Correlation between copy number variation genes (focal events) and molecular subtypes
Stomach and Esophageal carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1V40THV
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1V40THV
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 99 focal events and 10 molecular subtypes across 625 patients, 617 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • amp_1p34.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_1q21.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_2q12.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

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

  • amp_7p22.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • amp_8p23.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_8p11.21 cnv correlated to 'METHLYATION_CNMF'.

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

  • amp_9p24.1 cnv correlated to 'MIRSEQ_CNMF'.

  • amp_9p13.3 cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_10p11.22 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • amp_10q26.13 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • amp_12q15 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • amp_14q13.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • amp_18p11.32 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_19p13.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_19q13.43 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • del_1p13.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_1q44 cnv correlated to 'METHLYATION_CNMF'.

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

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

  • del_2q33.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_3p26.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_3q11.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • del_4p15.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

  • del_6q16.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_6q26 cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

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

  • del_9p23 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • del_9q21.11 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 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_10p11.21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_10q21.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

  • del_12q23.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_13q12.11 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_13q21.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_14q32.32 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_15q11.2 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

  • del_17p12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_17q24.3 cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

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

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

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

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

  • del_22q11.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

  • del_xq11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_xq21.33 cnv correlated to 'CN_CNMF',  'METHLYATION_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 99 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 617 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
amp 6p21 1 192 (31%) 433 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.0243
(0.0429) 		0.0108
(0.0208) 		0.0196
(0.0355) 		0.0205
(0.0371) 		7e-05
(0.000211) 		1e-05
(3.61e-05) 		0.00159
(0.00373) 		1e-05
(3.61e-05)
del 1p36 11 210 (34%) 415 1e-05
(3.61e-05) 		0.00034
(9e-04) 		0.0052
(0.0107) 		0.00247
(0.00553) 		0.00286
(0.00625) 		0.0234
(0.0416) 		6e-05
(0.000183) 		1e-05
(3.61e-05) 		0.00197
(0.0045) 		5e-05
(0.000155)
amp 5p15 33 228 (36%) 397 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.188
(0.249) 		0.00622
(0.0126) 		0.00135
(0.00322) 		0.00091
(0.00225) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05)
amp 11q13 3 218 (35%) 407 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.051
(0.0814) 		0.0412
(0.0682) 		0.00267
(0.00595) 		0.00217
(0.00492) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05)
del 2q22 1 126 (20%) 499 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.425
(0.492) 		0.0245
(0.0431) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05)
del 3p14 2 282 (45%) 343 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.461
(0.526) 		0.0371
(0.0622) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05)
amp 3q26 2 287 (46%) 338 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.493
(0.559) 		0.954
(0.969) 		2e-05
(6.71e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05)
amp 5p13 1 216 (35%) 409 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.944
(0.964) 		0.104
(0.15) 		0.0158
(0.0292) 		0.0327
(0.0558) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05)
amp 7p11 2 340 (54%) 285 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.796
(0.834) 		0.161
(0.219) 		0.0109
(0.0209) 		0.0395
(0.0661) 		6e-05
(0.000183) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.00014
(0.000397)
amp 8p23 1 229 (37%) 396 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.843
(0.874) 		0.687
(0.736) 		0.0141
(0.0263) 		7e-05
(0.000211) 		6e-05
(0.000183) 		0.00112
(0.00271) 		0.00015
(0.000424) 		0.00088
(0.00218)
amp 12p12 1 207 (33%) 418 1e-05
(3.61e-05) 		3e-05
(9.61e-05) 		0.528
(0.59) 		0.0864
(0.128) 		0.02
(0.0362) 		0.0291
(0.0503) 		0.0001
(0.000292) 		0.00245
(0.0055) 		0.00021
(0.000574) 		0.00054
(0.00139)
amp 14q13 3 113 (18%) 512 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.561
(0.624) 		0.123
(0.173) 		0.0327
(0.0558) 		0.00464
(0.00973) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		8e-05
(0.000237) 		1e-05
(3.61e-05)
amp 15q26 1 168 (27%) 457 1e-05
(3.61e-05) 		0.0652
(0.101) 		0.00227
(0.00512) 		0.0069
(0.0138) 		0.0661
(0.102) 		0.0446
(0.0723) 		0.00052
(0.00134) 		6e-05
(0.000183) 		0.0345
(0.0583) 		0.00017
(0.000469)
del 2q37 2 122 (20%) 503 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.566
(0.628) 		0.29
(0.354) 		0.00181
(0.00418) 		0.00149
(0.00352) 		0.00016
(0.000449) 		1e-05
(3.61e-05) 		0.027
(0.0471) 		1e-05
(3.61e-05)
del 3p26 2 250 (40%) 375 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.913
(0.935) 		0.212
(0.273) 		0.00029
(0.000776) 		3e-05
(9.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05)
del 4q22 1 298 (48%) 327 1e-05
(3.61e-05) 		0.0035
(0.00752) 		0.443
(0.511) 		0.0931
(0.136) 		0.00452
(0.00952) 		0.0293
(0.0505) 		0.00658
(0.0132) 		1e-05
(3.61e-05) 		0.00912
(0.0177) 		0.0131
(0.0246)
del 5q12 1 282 (45%) 343 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.00164
(0.00383) 		0.00269
(0.00597) 		0.319
(0.383) 		0.498
(0.562) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05)
del 8p23 2 212 (34%) 413 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.644
(0.7) 		0.0189
(0.0345) 		0.0726
(0.11) 		0.0473
(0.0763) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05)
del 10p15 3 131 (21%) 494 1e-05
(3.61e-05) 		0.00193
(0.00442) 		0.848
(0.878) 		0.804
(0.842) 		0.0428
(0.0705) 		0.0239
(0.0424) 		0.00212
(0.00482) 		1e-05
(3.61e-05) 		0.00864
(0.0169) 		3e-05
(9.61e-05)
del 10p11 21 102 (16%) 523 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.734
(0.781) 		0.928
(0.95) 		3e-05
(9.61e-05) 		2e-05
(6.71e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		8e-05
(0.000237) 		1e-05
(3.61e-05)
del 11p15 5 175 (28%) 450 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.0131
(0.0247) 		0.00531
(0.011) 		0.303
(0.368) 		0.409
(0.476) 		2e-05
(6.71e-05) 		1e-05
(3.61e-05) 		0.00024
(0.000649) 		0.00023
(0.000624)
del 13q12 11 138 (22%) 487 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.44
(0.508) 		0.121
(0.171) 		0.00663
(0.0133) 		0.0058
(0.0119) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05)
del 13q14 2 125 (20%) 500 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.639
(0.697) 		0.181
(0.241) 		0.0189
(0.0345) 		0.0211
(0.0379) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05)
del 16p13 3 178 (28%) 447 1e-05
(3.61e-05) 		0.00451
(0.00952) 		0.243
(0.305) 		0.245
(0.307) 		0.00067
(0.0017) 		0.0001
(0.000292) 		0.00193
(0.00442) 		1e-05
(3.61e-05) 		0.00133
(0.00318) 		1e-05
(3.61e-05)
del 16p13 3 148 (24%) 477 1e-05
(3.61e-05) 		0.0145
(0.027) 		0.313
(0.378) 		0.616
(0.676) 		0.00071
(0.0018) 		0.00063
(0.0016) 		0.00047
(0.00122) 		1e-05
(3.61e-05) 		0.00191
(0.0044) 		1e-05
(3.61e-05)
del 16q23 1 265 (42%) 360 1e-05
(3.61e-05) 		0.00088
(0.00218) 		0.977
(0.987) 		0.145
(0.199) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.0122
(0.0233) 		1e-05
(3.61e-05) 		0.00797
(0.0157) 		1e-05
(3.61e-05)
del 17p12 267 (43%) 358 1e-05
(3.61e-05) 		2e-05
(6.71e-05) 		0.196
(0.257) 		0.15
(0.204) 		3e-05
(9.61e-05) 		1e-05
(3.61e-05) 		0.00076
(0.00191) 		1e-05
(3.61e-05) 		0.043
(0.0705) 		1e-05
(3.61e-05)
del 19p13 3 249 (40%) 376 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.00318
(0.00689) 		0.00078
(0.00195) 		0.154
(0.211) 		0.439
(0.507) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05)
del 22q13 31 235 (38%) 390 1e-05
(3.61e-05) 		0.00245
(0.0055) 		0.682
(0.734) 		0.238
(0.302) 		0.0089
(0.0173) 		0.00127
(0.00305) 		0.0001
(0.000292) 		1e-05
(3.61e-05) 		0.0338
(0.0574) 		5e-05
(0.000155)
del xp11 3 146 (23%) 479 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.779
(0.821) 		0.314
(0.378) 		0.00869
(0.017) 		0.0229
(0.0409) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.00605
(0.0123) 		1e-05
(3.61e-05)
amp 1q21 3 249 (40%) 376 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.887
(0.912) 		0.0134
(0.0251) 		0.989
(0.996) 		0.809
(0.845) 		0.00011
(0.000317) 		1e-05
(3.61e-05) 		8e-05
(0.000237) 		2e-05
(6.71e-05)
amp 1q42 3 244 (39%) 381 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.706
(0.755) 		0.0455
(0.0738) 		0.77
(0.812) 		0.717
(0.765) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		3e-05
(9.61e-05)
amp 7p22 3 353 (56%) 272 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.999
(1.00) 		0.167
(0.226) 		0.00149
(0.00352) 		0.191
(0.252) 		2e-05
(6.71e-05) 		1e-05
(3.61e-05) 		2e-05
(6.71e-05) 		6e-05
(0.000183)
amp 13q22 1 243 (39%) 382 1e-05
(3.61e-05) 		0.00216
(0.0049) 		0.413
(0.48) 		0.26
(0.323) 		0.0276
(0.0479) 		0.0008
(0.00199) 		0.0316
(0.054) 		1e-05
(3.61e-05) 		0.118
(0.167) 		2e-05
(6.71e-05)
amp 17q12 222 (36%) 403 1e-05
(3.61e-05) 		0.00016
(0.000449) 		0.0561
(0.0883) 		0.137
(0.19) 		0.0297
(0.0511) 		0.00274
(0.00603) 		0.0215
(0.0386) 		2e-05
(6.71e-05) 		0.0549
(0.0867) 		0.00085
(0.00211)
amp 18q11 2 198 (32%) 427 1e-05
(3.61e-05) 		0.0846
(0.125) 		0.877
(0.905) 		0.269
(0.333) 		0.0397
(0.0661) 		0.00465
(0.00973) 		0.0465
(0.0752) 		0.00023
(0.000624) 		0.0332
(0.0566) 		0.00469
(0.00977)
amp 19q12 185 (30%) 440 1e-05
(3.61e-05) 		4e-05
(0.000126) 		0.00031
(0.000825) 		0.00112
(0.00271) 		0.373
(0.438) 		0.167
(0.225) 		0.0244
(0.043) 		1e-05
(3.61e-05) 		0.0924
(0.135) 		0.00017
(0.000469)
amp 20q13 2 416 (67%) 209 1e-05
(3.61e-05) 		0.0725
(0.11) 		0.294
(0.358) 		0.0242
(0.0429) 		0.00017
(0.000469) 		5e-05
(0.000155) 		0.0434
(0.071) 		1e-05
(3.61e-05) 		0.178
(0.238) 		1e-05
(3.61e-05)
amp xq28 154 (25%) 471 1e-05
(3.61e-05) 		3e-05
(9.61e-05) 		0.885
(0.911) 		0.282
(0.346) 		0.0581
(0.0904) 		0.0263
(0.046) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.00452
(0.00952) 		1e-05
(3.61e-05)
del 2q33 3 85 (14%) 540 2e-05
(6.71e-05) 		7e-05
(0.000211) 		0.822
(0.855) 		0.121
(0.172) 		0.0589
(0.0915) 		0.0274
(0.0477) 		0.00062
(0.00158) 		0.00011
(0.000317) 		0.00275
(0.00604) 		0.00132
(0.00316)
del 4p16 3 271 (43%) 354 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.519
(0.581) 		0.899
(0.923) 		0.0398
(0.0662) 		0.695
(0.744) 		2e-05
(6.71e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05)
del 4q34 3 300 (48%) 325 1e-05
(3.61e-05) 		0.00162
(0.00379) 		0.21
(0.271) 		0.336
(0.399) 		0.00785
(0.0156) 		0.00423
(0.00897) 		0.0124
(0.0236) 		1e-05
(3.61e-05) 		0.112
(0.161) 		0.00011
(0.000317)
del 7q36 3 163 (26%) 462 1e-05
(3.61e-05) 		8e-05
(0.000237) 		0.446
(0.513) 		0.325
(0.389) 		0.0397
(0.0661) 		0.227
(0.29) 		3e-05
(9.61e-05) 		1e-05
(3.61e-05) 		0.00035
(0.000924) 		0.00033
(0.000876)
del 9p21 3 334 (53%) 291 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.196
(0.257) 		0.494
(0.559) 		0.0698
(0.106) 		0.0209
(0.0376) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05)
del 10q22 3 135 (22%) 490 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.227
(0.291) 		0.185
(0.246) 		0.0771
(0.115) 		0.0482
(0.0776) 		5e-05
(0.000155) 		1e-05
(3.61e-05) 		3e-05
(9.61e-05) 		1e-05
(3.61e-05)
del 10q23 31 183 (29%) 442 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.00773
(0.0154) 		0.0546
(0.0864) 		0.275
(0.338) 		0.181
(0.241) 		2e-05
(6.71e-05) 		1e-05
(3.61e-05) 		0.0005
(0.0013) 		0.00011
(0.000317)
del 11q25 178 (28%) 447 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.156
(0.212) 		0.224
(0.287) 		0.124
(0.174) 		0.0372
(0.0623) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05)
del 18q21 2 323 (52%) 302 1e-05
(3.61e-05) 		0.00061
(0.00156) 		0.968
(0.98) 		0.182
(0.242) 		0.00467
(0.00975) 		0.00977
(0.0189) 		0.0167
(0.0309) 		2e-05
(6.71e-05) 		0.132
(0.183) 		0.0194
(0.0352)
del 21q22 13 305 (49%) 320 1e-05
(3.61e-05) 		0.0209
(0.0376) 		0.964
(0.976) 		0.992
(0.998) 		0.035
(0.059) 		0.143
(0.197) 		0.00092
(0.00226) 		1e-05
(3.61e-05) 		0.00251
(0.00561) 		0.00674
(0.0135)
del 22q11 1 230 (37%) 395 1e-05
(3.61e-05) 		0.00649
(0.0131) 		0.101
(0.146) 		0.154
(0.211) 		4e-05
(0.000126) 		4e-05
(0.000126) 		0.00111
(0.0027) 		1e-05
(3.61e-05) 		0.0898
(0.132) 		3e-05
(9.61e-05)
del xp21 1 143 (23%) 482 1e-05
(3.61e-05) 		3e-05
(9.61e-05) 		0.459
(0.524) 		0.207
(0.269) 		0.0128
(0.0242) 		0.195
(0.256) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.00655
(0.0132) 		2e-05
(6.71e-05)
amp 2q12 2 155 (25%) 470 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.458
(0.524) 		0.678
(0.731) 		0.77
(0.812) 		0.39
(0.457) 		2e-05
(6.71e-05) 		1e-05
(3.61e-05) 		0.00013
(0.000371) 		0.0002
(0.000548)
amp 6q12 141 (23%) 484 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.47
(0.535) 		0.231
(0.293) 		0.391
(0.457) 		0.203
(0.264) 		0.0101
(0.0195) 		1e-05
(3.61e-05) 		0.0011
(0.00268) 		0.00042
(0.00111)
amp 7q21 2 317 (51%) 308 1e-05
(3.61e-05) 		0.00012
(0.000343) 		0.245
(0.307) 		0.173
(0.233) 		0.686
(0.736) 		0.952
(0.969) 		0.00273
(0.00603) 		0.00155
(0.00365) 		2e-05
(6.71e-05) 		0.00545
(0.0112)
amp 8q24 21 454 (73%) 171 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.333
(0.396) 		0.148
(0.203) 		0.0839
(0.125) 		0.114
(0.162) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.00022
(6e-04) 		0.00027
(0.000728)
amp 10q26 13 119 (19%) 506 3e-05
(9.61e-05) 		0.792
(0.831) 		0.421
(0.489) 		0.243
(0.305) 		0.0154
(0.0286) 		0.0106
(0.0204) 		0.0191
(0.0348) 		0.001
(0.00245) 		0.097
(0.141) 		0.00181
(0.00418)
amp 13q12 3 216 (35%) 409 1e-05
(3.61e-05) 		0.0862
(0.127) 		0.0506
(0.0808) 		0.826
(0.858) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.00393
(0.0084) 		1e-05
(3.61e-05) 		0.523
(0.586) 		1e-05
(3.61e-05)
amp 18p11 32 178 (28%) 447 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.745
(0.791) 		0.0558
(0.088) 		0.134
(0.186) 		0.173
(0.233) 		2e-05
(6.71e-05) 		1e-05
(3.61e-05) 		0.00061
(0.00156) 		0.00028
(0.000753)
amp 19q13 43 164 (26%) 461 1e-05
(3.61e-05) 		0.0434
(0.071) 		0.0129
(0.0243) 		0.1
(0.145) 		0.81
(0.845) 		0.0878
(0.129) 		0.603
(0.666) 		4e-05
(0.000126) 		0.00173
(0.00402) 		0.00414
(0.00881)
del 1p13 2 156 (25%) 469 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.123
(0.173) 		0.137
(0.19) 		0.217
(0.279) 		0.595
(0.659) 		0.00513
(0.0106) 		1e-05
(3.61e-05) 		0.00544
(0.0112) 		0.00828
(0.0163)
del 3q26 31 63 (10%) 562 1e-05
(3.61e-05) 		0.00791
(0.0156) 		0.186
(0.247) 		0.566
(0.628) 		0.00888
(0.0173) 		0.00017
(0.000469) 		0.0932
(0.136) 		1e-05
(3.61e-05) 		0.077
(0.115) 		0.00139
(0.00331)
del 4p15 2 269 (43%) 356 1e-05
(3.61e-05) 		2e-05
(6.71e-05) 		0.651
(0.706) 		0.958
(0.972) 		0.103
(0.148) 		0.474
(0.538) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05)
del 10q21 1 112 (18%) 513 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.318
(0.383) 		0.24
(0.303) 		0.0642
(0.0991) 		0.0667
(0.102) 		0.00092
(0.00226) 		1e-05
(3.61e-05) 		0.00641
(0.013) 		3e-05
(9.61e-05)
del 12p13 1 113 (18%) 512 1e-05
(3.61e-05) 		0.0443
(0.072) 		0.369
(0.434) 		0.723
(0.769) 		4e-05
(0.000126) 		2e-05
(6.71e-05) 		0.602
(0.665) 		1e-05
(3.61e-05) 		0.448
(0.514) 		0.00319
(0.0069)
del 13q21 31 126 (20%) 499 1e-05
(3.61e-05) 		2e-05
(6.71e-05) 		0.259
(0.323) 		0.138
(0.19) 		0.178
(0.238) 		0.115
(0.164) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		6e-05
(0.000183) 		1e-05
(3.61e-05)
del 14q23 3 187 (30%) 438 1e-05
(3.61e-05) 		0.00303
(0.00659) 		0.635
(0.694) 		0.102
(0.148) 		0.00713
(0.0142) 		0.0438
(0.0715) 		0.121
(0.172) 		1e-05
(3.61e-05) 		0.124
(0.174) 		0.00046
(0.0012)
del 18q12 2 292 (47%) 333 1e-05
(3.61e-05) 		0.00176
(0.00408) 		0.956
(0.971) 		0.177
(0.237) 		0.023
(0.041) 		0.0748
(0.113) 		0.0364
(0.0612) 		0.00017
(0.000469) 		0.111
(0.159) 		0.012
(0.023)
del 19q13 11 120 (19%) 505 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.333
(0.396) 		0.66
(0.713) 		0.0793
(0.118) 		0.0572
(0.0894) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		8e-05
(0.000237) 		0.0001
(0.000292)
del 21q11 2 290 (46%) 335 1e-05
(3.61e-05) 		0.0108
(0.0207) 		0.935
(0.957) 		0.634
(0.694) 		0.204
(0.265) 		0.215
(0.277) 		0.00012
(0.000343) 		1e-05
(3.61e-05) 		0.00268
(0.00596) 		0.00503
(0.0104)
del xp22 2 150 (24%) 475 1e-05
(3.61e-05) 		2e-05
(6.71e-05) 		0.311
(0.376) 		0.125
(0.175) 		0.043
(0.0705) 		0.203
(0.264) 		1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.0503
(0.0805) 		0.00074
(0.00187)
del xq21 33 96 (15%) 529 1e-05
(3.61e-05) 		0.0079
(0.0156) 		0.248
(0.31) 		0.271
(0.335) 		0.242
(0.305) 		0.275
(0.338) 		0.0123
(0.0234) 		9e-05
(0.000266) 		0.0462
(0.0748) 		0.00958
(0.0186)
amp 1p36 22 101 (16%) 524 1e-05
(3.61e-05) 		0.00543
(0.0112) 		0.462
(0.527) 		0.385
(0.452) 		0.45
(0.516) 		0.191
(0.251) 		0.0262
(0.0459) 		0.00018
(0.000495) 		0.189
(0.25) 		0.00062
(0.00158)
amp 1p34 2 95 (15%) 530 1e-05
(3.61e-05) 		0.00461
(0.00969) 		0.64
(0.697) 		0.984
(0.992) 		0.689
(0.738) 		0.815
(0.849) 		0.0403
(0.0669) 		0.0146
(0.0272) 		0.0613
(0.095) 		0.00399
(0.00851)
amp 6q21 111 (18%) 514 1e-05
(3.61e-05) 		0.00211
(0.00481) 		0.0571
(0.0893) 		0.494
(0.559) 		0.117
(0.167) 		0.0191
(0.0348) 		0.233
(0.296) 		1e-05
(3.61e-05) 		0.183
(0.243) 		0.0003
(0.000801)
amp 19p13 2 79 (13%) 546 1e-05
(3.61e-05) 		0.0017
(0.00396) 		0.755
(0.8) 		0.766
(0.809) 		0.317
(0.382) 		0.355
(0.419) 		0.417
(0.484) 		0.0407
(0.0674) 		0.0441
(0.0718) 		0.0425
(0.0701)
del 6p25 3 188 (30%) 437 1e-05
(3.61e-05) 		0.00014
(0.000397) 		0.413
(0.48) 		0.107
(0.154) 		0.105
(0.151) 		0.328
(0.392) 		3e-05
(9.61e-05) 		1e-05
(3.61e-05) 		0.0511
(0.0814) 		0.00321
(0.00692)
del 6q16 3 147 (24%) 478 1e-05
(3.61e-05) 		0.0259
(0.0456) 		0.517
(0.58) 		0.611
(0.672) 		0.467
(0.531) 		0.605
(0.666) 		0.0336
(0.057) 		0.00127
(0.00305) 		0.11
(0.159) 		0.0284
(0.0492)
del 7q31 1 127 (20%) 498 1e-05
(3.61e-05) 		0.00416
(0.00884) 		0.546
(0.609) 		0.576
(0.639) 		0.0735
(0.111) 		0.458
(0.524) 		0.0061
(0.0124) 		0.00108
(0.00264) 		0.132
(0.184) 		0.00016
(0.000449)
del 9q21 11 176 (28%) 449 1e-05
(3.61e-05) 		8e-05
(0.000237) 		0.272
(0.336) 		0.295
(0.358) 		0.378
(0.444) 		0.264
(0.327) 		0.00029
(0.000776) 		1e-05
(3.61e-05) 		0.00046
(0.0012) 		0.0929
(0.136)
del 15q11 2 183 (29%) 442 1e-05
(3.61e-05) 		0.0853
(0.126) 		0.0291
(0.0503) 		0.0303
(0.0519) 		0.243
(0.305) 		0.239
(0.302) 		0.00678
(0.0136) 		1e-05
(3.61e-05) 		0.0696
(0.106) 		0.274
(0.337)
del xq11 2 103 (16%) 522 1e-05
(3.61e-05) 		0.0188
(0.0345) 		0.0748
(0.113) 		0.306
(0.37) 		0.502
(0.567) 		0.907
(0.93) 		0.00615
(0.0125) 		0.00313
(0.0068) 		0.0888
(0.131) 		0.0281
(0.0488)
amp 9q34 3 185 (30%) 440 1e-05
(3.61e-05) 		0.0039
(0.00836) 		0.749
(0.794) 		0.495
(0.559) 		0.192
(0.252) 		0.791
(0.83) 		0.00492
(0.0102) 		0.0762
(0.114) 		0.0136
(0.0255) 		0.0503
(0.0805)
amp 12q15 161 (26%) 464 1e-05
(3.61e-05) 		0.0218
(0.0391) 		0.833
(0.865) 		0.293
(0.357) 		0.271
(0.335) 		0.863
(0.892) 		0.0676
(0.104) 		0.0186
(0.0342) 		0.0347
(0.0585) 		0.128
(0.178)
del 6q26 152 (24%) 473 1e-05
(3.61e-05) 		0.0691
(0.106) 		0.635
(0.694) 		0.201
(0.262) 		0.596
(0.66) 		0.199
(0.26) 		0.00274
(0.00603) 		0.0156
(0.0289) 		0.0306
(0.0525) 		0.0667
(0.102)
del 9p23 302 (48%) 323 1e-05
(3.61e-05) 		0.0012
(0.0029) 		0.202
(0.263) 		0.511
(0.575) 		0.19
(0.251) 		0.118
(0.168) 		0.0014
(0.00332) 		1e-05
(3.61e-05) 		0.0635
(0.0983) 		0.0842
(0.125)
del 14q32 32 190 (30%) 435 1e-05
(3.61e-05) 		0.0222
(0.0397) 		0.762
(0.806) 		0.531
(0.592) 		0.0569
(0.0891) 		0.112
(0.161) 		0.361
(0.426) 		0.00017
(0.000469) 		0.511
(0.575) 		0.00272
(0.00602)
del 20p12 1 72 (12%) 553 0.00012
(0.000343) 		0.0271
(0.0472) 		0.082
(0.122) 		0.628
(0.69) 		0.0734
(0.111) 		0.00794
(0.0157) 		0.396
(0.463) 		0.0028
(0.00613) 		0.267
(0.331) 		0.227
(0.29)
amp 9p13 3 132 (21%) 493 0.00043
(0.00113) 		0.401
(0.468) 		0.21
(0.271) 		0.328
(0.392) 		0.884
(0.911) 		0.684
(0.735) 		0.0136
(0.0255) 		0.333
(0.396) 		0.0595
(0.0923) 		0.0424
(0.07)
amp 10p11 22 169 (27%) 456 1e-05
(3.61e-05) 		0.00218
(0.00493) 		0.998
(1.00) 		0.674
(0.727) 		0.189
(0.25) 		0.216
(0.278) 		0.527
(0.589) 		1e-05
(3.61e-05) 		0.0931
(0.136) 		0.0543
(0.086)
amp 11p13 138 (22%) 487 1e-05
(3.61e-05) 		0.00158
(0.00372) 		0.265
(0.328) 		0.954
(0.969) 		0.657
(0.711) 		1
(1.00) 		0.122
(0.172) 		0.00079
(0.00197) 		0.0514
(0.0817) 		0.133
(0.185)
del 2q32 1 87 (14%) 538 0.00075
(0.00189) 		0.00869
(0.017) 		0.898
(0.923) 		0.239
(0.302) 		0.353
(0.417) 		0.0764
(0.115) 		0.229
(0.292) 		0.0182
(0.0335) 		0.173
(0.233) 		0.453
(0.519)
del 3q11 1 98 (16%) 527 1e-05
(3.61e-05) 		1e-05
(3.61e-05) 		0.253
(0.316) 		0.289
(0.353) 		0.35
(0.414) 		0.818
(0.852) 		0.125
(0.175) 		4e-05
(0.000126) 		0.143
(0.197) 		0.323
(0.387)
del 12q23 1 109 (17%) 516 1e-05
(3.61e-05) 		0.00302
(0.00659) 		0.333
(0.396) 		0.641
(0.698) 		0.0565
(0.0887) 		0.0716
(0.109) 		0.131
(0.183) 		0.00048
(0.00125) 		0.22
(0.283) 		0.0568
(0.0891)
del 17q24 3 103 (16%) 522 1e-05
(3.61e-05) 		0.0811
(0.121) 		0.646
(0.702) 		0.655
(0.71) 		0.708
(0.756) 		0.79
(0.83) 		0.0486
(0.0781) 		0.0339
(0.0574) 		0.554
(0.617) 		0.979
(0.988)
amp 10q22 2 125 (20%) 500 1e-05
(3.61e-05) 		0.0491
(0.0788) 		0.806
(0.842) 		0.3
(0.364) 		0.29
(0.354) 		0.388
(0.455) 		0.736
(0.781) 		0.145
(0.199) 		0.144
(0.197) 		0.163
(0.221)
del 1q44 46 (7%) 579 0.0136
(0.0255) 		0.0531
(0.0842) 		0.165
(0.224) 		0.2
(0.261) 		0.974
(0.985) 		0.517
(0.58) 		0.00337
(0.00725) 		0.171
(0.231) 		0.324
(0.389) 		0.28
(0.343)
amp 8p11 21 272 (44%) 353 0.284
(0.348) 		0.024
(0.0425) 		0.657
(0.711) 		0.635
(0.694) 		1
(1.00) 		0.0742
(0.112) 		0.0693
(0.106) 		0.24
(0.303) 		0.425
(0.492) 		0.445
(0.512)
amp 9p24 1 91 (15%) 534 0.238
(0.302) 		0.35
(0.414) 		0.953
(0.969) 		1
(1.00) 		0.344
(0.407) 		0.786
(0.827) 		0.0397
(0.0661) 		0.638
(0.696) 		0.0894
(0.131) 		0.155
(0.211)
del 1q44 43 (7%) 582 0.0576
(0.0899) 		0.0115
(0.022) 		0.117
(0.166) 		0.229
(0.292) 		0.95
(0.969) 		0.613
(0.674) 		0.262
(0.326) 		0.862
(0.892) 		1
(1.00) 		0.722
(0.769)
'amp_1p36.22' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 1(1P36.22) MUTATED 45 45 11
AMP PEAK 1(1P36.22) WILD-TYPE 121 165 238

