Correlation between copy number variation genes (focal events) and molecular subtypes
Breast Invasive Carcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1KH0KW6
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1KH0KW6
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 68 focal events and 12 molecular subtypes across 1033 patients, 623 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

  • amp_1q44 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

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

  • amp_3q26.32 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_4q13.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_6p23 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_6q21 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_8p11.23 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_8p11.21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

  • amp_10q22.3 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • amp_11q13.3 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

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

  • amp_12q15 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • amp_14q21.1 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

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

  • amp_17q23.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_19p13.12 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_19q13.42 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • del_1p36.13 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_1p21.2 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_2q37.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3p21.31 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • del_5q11.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_5q21.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_6p25.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_6q15 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_6q27 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

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

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

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

  • del_8p11.21 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

  • del_10q26.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_11q13.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_11q23.2 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_12p13.2 cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • del_12q24.31 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_14q24.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_15q13.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_16q24.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

  • del_19q13.32 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_20p13 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_21q11.2 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_22q11.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_22q13.32 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 68 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 623 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Chi-square test Fisher's exact test Chi-square test Chi-square test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test
amp 1p22 3 242 (23%) 791 3.79e-13
(2.09e-10) 		1.17e-11
(5.93e-09) 		1.8e-19
(1.2e-16) 		1.06e-16
(6.59e-14) 		0.000472
(0.101) 		6.95e-07
(0.000242) 		6.26e-23
(4.46e-20) 		7.79e-21
(5.38e-18) 		1.35e-14
(7.88e-12) 		9.05e-16
(5.46e-13) 		3.16e-14
(1.82e-11) 		6.53e-16
(3.95e-13)
amp 3q26 32 328 (32%) 705 1.59e-10
(7.61e-08) 		5.06e-11
(2.5e-08) 		1.15e-39
(9.03e-37) 		3.15e-20
(2.14e-17) 		3.01e-06
(0.000953) 		1.16e-05
(0.00326) 		9.43e-28
(7.08e-25) 		9.32e-25
(6.8e-22) 		3.34e-21
(2.32e-18) 		9.9e-22
(6.93e-19) 		6.12e-18
(3.93e-15) 		5.39e-15
(3.19e-12)
amp 6p23 287 (28%) 746 1.36e-07
(5.15e-05) 		4.12e-07
(0.000148) 		2.37e-39
(1.86e-36) 		3.26e-23
(2.34e-20) 		3.98e-07
(0.000144) 		0.000129
(0.0304) 		1.37e-23
(9.89e-21) 		2.66e-16
(1.64e-13) 		6.26e-20
(4.22e-17) 		1.36e-19
(9.07e-17) 		6e-15
(3.53e-12) 		1.07e-09
(4.78e-07)
amp 6q21 196 (19%) 837 7.25e-14
(4.1e-11) 		1.69e-10
(8.05e-08) 		2.66e-47
(2.13e-44) 		5.27e-23
(3.77e-20) 		1.11e-08
(4.64e-06) 		4.44e-07
(0.000158) 		8.9e-32
(6.82e-29) 		4.36e-25
(3.19e-22) 		1.52e-27
(1.14e-24) 		2.15e-29
(1.63e-26) 		1.95e-21
(1.36e-18) 		3.19e-18
(2.06e-15)
amp 8q24 21 656 (64%) 377 1.61e-15
(9.67e-13) 		4.21e-08
(1.67e-05) 		6.65e-58
(5.38e-55) 		1.17e-28
(8.89e-26) 		1.22e-07
(4.67e-05) 		2.49e-06
(0.000808) 		3.84e-35
(2.97e-32) 		1.58e-24
(1.15e-21) 		1.93e-30
(1.47e-27) 		4.84e-28
(3.64e-25) 		3.62e-26
(2.67e-23) 		6.5e-21
(4.49e-18)
amp 10p15 1 292 (28%) 741 1.27e-20
(8.71e-18) 		6.33e-19
(4.15e-16) 		5.71e-49
(4.58e-46) 		1.19e-29
(9.03e-27) 		7.17e-11
(3.5e-08) 		2.17e-12
(1.15e-09) 		6.17e-38
(4.83e-35) 		4.7e-35
(3.63e-32) 		4.08e-35
(3.16e-32) 		5.11e-36
(3.98e-33) 		1.78e-21
(1.24e-18) 		4.81e-23
(3.45e-20)
amp 12p13 33 276 (27%) 757 3.08e-11
(1.54e-08) 		1.13e-11
(5.77e-09) 		9.75e-38
(7.63e-35) 		9.67e-20
(6.49e-17) 		3.18e-08
(1.28e-05) 		2.82e-06
(0.000902) 		4.82e-27
(3.59e-24) 		8.24e-23
(5.84e-20) 		1.73e-27
(1.29e-24) 		2.76e-17
(1.75e-14) 		8.76e-19
(5.7e-16) 		1.93e-16
(1.19e-13)
amp 13q34 175 (17%) 858 2.44e-09
(1.07e-06) 		5.48e-09
(2.33e-06) 		3.55e-22
(2.49e-19) 		1.39e-13
(7.75e-11) 		1.4e-05
(0.00392) 		8.83e-08
(3.43e-05) 		6.4e-21
(4.43e-18) 		2.76e-19
(1.82e-16) 		1.39e-19
(9.27e-17) 		8.23e-19
(5.37e-16) 		1.49e-11
(7.53e-09) 		4.05e-12
(2.1e-09)
amp 19q12 270 (26%) 763 3.61e-11
(1.79e-08) 		5.38e-10
(2.44e-07) 		8.46e-32
(6.49e-29) 		3.81e-12
(1.99e-09) 		1.9e-06
(0.000629) 		2.74e-06
(0.000879) 		8.09e-23
(5.74e-20) 		4.03e-20
(2.73e-17) 		5.07e-14
(2.88e-11) 		4.51e-19
(2.97e-16) 		5.75e-13
(3.14e-10) 		3.06e-13
(1.69e-10)
del 2q37 3 307 (30%) 726 2.53e-07
(9.26e-05) 		8.21e-10
(3.69e-07) 		1.66e-27
(1.24e-24) 		1.41e-12
(7.54e-10) 		3.45e-10
(1.59e-07) 		2.74e-09
(1.19e-06) 		2.88e-15
(1.71e-12) 		2.19e-14
(1.27e-11) 		2.72e-14
(1.57e-11) 		8.07e-12
(4.15e-09) 		1.33e-15
(7.97e-13) 		1.04e-09
(4.64e-07)
del 3p21 31 333 (32%) 700 4.41e-12
(2.29e-09) 		2.05e-08
(8.44e-06) 		5.91e-41
(4.67e-38) 		6.64e-19
(4.34e-16) 		3.63e-09
(1.56e-06) 		4.15e-06
(0.00128) 		2.58e-22
(1.82e-19) 		5.33e-13
(2.92e-10) 		1.14e-17
(7.3e-15) 		1.36e-13
(7.61e-11) 		7.19e-13
(3.92e-10) 		2.06e-08
(8.47e-06)
del 4p16 3 327 (32%) 706 9.53e-13
(5.15e-10) 		2.8e-12
(1.48e-09) 		3.45e-35
(2.68e-32) 		8.72e-18
(5.58e-15) 		1.78e-07
(6.67e-05) 		5.2e-07
(0.000183) 		1.07e-25
(7.85e-23) 		3.18e-23
(2.29e-20) 		1.1e-18
(7.14e-16) 		4.62e-20
(3.13e-17) 		9.04e-15
(5.3e-12) 		4.47e-13
(2.46e-10)
del 4q35 2 334 (32%) 699 7.03e-07
(0.000243) 		1.71e-06
(0.000571) 		8.03e-41
(6.32e-38) 		2.48e-18
(1.6e-15) 		8.21e-08
(3.21e-05) 		6.93e-06
(0.00203) 		1.05e-26
(7.8e-24) 		1.69e-19
(1.12e-16) 		8.06e-20
(5.42e-17) 		4.86e-22
(3.4e-19) 		2.08e-17
(1.32e-14) 		5.52e-15
(3.26e-12)
del 5q11 2 269 (26%) 764 3.26e-28
(2.46e-25) 		3.49e-25
(2.56e-22) 		5.33e-81
(4.34e-78) 		6.67e-48
(5.34e-45) 		1.32e-16
(8.17e-14) 		2.45e-19
(1.62e-16) 		8.1e-65
(6.59e-62) 		2.38e-56
(1.92e-53) 		7.28e-46
(5.81e-43) 		2.14e-51
(1.73e-48) 		8.05e-43
(6.38e-40) 		1.41e-36
(1.1e-33)
del 5q21 3 261 (25%) 772 7.19e-31
(5.48e-28) 		1.14e-27
(8.52e-25) 		3.29e-92
(2.69e-89) 		3.74e-59
(3.03e-56) 		1.04e-15
(6.29e-13) 		2.68e-16
(1.65e-13) 		1.94e-76
(1.58e-73) 		9.08e-63
(7.37e-60) 		3.12e-51
(2.51e-48) 		8.56e-60
(6.94e-57) 		6.27e-46
(5e-43) 		4.71e-44
(3.73e-41)
del 9q34 2 292 (28%) 741 3.61e-09
(1.55e-06) 		1.75e-09
(7.73e-07) 		1.2e-42
(9.48e-40) 		6.39e-21
(4.43e-18) 		1.09e-06
(0.000371) 		9.56e-05
(0.0234) 		1.07e-26
(7.96e-24) 		1.34e-19
(8.97e-17) 		8.45e-23
(5.98e-20) 		1.29e-24
(9.41e-22) 		1.94e-19
(1.29e-16) 		1.29e-19
(8.67e-17)
del 10q23 31 311 (30%) 722 8.49e-07
(0.000292) 		4.49e-06
(0.00137) 		6.69e-24
(4.84e-21) 		2.39e-15
(1.43e-12) 		1.98e-07
(7.34e-05) 		4.1e-05
(0.0107) 		6.08e-17
(3.82e-14) 		4e-14
(2.28e-11) 		7.05e-12
(3.64e-09) 		2.05e-15
(1.22e-12) 		2e-09
(8.76e-07) 		1.42e-08
(5.92e-06)
del 10q26 3 308 (30%) 725 1.72e-10
(8.14e-08) 		2.65e-08
(1.08e-05) 		2.01e-28
(1.52e-25) 		6.1e-17
(3.82e-14) 		2.63e-08
(1.07e-05) 		1.96e-07
(7.29e-05) 		4.19e-24
(3.04e-21) 		2.1e-18
(1.36e-15) 		4.7e-16
(2.87e-13) 		4.78e-19
(3.14e-16) 		1.05e-10
(5.09e-08) 		3.13e-12
(1.65e-09)
del 11p15 5 301 (29%) 732 2.94e-08
(1.18e-05) 		2.7e-08
(1.1e-05) 		7.15e-41
(5.63e-38) 		1.02e-14
(5.96e-12) 		1.9e-09
(8.34e-07) 		1.86e-06
(0.000615) 		1.46e-21
(1.02e-18) 		1.91e-16
(1.18e-13) 		3.44e-17
(2.17e-14) 		4.67e-16
(2.86e-13) 		1.83e-14
(1.06e-11) 		2.26e-11
(1.13e-08)
del 12q23 1 196 (19%) 837 8.74e-14
(4.92e-11) 		9.86e-13
(5.32e-10) 		1.2e-29
(9.08e-27) 		5.89e-23
(4.2e-20) 		3.98e-07
(0.000144) 		3.66e-08
(1.46e-05) 		4.39e-23
(3.16e-20) 		1.92e-22
(1.35e-19) 		2.26e-16
(1.39e-13) 		1.27e-18
(8.27e-16) 		7.7e-13
(4.18e-10) 		5.86e-14
(3.32e-11)
del 12q24 31 203 (20%) 830 1.46e-10
(7.02e-08) 		1.68e-10
(8.02e-08) 		6.84e-26
(5.03e-23) 		9.27e-21
(6.39e-18) 		7.73e-06
(0.00224) 		2.47e-07
(9.08e-05) 		1.31e-20
(9.02e-18) 		1.82e-20
(1.24e-17) 		7.42e-12
(3.82e-09) 		6.36e-15
(3.73e-12) 		1.17e-09
(5.23e-07) 		3.14e-10
(1.45e-07)
del 14q24 1 337 (33%) 696 5.85e-16
(3.55e-13) 		4.83e-10
(2.21e-07) 		2.05e-44
(1.63e-41) 		1.85e-22
(1.3e-19) 		3.27e-08
(1.31e-05) 		2.82e-07
(0.000103) 		2.04e-34
(1.57e-31) 		1.41e-23
(1.02e-20) 		1.06e-22
(7.49e-20) 		7.65e-23
(5.44e-20) 		2.96e-20
(2.01e-17) 		2.25e-16
(1.39e-13)
del 15q13 1 360 (35%) 673 1.29e-07
(4.92e-05) 		4.27e-08
(1.69e-05) 		5.3e-45
(4.22e-42) 		3.53e-18
(2.28e-15) 		9.66e-05
(0.0236) 		7.54e-06
(0.0022) 		5.23e-25
(3.82e-22) 		1.39e-20
(9.53e-18) 		2.72e-22
(1.91e-19) 		2.11e-24
(1.54e-21) 		1.55e-19
(1.03e-16) 		4.31e-17
(2.71e-14)
del 16q24 3 665 (64%) 368 9.32e-17
(5.83e-14) 		2.85e-14
(1.64e-11) 		1.15e-13
(6.42e-11) 		4.58e-12
(2.37e-09) 		1.21e-09
(5.37e-07) 		3.55e-11
(1.76e-08) 		6.73e-32
(5.17e-29) 		1.16e-26
(8.56e-24) 		6.07e-16
(3.68e-13) 		9.46e-17
(5.9e-14) 		2.08e-11
(1.04e-08) 		2.86e-13
(1.59e-10)
del 17q21 31 360 (35%) 673 5.96e-16
(3.62e-13) 		4.27e-08
(1.69e-05) 		6.83e-31
(5.22e-28) 		7.01e-18
(4.49e-15) 		3.71e-12
(1.94e-09) 		3.98e-12
(2.07e-09) 		5.57e-36
(4.34e-33) 		9.26e-18
(5.92e-15) 		1.66e-16
(1.03e-13) 		3e-13
(1.66e-10) 		1.02e-13
(5.73e-11) 		7.79e-09
(3.27e-06)
del 19p13 3 345 (33%) 688 1.15e-11
(5.87e-09) 		4.92e-09
(2.1e-06) 		3.35e-55
(2.7e-52) 		6.13e-24
(4.44e-21) 		8.17e-07
(0.000282) 		3.6e-06
(0.00112) 		7.24e-27
(5.38e-24) 		5.26e-19
(3.45e-16) 		2.84e-25
(2.09e-22) 		2.61e-21
(1.81e-18) 		6.57e-19
(4.3e-16) 		1.62e-12
(8.61e-10)
del 19q13 32 204 (20%) 829 1.72e-06
(0.000573) 		4.65e-06
(0.00141) 		3.51e-27
(2.62e-24) 		4.2e-14
(2.4e-11) 		0.000458
(0.099) 		2.51e-05
(0.00681) 		3.86e-15
(2.29e-12) 		1.52e-14
(8.84e-12) 		3.92e-12
(2.05e-09) 		1.02e-10
(4.96e-08) 		1.36e-15
(8.18e-13) 		2.8e-08
(1.14e-05)
amp 19p13 12 216 (21%) 817 3.23e-05
(0.00851) 		0.000109
(0.026) 		2.33e-15
(1.39e-12) 		0.000187
(0.0421) 		0.00069
(0.142) 		0.00384
(0.631) 		2.65e-11
(1.33e-08) 		7.54e-09
(3.16e-06) 		1.01e-05
(0.00289) 		4.13e-08
(1.65e-05) 		5.92e-05
(0.0148) 		1.11e-05
(0.00315)
amp 20q13 2 530 (51%) 503 2.78e-10
(1.3e-07) 		5.66e-05
(0.0144) 		7.91e-57
(6.39e-54) 		4.77e-23
(3.42e-20) 		0.000529
(0.112) 		0.0189
(1.00) 		1.18e-20
(8.1e-18) 		8.73e-13
(4.72e-10) 		3.61e-13
(1.99e-10) 		2.99e-11
(1.49e-08) 		4.44e-08
(1.75e-05) 		5.73e-06
(0.00172)
del 20p13 153 (15%) 880 2.72e-06
(0.000877) 		1.15e-05
(0.00326) 		1.98e-20
(1.35e-17) 		1.96e-12
(1.04e-09) 		0.000985
(0.196) 		0.00666
(1) 		9.71e-14
(5.46e-11) 		1.43e-12
(7.63e-10) 		1.99e-17
(1.27e-14) 		3.8e-14
(2.17e-11) 		8.82e-11
(4.3e-08) 		6.75e-11
(3.32e-08)
amp 4q13 3 159 (15%) 874 2.97e-05
(0.00786) 		0.000175
(0.0396) 		3e-19
(1.98e-16) 		6.94e-09
(2.93e-06) 		0.0795
(1.00) 		0.618
(1.00) 		1.18e-09
(5.23e-07) 		3.02e-07
(0.00011) 		2.19e-07
(8.08e-05) 		1.68e-09
(7.44e-07) 		3.98e-06
(0.00123) 		1.13e-05
(0.0032)
amp 17q23 1 414 (40%) 619 8.3e-17
(5.19e-14) 		0.000143
(0.0329) 		5.06e-48
(4.06e-45) 		4.52e-13
(2.48e-10) 		0.378
(1.00) 		0.454
(1.00) 		1.96e-28
(1.48e-25) 		7.19e-09
(3.03e-06) 		5.2e-15
(3.08e-12) 		7.61e-05
(0.0188) 		5.87e-06
(0.00175) 		0.00113
(0.218)
del 7p22 3 133 (13%) 900 0.000111
(0.0263) 		2.05e-05
(0.00559) 		7.01e-20
(4.72e-17) 		1.97e-06
(0.000647) 		0.00687
(1.00) 		0.00144
(0.278) 		1.33e-10
(6.4e-08) 		1.36e-11
(6.93e-09) 		3.89e-10
(1.78e-07) 		1.55e-11
(7.83e-09) 		1.68e-08
(6.92e-06) 		4.8e-07
(0.00017)
del 8p23 2 534 (52%) 499 2.66e-09
(1.16e-06) 		1.9e-05
(0.00522) 		1.43e-36
(1.11e-33) 		6.49e-11
(3.2e-08) 		0.0128
(1.00) 		0.0505
(1.00) 		2.58e-20
(1.76e-17) 		1.52e-13
(8.46e-11) 		3.36e-12
(1.77e-09) 		3.28e-10
(1.52e-07) 		3.76e-09
(1.61e-06) 		9.74e-07
(0.000331)
del 9p23 316 (31%) 717 2.37e-07
(8.71e-05) 		7.54e-06
(0.0022) 		1.37e-46
(1.09e-43) 		1.57e-20
(1.07e-17) 		0.00729
(1.00) 		0.366
(1.00) 		2.4e-19
(1.59e-16) 		1.58e-11
(7.94e-09) 		6.24e-10
(2.82e-07) 		1.2e-08
(4.99e-06) 		1.45e-06
(0.000485) 		0.00106
(0.209)
del 9p21 3 354 (34%) 679 2.15e-06
(0.000704) 		2.64e-05
(0.00713) 		8.78e-45
(6.98e-42) 		1.12e-16
(6.99e-14) 		0.00313
(0.541) 		0.292
(1.00) 		1.17e-17
(7.48e-15) 		4.48e-14
(2.54e-11) 		3.11e-10
(1.45e-07) 		1.56e-11
(7.87e-09) 		5.45e-09
(2.32e-06) 		3.35e-07
(0.000121)
del 9q21 11 288 (28%) 745 0.00148
(0.284) 		6.43e-06
(0.0019) 		5.83e-27
(4.34e-24) 		1.73e-13
(9.61e-11) 		2.87e-06
(0.000913) 		0.00199
(0.369) 		6.93e-11
(3.4e-08) 		2.28e-12
(1.2e-09) 		3.4e-14
(1.95e-11) 		2.99e-15
(1.78e-12) 		6.89e-10
(3.11e-07) 		7.31e-10
(3.29e-07)
del 13q14 2 481 (47%) 552 6.78e-06
(0.00199) 		2.41e-06
(0.000787) 		9.2e-32
(7.04e-29) 		6.86e-09
(2.9e-06) 		0.286
(1.00) 		0.034
(1.00) 		2.45e-14
(1.42e-11) 		1.13e-12
(6.08e-10) 		1.72e-10
(8.14e-08) 		1.74e-10
(8.18e-08) 		6.09e-09
(2.58e-06) 		9.5e-07
(0.000324)
del 17p12 622 (60%) 411 1.14e-12
(6.08e-10) 		0.0475
(1.00) 		4.31e-30
(3.28e-27) 		1.17e-10
(5.68e-08) 		3.52e-06
(0.0011) 		0.0007
(0.143) 		4.35e-21
(3.02e-18) 		2.33e-05
(0.00634) 		1.08e-10
(5.22e-08) 		9.32e-07
(0.000319) 		6.01e-05
(0.015) 		0.0101
(1.00)
amp 15q26 3 185 (18%) 848 4.19e-07
(0.00015) 		0.00535
(0.839) 		2.52e-20
(1.72e-17) 		2.81e-05
(0.00754) 		0.00169
(0.323) 		0.0909
(1.00) 		2.62e-10
(1.23e-07) 		8.2e-08
(3.21e-05) 		2.25e-08
(9.23e-06) 		1.81e-10
(8.51e-08) 		9.95e-05
(0.024) 		3.19e-05
(0.00843)
amp 17q12 319 (31%) 714 7.5e-16
(4.53e-13) 		9.88e-06
(0.00284) 		1.58e-40
(1.24e-37) 		3.19e-10
(1.48e-07) 		0.0756
(1.00) 		0.012
(1.00) 		4.46e-28
(3.36e-25) 		1.65e-08
(6.85e-06) 		1.02e-07
(3.95e-05) 		0.000702
(0.143) 		0.00173
(0.328) 		0.000684
(0.142)
del 18q23 340 (33%) 693 0.000145
(0.0332) 		0.0482
(1.00) 		3.17e-17
(2e-14) 		6.68e-10
(3.02e-07) 		0.00256
(0.456) 		0.408
(1.00) 		1.65e-10
(7.89e-08) 		0.000286
(0.0634) 		2.38e-08
(9.74e-06) 		2.83e-06
(0.000903) 		4.21e-07
(0.00015) 		0.00013
(0.0304)
amp 3p25 1 195 (19%) 838 0.00229
(0.415) 		5.72e-05
(0.0145) 		3.64e-16
(2.23e-13) 		8.24e-05
(0.0203) 		0.205
(1.00) 		0.277
(1.00) 		8.96e-07
(0.000307) 		5.29e-10
(2.41e-07) 		1.06e-07
(4.1e-05) 		2.7e-06
(0.000874) 		0.000209
(0.0467) 		0.00675
(1.00)
amp 5p15 33 377 (36%) 656 0.00954
(1.00) 		0.00605
(0.931) 		4.99e-24
(3.62e-21) 		6.38e-07
(0.000223) 		0.056
(1.00) 		0.577
(1.00) 		5.52e-06
(0.00166) 		1.11e-06
(0.000377) 		5.4e-08
(2.12e-05) 		1.65e-07
(6.17e-05) 		0.000113
(0.0267) 		9.84e-05
(0.0239)
amp 11p13 214 (21%) 819 0.194
(1.00) 		0.128
(1.00) 		5.3e-16
(3.23e-13) 		5.15e-06
(0.00155) 		0.0932
(1.00) 		0.175
(1.00) 		1.52e-09
(6.75e-07) 		1.36e-07
(5.15e-05) 		1.09e-07
(4.18e-05) 		4.48e-11
(2.22e-08) 		1.5e-07
(5.65e-05) 		2.95e-05
(0.00785)
amp 11q14 1 255 (25%) 778 0.00766
(1.00) 		0.125
(1.00) 		5.66e-20
(3.82e-17) 		0.000105
(0.0251) 		0.113
(1.00) 		0.235
(1.00) 		5.37e-08
(2.11e-05) 		4.94e-05
(0.0127) 		3.39e-09
(1.46e-06) 		3.36e-06
(0.00105) 		6.12e-06
(0.00182) 		0.0011
(0.216)
amp 12q15 268 (26%) 765 1.91e-07
(7.12e-05) 		1.41e-06
(0.000473) 		3.73e-34
(2.87e-31) 		3.21e-18
(2.07e-15) 		0.303
(1.00) 		0.108
(1.00) 		7.31e-13
(3.98e-10) 		7.53e-14
(4.25e-11) 		4.76e-08
(1.87e-05) 		4.21e-06
(0.00129) 		0.00926
(1.00) 		0.00223
(0.407)
del 1p36 13 432 (42%) 601 5.78e-05
(0.0145) 		4.92e-05
(0.0126) 		1.07e-34
(8.29e-32) 		1.11e-12
(5.97e-10) 		0.0035
(0.589) 		0.0631
(1.00) 		2.58e-09
(1.13e-06) 		1.7e-10
(8.05e-08) 		8.63e-08
(3.36e-05) 		2.93e-05
(0.00782) 		0.00936
(1.00) 		0.14
(1.00)
amp 10q22 3 144 (14%) 889 2.78e-05
(0.00748) 		0.134
(1.00) 		2.36e-10
(1.11e-07) 		0.00571
(0.885) 		0.00335
(0.575) 		0.0322
(1.00) 		2.16e-07
(7.98e-05) 		0.000134
(0.031) 		0.000465
(0.1) 		5.73e-05
(0.0145) 		0.000114
(0.0269) 		0.00345
(0.582)
del 1p21 2 340 (33%) 693 0.00387
(0.632) 		0.000469
(0.1) 		6.49e-26
(4.78e-23) 		2.98e-09
(1.29e-06) 		0.000478
(0.101) 		0.00688
(1.00) 		3.69e-06
(0.00115) 		1.6e-10
(7.62e-08) 		0.00377
(0.626) 		0.000137
(0.0316) 		0.439
(1.00) 		0.411
(1.00)
del 6q15 338 (33%) 695 4.02e-06
(0.00124) 		0.00337
(0.577) 		9.92e-36
(7.7e-33) 		3.8e-10
(1.74e-07) 		0.53
(1.00) 		0.143
(1.00) 		1.2e-14
(7.03e-12) 		2.93e-08
(1.18e-05) 		0.00246
(0.442) 		2.46e-06
(0.000802) 		0.00255
(0.456) 		0.000715
(0.144)
del 7q36 1 194 (19%) 839 0.00282
(0.494) 		0.0219
(1.00) 		6.9e-11
(3.39e-08) 		0.187
(1.00) 		0.468
(1.00) 		0.0362
(1.00) 		5.79e-07
(0.000203) 		1.31e-05
(0.00367) 		4.51e-06
(0.00138) 		1.08e-07
(4.16e-05) 		5.1e-07
(0.00018) 		3.15e-06
(0.000994)
del 8p11 21 197 (19%) 836 0.000172
(0.039) 		0.00179
(0.339) 		1e-11
(5.13e-09) 		0.00523
(0.826) 		0.0231
(1.00) 		0.00808
(1.00) 		1.43e-10
(6.89e-08) 		0.00055
(0.115) 		0.00658
(0.994) 		3.03e-07
(0.00011) 		2.46e-06
(0.000802) 		0.000693
(0.142)
del 11q23 2 527 (51%) 506 1.25e-07
(4.76e-05) 		0.0202
(1.00) 		3.8e-33
(2.92e-30) 		1.3e-12
(6.96e-10) 		0.86
(1.00) 		0.59
(1.00) 		5.38e-18
(3.46e-15) 		3.33e-06
(0.00105) 		0.000152
(0.0345) 		3.46e-05
(0.00907) 		0.154
(1.00) 		0.0897
(1.00)
amp 1q21 3 748 (72%) 285 1.25e-06
(0.000421) 		0.000535
(0.112) 		8.42e-13
(4.56e-10) 		6.71e-06
(0.00198) 		0.0597
(1.00) 		0.00695
(1.00) 		3.73e-14
(2.14e-11) 		0.0201
(1.00) 		0.000372
(0.0818) 		0.00221
(0.406) 		0.0522
(1.00) 		0.0275
(1.00)
amp 11q13 3 382 (37%) 651 0.000273
(0.061) 		0.00479
(0.762) 		4.73e-42
(3.73e-39) 		4.03e-13
(2.22e-10) 		0.966
(1.00) 		0.146
(1.00) 		2.6e-14
(1.5e-11) 		1.68e-05
(0.00467) 		4.97e-06
(0.00151) 		0.00308
(0.535) 		0.0114
(1.00) 		0.197
(1.00)
amp 14q21 1 213 (21%) 820 9.91e-05
(0.024) 		0.00443
(0.709) 		3.74e-17
(2.35e-14) 		1.42e-07
(5.36e-05) 		0.0947
(1.00) 		0.0293
(1.00) 		3.31e-09
(1.43e-06) 		4.75e-07
(0.000168) 		4.27e-05
(0.011) 		0.00791
(1.00) 		0.0954
(1.00) 		0.0274
(1.00)
amp 19q13 42 266 (26%) 767 0.000392
(0.0854) 		0.00433
(0.698) 		1.9e-17
(1.21e-14) 		4.19e-05
(0.0109) 		0.00193
(0.363) 		0.0564
(1.00) 		5.75e-06
(0.00172) 		0.00195
(0.364) 		8.95e-06
(0.00259) 		0.000133
(0.031) 		0.0778
(1.00) 		0.215
(1.00)
amp 8p11 23 394 (38%) 639 1.72e-06
(0.000572) 		0.0107
(1.00) 		1.59e-26
(1.18e-23) 		1.38e-10
(6.63e-08) 		0.0383
(1.00) 		0.0063
(0.957) 		4.36e-14
(2.48e-11) 		1.56e-07
(5.86e-05) 		0.00703
(1.00) 		0.269
(1.00) 		0.352
(1.00) 		0.152
(1.00)
del 21q11 2 205 (20%) 828 0.000299
(0.0661) 		0.0237
(1.00) 		5.97e-15
(3.52e-12) 		1.92e-05
(0.00525) 		0.0825
(1.00) 		0.543
(1.00) 		1.89e-05
(0.0052) 		4.73e-05
(0.0122) 		0.00406
(0.657) 		0.0232
(1.00) 		0.0116
(1.00) 		0.0626
(1.00)
amp 1q44 754 (73%) 279 1.53e-05
(0.00428) 		0.133
(1.00) 		5.6e-12
(2.9e-09) 		6.47e-05
(0.016) 		0.89
(1.00) 		0.321
(1.00) 		3.4e-10
(1.57e-07) 		0.913
(1.00) 		0.195
(1.00) 		0.41
(1.00) 		0.217
(1.00) 		0.0149
(1.00)
amp 8p11 21 406 (39%) 627 0.0456
(1.00) 		0.0633
(1.00) 		5.81e-23
(4.15e-20) 		6.98e-07
(0.000242) 		0.774
(1.00) 		0.647
(1.00) 		4.99e-10
(2.27e-07) 		1.52e-08
(6.32e-06) 		0.00371
(0.62) 		0.00768
(1.00) 		0.00339
(0.577) 		0.00199
(0.369)
del 11q13 1 229 (22%) 804 0.00262
(0.463) 		0.108
(1.00) 		1.09e-12
(5.87e-10) 		5.95e-07
(0.000208) 		0.396
(1.00) 		0.5
(1.00) 		1.38e-11
(7e-09) 		0.00107
(0.21) 		0.00881
(1.00) 		0.0549
(1.00) 		0.268
(1.00) 		0.0627
(1.00)
del 12p13 2 180 (17%) 853 0.0485
(1.00) 		0.0572
(1.00) 		0.00064
(0.133) 		0.00266
(0.469) 		0.387
(1.00) 		0.0982
(1.00) 		0.00565
(0.882) 		0.000885
(0.177) 		0.00111
(0.216) 		1.84e-05
(0.00509) 		0.00845
(1.00) 		0.0939
(1.00)
del 6p25 3 199 (19%) 834 0.38
(1.00) 		0.575
(1.00) 		1.79e-09
(7.89e-07) 		0.00221
(0.406) 		0.334
(1.00) 		0.479
(1.00) 		0.000381
(0.0835) 		0.0062
(0.949) 		0.0225
(1.00) 		0.000859
(0.173) 		0.0396
(1.00) 		0.0363
(1.00)
del 6q27 356 (34%) 677 0.0264
(1.00) 		0.36
(1.00) 		5.26e-16
(3.21e-13) 		0.0102
(1.00) 		0.0563
(1.00) 		0.596
(1.00) 		5.15e-05
(0.0131) 		0.116
(1.00) 		0.178
(1.00) 		0.086
(1.00) 		0.326
(1.00) 		0.832
(1.00)
del 22q11 1 448 (43%) 585 0.364
(1.00) 		0.573
(1.00) 		2.38e-10
(1.12e-07) 		1.04e-05
(0.00296) 		0.297
(1.00) 		0.219
(1.00) 		0.381
(1.00) 		0.267
(1.00) 		0.00787
(1.00) 		0.057
(1.00) 		0.689
(1.00) 		0.946
(1.00)
del 22q13 32 477 (46%) 556 0.251
(1.00) 		0.101
(1.00) 		9.53e-12
(4.89e-09) 		0.000417
(0.0906) 		0.157
(1.00) 		0.0292
(1.00) 		0.142
(1.00) 		0.0315
(1.00) 		0.00379
(0.626) 		0.0135
(1.00) 		0.634
(1.00) 		0.712
(1.00)
'amp_1p22.3' versus 'MRNA_CNMF'

