 18 37 15
DEL PEAK 42(17Q25.3) WILD-TYPE 74 132 122 68

Figure S476.  Get High-res Image Gene #72: 'del_17q25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17q25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00127 (Fisher's exact test), Q value = 0.0043

Table S477.  Gene #72: 'del_17q25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 42(17Q25.3) MUTATED 51 25 26
DEL PEAK 42(17Q25.3) WILD-TYPE 127 164 105

Figure S477.  Get High-res Image Gene #72: 'del_17q25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17q25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.03

Table S478.  Gene #72: 'del_17q25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 42(17Q25.3) MUTATED 8 28 48 15
DEL PEAK 42(17Q25.3) WILD-TYPE 81 90 151 54

Figure S478.  Get High-res Image Gene #72: 'del_17q25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q23' versus 'CN_CNMF'

P value = 0.00154 (Fisher's exact test), Q value = 0.005

Table S479.  Gene #73: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 43(18Q23) MUTATED 31 39 15 40 80 29
DEL PEAK 43(18Q23) WILD-TYPE 12 76 14 47 89 29

Figure S479.  Get High-res Image Gene #73: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00708 (Fisher's exact test), Q value = 0.018

Table S480.  Gene #73: 'del_18q23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 43(18Q23) MUTATED 23 52 26 57
DEL PEAK 43(18Q23) WILD-TYPE 38 63 40 35

Figure S480.  Get High-res Image Gene #73: 'del_18q23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S481.  Gene #74: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 44(19P13.3) MUTATED 27 34 14 50 72 39
DEL PEAK 44(19P13.3) WILD-TYPE 16 81 15 37 97 19

Figure S481.  Get High-res Image Gene #74: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0219 (Fisher's exact test), Q value = 0.045

Table S482.  Gene #74: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 44(19P13.3) MUTATED 86 76 73
DEL PEAK 44(19P13.3) WILD-TYPE 92 113 58

Figure S482.  Get High-res Image Gene #74: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 0.0273 (Fisher's exact test), Q value = 0.055

Table S483.  Gene #74: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 44(19P13.3) MUTATED 99 45 49 31
DEL PEAK 44(19P13.3) WILD-TYPE 85 42 75 49

Figure S483.  Get High-res Image Gene #74: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00086 (Fisher's exact test), Q value = 0.0031

Table S484.  Gene #74: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 44(19P13.3) MUTATED 30 57 112 25
DEL PEAK 44(19P13.3) WILD-TYPE 59 61 87 44

Figure S484.  Get High-res Image Gene #74: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00384 (Fisher's exact test), Q value = 0.011

Table S485.  Gene #74: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 44(19P13.3) MUTATED 30 63 18 41
DEL PEAK 44(19P13.3) WILD-TYPE 31 52 48 51

Figure S485.  Get High-res Image Gene #74: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00426 (Fisher's exact test), Q value = 0.012

Table S486.  Gene #74: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
DEL PEAK 44(19P13.3) MUTATED 21 95 36
DEL PEAK 44(19P13.3) WILD-TYPE 16 93 73

Figure S486.  Get High-res Image Gene #74: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S487.  Gene #75: 'del_19q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 45(19Q13.32) MUTATED 18 13 9 22 73 14
DEL PEAK 45(19Q13.32) WILD-TYPE 25 102 20 65 96 44

Figure S487.  Get High-res Image Gene #75: 'del_19q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.32' versus 'METHLYATION_CNMF'

P value = 0.0017 (Fisher's exact test), Q value = 0.0054

Table S488.  Gene #75: 'del_19q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 45(19Q13.32) MUTATED 30 36 20 21
DEL PEAK 45(19Q13.32) WILD-TYPE 60 59 37 104

Figure S488.  Get High-res Image Gene #75: 'del_19q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.32' versus 'RPPA_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.032

Table S489.  Gene #75: 'del_19q13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
DEL PEAK 45(19Q13.32) MUTATED 33 24 37 6
DEL PEAK 45(19Q13.32) WILD-TYPE 72 85 49 20