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

'amp_1p36.22' versus 'METHLYATION_CNMF'

P value = 0.00543 (Fisher's exact test), Q value = 0.011

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 1(1P36.22) MUTATED 40 36 17
AMP PEAK 1(1P36.22) WILD-TYPE 208 121 155

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

'amp_1p36.22' versus 'MIRSEQ_CNMF'

P value = 0.0262 (Fisher's exact test), Q value = 0.046

Table S3.  Gene #1: 'amp_1p36.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 1(1P36.22) MUTATED 32 56 11
AMP PEAK 1(1P36.22) WILD-TYPE 131 272 115

Figure S3.  Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1p36.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00049

Table S4.  Gene #1: 'amp_1p36.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 1(1P36.22) MUTATED 34 29 17 13 6
AMP PEAK 1(1P36.22) WILD-TYPE 93 114 147 81 83

Figure S4.  Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1p36.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0016

Table S5.  Gene #1: 'amp_1p36.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 1(1P36.22) MUTATED 48 14 8 13
AMP PEAK 1(1P36.22) WILD-TYPE 150 116 91 79

Figure S5.  Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1p34.2' versus 'CN_CNMF'

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

Table S6.  Gene #2: 'amp_1p34.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 2(1P34.2) MUTATED 34 51 10
AMP PEAK 2(1P34.2) WILD-TYPE 132 159 239

Figure S6.  Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1p34.2' versus 'METHLYATION_CNMF'

P value = 0.00461 (Fisher's exact test), Q value = 0.0097

Table S7.  Gene #2: 'amp_1p34.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 2(1P34.2) MUTATED 36 36 17
AMP PEAK 2(1P34.2) WILD-TYPE 212 121 155

Figure S7.  Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1p34.2' versus 'MIRSEQ_CNMF'

P value = 0.0403 (Fisher's exact test), Q value = 0.067

Table S8.  Gene #2: 'amp_1p34.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 2(1P34.2) MUTATED 33 49 12
AMP PEAK 2(1P34.2) WILD-TYPE 130 279 114

Figure S8.  Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1p34.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0146 (Fisher's exact test), Q value = 0.027

Table S9.  Gene #2: 'amp_1p34.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 2(1P34.2) MUTATED 28 22 15 19 10
AMP PEAK 2(1P34.2) WILD-TYPE 99 121 149 75 79

Figure S9.  Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1p34.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00399 (Fisher's exact test), Q value = 0.0085

Table S10.  Gene #2: 'amp_1p34.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 2(1P34.2) MUTATED 39 12 8 19
AMP PEAK 2(1P34.2) WILD-TYPE 159 118 91 73

Figure S10.  Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q21.3' versus 'CN_CNMF'

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

Table S11.  Gene #3: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 3(1Q21.3) MUTATED 98 121 30
AMP PEAK 3(1Q21.3) WILD-TYPE 68 89 219

Figure S11.  Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q21.3' versus 'METHLYATION_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 3(1Q21.3) MUTATED 99 96 37
AMP PEAK 3(1Q21.3) WILD-TYPE 149 61 135

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

'amp_1q21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.025

Table S13.  Gene #3: 'amp_1q21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
AMP PEAK 3(1Q21.3) MUTATED 123 39 29
AMP PEAK 3(1Q21.3) WILD-TYPE 150 71 70

Figure S13.  Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 3(1Q21.3) MUTATED 81 133 31
AMP PEAK 3(1Q21.3) WILD-TYPE 82 195 95

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

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 3(1Q21.3) MUTATED 75 73 31 45 21
AMP PEAK 3(1Q21.3) WILD-TYPE 52 70 133 49 68

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

'amp_1q21.3' versus 'MIRSEQ_MATURE_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
AMP PEAK 3(1Q21.3) MUTATED 76 83 47
AMP PEAK 3(1Q21.3) WILD-TYPE 69 122 122

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

'amp_1q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.7e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 3(1Q21.3) MUTATED 98 36 27 45
AMP PEAK 3(1Q21.3) WILD-TYPE 100 94 72 47

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

'amp_1q42.3' versus 'CN_CNMF'

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

Table S18.  Gene #4: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 4(1Q42.3) MUTATED 97 116 31
AMP PEAK 4(1Q42.3) WILD-TYPE 69 94 218

Figure S18.  Get High-res Image Gene #4: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q42.3' versus 'METHLYATION_CNMF'

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

Table S19.  Gene #4: 'amp_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 4(1Q42.3) MUTATED 86 99 43
AMP PEAK 4(1Q42.3) WILD-TYPE 162 58 129

Figure S19.  Get High-res Image Gene #4: 'amp_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q42.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0455 (Fisher's exact test), Q value = 0.074

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
AMP PEAK 4(1Q42.3) MUTATED 118 41 29
AMP PEAK 4(1Q42.3) WILD-TYPE 155 69 70

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

'amp_1q42.3' versus 'MIRSEQ_CNMF'

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

Table S21.  Gene #4: 'amp_1q42.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 4(1Q42.3) MUTATED 92 113 36
AMP PEAK 4(1Q42.3) WILD-TYPE 71 215 90

Figure S21.  Get High-res Image Gene #4: 'amp_1q42.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q42.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S22.  Gene #4: 'amp_1q42.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 4(1Q42.3) MUTATED 78 64 25 50 24
AMP PEAK 4(1Q42.3) WILD-TYPE 49 79 139 44 65

Figure S22.  Get High-res Image Gene #4: 'amp_1q42.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q42.3' versus 'MIRSEQ_MATURE_CNMF'

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

Table S23.  Gene #4: 'amp_1q42.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
AMP PEAK 4(1Q42.3) MUTATED 83 72 51
AMP PEAK 4(1Q42.3) WILD-TYPE 62 133 118

Figure S23.  Get High-res Image Gene #4: 'amp_1q42.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_1q42.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.6e-05

Table S24.  Gene #4: 'amp_1q42.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 4(1Q42.3) MUTATED 92 33 32 49
AMP PEAK 4(1Q42.3) WILD-TYPE 106 97 67 43

Figure S24.  Get High-res Image Gene #4: 'amp_1q42.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_2q12.2' versus 'CN_CNMF'

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

Table S25.  Gene #5: 'amp_2q12.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 5(2Q12.2) MUTATED 61 76 18
AMP PEAK 5(2Q12.2) WILD-TYPE 105 134 231

Figure S25.  Get High-res Image Gene #5: 'amp_2q12.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2q12.2' versus 'METHLYATION_CNMF'

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

Table S26.  Gene #5: 'amp_2q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 5(2Q12.2) MUTATED 59 62 26
AMP PEAK 5(2Q12.2) WILD-TYPE 189 95 146

Figure S26.  Get High-res Image Gene #5: 'amp_2q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_2q12.2' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.7e-05

Table S27.  Gene #5: 'amp_2q12.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 5(2Q12.2) MUTATED 63 73 18
AMP PEAK 5(2Q12.2) WILD-TYPE 100 255 108

Figure S27.  Get High-res Image Gene #5: 'amp_2q12.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_2q12.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S28.  Gene #5: 'amp_2q12.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 5(2Q12.2) MUTATED 41 36 26 39 12
AMP PEAK 5(2Q12.2) WILD-TYPE 86 107 138 55 77

Figure S28.  Get High-res Image Gene #5: 'amp_2q12.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_2q12.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00037

Table S29.  Gene #5: 'amp_2q12.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
AMP PEAK 5(2Q12.2) MUTATED 56 48 30
AMP PEAK 5(2Q12.2) WILD-TYPE 89 157 139

Figure S29.  Get High-res Image Gene #5: 'amp_2q12.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_2q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00055

Table S30.  Gene #5: 'amp_2q12.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 5(2Q12.2) MUTATED 56 24 16 38
AMP PEAK 5(2Q12.2) WILD-TYPE 142 106 83 54

Figure S30.  Get High-res Image Gene #5: 'amp_2q12.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.2' versus 'CN_CNMF'

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

Table S31.  Gene #6: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 6(3Q26.2) MUTATED 68 170 49
AMP PEAK 6(3Q26.2) WILD-TYPE 98 40 200

Figure S31.  Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

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

Table S32.  Gene #6: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 6(3Q26.2) MUTATED 94 118 56
AMP PEAK 6(3Q26.2) WILD-TYPE 154 39 116

Figure S32.  Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.7e-05

Table S33.  Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
AMP PEAK 6(3Q26.2) MUTATED 43 61 15 8
AMP PEAK 6(3Q26.2) WILD-TYPE 38 8 7 3

Figure S33.  Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S34.  Gene #6: 'amp_3q26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 6(3Q26.2) MUTATED 38 7 82
AMP PEAK 6(3Q26.2) WILD-TYPE 29 13 14

Figure S34.  Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_CNMF'

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

Table S35.  Gene #6: 'amp_3q26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 6(3Q26.2) MUTATED 117 131 36
AMP PEAK 6(3Q26.2) WILD-TYPE 46 197 90

Figure S35.  Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S36.  Gene #6: 'amp_3q26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 6(3Q26.2) MUTATED 62 57 60 81 24
AMP PEAK 6(3Q26.2) WILD-TYPE 65 86 104 13 65

Figure S36.  Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CNMF'

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

Table S37.  Gene #6: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
AMP PEAK 6(3Q26.2) MUTATED 104 78 62
AMP PEAK 6(3Q26.2) WILD-TYPE 41 127 107

Figure S37.  Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S38.  Gene #6: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 6(3Q26.2) MUTATED 90 46 28 80
AMP PEAK 6(3Q26.2) WILD-TYPE 108 84 71 12

Figure S38.  Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

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

Table S39.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 7(5P15.33) MUTATED 85 116 27
AMP PEAK 7(5P15.33) WILD-TYPE 81 94 222

Figure S39.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

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

Table S40.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 7(5P15.33) MUTATED 69 104 42
AMP PEAK 7(5P15.33) WILD-TYPE 179 53 130

Figure S40.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.00622 (Fisher's exact test), Q value = 0.013

Table S41.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
AMP PEAK 7(5P15.33) MUTATED 112 32 25
AMP PEAK 7(5P15.33) WILD-TYPE 161 78 74

Figure S41.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.0032

Table S42.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
AMP PEAK 7(5P15.33) MUTATED 32 49 12 5
AMP PEAK 7(5P15.33) WILD-TYPE 49 20 10 6

Figure S42.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00091 (Fisher's exact test), Q value = 0.0022

Table S43.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 7(5P15.33) MUTATED 30 5 63
AMP PEAK 7(5P15.33) WILD-TYPE 37 15 33

Figure S43.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

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

Table S44.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 7(5P15.33) MUTATED 95 103 28
AMP PEAK 7(5P15.33) WILD-TYPE 68 225 98

Figure S44.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S45.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 7(5P15.33) MUTATED 66 42 37 63 18
AMP PEAK 7(5P15.33) WILD-TYPE 61 101 127 31 71

Figure S45.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

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

Table S46.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
AMP PEAK 7(5P15.33) MUTATED 87 75 38
AMP PEAK 7(5P15.33) WILD-TYPE 58 130 131

Figure S46.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S47.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 7(5P15.33) MUTATED 79 40 18 63
AMP PEAK 7(5P15.33) WILD-TYPE 119 90 81 29

Figure S47.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p13.1' versus 'CN_CNMF'

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

Table S48.  Gene #8: 'amp_5p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 8(5P13.1) MUTATED 85 102 29
AMP PEAK 8(5P13.1) WILD-TYPE 81 108 220

Figure S48.  Get High-res Image Gene #8: 'amp_5p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p13.1' versus 'METHLYATION_CNMF'

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

Table S49.  Gene #8: 'amp_5p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 8(5P13.1) MUTATED 65 93 43
AMP PEAK 8(5P13.1) WILD-TYPE 183 64 129

Figure S49.  Get High-res Image Gene #8: 'amp_5p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p13.1' versus 'MRNASEQ_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.029

Table S50.  Gene #8: 'amp_5p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
AMP PEAK 8(5P13.1) MUTATED 30 41 14 4
AMP PEAK 8(5P13.1) WILD-TYPE 51 28 8 7

Figure S50.  Get High-res Image Gene #8: 'amp_5p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0327 (Fisher's exact test), Q value = 0.056

Table S51.  Gene #8: 'amp_5p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 8(5P13.1) MUTATED 28 6 55
AMP PEAK 8(5P13.1) WILD-TYPE 39 14 41

Figure S51.  Get High-res Image Gene #8: 'amp_5p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5p13.1' versus 'MIRSEQ_CNMF'

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

Table S52.  Gene #8: 'amp_5p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 8(5P13.1) MUTATED 87 95 33
AMP PEAK 8(5P13.1) WILD-TYPE 76 233 93

Figure S52.  Get High-res Image Gene #8: 'amp_5p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5p13.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S53.  Gene #8: 'amp_5p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 8(5P13.1) MUTATED 65 37 37 55 21
AMP PEAK 8(5P13.1) WILD-TYPE 62 106 127 39 68

Figure S53.  Get High-res Image Gene #8: 'amp_5p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p13.1' versus 'MIRSEQ_MATURE_CNMF'

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

Table S54.  Gene #8: 'amp_5p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
AMP PEAK 8(5P13.1) MUTATED 79 64 46
AMP PEAK 8(5P13.1) WILD-TYPE 66 141 123

Figure S54.  Get High-res Image Gene #8: 'amp_5p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_5p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S55.  Gene #8: 'amp_5p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 8(5P13.1) MUTATED 72 41 21 55
AMP PEAK 8(5P13.1) WILD-TYPE 126 89 78 37

Figure S55.  Get High-res Image Gene #8: 'amp_5p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6p21.1' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 9(6P21.1) MUTATED 94 74 24
AMP PEAK 9(6P21.1) WILD-TYPE 72 136 225

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

'amp_6p21.1' versus 'METHLYATION_CNMF'

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

Table S57.  Gene #9: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 9(6P21.1) MUTATED 80 69 27
AMP PEAK 9(6P21.1) WILD-TYPE 168 88 145

Figure S57.  Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p21.1' versus 'RPPA_CNMF'

P value = 0.0243 (Fisher's exact test), Q value = 0.043

Table S58.  Gene #9: 'amp_6p21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 137 136 64
AMP PEAK 9(6P21.1) MUTATED 45 50 29 24
AMP PEAK 9(6P21.1) WILD-TYPE 100 87 107 40

Figure S58.  Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_6p21.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.021

Table S59.  Gene #9: 'amp_6p21.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
AMP PEAK 9(6P21.1) MUTATED 88 41 19
AMP PEAK 9(6P21.1) WILD-TYPE 185 69 80

Figure S59.  Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_6p21.1' versus 'MRNASEQ_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.036

Table S60.  Gene #9: 'amp_6p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
AMP PEAK 9(6P21.1) MUTATED 39 20 8 1
AMP PEAK 9(6P21.1) WILD-TYPE 42 49 14 10

Figure S60.  Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0205 (Fisher's exact test), Q value = 0.037

Table S61.  Gene #9: 'amp_6p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 9(6P21.1) MUTATED 30 11 27
AMP PEAK 9(6P21.1) WILD-TYPE 37 9 69

Figure S61.  Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00021

Table S62.  Gene #9: 'amp_6p21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 9(6P21.1) MUTATED 60 110 19
AMP PEAK 9(6P21.1) WILD-TYPE 103 218 107

Figure S62.  Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6p21.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S63.  Gene #9: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 9(6P21.1) MUTATED 67 56 28 26 12
AMP PEAK 9(6P21.1) WILD-TYPE 60 87 136 68 77

Figure S63.  Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00159 (Fisher's exact test), Q value = 0.0037

Table S64.  Gene #9: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
AMP PEAK 9(6P21.1) MUTATED 58 70 37
AMP PEAK 9(6P21.1) WILD-TYPE 87 135 132

Figure S64.  Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S65.  Gene #9: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 9(6P21.1) MUTATED 95 27 17 26
AMP PEAK 9(6P21.1) WILD-TYPE 103 103 82 66

Figure S65.  Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q12' versus 'CN_CNMF'

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

Table S66.  Gene #10: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 10(6Q12) MUTATED 67 53 21
AMP PEAK 10(6Q12) WILD-TYPE 99 157 228

Figure S66.  Get High-res Image Gene #10: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q12' versus 'METHLYATION_CNMF'

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

Table S67.  Gene #10: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 10(6Q12) MUTATED 55 55 17
AMP PEAK 10(6Q12) WILD-TYPE 193 102 155

Figure S67.  Get High-res Image Gene #10: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q12' versus 'MIRSEQ_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.02

Table S68.  Gene #10: 'amp_6q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 10(6Q12) MUTATED 49 71 19
AMP PEAK 10(6Q12) WILD-TYPE 114 257 107

Figure S68.  Get High-res Image Gene #10: 'amp_6q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6q12' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S69.  Gene #10: 'amp_6q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 10(6Q12) MUTATED 50 37 20 22 10
AMP PEAK 10(6Q12) WILD-TYPE 77 106 144 72 79

Figure S69.  Get High-res Image Gene #10: 'amp_6q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0011 (Fisher's exact test), Q value = 0.0027

Table S70.  Gene #10: 'amp_6q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
AMP PEAK 10(6Q12) MUTATED 47 46 25
AMP PEAK 10(6Q12) WILD-TYPE 98 159 144

Figure S70.  Get High-res Image Gene #10: 'amp_6q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.0011

Table S71.  Gene #10: 'amp_6q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 10(6Q12) MUTATED 63 19 14 22
AMP PEAK 10(6Q12) WILD-TYPE 135 111 85 70

Figure S71.  Get High-res Image Gene #10: 'amp_6q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q21' versus 'CN_CNMF'

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

Table S72.  Gene #11: 'amp_6q21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 11(6Q21) MUTATED 57 34 20
AMP PEAK 11(6Q21) WILD-TYPE 109 176 229

Figure S72.  Get High-res Image Gene #11: 'amp_6q21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q21' versus 'METHLYATION_CNMF'

P value = 0.00211 (Fisher's exact test), Q value = 0.0048

Table S73.  Gene #11: 'amp_6q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 11(6Q21) MUTATED 43 38 17
AMP PEAK 11(6Q21) WILD-TYPE 205 119 155

Figure S73.  Get High-res Image Gene #11: 'amp_6q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0191 (Fisher's exact test), Q value = 0.035

Table S74.  Gene #11: 'amp_6q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 11(6Q21) MUTATED 14 6 9
AMP PEAK 11(6Q21) WILD-TYPE 53 14 87

Figure S74.  Get High-res Image Gene #11: 'amp_6q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S75.  Gene #11: 'amp_6q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 11(6Q21) MUTATED 45 30 19 9 7
AMP PEAK 11(6Q21) WILD-TYPE 82 113 145 85 82

Figure S75.  Get High-res Image Gene #11: 'amp_6q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 8e-04

Table S76.  Gene #11: 'amp_6q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 11(6Q21) MUTATED 53 15 13 9
AMP PEAK 11(6Q21) WILD-TYPE 145 115 86 83

Figure S76.  Get High-res Image Gene #11: 'amp_6q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p22.3' versus 'CN_CNMF'

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

Table S77.  Gene #12: 'amp_7p22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 12(7P22.3) MUTATED 128 148 77
AMP PEAK 12(7P22.3) WILD-TYPE 38 62 172

Figure S77.  Get High-res Image Gene #12: 'amp_7p22.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p22.3' versus 'METHLYATION_CNMF'

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

Table S78.  Gene #12: 'amp_7p22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 12(7P22.3) MUTATED 154 106 67
AMP PEAK 12(7P22.3) WILD-TYPE 94 51 105

Figure S78.  Get High-res Image Gene #12: 'amp_7p22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p22.3' versus 'MRNASEQ_CNMF'

P value = 0.00149 (Fisher's exact test), Q value = 0.0035

Table S79.  Gene #12: 'amp_7p22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
AMP PEAK 12(7P22.3) MUTATED 63 48 15 2
AMP PEAK 12(7P22.3) WILD-TYPE 18 21 7 9

Figure S79.  Get High-res Image Gene #12: 'amp_7p22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p22.3' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.7e-05

Table S80.  Gene #12: 'amp_7p22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 12(7P22.3) MUTATED 109 191 48
AMP PEAK 12(7P22.3) WILD-TYPE 54 137 78