P value = 3.79e-13 (Chi-square test), Q value = 2.1e-10

Table S1.  Gene #1: 'amp_1p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 1(1P22.3) MUTATED 4 3 14 51 24 15 2 2
AMP PEAK 1(1P22.3) WILD-TYPE 17 33 105 45 85 57 18 38

Figure S1.  Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1p22.3' versus 'MRNA_CHIERARCHICAL'

P value = 1.17e-11 (Fisher's exact test), Q value = 5.9e-09

Table S2.  Gene #1: 'amp_1p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 1(1P22.3) MUTATED 10 56 49
AMP PEAK 1(1P22.3) WILD-TYPE 112 69 217

Figure S2.  Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_1p22.3' versus 'CN_CNMF'

P value = 1.8e-19 (Chi-square test), Q value = 1.2e-16

Table S3.  Gene #1: 'amp_1p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
AMP PEAK 1(1P22.3) MUTATED 47 38 36 107 14
AMP PEAK 1(1P22.3) WILD-TYPE 330 214 68 145 34

Figure S3.  Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1p22.3' versus 'METHLYATION_CNMF'

P value = 1.06e-16 (Chi-square test), Q value = 6.6e-14

Table S4.  Gene #1: 'amp_1p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
AMP PEAK 1(1P22.3) MUTATED 67 30 24 19 4 23
AMP PEAK 1(1P22.3) WILD-TYPE 57 146 80 116 52 93

Figure S4.  Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1p22.3' versus 'RPPA_CNMF'

P value = 0.000472 (Fisher's exact test), Q value = 0.1

Table S5.  Gene #1: 'amp_1p22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 1(1P22.3) MUTATED 51 28 17
AMP PEAK 1(1P22.3) WILD-TYPE 96 105 100

Figure S5.  Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_1p22.3' versus 'RPPA_CHIERARCHICAL'

P value = 6.95e-07 (Fisher's exact test), Q value = 0.00024

Table S6.  Gene #1: 'amp_1p22.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 1(1P22.3) MUTATED 32 13 51
AMP PEAK 1(1P22.3) WILD-TYPE 129 97 75

Figure S6.  Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_1p22.3' versus 'MRNASEQ_CNMF'

P value = 6.26e-23 (Chi-square test), Q value = 4.5e-20

Table S7.  Gene #1: 'amp_1p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
AMP PEAK 1(1P22.3) MUTATED 98 14 51 34 37 2
AMP PEAK 1(1P22.3) WILD-TYPE 92 81 206 135 223 46

Figure S7.  Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1p22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.79e-21 (Fisher's exact test), Q value = 5.4e-18

Table S8.  Gene #1: 'amp_1p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
AMP PEAK 1(1P22.3) MUTATED 43 79 114
AMP PEAK 1(1P22.3) WILD-TYPE 296 354 133

Figure S8.  Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1p22.3' versus 'MIRSEQ_CNMF'

P value = 1.35e-14 (Chi-square test), Q value = 7.9e-12

Table S9.  Gene #1: 'amp_1p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
AMP PEAK 1(1P22.3) MUTATED 26 29 40 107 26 11
AMP PEAK 1(1P22.3) WILD-TYPE 168 141 187 144 114 21

Figure S9.  Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1p22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.05e-16 (Fisher's exact test), Q value = 5.5e-13

Table S10.  Gene #1: 'amp_1p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
AMP PEAK 1(1P22.3) MUTATED 91 116 32
AMP PEAK 1(1P22.3) WILD-TYPE 440 157 178

Figure S10.  Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1p22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.16e-14 (Fisher's exact test), Q value = 1.8e-11

Table S11.  Gene #1: 'amp_1p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
AMP PEAK 1(1P22.3) MUTATED 35 38 94
AMP PEAK 1(1P22.3) WILD-TYPE 213 200 124

Figure S11.  Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.53e-16 (Fisher's exact test), Q value = 4e-13

Table S12.  Gene #1: 'amp_1p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
AMP PEAK 1(1P22.3) MUTATED 81 60 26
AMP PEAK 1(1P22.3) WILD-TYPE 84 298 155

Figure S12.  Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q21.3' versus 'MRNA_CNMF'

P value = 1.25e-06 (Chi-square test), Q value = 0.00042

Table S13.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 2(1Q21.3) MUTATED 16 19 75 88 88 54 10 29
AMP PEAK 2(1Q21.3) WILD-TYPE 5 17 44 8 21 18 10 11

Figure S13.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1q21.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.000535 (Fisher's exact test), Q value = 0.11

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 2(1Q21.3) MUTATED 76 105 198
AMP PEAK 2(1Q21.3) WILD-TYPE 46 20 68

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

'amp_1q21.3' versus 'CN_CNMF'

P value = 8.42e-13 (Chi-square test), Q value = 4.6e-10

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
AMP PEAK 2(1Q21.3) MUTATED 231 183 102 198 34
AMP PEAK 2(1Q21.3) WILD-TYPE 146 69 2 54 14

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

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 6.71e-06 (Chi-square test), Q value = 0.002

Table S16.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
AMP PEAK 2(1Q21.3) MUTATED 104 137 82 87 34 68
AMP PEAK 2(1Q21.3) WILD-TYPE 20 39 22 48 22 48

Figure S16.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 3.73e-14 (Chi-square test), Q value = 2.1e-11

Table S17.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
AMP PEAK 2(1Q21.3) MUTATED 163 54 219 116 158 29
AMP PEAK 2(1Q21.3) WILD-TYPE 27 41 38 53 102 19

Figure S17.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 0.000372 (Chi-square test), Q value = 0.082

Table S18.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
AMP PEAK 2(1Q21.3) MUTATED 134 113 153 206 97 28
AMP PEAK 2(1Q21.3) WILD-TYPE 60 57 74 45 43 4

Figure S18.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q44' versus 'MRNA_CNMF'

P value = 1.53e-05 (Chi-square test), Q value = 0.0043

Table S19.  Gene #3: 'amp_1q44' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 3(1Q44) MUTATED 16 20 69 78 91 57 11 32
AMP PEAK 3(1Q44) WILD-TYPE 5 16 50 18 18 15 9 8

Figure S19.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1q44' versus 'CN_CNMF'

P value = 5.6e-12 (Chi-square test), Q value = 2.9e-09

Table S20.  Gene #3: 'amp_1q44' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
AMP PEAK 3(1Q44) MUTATED 242 187 104 192 29
AMP PEAK 3(1Q44) WILD-TYPE 135 65 0 60 19

Figure S20.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q44' versus 'METHLYATION_CNMF'

P value = 6.47e-05 (Chi-square test), Q value = 0.016

Table S21.  Gene #3: 'amp_1q44' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
AMP PEAK 3(1Q44) MUTATED 94 141 88 85 38 72
AMP PEAK 3(1Q44) WILD-TYPE 30 35 16 50 18 44

Figure S21.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q44' versus 'MRNASEQ_CNMF'

P value = 3.4e-10 (Chi-square test), Q value = 1.6e-07

Table S22.  Gene #3: 'amp_1q44' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
AMP PEAK 3(1Q44) MUTATED 147 62 222 123 154 35
AMP PEAK 3(1Q44) WILD-TYPE 43 33 35 46 106 13