Figure S489.  Get High-res Image Gene #75: 'del_19q13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19q13.32' versus 'MRNASEQ_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.038

Table S490.  Gene #75: 'del_19q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 45(19Q13.32) MUTATED 26 60 41 22
DEL PEAK 45(19Q13.32) WILD-TYPE 80 90 118 61

Figure S490.  Get High-res Image Gene #75: 'del_19q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00713 (Fisher's exact test), Q value = 0.018

Table S491.  Gene #75: 'del_19q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 45(19Q13.32) MUTATED 42 72 35
DEL PEAK 45(19Q13.32) WILD-TYPE 136 117 96

Figure S491.  Get High-res Image Gene #75: 'del_19q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.32' versus 'MIRSEQ_CNMF'

P value = 0.00435 (Fisher's exact test), Q value = 0.012

Table S492.  Gene #75: 'del_19q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 45(19Q13.32) MUTATED 65 26 22 28
DEL PEAK 45(19Q13.32) WILD-TYPE 119 61 102 52

Figure S492.  Get High-res Image Gene #75: 'del_19q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_21q11.2' versus 'CN_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.0032

Table S493.  Gene #76: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 46(21Q11.2) MUTATED 19 40 19 37 93 36
DEL PEAK 46(21Q11.2) WILD-TYPE 24 75 10 50 76 22

Figure S493.  Get High-res Image Gene #76: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.039

Table S494.  Gene #76: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 46(21Q11.2) MUTATED 45 56 31 48
DEL PEAK 46(21Q11.2) WILD-TYPE 45 39 26 77

Figure S494.  Get High-res Image Gene #76: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S495.  Gene #76: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 46(21Q11.2) MUTATED 106 52 41 34
DEL PEAK 46(21Q11.2) WILD-TYPE 78 35 83 46

Figure S495.  Get High-res Image Gene #76: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_21q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00025

Table S496.  Gene #76: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 46(21Q11.2) MUTATED 42 66 108 17
DEL PEAK 46(21Q11.2) WILD-TYPE 47 52 91 52

Figure S496.  Get High-res Image Gene #76: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00151 (Fisher's exact test), Q value = 0.0049

Table S497.  Gene #76: 'del_21q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 46(21Q11.2) MUTATED 29 68 19 47
DEL PEAK 46(21Q11.2) WILD-TYPE 32 47 47 45

Figure S497.  Get High-res Image Gene #76: 'del_21q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_21q22.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S498.  Gene #77: 'del_21q22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 47(21Q22.3) MUTATED 25 42 22 41 111 40
DEL PEAK 47(21Q22.3) WILD-TYPE 18 73 7 46 58 18

Figure S498.  Get High-res Image Gene #77: 'del_21q22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q22.3' versus 'METHLYATION_CNMF'

P value = 0.00399 (Fisher's exact test), Q value = 0.011

Table S499.  Gene #77: 'del_21q22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 47(21Q22.3) MUTATED 51 61 35 52
DEL PEAK 47(21Q22.3) WILD-TYPE 39 34 22 73

Figure S499.  Get High-res Image Gene #77: 'del_21q22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_21q22.3' versus 'MIRSEQ_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0022

Table S500.  Gene #77: 'del_21q22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 47(21Q22.3) MUTATED 119 55 52 43
DEL PEAK 47(21Q22.3) WILD-TYPE 65 32 72 37

Figure S500.  Get High-res Image Gene #77: 'del_21q22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_21q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.002

Table S501.  Gene #77: 'del_21q22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 47(21Q22.3) MUTATED 55 70 121 23
DEL PEAK 47(21Q22.3) WILD-TYPE 34 48 78 46

Figure S501.  Get High-res Image Gene #77: 'del_21q22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_21q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0273 (Fisher's exact test), Q value = 0.055

Table S502.  Gene #77: 'del_21q22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 47(21Q22.3) MUTATED 31 67 25 55
DEL PEAK 47(21Q22.3) WILD-TYPE 30 48 41 37

Figure S502.  Get High-res Image Gene #77: 'del_21q22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_22q11.21' versus 'CN_CNMF'