Figure S80.  Get High-res Image Gene #12: 'amp_7p22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7p22.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S81.  Gene #12: 'amp_7p22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 12(7P22.3) MUTATED 88 92 76 61 31
AMP PEAK 12(7P22.3) WILD-TYPE 39 51 88 33 58

Figure S81.  Get High-res Image Gene #12: 'amp_7p22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7p22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.7e-05

Table S82.  Gene #12: 'amp_7p22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
AMP PEAK 12(7P22.3) MUTATED 103 118 75
AMP PEAK 12(7P22.3) WILD-TYPE 42 87 94

Figure S82.  Get High-res Image Gene #12: 'amp_7p22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00018

Table S83.  Gene #12: 'amp_7p22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 12(7P22.3) MUTATED 130 67 39 60
AMP PEAK 12(7P22.3) WILD-TYPE 68 63 60 32

Figure S83.  Get High-res Image Gene #12: 'amp_7p22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

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

Table S84.  Gene #13: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 13(7P11.2) MUTATED 117 143 80
AMP PEAK 13(7P11.2) WILD-TYPE 49 67 169

Figure S84.  Get High-res Image Gene #13: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

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

Table S85.  Gene #13: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 13(7P11.2) MUTATED 150 103 64
AMP PEAK 13(7P11.2) WILD-TYPE 98 54 108

Figure S85.  Get High-res Image Gene #13: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.021

Table S86.  Gene #13: 'amp_7p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
AMP PEAK 13(7P11.2) MUTATED 62 45 16 3
AMP PEAK 13(7P11.2) WILD-TYPE 19 24 6 8

Figure S86.  Get High-res Image Gene #13: 'amp_7p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0395 (Fisher's exact test), Q value = 0.066

Table S87.  Gene #13: 'amp_7p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 13(7P11.2) MUTATED 48 18 60
AMP PEAK 13(7P11.2) WILD-TYPE 19 2 36

Figure S87.  Get High-res Image Gene #13: 'amp_7p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00018

Table S88.  Gene #13: 'amp_7p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 13(7P11.2) MUTATED 103 184 47
AMP PEAK 13(7P11.2) WILD-TYPE 60 144 79

Figure S88.  Get High-res Image Gene #13: 'amp_7p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S89.  Gene #13: 'amp_7p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 13(7P11.2) MUTATED 78 93 74 59 30
AMP PEAK 13(7P11.2) WILD-TYPE 49 50 90 35 59

Figure S89.  Get High-res Image Gene #13: 'amp_7p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CNMF'

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

Table S90.  Gene #13: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
AMP PEAK 13(7P11.2) MUTATED 101 111 70
AMP PEAK 13(7P11.2) WILD-TYPE 44 94 99

Figure S90.  Get High-res Image Gene #13: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 4e-04

Table S91.  Gene #13: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 13(7P11.2) MUTATED 123 64 37 58
AMP PEAK 13(7P11.2) WILD-TYPE 75 66 62 34

Figure S91.  Get High-res Image Gene #13: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q21.2' versus 'CN_CNMF'

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

Table S92.  Gene #14: 'amp_7q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 14(7Q21.2) MUTATED 99 139 79
AMP PEAK 14(7Q21.2) WILD-TYPE 67 71 170

Figure S92.  Get High-res Image Gene #14: 'amp_7q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q21.2' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00034

Table S93.  Gene #14: 'amp_7q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 14(7Q21.2) MUTATED 132 95 65
AMP PEAK 14(7Q21.2) WILD-TYPE 116 62 107

Figure S93.  Get High-res Image Gene #14: 'amp_7q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q21.2' versus 'MIRSEQ_CNMF'

P value = 0.00273 (Fisher's exact test), Q value = 0.006

Table S94.  Gene #14: 'amp_7q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 14(7Q21.2) MUTATED 92 173 47
AMP PEAK 14(7Q21.2) WILD-TYPE 71 155 79

Figure S94.  Get High-res Image Gene #14: 'amp_7q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00155 (Fisher's exact test), Q value = 0.0037

Table S95.  Gene #14: 'amp_7q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 14(7Q21.2) MUTATED 69 78 77 58 30
AMP PEAK 14(7Q21.2) WILD-TYPE 58 65 87 36 59

Figure S95.  Get High-res Image Gene #14: 'amp_7q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.7e-05

Table S96.  Gene #14: 'amp_7q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
AMP PEAK 14(7Q21.2) MUTATED 96 100 66
AMP PEAK 14(7Q21.2) WILD-TYPE 49 105 103

Figure S96.  Get High-res Image Gene #14: 'amp_7q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00545 (Fisher's exact test), Q value = 0.011

Table S97.  Gene #14: 'amp_7q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 14(7Q21.2) MUTATED 107 60 38 57
AMP PEAK 14(7Q21.2) WILD-TYPE 91 70 61 35

Figure S97.  Get High-res Image Gene #14: 'amp_7q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p23.1' versus 'CN_CNMF'

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

Table S98.  Gene #15: 'amp_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 15(8P23.1) MUTATED 59 54 116
AMP PEAK 15(8P23.1) WILD-TYPE 107 156 133

Figure S98.  Get High-res Image Gene #15: 'amp_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p23.1' versus 'METHLYATION_CNMF'

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

Table S99.  Gene #15: 'amp_8p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 15(8P23.1) MUTATED 119 33 54
AMP PEAK 15(8P23.1) WILD-TYPE 129 124 118

Figure S99.  Get High-res Image Gene #15: 'amp_8p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8p23.1' versus 'MRNASEQ_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.026

Table S100.  Gene #15: 'amp_8p23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
AMP PEAK 15(8P23.1) MUTATED 33 13 4 2
AMP PEAK 15(8P23.1) WILD-TYPE 48 56 18 9

Figure S100.  Get High-res Image Gene #15: 'amp_8p23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8p23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00021

Table S101.  Gene #15: 'amp_8p23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 15(8P23.1) MUTATED 32 2 18
AMP PEAK 15(8P23.1) WILD-TYPE 35 18 78

Figure S101.  Get High-res Image Gene #15: 'amp_8p23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8p23.1' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00018

Table S102.  Gene #15: 'amp_8p23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 15(8P23.1) MUTATED 39 144 41
AMP PEAK 15(8P23.1) WILD-TYPE 124 184 85

Figure S102.  Get High-res Image Gene #15: 'amp_8p23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8p23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00112 (Fisher's exact test), Q value = 0.0027

Table S103.  Gene #15: 'amp_8p23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 15(8P23.1) MUTATED 43 64 65 18 34
AMP PEAK 15(8P23.1) WILD-TYPE 84 79 99 76 55

Figure S103.  Get High-res Image Gene #15: 'amp_8p23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8p23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00042

Table S104.  Gene #15: 'amp_8p23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
AMP PEAK 15(8P23.1) MUTATED 33 90 58
AMP PEAK 15(8P23.1) WILD-TYPE 112 115 111

Figure S104.  Get High-res Image Gene #15: 'amp_8p23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8p23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00088 (Fisher's exact test), Q value = 0.0022

Table S105.  Gene #15: 'amp_8p23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 15(8P23.1) MUTATED 74 53 38 16
AMP PEAK 15(8P23.1) WILD-TYPE 124 77 61 76

Figure S105.  Get High-res Image Gene #15: 'amp_8p23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p11.21' versus 'METHLYATION_CNMF'

P value = 0.024 (Fisher's exact test), Q value = 0.043

Table S106.  Gene #16: 'amp_8p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 16(8P11.21) MUTATED 120 68 60
AMP PEAK 16(8P11.21) WILD-TYPE 128 89 112

Figure S106.  Get High-res Image Gene #16: 'amp_8p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

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

Table S107.  Gene #17: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 17(8Q24.21) MUTATED 143 164 147
AMP PEAK 17(8Q24.21) WILD-TYPE 23 46 102

Figure S107.  Get High-res Image Gene #17: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

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

Table S108.  Gene #17: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 17(8Q24.21) MUTATED 186 132 99
AMP PEAK 17(8Q24.21) WILD-TYPE 62 25 73

Figure S108.  Get High-res Image Gene #17: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

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

Table S109.  Gene #17: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 17(8Q24.21) MUTATED 138 241 70
AMP PEAK 17(8Q24.21) WILD-TYPE 25 87 56

Figure S109.  Get High-res Image Gene #17: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S110.  Gene #17: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 17(8Q24.21) MUTATED 105 123 92 77 52
AMP PEAK 17(8Q24.21) WILD-TYPE 22 20 72 17 37

Figure S110.  Get High-res Image Gene #17: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 6e-04

Table S111.  Gene #17: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
AMP PEAK 17(8Q24.21) MUTATED 122 147 108
AMP PEAK 17(8Q24.21) WILD-TYPE 23 58 61

Figure S111.  Get High-res Image Gene #17: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.00073

Table S112.  Gene #17: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 17(8Q24.21) MUTATED 158 86 59 74
AMP PEAK 17(8Q24.21) WILD-TYPE 40 44 40 18

Figure S112.  Get High-res Image Gene #17: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9p24.1' versus 'MIRSEQ_CNMF'

P value = 0.0397 (Fisher's exact test), Q value = 0.066

Table S113.  Gene #18: 'amp_9p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 18(9P24.1) MUTATED 33 43 13
AMP PEAK 18(9P24.1) WILD-TYPE 130 285 113

Figure S113.  Get High-res Image Gene #18: 'amp_9p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_9p13.3' versus 'CN_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.0011

Table S114.  Gene #19: 'amp_9p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 19(9P13.3) MUTATED 50 47 35
AMP PEAK 19(9P13.3) WILD-TYPE 116 163 214

Figure S114.  Get High-res Image Gene #19: 'amp_9p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p13.3' versus 'MIRSEQ_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.025

Table S115.  Gene #19: 'amp_9p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 19(9P13.3) MUTATED 45 68 17
AMP PEAK 19(9P13.3) WILD-TYPE 118 260 109

Figure S115.  Get High-res Image Gene #19: 'amp_9p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_9p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0424 (Fisher's exact test), Q value = 0.07

Table S116.  Gene #19: 'amp_9p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 19(9P13.3) MUTATED 54 26 13 19
AMP PEAK 19(9P13.3) WILD-TYPE 144 104 86 73

Figure S116.  Get High-res Image Gene #19: 'amp_9p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9q34.3' versus 'CN_CNMF'

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

Table S117.  Gene #20: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 20(9Q34.3) MUTATED 68 78 39
AMP PEAK 20(9Q34.3) WILD-TYPE 98 132 210

Figure S117.  Get High-res Image Gene #20: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9q34.3' versus 'METHLYATION_CNMF'

P value = 0.0039 (Fisher's exact test), Q value = 0.0084

Table S118.  Gene #20: 'amp_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 20(9Q34.3) MUTATED 71 61 38
AMP PEAK 20(9Q34.3) WILD-TYPE 177 96 134

Figure S118.  Get High-res Image Gene #20: 'amp_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9q34.3' versus 'MIRSEQ_CNMF'

P value = 0.00492 (Fisher's exact test), Q value = 0.01

Table S119.  Gene #20: 'amp_9q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 20(9Q34.3) MUTATED 62 94 26
AMP PEAK 20(9Q34.3) WILD-TYPE 101 234 100

Figure S119.  Get High-res Image Gene #20: 'amp_9q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_9q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.025

Table S120.  Gene #20: 'amp_9q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
AMP PEAK 20(9Q34.3) MUTATED 55 52 41
AMP PEAK 20(9Q34.3) WILD-TYPE 90 153 128

Figure S120.  Get High-res Image Gene #20: 'amp_9q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_10p11.22' versus 'CN_CNMF'

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

Table S121.  Gene #21: 'amp_10p11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 21(10P11.22) MUTATED 75 65 29
AMP PEAK 21(10P11.22) WILD-TYPE 91 145 220

Figure S121.  Get High-res Image Gene #21: 'amp_10p11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10p11.22' versus 'METHLYATION_CNMF'

P value = 0.00218 (Fisher's exact test), Q value = 0.0049

Table S122.  Gene #21: 'amp_10p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 21(10P11.22) MUTATED 72 54 31
AMP PEAK 21(10P11.22) WILD-TYPE 176 103 141

Figure S122.  Get High-res Image Gene #21: 'amp_10p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_10p11.22' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S123.  Gene #21: 'amp_10p11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 21(10P11.22) MUTATED 57 42 28 21 18
AMP PEAK 21(10P11.22) WILD-TYPE 70 101 136 73 71

Figure S123.  Get High-res Image Gene #21: 'amp_10p11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_10q22.2' versus 'CN_CNMF'

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

Table S124.  Gene #22: 'amp_10q22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 22(10Q22.2) MUTATED 43 56 26
AMP PEAK 22(10Q22.2) WILD-TYPE 123 154 223

Figure S124.  Get High-res Image Gene #22: 'amp_10q22.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10q22.2' versus 'METHLYATION_CNMF'

P value = 0.0491 (Fisher's exact test), Q value = 0.079

Table S125.  Gene #22: 'amp_10q22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 22(10Q22.2) MUTATED 57 35 24
AMP PEAK 22(10Q22.2) WILD-TYPE 191 122 148

Figure S125.  Get High-res Image Gene #22: 'amp_10q22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_10q26.13' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.6e-05

Table S126.  Gene #23: 'amp_10q26.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 23(10Q26.13) MUTATED 48 42 29
AMP PEAK 23(10Q26.13) WILD-TYPE 118 168 220

Figure S126.  Get High-res Image Gene #23: 'amp_10q26.13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10q26.13' versus 'MRNASEQ_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.029

Table S127.  Gene #23: 'amp_10q26.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
AMP PEAK 23(10Q26.13) MUTATED 21 6 4 0
AMP PEAK 23(10Q26.13) WILD-TYPE 60 63 18 11

Figure S127.  Get High-res Image Gene #23: 'amp_10q26.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_10q26.13' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S128.  Gene #23: 'amp_10q26.13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 23(10Q26.13) MUTATED 16 6 9
AMP PEAK 23(10Q26.13) WILD-TYPE 51 14 87

Figure S128.  Get High-res Image Gene #23: 'amp_10q26.13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_10q26.13' versus 'MIRSEQ_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.035

Table S129.  Gene #23: 'amp_10q26.13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 23(10Q26.13) MUTATED 20 66 31
AMP PEAK 23(10Q26.13) WILD-TYPE 143 262 95

Figure S129.  Get High-res Image Gene #23: 'amp_10q26.13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_10q26.13' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S130.  Gene #23: 'amp_10q26.13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 23(10Q26.13) MUTATED 37 30 26 7 17
AMP PEAK 23(10Q26.13) WILD-TYPE 90 113 138 87 72

Figure S130.  Get High-res Image Gene #23: 'amp_10q26.13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_10q26.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00181 (Fisher's exact test), Q value = 0.0042

Table S131.  Gene #23: 'amp_10q26.13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 23(10Q26.13) MUTATED 48 24 21 6
AMP PEAK 23(10Q26.13) WILD-TYPE 150 106 78 86

Figure S131.  Get High-res Image Gene #23: 'amp_10q26.13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11p13' versus 'CN_CNMF'

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

Table S132.  Gene #24: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 24(11P13) MUTATED 55 60 23
AMP PEAK 24(11P13) WILD-TYPE 111 150 226

Figure S132.  Get High-res Image Gene #24: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11p13' versus 'METHLYATION_CNMF'

P value = 0.00158 (Fisher's exact test), Q value = 0.0037

Table S133.  Gene #24: 'amp_11p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 24(11P13) MUTATED 49 51 29
AMP PEAK 24(11P13) WILD-TYPE 199 106 143

Figure S133.  Get High-res Image Gene #24: 'amp_11p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11p13' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S134.  Gene #24: 'amp_11p13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 24(11P13) MUTATED 42 28 25 27 13
AMP PEAK 24(11P13) WILD-TYPE 85 115 139 67 76

Figure S134.  Get High-res Image Gene #24: 'amp_11p13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

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

Table S135.  Gene #25: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 25(11Q13.3) MUTATED 73 116 29
AMP PEAK 25(11Q13.3) WILD-TYPE 93 94 220

Figure S135.  Get High-res Image Gene #25: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

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

Table S136.  Gene #25: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 25(11Q13.3) MUTATED 76 88 41
AMP PEAK 25(11Q13.3) WILD-TYPE 172 69 131

Figure S136.  Get High-res Image Gene #25: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0412 (Fisher's exact test), Q value = 0.068

Table S137.  Gene #25: 'amp_11q13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
AMP PEAK 25(11Q13.3) MUTATED 92 47 26
AMP PEAK 25(11Q13.3) WILD-TYPE 181 63 73

Figure S137.  Get High-res Image Gene #25: 'amp_11q13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 0.00267 (Fisher's exact test), Q value = 0.006

Table S138.  Gene #25: 'amp_11q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
AMP PEAK 25(11Q13.3) MUTATED 35 49 14 4
AMP PEAK 25(11Q13.3) WILD-TYPE 46 20 8 7

Figure S138.  Get High-res Image Gene #25: 'amp_11q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00217 (Fisher's exact test), Q value = 0.0049

Table S139.  Gene #25: 'amp_11q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 25(11Q13.3) MUTATED 27 10 65
AMP PEAK 25(11Q13.3) WILD-TYPE 40 10 31

Figure S139.  Get High-res Image Gene #25: 'amp_11q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

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

Table S140.  Gene #25: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 25(11Q13.3) MUTATED 93 102 20
AMP PEAK 25(11Q13.3) WILD-TYPE 70 226 106

Figure S140.  Get High-res Image Gene #25: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S141.  Gene #25: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 25(11Q13.3) MUTATED 49 53 35 67 11
AMP PEAK 25(11Q13.3) WILD-TYPE 78 90 129 27 78

Figure S141.  Get High-res Image Gene #25: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CNMF'

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

Table S142.  Gene #25: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
AMP PEAK 25(11Q13.3) MUTATED 84 65 42
AMP PEAK 25(11Q13.3) WILD-TYPE 61 140 127

Figure S142.  Get High-res Image Gene #25: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S143.  Gene #25: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 25(11Q13.3) MUTATED 73 36 16 66
AMP PEAK 25(11Q13.3) WILD-TYPE 125 94 83 26

Figure S143.  Get High-res Image Gene #25: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p12.1' versus 'CN_CNMF'

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

Table S144.  Gene #26: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 26(12P12.1) MUTATED 48 113 46
AMP PEAK 26(12P12.1) WILD-TYPE 118 97 203

Figure S144.  Get High-res Image Gene #26: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p12.1' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.6e-05

Table S145.  Gene #26: 'amp_12p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 26(12P12.1) MUTATED 73 79 46
AMP PEAK 26(12P12.1) WILD-TYPE 175 78 126

Figure S145.  Get High-res Image Gene #26: 'amp_12p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.036

Table S146.  Gene #26: 'amp_12p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
AMP PEAK 26(12P12.1) MUTATED 25 36 13 5
AMP PEAK 26(12P12.1) WILD-TYPE 56 33 9 6

Figure S146.  Get High-res Image Gene #26: 'amp_12p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0291 (Fisher's exact test), Q value = 0.05

Table S147.  Gene #26: 'amp_12p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 26(12P12.1) MUTATED 21 8 50
AMP PEAK 26(12P12.1) WILD-TYPE 46 12 46

Figure S147.  Get High-res Image Gene #26: 'amp_12p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00029

Table S148.  Gene #26: 'amp_12p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 26(12P12.1) MUTATED 77 93 34
AMP PEAK 26(12P12.1) WILD-TYPE 86 235 92

Figure S148.  Get High-res Image Gene #26: 'amp_12p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_12p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00245 (Fisher's exact test), Q value = 0.0055

Table S149.  Gene #26: 'amp_12p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 26(12P12.1) MUTATED 44 43 49 47 21
AMP PEAK 26(12P12.1) WILD-TYPE 83 100 115 47 68

Figure S149.  Get High-res Image Gene #26: 'amp_12p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00057

Table S150.  Gene #26: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
AMP PEAK 26(12P12.1) MUTATED 70 62 46
AMP PEAK 26(12P12.1) WILD-TYPE 75 143 123

Figure S150.  Get High-res Image Gene #26: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.0014

Table S151.  Gene #26: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 26(12P12.1) MUTATED 65 44 22 47
AMP PEAK 26(12P12.1) WILD-TYPE 133 86 77 45

Figure S151.  Get High-res Image Gene #26: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

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

Table S152.  Gene #27: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 27(12Q15) MUTATED 35 86 40
AMP PEAK 27(12Q15) WILD-TYPE 131 124 209

Figure S152.  Get High-res Image Gene #27: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.039

Table S153.  Gene #27: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 27(12Q15) MUTATED 56 54 40
AMP PEAK 27(12Q15) WILD-TYPE 192 103 132

Figure S153.  Get High-res Image Gene #27: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0186 (Fisher's exact test), Q value = 0.034

Table S154.  Gene #27: 'amp_12q15' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 27(12Q15) MUTATED 40 25 50 26 17
AMP PEAK 27(12Q15) WILD-TYPE 87 118 114 68 72

Figure S154.  Get High-res Image Gene #27: 'amp_12q15' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0347 (Fisher's exact test), Q value = 0.059

Table S155.  Gene #27: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
AMP PEAK 27(12Q15) MUTATED 46 51 32
AMP PEAK 27(12Q15) WILD-TYPE 99 154 137

Figure S155.  Get High-res Image Gene #27: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_13q12.3' versus 'CN_CNMF'

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

Table S156.  Gene #28: 'amp_13q12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 28(13Q12.3) MUTATED 120 43 53
AMP PEAK 28(13Q12.3) WILD-TYPE 46 167 196

Figure S156.  Get High-res Image Gene #28: 'amp_13q12.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q12.3' versus 'MRNASEQ_CNMF'

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

Table S157.  Gene #28: 'amp_13q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
AMP PEAK 28(13Q12.3) MUTATED 34 8 1 3
AMP PEAK 28(13Q12.3) WILD-TYPE 47 61 21 8

Figure S157.  Get High-res Image Gene #28: 'amp_13q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q12.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S158.  Gene #28: 'amp_13q12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 28(13Q12.3) MUTATED 25 12 9
AMP PEAK 28(13Q12.3) WILD-TYPE 42 8 87

Figure S158.  Get High-res Image Gene #28: 'amp_13q12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_13q12.3' versus 'MIRSEQ_CNMF'

P value = 0.00393 (Fisher's exact test), Q value = 0.0084

Table S159.  Gene #28: 'amp_13q12.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 28(13Q12.3) MUTATED 44 133 36
AMP PEAK 28(13Q12.3) WILD-TYPE 119 195 90

Figure S159.  Get High-res Image Gene #28: 'amp_13q12.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_13q12.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S160.  Gene #28: 'amp_13q12.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 28(13Q12.3) MUTATED 72 68 38 9 26
AMP PEAK 28(13Q12.3) WILD-TYPE 55 75 126 85 63

Figure S160.  Get High-res Image Gene #28: 'amp_13q12.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_13q12.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S161.  Gene #28: 'amp_13q12.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 28(13Q12.3) MUTATED 88 42 36 9
AMP PEAK 28(13Q12.3) WILD-TYPE 110 88 63 83

Figure S161.  Get High-res Image Gene #28: 'amp_13q12.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q22.1' versus 'CN_CNMF'

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

Table S162.  Gene #29: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 29(13Q22.1) MUTATED 131 55 57
AMP PEAK 29(13Q22.1) WILD-TYPE 35 155 192

Figure S162.  Get High-res Image Gene #29: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q22.1' versus 'METHLYATION_CNMF'

P value = 0.00216 (Fisher's exact test), Q value = 0.0049

Table S163.  Gene #29: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 29(13Q22.1) MUTATED 101 72 48
AMP PEAK 29(13Q22.1) WILD-TYPE 147 85 124

Figure S163.  Get High-res Image Gene #29: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CNMF'

P value = 0.0276 (Fisher's exact test), Q value = 0.048

Table S164.  Gene #29: 'amp_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
AMP PEAK 29(13Q22.1) MUTATED 37 17 6 2
AMP PEAK 29(13Q22.1) WILD-TYPE 44 52 16 9

Figure S164.  Get High-res Image Gene #29: 'amp_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S165.  Gene #29: 'amp_13q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 29(13Q22.1) MUTATED 29 12 21
AMP PEAK 29(13Q22.1) WILD-TYPE 38 8 75

Figure S165.  Get High-res Image Gene #29: 'amp_13q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_CNMF'

P value = 0.0316 (Fisher's exact test), Q value = 0.054

Table S166.  Gene #29: 'amp_13q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 29(13Q22.1) MUTATED 66 136 36
AMP PEAK 29(13Q22.1) WILD-TYPE 97 192 90

Figure S166.  Get High-res Image Gene #29: 'amp_13q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_13q22.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S167.  Gene #29: 'amp_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 29(13Q22.1) MUTATED 78 76 38 19 27
AMP PEAK 29(13Q22.1) WILD-TYPE 49 67 126 75 62

Figure S167.  Get High-res Image Gene #29: 'amp_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.7e-05

Table S168.  Gene #29: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 29(13Q22.1) MUTATED 101 46 33 19
AMP PEAK 29(13Q22.1) WILD-TYPE 97 84 66 73

Figure S168.  Get High-res Image Gene #29: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_14q13.3' versus 'CN_CNMF'