Figure S22.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3p25.1' versus 'MRNA_CHIERARCHICAL'

P value = 5.72e-05 (Fisher's exact test), Q value = 0.014

Table S23.  Gene #4: 'amp_3p25.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 4(3P25.1) MUTATED 12 28 78
AMP PEAK 4(3P25.1) WILD-TYPE 110 97 188

Figure S23.  Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_3p25.1' versus 'CN_CNMF'

P value = 3.64e-16 (Chi-square test), Q value = 2.2e-13

Table S24.  Gene #4: 'amp_3p25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
AMP PEAK 4(3P25.1) MUTATED 18 73 25 67 12
AMP PEAK 4(3P25.1) WILD-TYPE 359 179 79 185 36

Figure S24.  Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3p25.1' versus 'METHLYATION_CNMF'

P value = 8.24e-05 (Chi-square test), Q value = 0.02

Table S25.  Gene #4: 'amp_3p25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
AMP PEAK 4(3P25.1) MUTATED 31 14 21 30 5 12
AMP PEAK 4(3P25.1) WILD-TYPE 93 162 83 105 51 104

Figure S25.  Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3p25.1' versus 'MRNASEQ_CNMF'

P value = 8.96e-07 (Chi-square test), Q value = 0.00031

Table S26.  Gene #4: 'amp_3p25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
AMP PEAK 4(3P25.1) MUTATED 46 7 34 49 56 2
AMP PEAK 4(3P25.1) WILD-TYPE 144 88 223 120 204 46

Figure S26.  Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3p25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.29e-10 (Fisher's exact test), Q value = 2.4e-07

Table S27.  Gene #4: 'amp_3p25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
AMP PEAK 4(3P25.1) MUTATED 28 107 59
AMP PEAK 4(3P25.1) WILD-TYPE 311 326 188

Figure S27.  Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3p25.1' versus 'MIRSEQ_CNMF'

P value = 1.06e-07 (Chi-square test), Q value = 4.1e-05

Table S28.  Gene #4: 'amp_3p25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
AMP PEAK 4(3P25.1) MUTATED 35 10 33 63 42 4
AMP PEAK 4(3P25.1) WILD-TYPE 159 160 194 188 98 28

Figure S28.  Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3p25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.7e-06 (Fisher's exact test), Q value = 0.00087

Table S29.  Gene #4: 'amp_3p25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
AMP PEAK 4(3P25.1) MUTATED 101 69 17
AMP PEAK 4(3P25.1) WILD-TYPE 430 204 193

Figure S29.  Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3p25.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000209 (Fisher's exact test), Q value = 0.047

Table S30.  Gene #4: 'amp_3p25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
AMP PEAK 4(3P25.1) MUTATED 44 26 56
AMP PEAK 4(3P25.1) WILD-TYPE 204 212 162

Figure S30.  Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.32' versus 'MRNA_CNMF'

P value = 1.59e-10 (Chi-square test), Q value = 7.6e-08

Table S31.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 5(3Q26.32) MUTATED 5 11 41 58 19 34 9 4
AMP PEAK 5(3Q26.32) WILD-TYPE 16 25 78 38 90 38 11 36

Figure S31.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.32' versus 'MRNA_CHIERARCHICAL'

P value = 5.06e-11 (Fisher's exact test), Q value = 2.5e-08

Table S32.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 5(3Q26.32) MUTATED 19 71 91
AMP PEAK 5(3Q26.32) WILD-TYPE 103 54 175

Figure S32.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_3q26.32' versus 'CN_CNMF'

P value = 1.15e-39 (Chi-square test), Q value = 9e-37

Table S33.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
AMP PEAK 5(3Q26.32) MUTATED 34 98 31 151 14
AMP PEAK 5(3Q26.32) WILD-TYPE 343 154 73 101 34

Figure S33.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.32' versus 'METHLYATION_CNMF'

P value = 3.15e-20 (Chi-square test), Q value = 2.1e-17

Table S34.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
AMP PEAK 5(3Q26.32) MUTATED 78 23 33 41 13 19
AMP PEAK 5(3Q26.32) WILD-TYPE 46 153 71 94 43 97

Figure S34.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.32' versus 'RPPA_CNMF'

P value = 3.01e-06 (Fisher's exact test), Q value = 0.00095

Table S35.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 5(3Q26.32) MUTATED 76 36 30
AMP PEAK 5(3Q26.32) WILD-TYPE 71 97 87

Figure S35.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_3q26.32' versus 'RPPA_CHIERARCHICAL'

P value = 1.16e-05 (Fisher's exact test), Q value = 0.0033

Table S36.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 5(3Q26.32) MUTATED 49 27 66
AMP PEAK 5(3Q26.32) WILD-TYPE 112 83 60

Figure S36.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_3q26.32' versus 'MRNASEQ_CNMF'

P value = 9.43e-28 (Chi-square test), Q value = 7.1e-25

Table S37.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
AMP PEAK 5(3Q26.32) MUTATED 119 14 48 68 71 4
AMP PEAK 5(3Q26.32) WILD-TYPE 71 81 209 101 189 44

Figure S37.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.32e-25 (Fisher's exact test), Q value = 6.8e-22

Table S38.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
AMP PEAK 5(3Q26.32) MUTATED 51 135 138
AMP PEAK 5(3Q26.32) WILD-TYPE 288 298 109

Figure S38.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.32' versus 'MIRSEQ_CNMF'

P value = 3.34e-21 (Chi-square test), Q value = 2.3e-18

Table S39.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
AMP PEAK 5(3Q26.32) MUTATED 59 23 46 136 51 4
AMP PEAK 5(3Q26.32) WILD-TYPE 135 147 181 115 89 28

Figure S39.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.9e-22 (Fisher's exact test), Q value = 6.9e-19

Table S40.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
AMP PEAK 5(3Q26.32) MUTATED 142 147 30
AMP PEAK 5(3Q26.32) WILD-TYPE 389 126 180

Figure S40.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.12e-18 (Fisher's exact test), Q value = 3.9e-15

Table S41.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
AMP PEAK 5(3Q26.32) MUTATED 57 36 113
AMP PEAK 5(3Q26.32) WILD-TYPE 191 202 105

Figure S41.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.39e-15 (Fisher's exact test), Q value = 3.2e-12

Table S42.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
AMP PEAK 5(3Q26.32) MUTATED 89 89 28
AMP PEAK 5(3Q26.32) WILD-TYPE 76 269 153

Figure S42.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q13.3' versus 'MRNA_CNMF'

P value = 2.97e-05 (Chi-square test), Q value = 0.0079

Table S43.  Gene #6: 'amp_4q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 6(4Q13.3) MUTATED 4 3 32 19 3 18 4 3
AMP PEAK 6(4Q13.3) WILD-TYPE 17 33 87 77 106 54 16 37

Figure S43.  Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_4q13.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.000175 (Fisher's exact test), Q value = 0.04

Table S44.  Gene #6: 'amp_4q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 6(4Q13.3) MUTATED 7 29 50
AMP PEAK 6(4Q13.3) WILD-TYPE 115 96 216

Figure S44.  Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_4q13.3' versus 'CN_CNMF'

P value = 3e-19 (Chi-square test), Q value = 2e-16

Table S45.  Gene #6: 'amp_4q13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
AMP PEAK 6(4Q13.3) MUTATED 20 73 1 58 7
AMP PEAK 6(4Q13.3) WILD-TYPE 357 179 103 194 41

Figure S45.  Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_4q13.3' versus 'METHLYATION_CNMF'

P value = 6.94e-09 (Chi-square test), Q value = 2.9e-06

Table S46.  Gene #6: 'amp_4q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
AMP PEAK 6(4Q13.3) MUTATED 30 8 11 36 5 10
AMP PEAK 6(4Q13.3) WILD-TYPE 94 168 93 99 51 106

Figure S46.  Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_4q13.3' versus 'MRNASEQ_CNMF'

P value = 1.18e-09 (Chi-square test), Q value = 5.2e-07

Table S47.  Gene #6: 'amp_4q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
AMP PEAK 6(4Q13.3) MUTATED 39 7 12 38 58 3
AMP PEAK 6(4Q13.3) WILD-TYPE 151 88 245 131 202 45

Figure S47.  Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_4q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.02e-07 (Fisher's exact test), Q value = 0.00011

Table S48.  Gene #6: 'amp_4q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
AMP PEAK 6(4Q13.3) MUTATED 26 73 58
AMP PEAK 6(4Q13.3) WILD-TYPE 313 360 189

Figure S48.  Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_4q13.3' versus 'MIRSEQ_CNMF'

P value = 2.19e-07 (Chi-square test), Q value = 8.1e-05

Table S49.  Gene #6: 'amp_4q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
AMP PEAK 6(4Q13.3) MUTATED 24 10 26 59 35 3
AMP PEAK 6(4Q13.3) WILD-TYPE 170 160 201 192 105 29

Figure S49.  Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_4q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.68e-09 (Fisher's exact test), Q value = 7.4e-07

Table S50.  Gene #6: 'amp_4q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
AMP PEAK 6(4Q13.3) MUTATED 76 70 11
AMP PEAK 6(4Q13.3) WILD-TYPE 455 203 199

Figure S50.  Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_4q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.98e-06 (Fisher's exact test), Q value = 0.0012

Table S51.  Gene #6: 'amp_4q13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
AMP PEAK 6(4Q13.3) MUTATED 38 16 50
AMP PEAK 6(4Q13.3) WILD-TYPE 210 222 168

Figure S51.  Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_4q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.13e-05 (Fisher's exact test), Q value = 0.0032

Table S52.  Gene #6: 'amp_4q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
AMP PEAK 6(4Q13.3) MUTATED 42 49 13
AMP PEAK 6(4Q13.3) WILD-TYPE 123 309 168

Figure S52.  Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 4.99e-24 (Chi-square test), Q value = 3.6e-21

Table S53.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
AMP PEAK 7(5P15.33) MUTATED 60 123 50 129 15
AMP PEAK 7(5P15.33) WILD-TYPE 317 129 54 123 33

Figure S53.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 6.38e-07 (Chi-square test), Q value = 0.00022

Table S54.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
AMP PEAK 7(5P15.33) MUTATED 66 50 48 45 12 29
AMP PEAK 7(5P15.33) WILD-TYPE 58 126 56 90 44 87

Figure S54.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 5.52e-06 (Chi-square test), Q value = 0.0017

Table S55.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
AMP PEAK 7(5P15.33) MUTATED 94 25 76 71 96 9
AMP PEAK 7(5P15.33) WILD-TYPE 96 70 181 98 164 39

Figure S55.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.11e-06 (Fisher's exact test), Q value = 0.00038

Table S56.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
AMP PEAK 7(5P15.33) MUTATED 92 160 119
AMP PEAK 7(5P15.33) WILD-TYPE 247 273 128

Figure S56.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 5.4e-08 (Chi-square test), Q value = 2.1e-05

Table S57.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
AMP PEAK 7(5P15.33) MUTATED 76 35 69 124 54 9
AMP PEAK 7(5P15.33) WILD-TYPE 118 135 158 127 86 23

Figure S57.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.65e-07 (Fisher's exact test), Q value = 6.2e-05

Table S58.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
AMP PEAK 7(5P15.33) MUTATED 190 129 48
AMP PEAK 7(5P15.33) WILD-TYPE 341 144 162

Figure S58.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000113 (Fisher's exact test), Q value = 0.027

Table S59.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
AMP PEAK 7(5P15.33) MUTATED 92 62 98
AMP PEAK 7(5P15.33) WILD-TYPE 156 176 120

Figure S59.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.84e-05 (Fisher's exact test), Q value = 0.024

Table S60.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
AMP PEAK 7(5P15.33) MUTATED 76 132 44
AMP PEAK 7(5P15.33) WILD-TYPE 89 226 137

Figure S60.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6p23' versus 'MRNA_CNMF'

P value = 1.36e-07 (Chi-square test), Q value = 5.1e-05

Table S61.  Gene #8: 'amp_6p23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 8(6P23) MUTATED 3 7 30 49 18 28 9 6
AMP PEAK 8(6P23) WILD-TYPE 18 29 89 47 91 44 11 34

Figure S61.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_6p23' versus 'MRNA_CHIERARCHICAL'

P value = 4.12e-07 (Fisher's exact test), Q value = 0.00015

Table S62.  Gene #8: 'amp_6p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 8(6P23) MUTATED 20 59 71
AMP PEAK 8(6P23) WILD-TYPE 102 66 195

Figure S62.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_6p23' versus 'CN_CNMF'

P value = 2.37e-39 (Chi-square test), Q value = 1.9e-36

Table S63.  Gene #8: 'amp_6p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
AMP PEAK 8(6P23) MUTATED 25 86 21 139 16
AMP PEAK 8(6P23) WILD-TYPE 352 166 83 113 32

Figure S63.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p23' versus 'METHLYATION_CNMF'

P value = 3.26e-23 (Chi-square test), Q value = 2.3e-20

Table S64.  Gene #8: 'amp_6p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
AMP PEAK 8(6P23) MUTATED 68 13 28 57 4 21
AMP PEAK 8(6P23) WILD-TYPE 56 163 76 78 52 95

Figure S64.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6p23' versus 'RPPA_CNMF'

P value = 3.98e-07 (Fisher's exact test), Q value = 0.00014

Table S65.  Gene #8: 'amp_6p23' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 8(6P23) MUTATED 67 25 24
AMP PEAK 8(6P23) WILD-TYPE 80 108 93

Figure S65.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_6p23' versus 'RPPA_CHIERARCHICAL'

P value = 0.000129 (Fisher's exact test), Q value = 0.03

Table S66.  Gene #8: 'amp_6p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 8(6P23) MUTATED 36 25 55
AMP PEAK 8(6P23) WILD-TYPE 125 85 71

Figure S66.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_6p23' versus 'MRNASEQ_CNMF'

P value = 1.37e-23 (Chi-square test), Q value = 9.9e-21

Table S67.  Gene #8: 'amp_6p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
AMP PEAK 8(6P23) MUTATED 99 14 31 66 66 4
AMP PEAK 8(6P23) WILD-TYPE 91 81 226 103 194 44

Figure S67.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.66e-16 (Fisher's exact test), Q value = 1.6e-13

Table S68.  Gene #8: 'amp_6p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
AMP PEAK 8(6P23) MUTATED 48 119 113
AMP PEAK 8(6P23) WILD-TYPE 291 314 134

Figure S68.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6p23' versus 'MIRSEQ_CNMF'

P value = 6.26e-20 (Chi-square test), Q value = 4.2e-17

Table S69.  Gene #8: 'amp_6p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
AMP PEAK 8(6P23) MUTATED 36 22 37 121 50 9
AMP PEAK 8(6P23) WILD-TYPE 158 148 190 130 90 23

Figure S69.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_6p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.36e-19 (Fisher's exact test), Q value = 9.1e-17

Table S70.  Gene #8: 'amp_6p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
AMP PEAK 8(6P23) MUTATED 127 127 21
AMP PEAK 8(6P23) WILD-TYPE 404 146 189

Figure S70.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-15 (Fisher's exact test), Q value = 3.5e-12

Table S71.  Gene #8: 'amp_6p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
AMP PEAK 8(6P23) MUTATED 49 33 100
AMP PEAK 8(6P23) WILD-TYPE 199 205 118

Figure S71.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_6p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.07e-09 (Fisher's exact test), Q value = 4.8e-07

Table S72.  Gene #8: 'amp_6p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
AMP PEAK 8(6P23) MUTATED 73 83 26
AMP PEAK 8(6P23) WILD-TYPE 92 275 155

Figure S72.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q21' versus 'MRNA_CNMF'

P value = 7.25e-14 (Chi-square test), Q value = 4.1e-11

Table S73.  Gene #9: 'amp_6q21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 9(6Q21) MUTATED 4 1 11 42 11 24 9 2
AMP PEAK 9(6Q21) WILD-TYPE 17 35 108 54 98 48 11 38

Figure S73.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_6q21' versus 'MRNA_CHIERARCHICAL'

P value = 1.69e-10 (Fisher's exact test), Q value = 8e-08

Table S74.  Gene #9: 'amp_6q21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 9(6Q21) MUTATED 9 51 44
AMP PEAK 9(6Q21) WILD-TYPE 113 74 222

Figure S74.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_6q21' versus 'CN_CNMF'

P value = 2.66e-47 (Chi-square test), Q value = 2.1e-44

Table S75.  Gene #9: 'amp_6q21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
AMP PEAK 9(6Q21) MUTATED 22 26 14 128 6
AMP PEAK 9(6Q21) WILD-TYPE 355 226 90 124 42

Figure S75.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6q21' versus 'METHLYATION_CNMF'

P value = 5.27e-23 (Chi-square test), Q value = 3.8e-20

Table S76.  Gene #9: 'amp_6q21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
AMP PEAK 9(6Q21) MUTATED 60 5 18 20 3 19
AMP PEAK 9(6Q21) WILD-TYPE 64 171 86 115 53 97

Figure S76.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6q21' versus 'RPPA_CNMF'

P value = 1.11e-08 (Fisher's exact test), Q value = 4.6e-06

Table S77.  Gene #9: 'amp_6q21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 9(6Q21) MUTATED 54 12 16
AMP PEAK 9(6Q21) WILD-TYPE 93 121 101

Figure S77.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_6q21' versus 'RPPA_CHIERARCHICAL'

P value = 4.44e-07 (Fisher's exact test), Q value = 0.00016

Table S78.  Gene #9: 'amp_6q21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 9(6Q21) MUTATED 20 15 47
AMP PEAK 9(6Q21) WILD-TYPE 141 95 79

Figure S78.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_6q21' versus 'MRNASEQ_CNMF'

P value = 8.9e-32 (Chi-square test), Q value = 6.8e-29

Table S79.  Gene #9: 'amp_6q21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
AMP PEAK 9(6Q21) MUTATED 85 6 22 54 22 2
AMP PEAK 9(6Q21) WILD-TYPE 105 89 235 115 238 46

Figure S79.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6q21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.36e-25 (Fisher's exact test), Q value = 3.2e-22

Table S80.  Gene #9: 'amp_6q21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
AMP PEAK 9(6Q21) MUTATED 22 67 102
AMP PEAK 9(6Q21) WILD-TYPE 317 366 145

Figure S80.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_CNMF'

P value = 1.52e-27 (Chi-square test), Q value = 1.1e-24

Table S81.  Gene #9: 'amp_6q21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
AMP PEAK 9(6Q21) MUTATED 23 14 12 105 25 7
AMP PEAK 9(6Q21) WILD-TYPE 171 156 215 146 115 25

Figure S81.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_6q21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.15e-29 (Fisher's exact test), Q value = 1.6e-26

Table S82.  Gene #9: 'amp_6q21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
AMP PEAK 9(6Q21) MUTATED 59 115 12
AMP PEAK 9(6Q21) WILD-TYPE 472 158 198

Figure S82.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.95e-21 (Fisher's exact test), Q value = 1.4e-18

Table S83.  Gene #9: 'amp_6q21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
AMP PEAK 9(6Q21) MUTATED 28 14 87
AMP PEAK 9(6Q21) WILD-TYPE 220 224 131

Figure S83.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_6q21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.19e-18 (Fisher's exact test), Q value = 2.1e-15

Table S84.  Gene #9: 'amp_6q21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
AMP PEAK 9(6Q21) MUTATED 71 45 13
AMP PEAK 9(6Q21) WILD-TYPE 94 313 168

Figure S84.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p11.23' versus 'MRNA_CNMF'

P value = 1.72e-06 (Chi-square test), Q value = 0.00057

Table S85.  Gene #10: 'amp_8p11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 10(8P11.23) MUTATED 11 18 74 33 36 23 5 9
AMP PEAK 10(8P11.23) WILD-TYPE 10 18 45 63 73 49 15 31

Figure S85.  Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8p11.23' versus 'CN_CNMF'

P value = 1.59e-26 (Chi-square test), Q value = 1.2e-23

Table S86.  Gene #10: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
AMP PEAK 10(8P11.23) MUTATED 100 133 42 72 47
AMP PEAK 10(8P11.23) WILD-TYPE 277 119 62 180 1

Figure S86.  Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.23' versus 'METHLYATION_CNMF'

P value = 1.38e-10 (Chi-square test), Q value = 6.6e-08

Table S87.  Gene #10: 'amp_8p11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
AMP PEAK 10(8P11.23) MUTATED 43 44 46 84 18 32
AMP PEAK 10(8P11.23) WILD-TYPE 81 132 58 51 38 84