P value = 0.00776 (Fisher's exact test), Q value = 0.019

Table S503.  Gene #78: 'del_22q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 48(22Q11.21) MUTATED 7 27 0 24 27 10
DEL PEAK 48(22Q11.21) WILD-TYPE 36 88 29 63 142 48

Figure S503.  Get High-res Image Gene #78: 'del_22q11.21' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00098

Table S504.  Gene #78: 'del_22q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 48(22Q11.21) MUTATED 23 31 41
DEL PEAK 48(22Q11.21) WILD-TYPE 155 158 90

Figure S504.  Get High-res Image Gene #78: 'del_22q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MRNA_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.002

Table S505.  Gene #79: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
DEL PEAK 49(22Q13.32) MUTATED 7 7 10 16
DEL PEAK 49(22Q13.32) WILD-TYPE 34 43 24 13

Figure S505.  Get High-res Image Gene #79: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_22q13.32' versus 'MRNA_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.025

Table S506.  Gene #79: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 49(22Q13.32) MUTATED 10 9 21
DEL PEAK 49(22Q13.32) WILD-TYPE 37 47 30

Figure S506.  Get High-res Image Gene #79: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00068

Table S507.  Gene #79: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 49(22Q13.32) MUTATED 10 33 0 29 33 22
DEL PEAK 49(22Q13.32) WILD-TYPE 33 82 29 58 136 36

Figure S507.  Get High-res Image Gene #79: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.32' versus 'RPPA_CNMF'

P value = 0.0433 (Fisher's exact test), Q value = 0.081

Table S508.  Gene #79: 'del_22q13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
DEL PEAK 49(22Q13.32) MUTATED 24 36 22 2
DEL PEAK 49(22Q13.32) WILD-TYPE 81 73 64 24

Figure S508.  Get High-res Image Gene #79: 'del_22q13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00054

Table S509.  Gene #79: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 49(22Q13.32) MUTATED 28 23 59 17
DEL PEAK 49(22Q13.32) WILD-TYPE 78 127 100 66

Figure S509.  Get High-res Image Gene #79: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S510.  Gene #79: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 49(22Q13.32) MUTATED 38 30 59
DEL PEAK 49(22Q13.32) WILD-TYPE 140 159 72

Figure S510.  Get High-res Image Gene #79: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.0022

Table S511.  Gene #79: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 49(22Q13.32) MUTATED 11 37 59 10
DEL PEAK 49(22Q13.32) WILD-TYPE 78 81 140 59

Figure S511.  Get High-res Image Gene #79: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_xp22.2' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00072

Table S512.  Gene #80: 'del_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 50(XP22.2) MUTATED 12 18 9 28 72 16
DEL PEAK 50(XP22.2) WILD-TYPE 31 97 20 59 97 42

Figure S512.  Get High-res Image Gene #80: 'del_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_xp22.2' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 3e-04

Table S513.  Gene #80: 'del_xp22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 50(XP22.2) MUTATED 37 40 15 21
DEL PEAK 50(XP22.2) WILD-TYPE 53 55 42 104

Figure S513.  Get High-res Image Gene #80: 'del_xp22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xp22.2' versus 'MRNASEQ_CNMF'

P value = 0.00461 (Fisher's exact test), Q value = 0.012

Table S514.  Gene #80: 'del_xp22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 50(XP22.2) MUTATED 33 60 45 15
DEL PEAK 50(XP22.2) WILD-TYPE 73 90 114 68

Figure S514.  Get High-res Image Gene #80: 'del_xp22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_xp22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00982 (Fisher's exact test), Q value = 0.024

Table S515.  Gene #80: 'del_xp22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 50(XP22.2) MUTATED 49 73 31
DEL PEAK 50(XP22.2) WILD-TYPE 129 116 100

Figure S515.  Get High-res Image Gene #80: 'del_xp22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_xp22.2' versus 'MIRSEQ_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 0.05

Table S516.  Gene #80: 'del_xp22.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 50(XP22.2) MUTATED 55 35 28 30
DEL PEAK 50(XP22.2) WILD-TYPE 129 52 96 50