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

Table S169.  Gene #30: 'amp_14q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 30(14Q13.3) MUTATED 34 69 10
AMP PEAK 30(14Q13.3) WILD-TYPE 132 141 239

Figure S169.  Get High-res Image Gene #30: 'amp_14q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_14q13.3' versus 'METHLYATION_CNMF'

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

Table S170.  Gene #30: 'amp_14q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 30(14Q13.3) MUTATED 34 53 20
AMP PEAK 30(14Q13.3) WILD-TYPE 214 104 152

Figure S170.  Get High-res Image Gene #30: 'amp_14q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_14q13.3' versus 'MRNASEQ_CNMF'

P value = 0.0327 (Fisher's exact test), Q value = 0.056

Table S171.  Gene #30: 'amp_14q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
AMP PEAK 30(14Q13.3) MUTATED 18 30 9 3
AMP PEAK 30(14Q13.3) WILD-TYPE 63 39 13 8

Figure S171.  Get High-res Image Gene #30: 'amp_14q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_14q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00464 (Fisher's exact test), Q value = 0.0097

Table S172.  Gene #30: 'amp_14q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 30(14Q13.3) MUTATED 17 2 41
AMP PEAK 30(14Q13.3) WILD-TYPE 50 18 55

Figure S172.  Get High-res Image Gene #30: 'amp_14q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_14q13.3' versus 'MIRSEQ_CNMF'

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

Table S173.  Gene #30: 'amp_14q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 30(14Q13.3) MUTATED 55 44 12
AMP PEAK 30(14Q13.3) WILD-TYPE 108 284 114

Figure S173.  Get High-res Image Gene #30: 'amp_14q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_14q13.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S174.  Gene #30: 'amp_14q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 30(14Q13.3) MUTATED 21 26 11 41 12
AMP PEAK 30(14Q13.3) WILD-TYPE 106 117 153 53 77

Figure S174.  Get High-res Image Gene #30: 'amp_14q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_14q13.3' versus 'MIRSEQ_MATURE_CNMF'

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

Table S175.  Gene #30: 'amp_14q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
AMP PEAK 30(14Q13.3) MUTATED 46 27 26
AMP PEAK 30(14Q13.3) WILD-TYPE 99 178 143

Figure S175.  Get High-res Image Gene #30: 'amp_14q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_14q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S176.  Gene #30: 'amp_14q13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 30(14Q13.3) MUTATED 35 13 10 41
AMP PEAK 30(14Q13.3) WILD-TYPE 163 117 89 51

Figure S176.  Get High-res Image Gene #30: 'amp_14q13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_15q26.1' versus 'CN_CNMF'

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

Table S177.  Gene #31: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 31(15Q26.1) MUTATED 67 75 26
AMP PEAK 31(15Q26.1) WILD-TYPE 99 135 223

Figure S177.  Get High-res Image Gene #31: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_15q26.1' versus 'RPPA_CNMF'

P value = 0.00227 (Fisher's exact test), Q value = 0.0051

Table S178.  Gene #31: 'amp_15q26.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 137 136 64
AMP PEAK 31(15Q26.1) MUTATED 37 43 22 25
AMP PEAK 31(15Q26.1) WILD-TYPE 108 94 114 39

Figure S178.  Get High-res Image Gene #31: 'amp_15q26.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_15q26.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0069 (Fisher's exact test), Q value = 0.014

Table S179.  Gene #31: 'amp_15q26.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
AMP PEAK 31(15Q26.1) MUTATED 75 37 15
AMP PEAK 31(15Q26.1) WILD-TYPE 198 73 84

Figure S179.  Get High-res Image Gene #31: 'amp_15q26.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_15q26.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0446 (Fisher's exact test), Q value = 0.072

Table S180.  Gene #31: 'amp_15q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 31(15Q26.1) MUTATED 24 9 21
AMP PEAK 31(15Q26.1) WILD-TYPE 43 11 75

Figure S180.  Get High-res Image Gene #31: 'amp_15q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.1' versus 'MIRSEQ_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0013

Table S181.  Gene #31: 'amp_15q26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 31(15Q26.1) MUTATED 57 90 19
AMP PEAK 31(15Q26.1) WILD-TYPE 106 238 107

Figure S181.  Get High-res Image Gene #31: 'amp_15q26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_15q26.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00018

Table S182.  Gene #31: 'amp_15q26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 31(15Q26.1) MUTATED 52 43 40 20 11
AMP PEAK 31(15Q26.1) WILD-TYPE 75 100 124 74 78

Figure S182.  Get High-res Image Gene #31: 'amp_15q26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_15q26.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0345 (Fisher's exact test), Q value = 0.058

Table S183.  Gene #31: 'amp_15q26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
AMP PEAK 31(15Q26.1) MUTATED 48 64 36
AMP PEAK 31(15Q26.1) WILD-TYPE 97 141 133

Figure S183.  Get High-res Image Gene #31: 'amp_15q26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_15q26.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00047

Table S184.  Gene #31: 'amp_15q26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 31(15Q26.1) MUTATED 77 34 16 21
AMP PEAK 31(15Q26.1) WILD-TYPE 121 96 83 71

Figure S184.  Get High-res Image Gene #31: 'amp_15q26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

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

Table S185.  Gene #32: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 32(17Q12) MUTATED 98 87 37
AMP PEAK 32(17Q12) WILD-TYPE 68 123 212

Figure S185.  Get High-res Image Gene #32: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00045

Table S186.  Gene #32: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 32(17Q12) MUTATED 95 71 42
AMP PEAK 32(17Q12) WILD-TYPE 153 86 130

Figure S186.  Get High-res Image Gene #32: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.051

Table S187.  Gene #32: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
AMP PEAK 32(17Q12) MUTATED 43 23 6 3
AMP PEAK 32(17Q12) WILD-TYPE 38 46 16 8

Figure S187.  Get High-res Image Gene #32: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00274 (Fisher's exact test), Q value = 0.006

Table S188.  Gene #32: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 32(17Q12) MUTATED 38 8 29
AMP PEAK 32(17Q12) WILD-TYPE 29 12 67

Figure S188.  Get High-res Image Gene #32: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.039

Table S189.  Gene #32: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 32(17Q12) MUTATED 66 120 32
AMP PEAK 32(17Q12) WILD-TYPE 97 208 94

Figure S189.  Get High-res Image Gene #32: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.7e-05

Table S190.  Gene #32: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 32(17Q12) MUTATED 64 59 47 29 19
AMP PEAK 32(17Q12) WILD-TYPE 63 84 117 65 70

Figure S190.  Get High-res Image Gene #32: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00085 (Fisher's exact test), Q value = 0.0021

Table S191.  Gene #32: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 32(17Q12) MUTATED 89 45 22 28
AMP PEAK 32(17Q12) WILD-TYPE 109 85 77 64

Figure S191.  Get High-res Image Gene #32: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18p11.32' versus 'CN_CNMF'

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

Table S192.  Gene #33: 'amp_18p11.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 33(18P11.32) MUTATED 55 90 33
AMP PEAK 33(18P11.32) WILD-TYPE 111 120 216

Figure S192.  Get High-res Image Gene #33: 'amp_18p11.32' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18p11.32' versus 'METHLYATION_CNMF'

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

Table S193.  Gene #33: 'amp_18p11.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 33(18P11.32) MUTATED 49 78 41
AMP PEAK 33(18P11.32) WILD-TYPE 199 79 131

Figure S193.  Get High-res Image Gene #33: 'amp_18p11.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_18p11.32' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.7e-05

Table S194.  Gene #33: 'amp_18p11.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 33(18P11.32) MUTATED 67 89 20
AMP PEAK 33(18P11.32) WILD-TYPE 96 239 106

Figure S194.  Get High-res Image Gene #33: 'amp_18p11.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_18p11.32' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S195.  Gene #33: 'amp_18p11.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 33(18P11.32) MUTATED 52 40 32 41 11
AMP PEAK 33(18P11.32) WILD-TYPE 75 103 132 53 78

Figure S195.  Get High-res Image Gene #33: 'amp_18p11.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_18p11.32' versus 'MIRSEQ_MATURE_CNMF'

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

Table S196.  Gene #33: 'amp_18p11.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
AMP PEAK 33(18P11.32) MUTATED 58 60 34
AMP PEAK 33(18P11.32) WILD-TYPE 87 145 135

Figure S196.  Get High-res Image Gene #33: 'amp_18p11.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_18p11.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.00075

Table S197.  Gene #33: 'amp_18p11.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 33(18P11.32) MUTATED 65 30 17 40
AMP PEAK 33(18P11.32) WILD-TYPE 133 100 82 52

Figure S197.  Get High-res Image Gene #33: 'amp_18p11.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18q11.2' versus 'CN_CNMF'

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

Table S198.  Gene #34: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 34(18Q11.2) MUTATED 76 77 45
AMP PEAK 34(18Q11.2) WILD-TYPE 90 133 204

Figure S198.  Get High-res Image Gene #34: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CNMF'

P value = 0.0397 (Fisher's exact test), Q value = 0.066

Table S199.  Gene #34: 'amp_18q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
AMP PEAK 34(18Q11.2) MUTATED 35 18 4 2
AMP PEAK 34(18Q11.2) WILD-TYPE 46 51 18 9

Figure S199.  Get High-res Image Gene #34: 'amp_18q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00465 (Fisher's exact test), Q value = 0.0097

Table S200.  Gene #34: 'amp_18q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 34(18Q11.2) MUTATED 28 10 21
AMP PEAK 34(18Q11.2) WILD-TYPE 39 10 75

Figure S200.  Get High-res Image Gene #34: 'amp_18q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_CNMF'

P value = 0.0465 (Fisher's exact test), Q value = 0.075

Table S201.  Gene #34: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 34(18Q11.2) MUTATED 49 117 30
AMP PEAK 34(18Q11.2) WILD-TYPE 114 211 96

Figure S201.  Get High-res Image Gene #34: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.00062

Table S202.  Gene #34: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 34(18Q11.2) MUTATED 60 50 43 21 22
AMP PEAK 34(18Q11.2) WILD-TYPE 67 93 121 73 67

Figure S202.  Get High-res Image Gene #34: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0332 (Fisher's exact test), Q value = 0.057

Table S203.  Gene #34: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
AMP PEAK 34(18Q11.2) MUTATED 42 76 42
AMP PEAK 34(18Q11.2) WILD-TYPE 103 129 127

Figure S203.  Get High-res Image Gene #34: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00469 (Fisher's exact test), Q value = 0.0098

Table S204.  Gene #34: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 34(18Q11.2) MUTATED 78 39 23 20
AMP PEAK 34(18Q11.2) WILD-TYPE 120 91 76 72

Figure S204.  Get High-res Image Gene #34: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

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

Table S205.  Gene #35: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 35(19P13.2) MUTATED 28 39 12
AMP PEAK 35(19P13.2) WILD-TYPE 138 171 237

Figure S205.  Get High-res Image Gene #35: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19p13.2' versus 'METHLYATION_CNMF'

P value = 0.0017 (Fisher's exact test), Q value = 0.004

Table S206.  Gene #35: 'amp_19p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 35(19P13.2) MUTATED 31 32 12
AMP PEAK 35(19P13.2) WILD-TYPE 217 125 160

Figure S206.  Get High-res Image Gene #35: 'amp_19p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0407 (Fisher's exact test), Q value = 0.067

Table S207.  Gene #35: 'amp_19p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 35(19P13.2) MUTATED 13 21 14 20 9
AMP PEAK 35(19P13.2) WILD-TYPE 114 122 150 74 80

Figure S207.  Get High-res Image Gene #35: 'amp_19p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0441 (Fisher's exact test), Q value = 0.072

Table S208.  Gene #35: 'amp_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
AMP PEAK 35(19P13.2) MUTATED 24 28 13
AMP PEAK 35(19P13.2) WILD-TYPE 121 177 156

Figure S208.  Get High-res Image Gene #35: 'amp_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0425 (Fisher's exact test), Q value = 0.07

Table S209.  Gene #35: 'amp_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 35(19P13.2) MUTATED 26 15 6 18
AMP PEAK 35(19P13.2) WILD-TYPE 172 115 93 74

Figure S209.  Get High-res Image Gene #35: 'amp_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

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

Table S210.  Gene #36: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 36(19Q12) MUTATED 86 75 24
AMP PEAK 36(19Q12) WILD-TYPE 80 135 225

Figure S210.  Get High-res Image Gene #36: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

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

Table S211.  Gene #36: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 36(19Q12) MUTATED 63 69 41
AMP PEAK 36(19Q12) WILD-TYPE 185 88 131

Figure S211.  Get High-res Image Gene #36: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q12' versus 'RPPA_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.00082

Table S212.  Gene #36: 'amp_19q12' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 137 136 64
AMP PEAK 36(19Q12) MUTATED 61 31 29 18
AMP PEAK 36(19Q12) WILD-TYPE 84 106 107 46

Figure S212.  Get High-res Image Gene #36: 'amp_19q12' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_19q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00112 (Fisher's exact test), Q value = 0.0027

Table S213.  Gene #36: 'amp_19q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
AMP PEAK 36(19Q12) MUTATED 97 23 19
AMP PEAK 36(19Q12) WILD-TYPE 176 87 80

Figure S213.  Get High-res Image Gene #36: 'amp_19q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 0.043

Table S214.  Gene #36: 'amp_19q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 36(19Q12) MUTATED 62 91 31
AMP PEAK 36(19Q12) WILD-TYPE 101 237 95

Figure S214.  Get High-res Image Gene #36: 'amp_19q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S215.  Gene #36: 'amp_19q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 36(19Q12) MUTATED 83 37 24 23 17
AMP PEAK 36(19Q12) WILD-TYPE 44 106 140 71 72

Figure S215.  Get High-res Image Gene #36: 'amp_19q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00047

Table S216.  Gene #36: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 36(19Q12) MUTATED 83 28 25 22
AMP PEAK 36(19Q12) WILD-TYPE 115 102 74 70

Figure S216.  Get High-res Image Gene #36: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q13.43' versus 'CN_CNMF'

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

Table S217.  Gene #37: 'amp_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 37(19Q13.43) MUTATED 62 71 31
AMP PEAK 37(19Q13.43) WILD-TYPE 104 139 218

Figure S217.  Get High-res Image Gene #37: 'amp_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q13.43' versus 'METHLYATION_CNMF'

P value = 0.0434 (Fisher's exact test), Q value = 0.071

Table S218.  Gene #37: 'amp_19q13.43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 37(19Q13.43) MUTATED 70 49 34
AMP PEAK 37(19Q13.43) WILD-TYPE 178 108 138

Figure S218.  Get High-res Image Gene #37: 'amp_19q13.43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q13.43' versus 'RPPA_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.024

Table S219.  Gene #37: 'amp_19q13.43' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 137 136 64
AMP PEAK 37(19Q13.43) MUTATED 50 27 29 12
AMP PEAK 37(19Q13.43) WILD-TYPE 95 110 107 52

Figure S219.  Get High-res Image Gene #37: 'amp_19q13.43' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_19q13.43' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S220.  Gene #37: 'amp_19q13.43' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 37(19Q13.43) MUTATED 52 44 29 23 14
AMP PEAK 37(19Q13.43) WILD-TYPE 75 99 135 71 75

Figure S220.  Get High-res Image Gene #37: 'amp_19q13.43' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_19q13.43' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00173 (Fisher's exact test), Q value = 0.004

Table S221.  Gene #37: 'amp_19q13.43' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
AMP PEAK 37(19Q13.43) MUTATED 50 57 29
AMP PEAK 37(19Q13.43) WILD-TYPE 95 148 140

Figure S221.  Get High-res Image Gene #37: 'amp_19q13.43' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_19q13.43' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00414 (Fisher's exact test), Q value = 0.0088

Table S222.  Gene #37: 'amp_19q13.43' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 37(19Q13.43) MUTATED 69 28 17 22
AMP PEAK 37(19Q13.43) WILD-TYPE 129 102 82 70

Figure S222.  Get High-res Image Gene #37: 'amp_19q13.43' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.2' versus 'CN_CNMF'

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

Table S223.  Gene #38: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 38(20Q13.2) MUTATED 153 154 109
AMP PEAK 38(20Q13.2) WILD-TYPE 13 56 140

Figure S223.  Get High-res Image Gene #38: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0242 (Fisher's exact test), Q value = 0.043

Table S224.  Gene #38: 'amp_20q13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
AMP PEAK 38(20Q13.2) MUTATED 190 75 54
AMP PEAK 38(20Q13.2) WILD-TYPE 83 35 45

Figure S224.  Get High-res Image Gene #38: 'amp_20q13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_20q13.2' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00047

Table S225.  Gene #38: 'amp_20q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
AMP PEAK 38(20Q13.2) MUTATED 68 38 11 6
AMP PEAK 38(20Q13.2) WILD-TYPE 13 31 11 5

Figure S225.  Get High-res Image Gene #38: 'amp_20q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_20q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00016

Table S226.  Gene #38: 'amp_20q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 38(20Q13.2) MUTATED 56 16 51
AMP PEAK 38(20Q13.2) WILD-TYPE 11 4 45

Figure S226.  Get High-res Image Gene #38: 'amp_20q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_CNMF'

P value = 0.0434 (Fisher's exact test), Q value = 0.071

Table S227.  Gene #38: 'amp_20q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 38(20Q13.2) MUTATED 110 228 72
AMP PEAK 38(20Q13.2) WILD-TYPE 53 100 54

Figure S227.  Get High-res Image Gene #38: 'amp_20q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_20q13.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S228.  Gene #38: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 38(20Q13.2) MUTATED 119 102 95 49 45
AMP PEAK 38(20Q13.2) WILD-TYPE 8 41 69 45 44

Figure S228.  Get High-res Image Gene #38: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S229.  Gene #38: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 38(20Q13.2) MUTATED 157 75 61 49
AMP PEAK 38(20Q13.2) WILD-TYPE 41 55 38 43

Figure S229.  Get High-res Image Gene #38: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xq28' versus 'CN_CNMF'

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

Table S230.  Gene #39: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
AMP PEAK 39(XQ28) MUTATED 47 78 29
AMP PEAK 39(XQ28) WILD-TYPE 119 132 220

Figure S230.  Get High-res Image Gene #39: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq28' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.6e-05

Table S231.  Gene #39: 'amp_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
AMP PEAK 39(XQ28) MUTATED 65 55 24
AMP PEAK 39(XQ28) WILD-TYPE 183 102 148

Figure S231.  Get High-res Image Gene #39: 'amp_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xq28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0263 (Fisher's exact test), Q value = 0.046

Table S232.  Gene #39: 'amp_xq28' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
AMP PEAK 39(XQ28) MUTATED 18 6 45
AMP PEAK 39(XQ28) WILD-TYPE 49 14 51

Figure S232.  Get High-res Image Gene #39: 'amp_xq28' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_CNMF'

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

Table S233.  Gene #39: 'amp_xq28' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
AMP PEAK 39(XQ28) MUTATED 62 75 15
AMP PEAK 39(XQ28) WILD-TYPE 101 253 111

Figure S233.  Get High-res Image Gene #39: 'amp_xq28' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_xq28' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S234.  Gene #39: 'amp_xq28' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
AMP PEAK 39(XQ28) MUTATED 30 42 21 45 14
AMP PEAK 39(XQ28) WILD-TYPE 97 101 143 49 75

Figure S234.  Get High-res Image Gene #39: 'amp_xq28' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00452 (Fisher's exact test), Q value = 0.0095

Table S235.  Gene #39: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
AMP PEAK 39(XQ28) MUTATED 51 47 33
AMP PEAK 39(XQ28) WILD-TYPE 94 158 136

Figure S235.  Get High-res Image Gene #39: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_xq28' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S236.  Gene #39: 'amp_xq28' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
AMP PEAK 39(XQ28) MUTATED 51 20 16 44
AMP PEAK 39(XQ28) WILD-TYPE 147 110 83 48

Figure S236.  Get High-res Image Gene #39: 'amp_xq28' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.11' versus 'CN_CNMF'

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

Table S237.  Gene #40: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 1(1P36.11) MUTATED 90 98 22
DEL PEAK 1(1P36.11) WILD-TYPE 76 112 227

Figure S237.  Get High-res Image Gene #40: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 9e-04

Table S238.  Gene #40: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 1(1P36.11) MUTATED 85 68 39
DEL PEAK 1(1P36.11) WILD-TYPE 163 89 133

Figure S238.  Get High-res Image Gene #40: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.11' versus 'RPPA_CNMF'

P value = 0.0052 (Fisher's exact test), Q value = 0.011

Table S239.  Gene #40: 'del_1p36.11' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 137 136 64
DEL PEAK 1(1P36.11) MUTATED 47 54 28 23
DEL PEAK 1(1P36.11) WILD-TYPE 98 83 108 41

Figure S239.  Get High-res Image Gene #40: 'del_1p36.11' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_1p36.11' versus 'RPPA_CHIERARCHICAL'

P value = 0.00247 (Fisher's exact test), Q value = 0.0055

Table S240.  Gene #40: 'del_1p36.11' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
DEL PEAK 1(1P36.11) MUTATED 88 45 19
DEL PEAK 1(1P36.11) WILD-TYPE 185 65 80

Figure S240.  Get High-res Image Gene #40: 'del_1p36.11' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 0.00286 (Fisher's exact test), Q value = 0.0063

Table S241.  Gene #40: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
DEL PEAK 1(1P36.11) MUTATED 44 21 9 1
DEL PEAK 1(1P36.11) WILD-TYPE 37 48 13 10

Figure S241.  Get High-res Image Gene #40: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0234 (Fisher's exact test), Q value = 0.042

Table S242.  Gene #40: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 1(1P36.11) MUTATED 36 8 31
DEL PEAK 1(1P36.11) WILD-TYPE 31 12 65

Figure S242.  Get High-res Image Gene #40: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00018

Table S243.  Gene #40: 'del_1p36.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 1(1P36.11) MUTATED 64 121 22
DEL PEAK 1(1P36.11) WILD-TYPE 99 207 104

Figure S243.  Get High-res Image Gene #40: 'del_1p36.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p36.11' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S244.  Gene #40: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 1(1P36.11) MUTATED 66 55 41 30 15
DEL PEAK 1(1P36.11) WILD-TYPE 61 88 123 64 74

Figure S244.  Get High-res Image Gene #40: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00197 (Fisher's exact test), Q value = 0.0045

Table S245.  Gene #40: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 1(1P36.11) MUTATED 61 75 41
DEL PEAK 1(1P36.11) WILD-TYPE 84 130 128

Figure S245.  Get High-res Image Gene #40: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00016

Table S246.  Gene #40: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 1(1P36.11) MUTATED 91 34 21 31
DEL PEAK 1(1P36.11) WILD-TYPE 107 96 78 61

Figure S246.  Get High-res Image Gene #40: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p13.2' versus 'CN_CNMF'

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

Table S247.  Gene #41: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 2(1P13.2) MUTATED 68 77 11
DEL PEAK 2(1P13.2) WILD-TYPE 98 133 238

Figure S247.  Get High-res Image Gene #41: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p13.2' versus 'METHLYATION_CNMF'

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

Table S248.  Gene #41: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 2(1P13.2) MUTATED 64 68 15
DEL PEAK 2(1P13.2) WILD-TYPE 184 89 157

Figure S248.  Get High-res Image Gene #41: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p13.2' versus 'MIRSEQ_CNMF'

P value = 0.00513 (Fisher's exact test), Q value = 0.011

Table S249.  Gene #41: 'del_1p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 2(1P13.2) MUTATED 48 88 18
DEL PEAK 2(1P13.2) WILD-TYPE 115 240 108

Figure S249.  Get High-res Image Gene #41: 'del_1p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p13.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S250.  Gene #41: 'del_1p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 2(1P13.2) MUTATED 41 46 25 32 10
DEL PEAK 2(1P13.2) WILD-TYPE 86 97 139 62 79

Figure S250.  Get High-res Image Gene #41: 'del_1p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00544 (Fisher's exact test), Q value = 0.011

Table S251.  Gene #41: 'del_1p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 2(1P13.2) MUTATED 50 54 31
DEL PEAK 2(1P13.2) WILD-TYPE 95 151 138

Figure S251.  Get High-res Image Gene #41: 'del_1p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00828 (Fisher's exact test), Q value = 0.016

Table S252.  Gene #41: 'del_1p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 2(1P13.2) MUTATED 58 30 15 32
DEL PEAK 2(1P13.2) WILD-TYPE 140 100 84 60

Figure S252.  Get High-res Image Gene #41: 'del_1p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1q44' versus 'CN_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.025

Table S253.  Gene #42: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 3(1Q44) MUTATED 19 17 10
DEL PEAK 3(1Q44) WILD-TYPE 147 193 239

Figure S253.  Get High-res Image Gene #42: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q44' versus 'MIRSEQ_CNMF'

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

Table S254.  Gene #42: 'del_1q44' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 3(1Q44) MUTATED 10 33 2
DEL PEAK 3(1Q44) WILD-TYPE 153 295 124

Figure S254.  Get High-res Image Gene #42: 'del_1q44' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1q44' versus 'METHLYATION_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.022

Table S255.  Gene #43: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 4(1Q44) MUTATED 21 17 5
DEL PEAK 4(1Q44) WILD-TYPE 227 140 167

Figure S255.  Get High-res Image Gene #43: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.1' versus 'CN_CNMF'