Figure S87.  Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8p11.23' versus 'MRNASEQ_CNMF'

P value = 4.36e-14 (Chi-square test), Q value = 2.5e-11

Table S88.  Gene #10: 'amp_8p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
AMP PEAK 10(8P11.23) MUTATED 61 37 72 49 154 13
AMP PEAK 10(8P11.23) WILD-TYPE 129 58 185 120 106 35

Figure S88.  Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.56e-07 (Fisher's exact test), Q value = 5.9e-05

Table S89.  Gene #10: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
AMP PEAK 10(8P11.23) MUTATED 104 207 75
AMP PEAK 10(8P11.23) WILD-TYPE 235 226 172

Figure S89.  Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'CN_CNMF'

P value = 5.81e-23 (Chi-square test), Q value = 4.1e-20

Table S90.  Gene #11: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
AMP PEAK 11(8P11.21) MUTATED 96 117 45 100 48
AMP PEAK 11(8P11.21) WILD-TYPE 281 135 59 152 0

Figure S90.  Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'METHLYATION_CNMF'

P value = 6.98e-07 (Chi-square test), Q value = 0.00024

Table S91.  Gene #11: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
AMP PEAK 11(8P11.21) MUTATED 66 46 42 70 16 38
AMP PEAK 11(8P11.21) WILD-TYPE 58 130 62 65 40 78

Figure S91.  Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CNMF'

P value = 4.99e-10 (Chi-square test), Q value = 2.3e-07

Table S92.  Gene #11: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
AMP PEAK 11(8P11.21) MUTATED 96 30 72 53 135 12
AMP PEAK 11(8P11.21) WILD-TYPE 94 65 185 116 125 36

Figure S92.  Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.52e-08 (Fisher's exact test), Q value = 6.3e-06

Table S93.  Gene #11: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
AMP PEAK 11(8P11.21) MUTATED 89 196 113
AMP PEAK 11(8P11.21) WILD-TYPE 250 237 134

Figure S93.  Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNA_CNMF'

P value = 1.61e-15 (Chi-square test), Q value = 9.7e-13

Table S94.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 12(8Q24.21) MUTATED 17 20 96 83 46 56 17 15
AMP PEAK 12(8Q24.21) WILD-TYPE 4 16 23 13 63 16 3 25

Figure S94.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8q24.21' versus 'MRNA_CHIERARCHICAL'

P value = 4.21e-08 (Fisher's exact test), Q value = 1.7e-05

Table S95.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 12(8Q24.21) MUTATED 59 103 188
AMP PEAK 12(8Q24.21) WILD-TYPE 63 22 78

Figure S95.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 6.65e-58 (Chi-square test), Q value = 5.4e-55

Table S96.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
AMP PEAK 12(8Q24.21) MUTATED 133 201 48 227 47
AMP PEAK 12(8Q24.21) WILD-TYPE 244 51 56 25 1

Figure S96.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 1.17e-28 (Chi-square test), Q value = 8.9e-26

Table S97.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
AMP PEAK 12(8Q24.21) MUTATED 112 54 71 105 24 61
AMP PEAK 12(8Q24.21) WILD-TYPE 12 122 33 30 32 55

Figure S97.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'RPPA_CNMF'

P value = 1.22e-07 (Fisher's exact test), Q value = 4.7e-05

Table S98.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 12(8Q24.21) MUTATED 124 72 76
AMP PEAK 12(8Q24.21) WILD-TYPE 23 61 41

Figure S98.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8q24.21' versus 'RPPA_CHIERARCHICAL'

P value = 2.49e-06 (Fisher's exact test), Q value = 0.00081

Table S99.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 12(8Q24.21) MUTATED 102 63 107
AMP PEAK 12(8Q24.21) WILD-TYPE 59 47 19

Figure S99.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 3.84e-35 (Chi-square test), Q value = 3e-32

Table S100.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
AMP PEAK 12(8Q24.21) MUTATED 168 45 94 129 189 21
AMP PEAK 12(8Q24.21) WILD-TYPE 22 50 163 40 71 27

Figure S100.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.58e-24 (Fisher's exact test), Q value = 1.1e-21

Table S101.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
AMP PEAK 12(8Q24.21) MUTATED 151 284 211
AMP PEAK 12(8Q24.21) WILD-TYPE 188 149 36

Figure S101.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 1.93e-30 (Chi-square test), Q value = 1.5e-27

Table S102.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
AMP PEAK 12(8Q24.21) MUTATED 106 71 109 225 107 23
AMP PEAK 12(8Q24.21) WILD-TYPE 88 99 118 26 33 9

Figure S102.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.84e-28 (Fisher's exact test), Q value = 3.6e-25

Table S103.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
AMP PEAK 12(8Q24.21) MUTATED 315 239 87
AMP PEAK 12(8Q24.21) WILD-TYPE 216 34 123

Figure S103.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.62e-26 (Fisher's exact test), Q value = 2.7e-23

Table S104.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
AMP PEAK 12(8Q24.21) MUTATED 137 98 191
AMP PEAK 12(8Q24.21) WILD-TYPE 111 140 27

Figure S104.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.5e-21 (Fisher's exact test), Q value = 4.5e-18

Table S105.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
AMP PEAK 12(8Q24.21) MUTATED 147 202 77
AMP PEAK 12(8Q24.21) WILD-TYPE 18 156 104

Figure S105.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10p15.1' versus 'MRNA_CNMF'

P value = 1.27e-20 (Chi-square test), Q value = 8.7e-18

Table S106.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 13(10P15.1) MUTATED 6 4 26 67 12 33 6 7
AMP PEAK 13(10P15.1) WILD-TYPE 15 32 93 29 97 39 14 33

Figure S106.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_10p15.1' versus 'MRNA_CHIERARCHICAL'

P value = 6.33e-19 (Fisher's exact test), Q value = 4.1e-16

Table S107.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 13(10P15.1) MUTATED 19 81 61
AMP PEAK 13(10P15.1) WILD-TYPE 103 44 205

Figure S107.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_10p15.1' versus 'CN_CNMF'

P value = 5.71e-49 (Chi-square test), Q value = 4.6e-46

Table S108.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
AMP PEAK 13(10P15.1) MUTATED 34 71 17 160 10
AMP PEAK 13(10P15.1) WILD-TYPE 343 181 87 92 38

Figure S108.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10p15.1' versus 'METHLYATION_CNMF'

P value = 1.19e-29 (Chi-square test), Q value = 9e-27

Table S109.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
AMP PEAK 13(10P15.1) MUTATED 82 12 26 31 5 31
AMP PEAK 13(10P15.1) WILD-TYPE 42 164 78 104 51 85

Figure S109.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_10p15.1' versus 'RPPA_CNMF'

P value = 7.17e-11 (Fisher's exact test), Q value = 3.5e-08

Table S110.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 13(10P15.1) MUTATED 78 22 29
AMP PEAK 13(10P15.1) WILD-TYPE 69 111 88

Figure S110.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_10p15.1' versus 'RPPA_CHIERARCHICAL'

P value = 2.17e-12 (Fisher's exact test), Q value = 1.1e-09

Table S111.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 13(10P15.1) MUTATED 30 26 73
AMP PEAK 13(10P15.1) WILD-TYPE 131 84 53

Figure S111.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_10p15.1' versus 'MRNASEQ_CNMF'

P value = 6.17e-38 (Chi-square test), Q value = 4.8e-35

Table S112.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
AMP PEAK 13(10P15.1) MUTATED 123 14 30 62 53 8
AMP PEAK 13(10P15.1) WILD-TYPE 67 81 227 107 207 40

Figure S112.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_10p15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.7e-35 (Fisher's exact test), Q value = 3.6e-32

Table S113.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
AMP PEAK 13(10P15.1) MUTATED 45 97 148
AMP PEAK 13(10P15.1) WILD-TYPE 294 336 99

Figure S113.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10p15.1' versus 'MIRSEQ_CNMF'

P value = 4.08e-35 (Chi-square test), Q value = 3.2e-32

Table S114.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
AMP PEAK 13(10P15.1) MUTATED 41 26 24 147 41 5
AMP PEAK 13(10P15.1) WILD-TYPE 153 144 203 104 99 27

Figure S114.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_10p15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.11e-36 (Fisher's exact test), Q value = 4e-33

Table S115.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
AMP PEAK 13(10P15.1) MUTATED 106 157 21
AMP PEAK 13(10P15.1) WILD-TYPE 425 116 189

Figure S115.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_10p15.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.78e-21 (Fisher's exact test), Q value = 1.2e-18

Table S116.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
AMP PEAK 13(10P15.1) MUTATED 45 31 112
AMP PEAK 13(10P15.1) WILD-TYPE 203 207 106

Figure S116.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_10p15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.81e-23 (Fisher's exact test), Q value = 3.4e-20

Table S117.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
AMP PEAK 13(10P15.1) MUTATED 96 68 24
AMP PEAK 13(10P15.1) WILD-TYPE 69 290 157

Figure S117.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10q22.3' versus 'MRNA_CNMF'

P value = 2.78e-05 (Chi-square test), Q value = 0.0075

Table S118.  Gene #14: 'amp_10q22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 14(10Q22.3) MUTATED 6 3 16 18 9 23 8 3
AMP PEAK 14(10Q22.3) WILD-TYPE 15 33 103 78 100 49 12 37

Figure S118.  Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_10q22.3' versus 'CN_CNMF'

P value = 2.36e-10 (Chi-square test), Q value = 1.1e-07

Table S119.  Gene #14: 'amp_10q22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
AMP PEAK 14(10Q22.3) MUTATED 21 40 12 64 7
AMP PEAK 14(10Q22.3) WILD-TYPE 356 212 92 188 41

Figure S119.  Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10q22.3' versus 'MRNASEQ_CNMF'

P value = 2.16e-07 (Chi-square test), Q value = 8e-05

Table S120.  Gene #14: 'amp_10q22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
AMP PEAK 14(10Q22.3) MUTATED 34 6 23 46 29 5
AMP PEAK 14(10Q22.3) WILD-TYPE 156 89 234 123 231 43

Figure S120.  Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_10q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000134 (Fisher's exact test), Q value = 0.031

Table S121.  Gene #14: 'amp_10q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
AMP PEAK 14(10Q22.3) MUTATED 27 69 47
AMP PEAK 14(10Q22.3) WILD-TYPE 312 364 200

Figure S121.  Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10q22.3' versus 'MIRSEQ_CNMF'

P value = 0.000465 (Chi-square test), Q value = 0.1

Table S122.  Gene #14: 'amp_10q22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
AMP PEAK 14(10Q22.3) MUTATED 29 14 17 46 29 5
AMP PEAK 14(10Q22.3) WILD-TYPE 165 156 210 205 111 27

Figure S122.  Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_10q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.73e-05 (Fisher's exact test), Q value = 0.014

Table S123.  Gene #14: 'amp_10q22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
AMP PEAK 14(10Q22.3) MUTATED 73 54 13
AMP PEAK 14(10Q22.3) WILD-TYPE 458 219 197

Figure S123.  Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_10q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000114 (Fisher's exact test), Q value = 0.027

Table S124.  Gene #14: 'amp_10q22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
AMP PEAK 14(10Q22.3) MUTATED 35 15 42
AMP PEAK 14(10Q22.3) WILD-TYPE 213 223 176

Figure S124.  Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_11p13' versus 'CN_CNMF'

P value = 5.3e-16 (Chi-square test), Q value = 3.2e-13

Table S125.  Gene #15: 'amp_11p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
AMP PEAK 15(11P13) MUTATED 29 74 17 85 9
AMP PEAK 15(11P13) WILD-TYPE 348 178 87 167 39

Figure S125.  Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11p13' versus 'METHLYATION_CNMF'

P value = 5.15e-06 (Chi-square test), Q value = 0.0016

Table S126.  Gene #15: 'amp_11p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
AMP PEAK 15(11P13) MUTATED 38 24 16 42 4 18
AMP PEAK 15(11P13) WILD-TYPE 86 152 88 93 52 98

Figure S126.  Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11p13' versus 'MRNASEQ_CNMF'

P value = 1.52e-09 (Chi-square test), Q value = 6.7e-07

Table S127.  Gene #15: 'amp_11p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
AMP PEAK 15(11P13) MUTATED 62 9 28 45 66 4
AMP PEAK 15(11P13) WILD-TYPE 128 86 229 124 194 44

Figure S127.  Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.36e-07 (Fisher's exact test), Q value = 5.1e-05

Table S128.  Gene #15: 'amp_11p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
AMP PEAK 15(11P13) MUTATED 39 104 71
AMP PEAK 15(11P13) WILD-TYPE 300 329 176

Figure S128.  Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11p13' versus 'MIRSEQ_CNMF'

P value = 1.09e-07 (Chi-square test), Q value = 4.2e-05

Table S129.  Gene #15: 'amp_11p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
AMP PEAK 15(11P13) MUTATED 39 16 34 82 34 6
AMP PEAK 15(11P13) WILD-TYPE 155 154 193 169 106 26

Figure S129.  Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.48e-11 (Fisher's exact test), Q value = 2.2e-08

Table S130.  Gene #15: 'amp_11p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
AMP PEAK 15(11P13) MUTATED 109 87 15
AMP PEAK 15(11P13) WILD-TYPE 422 186 195

Figure S130.  Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.5e-07 (Fisher's exact test), Q value = 5.6e-05

Table S131.  Gene #15: 'amp_11p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
AMP PEAK 15(11P13) MUTATED 49 21 63
AMP PEAK 15(11P13) WILD-TYPE 199 217 155

Figure S131.  Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_11p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.95e-05 (Fisher's exact test), Q value = 0.0079

Table S132.  Gene #15: 'amp_11p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
AMP PEAK 15(11P13) MUTATED 48 67 18
AMP PEAK 15(11P13) WILD-TYPE 117 291 163

Figure S132.  Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q13.3' versus 'MRNA_CNMF'

P value = 0.000273 (Chi-square test), Q value = 0.061

Table S133.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 16(11Q13.3) MUTATED 13 18 62 28 33 37 11 13
AMP PEAK 16(11Q13.3) WILD-TYPE 8 18 57 68 76 35 9 27

Figure S133.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11q13.3' versus 'CN_CNMF'

P value = 4.73e-42 (Chi-square test), Q value = 3.7e-39

Table S134.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
AMP PEAK 16(11Q13.3) MUTATED 62 180 30 93 17
AMP PEAK 16(11Q13.3) WILD-TYPE 315 72 74 159 31

Figure S134.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 4.03e-13 (Chi-square test), Q value = 2.2e-10

Table S135.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
AMP PEAK 16(11Q13.3) MUTATED 42 42 51 77 15 19
AMP PEAK 16(11Q13.3) WILD-TYPE 82 134 53 58 41 97

Figure S135.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 2.6e-14 (Chi-square test), Q value = 1.5e-11

Table S136.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
AMP PEAK 16(11Q13.3) MUTATED 62 30 56 78 142 11
AMP PEAK 16(11Q13.3) WILD-TYPE 128 65 201 91 118 37

Figure S136.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.68e-05 (Fisher's exact test), Q value = 0.0047

Table S137.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
AMP PEAK 16(11Q13.3) MUTATED 100 196 83
AMP PEAK 16(11Q13.3) WILD-TYPE 239 237 164

Figure S137.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

P value = 4.97e-06 (Chi-square test), Q value = 0.0015

Table S138.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
AMP PEAK 16(11Q13.3) MUTATED 70 37 83 103 72 9
AMP PEAK 16(11Q13.3) WILD-TYPE 124 133 144 148 68 23

Figure S138.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q14.1' versus 'CN_CNMF'

P value = 5.66e-20 (Chi-square test), Q value = 3.8e-17

Table S139.  Gene #17: 'amp_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
AMP PEAK 17(11Q14.1) MUTATED 35 98 21 92 9
AMP PEAK 17(11Q14.1) WILD-TYPE 342 154 83 160 39

Figure S139.  Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q14.1' versus 'METHLYATION_CNMF'

P value = 0.000105 (Chi-square test), Q value = 0.025

Table S140.  Gene #17: 'amp_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
AMP PEAK 17(11Q14.1) MUTATED 40 26 33 33 12 14
AMP PEAK 17(11Q14.1) WILD-TYPE 84 150 71 102 44 102

Figure S140.  Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q14.1' versus 'MRNASEQ_CNMF'

P value = 5.37e-08 (Chi-square test), Q value = 2.1e-05

Table S141.  Gene #17: 'amp_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
AMP PEAK 17(11Q14.1) MUTATED 64 16 35 57 76 6
AMP PEAK 17(11Q14.1) WILD-TYPE 126 79 222 112 184 42

Figure S141.  Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.94e-05 (Fisher's exact test), Q value = 0.013

Table S142.  Gene #17: 'amp_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
AMP PEAK 17(11Q14.1) MUTATED 59 113 82
AMP PEAK 17(11Q14.1) WILD-TYPE 280 320 165

Figure S142.  Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q14.1' versus 'MIRSEQ_CNMF'

P value = 3.39e-09 (Chi-square test), Q value = 1.5e-06

Table S143.  Gene #17: 'amp_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
AMP PEAK 17(11Q14.1) MUTATED 51 20 42 97 34 5
AMP PEAK 17(11Q14.1) WILD-TYPE 143 150 185 154 106 27

Figure S143.  Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.36e-06 (Fisher's exact test), Q value = 0.0011

Table S144.  Gene #17: 'amp_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
AMP PEAK 17(11Q14.1) MUTATED 129 91 29
AMP PEAK 17(11Q14.1) WILD-TYPE 402 182 181

Figure S144.  Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.12e-06 (Fisher's exact test), Q value = 0.0018

Table S145.  Gene #17: 'amp_11q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
AMP PEAK 17(11Q14.1) MUTATED 53 34 73
AMP PEAK 17(11Q14.1) WILD-TYPE 195 204 145

Figure S145.  Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_11q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0011 (Fisher's exact test), Q value = 0.22

Table S146.  Gene #17: 'amp_11q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
AMP PEAK 17(11Q14.1) MUTATED 53 79 28
AMP PEAK 17(11Q14.1) WILD-TYPE 112 279 153

Figure S146.  Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p13.33' versus 'MRNA_CNMF'

P value = 3.08e-11 (Chi-square test), Q value = 1.5e-08

Table S147.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 18(12P13.33) MUTATED 3 4 36 53 18 29 3 3
AMP PEAK 18(12P13.33) WILD-TYPE 18 32 83 43 91 43 17 37

Figure S147.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_12p13.33' versus 'MRNA_CHIERARCHICAL'

P value = 1.13e-11 (Fisher's exact test), Q value = 5.8e-09

Table S148.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 18(12P13.33) MUTATED 11 61 77
AMP PEAK 18(12P13.33) WILD-TYPE 111 64 189

Figure S148.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_12p13.33' versus 'CN_CNMF'

P value = 9.75e-38 (Chi-square test), Q value = 7.6e-35

Table S149.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
AMP PEAK 18(12P13.33) MUTATED 18 86 29 130 13
AMP PEAK 18(12P13.33) WILD-TYPE 359 166 75 122 35

Figure S149.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p13.33' versus 'METHLYATION_CNMF'

P value = 9.67e-20 (Chi-square test), Q value = 6.5e-17

Table S150.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
AMP PEAK 18(12P13.33) MUTATED 66 18 24 48 5 15
AMP PEAK 18(12P13.33) WILD-TYPE 58 158 80 87 51 101

Figure S150.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12p13.33' versus 'RPPA_CNMF'

P value = 3.18e-08 (Fisher's exact test), Q value = 1.3e-05

Table S151.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 18(12P13.33) MUTATED 70 31 19
AMP PEAK 18(12P13.33) WILD-TYPE 77 102 98

Figure S151.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_12p13.33' versus 'RPPA_CHIERARCHICAL'

P value = 2.82e-06 (Fisher's exact test), Q value = 9e-04

Table S152.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 18(12P13.33) MUTATED 44 18 58
AMP PEAK 18(12P13.33) WILD-TYPE 117 92 68

Figure S152.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_12p13.33' versus 'MRNASEQ_CNMF'

P value = 4.82e-27 (Chi-square test), Q value = 3.6e-24

Table S153.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
AMP PEAK 18(12P13.33) MUTATED 107 10 32 49 70 4
AMP PEAK 18(12P13.33) WILD-TYPE 83 85 225 120 190 44

Figure S153.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12p13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.24e-23 (Fisher's exact test), Q value = 5.8e-20