Figure S516.  Get High-res Image Gene #80: 'del_xp22.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_xp22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0014

Table S517.  Gene #80: 'del_xp22.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 50(XP22.2) MUTATED 14 45 9 36
DEL PEAK 50(XP22.2) WILD-TYPE 47 70 57 56

Figure S517.  Get High-res Image Gene #80: 'del_xp22.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_xp22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00598 (Fisher's exact test), Q value = 0.016

Table S518.  Gene #80: 'del_xp22.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
DEL PEAK 50(XP22.2) MUTATED 8 72 24
DEL PEAK 50(XP22.2) WILD-TYPE 29 116 85

Figure S518.  Get High-res Image Gene #80: 'del_xp22.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S519.  Gene #81: 'del_xp21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 51(XP21.1) MUTATED 10 14 10 27 75 15
DEL PEAK 51(XP21.1) WILD-TYPE 33 101 19 60 94 43

Figure S519.  Get High-res Image Gene #81: 'del_xp21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S520.  Gene #81: 'del_xp21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 51(XP21.1) MUTATED 36 40 18 15
DEL PEAK 51(XP21.1) WILD-TYPE 54 55 39 110

Figure S520.  Get High-res Image Gene #81: 'del_xp21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xp21.1' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 3e-04

Table S521.  Gene #81: 'del_xp21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
DEL PEAK 51(XP21.1) MUTATED 32 66 36 15
DEL PEAK 51(XP21.1) WILD-TYPE 74 84 123 68

Figure S521.  Get High-res Image Gene #81: 'del_xp21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_xp21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0025

Table S522.  Gene #81: 'del_xp21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 51(XP21.1) MUTATED 47 75 27
DEL PEAK 51(XP21.1) WILD-TYPE 131 114 104

Figure S522.  Get High-res Image Gene #81: 'del_xp21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.0047

Table S523.  Gene #81: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
DEL PEAK 51(XP21.1) MUTATED 61 31 22 32
DEL PEAK 51(XP21.1) WILD-TYPE 123 56 102 48

Figure S523.  Get High-res Image Gene #81: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_xp21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00119 (Fisher's exact test), Q value = 0.004

Table S524.  Gene #81: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 51(XP21.1) MUTATED 38 40 58 10
DEL PEAK 51(XP21.1) WILD-TYPE 51 78 141 59

Figure S524.  Get High-res Image Gene #81: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0016

Table S525.  Gene #81: 'del_xp21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
DEL PEAK 51(XP21.1) MUTATED 11 46 10 32
DEL PEAK 51(XP21.1) WILD-TYPE 50 69 56 60

Figure S525.  Get High-res Image Gene #81: 'del_xp21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_xp21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00108 (Fisher's exact test), Q value = 0.0037

Table S526.  Gene #81: 'del_xp21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
DEL PEAK 51(XP21.1) MUTATED 6 71 22
DEL PEAK 51(XP21.1) WILD-TYPE 31 117 87

Figure S526.  Get High-res Image Gene #81: 'del_xp21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp11.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S527.  Gene #82: 'del_xp11.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
DEL PEAK 52(XP11.3) MUTATED 11 13 10 26 77 12
DEL PEAK 52(XP11.3) WILD-TYPE 32 102 19 61 92 46

Figure S527.  Get High-res Image Gene #82: 'del_xp11.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_xp11.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S528.  Gene #82: 'del_xp11.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
DEL PEAK 52(XP11.3) MUTATED 34 41 21 12
DEL PEAK 52(XP11.3) WILD-TYPE 56 54 36 113

Figure S528.  Get High-res Image Gene #82: 'del_xp11.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xp11.3' versus 'RPPA_CNMF'

P value = 0.0132 (Fisher's exact test), Q value = 0.03

Table S529.  Gene #82: 'del_xp11.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
DEL PEAK 52(XP11.3) MUTATED 28 25 37 10
DEL PEAK 52(XP11.3) WILD-TYPE 77 84 49 16

Figure S529.  Get High-res Image Gene #82: 'del_xp11.3' versus Molecular Subtype #5: 'RPPA_CNMF'