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

Table S256.  Gene #44: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 5(2Q22.1) MUTATED 34 74 18
DEL PEAK 5(2Q22.1) WILD-TYPE 132 136 231

Figure S256.  Get High-res Image Gene #44: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

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

Table S257.  Gene #44: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 5(2Q22.1) MUTATED 31 68 20
DEL PEAK 5(2Q22.1) WILD-TYPE 217 89 152

Figure S257.  Get High-res Image Gene #44: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0245 (Fisher's exact test), Q value = 0.043

Table S258.  Gene #44: 'del_2q22.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
DEL PEAK 5(2Q22.1) MUTATED 67 20 12
DEL PEAK 5(2Q22.1) WILD-TYPE 206 90 87

Figure S258.  Get High-res Image Gene #44: 'del_2q22.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_2q22.1' versus 'MRNASEQ_CNMF'

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

Table S259.  Gene #44: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
DEL PEAK 5(2Q22.1) MUTATED 11 34 12 1
DEL PEAK 5(2Q22.1) WILD-TYPE 70 35 10 10

Figure S259.  Get High-res Image Gene #44: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q22.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S260.  Gene #44: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 5(2Q22.1) MUTATED 6 6 46
DEL PEAK 5(2Q22.1) WILD-TYPE 61 14 50

Figure S260.  Get High-res Image Gene #44: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_CNMF'

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

Table S261.  Gene #44: 'del_2q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 5(2Q22.1) MUTATED 59 56 10
DEL PEAK 5(2Q22.1) WILD-TYPE 104 272 116

Figure S261.  Get High-res Image Gene #44: 'del_2q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S262.  Gene #44: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 5(2Q22.1) MUTATED 33 18 21 46 7
DEL PEAK 5(2Q22.1) WILD-TYPE 94 125 143 48 82

Figure S262.  Get High-res Image Gene #44: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_MATURE_CNMF'

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

Table S263.  Gene #44: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 5(2Q22.1) MUTATED 58 31 19
DEL PEAK 5(2Q22.1) WILD-TYPE 87 174 150

Figure S263.  Get High-res Image Gene #44: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_2q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S264.  Gene #44: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 5(2Q22.1) MUTATED 37 17 8 46
DEL PEAK 5(2Q22.1) WILD-TYPE 161 113 91 46

Figure S264.  Get High-res Image Gene #44: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q32.1' versus 'CN_CNMF'

P value = 0.00075 (Fisher's exact test), Q value = 0.0019

Table S265.  Gene #45: 'del_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 6(2Q32.1) MUTATED 34 33 20
DEL PEAK 6(2Q32.1) WILD-TYPE 132 177 229

Figure S265.  Get High-res Image Gene #45: 'del_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q32.1' versus 'METHLYATION_CNMF'

P value = 0.00869 (Fisher's exact test), Q value = 0.017

Table S266.  Gene #45: 'del_2q32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 6(2Q32.1) MUTATED 34 31 14
DEL PEAK 6(2Q32.1) WILD-TYPE 214 126 158

Figure S266.  Get High-res Image Gene #45: 'del_2q32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q32.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0182 (Fisher's exact test), Q value = 0.033

Table S267.  Gene #45: 'del_2q32.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 6(2Q32.1) MUTATED 29 14 17 15 11
DEL PEAK 6(2Q32.1) WILD-TYPE 98 129 147 79 78

Figure S267.  Get High-res Image Gene #45: 'del_2q32.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q33.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.7e-05

Table S268.  Gene #46: 'del_2q33.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 7(2Q33.3) MUTATED 31 39 15
DEL PEAK 7(2Q33.3) WILD-TYPE 135 171 234

Figure S268.  Get High-res Image Gene #46: 'del_2q33.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q33.3' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00021

Table S269.  Gene #46: 'del_2q33.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 7(2Q33.3) MUTATED 29 39 14
DEL PEAK 7(2Q33.3) WILD-TYPE 219 118 158

Figure S269.  Get High-res Image Gene #46: 'del_2q33.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q33.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0274 (Fisher's exact test), Q value = 0.048

Table S270.  Gene #46: 'del_2q33.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 7(2Q33.3) MUTATED 7 3 26
DEL PEAK 7(2Q33.3) WILD-TYPE 60 17 70

Figure S270.  Get High-res Image Gene #46: 'del_2q33.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q33.3' versus 'MIRSEQ_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.0016

Table S271.  Gene #46: 'del_2q33.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 7(2Q33.3) MUTATED 36 38 9
DEL PEAK 7(2Q33.3) WILD-TYPE 127 290 117

Figure S271.  Get High-res Image Gene #46: 'del_2q33.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q33.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S272.  Gene #46: 'del_2q33.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 7(2Q33.3) MUTATED 23 15 15 25 5
DEL PEAK 7(2Q33.3) WILD-TYPE 104 128 149 69 84

Figure S272.  Get High-res Image Gene #46: 'del_2q33.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q33.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00275 (Fisher's exact test), Q value = 0.006

Table S273.  Gene #46: 'del_2q33.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 7(2Q33.3) MUTATED 32 19 20
DEL PEAK 7(2Q33.3) WILD-TYPE 113 186 149

Figure S273.  Get High-res Image Gene #46: 'del_2q33.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_2q33.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00132 (Fisher's exact test), Q value = 0.0032

Table S274.  Gene #46: 'del_2q33.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 7(2Q33.3) MUTATED 23 15 8 25
DEL PEAK 7(2Q33.3) WILD-TYPE 175 115 91 67

Figure S274.  Get High-res Image Gene #46: 'del_2q33.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q37.2' versus 'CN_CNMF'

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

Table S275.  Gene #47: 'del_2q37.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 8(2Q37.2) MUTATED 41 63 18
DEL PEAK 8(2Q37.2) WILD-TYPE 125 147 231

Figure S275.  Get High-res Image Gene #47: 'del_2q37.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.2' versus 'METHLYATION_CNMF'

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

Table S276.  Gene #47: 'del_2q37.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 8(2Q37.2) MUTATED 39 55 23
DEL PEAK 8(2Q37.2) WILD-TYPE 209 102 149

Figure S276.  Get High-res Image Gene #47: 'del_2q37.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.2' versus 'MRNASEQ_CNMF'

P value = 0.00181 (Fisher's exact test), Q value = 0.0042

Table S277.  Gene #47: 'del_2q37.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
DEL PEAK 8(2Q37.2) MUTATED 12 29 7 2
DEL PEAK 8(2Q37.2) WILD-TYPE 69 40 15 9

Figure S277.  Get High-res Image Gene #47: 'del_2q37.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q37.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00149 (Fisher's exact test), Q value = 0.0035

Table S278.  Gene #47: 'del_2q37.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 8(2Q37.2) MUTATED 10 3 37
DEL PEAK 8(2Q37.2) WILD-TYPE 57 17 59

Figure S278.  Get High-res Image Gene #47: 'del_2q37.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.2' versus 'MIRSEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00045

Table S279.  Gene #47: 'del_2q37.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 8(2Q37.2) MUTATED 49 57 14
DEL PEAK 8(2Q37.2) WILD-TYPE 114 271 112

Figure S279.  Get High-res Image Gene #47: 'del_2q37.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q37.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S280.  Gene #47: 'del_2q37.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 8(2Q37.2) MUTATED 33 25 19 36 7
DEL PEAK 8(2Q37.2) WILD-TYPE 94 118 145 58 82

Figure S280.  Get High-res Image Gene #47: 'del_2q37.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.027 (Fisher's exact test), Q value = 0.047

Table S281.  Gene #47: 'del_2q37.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 8(2Q37.2) MUTATED 41 38 28
DEL PEAK 8(2Q37.2) WILD-TYPE 104 167 141

Figure S281.  Get High-res Image Gene #47: 'del_2q37.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_2q37.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S282.  Gene #47: 'del_2q37.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 8(2Q37.2) MUTATED 42 18 12 35
DEL PEAK 8(2Q37.2) WILD-TYPE 156 112 87 57

Figure S282.  Get High-res Image Gene #47: 'del_2q37.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p26.2' versus 'CN_CNMF'

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

Table S283.  Gene #48: 'del_3p26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 9(3P26.2) MUTATED 91 129 30
DEL PEAK 9(3P26.2) WILD-TYPE 75 81 219

Figure S283.  Get High-res Image Gene #48: 'del_3p26.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p26.2' versus 'METHLYATION_CNMF'

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

Table S284.  Gene #48: 'del_3p26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 9(3P26.2) MUTATED 86 104 45
DEL PEAK 9(3P26.2) WILD-TYPE 162 53 127

Figure S284.  Get High-res Image Gene #48: 'del_3p26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p26.2' versus 'MRNASEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.00078

Table S285.  Gene #48: 'del_3p26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
DEL PEAK 9(3P26.2) MUTATED 38 55 11 6
DEL PEAK 9(3P26.2) WILD-TYPE 43 14 11 5

Figure S285.  Get High-res Image Gene #48: 'del_3p26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.6e-05

Table S286.  Gene #48: 'del_3p26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 9(3P26.2) MUTATED 27 11 72
DEL PEAK 9(3P26.2) WILD-TYPE 40 9 24

Figure S286.  Get High-res Image Gene #48: 'del_3p26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_CNMF'

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

Table S287.  Gene #48: 'del_3p26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 9(3P26.2) MUTATED 99 120 28
DEL PEAK 9(3P26.2) WILD-TYPE 64 208 98

Figure S287.  Get High-res Image Gene #48: 'del_3p26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p26.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S288.  Gene #48: 'del_3p26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 9(3P26.2) MUTATED 63 56 39 74 15
DEL PEAK 9(3P26.2) WILD-TYPE 64 87 125 20 74

Figure S288.  Get High-res Image Gene #48: 'del_3p26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_MATURE_CNMF'

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

Table S289.  Gene #48: 'del_3p26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 9(3P26.2) MUTATED 94 69 53
DEL PEAK 9(3P26.2) WILD-TYPE 51 136 116

Figure S289.  Get High-res Image Gene #48: 'del_3p26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S290.  Gene #48: 'del_3p26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 9(3P26.2) MUTATED 80 38 25 73
DEL PEAK 9(3P26.2) WILD-TYPE 118 92 74 19

Figure S290.  Get High-res Image Gene #48: 'del_3p26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.2' versus 'CN_CNMF'

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

Table S291.  Gene #49: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 10(3P14.2) MUTATED 95 142 45
DEL PEAK 10(3P14.2) WILD-TYPE 71 68 204

Figure S291.  Get High-res Image Gene #49: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.2' versus 'METHLYATION_CNMF'

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

Table S292.  Gene #49: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 10(3P14.2) MUTATED 107 117 45
DEL PEAK 10(3P14.2) WILD-TYPE 141 40 127

Figure S292.  Get High-res Image Gene #49: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p14.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0371 (Fisher's exact test), Q value = 0.062

Table S293.  Gene #49: 'del_3p14.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
DEL PEAK 10(3P14.2) MUTATED 135 41 38
DEL PEAK 10(3P14.2) WILD-TYPE 138 69 61

Figure S293.  Get High-res Image Gene #49: 'del_3p14.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_3p14.2' versus 'MRNASEQ_CNMF'

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

Table S294.  Gene #49: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
DEL PEAK 10(3P14.2) MUTATED 43 61 14 6
DEL PEAK 10(3P14.2) WILD-TYPE 38 8 8 5

Figure S294.  Get High-res Image Gene #49: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S295.  Gene #49: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 10(3P14.2) MUTATED 31 12 81
DEL PEAK 10(3P14.2) WILD-TYPE 36 8 15

Figure S295.  Get High-res Image Gene #49: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_CNMF'

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

Table S296.  Gene #49: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 10(3P14.2) MUTATED 110 137 32
DEL PEAK 10(3P14.2) WILD-TYPE 53 191 94

Figure S296.  Get High-res Image Gene #49: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p14.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S297.  Gene #49: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 10(3P14.2) MUTATED 68 64 47 83 17
DEL PEAK 10(3P14.2) WILD-TYPE 59 79 117 11 72

Figure S297.  Get High-res Image Gene #49: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CNMF'

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

Table S298.  Gene #49: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 10(3P14.2) MUTATED 103 85 57
DEL PEAK 10(3P14.2) WILD-TYPE 42 120 112

Figure S298.  Get High-res Image Gene #49: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S299.  Gene #49: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 10(3P14.2) MUTATED 90 47 26 82
DEL PEAK 10(3P14.2) WILD-TYPE 108 83 73 10

Figure S299.  Get High-res Image Gene #49: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q11.1' versus 'CN_CNMF'

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

Table S300.  Gene #50: 'del_3q11.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 11(3Q11.1) MUTATED 53 33 12
DEL PEAK 11(3Q11.1) WILD-TYPE 113 177 237

Figure S300.  Get High-res Image Gene #50: 'del_3q11.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q11.1' versus 'METHLYATION_CNMF'

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

Table S301.  Gene #50: 'del_3q11.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 11(3Q11.1) MUTATED 46 36 10
DEL PEAK 11(3Q11.1) WILD-TYPE 202 121 162

Figure S301.  Get High-res Image Gene #50: 'del_3q11.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q11.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S302.  Gene #50: 'del_3q11.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 11(3Q11.1) MUTATED 34 27 11 16 9
DEL PEAK 11(3Q11.1) WILD-TYPE 93 116 153 78 80

Figure S302.  Get High-res Image Gene #50: 'del_3q11.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3q26.31' versus 'CN_CNMF'

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

Table S303.  Gene #51: 'del_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 12(3Q26.31) MUTATED 47 7 9
DEL PEAK 12(3Q26.31) WILD-TYPE 119 203 240

Figure S303.  Get High-res Image Gene #51: 'del_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q26.31' versus 'METHLYATION_CNMF'

P value = 0.00791 (Fisher's exact test), Q value = 0.016

Table S304.  Gene #51: 'del_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 12(3Q26.31) MUTATED 33 18 8
DEL PEAK 12(3Q26.31) WILD-TYPE 215 139 164

Figure S304.  Get High-res Image Gene #51: 'del_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q26.31' versus 'MRNASEQ_CNMF'

P value = 0.00888 (Fisher's exact test), Q value = 0.017

Table S305.  Gene #51: 'del_3q26.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
DEL PEAK 12(3Q26.31) MUTATED 13 1 1 1
DEL PEAK 12(3Q26.31) WILD-TYPE 68 68 21 10

Figure S305.  Get High-res Image Gene #51: 'del_3q26.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3q26.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00047

Table S306.  Gene #51: 'del_3q26.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 12(3Q26.31) MUTATED 12 3 1
DEL PEAK 12(3Q26.31) WILD-TYPE 55 17 95

Figure S306.  Get High-res Image Gene #51: 'del_3q26.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3q26.31' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S307.  Gene #51: 'del_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 12(3Q26.31) MUTATED 26 22 6 2 6
DEL PEAK 12(3Q26.31) WILD-TYPE 101 121 158 92 83

Figure S307.  Get High-res Image Gene #51: 'del_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3q26.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00139 (Fisher's exact test), Q value = 0.0033

Table S308.  Gene #51: 'del_3q26.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 12(3Q26.31) MUTATED 31 9 10 2
DEL PEAK 12(3Q26.31) WILD-TYPE 167 121 89 90

Figure S308.  Get High-res Image Gene #51: 'del_3q26.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p16.3' versus 'CN_CNMF'

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

Table S309.  Gene #52: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 13(4P16.3) MUTATED 104 120 47
DEL PEAK 13(4P16.3) WILD-TYPE 62 90 202

Figure S309.  Get High-res Image Gene #52: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

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

Table S310.  Gene #52: 'del_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 13(4P16.3) MUTATED 98 95 59
DEL PEAK 13(4P16.3) WILD-TYPE 150 62 113

Figure S310.  Get High-res Image Gene #52: 'del_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4p16.3' versus 'MRNASEQ_CNMF'

P value = 0.0398 (Fisher's exact test), Q value = 0.066

Table S311.  Gene #52: 'del_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
DEL PEAK 13(4P16.3) MUTATED 43 44 12 2
DEL PEAK 13(4P16.3) WILD-TYPE 38 25 10 9

Figure S311.  Get High-res Image Gene #52: 'del_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4p16.3' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.7e-05

Table S312.  Gene #52: 'del_4p16.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 13(4P16.3) MUTATED 97 129 44
DEL PEAK 13(4P16.3) WILD-TYPE 66 199 82

Figure S312.  Get High-res Image Gene #52: 'del_4p16.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S313.  Gene #52: 'del_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 13(4P16.3) MUTATED 79 67 41 53 30
DEL PEAK 13(4P16.3) WILD-TYPE 48 76 123 41 59

Figure S313.  Get High-res Image Gene #52: 'del_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

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

Table S314.  Gene #52: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 13(4P16.3) MUTATED 94 72 68
DEL PEAK 13(4P16.3) WILD-TYPE 51 133 101

Figure S314.  Get High-res Image Gene #52: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S315.  Gene #52: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 13(4P16.3) MUTATED 103 34 44 53
DEL PEAK 13(4P16.3) WILD-TYPE 95 96 55 39

Figure S315.  Get High-res Image Gene #52: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p15.2' versus 'CN_CNMF'

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

Table S316.  Gene #53: 'del_4p15.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 14(4P15.2) MUTATED 98 126 45
DEL PEAK 14(4P15.2) WILD-TYPE 68 84 204

Figure S316.  Get High-res Image Gene #53: 'del_4p15.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_4p15.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.7e-05

Table S317.  Gene #53: 'del_4p15.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 14(4P15.2) MUTATED 94 96 59
DEL PEAK 14(4P15.2) WILD-TYPE 154 61 113

Figure S317.  Get High-res Image Gene #53: 'del_4p15.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4p15.2' versus 'MIRSEQ_CNMF'

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

Table S318.  Gene #53: 'del_4p15.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 14(4P15.2) MUTATED 99 126 43
DEL PEAK 14(4P15.2) WILD-TYPE 64 202 83

Figure S318.  Get High-res Image Gene #53: 'del_4p15.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4p15.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S319.  Gene #53: 'del_4p15.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 14(4P15.2) MUTATED 81 63 39 55 30
DEL PEAK 14(4P15.2) WILD-TYPE 46 80 125 39 59

Figure S319.  Get High-res Image Gene #53: 'del_4p15.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4p15.2' versus 'MIRSEQ_MATURE_CNMF'

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

Table S320.  Gene #53: 'del_4p15.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 14(4P15.2) MUTATED 94 70 64
DEL PEAK 14(4P15.2) WILD-TYPE 51 135 105

Figure S320.  Get High-res Image Gene #53: 'del_4p15.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4p15.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S321.  Gene #53: 'del_4p15.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 14(4P15.2) MUTATED 98 36 39 55
DEL PEAK 14(4P15.2) WILD-TYPE 100 94 60 37

Figure S321.  Get High-res Image Gene #53: 'del_4p15.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

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

Table S322.  Gene #54: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 15(4Q22.1) MUTATED 111 138 49
DEL PEAK 15(4Q22.1) WILD-TYPE 55 72 200

Figure S322.  Get High-res Image Gene #54: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 0.0035 (Fisher's exact test), Q value = 0.0075

Table S323.  Gene #54: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 15(4Q22.1) MUTATED 122 89 66
DEL PEAK 15(4Q22.1) WILD-TYPE 126 68 106

Figure S323.  Get High-res Image Gene #54: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00452 (Fisher's exact test), Q value = 0.0095

Table S324.  Gene #54: 'del_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
DEL PEAK 15(4Q22.1) MUTATED 55 39 9 2
DEL PEAK 15(4Q22.1) WILD-TYPE 26 30 13 9

Figure S324.  Get High-res Image Gene #54: 'del_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0293 (Fisher's exact test), Q value = 0.05

Table S325.  Gene #54: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 15(4Q22.1) MUTATED 47 10 48
DEL PEAK 15(4Q22.1) WILD-TYPE 20 10 48

Figure S325.  Get High-res Image Gene #54: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_CNMF'

P value = 0.00658 (Fisher's exact test), Q value = 0.013

Table S326.  Gene #54: 'del_4q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 15(4Q22.1) MUTATED 88 161 45
DEL PEAK 15(4Q22.1) WILD-TYPE 75 167 81

Figure S326.  Get High-res Image Gene #54: 'del_4q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q22.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S327.  Gene #54: 'del_4q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 15(4Q22.1) MUTATED 81 79 57 47 30
DEL PEAK 15(4Q22.1) WILD-TYPE 46 64 107 47 59

Figure S327.  Get High-res Image Gene #54: 'del_4q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00912 (Fisher's exact test), Q value = 0.018

Table S328.  Gene #54: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 15(4Q22.1) MUTATED 85 92 72
DEL PEAK 15(4Q22.1) WILD-TYPE 60 113 97

Figure S328.  Get High-res Image Gene #54: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 0.025

Table S329.  Gene #54: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 15(4Q22.1) MUTATED 110 50 42 47
DEL PEAK 15(4Q22.1) WILD-TYPE 88 80 57 45

Figure S329.  Get High-res Image Gene #54: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

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

Table S330.  Gene #55: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 16(4Q34.3) MUTATED 115 136 49
DEL PEAK 16(4Q34.3) WILD-TYPE 51 74 200

Figure S330.  Get High-res Image Gene #55: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 0.00162 (Fisher's exact test), Q value = 0.0038

Table S331.  Gene #55: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 16(4Q34.3) MUTATED 122 92 67
DEL PEAK 16(4Q34.3) WILD-TYPE 126 65 105

Figure S331.  Get High-res Image Gene #55: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 0.00785 (Fisher's exact test), Q value = 0.016

Table S332.  Gene #55: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
DEL PEAK 16(4Q34.3) MUTATED 55 32 10 3
DEL PEAK 16(4Q34.3) WILD-TYPE 26 37 12 8

Figure S332.  Get High-res Image Gene #55: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00423 (Fisher's exact test), Q value = 0.009

Table S333.  Gene #55: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 16(4Q34.3) MUTATED 47 10 43
DEL PEAK 16(4Q34.3) WILD-TYPE 20 10 53

Figure S333.  Get High-res Image Gene #55: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.024

Table S334.  Gene #55: 'del_4q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 16(4Q34.3) MUTATED 89 162 47
DEL PEAK 16(4Q34.3) WILD-TYPE 74 166 79

Figure S334.  Get High-res Image Gene #55: 'del_4q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S335.  Gene #55: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 16(4Q34.3) MUTATED 90 80 56 42 30
DEL PEAK 16(4Q34.3) WILD-TYPE 37 63 108 52 59

Figure S335.  Get High-res Image Gene #55: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S336.  Gene #55: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 16(4Q34.3) MUTATED 122 50 43 42
DEL PEAK 16(4Q34.3) WILD-TYPE 76 80 56 50

Figure S336.  Get High-res Image Gene #55: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

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

Table S337.  Gene #56: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 17(5Q12.1) MUTATED 115 132 35
DEL PEAK 17(5Q12.1) WILD-TYPE 51 78 214

Figure S337.  Get High-res Image Gene #56: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

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

Table S338.  Gene #56: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 17(5Q12.1) MUTATED 105 115 48
DEL PEAK 17(5Q12.1) WILD-TYPE 143 42 124

Figure S338.  Get High-res Image Gene #56: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q12.1' versus 'RPPA_CNMF'

P value = 0.00164 (Fisher's exact test), Q value = 0.0038

Table S339.  Gene #56: 'del_5q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 137 136 64
DEL PEAK 17(5Q12.1) MUTATED 73 61 40 32
DEL PEAK 17(5Q12.1) WILD-TYPE 72 76 96 32

Figure S339.  Get High-res Image Gene #56: 'del_5q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_5q12.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00269 (Fisher's exact test), Q value = 0.006

Table S340.  Gene #56: 'del_5q12.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
DEL PEAK 17(5Q12.1) MUTATED 131 47 28
DEL PEAK 17(5Q12.1) WILD-TYPE 142 63 71

Figure S340.  Get High-res Image Gene #56: 'del_5q12.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_CNMF'

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

Table S341.  Gene #56: 'del_5q12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 17(5Q12.1) MUTATED 104 145 29
DEL PEAK 17(5Q12.1) WILD-TYPE 59 183 97

Figure S341.  Get High-res Image Gene #56: 'del_5q12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S342.  Gene #56: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 17(5Q12.1) MUTATED 97 70 42 54 15
DEL PEAK 17(5Q12.1) WILD-TYPE 30 73 122 40 74

Figure S342.  Get High-res Image Gene #56: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_MATURE_CNMF'

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

Table S343.  Gene #56: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 17(5Q12.1) MUTATED 96 93 59
DEL PEAK 17(5Q12.1) WILD-TYPE 49 112 110

Figure S343.  Get High-res Image Gene #56: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S344.  Gene #56: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 17(5Q12.1) MUTATED 116 50 28 54
DEL PEAK 17(5Q12.1) WILD-TYPE 82 80 71 38

Figure S344.  Get High-res Image Gene #56: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

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

Table S345.  Gene #57: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 18(6P25.3) MUTATED 67 89 32
DEL PEAK 18(6P25.3) WILD-TYPE 99 121 217

Figure S345.  Get High-res Image Gene #57: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 4e-04

Table S346.  Gene #57: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 18(6P25.3) MUTATED 81 65 35
DEL PEAK 18(6P25.3) WILD-TYPE 167 92 137