Table S154.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
AMP PEAK 18(12P13.33) MUTATED 36 119 117
AMP PEAK 18(12P13.33) WILD-TYPE 303 314 130

Figure S154.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12p13.33' versus 'MIRSEQ_CNMF'

P value = 1.73e-27 (Chi-square test), Q value = 1.3e-24

Table S155.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
AMP PEAK 18(12P13.33) MUTATED 27 18 39 131 44 8
AMP PEAK 18(12P13.33) WILD-TYPE 167 152 188 120 96 24

Figure S155.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12p13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.76e-17 (Fisher's exact test), Q value = 1.7e-14

Table S156.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
AMP PEAK 18(12P13.33) MUTATED 115 125 27
AMP PEAK 18(12P13.33) WILD-TYPE 416 148 183

Figure S156.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p13.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.76e-19 (Fisher's exact test), Q value = 5.7e-16

Table S157.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
AMP PEAK 18(12P13.33) MUTATED 41 31 104
AMP PEAK 18(12P13.33) WILD-TYPE 207 207 114

Figure S157.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12p13.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.93e-16 (Fisher's exact test), Q value = 1.2e-13

Table S158.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
AMP PEAK 18(12P13.33) MUTATED 84 67 25
AMP PEAK 18(12P13.33) WILD-TYPE 81 291 156

Figure S158.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q15' versus 'MRNA_CNMF'

P value = 1.91e-07 (Chi-square test), Q value = 7.1e-05

Table S159.  Gene #19: 'amp_12q15' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 19(12Q15) MUTATED 4 6 54 21 20 35 7 6
AMP PEAK 19(12Q15) WILD-TYPE 17 30 65 75 89 37 13 34

Figure S159.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_12q15' versus 'MRNA_CHIERARCHICAL'

P value = 1.41e-06 (Fisher's exact test), Q value = 0.00047

Table S160.  Gene #19: 'amp_12q15' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 19(12Q15) MUTATED 19 29 105
AMP PEAK 19(12Q15) WILD-TYPE 103 96 161

Figure S160.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

P value = 3.73e-34 (Chi-square test), Q value = 2.9e-31

Table S161.  Gene #19: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
AMP PEAK 19(12Q15) MUTATED 27 132 33 64 12
AMP PEAK 19(12Q15) WILD-TYPE 350 120 71 188 36

Figure S161.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 3.21e-18 (Chi-square test), Q value = 2.1e-15

Table S162.  Gene #19: 'amp_12q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
AMP PEAK 19(12Q15) MUTATED 19 27 25 73 9 14
AMP PEAK 19(12Q15) WILD-TYPE 105 149 79 62 47 102

Figure S162.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q15' versus 'MRNASEQ_CNMF'

P value = 7.31e-13 (Chi-square test), Q value = 4e-10

Table S163.  Gene #19: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
AMP PEAK 19(12Q15) MUTATED 32 16 42 64 102 6
AMP PEAK 19(12Q15) WILD-TYPE 158 79 215 105 158 42

Figure S163.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.53e-14 (Fisher's exact test), Q value = 4.2e-11

Table S164.  Gene #19: 'amp_12q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
AMP PEAK 19(12Q15) MUTATED 53 165 44
AMP PEAK 19(12Q15) WILD-TYPE 286 268 203

Figure S164.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_CNMF'

P value = 4.76e-08 (Chi-square test), Q value = 1.9e-05

Table S165.  Gene #19: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
AMP PEAK 19(12Q15) MUTATED 52 18 53 69 59 11
AMP PEAK 19(12Q15) WILD-TYPE 142 152 174 182 81 21

Figure S165.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.21e-06 (Fisher's exact test), Q value = 0.0013

Table S166.  Gene #19: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
AMP PEAK 19(12Q15) MUTATED 169 61 32
AMP PEAK 19(12Q15) WILD-TYPE 362 212 178

Figure S166.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_13q34' versus 'MRNA_CNMF'

P value = 2.44e-09 (Chi-square test), Q value = 1.1e-06

Table S167.  Gene #20: 'amp_13q34' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 20(13Q34) MUTATED 3 5 19 43 16 10 4 0
AMP PEAK 20(13Q34) WILD-TYPE 18 31 100 53 93 62 16 40

Figure S167.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_13q34' versus 'MRNA_CHIERARCHICAL'

P value = 5.48e-09 (Fisher's exact test), Q value = 2.3e-06

Table S168.  Gene #20: 'amp_13q34' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 20(13Q34) MUTATED 10 48 42
AMP PEAK 20(13Q34) WILD-TYPE 112 77 224

Figure S168.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_13q34' versus 'CN_CNMF'

P value = 3.55e-22 (Chi-square test), Q value = 2.5e-19

Table S169.  Gene #20: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
AMP PEAK 20(13Q34) MUTATED 25 39 11 94 6
AMP PEAK 20(13Q34) WILD-TYPE 352 213 93 158 42

Figure S169.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q34' versus 'METHLYATION_CNMF'

P value = 1.39e-13 (Chi-square test), Q value = 7.7e-11

Table S170.  Gene #20: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
AMP PEAK 20(13Q34) MUTATED 47 10 14 23 2 13
AMP PEAK 20(13Q34) WILD-TYPE 77 166 90 112 54 103

Figure S170.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q34' versus 'RPPA_CNMF'

P value = 1.4e-05 (Fisher's exact test), Q value = 0.0039

Table S171.  Gene #20: 'amp_13q34' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 20(13Q34) MUTATED 49 23 12
AMP PEAK 20(13Q34) WILD-TYPE 98 110 105

Figure S171.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_13q34' versus 'RPPA_CHIERARCHICAL'

P value = 8.83e-08 (Fisher's exact test), Q value = 3.4e-05

Table S172.  Gene #20: 'amp_13q34' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 20(13Q34) MUTATED 26 10 48
AMP PEAK 20(13Q34) WILD-TYPE 135 100 78

Figure S172.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_13q34' versus 'MRNASEQ_CNMF'

P value = 6.4e-21 (Chi-square test), Q value = 4.4e-18

Table S173.  Gene #20: 'amp_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
AMP PEAK 20(13Q34) MUTATED 78 7 24 29 35 1
AMP PEAK 20(13Q34) WILD-TYPE 112 88 233 140 225 47

Figure S173.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.76e-19 (Fisher's exact test), Q value = 1.8e-16

Table S174.  Gene #20: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
AMP PEAK 20(13Q34) MUTATED 26 57 91
AMP PEAK 20(13Q34) WILD-TYPE 313 376 156

Figure S174.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q34' versus 'MIRSEQ_CNMF'

P value = 1.39e-19 (Chi-square test), Q value = 9.3e-17

Table S175.  Gene #20: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
AMP PEAK 20(13Q34) MUTATED 20 12 25 93 19 3
AMP PEAK 20(13Q34) WILD-TYPE 174 158 202 158 121 29

Figure S175.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.23e-19 (Fisher's exact test), Q value = 5.4e-16

Table S176.  Gene #20: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
AMP PEAK 20(13Q34) MUTATED 65 95 12
AMP PEAK 20(13Q34) WILD-TYPE 466 178 198

Figure S176.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_13q34' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.49e-11 (Fisher's exact test), Q value = 7.5e-09

Table S177.  Gene #20: 'amp_13q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
AMP PEAK 20(13Q34) MUTATED 23 18 65
AMP PEAK 20(13Q34) WILD-TYPE 225 220 153

Figure S177.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_13q34' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.05e-12 (Fisher's exact test), Q value = 2.1e-09

Table S178.  Gene #20: 'amp_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
AMP PEAK 20(13Q34) MUTATED 56 35 15
AMP PEAK 20(13Q34) WILD-TYPE 109 323 166

Figure S178.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_14q21.1' versus 'MRNA_CNMF'

P value = 9.91e-05 (Chi-square test), Q value = 0.024

Table S179.  Gene #21: 'amp_14q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 21(14Q21.1) MUTATED 5 9 33 11 21 26 6 0
AMP PEAK 21(14Q21.1) WILD-TYPE 16 27 86 85 88 46 14 40

Figure S179.  Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_14q21.1' versus 'CN_CNMF'

P value = 3.74e-17 (Chi-square test), Q value = 2.4e-14

Table S180.  Gene #21: 'amp_14q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
AMP PEAK 21(14Q21.1) MUTATED 33 97 24 47 12
AMP PEAK 21(14Q21.1) WILD-TYPE 344 155 80 205 36

Figure S180.  Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_14q21.1' versus 'METHLYATION_CNMF'

P value = 1.42e-07 (Chi-square test), Q value = 5.4e-05

Table S181.  Gene #21: 'amp_14q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
AMP PEAK 21(14Q21.1) MUTATED 16 25 28 46 4 13
AMP PEAK 21(14Q21.1) WILD-TYPE 108 151 76 89 52 103

Figure S181.  Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_14q21.1' versus 'MRNASEQ_CNMF'

P value = 3.31e-09 (Chi-square test), Q value = 1.4e-06

Table S182.  Gene #21: 'amp_14q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
AMP PEAK 21(14Q21.1) MUTATED 22 14 40 59 71 4
AMP PEAK 21(14Q21.1) WILD-TYPE 168 81 217 110 189 44

Figure S182.  Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_14q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.75e-07 (Fisher's exact test), Q value = 0.00017

Table S183.  Gene #21: 'amp_14q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
AMP PEAK 21(14Q21.1) MUTATED 50 124 36
AMP PEAK 21(14Q21.1) WILD-TYPE 289 309 211

Figure S183.  Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_14q21.1' versus 'MIRSEQ_CNMF'

P value = 4.27e-05 (Chi-square test), Q value = 0.011

Table S184.  Gene #21: 'amp_14q21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
AMP PEAK 21(14Q21.1) MUTATED 43 14 46 51 42 11
AMP PEAK 21(14Q21.1) WILD-TYPE 151 156 181 200 98 21

Figure S184.  Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_15q26.3' versus 'MRNA_CNMF'

P value = 4.19e-07 (Chi-square test), Q value = 0.00015

Table S185.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 22(15Q26.3) MUTATED 3 8 31 32 4 16 8 2
AMP PEAK 22(15Q26.3) WILD-TYPE 18 28 88 64 105 56 12 38

Figure S185.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_15q26.3' versus 'CN_CNMF'

P value = 2.52e-20 (Chi-square test), Q value = 1.7e-17

Table S186.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
AMP PEAK 22(15Q26.3) MUTATED 26 63 7 86 3
AMP PEAK 22(15Q26.3) WILD-TYPE 351 189 97 166 45

Figure S186.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_15q26.3' versus 'METHLYATION_CNMF'

P value = 2.81e-05 (Chi-square test), Q value = 0.0075

Table S187.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
AMP PEAK 22(15Q26.3) MUTATED 33 10 15 29 8 16
AMP PEAK 22(15Q26.3) WILD-TYPE 91 166 89 106 48 100

Figure S187.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CNMF'

P value = 2.62e-10 (Chi-square test), Q value = 1.2e-07

Table S188.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
AMP PEAK 22(15Q26.3) MUTATED 62 12 19 33 54 4
AMP PEAK 22(15Q26.3) WILD-TYPE 128 83 238 136 206 44

Figure S188.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.2e-08 (Fisher's exact test), Q value = 3.2e-05

Table S189.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
AMP PEAK 22(15Q26.3) MUTATED 34 80 70
AMP PEAK 22(15Q26.3) WILD-TYPE 305 353 177

Figure S189.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'MIRSEQ_CNMF'

P value = 2.25e-08 (Chi-square test), Q value = 9.2e-06

Table S190.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
AMP PEAK 22(15Q26.3) MUTATED 27 17 25 74 32 3
AMP PEAK 22(15Q26.3) WILD-TYPE 167 153 202 177 108 29

Figure S190.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_15q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.81e-10 (Fisher's exact test), Q value = 8.5e-08

Table S191.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
AMP PEAK 22(15Q26.3) MUTATED 84 80 14
AMP PEAK 22(15Q26.3) WILD-TYPE 447 193 196

Figure S191.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.95e-05 (Fisher's exact test), Q value = 0.024

Table S192.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
AMP PEAK 22(15Q26.3) MUTATED 40 25 56
AMP PEAK 22(15Q26.3) WILD-TYPE 208 213 162

Figure S192.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_15q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.19e-05 (Fisher's exact test), Q value = 0.0084

Table S193.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
AMP PEAK 22(15Q26.3) MUTATED 45 60 16
AMP PEAK 22(15Q26.3) WILD-TYPE 120 298 165

Figure S193.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q12' versus 'MRNA_CNMF'

P value = 7.5e-16 (Chi-square test), Q value = 4.5e-13

Table S194.  Gene #23: 'amp_17q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 23(17Q12) MUTATED 9 11 53 19 14 49 7 4
AMP PEAK 23(17Q12) WILD-TYPE 12 25 66 77 95 23 13 36

Figure S194.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q12' versus 'MRNA_CHIERARCHICAL'

P value = 9.88e-06 (Fisher's exact test), Q value = 0.0028

Table S195.  Gene #23: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 23(17Q12) MUTATED 20 39 107
AMP PEAK 23(17Q12) WILD-TYPE 102 86 159

Figure S195.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1.58e-40 (Chi-square test), Q value = 1.2e-37

Table S196.  Gene #23: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
AMP PEAK 23(17Q12) MUTATED 56 164 23 61 15
AMP PEAK 23(17Q12) WILD-TYPE 321 88 81 191 33

Figure S196.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 3.19e-10 (Chi-square test), Q value = 1.5e-07

Table S197.  Gene #23: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
AMP PEAK 23(17Q12) MUTATED 30 34 41 71 14 25
AMP PEAK 23(17Q12) WILD-TYPE 94 142 63 64 42 91

Figure S197.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 4.46e-28 (Chi-square test), Q value = 3.4e-25

Table S198.  Gene #23: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
AMP PEAK 23(17Q12) MUTATED 36 18 39 103 110 10
AMP PEAK 23(17Q12) WILD-TYPE 154 77 218 66 150 38

Figure S198.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.65e-08 (Fisher's exact test), Q value = 6.8e-06

Table S199.  Gene #23: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
AMP PEAK 23(17Q12) MUTATED 69 174 73
AMP PEAK 23(17Q12) WILD-TYPE 270 259 174

Figure S199.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 1.02e-07 (Chi-square test), Q value = 4e-05

Table S200.  Gene #23: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
AMP PEAK 23(17Q12) MUTATED 64 33 58 73 70 14
AMP PEAK 23(17Q12) WILD-TYPE 130 137 169 178 70 18

Figure S200.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000702 (Fisher's exact test), Q value = 0.14

Table S201.  Gene #23: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
AMP PEAK 23(17Q12) MUTATED 186 82 44
AMP PEAK 23(17Q12) WILD-TYPE 345 191 166

Figure S201.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000684 (Fisher's exact test), Q value = 0.14

Table S202.  Gene #23: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
AMP PEAK 23(17Q12) MUTATED 44 133 40
AMP PEAK 23(17Q12) WILD-TYPE 121 225 141

Figure S202.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q23.1' versus 'MRNA_CNMF'

P value = 8.3e-17 (Chi-square test), Q value = 5.2e-14

Table S203.  Gene #24: 'amp_17q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 24(17Q23.1) MUTATED 9 17 81 29 16 44 11 9
AMP PEAK 24(17Q23.1) WILD-TYPE 12 19 38 67 93 28 9 31

Figure S203.  Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q23.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.000143 (Fisher's exact test), Q value = 0.033

Table S204.  Gene #24: 'amp_17q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 24(17Q23.1) MUTATED 35 47 134
AMP PEAK 24(17Q23.1) WILD-TYPE 87 78 132

Figure S204.  Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q23.1' versus 'CN_CNMF'

P value = 5.06e-48 (Chi-square test), Q value = 4.1e-45

Table S205.  Gene #24: 'amp_17q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
AMP PEAK 24(17Q23.1) MUTATED 67 193 27 106 21
AMP PEAK 24(17Q23.1) WILD-TYPE 310 59 77 146 27

Figure S205.  Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q23.1' versus 'METHLYATION_CNMF'

P value = 4.52e-13 (Chi-square test), Q value = 2.5e-10

Table S206.  Gene #24: 'amp_17q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
AMP PEAK 24(17Q23.1) MUTATED 50 40 47 88 20 32
AMP PEAK 24(17Q23.1) WILD-TYPE 74 136 57 47 36 84

Figure S206.  Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q23.1' versus 'MRNASEQ_CNMF'

P value = 1.96e-28 (Chi-square test), Q value = 1.5e-25

Table S207.  Gene #24: 'amp_17q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
AMP PEAK 24(17Q23.1) MUTATED 65 26 42 101 156 18
AMP PEAK 24(17Q23.1) WILD-TYPE 125 69 215 68 104 30

Figure S207.  Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.19e-09 (Fisher's exact test), Q value = 3e-06

Table S208.  Gene #24: 'amp_17q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
AMP PEAK 24(17Q23.1) MUTATED 97 217 94
AMP PEAK 24(17Q23.1) WILD-TYPE 242 216 153

Figure S208.  Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q23.1' versus 'MIRSEQ_CNMF'

P value = 5.2e-15 (Chi-square test), Q value = 3.1e-12

Table S209.  Gene #24: 'amp_17q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
AMP PEAK 24(17Q23.1) MUTATED 75 34 79 119 91 8
AMP PEAK 24(17Q23.1) WILD-TYPE 119 136 148 132 49 24

Figure S209.  Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.61e-05 (Fisher's exact test), Q value = 0.019

Table S210.  Gene #24: 'amp_17q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
AMP PEAK 24(17Q23.1) MUTATED 232 117 57
AMP PEAK 24(17Q23.1) WILD-TYPE 299 156 153

Figure S210.  Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.87e-06 (Fisher's exact test), Q value = 0.0017

Table S211.  Gene #24: 'amp_17q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
AMP PEAK 24(17Q23.1) MUTATED 97 65 108
AMP PEAK 24(17Q23.1) WILD-TYPE 151 173 110

Figure S211.  Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00113 (Fisher's exact test), Q value = 0.22

Table S212.  Gene #24: 'amp_17q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
AMP PEAK 24(17Q23.1) MUTATED 68 153 49
AMP PEAK 24(17Q23.1) WILD-TYPE 97 205 132

Figure S212.  Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.12' versus 'MRNA_CNMF'

P value = 3.23e-05 (Chi-square test), Q value = 0.0085

Table S213.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 25(19P13.12) MUTATED 5 6 22 40 16 11 5 4
AMP PEAK 25(19P13.12) WILD-TYPE 16 30 97 56 93 61 15 36

Figure S213.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19p13.12' versus 'MRNA_CHIERARCHICAL'

P value = 0.000109 (Fisher's exact test), Q value = 0.026

Table S214.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 25(19P13.12) MUTATED 18 44 47
AMP PEAK 25(19P13.12) WILD-TYPE 104 81 219

Figure S214.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19p13.12' versus 'CN_CNMF'

P value = 2.33e-15 (Chi-square test), Q value = 1.4e-12

Table S215.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
AMP PEAK 25(19P13.12) MUTATED 35 48 28 94 11
AMP PEAK 25(19P13.12) WILD-TYPE 342 204 76 158 37

Figure S215.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.12' versus 'METHLYATION_CNMF'

P value = 0.000187 (Chi-square test), Q value = 0.042

Table S216.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
AMP PEAK 25(19P13.12) MUTATED 43 23 19 23 8 24
AMP PEAK 25(19P13.12) WILD-TYPE 81 153 85 112 48 92

Figure S216.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.12' versus 'RPPA_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.14

Table S217.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 25(19P13.12) MUTATED 49 25 17
AMP PEAK 25(19P13.12) WILD-TYPE 98 108 100

Figure S217.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19p13.12' versus 'MRNASEQ_CNMF'

P value = 2.65e-11 (Chi-square test), Q value = 1.3e-08

Table S218.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
AMP PEAK 25(19P13.12) MUTATED 77 18 33 32 45 7
AMP PEAK 25(19P13.12) WILD-TYPE 113 77 224 137 215 41

Figure S218.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19p13.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.54e-09 (Fisher's exact test), Q value = 3.2e-06

Table S219.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
AMP PEAK 25(19P13.12) MUTATED 49 77 86
AMP PEAK 25(19P13.12) WILD-TYPE 290 356 161

Figure S219.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.12' versus 'MIRSEQ_CNMF'