Figure S346.  Get High-res Image Gene #57: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p25.3' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.6e-05

Table S347.  Gene #57: 'del_6p25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 18(6P25.3) MUTATED 59 108 18
DEL PEAK 18(6P25.3) WILD-TYPE 104 220 108

Figure S347.  Get High-res Image Gene #57: 'del_6p25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6p25.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S348.  Gene #57: 'del_6p25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 18(6P25.3) MUTATED 55 50 34 33 13
DEL PEAK 18(6P25.3) WILD-TYPE 72 93 130 61 76

Figure S348.  Get High-res Image Gene #57: 'del_6p25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6p25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00321 (Fisher's exact test), Q value = 0.0069

Table S349.  Gene #57: 'del_6p25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 18(6P25.3) MUTATED 78 34 20 32
DEL PEAK 18(6P25.3) WILD-TYPE 120 96 79 60

Figure S349.  Get High-res Image Gene #57: 'del_6p25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q16.3' versus 'CN_CNMF'

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

Table S350.  Gene #58: 'del_6q16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 19(6Q16.3) MUTATED 41 83 23
DEL PEAK 19(6Q16.3) WILD-TYPE 125 127 226

Figure S350.  Get High-res Image Gene #58: 'del_6q16.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q16.3' versus 'METHLYATION_CNMF'

P value = 0.0259 (Fisher's exact test), Q value = 0.046

Table S351.  Gene #58: 'del_6q16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 19(6Q16.3) MUTATED 53 50 35
DEL PEAK 19(6Q16.3) WILD-TYPE 195 107 137

Figure S351.  Get High-res Image Gene #58: 'del_6q16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q16.3' versus 'MIRSEQ_CNMF'

P value = 0.0336 (Fisher's exact test), Q value = 0.057

Table S352.  Gene #58: 'del_6q16.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 19(6Q16.3) MUTATED 47 78 20
DEL PEAK 19(6Q16.3) WILD-TYPE 116 250 106

Figure S352.  Get High-res Image Gene #58: 'del_6q16.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6q16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00127 (Fisher's exact test), Q value = 0.0031

Table S353.  Gene #58: 'del_6q16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 19(6Q16.3) MUTATED 36 32 36 32 9
DEL PEAK 19(6Q16.3) WILD-TYPE 91 111 128 62 80

Figure S353.  Get High-res Image Gene #58: 'del_6q16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0284 (Fisher's exact test), Q value = 0.049

Table S354.  Gene #58: 'del_6q16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 19(6Q16.3) MUTATED 51 27 17 32
DEL PEAK 19(6Q16.3) WILD-TYPE 147 103 82 60

Figure S354.  Get High-res Image Gene #58: 'del_6q16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

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

Table S355.  Gene #59: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 20(6Q26) MUTATED 46 80 26
DEL PEAK 20(6Q26) WILD-TYPE 120 130 223

Figure S355.  Get High-res Image Gene #59: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 0.00274 (Fisher's exact test), Q value = 0.006

Table S356.  Gene #59: 'del_6q26' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 20(6Q26) MUTATED 49 84 17
DEL PEAK 20(6Q26) WILD-TYPE 114 244 109

Figure S356.  Get High-res Image Gene #59: 'del_6q26' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0156 (Fisher's exact test), Q value = 0.029

Table S357.  Gene #59: 'del_6q26' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 20(6Q26) MUTATED 37 33 39 30 11
DEL PEAK 20(6Q26) WILD-TYPE 90 110 125 64 78

Figure S357.  Get High-res Image Gene #59: 'del_6q26' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 0.052

Table S358.  Gene #59: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 20(6Q26) MUTATED 46 45 33
DEL PEAK 20(6Q26) WILD-TYPE 99 160 136

Figure S358.  Get High-res Image Gene #59: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_7q31.1' versus 'CN_CNMF'

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

Table S359.  Gene #60: 'del_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 21(7Q31.1) MUTATED 44 65 18
DEL PEAK 21(7Q31.1) WILD-TYPE 122 145 231

Figure S359.  Get High-res Image Gene #60: 'del_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q31.1' versus 'METHLYATION_CNMF'

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

Table S360.  Gene #60: 'del_7q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 21(7Q31.1) MUTATED 55 42 22
DEL PEAK 21(7Q31.1) WILD-TYPE 193 115 150

Figure S360.  Get High-res Image Gene #60: 'del_7q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q31.1' versus 'MIRSEQ_CNMF'

P value = 0.0061 (Fisher's exact test), Q value = 0.012

Table S361.  Gene #60: 'del_7q31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 21(7Q31.1) MUTATED 46 61 17
DEL PEAK 21(7Q31.1) WILD-TYPE 117 267 109

Figure S361.  Get High-res Image Gene #60: 'del_7q31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_7q31.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S362.  Gene #60: 'del_7q31.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 21(7Q31.1) MUTATED 38 30 21 24 11
DEL PEAK 21(7Q31.1) WILD-TYPE 89 113 143 70 78

Figure S362.  Get High-res Image Gene #60: 'del_7q31.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_7q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00045

Table S363.  Gene #60: 'del_7q31.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 21(7Q31.1) MUTATED 58 16 13 24
DEL PEAK 21(7Q31.1) WILD-TYPE 140 114 86 68

Figure S363.  Get High-res Image Gene #60: 'del_7q31.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q36.3' versus 'CN_CNMF'

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

Table S364.  Gene #61: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 22(7Q36.3) MUTATED 60 86 17
DEL PEAK 22(7Q36.3) WILD-TYPE 106 124 232

Figure S364.  Get High-res Image Gene #61: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q36.3' versus 'METHLYATION_CNMF'

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

Table S365.  Gene #61: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 22(7Q36.3) MUTATED 57 63 35
DEL PEAK 22(7Q36.3) WILD-TYPE 191 94 137

Figure S365.  Get High-res Image Gene #61: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q36.3' versus 'MRNASEQ_CNMF'

P value = 0.0397 (Fisher's exact test), Q value = 0.066

Table S366.  Gene #61: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
DEL PEAK 22(7Q36.3) MUTATED 32 28 7 0
DEL PEAK 22(7Q36.3) WILD-TYPE 49 41 15 11

Figure S366.  Get High-res Image Gene #61: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_7q36.3' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.6e-05

Table S367.  Gene #61: 'del_7q36.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 22(7Q36.3) MUTATED 64 77 20
DEL PEAK 22(7Q36.3) WILD-TYPE 99 251 106

Figure S367.  Get High-res Image Gene #61: 'del_7q36.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_7q36.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S368.  Gene #61: 'del_7q36.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 22(7Q36.3) MUTATED 52 37 29 33 10
DEL PEAK 22(7Q36.3) WILD-TYPE 75 106 135 61 79

Figure S368.  Get High-res Image Gene #61: 'del_7q36.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_7q36.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.00092

Table S369.  Gene #61: 'del_7q36.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 22(7Q36.3) MUTATED 58 54 34
DEL PEAK 22(7Q36.3) WILD-TYPE 87 151 135

Figure S369.  Get High-res Image Gene #61: 'del_7q36.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_7q36.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.00088

Table S370.  Gene #61: 'del_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 22(7Q36.3) MUTATED 70 28 15 33
DEL PEAK 22(7Q36.3) WILD-TYPE 128 102 84 59

Figure S370.  Get High-res Image Gene #61: 'del_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

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

Table S371.  Gene #62: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 23(8P23.2) MUTATED 77 109 26
DEL PEAK 23(8P23.2) WILD-TYPE 89 101 223

Figure S371.  Get High-res Image Gene #62: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

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

Table S372.  Gene #62: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 23(8P23.2) MUTATED 72 87 41
DEL PEAK 23(8P23.2) WILD-TYPE 176 70 131

Figure S372.  Get High-res Image Gene #62: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.035

Table S373.  Gene #62: 'del_8p23.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
DEL PEAK 23(8P23.2) MUTATED 105 26 32
DEL PEAK 23(8P23.2) WILD-TYPE 168 84 67

Figure S373.  Get High-res Image Gene #62: 'del_8p23.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0473 (Fisher's exact test), Q value = 0.076

Table S374.  Gene #62: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 23(8P23.2) MUTATED 27 7 55
DEL PEAK 23(8P23.2) WILD-TYPE 40 13 41

Figure S374.  Get High-res Image Gene #62: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

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

Table S375.  Gene #62: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 23(8P23.2) MUTATED 84 100 26
DEL PEAK 23(8P23.2) WILD-TYPE 79 228 100

Figure S375.  Get High-res Image Gene #62: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S376.  Gene #62: 'del_8p23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 23(8P23.2) MUTATED 61 47 30 55 17
DEL PEAK 23(8P23.2) WILD-TYPE 66 96 134 39 72

Figure S376.  Get High-res Image Gene #62: 'del_8p23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

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

Table S377.  Gene #62: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 23(8P23.2) MUTATED 76 63 44
DEL PEAK 23(8P23.2) WILD-TYPE 69 142 125

Figure S377.  Get High-res Image Gene #62: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S378.  Gene #62: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 23(8P23.2) MUTATED 75 38 18 52
DEL PEAK 23(8P23.2) WILD-TYPE 123 92 81 40

Figure S378.  Get High-res Image Gene #62: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

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

Table S379.  Gene #63: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 24(9P23) MUTATED 113 135 54
DEL PEAK 24(9P23) WILD-TYPE 53 75 195

Figure S379.  Get High-res Image Gene #63: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

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

Table S380.  Gene #63: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 24(9P23) MUTATED 118 95 70
DEL PEAK 24(9P23) WILD-TYPE 130 62 102

Figure S380.  Get High-res Image Gene #63: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 0.0014 (Fisher's exact test), Q value = 0.0033

Table S381.  Gene #63: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 24(9P23) MUTATED 93 161 45
DEL PEAK 24(9P23) WILD-TYPE 70 167 81

Figure S381.  Get High-res Image Gene #63: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S382.  Gene #63: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 24(9P23) MUTATED 83 72 61 54 29
DEL PEAK 24(9P23) WILD-TYPE 44 71 103 40 60

Figure S382.  Get High-res Image Gene #63: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

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

Table S383.  Gene #64: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 25(9P21.3) MUTATED 114 164 56
DEL PEAK 25(9P21.3) WILD-TYPE 52 46 193

Figure S383.  Get High-res Image Gene #64: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

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

Table S384.  Gene #64: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 25(9P21.3) MUTATED 121 120 75
DEL PEAK 25(9P21.3) WILD-TYPE 127 37 97

Figure S384.  Get High-res Image Gene #64: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0209 (Fisher's exact test), Q value = 0.038

Table S385.  Gene #64: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 25(9P21.3) MUTATED 49 11 80
DEL PEAK 25(9P21.3) WILD-TYPE 18 9 16

Figure S385.  Get High-res Image Gene #64: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

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

Table S386.  Gene #64: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 25(9P21.3) MUTATED 123 159 49
DEL PEAK 25(9P21.3) WILD-TYPE 40 169 77

Figure S386.  Get High-res Image Gene #64: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S387.  Gene #64: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 25(9P21.3) MUTATED 87 75 60 80 29
DEL PEAK 25(9P21.3) WILD-TYPE 40 68 104 14 60

Figure S387.  Get High-res Image Gene #64: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

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

Table S388.  Gene #64: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 25(9P21.3) MUTATED 109 99 85
DEL PEAK 25(9P21.3) WILD-TYPE 36 106 84

Figure S388.  Get High-res Image Gene #64: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S389.  Gene #64: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 25(9P21.3) MUTATED 114 55 44 80
DEL PEAK 25(9P21.3) WILD-TYPE 84 75 55 12

Figure S389.  Get High-res Image Gene #64: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q21.11' versus 'CN_CNMF'

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

Table S390.  Gene #65: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 26(9Q21.11) MUTATED 68 83 25
DEL PEAK 26(9Q21.11) WILD-TYPE 98 127 224

Figure S390.  Get High-res Image Gene #65: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q21.11' versus 'METHLYATION_CNMF'

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

Table S391.  Gene #65: 'del_9q21.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 26(9Q21.11) MUTATED 58 67 42
DEL PEAK 26(9Q21.11) WILD-TYPE 190 90 130

Figure S391.  Get High-res Image Gene #65: 'del_9q21.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9q21.11' versus 'MIRSEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.00078

Table S392.  Gene #65: 'del_9q21.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 26(9Q21.11) MUTATED 66 80 28
DEL PEAK 26(9Q21.11) WILD-TYPE 97 248 98

Figure S392.  Get High-res Image Gene #65: 'del_9q21.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9q21.11' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S393.  Gene #65: 'del_9q21.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 26(9Q21.11) MUTATED 61 31 29 36 17
DEL PEAK 26(9Q21.11) WILD-TYPE 66 112 135 58 72

Figure S393.  Get High-res Image Gene #65: 'del_9q21.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_MATURE_CNMF'

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

Table S394.  Gene #65: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 26(9Q21.11) MUTATED 59 44 49
DEL PEAK 26(9Q21.11) WILD-TYPE 86 161 120

Figure S394.  Get High-res Image Gene #65: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10p15.3' versus 'CN_CNMF'

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

Table S395.  Gene #66: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 27(10P15.3) MUTATED 39 74 18
DEL PEAK 27(10P15.3) WILD-TYPE 127 136 231

Figure S395.  Get High-res Image Gene #66: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 0.00193 (Fisher's exact test), Q value = 0.0044

Table S396.  Gene #66: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 27(10P15.3) MUTATED 42 49 31
DEL PEAK 27(10P15.3) WILD-TYPE 206 108 141

Figure S396.  Get High-res Image Gene #66: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 0.0428 (Fisher's exact test), Q value = 0.07

Table S397.  Gene #66: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
DEL PEAK 27(10P15.3) MUTATED 16 28 7 3
DEL PEAK 27(10P15.3) WILD-TYPE 65 41 15 8

Figure S397.  Get High-res Image Gene #66: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0239 (Fisher's exact test), Q value = 0.042

Table S398.  Gene #66: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 27(10P15.3) MUTATED 12 6 36
DEL PEAK 27(10P15.3) WILD-TYPE 55 14 60

Figure S398.  Get High-res Image Gene #66: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_CNMF'

P value = 0.00212 (Fisher's exact test), Q value = 0.0048

Table S399.  Gene #66: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 27(10P15.3) MUTATED 50 60 20
DEL PEAK 27(10P15.3) WILD-TYPE 113 268 106

Figure S399.  Get High-res Image Gene #66: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10p15.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S400.  Gene #66: 'del_10p15.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 27(10P15.3) MUTATED 31 31 25 36 7
DEL PEAK 27(10P15.3) WILD-TYPE 96 112 139 58 82

Figure S400.  Get High-res Image Gene #66: 'del_10p15.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00864 (Fisher's exact test), Q value = 0.017

Table S401.  Gene #66: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 27(10P15.3) MUTATED 44 39 28
DEL PEAK 27(10P15.3) WILD-TYPE 101 166 141

Figure S401.  Get High-res Image Gene #66: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10p15.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.6e-05

Table S402.  Gene #66: 'del_10p15.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 27(10P15.3) MUTATED 43 17 15 36
DEL PEAK 27(10P15.3) WILD-TYPE 155 113 84 56

Figure S402.  Get High-res Image Gene #66: 'del_10p15.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p11.21' versus 'CN_CNMF'

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

Table S403.  Gene #67: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 28(10P11.21) MUTATED 25 67 10
DEL PEAK 28(10P11.21) WILD-TYPE 141 143 239

Figure S403.  Get High-res Image Gene #67: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p11.21' versus 'METHLYATION_CNMF'

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

Table S404.  Gene #67: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 28(10P11.21) MUTATED 23 53 21
DEL PEAK 28(10P11.21) WILD-TYPE 225 104 151

Figure S404.  Get High-res Image Gene #67: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p11.21' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.6e-05

Table S405.  Gene #67: 'del_10p11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
DEL PEAK 28(10P11.21) MUTATED 9 29 10 3
DEL PEAK 28(10P11.21) WILD-TYPE 72 40 12 8

Figure S405.  Get High-res Image Gene #67: 'del_10p11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.7e-05

Table S406.  Gene #67: 'del_10p11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 28(10P11.21) MUTATED 7 3 41
DEL PEAK 28(10P11.21) WILD-TYPE 60 17 55

Figure S406.  Get High-res Image Gene #67: 'del_10p11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10p11.21' versus 'MIRSEQ_CNMF'

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

Table S407.  Gene #67: 'del_10p11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 28(10P11.21) MUTATED 49 39 12
DEL PEAK 28(10P11.21) WILD-TYPE 114 289 114

Figure S407.  Get High-res Image Gene #67: 'del_10p11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10p11.21' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S408.  Gene #67: 'del_10p11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 28(10P11.21) MUTATED 25 18 14 40 3
DEL PEAK 28(10P11.21) WILD-TYPE 102 125 150 54 86

Figure S408.  Get High-res Image Gene #67: 'del_10p11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10p11.21' versus 'MIRSEQ_MATURE_CNMF'

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

Table S409.  Gene #67: 'del_10p11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 28(10P11.21) MUTATED 42 25 21
DEL PEAK 28(10P11.21) WILD-TYPE 103 180 148

Figure S409.  Get High-res Image Gene #67: 'del_10p11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S410.  Gene #67: 'del_10p11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 28(10P11.21) MUTATED 27 11 10 40
DEL PEAK 28(10P11.21) WILD-TYPE 171 119 89 52

Figure S410.  Get High-res Image Gene #67: 'del_10p11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q21.1' versus 'CN_CNMF'

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

Table S411.  Gene #68: 'del_10q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 29(10Q21.1) MUTATED 39 57 16
DEL PEAK 29(10Q21.1) WILD-TYPE 127 153 233

Figure S411.  Get High-res Image Gene #68: 'del_10q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q21.1' versus 'METHLYATION_CNMF'

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

Table S412.  Gene #68: 'del_10q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 29(10Q21.1) MUTATED 28 54 22
DEL PEAK 29(10Q21.1) WILD-TYPE 220 103 150

Figure S412.  Get High-res Image Gene #68: 'del_10q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q21.1' versus 'MIRSEQ_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.0023

Table S413.  Gene #68: 'del_10q21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 29(10Q21.1) MUTATED 43 56 12
DEL PEAK 29(10Q21.1) WILD-TYPE 120 272 114

Figure S413.  Get High-res Image Gene #68: 'del_10q21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q21.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S414.  Gene #68: 'del_10q21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 29(10Q21.1) MUTATED 38 26 14 31 2
DEL PEAK 29(10Q21.1) WILD-TYPE 89 117 150 63 87

Figure S414.  Get High-res Image Gene #68: 'del_10q21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00641 (Fisher's exact test), Q value = 0.013

Table S415.  Gene #68: 'del_10q21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 29(10Q21.1) MUTATED 39 32 23
DEL PEAK 29(10Q21.1) WILD-TYPE 106 173 146

Figure S415.  Get High-res Image Gene #68: 'del_10q21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.6e-05

Table S416.  Gene #68: 'del_10q21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 29(10Q21.1) MUTATED 39 11 13 31
DEL PEAK 29(10Q21.1) WILD-TYPE 159 119 86 61

Figure S416.  Get High-res Image Gene #68: 'del_10q21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q22.3' versus 'CN_CNMF'

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

Table S417.  Gene #69: 'del_10q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 30(10Q22.3) MUTATED 54 65 16
DEL PEAK 30(10Q22.3) WILD-TYPE 112 145 233

Figure S417.  Get High-res Image Gene #69: 'del_10q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q22.3' versus 'METHLYATION_CNMF'

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

Table S418.  Gene #69: 'del_10q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 30(10Q22.3) MUTATED 45 58 23
DEL PEAK 30(10Q22.3) WILD-TYPE 203 99 149

Figure S418.  Get High-res Image Gene #69: 'del_10q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0482 (Fisher's exact test), Q value = 0.078

Table S419.  Gene #69: 'del_10q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 30(10Q22.3) MUTATED 14 5 37
DEL PEAK 30(10Q22.3) WILD-TYPE 53 15 59

Figure S419.  Get High-res Image Gene #69: 'del_10q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q22.3' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00016

Table S420.  Gene #69: 'del_10q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 30(10Q22.3) MUTATED 51 70 13
DEL PEAK 30(10Q22.3) WILD-TYPE 112 258 113

Figure S420.  Get High-res Image Gene #69: 'del_10q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q22.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S421.  Gene #69: 'del_10q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 30(10Q22.3) MUTATED 40 37 16 36 5
DEL PEAK 30(10Q22.3) WILD-TYPE 87 106 148 58 84

Figure S421.  Get High-res Image Gene #69: 'del_10q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.6e-05

Table S422.  Gene #69: 'del_10q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 30(10Q22.3) MUTATED 49 39 23
DEL PEAK 30(10Q22.3) WILD-TYPE 96 166 146

Figure S422.  Get High-res Image Gene #69: 'del_10q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S423.  Gene #69: 'del_10q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 30(10Q22.3) MUTATED 49 14 12 36
DEL PEAK 30(10Q22.3) WILD-TYPE 149 116 87 56

Figure S423.  Get High-res Image Gene #69: 'del_10q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

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

Table S424.  Gene #70: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 31(10Q23.31) MUTATED 69 91 23
DEL PEAK 31(10Q23.31) WILD-TYPE 97 119 226

Figure S424.  Get High-res Image Gene #70: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

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

Table S425.  Gene #70: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 31(10Q23.31) MUTATED 59 73 37
DEL PEAK 31(10Q23.31) WILD-TYPE 189 84 135

Figure S425.  Get High-res Image Gene #70: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CNMF'

P value = 0.00773 (Fisher's exact test), Q value = 0.015

Table S426.  Gene #70: 'del_10q23.31' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 137 136 64
DEL PEAK 31(10Q23.31) MUTATED 53 37 28 25
DEL PEAK 31(10Q23.31) WILD-TYPE 92 100 108 39

Figure S426.  Get High-res Image Gene #70: 'del_10q23.31' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.7e-05

Table S427.  Gene #70: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 31(10Q23.31) MUTATED 62 100 19
DEL PEAK 31(10Q23.31) WILD-TYPE 101 228 107

Figure S427.  Get High-res Image Gene #70: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S428.  Gene #70: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 31(10Q23.31) MUTATED 56 45 31 40 9
DEL PEAK 31(10Q23.31) WILD-TYPE 71 98 133 54 80

Figure S428.  Get High-res Image Gene #70: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0013

Table S429.  Gene #70: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 31(10Q23.31) MUTATED 60 57 36
DEL PEAK 31(10Q23.31) WILD-TYPE 85 148 133

Figure S429.  Get High-res Image Gene #70: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S430.  Gene #70: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 31(10Q23.31) MUTATED 68 26 19 40
DEL PEAK 31(10Q23.31) WILD-TYPE 130 104 80 52

Figure S430.  Get High-res Image Gene #70: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

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

Table S431.  Gene #71: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 32(11P15.5) MUTATED 61 95 19
DEL PEAK 32(11P15.5) WILD-TYPE 105 115 230

Figure S431.  Get High-res Image Gene #71: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

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

Table S432.  Gene #71: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 32(11P15.5) MUTATED 62 71 28
DEL PEAK 32(11P15.5) WILD-TYPE 186 86 144

Figure S432.  Get High-res Image Gene #71: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.5' versus 'RPPA_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.025

Table S433.  Gene #71: 'del_11p15.5' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 137 136 64
DEL PEAK 32(11P15.5) MUTATED 52 31 30 23
DEL PEAK 32(11P15.5) WILD-TYPE 93 106 106 41

Figure S433.  Get High-res Image Gene #71: 'del_11p15.5' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_11p15.5' versus 'RPPA_CHIERARCHICAL'

P value = 0.00531 (Fisher's exact test), Q value = 0.011

Table S434.  Gene #71: 'del_11p15.5' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
DEL PEAK 32(11P15.5) MUTATED 93 23 20
DEL PEAK 32(11P15.5) WILD-TYPE 180 87 79

Figure S434.  Get High-res Image Gene #71: 'del_11p15.5' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.7e-05

Table S435.  Gene #71: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 32(11P15.5) MUTATED 67 81 24
DEL PEAK 32(11P15.5) WILD-TYPE 96 247 102

Figure S435.  Get High-res Image Gene #71: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S436.  Gene #71: 'del_11p15.5' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 32(11P15.5) MUTATED 46 41 29 43 13
DEL PEAK 32(11P15.5) WILD-TYPE 81 102 135 51 76

Figure S436.  Get High-res Image Gene #71: 'del_11p15.5' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00065

Table S437.  Gene #71: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 32(11P15.5) MUTATED 60 47 39
DEL PEAK 32(11P15.5) WILD-TYPE 85 158 130

Figure S437.  Get High-res Image Gene #71: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.00062

Table S438.  Gene #71: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 32(11P15.5) MUTATED 57 28 19 42
DEL PEAK 32(11P15.5) WILD-TYPE 141 102 80 50

Figure S438.  Get High-res Image Gene #71: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q25' versus 'CN_CNMF'

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

Table S439.  Gene #72: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 33(11Q25) MUTATED 58 101 19
DEL PEAK 33(11Q25) WILD-TYPE 108 109 230

Figure S439.  Get High-res Image Gene #72: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q25' versus 'METHLYATION_CNMF'

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

Table S440.  Gene #72: 'del_11q25' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 33(11Q25) MUTATED 63 77 30
DEL PEAK 33(11Q25) WILD-TYPE 185 80 142

Figure S440.  Get High-res Image Gene #72: 'del_11q25' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q25' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0372 (Fisher's exact test), Q value = 0.062

Table S441.  Gene #72: 'del_11q25' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 33(11Q25) MUTATED 22 7 50
DEL PEAK 33(11Q25) WILD-TYPE 45 13 46

Figure S441.  Get High-res Image Gene #72: 'del_11q25' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q25' versus 'MIRSEQ_CNMF'

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

Table S442.  Gene #72: 'del_11q25' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 33(11Q25) MUTATED 73 80 23
DEL PEAK 33(11Q25) WILD-TYPE 90 248 103

Figure S442.  Get High-res Image Gene #72: 'del_11q25' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11q25' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S443.  Gene #72: 'del_11q25' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 33(11Q25) MUTATED 40 39 32 51 14
DEL PEAK 33(11Q25) WILD-TYPE 87 104 132 43 75

Figure S443.  Get High-res Image Gene #72: 'del_11q25' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11q25' versus 'MIRSEQ_MATURE_CNMF'

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

Table S444.  Gene #72: 'del_11q25' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 33(11Q25) MUTATED 66 52 37
DEL PEAK 33(11Q25) WILD-TYPE 79 153 132

Figure S444.  Get High-res Image Gene #72: 'del_11q25' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q25' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S445.  Gene #72: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 33(11Q25) MUTATED 57 31 17 50
DEL PEAK 33(11Q25) WILD-TYPE 141 99 82 42

Figure S445.  Get High-res Image Gene #72: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12p13.1' versus 'CN_CNMF'

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

Table S446.  Gene #73: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 34(12P13.1) MUTATED 64 32 17
DEL PEAK 34(12P13.1) WILD-TYPE 102 178 232

Figure S446.  Get High-res Image Gene #73: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 0.0443 (Fisher's exact test), Q value = 0.072

Table S447.  Gene #73: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 34(12P13.1) MUTATED 50 34 21
DEL PEAK 34(12P13.1) WILD-TYPE 198 123 151

Figure S447.  Get High-res Image Gene #73: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12p13.1' versus 'MRNASEQ_CNMF'

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

Table S448.  Gene #73: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
DEL PEAK 34(12P13.1) MUTATED 28 7 0 1
DEL PEAK 34(12P13.1) WILD-TYPE 53 62 22 10

Figure S448.  Get High-res Image Gene #73: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.7e-05

Table S449.  Gene #73: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 34(12P13.1) MUTATED 21 8 7
DEL PEAK 34(12P13.1) WILD-TYPE 46 12 89

Figure S449.  Get High-res Image Gene #73: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S450.  Gene #73: 'del_12p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 34(12P13.1) MUTATED 44 28 21 7 12
DEL PEAK 34(12P13.1) WILD-TYPE 83 115 143 87 77

Figure S450.  Get High-res Image Gene #73: 'del_12p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00319 (Fisher's exact test), Q value = 0.0069

Table S451.  Gene #73: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 34(12P13.1) MUTATED 50 26 18 7
DEL PEAK 34(12P13.1) WILD-TYPE 148 104 81 85

Figure S451.  Get High-res Image Gene #73: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q23.1' versus 'CN_CNMF'

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

Table S452.  Gene #74: 'del_12q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 35(12Q23.1) MUTATED 51 51 7
DEL PEAK 35(12Q23.1) WILD-TYPE 115 159 242

Figure S452.  Get High-res Image Gene #74: 'del_12q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q23.1' versus 'METHLYATION_CNMF'

P value = 0.00302 (Fisher's exact test), Q value = 0.0066

Table S453.  Gene #74: 'del_12q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 35(12Q23.1) MUTATED 42 41 20
DEL PEAK 35(12Q23.1) WILD-TYPE 206 116 152

Figure S453.  Get High-res Image Gene #74: 'del_12q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00048 (Fisher's exact test), Q value = 0.0012

Table S454.  Gene #74: 'del_12q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 35(12Q23.1) MUTATED 33 31 16 19 8
DEL PEAK 35(12Q23.1) WILD-TYPE 94 112 148 75 81

Figure S454.  Get High-res Image Gene #74: 'del_12q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q12.11' versus 'CN_CNMF'

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

Table S455.  Gene #75: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 36(13Q12.11) MUTATED 20 101 17
DEL PEAK 36(13Q12.11) WILD-TYPE 146 109 232

Figure S455.  Get High-res Image Gene #75: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q12.11' versus 'METHLYATION_CNMF'

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

Table S456.  Gene #75: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 36(13Q12.11) MUTATED 49 60 22
DEL PEAK 36(13Q12.11) WILD-TYPE 199 97 150

Figure S456.  Get High-res Image Gene #75: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q12.11' versus 'MRNASEQ_CNMF'

P value = 0.00663 (Fisher's exact test), Q value = 0.013

Table S457.  Gene #75: 'del_13q12.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
DEL PEAK 36(13Q12.11) MUTATED 25 39 6 4
DEL PEAK 36(13Q12.11) WILD-TYPE 56 30 16 7

Figure S457.  Get High-res Image Gene #75: 'del_13q12.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q12.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0058 (Fisher's exact test), Q value = 0.012

Table S458.  Gene #75: 'del_13q12.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 36(13Q12.11) MUTATED 23 3 48
DEL PEAK 36(13Q12.11) WILD-TYPE 44 17 48

Figure S458.  Get High-res Image Gene #75: 'del_13q12.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q12.11' versus 'MIRSEQ_CNMF'

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

Table S459.  Gene #75: 'del_13q12.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 36(13Q12.11) MUTATED 67 50 21
DEL PEAK 36(13Q12.11) WILD-TYPE 96 278 105

Figure S459.  Get High-res Image Gene #75: 'del_13q12.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_13q12.11' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S460.  Gene #75: 'del_13q12.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 36(13Q12.11) MUTATED 30 25 24 50 9
DEL PEAK 36(13Q12.11) WILD-TYPE 97 118 140 44 80

Figure S460.  Get High-res Image Gene #75: 'del_13q12.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q12.11' versus 'MIRSEQ_MATURE_CNMF'

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

Table S461.  Gene #75: 'del_13q12.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 36(13Q12.11) MUTATED 58 34 31
DEL PEAK 36(13Q12.11) WILD-TYPE 87 171 138

Figure S461.  Get High-res Image Gene #75: 'del_13q12.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_13q12.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S462.  Gene #75: 'del_13q12.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 36(13Q12.11) MUTATED 38 22 14 49
DEL PEAK 36(13Q12.11) WILD-TYPE 160 108 85 43

Figure S462.  Get High-res Image Gene #75: 'del_13q12.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

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

Table S463.  Gene #76: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 37(13Q14.2) MUTATED 9 99 17
DEL PEAK 37(13Q14.2) WILD-TYPE 157 111 232

Figure S463.  Get High-res Image Gene #76: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

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

Table S464.  Gene #76: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 37(13Q14.2) MUTATED 41 55 21
DEL PEAK 37(13Q14.2) WILD-TYPE 207 102 151

Figure S464.  Get High-res Image Gene #76: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 0.0189 (Fisher's exact test), Q value = 0.035

Table S465.  Gene #76: 'del_13q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
DEL PEAK 37(13Q14.2) MUTATED 25 38 7 4
DEL PEAK 37(13Q14.2) WILD-TYPE 56 31 15 7

Figure S465.  Get High-res Image Gene #76: 'del_13q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0211 (Fisher's exact test), Q value = 0.038

Table S466.  Gene #76: 'del_13q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 37(13Q14.2) MUTATED 21 5 48
DEL PEAK 37(13Q14.2) WILD-TYPE 46 15 48

Figure S466.  Get High-res Image Gene #76: 'del_13q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

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

Table S467.  Gene #76: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 37(13Q14.2) MUTATED 63 44 17
DEL PEAK 37(13Q14.2) WILD-TYPE 100 284 109

Figure S467.  Get High-res Image Gene #76: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S468.  Gene #76: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 37(13Q14.2) MUTATED 26 22 21 47 8
DEL PEAK 37(13Q14.2) WILD-TYPE 101 121 143 47 81

Figure S468.  Get High-res Image Gene #76: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CNMF'

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

Table S469.  Gene #76: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 37(13Q14.2) MUTATED 54 28 25
DEL PEAK 37(13Q14.2) WILD-TYPE 91 177 144

Figure S469.  Get High-res Image Gene #76: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S470.  Gene #76: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 37(13Q14.2) MUTATED 31 18 12 46
DEL PEAK 37(13Q14.2) WILD-TYPE 167 112 87 46

Figure S470.  Get High-res Image Gene #76: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q21.31' versus 'CN_CNMF'

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

Table S471.  Gene #77: 'del_13q21.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 38(13Q21.31) MUTATED 8 98 20
DEL PEAK 38(13Q21.31) WILD-TYPE 158 112 229

Figure S471.  Get High-res Image Gene #77: 'del_13q21.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q21.31' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.7e-05

Table S472.  Gene #77: 'del_13q21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 38(13Q21.31) MUTATED 43 52 22
DEL PEAK 38(13Q21.31) WILD-TYPE 205 105 150

Figure S472.  Get High-res Image Gene #77: 'del_13q21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q21.31' versus 'MIRSEQ_CNMF'

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

Table S473.  Gene #77: 'del_13q21.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 38(13Q21.31) MUTATED 58 52 16
DEL PEAK 38(13Q21.31) WILD-TYPE 105 276 110

Figure S473.  Get High-res Image Gene #77: 'del_13q21.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_13q21.31' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S474.  Gene #77: 'del_13q21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 38(13Q21.31) MUTATED 27 21 28 44 6
DEL PEAK 38(13Q21.31) WILD-TYPE 100 122 136 50 83

Figure S474.  Get High-res Image Gene #77: 'del_13q21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q21.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00018

Table S475.  Gene #77: 'del_13q21.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 38(13Q21.31) MUTATED 50 32 27
DEL PEAK 38(13Q21.31) WILD-TYPE 95 173 142

Figure S475.  Get High-res Image Gene #77: 'del_13q21.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_13q21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S476.  Gene #77: 'del_13q21.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 38(13Q21.31) MUTATED 37 17 12 43
DEL PEAK 38(13Q21.31) WILD-TYPE 161 113 87 49

Figure S476.  Get High-res Image Gene #77: 'del_13q21.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q23.3' versus 'CN_CNMF'

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

Table S477.  Gene #78: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 39(14Q23.3) MUTATED 80 74 33
DEL PEAK 39(14Q23.3) WILD-TYPE 86 136 216

Figure S477.  Get High-res Image Gene #78: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q23.3' versus 'METHLYATION_CNMF'

P value = 0.00303 (Fisher's exact test), Q value = 0.0066

Table S478.  Gene #78: 'del_14q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 39(14Q23.3) MUTATED 74 62 38
DEL PEAK 39(14Q23.3) WILD-TYPE 174 95 134

Figure S478.  Get High-res Image Gene #78: 'del_14q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q23.3' versus 'MRNASEQ_CNMF'

P value = 0.00713 (Fisher's exact test), Q value = 0.014

Table S479.  Gene #78: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
DEL PEAK 39(14Q23.3) MUTATED 31 17 1 2
DEL PEAK 39(14Q23.3) WILD-TYPE 50 52 21 9

Figure S479.  Get High-res Image Gene #78: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0438 (Fisher's exact test), Q value = 0.071

Table S480.  Gene #78: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 39(14Q23.3) MUTATED 26 5 20
DEL PEAK 39(14Q23.3) WILD-TYPE 41 15 76

Figure S480.  Get High-res Image Gene #78: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S481.  Gene #78: 'del_14q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 39(14Q23.3) MUTATED 69 44 34 19 17
DEL PEAK 39(14Q23.3) WILD-TYPE 58 99 130 75 72

Figure S481.  Get High-res Image Gene #78: 'del_14q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S482.  Gene #78: 'del_14q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 39(14Q23.3) MUTATED 80 33 22 19
DEL PEAK 39(14Q23.3) WILD-TYPE 118 97 77 73

Figure S482.  Get High-res Image Gene #78: 'del_14q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q32.32' versus 'CN_CNMF'

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

Table S483.  Gene #79: 'del_14q32.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 40(14Q32.32) MUTATED 74 81 35
DEL PEAK 40(14Q32.32) WILD-TYPE 92 129 214

Figure S483.  Get High-res Image Gene #79: 'del_14q32.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.32' versus 'METHLYATION_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 0.04

Table S484.  Gene #79: 'del_14q32.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 40(14Q32.32) MUTATED 78 58 40
DEL PEAK 40(14Q32.32) WILD-TYPE 170 99 132

Figure S484.  Get High-res Image Gene #79: 'del_14q32.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q32.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00047

Table S485.  Gene #79: 'del_14q32.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 40(14Q32.32) MUTATED 59 45 39 24 20
DEL PEAK 40(14Q32.32) WILD-TYPE 68 98 125 70 69

Figure S485.  Get High-res Image Gene #79: 'del_14q32.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_14q32.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00272 (Fisher's exact test), Q value = 0.006

Table S486.  Gene #79: 'del_14q32.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 40(14Q32.32) MUTATED 79 30 24 24
DEL PEAK 40(14Q32.32) WILD-TYPE 119 100 75 68

Figure S486.  Get High-res Image Gene #79: 'del_14q32.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q11.2' versus 'CN_CNMF'

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

Table S487.  Gene #80: 'del_15q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 41(15Q11.2) MUTATED 72 85 26
DEL PEAK 41(15Q11.2) WILD-TYPE 94 125 223

Figure S487.  Get High-res Image Gene #80: 'del_15q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q11.2' versus 'RPPA_CNMF'

P value = 0.0291 (Fisher's exact test), Q value = 0.05

Table S488.  Gene #80: 'del_15q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 137 136 64
DEL PEAK 41(15Q11.2) MUTATED 54 34 30 18
DEL PEAK 41(15Q11.2) WILD-TYPE 91 103 106 46

Figure S488.  Get High-res Image Gene #80: 'del_15q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_15q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0303 (Fisher's exact test), Q value = 0.052

Table S489.  Gene #80: 'del_15q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
DEL PEAK 41(15Q11.2) MUTATED 90 25 21
DEL PEAK 41(15Q11.2) WILD-TYPE 183 85 78

Figure S489.  Get High-res Image Gene #80: 'del_15q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00678 (Fisher's exact test), Q value = 0.014

Table S490.  Gene #80: 'del_15q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 41(15Q11.2) MUTATED 51 107 23
DEL PEAK 41(15Q11.2) WILD-TYPE 112 221 103

Figure S490.  Get High-res Image Gene #80: 'del_15q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_15q11.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S491.  Gene #80: 'del_15q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 41(15Q11.2) MUTATED 59 46 34 29 13
DEL PEAK 41(15Q11.2) WILD-TYPE 68 97 130 65 76

Figure S491.  Get High-res Image Gene #80: 'del_15q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'CN_CNMF'

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

Table S492.  Gene #81: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 42(16P13.3) MUTATED 87 67 24
DEL PEAK 42(16P13.3) WILD-TYPE 79 143 225

Figure S492.  Get High-res Image Gene #81: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16p13.3' versus 'METHLYATION_CNMF'

P value = 0.00451 (Fisher's exact test), Q value = 0.0095

Table S493.  Gene #81: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 42(16P13.3) MUTATED 75 57 35
DEL PEAK 42(16P13.3) WILD-TYPE 173 100 137

Figure S493.  Get High-res Image Gene #81: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0017

Table S494.  Gene #81: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
DEL PEAK 42(16P13.3) MUTATED 42 15 6 2
DEL PEAK 42(16P13.3) WILD-TYPE 39 54 16 9

Figure S494.  Get High-res Image Gene #81: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00029

Table S495.  Gene #81: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 42(16P13.3) MUTATED 34 11 20
DEL PEAK 42(16P13.3) WILD-TYPE 33 9 76

Figure S495.  Get High-res Image Gene #81: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_CNMF'

P value = 0.00193 (Fisher's exact test), Q value = 0.0044

Table S496.  Gene #81: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 42(16P13.3) MUTATED 60 93 23
DEL PEAK 42(16P13.3) WILD-TYPE 103 235 103

Figure S496.  Get High-res Image Gene #81: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16p13.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S497.  Gene #81: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 42(16P13.3) MUTATED 65 56 26 18 11
DEL PEAK 42(16P13.3) WILD-TYPE 62 87 138 76 78

Figure S497.  Get High-res Image Gene #81: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00133 (Fisher's exact test), Q value = 0.0032

Table S498.  Gene #81: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 42(16P13.3) MUTATED 58 59 36
DEL PEAK 42(16P13.3) WILD-TYPE 87 146 133

Figure S498.  Get High-res Image Gene #81: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S499.  Gene #81: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 42(16P13.3) MUTATED 89 27 19 18
DEL PEAK 42(16P13.3) WILD-TYPE 109 103 80 74

Figure S499.  Get High-res Image Gene #81: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16p13.3' versus 'CN_CNMF'

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

Table S500.  Gene #82: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 43(16P13.3) MUTATED 69 59 20
DEL PEAK 43(16P13.3) WILD-TYPE 97 151 229

Figure S500.  Get High-res Image Gene #82: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16p13.3' versus 'METHLYATION_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.027

Table S501.  Gene #82: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 43(16P13.3) MUTATED 58 50 31
DEL PEAK 43(16P13.3) WILD-TYPE 190 107 141

Figure S501.  Get High-res Image Gene #82: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0018

Table S502.  Gene #82: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
DEL PEAK 43(16P13.3) MUTATED 37 12 4 2
DEL PEAK 43(16P13.3) WILD-TYPE 44 57 18 9

Figure S502.  Get High-res Image Gene #82: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00063 (Fisher's exact test), Q value = 0.0016

Table S503.  Gene #82: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 43(16P13.3) MUTATED 30 8 17
DEL PEAK 43(16P13.3) WILD-TYPE 37 12 79

Figure S503.  Get High-res Image Gene #82: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0012

Table S504.  Gene #82: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 43(16P13.3) MUTATED 56 71 19
DEL PEAK 43(16P13.3) WILD-TYPE 107 257 107

Figure S504.  Get High-res Image Gene #82: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16p13.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S505.  Gene #82: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 43(16P13.3) MUTATED 59 44 17 15 11
DEL PEAK 43(16P13.3) WILD-TYPE 68 99 147 79 78

Figure S505.  Get High-res Image Gene #82: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00191 (Fisher's exact test), Q value = 0.0044

Table S506.  Gene #82: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 43(16P13.3) MUTATED 49 49 28
DEL PEAK 43(16P13.3) WILD-TYPE 96 156 141

Figure S506.  Get High-res Image Gene #82: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S507.  Gene #82: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 43(16P13.3) MUTATED 77 18 16 15
DEL PEAK 43(16P13.3) WILD-TYPE 121 112 83 77

Figure S507.  Get High-res Image Gene #82: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

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

Table S508.  Gene #83: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 44(16Q23.1) MUTATED 109 91 65
DEL PEAK 44(16Q23.1) WILD-TYPE 57 119 184

Figure S508.  Get High-res Image Gene #83: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 0.00088 (Fisher's exact test), Q value = 0.0022

Table S509.  Gene #83: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 44(16Q23.1) MUTATED 125 65 55
DEL PEAK 44(16Q23.1) WILD-TYPE 123 92 117

Figure S509.  Get High-res Image Gene #83: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

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

Table S510.  Gene #83: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
DEL PEAK 44(16Q23.1) MUTATED 57 18 7 2
DEL PEAK 44(16Q23.1) WILD-TYPE 24 51 15 9

Figure S510.  Get High-res Image Gene #83: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S511.  Gene #83: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 44(16Q23.1) MUTATED 49 12 23
DEL PEAK 44(16Q23.1) WILD-TYPE 18 8 73

Figure S511.  Get High-res Image Gene #83: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

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

Table S512.  Gene #83: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 44(16Q23.1) MUTATED 67 154 40
DEL PEAK 44(16Q23.1) WILD-TYPE 96 174 86

Figure S512.  Get High-res Image Gene #83: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S513.  Gene #83: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 44(16Q23.1) MUTATED 73 75 65 21 27
DEL PEAK 44(16Q23.1) WILD-TYPE 54 68 99 73 62

Figure S513.  Get High-res Image Gene #83: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00797 (Fisher's exact test), Q value = 0.016

Table S514.  Gene #83: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 44(16Q23.1) MUTATED 65 98 55
DEL PEAK 44(16Q23.1) WILD-TYPE 80 107 114

Figure S514.  Get High-res Image Gene #83: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S515.  Gene #83: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 44(16Q23.1) MUTATED 111 53 33 21
DEL PEAK 44(16Q23.1) WILD-TYPE 87 77 66 71

Figure S515.  Get High-res Image Gene #83: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

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

Table S516.  Gene #84: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 45(17P12) MUTATED 121 103 43
DEL PEAK 45(17P12) WILD-TYPE 45 107 206

Figure S516.  Get High-res Image Gene #84: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.7e-05

Table S517.  Gene #84: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 45(17P12) MUTATED 120 80 51
DEL PEAK 45(17P12) WILD-TYPE 128 77 121

Figure S517.  Get High-res Image Gene #84: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.6e-05

Table S518.  Gene #84: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
DEL PEAK 45(17P12) MUTATED 55 21 7 3
DEL PEAK 45(17P12) WILD-TYPE 26 48 15 8

Figure S518.  Get High-res Image Gene #84: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S519.  Gene #84: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 45(17P12) MUTATED 46 11 29
DEL PEAK 45(17P12) WILD-TYPE 21 9 67

Figure S519.  Get High-res Image Gene #84: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_CNMF'

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

Table S520.  Gene #84: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 45(17P12) MUTATED 74 153 35
DEL PEAK 45(17P12) WILD-TYPE 89 175 91

Figure S520.  Get High-res Image Gene #84: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17p12' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S521.  Gene #84: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 45(17P12) MUTATED 87 74 55 27 19
DEL PEAK 45(17P12) WILD-TYPE 40 69 109 67 70

Figure S521.  Get High-res Image Gene #84: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.043 (Fisher's exact test), Q value = 0.071

Table S522.  Gene #84: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 45(17P12) MUTATED 69 96 60
DEL PEAK 45(17P12) WILD-TYPE 76 109 109

Figure S522.  Get High-res Image Gene #84: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S523.  Gene #84: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 45(17P12) MUTATED 116 51 30 28
DEL PEAK 45(17P12) WILD-TYPE 82 79 69 64

Figure S523.  Get High-res Image Gene #84: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q24.3' versus 'CN_CNMF'

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

Table S524.  Gene #85: 'del_17q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 46(17Q24.3) MUTATED 48 36 19
DEL PEAK 46(17Q24.3) WILD-TYPE 118 174 230

Figure S524.  Get High-res Image Gene #85: 'del_17q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q24.3' versus 'MIRSEQ_CNMF'

P value = 0.0486 (Fisher's exact test), Q value = 0.078

Table S525.  Gene #85: 'del_17q24.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 46(17Q24.3) MUTATED 24 64 13
DEL PEAK 46(17Q24.3) WILD-TYPE 139 264 113

Figure S525.  Get High-res Image Gene #85: 'del_17q24.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0339 (Fisher's exact test), Q value = 0.057

Table S526.  Gene #85: 'del_17q24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 46(17Q24.3) MUTATED 30 27 17 15 12
DEL PEAK 46(17Q24.3) WILD-TYPE 97 116 147 79 77

Figure S526.  Get High-res Image Gene #85: 'del_17q24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q12.2' versus 'CN_CNMF'

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

Table S527.  Gene #86: 'del_18q12.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 47(18Q12.2) MUTATED 107 132 53
DEL PEAK 47(18Q12.2) WILD-TYPE 59 78 196

Figure S527.  Get High-res Image Gene #86: 'del_18q12.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q12.2' versus 'METHLYATION_CNMF'

P value = 0.00176 (Fisher's exact test), Q value = 0.0041

Table S528.  Gene #86: 'del_18q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 47(18Q12.2) MUTATED 119 88 63
DEL PEAK 47(18Q12.2) WILD-TYPE 129 69 109

Figure S528.  Get High-res Image Gene #86: 'del_18q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q12.2' versus 'MRNASEQ_CNMF'

P value = 0.023 (Fisher's exact test), Q value = 0.041

Table S529.  Gene #86: 'del_18q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
DEL PEAK 47(18Q12.2) MUTATED 57 38 8 7
DEL PEAK 47(18Q12.2) WILD-TYPE 24 31 14 4

Figure S529.  Get High-res Image Gene #86: 'del_18q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q12.2' versus 'MIRSEQ_CNMF'

P value = 0.0364 (Fisher's exact test), Q value = 0.061

Table S530.  Gene #86: 'del_18q12.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 47(18Q12.2) MUTATED 85 157 47
DEL PEAK 47(18Q12.2) WILD-TYPE 78 171 79

Figure S530.  Get High-res Image Gene #86: 'del_18q12.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00047

Table S531.  Gene #86: 'del_18q12.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 47(18Q12.2) MUTATED 76 69 63 51 30
DEL PEAK 47(18Q12.2) WILD-TYPE 51 74 101 43 59

Figure S531.  Get High-res Image Gene #86: 'del_18q12.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.023