P value = 1.01e-05 (Chi-square test), Q value = 0.0029

Table S220.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
AMP PEAK 25(19P13.12) MUTATED 31 30 37 82 27 3
AMP PEAK 25(19P13.12) WILD-TYPE 163 140 190 169 113 29

Figure S220.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19p13.12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.13e-08 (Fisher's exact test), Q value = 1.6e-05

Table S221.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
AMP PEAK 25(19P13.12) MUTATED 87 91 32
AMP PEAK 25(19P13.12) WILD-TYPE 444 182 178

Figure S221.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19p13.12' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.92e-05 (Fisher's exact test), Q value = 0.015

Table S222.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
AMP PEAK 25(19P13.12) MUTATED 39 42 69
AMP PEAK 25(19P13.12) WILD-TYPE 209 196 149

Figure S222.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19p13.12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0032

Table S223.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
AMP PEAK 25(19P13.12) MUTATED 58 62 30
AMP PEAK 25(19P13.12) WILD-TYPE 107 296 151

Figure S223.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q12' versus 'MRNA_CNMF'

P value = 3.61e-11 (Chi-square test), Q value = 1.8e-08

Table S224.  Gene #26: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 26(19Q12) MUTATED 4 5 29 55 15 20 7 5
AMP PEAK 26(19Q12) WILD-TYPE 17 31 90 41 94 52 13 35

Figure S224.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q12' versus 'MRNA_CHIERARCHICAL'

P value = 5.38e-10 (Fisher's exact test), Q value = 2.4e-07

Table S225.  Gene #26: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 26(19Q12) MUTATED 20 63 57
AMP PEAK 26(19Q12) WILD-TYPE 102 62 209

Figure S225.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 8.46e-32 (Chi-square test), Q value = 6.5e-29

Table S226.  Gene #26: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
AMP PEAK 26(19Q12) MUTATED 36 56 30 134 14
AMP PEAK 26(19Q12) WILD-TYPE 341 196 74 118 34

Figure S226.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 3.81e-12 (Chi-square test), Q value = 2e-09

Table S227.  Gene #26: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
AMP PEAK 26(19Q12) MUTATED 63 24 21 36 7 27
AMP PEAK 26(19Q12) WILD-TYPE 61 152 83 99 49 89

Figure S227.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19q12' versus 'RPPA_CNMF'

P value = 1.9e-06 (Fisher's exact test), Q value = 0.00063

Table S228.  Gene #26: 'amp_19q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 26(19Q12) MUTATED 63 23 24
AMP PEAK 26(19Q12) WILD-TYPE 84 110 93

Figure S228.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19q12' versus 'RPPA_CHIERARCHICAL'

P value = 2.74e-06 (Fisher's exact test), Q value = 0.00088

Table S229.  Gene #26: 'amp_19q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 26(19Q12) MUTATED 29 25 56
AMP PEAK 26(19Q12) WILD-TYPE 132 85 70

Figure S229.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 8.09e-23 (Chi-square test), Q value = 5.7e-20

Table S230.  Gene #26: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
AMP PEAK 26(19Q12) MUTATED 105 15 38 49 56 6
AMP PEAK 26(19Q12) WILD-TYPE 85 80 219 120 204 42

Figure S230.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.03e-20 (Fisher's exact test), Q value = 2.7e-17

Table S231.  Gene #26: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
AMP PEAK 26(19Q12) MUTATED 53 93 123
AMP PEAK 26(19Q12) WILD-TYPE 286 340 124

Figure S231.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 5.07e-14 (Chi-square test), Q value = 2.9e-11

Table S232.  Gene #26: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
AMP PEAK 26(19Q12) MUTATED 40 31 36 115 37 7
AMP PEAK 26(19Q12) WILD-TYPE 154 139 191 136 103 25

Figure S232.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.51e-19 (Fisher's exact test), Q value = 3e-16

Table S233.  Gene #26: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
AMP PEAK 26(19Q12) MUTATED 104 130 32
AMP PEAK 26(19Q12) WILD-TYPE 427 143 178

Figure S233.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.75e-13 (Fisher's exact test), Q value = 3.1e-10

Table S234.  Gene #26: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
AMP PEAK 26(19Q12) MUTATED 44 44 100
AMP PEAK 26(19Q12) WILD-TYPE 204 194 118

Figure S234.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.06e-13 (Fisher's exact test), Q value = 1.7e-10

Table S235.  Gene #26: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
AMP PEAK 26(19Q12) MUTATED 83 74 31
AMP PEAK 26(19Q12) WILD-TYPE 82 284 150

Figure S235.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q13.42' versus 'MRNA_CNMF'

P value = 0.000392 (Chi-square test), Q value = 0.085

Table S236.  Gene #27: 'amp_19q13.42' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 27(19Q13.42) MUTATED 5 8 36 40 17 20 10 6
AMP PEAK 27(19Q13.42) WILD-TYPE 16 28 83 56 92 52 10 34

Figure S236.  Get High-res Image Gene #27: 'amp_19q13.42' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q13.42' versus 'CN_CNMF'

P value = 1.9e-17 (Chi-square test), Q value = 1.2e-14

Table S237.  Gene #27: 'amp_19q13.42' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
AMP PEAK 27(19Q13.42) MUTATED 38 75 33 102 18
AMP PEAK 27(19Q13.42) WILD-TYPE 339 177 71 150 30

Figure S237.  Get High-res Image Gene #27: 'amp_19q13.42' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q13.42' versus 'METHLYATION_CNMF'

P value = 4.19e-05 (Chi-square test), Q value = 0.011

Table S238.  Gene #27: 'amp_19q13.42' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
AMP PEAK 27(19Q13.42) MUTATED 39 27 25 50 9 21
AMP PEAK 27(19Q13.42) WILD-TYPE 85 149 79 85 47 95

Figure S238.  Get High-res Image Gene #27: 'amp_19q13.42' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19q13.42' versus 'MRNASEQ_CNMF'

P value = 5.75e-06 (Chi-square test), Q value = 0.0017

Table S239.  Gene #27: 'amp_19q13.42' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
AMP PEAK 27(19Q13.42) MUTATED 66 18 41 54 78 7
AMP PEAK 27(19Q13.42) WILD-TYPE 124 77 216 115 182 41

Figure S239.  Get High-res Image Gene #27: 'amp_19q13.42' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q13.42' versus 'MIRSEQ_CNMF'

P value = 8.95e-06 (Chi-square test), Q value = 0.0026

Table S240.  Gene #27: 'amp_19q13.42' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
AMP PEAK 27(19Q13.42) MUTATED 49 25 48 89 46 5
AMP PEAK 27(19Q13.42) WILD-TYPE 145 145 179 162 94 27

Figure S240.  Get High-res Image Gene #27: 'amp_19q13.42' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19q13.42' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000133 (Fisher's exact test), Q value = 0.031

Table S241.  Gene #27: 'amp_19q13.42' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
AMP PEAK 27(19Q13.42) MUTATED 121 97 44
AMP PEAK 27(19Q13.42) WILD-TYPE 410 176 166

Figure S241.  Get High-res Image Gene #27: 'amp_19q13.42' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MRNA_CNMF'

P value = 2.78e-10 (Chi-square test), Q value = 1.3e-07

Table S242.  Gene #28: 'amp_20q13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 28(20Q13.2) MUTATED 12 18 85 52 35 49 15 10
AMP PEAK 28(20Q13.2) WILD-TYPE 9 18 34 44 74 23 5 30

Figure S242.  Get High-res Image Gene #28: 'amp_20q13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q13.2' versus 'MRNA_CHIERARCHICAL'

P value = 5.66e-05 (Fisher's exact test), Q value = 0.014

Table S243.  Gene #28: 'amp_20q13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 28(20Q13.2) MUTATED 45 69 162
AMP PEAK 28(20Q13.2) WILD-TYPE 77 56 104

Figure S243.  Get High-res Image Gene #28: 'amp_20q13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q13.2' versus 'CN_CNMF'

P value = 7.91e-57 (Chi-square test), Q value = 6.4e-54

Table S244.  Gene #28: 'amp_20q13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
AMP PEAK 28(20Q13.2) MUTATED 72 204 61 164 29
AMP PEAK 28(20Q13.2) WILD-TYPE 305 48 43 88 19

Figure S244.  Get High-res Image Gene #28: 'amp_20q13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.2' versus 'METHLYATION_CNMF'

P value = 4.77e-23 (Chi-square test), Q value = 3.4e-20

Table S245.  Gene #28: 'amp_20q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
AMP PEAK 28(20Q13.2) MUTATED 75 47 61 107 14 43
AMP PEAK 28(20Q13.2) WILD-TYPE 49 129 43 28 42 73

Figure S245.  Get High-res Image Gene #28: 'amp_20q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.2' versus 'RPPA_CNMF'

P value = 0.000529 (Fisher's exact test), Q value = 0.11

Table S246.  Gene #28: 'amp_20q13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 28(20Q13.2) MUTATED 100 67 54
AMP PEAK 28(20Q13.2) WILD-TYPE 47 66 63

Figure S246.  Get High-res Image Gene #28: 'amp_20q13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q13.2' versus 'MRNASEQ_CNMF'

P value = 1.18e-20 (Chi-square test), Q value = 8.1e-18

Table S247.  Gene #28: 'amp_20q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
AMP PEAK 28(20Q13.2) MUTATED 106 32 80 113 175 17
AMP PEAK 28(20Q13.2) WILD-TYPE 84 63 177 56 85 31

Figure S247.  Get High-res Image Gene #28: 'amp_20q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.73e-13 (Fisher's exact test), Q value = 4.7e-10

Table S248.  Gene #28: 'amp_20q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
AMP PEAK 28(20Q13.2) MUTATED 119 265 139
AMP PEAK 28(20Q13.2) WILD-TYPE 220 168 108

Figure S248.  Get High-res Image Gene #28: 'amp_20q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_CNMF'

P value = 3.61e-13 (Chi-square test), Q value = 2e-10

Table S249.  Gene #28: 'amp_20q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
AMP PEAK 28(20Q13.2) MUTATED 97 51 100 158 94 22
AMP PEAK 28(20Q13.2) WILD-TYPE 97 119 127 93 46 10

Figure S249.  Get High-res Image Gene #28: 'amp_20q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.99e-11 (Fisher's exact test), Q value = 1.5e-08

Table S250.  Gene #28: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
AMP PEAK 28(20Q13.2) MUTATED 296 162 64
AMP PEAK 28(20Q13.2) WILD-TYPE 235 111 146

Figure S250.  Get High-res Image Gene #28: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.44e-08 (Fisher's exact test), Q value = 1.8e-05

Table S251.  Gene #28: 'amp_20q13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
AMP PEAK 28(20Q13.2) MUTATED 138 86 135
AMP PEAK 28(20Q13.2) WILD-TYPE 110 152 83

Figure S251.  Get High-res Image Gene #28: 'amp_20q13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.73e-06 (Fisher's exact test), Q value = 0.0017

Table S252.  Gene #28: 'amp_20q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
AMP PEAK 28(20Q13.2) MUTATED 95 200 64
AMP PEAK 28(20Q13.2) WILD-TYPE 70 158 117

Figure S252.  Get High-res Image Gene #28: 'amp_20q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.13' versus 'MRNA_CNMF'

P value = 5.78e-05 (Chi-square test), Q value = 0.015

Table S253.  Gene #29: 'del_1p36.13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 1(1P36.13) MUTATED 9 11 61 42 31 46 7 12
DEL PEAK 1(1P36.13) WILD-TYPE 12 25 58 54 78 26 13 28

Figure S253.  Get High-res Image Gene #29: 'del_1p36.13' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.13' versus 'MRNA_CHIERARCHICAL'

P value = 4.92e-05 (Fisher's exact test), Q value = 0.013

Table S254.  Gene #29: 'del_1p36.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 1(1P36.13) MUTATED 33 51 135
DEL PEAK 1(1P36.13) WILD-TYPE 89 74 131

Figure S254.  Get High-res Image Gene #29: 'del_1p36.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.13' versus 'CN_CNMF'

P value = 1.07e-34 (Chi-square test), Q value = 8.3e-32

Table S255.  Gene #29: 'del_1p36.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 1(1P36.13) MUTATED 64 161 60 128 19
DEL PEAK 1(1P36.13) WILD-TYPE 313 91 44 124 29

Figure S255.  Get High-res Image Gene #29: 'del_1p36.13' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.13' versus 'METHLYATION_CNMF'

P value = 1.11e-12 (Chi-square test), Q value = 6e-10

Table S256.  Gene #29: 'del_1p36.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 1(1P36.13) MUTATED 54 42 63 78 19 31
DEL PEAK 1(1P36.13) WILD-TYPE 70 134 41 57 37 85

Figure S256.  Get High-res Image Gene #29: 'del_1p36.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.13' versus 'MRNASEQ_CNMF'

P value = 2.58e-09 (Chi-square test), Q value = 1.1e-06

Table S257.  Gene #29: 'del_1p36.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 1(1P36.13) MUTATED 79 25 77 94 135 18
DEL PEAK 1(1P36.13) WILD-TYPE 111 70 180 75 125 30

Figure S257.  Get High-res Image Gene #29: 'del_1p36.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.7e-10 (Fisher's exact test), Q value = 8.1e-08

Table S258.  Gene #29: 'del_1p36.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 1(1P36.13) MUTATED 101 231 96
DEL PEAK 1(1P36.13) WILD-TYPE 238 202 151

Figure S258.  Get High-res Image Gene #29: 'del_1p36.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.13' versus 'MIRSEQ_CNMF'

P value = 8.63e-08 (Chi-square test), Q value = 3.4e-05

Table S259.  Gene #29: 'del_1p36.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 1(1P36.13) MUTATED 89 37 85 128 65 14
DEL PEAK 1(1P36.13) WILD-TYPE 105 133 142 123 75 18

Figure S259.  Get High-res Image Gene #29: 'del_1p36.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.93e-05 (Fisher's exact test), Q value = 0.0078

Table S260.  Gene #29: 'del_1p36.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 1(1P36.13) MUTATED 239 121 58
DEL PEAK 1(1P36.13) WILD-TYPE 292 152 152

Figure S260.  Get High-res Image Gene #29: 'del_1p36.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p21.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.000469 (Fisher's exact test), Q value = 0.1

Table S261.  Gene #30: 'del_1p21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 2(1P21.2) MUTATED 32 33 114
DEL PEAK 2(1P21.2) WILD-TYPE 90 92 152

Figure S261.  Get High-res Image Gene #30: 'del_1p21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p21.2' versus 'CN_CNMF'

P value = 6.49e-26 (Chi-square test), Q value = 4.8e-23

Table S262.  Gene #30: 'del_1p21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 2(1P21.2) MUTATED 57 129 61 80 13
DEL PEAK 2(1P21.2) WILD-TYPE 320 123 43 172 35

Figure S262.  Get High-res Image Gene #30: 'del_1p21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p21.2' versus 'METHLYATION_CNMF'

P value = 2.98e-09 (Chi-square test), Q value = 1.3e-06

Table S263.  Gene #30: 'del_1p21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 2(1P21.2) MUTATED 31 38 50 63 16 21
DEL PEAK 2(1P21.2) WILD-TYPE 93 138 54 72 40 95

Figure S263.  Get High-res Image Gene #30: 'del_1p21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p21.2' versus 'RPPA_CNMF'

P value = 0.000478 (Fisher's exact test), Q value = 0.1

Table S264.  Gene #30: 'del_1p21.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 2(1P21.2) MUTATED 60 50 23
DEL PEAK 2(1P21.2) WILD-TYPE 87 83 94

Figure S264.  Get High-res Image Gene #30: 'del_1p21.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p21.2' versus 'MRNASEQ_CNMF'

P value = 3.69e-06 (Chi-square test), Q value = 0.0011

Table S265.  Gene #30: 'del_1p21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 2(1P21.2) MUTATED 44 23 75 78 104 13
DEL PEAK 2(1P21.2) WILD-TYPE 146 72 182 91 156 35

Figure S265.  Get High-res Image Gene #30: 'del_1p21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.6e-10 (Fisher's exact test), Q value = 7.6e-08

Table S266.  Gene #30: 'del_1p21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 2(1P21.2) MUTATED 87 193 57
DEL PEAK 2(1P21.2) WILD-TYPE 252 240 190

Figure S266.  Get High-res Image Gene #30: 'del_1p21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000137 (Fisher's exact test), Q value = 0.032

Table S267.  Gene #30: 'del_1p21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 2(1P21.2) MUTATED 204 80 49
DEL PEAK 2(1P21.2) WILD-TYPE 327 193 161

Figure S267.  Get High-res Image Gene #30: 'del_1p21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MRNA_CNMF'

P value = 2.53e-07 (Chi-square test), Q value = 9.3e-05

Table S268.  Gene #31: 'del_2q37.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 3(2Q37.3) MUTATED 5 9 42 49 24 28 6 0
DEL PEAK 3(2Q37.3) WILD-TYPE 16 27 77 47 85 44 14 40

Figure S268.  Get High-res Image Gene #31: 'del_2q37.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_2q37.3' versus 'MRNA_CHIERARCHICAL'

P value = 8.21e-10 (Fisher's exact test), Q value = 3.7e-07

Table S269.  Gene #31: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 3(2Q37.3) MUTATED 14 60 89
DEL PEAK 3(2Q37.3) WILD-TYPE 108 65 177

Figure S269.  Get High-res Image Gene #31: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 1.66e-27 (Chi-square test), Q value = 1.2e-24

Table S270.  Gene #31: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 3(2Q37.3) MUTATED 38 99 27 126 17
DEL PEAK 3(2Q37.3) WILD-TYPE 339 153 77 126 31

Figure S270.  Get High-res Image Gene #31: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 1.41e-12 (Chi-square test), Q value = 7.5e-10

Table S271.  Gene #31: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 3(2Q37.3) MUTATED 58 29 25 55 7 16
DEL PEAK 3(2Q37.3) WILD-TYPE 66 147 79 80 49 100

Figure S271.  Get High-res Image Gene #31: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q37.3' versus 'RPPA_CNMF'

P value = 3.45e-10 (Fisher's exact test), Q value = 1.6e-07

Table S272.  Gene #31: 'del_2q37.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 3(2Q37.3) MUTATED 72 40 14
DEL PEAK 3(2Q37.3) WILD-TYPE 75 93 103

Figure S272.  Get High-res Image Gene #31: 'del_2q37.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_2q37.3' versus 'RPPA_CHIERARCHICAL'

P value = 2.74e-09 (Fisher's exact test), Q value = 1.2e-06

Table S273.  Gene #31: 'del_2q37.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 3(2Q37.3) MUTATED 59 11 56
DEL PEAK 3(2Q37.3) WILD-TYPE 102 99 70

Figure S273.  Get High-res Image Gene #31: 'del_2q37.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 2.88e-15 (Chi-square test), Q value = 1.7e-12

Table S274.  Gene #31: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 3(2Q37.3) MUTATED 93 15 47 59 87 2
DEL PEAK 3(2Q37.3) WILD-TYPE 97 80 210 110 173 46

Figure S274.  Get High-res Image Gene #31: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.19e-14 (Fisher's exact test), Q value = 1.3e-11

Table S275.  Gene #31: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 3(2Q37.3) MUTATED 51 145 107
DEL PEAK 3(2Q37.3) WILD-TYPE 288 288 140

Figure S275.  Get High-res Image Gene #31: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 2.72e-14 (Chi-square test), Q value = 1.6e-11

Table S276.  Gene #31: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 3(2Q37.3) MUTATED 53 21 45 114 56 10
DEL PEAK 3(2Q37.3) WILD-TYPE 141 149 182 137 84 22

Figure S276.  Get High-res Image Gene #31: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.07e-12 (Fisher's exact test), Q value = 4.1e-09

Table S277.  Gene #31: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 3(2Q37.3) MUTATED 155 116 28
DEL PEAK 3(2Q37.3) WILD-TYPE 376 157 182

Figure S277.  Get High-res Image Gene #31: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.33e-15 (Fisher's exact test), Q value = 8e-13

Table S278.  Gene #31: 'del_2q37.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
DEL PEAK 3(2Q37.3) MUTATED 65 32 105
DEL PEAK 3(2Q37.3) WILD-TYPE 183 206 113

Figure S278.  Get High-res Image Gene #31: 'del_2q37.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_2q37.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.04e-09 (Fisher's exact test), Q value = 4.6e-07