Table S532.  Gene #86: 'del_18q12.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 47(18Q12.2) MUTATED 103 57 34 50
DEL PEAK 47(18Q12.2) WILD-TYPE 95 73 65 42

Figure S532.  Get High-res Image Gene #86: 'del_18q12.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q21.2' versus 'CN_CNMF'

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

Table S533.  Gene #87: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 48(18Q21.2) MUTATED 116 145 62
DEL PEAK 48(18Q21.2) WILD-TYPE 50 65 187

Figure S533.  Get High-res Image Gene #87: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

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

Table S534.  Gene #87: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 48(18Q21.2) MUTATED 138 94 69
DEL PEAK 48(18Q21.2) WILD-TYPE 110 63 103

Figure S534.  Get High-res Image Gene #87: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 0.00467 (Fisher's exact test), Q value = 0.0098

Table S535.  Gene #87: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
DEL PEAK 48(18Q21.2) MUTATED 63 38 10 7
DEL PEAK 48(18Q21.2) WILD-TYPE 18 31 12 4

Figure S535.  Get High-res Image Gene #87: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00977 (Fisher's exact test), Q value = 0.019

Table S536.  Gene #87: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 48(18Q21.2) MUTATED 51 15 52
DEL PEAK 48(18Q21.2) WILD-TYPE 16 5 44

Figure S536.  Get High-res Image Gene #87: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.031

Table S537.  Gene #87: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 48(18Q21.2) MUTATED 90 179 51
DEL PEAK 48(18Q21.2) WILD-TYPE 73 149 75

Figure S537.  Get High-res Image Gene #87: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.7e-05

Table S538.  Gene #87: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 48(18Q21.2) MUTATED 82 83 69 54 32
DEL PEAK 48(18Q21.2) WILD-TYPE 45 60 95 40 57

Figure S538.  Get High-res Image Gene #87: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0194 (Fisher's exact test), Q value = 0.035

Table S539.  Gene #87: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 48(18Q21.2) MUTATED 113 64 39 53
DEL PEAK 48(18Q21.2) WILD-TYPE 85 66 60 39

Figure S539.  Get High-res Image Gene #87: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

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

Table S540.  Gene #88: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 49(19P13.3) MUTATED 111 113 25
DEL PEAK 49(19P13.3) WILD-TYPE 55 97 224

Figure S540.  Get High-res Image Gene #88: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

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

Table S541.  Gene #88: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 49(19P13.3) MUTATED 92 96 45
DEL PEAK 49(19P13.3) WILD-TYPE 156 61 127

Figure S541.  Get High-res Image Gene #88: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'RPPA_CNMF'

P value = 0.00318 (Fisher's exact test), Q value = 0.0069

Table S542.  Gene #88: 'del_19p13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 137 136 64
DEL PEAK 49(19P13.3) MUTATED 70 49 39 30
DEL PEAK 49(19P13.3) WILD-TYPE 75 88 97 34

Figure S542.  Get High-res Image Gene #88: 'del_19p13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_19p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.002

Table S543.  Gene #88: 'del_19p13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
DEL PEAK 49(19P13.3) MUTATED 126 35 27
DEL PEAK 49(19P13.3) WILD-TYPE 147 75 72

Figure S543.  Get High-res Image Gene #88: 'del_19p13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

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

Table S544.  Gene #88: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 49(19P13.3) MUTATED 94 127 25
DEL PEAK 49(19P13.3) WILD-TYPE 69 201 101

Figure S544.  Get High-res Image Gene #88: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S545.  Gene #88: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 49(19P13.3) MUTATED 100 62 32 43 9
DEL PEAK 49(19P13.3) WILD-TYPE 27 81 132 51 80

Figure S545.  Get High-res Image Gene #88: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

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

Table S546.  Gene #88: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 49(19P13.3) MUTATED 90 79 43
DEL PEAK 49(19P13.3) WILD-TYPE 55 126 126

Figure S546.  Get High-res Image Gene #88: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S547.  Gene #88: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 49(19P13.3) MUTATED 112 34 24 42
DEL PEAK 49(19P13.3) WILD-TYPE 86 96 75 50

Figure S547.  Get High-res Image Gene #88: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.11' versus 'CN_CNMF'

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

Table S548.  Gene #89: 'del_19q13.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 50(19Q13.11) MUTATED 58 51 11
DEL PEAK 50(19Q13.11) WILD-TYPE 108 159 238

Figure S548.  Get High-res Image Gene #89: 'del_19q13.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.11' versus 'METHLYATION_CNMF'

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

Table S549.  Gene #89: 'del_19q13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 50(19Q13.11) MUTATED 38 63 12
DEL PEAK 50(19Q13.11) WILD-TYPE 210 94 160

Figure S549.  Get High-res Image Gene #89: 'del_19q13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.11' versus 'MIRSEQ_CNMF'

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

Table S550.  Gene #89: 'del_19q13.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 50(19Q13.11) MUTATED 51 56 11
DEL PEAK 50(19Q13.11) WILD-TYPE 112 272 115

Figure S550.  Get High-res Image Gene #89: 'del_19q13.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19q13.11' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S551.  Gene #89: 'del_19q13.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 50(19Q13.11) MUTATED 47 25 14 27 5
DEL PEAK 50(19Q13.11) WILD-TYPE 80 118 150 67 84

Figure S551.  Get High-res Image Gene #89: 'del_19q13.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.11' versus 'MIRSEQ_MATURE_CNMF'

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

Table S552.  Gene #89: 'del_19q13.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 50(19Q13.11) MUTATED 46 38 19
DEL PEAK 50(19Q13.11) WILD-TYPE 99 167 150

Figure S552.  Get High-res Image Gene #89: 'del_19q13.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19q13.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00029

Table S553.  Gene #89: 'del_19q13.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 50(19Q13.11) MUTATED 51 13 12 27
DEL PEAK 50(19Q13.11) WILD-TYPE 147 117 87 65

Figure S553.  Get High-res Image Gene #89: 'del_19q13.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p12.1' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00034

Table S554.  Gene #90: 'del_20p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 51(20P12.1) MUTATED 19 39 14
DEL PEAK 51(20P12.1) WILD-TYPE 147 171 235

Figure S554.  Get High-res Image Gene #90: 'del_20p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_20p12.1' versus 'METHLYATION_CNMF'

P value = 0.0271 (Fisher's exact test), Q value = 0.047

Table S555.  Gene #90: 'del_20p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 51(20P12.1) MUTATED 28 28 14
DEL PEAK 51(20P12.1) WILD-TYPE 220 129 158

Figure S555.  Get High-res Image Gene #90: 'del_20p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00794 (Fisher's exact test), Q value = 0.016

Table S556.  Gene #90: 'del_20p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 51(20P12.1) MUTATED 20 2 11
DEL PEAK 51(20P12.1) WILD-TYPE 47 18 85

Figure S556.  Get High-res Image Gene #90: 'del_20p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0028 (Fisher's exact test), Q value = 0.0061

Table S557.  Gene #90: 'del_20p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 51(20P12.1) MUTATED 27 13 16 12 4
DEL PEAK 51(20P12.1) WILD-TYPE 100 130 148 82 85

Figure S557.  Get High-res Image Gene #90: 'del_20p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_21q11.2' versus 'CN_CNMF'

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

Table S558.  Gene #91: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 52(21Q11.2) MUTATED 103 125 62
DEL PEAK 52(21Q11.2) WILD-TYPE 63 85 187

Figure S558.  Get High-res Image Gene #91: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.021

Table S559.  Gene #91: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 52(21Q11.2) MUTATED 121 87 67
DEL PEAK 52(21Q11.2) WILD-TYPE 127 70 105

Figure S559.  Get High-res Image Gene #91: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00034

Table S560.  Gene #91: 'del_21q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 52(21Q11.2) MUTATED 94 151 42
DEL PEAK 52(21Q11.2) WILD-TYPE 69 177 84

Figure S560.  Get High-res Image Gene #91: 'del_21q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_21q11.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S561.  Gene #91: 'del_21q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 52(21Q11.2) MUTATED 77 75 55 52 28
DEL PEAK 52(21Q11.2) WILD-TYPE 50 68 109 42 61

Figure S561.  Get High-res Image Gene #91: 'del_21q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00268 (Fisher's exact test), Q value = 0.006

Table S562.  Gene #91: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 52(21Q11.2) MUTATED 86 96 68
DEL PEAK 52(21Q11.2) WILD-TYPE 59 109 101

Figure S562.  Get High-res Image Gene #91: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_21q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00503 (Fisher's exact test), Q value = 0.01

Table S563.  Gene #91: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 52(21Q11.2) MUTATED 109 51 39 51
DEL PEAK 52(21Q11.2) WILD-TYPE 89 79 60 41

Figure S563.  Get High-res Image Gene #91: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q22.13' versus 'CN_CNMF'

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

Table S564.  Gene #92: 'del_21q22.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 53(21Q22.13) MUTATED 104 136 65
DEL PEAK 53(21Q22.13) WILD-TYPE 62 74 184

Figure S564.  Get High-res Image Gene #92: 'del_21q22.13' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q22.13' versus 'METHLYATION_CNMF'

P value = 0.0209 (Fisher's exact test), Q value = 0.038

Table S565.  Gene #92: 'del_21q22.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 53(21Q22.13) MUTATED 132 84 70
DEL PEAK 53(21Q22.13) WILD-TYPE 116 73 102

Figure S565.  Get High-res Image Gene #92: 'del_21q22.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q22.13' versus 'MRNASEQ_CNMF'

P value = 0.035 (Fisher's exact test), Q value = 0.059

Table S566.  Gene #92: 'del_21q22.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
DEL PEAK 53(21Q22.13) MUTATED 55 36 14 3
DEL PEAK 53(21Q22.13) WILD-TYPE 26 33 8 8

Figure S566.  Get High-res Image Gene #92: 'del_21q22.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_21q22.13' versus 'MIRSEQ_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.0023

Table S567.  Gene #92: 'del_21q22.13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 53(21Q22.13) MUTATED 92 166 44
DEL PEAK 53(21Q22.13) WILD-TYPE 71 162 82

Figure S567.  Get High-res Image Gene #92: 'del_21q22.13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_21q22.13' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S568.  Gene #92: 'del_21q22.13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 53(21Q22.13) MUTATED 79 81 61 52 29
DEL PEAK 53(21Q22.13) WILD-TYPE 48 62 103 42 60

Figure S568.  Get High-res Image Gene #92: 'del_21q22.13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_21q22.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00251 (Fisher's exact test), Q value = 0.0056

Table S569.  Gene #92: 'del_21q22.13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 53(21Q22.13) MUTATED 89 101 71
DEL PEAK 53(21Q22.13) WILD-TYPE 56 104 98

Figure S569.  Get High-res Image Gene #92: 'del_21q22.13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_21q22.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00674 (Fisher's exact test), Q value = 0.014

Table S570.  Gene #92: 'del_21q22.13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 53(21Q22.13) MUTATED 114 57 39 51
DEL PEAK 53(21Q22.13) WILD-TYPE 84 73 60 41

Figure S570.  Get High-res Image Gene #92: 'del_21q22.13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q11.1' versus 'CN_CNMF'

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

Table S571.  Gene #93: 'del_22q11.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 54(22Q11.1) MUTATED 101 97 32
DEL PEAK 54(22Q11.1) WILD-TYPE 65 113 217

Figure S571.  Get High-res Image Gene #93: 'del_22q11.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q11.1' versus 'METHLYATION_CNMF'

P value = 0.00649 (Fisher's exact test), Q value = 0.013

Table S572.  Gene #93: 'del_22q11.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 54(22Q11.1) MUTATED 99 67 47
DEL PEAK 54(22Q11.1) WILD-TYPE 149 90 125

Figure S572.  Get High-res Image Gene #93: 'del_22q11.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q11.1' versus 'MRNASEQ_CNMF'

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

Table S573.  Gene #93: 'del_22q11.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
DEL PEAK 54(22Q11.1) MUTATED 51 20 5 3
DEL PEAK 54(22Q11.1) WILD-TYPE 30 49 17 8

Figure S573.  Get High-res Image Gene #93: 'del_22q11.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q11.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S574.  Gene #93: 'del_22q11.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 54(22Q11.1) MUTATED 43 10 26
DEL PEAK 54(22Q11.1) WILD-TYPE 24 10 70

Figure S574.  Get High-res Image Gene #93: 'del_22q11.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q11.1' versus 'MIRSEQ_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0027

Table S575.  Gene #93: 'del_22q11.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 54(22Q11.1) MUTATED 65 133 29
DEL PEAK 54(22Q11.1) WILD-TYPE 98 195 97

Figure S575.  Get High-res Image Gene #93: 'del_22q11.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q11.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S576.  Gene #93: 'del_22q11.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 54(22Q11.1) MUTATED 76 72 34 25 20
DEL PEAK 54(22Q11.1) WILD-TYPE 51 71 130 69 69

Figure S576.  Get High-res Image Gene #93: 'del_22q11.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q11.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.6e-05

Table S577.  Gene #93: 'del_22q11.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 54(22Q11.1) MUTATED 98 41 28 24
DEL PEAK 54(22Q11.1) WILD-TYPE 100 89 71 68

Figure S577.  Get High-res Image Gene #93: 'del_22q11.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.31' versus 'CN_CNMF'

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

Table S578.  Gene #94: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 55(22Q13.31) MUTATED 96 106 33
DEL PEAK 55(22Q13.31) WILD-TYPE 70 104 216

Figure S578.  Get High-res Image Gene #94: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.31' versus 'METHLYATION_CNMF'

P value = 0.00245 (Fisher's exact test), Q value = 0.0055

Table S579.  Gene #94: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 55(22Q13.31) MUTATED 98 72 48
DEL PEAK 55(22Q13.31) WILD-TYPE 150 85 124

Figure S579.  Get High-res Image Gene #94: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.31' versus 'MRNASEQ_CNMF'

P value = 0.0089 (Fisher's exact test), Q value = 0.017

Table S580.  Gene #94: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
DEL PEAK 55(22Q13.31) MUTATED 44 21 6 3
DEL PEAK 55(22Q13.31) WILD-TYPE 37 48 16 8

Figure S580.  Get High-res Image Gene #94: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00127 (Fisher's exact test), Q value = 0.0031

Table S581.  Gene #94: 'del_22q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 55(22Q13.31) MUTATED 38 9 27
DEL PEAK 55(22Q13.31) WILD-TYPE 29 11 69

Figure S581.  Get High-res Image Gene #94: 'del_22q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00029

Table S582.  Gene #94: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 55(22Q13.31) MUTATED 66 139 27
DEL PEAK 55(22Q13.31) WILD-TYPE 97 189 99

Figure S582.  Get High-res Image Gene #94: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.31' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S583.  Gene #94: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 55(22Q13.31) MUTATED 78 67 40 27 20
DEL PEAK 55(22Q13.31) WILD-TYPE 49 76 124 67 69

Figure S583.  Get High-res Image Gene #94: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0338 (Fisher's exact test), Q value = 0.057

Table S584.  Gene #94: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 55(22Q13.31) MUTATED 62 87 52
DEL PEAK 55(22Q13.31) WILD-TYPE 83 118 117

Figure S584.  Get High-res Image Gene #94: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00016

Table S585.  Gene #94: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 55(22Q13.31) MUTATED 102 45 28 26
DEL PEAK 55(22Q13.31) WILD-TYPE 96 85 71 66

Figure S585.  Get High-res Image Gene #94: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp22.2' versus 'CN_CNMF'

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

Table S586.  Gene #95: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 56(XP22.2) MUTATED 51 81 18
DEL PEAK 56(XP22.2) WILD-TYPE 115 129 231

Figure S586.  Get High-res Image Gene #95: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp22.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.7e-05

Table S587.  Gene #95: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 56(XP22.2) MUTATED 57 60 27
DEL PEAK 56(XP22.2) WILD-TYPE 191 97 145

Figure S587.  Get High-res Image Gene #95: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp22.2' versus 'MRNASEQ_CNMF'

P value = 0.043 (Fisher's exact test), Q value = 0.071

Table S588.  Gene #95: 'del_xp22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
DEL PEAK 56(XP22.2) MUTATED 24 32 4 5
DEL PEAK 56(XP22.2) WILD-TYPE 57 37 18 6

Figure S588.  Get High-res Image Gene #95: 'del_xp22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp22.2' versus 'MIRSEQ_CNMF'

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

Table S589.  Gene #95: 'del_xp22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 56(XP22.2) MUTATED 61 72 16
DEL PEAK 56(XP22.2) WILD-TYPE 102 256 110

Figure S589.  Get High-res Image Gene #95: 'del_xp22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xp22.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S590.  Gene #95: 'del_xp22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 56(XP22.2) MUTATED 44 31 23 39 12
DEL PEAK 56(XP22.2) WILD-TYPE 83 112 141 55 77

Figure S590.  Get High-res Image Gene #95: 'del_xp22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xp22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00074 (Fisher's exact test), Q value = 0.0019

Table S591.  Gene #95: 'del_xp22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 56(XP22.2) MUTATED 53 26 19 39
DEL PEAK 56(XP22.2) WILD-TYPE 145 104 80 53

Figure S591.  Get High-res Image Gene #95: 'del_xp22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp21.1' versus 'CN_CNMF'

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

Table S592.  Gene #96: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 57(XP21.1) MUTATED 47 83 13
DEL PEAK 57(XP21.1) WILD-TYPE 119 127 236

Figure S592.  Get High-res Image Gene #96: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.6e-05

Table S593.  Gene #96: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 57(XP21.1) MUTATED 54 57 24
DEL PEAK 57(XP21.1) WILD-TYPE 194 100 148

Figure S593.  Get High-res Image Gene #96: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp21.1' versus 'MRNASEQ_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.024

Table S594.  Gene #96: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
DEL PEAK 57(XP21.1) MUTATED 27 34 3 5
DEL PEAK 57(XP21.1) WILD-TYPE 54 35 19 6

Figure S594.  Get High-res Image Gene #96: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp21.1' versus 'MIRSEQ_CNMF'

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

Table S595.  Gene #96: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 57(XP21.1) MUTATED 61 66 13
DEL PEAK 57(XP21.1) WILD-TYPE 102 262 113

Figure S595.  Get High-res Image Gene #96: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xp21.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S596.  Gene #96: 'del_xp21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 57(XP21.1) MUTATED 35 30 22 41 12
DEL PEAK 57(XP21.1) WILD-TYPE 92 113 142 53 77

Figure S596.  Get High-res Image Gene #96: 'del_xp21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00655 (Fisher's exact test), Q value = 0.013

Table S597.  Gene #96: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 57(XP21.1) MUTATED 50 44 34
DEL PEAK 57(XP21.1) WILD-TYPE 95 161 135

Figure S597.  Get High-res Image Gene #96: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xp21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.7e-05

Table S598.  Gene #96: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 57(XP21.1) MUTATED 49 22 16 41
DEL PEAK 57(XP21.1) WILD-TYPE 149 108 83 51

Figure S598.  Get High-res Image Gene #96: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp11.3' versus 'CN_CNMF'

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

Table S599.  Gene #97: 'del_xp11.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 58(XP11.3) MUTATED 44 90 12
DEL PEAK 58(XP11.3) WILD-TYPE 122 120 237

Figure S599.  Get High-res Image Gene #97: 'del_xp11.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp11.3' versus 'METHLYATION_CNMF'

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

Table S600.  Gene #97: 'del_xp11.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 58(XP11.3) MUTATED 55 61 22
DEL PEAK 58(XP11.3) WILD-TYPE 193 96 150

Figure S600.  Get High-res Image Gene #97: 'del_xp11.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp11.3' versus 'MRNASEQ_CNMF'

P value = 0.00869 (Fisher's exact test), Q value = 0.017

Table S601.  Gene #97: 'del_xp11.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
DEL PEAK 58(XP11.3) MUTATED 26 38 5 5
DEL PEAK 58(XP11.3) WILD-TYPE 55 31 17 6

Figure S601.  Get High-res Image Gene #97: 'del_xp11.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp11.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0229 (Fisher's exact test), Q value = 0.041

Table S602.  Gene #97: 'del_xp11.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
DEL PEAK 58(XP11.3) MUTATED 20 6 48
DEL PEAK 58(XP11.3) WILD-TYPE 47 14 48

Figure S602.  Get High-res Image Gene #97: 'del_xp11.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp11.3' versus 'MIRSEQ_CNMF'

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

Table S603.  Gene #97: 'del_xp11.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 58(XP11.3) MUTATED 62 70 12
DEL PEAK 58(XP11.3) WILD-TYPE 101 258 114

Figure S603.  Get High-res Image Gene #97: 'del_xp11.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xp11.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S604.  Gene #97: 'del_xp11.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 58(XP11.3) MUTATED 35 29 22 47 11
DEL PEAK 58(XP11.3) WILD-TYPE 92 114 142 47 78

Figure S604.  Get High-res Image Gene #97: 'del_xp11.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xp11.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00605 (Fisher's exact test), Q value = 0.012

Table S605.  Gene #97: 'del_xp11.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 58(XP11.3) MUTATED 51 46 34
DEL PEAK 58(XP11.3) WILD-TYPE 94 159 135

Figure S605.  Get High-res Image Gene #97: 'del_xp11.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xp11.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S606.  Gene #97: 'del_xp11.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 58(XP11.3) MUTATED 48 21 15 47
DEL PEAK 58(XP11.3) WILD-TYPE 150 109 84 45

Figure S606.  Get High-res Image Gene #97: 'del_xp11.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xq11.2' versus 'CN_CNMF'

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

Table S607.  Gene #98: 'del_xq11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 59(XQ11.2) MUTATED 37 54 12
DEL PEAK 59(XQ11.2) WILD-TYPE 129 156 237

Figure S607.  Get High-res Image Gene #98: 'del_xq11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq11.2' versus 'METHLYATION_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.035

Table S608.  Gene #98: 'del_xq11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 59(XQ11.2) MUTATED 43 34 18
DEL PEAK 59(XQ11.2) WILD-TYPE 205 123 154

Figure S608.  Get High-res Image Gene #98: 'del_xq11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq11.2' versus 'MIRSEQ_CNMF'

P value = 0.00615 (Fisher's exact test), Q value = 0.013

Table S609.  Gene #98: 'del_xq11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 59(XQ11.2) MUTATED 34 58 10
DEL PEAK 59(XQ11.2) WILD-TYPE 129 270 116

Figure S609.  Get High-res Image Gene #98: 'del_xq11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xq11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00313 (Fisher's exact test), Q value = 0.0068

Table S610.  Gene #98: 'del_xq11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 59(XQ11.2) MUTATED 25 32 19 20 6
DEL PEAK 59(XQ11.2) WILD-TYPE 102 111 145 74 83

Figure S610.  Get High-res Image Gene #98: 'del_xq11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xq11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0281 (Fisher's exact test), Q value = 0.049

Table S611.  Gene #98: 'del_xq11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 59(XQ11.2) MUTATED 41 16 10 20
DEL PEAK 59(XQ11.2) WILD-TYPE 157 114 89 72

Figure S611.  Get High-res Image Gene #98: 'del_xq11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xq21.33' versus 'CN_CNMF'

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

Table S612.  Gene #99: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 166 210 249
DEL PEAK 60(XQ21.33) MUTATED 37 47 12
DEL PEAK 60(XQ21.33) WILD-TYPE 129 163 237

Figure S612.  Get High-res Image Gene #99: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq21.33' versus 'METHLYATION_CNMF'

P value = 0.0079 (Fisher's exact test), Q value = 0.016

Table S613.  Gene #99: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 157 172
DEL PEAK 60(XQ21.33) MUTATED 38 34 16
DEL PEAK 60(XQ21.33) WILD-TYPE 210 123 156

Figure S613.  Get High-res Image Gene #99: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq21.33' versus 'MIRSEQ_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.023

Table S614.  Gene #99: 'del_xq21.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 328 126
DEL PEAK 60(XQ21.33) MUTATED 33 52 10
DEL PEAK 60(XQ21.33) WILD-TYPE 130 276 116

Figure S614.  Get High-res Image Gene #99: 'del_xq21.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xq21.33' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S615.  Gene #99: 'del_xq21.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
DEL PEAK 60(XQ21.33) MUTATED 29 30 14 17 5
DEL PEAK 60(XQ21.33) WILD-TYPE 98 113 150 77 84

Figure S615.  Get High-res Image Gene #99: 'del_xq21.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xq21.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0462 (Fisher's exact test), Q value = 0.075

Table S616.  Gene #99: 'del_xq21.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 205 169
DEL PEAK 60(XQ21.33) MUTATED 31 30 19
DEL PEAK 60(XQ21.33) WILD-TYPE 114 175 150

Figure S616.  Get High-res Image Gene #99: 'del_xq21.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xq21.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00958 (Fisher's exact test), Q value = 0.019

Table S617.  Gene #99: 'del_xq21.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 198 130 99 92
DEL PEAK 60(XQ21.33) MUTATED 41 11 11 17
DEL PEAK 60(XQ21.33) WILD-TYPE 157 119 88 75

Figure S617.  Get High-res Image Gene #99: 'del_xq21.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = all_lesions.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/STES-TP/19785970/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/STES-TP/20144037/STES-TP.transferedmergedcluster.txt

  • Number of patients = 625

  • Number of significantly focal cnvs = 99

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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