Table S279.  Gene #31: 'del_2q37.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
DEL PEAK 3(2Q37.3) MUTATED 75 101 26
DEL PEAK 3(2Q37.3) WILD-TYPE 90 257 155

Figure S279.  Get High-res Image Gene #31: 'del_2q37.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p21.31' versus 'MRNA_CNMF'

P value = 4.41e-12 (Chi-square test), Q value = 2.3e-09

Table S280.  Gene #32: 'del_3p21.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 4(3P21.31) MUTATED 5 15 38 52 8 35 9 7
DEL PEAK 4(3P21.31) WILD-TYPE 16 21 81 44 101 37 11 33

Figure S280.  Get High-res Image Gene #32: 'del_3p21.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p21.31' versus 'MRNA_CHIERARCHICAL'

P value = 2.05e-08 (Fisher's exact test), Q value = 8.4e-06

Table S281.  Gene #32: 'del_3p21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 4(3P21.31) MUTATED 31 69 69
DEL PEAK 4(3P21.31) WILD-TYPE 91 56 197

Figure S281.  Get High-res Image Gene #32: 'del_3p21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p21.31' versus 'CN_CNMF'

P value = 5.91e-41 (Chi-square test), Q value = 4.7e-38

Table S282.  Gene #32: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 4(3P21.31) MUTATED 51 96 21 160 5
DEL PEAK 4(3P21.31) WILD-TYPE 326 156 83 92 43

Figure S282.  Get High-res Image Gene #32: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p21.31' versus 'METHLYATION_CNMF'

P value = 6.64e-19 (Chi-square test), Q value = 4.3e-16

Table S283.  Gene #32: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 4(3P21.31) MUTATED 67 15 48 52 17 22
DEL PEAK 4(3P21.31) WILD-TYPE 57 161 56 83 39 94

Figure S283.  Get High-res Image Gene #32: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p21.31' versus 'RPPA_CNMF'

P value = 3.63e-09 (Fisher's exact test), Q value = 1.6e-06

Table S284.  Gene #32: 'del_3p21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 4(3P21.31) MUTATED 81 27 36
DEL PEAK 4(3P21.31) WILD-TYPE 66 106 81

Figure S284.  Get High-res Image Gene #32: 'del_3p21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p21.31' versus 'RPPA_CHIERARCHICAL'

P value = 4.15e-06 (Fisher's exact test), Q value = 0.0013

Table S285.  Gene #32: 'del_3p21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 4(3P21.31) MUTATED 43 33 68
DEL PEAK 4(3P21.31) WILD-TYPE 118 77 58

Figure S285.  Get High-res Image Gene #32: 'del_3p21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p21.31' versus 'MRNASEQ_CNMF'

P value = 2.58e-22 (Chi-square test), Q value = 1.8e-19

Table S286.  Gene #32: 'del_3p21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 4(3P21.31) MUTATED 102 22 32 81 80 11
DEL PEAK 4(3P21.31) WILD-TYPE 88 73 225 88 180 37

Figure S286.  Get High-res Image Gene #32: 'del_3p21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.33e-13 (Fisher's exact test), Q value = 2.9e-10

Table S287.  Gene #32: 'del_3p21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 4(3P21.31) MUTATED 74 128 126
DEL PEAK 4(3P21.31) WILD-TYPE 265 305 121

Figure S287.  Get High-res Image Gene #32: 'del_3p21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_CNMF'

P value = 1.14e-17 (Chi-square test), Q value = 7.3e-15

Table S288.  Gene #32: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 4(3P21.31) MUTATED 53 25 52 134 53 9
DEL PEAK 4(3P21.31) WILD-TYPE 141 145 175 117 87 23

Figure S288.  Get High-res Image Gene #32: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.36e-13 (Fisher's exact test), Q value = 7.6e-11

Table S289.  Gene #32: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 4(3P21.31) MUTATED 151 136 39
DEL PEAK 4(3P21.31) WILD-TYPE 380 137 171

Figure S289.  Get High-res Image Gene #32: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.19e-13 (Fisher's exact test), Q value = 3.9e-10

Table S290.  Gene #32: 'del_3p21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
DEL PEAK 4(3P21.31) MUTATED 64 48 112
DEL PEAK 4(3P21.31) WILD-TYPE 184 190 106

Figure S290.  Get High-res Image Gene #32: 'del_3p21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.06e-08 (Fisher's exact test), Q value = 8.5e-06

Table S291.  Gene #32: 'del_3p21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
DEL PEAK 4(3P21.31) MUTATED 83 102 39
DEL PEAK 4(3P21.31) WILD-TYPE 82 256 142

Figure S291.  Get High-res Image Gene #32: 'del_3p21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p16.3' versus 'MRNA_CNMF'

P value = 9.53e-13 (Chi-square test), Q value = 5.1e-10

Table S292.  Gene #33: 'del_4p16.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 5(4P16.3) MUTATED 3 10 25 58 22 38 7 6
DEL PEAK 5(4P16.3) WILD-TYPE 18 26 94 38 87 34 13 34

Figure S292.  Get High-res Image Gene #33: 'del_4p16.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4p16.3' versus 'MRNA_CHIERARCHICAL'

P value = 2.8e-12 (Fisher's exact test), Q value = 1.5e-09

Table S293.  Gene #33: 'del_4p16.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 5(4P16.3) MUTATED 22 74 73
DEL PEAK 5(4P16.3) WILD-TYPE 100 51 193

Figure S293.  Get High-res Image Gene #33: 'del_4p16.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4p16.3' versus 'CN_CNMF'

P value = 3.45e-35 (Chi-square test), Q value = 2.7e-32

Table S294.  Gene #33: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 5(4P16.3) MUTATED 49 69 44 153 12
DEL PEAK 5(4P16.3) WILD-TYPE 328 183 60 99 36

Figure S294.  Get High-res Image Gene #33: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

P value = 8.72e-18 (Chi-square test), Q value = 5.6e-15

Table S295.  Gene #33: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 5(4P16.3) MUTATED 80 35 29 33 7 31
DEL PEAK 5(4P16.3) WILD-TYPE 44 141 75 102 49 85

Figure S295.  Get High-res Image Gene #33: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p16.3' versus 'RPPA_CNMF'

P value = 1.78e-07 (Fisher's exact test), Q value = 6.7e-05

Table S296.  Gene #33: 'del_4p16.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 5(4P16.3) MUTATED 77 38 25
DEL PEAK 5(4P16.3) WILD-TYPE 70 95 92

Figure S296.  Get High-res Image Gene #33: 'del_4p16.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4p16.3' versus 'RPPA_CHIERARCHICAL'

P value = 5.2e-07 (Fisher's exact test), Q value = 0.00018

Table S297.  Gene #33: 'del_4p16.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 5(4P16.3) MUTATED 47 25 68
DEL PEAK 5(4P16.3) WILD-TYPE 114 85 58

Figure S297.  Get High-res Image Gene #33: 'del_4p16.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4p16.3' versus 'MRNASEQ_CNMF'

P value = 1.07e-25 (Chi-square test), Q value = 7.8e-23

Table S298.  Gene #33: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 5(4P16.3) MUTATED 116 13 58 73 55 9
DEL PEAK 5(4P16.3) WILD-TYPE 74 82 199 96 205 39

Figure S298.  Get High-res Image Gene #33: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.18e-23 (Fisher's exact test), Q value = 2.3e-20

Table S299.  Gene #33: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 5(4P16.3) MUTATED 62 120 142
DEL PEAK 5(4P16.3) WILD-TYPE 277 313 105

Figure S299.  Get High-res Image Gene #33: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_CNMF'

P value = 1.1e-18 (Chi-square test), Q value = 7.1e-16

Table S300.  Gene #33: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 5(4P16.3) MUTATED 61 35 37 135 37 11
DEL PEAK 5(4P16.3) WILD-TYPE 133 135 190 116 103 21

Figure S300.  Get High-res Image Gene #33: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.62e-20 (Fisher's exact test), Q value = 3.1e-17

Table S301.  Gene #33: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 5(4P16.3) MUTATED 143 143 30
DEL PEAK 5(4P16.3) WILD-TYPE 388 130 180

Figure S301.  Get High-res Image Gene #33: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.04e-15 (Fisher's exact test), Q value = 5.3e-12

Table S302.  Gene #33: 'del_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
DEL PEAK 5(4P16.3) MUTATED 66 42 113
DEL PEAK 5(4P16.3) WILD-TYPE 182 196 105

Figure S302.  Get High-res Image Gene #33: 'del_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.47e-13 (Fisher's exact test), Q value = 2.5e-10

Table S303.  Gene #33: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
DEL PEAK 5(4P16.3) MUTATED 91 95 35
DEL PEAK 5(4P16.3) WILD-TYPE 74 263 146

Figure S303.  Get High-res Image Gene #33: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q35.2' versus 'MRNA_CNMF'

P value = 7.03e-07 (Chi-square test), Q value = 0.00024

Table S304.  Gene #34: 'del_4q35.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 6(4Q35.2) MUTATED 7 10 26 52 24 32 10 9
DEL PEAK 6(4Q35.2) WILD-TYPE 14 26 93 44 85 40 10 31

Figure S304.  Get High-res Image Gene #34: 'del_4q35.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q35.2' versus 'MRNA_CHIERARCHICAL'

P value = 1.71e-06 (Fisher's exact test), Q value = 0.00057

Table S305.  Gene #34: 'del_4q35.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 6(4Q35.2) MUTATED 26 64 80
DEL PEAK 6(4Q35.2) WILD-TYPE 96 61 186

Figure S305.  Get High-res Image Gene #34: 'del_4q35.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q35.2' versus 'CN_CNMF'

P value = 8.03e-41 (Chi-square test), Q value = 6.3e-38

Table S306.  Gene #34: 'del_4q35.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 6(4Q35.2) MUTATED 50 63 48 161 12
DEL PEAK 6(4Q35.2) WILD-TYPE 327 189 56 91 36

Figure S306.  Get High-res Image Gene #34: 'del_4q35.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q35.2' versus 'METHLYATION_CNMF'

P value = 2.48e-18 (Chi-square test), Q value = 1.6e-15

Table S307.  Gene #34: 'del_4q35.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 6(4Q35.2) MUTATED 81 34 31 27 10 36
DEL PEAK 6(4Q35.2) WILD-TYPE 43 142 73 108 46 80

Figure S307.  Get High-res Image Gene #34: 'del_4q35.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q35.2' versus 'RPPA_CNMF'

P value = 8.21e-08 (Fisher's exact test), Q value = 3.2e-05

Table S308.  Gene #34: 'del_4q35.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 6(4Q35.2) MUTATED 78 36 26
DEL PEAK 6(4Q35.2) WILD-TYPE 69 97 91

Figure S308.  Get High-res Image Gene #34: 'del_4q35.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4q35.2' versus 'RPPA_CHIERARCHICAL'

P value = 6.93e-06 (Fisher's exact test), Q value = 0.002

Table S309.  Gene #34: 'del_4q35.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 6(4Q35.2) MUTATED 47 27 66
DEL PEAK 6(4Q35.2) WILD-TYPE 114 83 60

Figure S309.  Get High-res Image Gene #34: 'del_4q35.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4q35.2' versus 'MRNASEQ_CNMF'

P value = 1.05e-26 (Chi-square test), Q value = 7.8e-24

Table S310.  Gene #34: 'del_4q35.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 6(4Q35.2) MUTATED 119 15 62 74 50 11
DEL PEAK 6(4Q35.2) WILD-TYPE 71 80 195 95 210 37

Figure S310.  Get High-res Image Gene #34: 'del_4q35.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q35.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.69e-19 (Fisher's exact test), Q value = 1.1e-16

Table S311.  Gene #34: 'del_4q35.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 6(4Q35.2) MUTATED 67 126 138
DEL PEAK 6(4Q35.2) WILD-TYPE 272 307 109

Figure S311.  Get High-res Image Gene #34: 'del_4q35.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.2' versus 'MIRSEQ_CNMF'

P value = 8.06e-20 (Chi-square test), Q value = 5.4e-17

Table S312.  Gene #34: 'del_4q35.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 6(4Q35.2) MUTATED 67 33 38 137 36 10
DEL PEAK 6(4Q35.2) WILD-TYPE 127 137 189 114 104 22

Figure S312.  Get High-res Image Gene #34: 'del_4q35.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q35.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.86e-22 (Fisher's exact test), Q value = 3.4e-19

Table S313.  Gene #34: 'del_4q35.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 6(4Q35.2) MUTATED 143 148 30
DEL PEAK 6(4Q35.2) WILD-TYPE 388 125 180

Figure S313.  Get High-res Image Gene #34: 'del_4q35.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q35.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.08e-17 (Fisher's exact test), Q value = 1.3e-14

Table S314.  Gene #34: 'del_4q35.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
DEL PEAK 6(4Q35.2) MUTATED 63 41 118
DEL PEAK 6(4Q35.2) WILD-TYPE 185 197 100

Figure S314.  Get High-res Image Gene #34: 'del_4q35.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q35.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.52e-15 (Fisher's exact test), Q value = 3.3e-12

Table S315.  Gene #34: 'del_4q35.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
DEL PEAK 6(4Q35.2) MUTATED 94 95 33
DEL PEAK 6(4Q35.2) WILD-TYPE 71 263 148

Figure S315.  Get High-res Image Gene #34: 'del_4q35.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q11.2' versus 'MRNA_CNMF'

P value = 3.26e-28 (Chi-square test), Q value = 2.5e-25

Table S316.  Gene #35: 'del_5q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 7(5Q11.2) MUTATED 3 5 19 69 7 26 3 4
DEL PEAK 7(5Q11.2) WILD-TYPE 18 31 100 27 102 46 17 36

Figure S316.  Get High-res Image Gene #35: 'del_5q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 3.49e-25 (Fisher's exact test), Q value = 2.6e-22

Table S317.  Gene #35: 'del_5q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 7(5Q11.2) MUTATED 12 80 44
DEL PEAK 7(5Q11.2) WILD-TYPE 110 45 222

Figure S317.  Get High-res Image Gene #35: 'del_5q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q11.2' versus 'CN_CNMF'

P value = 5.33e-81 (Chi-square test), Q value = 4.3e-78

Table S318.  Gene #35: 'del_5q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 7(5Q11.2) MUTATED 27 43 7 182 10
DEL PEAK 7(5Q11.2) WILD-TYPE 350 209 97 70 38

Figure S318.  Get High-res Image Gene #35: 'del_5q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q11.2' versus 'METHLYATION_CNMF'

P value = 6.67e-48 (Chi-square test), Q value = 5.3e-45

Table S319.  Gene #35: 'del_5q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 7(5Q11.2) MUTATED 96 7 13 31 8 28
DEL PEAK 7(5Q11.2) WILD-TYPE 28 169 91 104 48 88

Figure S319.  Get High-res Image Gene #35: 'del_5q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q11.2' versus 'RPPA_CNMF'

P value = 1.32e-16 (Fisher's exact test), Q value = 8.2e-14

Table S320.  Gene #35: 'del_5q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 7(5Q11.2) MUTATED 79 13 23
DEL PEAK 7(5Q11.2) WILD-TYPE 68 120 94

Figure S320.  Get High-res Image Gene #35: 'del_5q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_5q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 2.45e-19 (Fisher's exact test), Q value = 1.6e-16

Table S321.  Gene #35: 'del_5q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 7(5Q11.2) MUTATED 26 13 76
DEL PEAK 7(5Q11.2) WILD-TYPE 135 97 50

Figure S321.  Get High-res Image Gene #35: 'del_5q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_5q11.2' versus 'MRNASEQ_CNMF'

P value = 8.1e-65 (Chi-square test), Q value = 6.6e-62

Table S322.  Gene #35: 'del_5q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 7(5Q11.2) MUTATED 137 9 15 61 41 3
DEL PEAK 7(5Q11.2) WILD-TYPE 53 86 242 108 219 45

Figure S322.  Get High-res Image Gene #35: 'del_5q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.38e-56 (Fisher's exact test), Q value = 1.9e-53

Table S323.  Gene #35: 'del_5q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 7(5Q11.2) MUTATED 28 76 162
DEL PEAK 7(5Q11.2) WILD-TYPE 311 357 85

Figure S323.  Get High-res Image Gene #35: 'del_5q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_CNMF'

P value = 7.28e-46 (Chi-square test), Q value = 5.8e-43

Table S324.  Gene #35: 'del_5q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 7(5Q11.2) MUTATED 31 17 16 148 39 6
DEL PEAK 7(5Q11.2) WILD-TYPE 163 153 211 103 101 26

Figure S324.  Get High-res Image Gene #35: 'del_5q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.14e-51 (Fisher's exact test), Q value = 1.7e-48

Table S325.  Gene #35: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 7(5Q11.2) MUTATED 77 165 15
DEL PEAK 7(5Q11.2) WILD-TYPE 454 108 195

Figure S325.  Get High-res Image Gene #35: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.05e-43 (Fisher's exact test), Q value = 6.4e-40

Table S326.  Gene #35: 'del_5q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
DEL PEAK 7(5Q11.2) MUTATED 38 14 131
DEL PEAK 7(5Q11.2) WILD-TYPE 210 224 87

Figure S326.  Get High-res Image Gene #35: 'del_5q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.41e-36 (Fisher's exact test), Q value = 1.1e-33

Table S327.  Gene #35: 'del_5q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
DEL PEAK 7(5Q11.2) MUTATED 108 59 16
DEL PEAK 7(5Q11.2) WILD-TYPE 57 299 165

Figure S327.  Get High-res Image Gene #35: 'del_5q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q21.3' versus 'MRNA_CNMF'

P value = 7.19e-31 (Chi-square test), Q value = 5.5e-28

Table S328.  Gene #36: 'del_5q21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 8(5Q21.3) MUTATED 2 5 19 71 7 24 5 2
DEL PEAK 8(5Q21.3) WILD-TYPE 19 31 100 25 102 48 15 38

Figure S328.  Get High-res Image Gene #36: 'del_5q21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q21.3' versus 'MRNA_CHIERARCHICAL'

P value = 1.14e-27 (Fisher's exact test), Q value = 8.5e-25

Table S329.  Gene #36: 'del_5q21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 8(5Q21.3) MUTATED 11 82 42
DEL PEAK 8(5Q21.3) WILD-TYPE 111 43 224

Figure S329.  Get High-res Image Gene #36: 'del_5q21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q21.3' versus 'CN_CNMF'

P value = 3.29e-92 (Chi-square test), Q value = 2.7e-89

Table S330.  Gene #36: 'del_5q21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 8(5Q21.3) MUTATED 21 37 7 187 9
DEL PEAK 8(5Q21.3) WILD-TYPE 356 215 97 65 39

Figure S330.  Get High-res Image Gene #36: 'del_5q21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q21.3' versus 'METHLYATION_CNMF'

P value = 3.74e-59 (Chi-square test), Q value = 3e-56

Table S331.  Gene #36: 'del_5q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 8(5Q21.3) MUTATED 102 5 11 28 6 25
DEL PEAK 8(5Q21.3) WILD-TYPE 22 171 93 107 50 91

Figure S331.  Get High-res Image Gene #36: 'del_5q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q21.3' versus 'RPPA_CNMF'

P value = 1.04e-15 (Fisher's exact test), Q value = 6.3e-13

Table S332.  Gene #36: 'del_5q21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 8(5Q21.3) MUTATED 77 13 23
DEL PEAK 8(5Q21.3) WILD-TYPE 70 120 94

Figure S332.  Get High-res Image Gene #36: 'del_5q21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_5q21.3' versus 'RPPA_CHIERARCHICAL'

P value = 2.68e-16 (Fisher's exact test), Q value = 1.6e-13

Table S333.  Gene #36: 'del_5q21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 8(5Q21.3) MUTATED 26 15 72
DEL PEAK 8(5Q21.3) WILD-TYPE 135 95 54

Figure S333.  Get High-res Image Gene #36: 'del_5q21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_5q21.3' versus 'MRNASEQ_CNMF'

P value = 1.94e-76 (Chi-square test), Q value = 1.6e-73

Table S334.  Gene #36: 'del_5q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 8(5Q21.3) MUTATED 144 9 12 57 36 1
DEL PEAK 8(5Q21.3) WILD-TYPE 46 86 245 112 224 47

Figure S334.  Get High-res Image Gene #36: 'del_5q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.08e-63 (Fisher's exact test), Q value = 7.4e-60

Table S335.  Gene #36: 'del_5q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 8(5Q21.3) MUTATED 26 67 166
DEL PEAK 8(5Q21.3) WILD-TYPE 313 366 81

Figure S335.  Get High-res Image Gene #36: 'del_5q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q21.3' versus 'MIRSEQ_CNMF'

P value = 3.12e-51 (Chi-square test), Q value = 2.5e-48

Table S336.  Gene #36: 'del_5q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 8(5Q21.3) MUTATED 27 18 12 151 37 6
DEL PEAK 8(5Q21.3) WILD-TYPE 167 152 215 100 103 26

Figure S336.  Get High-res Image Gene #36: 'del_5q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.56e-60 (Fisher's exact test), Q value = 6.9e-57

Table S337.  Gene #36: 'del_5q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 8(5Q21.3) MUTATED 70 170 11
DEL PEAK 8(5Q21.3) WILD-TYPE 461 103 199

Figure S337.  Get High-res Image Gene #36: 'del_5q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.27e-46 (Fisher's exact test), Q value = 5e-43

Table S338.  Gene #36: 'del_5q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
DEL PEAK 8(5Q21.3) MUTATED 29 13 130
DEL PEAK 8(5Q21.3) WILD-TYPE 219 225 88

Figure S338.  Get High-res Image Gene #36: 'del_5q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.71e-44 (Fisher's exact test), Q value = 3.7e-41

Table S339.  Gene #36: 'del_5q21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
DEL PEAK 8(5Q21.3) MUTATED 111 49 12
DEL PEAK 8(5Q21.3) WILD-TYPE 54 309 169

Figure S339.  Get High-res Image Gene #36: 'del_5q21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

P value = 1.79e-09 (Chi-square test), Q value = 7.9e-07

Table S340.  Gene #37: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 9(6P25.3) MUTATED 34 75 21 56 13
DEL PEAK 9(6P25.3) WILD-TYPE 343 177 83 196 35

Figure S340.  Get High-res Image Gene #37: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 0.000381 (Chi-square test), Q value = 0.083

Table S341.  Gene #37: 'del_6p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 9(6P25.3) MUTATED 44 8 38 31 69 6
DEL PEAK 9(6P25.3) WILD-TYPE 146 87 219 138 191 42

Figure S341.  Get High-res Image Gene #37: 'del_6p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000859 (Fisher's exact test), Q value = 0.17

Table S342.  Gene #37: 'del_6p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 9(6P25.3) MUTATED 107 65 23
DEL PEAK 9(6P25.3) WILD-TYPE 424 208 187

Figure S342.  Get High-res Image Gene #37: 'del_6p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q15' versus 'MRNA_CNMF'

P value = 4.02e-06 (Chi-square test), Q value = 0.0012

Table S343.  Gene #38: 'del_6q15' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 10(6Q15) MUTATED 6 13 63 20 24 29 4 16
DEL PEAK 10(6Q15) WILD-TYPE 15 23 56 76 85 43 16 24

Figure S343.  Get High-res Image Gene #38: 'del_6q15' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_6q15' versus 'CN_CNMF'

P value = 9.92e-36 (Chi-square test), Q value = 7.7e-33

Table S344.  Gene #38: 'del_6q15' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 10(6Q15) MUTATED 73 156 35 45 29
DEL PEAK 10(6Q15) WILD-TYPE 304 96 69 207 19

Figure S344.  Get High-res Image Gene #38: 'del_6q15' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q15' versus 'METHLYATION_CNMF'

P value = 3.8e-10 (Chi-square test), Q value = 1.7e-07

Table S345.  Gene #38: 'del_6q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 10(6Q15) MUTATED 20 61 36 71 11 24
DEL PEAK 10(6Q15) WILD-TYPE 104 115 68 64 45 92

Figure S345.  Get High-res Image Gene #38: 'del_6q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q15' versus 'MRNASEQ_CNMF'

P value = 1.2e-14 (Chi-square test), Q value = 7e-12

Table S346.  Gene #38: 'del_6q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 10(6Q15) MUTATED 32 25 68 58 136 13
DEL PEAK 10(6Q15) WILD-TYPE 158 70 189 111 124 35

Figure S346.  Get High-res Image Gene #38: 'del_6q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.93e-08 (Fisher's exact test), Q value = 1.2e-05

Table S347.  Gene #38: 'del_6q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 10(6Q15) MUTATED 100 181 51
DEL PEAK 10(6Q15) WILD-TYPE 239 252 196

Figure S347.  Get High-res Image Gene #38: 'del_6q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.46e-06 (Fisher's exact test), Q value = 8e-04

Table S348.  Gene #38: 'del_6q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 10(6Q15) MUTATED 212 63 60
DEL PEAK 10(6Q15) WILD-TYPE 319 210 150

Figure S348.  Get High-res Image Gene #38: 'del_6q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q15' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000715 (Fisher's exact test), Q value = 0.14

Table S349.  Gene #38: 'del_6q15' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
DEL PEAK 10(6Q15) MUTATED 35 135 58
DEL PEAK 10(6Q15) WILD-TYPE 130 223 123

Figure S349.  Get High-res Image Gene #38: 'del_6q15' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q27' versus 'CN_CNMF'

P value = 5.26e-16 (Chi-square test), Q value = 3.2e-13

Table S350.  Gene #39: 'del_6q27' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 11(6Q27) MUTATED 82 133 34 79 28
DEL PEAK 11(6Q27) WILD-TYPE 295 119 70 173 20

Figure S350.  Get High-res Image Gene #39: 'del_6q27' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q27' versus 'MRNASEQ_CNMF'

P value = 5.15e-05 (Chi-square test), Q value = 0.013

Table S351.  Gene #39: 'del_6q27' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 11(6Q27) MUTATED 64 28 63 64 117 13
DEL PEAK 11(6Q27) WILD-TYPE 126 67 194 105 143 35

Figure S351.  Get High-res Image Gene #39: 'del_6q27' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7p22.3' versus 'MRNA_CNMF'

P value = 0.000111 (Chi-square test), Q value = 0.026

Table S352.  Gene #40: 'del_7p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 12(7P22.3) MUTATED 4 3 24 25 2 12 2 4
DEL PEAK 12(7P22.3) WILD-TYPE 17 33 95 71 107 60 18 36

Figure S352.  Get High-res Image Gene #40: 'del_7p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_7p22.3' versus 'MRNA_CHIERARCHICAL'

P value = 2.05e-05 (Fisher's exact test), Q value = 0.0056

Table S353.  Gene #40: 'del_7p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 12(7P22.3) MUTATED 5 30 41
DEL PEAK 12(7P22.3) WILD-TYPE 117 95 225

Figure S353.  Get High-res Image Gene #40: 'del_7p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_7p22.3' versus 'CN_CNMF'

P value = 7.01e-20 (Chi-square test), Q value = 4.7e-17

Table S354.  Gene #40: 'del_7p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 12(7P22.3) MUTATED 11 53 3 64 2
DEL PEAK 12(7P22.3) WILD-TYPE 366 199 101 188 46

Figure S354.  Get High-res Image Gene #40: 'del_7p22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_7p22.3' versus 'METHLYATION_CNMF'

P value = 1.97e-06 (Chi-square test), Q value = 0.00065

Table S355.  Gene #40: 'del_7p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 12(7P22.3) MUTATED 29 10 14 17 2 5
DEL PEAK 12(7P22.3) WILD-TYPE 95 166 90 118 54 111

Figure S355.  Get High-res Image Gene #40: 'del_7p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_7p22.3' versus 'MRNASEQ_CNMF'

P value = 1.33e-10 (Chi-square test), Q value = 6.4e-08

Table S356.  Gene #40: 'del_7p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 12(7P22.3) MUTATED 49 3 13 29 34 3
DEL PEAK 12(7P22.3) WILD-TYPE 141 92 244 140 226 45

Figure S356.  Get High-res Image Gene #40: 'del_7p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7p22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.36e-11 (Fisher's exact test), Q value = 6.9e-09

Table S357.  Gene #40: 'del_7p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 12(7P22.3) MUTATED 13 63 55
DEL PEAK 12(7P22.3) WILD-TYPE 326 370 192

Figure S357.  Get High-res Image Gene #40: 'del_7p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7p22.3' versus 'MIRSEQ_CNMF'

P value = 3.89e-10 (Chi-square test), Q value = 1.8e-07

Table S358.  Gene #40: 'del_7p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 12(7P22.3) MUTATED 20 4 17 59 25 4
DEL PEAK 12(7P22.3) WILD-TYPE 174 166 210 192 115 28

Figure S358.  Get High-res Image Gene #40: 'del_7p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_7p22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.55e-11 (Fisher's exact test), Q value = 7.8e-09

Table S359.  Gene #40: 'del_7p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 12(7P22.3) MUTATED 59 64 6
DEL PEAK 12(7P22.3) WILD-TYPE 472 209 204

Figure S359.  Get High-res Image Gene #40: 'del_7p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7p22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.68e-08 (Fisher's exact test), Q value = 6.9e-06

Table S360.  Gene #40: 'del_7p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
DEL PEAK 12(7P22.3) MUTATED 22 9 46
DEL PEAK 12(7P22.3) WILD-TYPE 226 229 172

Figure S360.  Get High-res Image Gene #40: 'del_7p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.8e-07 (Fisher's exact test), Q value = 0.00017

Table S361.  Gene #40: 'del_7p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
DEL PEAK 12(7P22.3) MUTATED 37 32 8
DEL PEAK 12(7P22.3) WILD-TYPE 128 326 173

Figure S361.  Get High-res Image Gene #40: 'del_7p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q36.1' versus 'CN_CNMF'

P value = 6.9e-11 (Chi-square test), Q value = 3.4e-08

Table S362.  Gene #41: 'del_7q36.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 13(7Q36.1) MUTATED 35 67 13 73 6
DEL PEAK 13(7Q36.1) WILD-TYPE 342 185 91 179 42

Figure S362.  Get High-res Image Gene #41: 'del_7q36.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_7q36.1' versus 'MRNASEQ_CNMF'

P value = 5.79e-07 (Chi-square test), Q value = 2e-04

Table S363.  Gene #41: 'del_7q36.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 13(7Q36.1) MUTATED 46 10 28 53 49 6
DEL PEAK 13(7Q36.1) WILD-TYPE 144 85 229 116 211 42

Figure S363.  Get High-res Image Gene #41: 'del_7q36.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7q36.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.31e-05 (Fisher's exact test), Q value = 0.0037

Table S364.  Gene #41: 'del_7q36.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 13(7Q36.1) MUTATED 37 97 58
DEL PEAK 13(7Q36.1) WILD-TYPE 302 336 189

Figure S364.  Get High-res Image Gene #41: 'del_7q36.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7q36.1' versus 'MIRSEQ_CNMF'

P value = 4.51e-06 (Chi-square test), Q value = 0.0014

Table S365.  Gene #41: 'del_7q36.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 13(7Q36.1) MUTATED 40 17 26 69 33 4
DEL PEAK 13(7Q36.1) WILD-TYPE 154 153 201 182 107 28

Figure S365.  Get High-res Image Gene #41: 'del_7q36.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_7q36.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.08e-07 (Fisher's exact test), Q value = 4.2e-05

Table S366.  Gene #41: 'del_7q36.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 13(7Q36.1) MUTATED 96 76 17
DEL PEAK 13(7Q36.1) WILD-TYPE 435 197 193

Figure S366.  Get High-res Image Gene #41: 'del_7q36.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7q36.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.1e-07 (Fisher's exact test), Q value = 0.00018

Table S367.  Gene #41: 'del_7q36.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
DEL PEAK 13(7Q36.1) MUTATED 46 21 61
DEL PEAK 13(7Q36.1) WILD-TYPE 202 217 157

Figure S367.  Get High-res Image Gene #41: 'del_7q36.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7q36.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.15e-06 (Fisher's exact test), Q value = 0.00099

Table S368.  Gene #41: 'del_7q36.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
DEL PEAK 13(7Q36.1) MUTATED 46 68 14
DEL PEAK 13(7Q36.1) WILD-TYPE 119 290 167

Figure S368.  Get High-res Image Gene #41: 'del_7q36.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'MRNA_CNMF'

P value = 2.66e-09 (Chi-square test), Q value = 1.2e-06

Table S369.  Gene #42: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 14(8P23.2) MUTATED 12 15 78 64 29 47 13 18
DEL PEAK 14(8P23.2) WILD-TYPE 9 21 41 32 80 25 7 22

Figure S369.  Get High-res Image Gene #42: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p23.2' versus 'MRNA_CHIERARCHICAL'

P value = 1.9e-05 (Fisher's exact test), Q value = 0.0052

Table S370.  Gene #42: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 14(8P23.2) MUTATED 47 85 144
DEL PEAK 14(8P23.2) WILD-TYPE 75 40 122

Figure S370.  Get High-res Image Gene #42: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 1.43e-36 (Chi-square test), Q value = 1.1e-33

Table S371.  Gene #42: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 14(8P23.2) MUTATED 119 175 25 177 38
DEL PEAK 14(8P23.2) WILD-TYPE 258 77 79 75 10

Figure S371.  Get High-res Image Gene #42: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 6.49e-11 (Chi-square test), Q value = 3.2e-08

Table S372.  Gene #42: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 14(8P23.2) MUTATED 82 55 53 89 21 51
DEL PEAK 14(8P23.2) WILD-TYPE 42 121 51 46 35 65

Figure S372.  Get High-res Image Gene #42: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 2.58e-20 (Chi-square test), Q value = 1.8e-17

Table S373.  Gene #42: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 14(8P23.2) MUTATED 120 37 74 118 157 21
DEL PEAK 14(8P23.2) WILD-TYPE 70 58 183 51 103 27

Figure S373.  Get High-res Image Gene #42: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.52e-13 (Fisher's exact test), Q value = 8.5e-11

Table S374.  Gene #42: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 14(8P23.2) MUTATED 121 243 163
DEL PEAK 14(8P23.2) WILD-TYPE 218 190 84

Figure S374.  Get High-res Image Gene #42: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 3.36e-12 (Chi-square test), Q value = 1.8e-09

Table S375.  Gene #42: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 14(8P23.2) MUTATED 95 57 97 164 94 15
DEL PEAK 14(8P23.2) WILD-TYPE 99 113 130 87 46 17

Figure S375.  Get High-res Image Gene #42: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.28e-10 (Fisher's exact test), Q value = 1.5e-07

Table S376.  Gene #42: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 14(8P23.2) MUTATED 264 181 77
DEL PEAK 14(8P23.2) WILD-TYPE 267 92 133

Figure S376.  Get High-res Image Gene #42: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.76e-09 (Fisher's exact test), Q value = 1.6e-06

Table S377.  Gene #42: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
DEL PEAK 14(8P23.2) MUTATED 125 87 143
DEL PEAK 14(8P23.2) WILD-TYPE 123 151 75

Figure S377.  Get High-res Image Gene #42: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.74e-07 (Fisher's exact test), Q value = 0.00033

Table S378.  Gene #42: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
DEL PEAK 14(8P23.2) MUTATED 112 167 76
DEL PEAK 14(8P23.2) WILD-TYPE 53 191 105

Figure S378.  Get High-res Image Gene #42: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p11.21' versus 'MRNA_CNMF'

P value = 0.000172 (Chi-square test), Q value = 0.039

Table S379.  Gene #43: 'del_8p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 15(8P11.21) MUTATED 4 4 23 23 9 27 7 7
DEL PEAK 15(8P11.21) WILD-TYPE 17 32 96 73 100 45 13 33

Figure S379.  Get High-res Image Gene #43: 'del_8p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p11.21' versus 'CN_CNMF'

P value = 1e-11 (Chi-square test), Q value = 5.1e-09

Table S380.  Gene #43: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 15(8P11.21) MUTATED 42 59 14 81 1
DEL PEAK 15(8P11.21) WILD-TYPE 335 193 90 171 47

Figure S380.  Get High-res Image Gene #43: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p11.21' versus 'MRNASEQ_CNMF'

P value = 1.43e-10 (Chi-square test), Q value = 6.9e-08

Table S381.  Gene #43: 'del_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 15(8P11.21) MUTATED 40 12 31 65 39 9
DEL PEAK 15(8P11.21) WILD-TYPE 150 83 226 104 221 39

Figure S381.  Get High-res Image Gene #43: 'del_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.12

Table S382.  Gene #43: 'del_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 15(8P11.21) MUTATED 46 85 65
DEL PEAK 15(8P11.21) WILD-TYPE 293 348 182

Figure S382.  Get High-res Image Gene #43: 'del_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.03e-07 (Fisher's exact test), Q value = 0.00011

Table S383.  Gene #43: 'del_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 15(8P11.21) MUTATED 101 76 18
DEL PEAK 15(8P11.21) WILD-TYPE 430 197 192

Figure S383.  Get High-res Image Gene #43: 'del_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.46e-06 (Fisher's exact test), Q value = 8e-04

Table S384.  Gene #43: 'del_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
DEL PEAK 15(8P11.21) MUTATED 58 23 58
DEL PEAK 15(8P11.21) WILD-TYPE 190 215 160

Figure S384.  Get High-res Image Gene #43: 'del_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000693 (Fisher's exact test), Q value = 0.14

Table S385.  Gene #43: 'del_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
DEL PEAK 15(8P11.21) MUTATED 47 70 22
DEL PEAK 15(8P11.21) WILD-TYPE 118 288 159

Figure S385.  Get High-res Image Gene #43: 'del_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'MRNA_CNMF'

P value = 2.37e-07 (Chi-square test), Q value = 8.7e-05

Table S386.  Gene #44: 'del_9p23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 16(9P23) MUTATED 9 15 57 21 22 34 10 5
DEL PEAK 16(9P23) WILD-TYPE 12 21 62 75 87 38 10 35

Figure S386.  Get High-res Image Gene #44: 'del_9p23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p23' versus 'MRNA_CHIERARCHICAL'

P value = 7.54e-06 (Fisher's exact test), Q value = 0.0022

Table S387.  Gene #44: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 16(9P23) MUTATED 25 33 115
DEL PEAK 16(9P23) WILD-TYPE 97 92 151

Figure S387.  Get High-res Image Gene #44: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1.37e-46 (Chi-square test), Q value = 1.1e-43

Table S388.  Gene #44: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 16(9P23) MUTATED 39 162 17 87 11
DEL PEAK 16(9P23) WILD-TYPE 338 90 87 165 37

Figure S388.  Get High-res Image Gene #44: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 1.57e-20 (Chi-square test), Q value = 1.1e-17

Table S389.  Gene #44: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 16(9P23) MUTATED 33 21 45 78 11 18
DEL PEAK 16(9P23) WILD-TYPE 91 155 59 57 45 98

Figure S389.  Get High-res Image Gene #44: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 2.4e-19 (Chi-square test), Q value = 1.6e-16

Table S390.  Gene #44: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 16(9P23) MUTATED 40 20 39 80 121 10
DEL PEAK 16(9P23) WILD-TYPE 150 75 218 89 139 38

Figure S390.  Get High-res Image Gene #44: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.58e-11 (Fisher's exact test), Q value = 7.9e-09

Table S391.  Gene #44: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 16(9P23) MUTATED 63 180 67
DEL PEAK 16(9P23) WILD-TYPE 276 253 180

Figure S391.  Get High-res Image Gene #44: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 6.24e-10 (Chi-square test), Q value = 2.8e-07

Table S392.  Gene #44: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 16(9P23) MUTATED 64 22 58 90 67 8
DEL PEAK 16(9P23) WILD-TYPE 130 148 169 161 73 24

Figure S392.  Get High-res Image Gene #44: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.2e-08 (Fisher's exact test), Q value = 5e-06

Table S393.  Gene #44: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 16(9P23) MUTATED 188 91 30
DEL PEAK 16(9P23) WILD-TYPE 343 182 180

Figure S393.  Get High-res Image Gene #44: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.45e-06 (Fisher's exact test), Q value = 0.00049

Table S394.  Gene #44: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
DEL PEAK 16(9P23) MUTATED 82 40 80
DEL PEAK 16(9P23) WILD-TYPE 166 198 138

Figure S394.  Get High-res Image Gene #44: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00106 (Fisher's exact test), Q value = 0.21

Table S395.  Gene #44: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
DEL PEAK 16(9P23) MUTATED 54 115 33
DEL PEAK 16(9P23) WILD-TYPE 111 243 148

Figure S395.  Get High-res Image Gene #44: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'MRNA_CNMF'

P value = 2.15e-06 (Chi-square test), Q value = 7e-04

Table S396.  Gene #45: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 17(9P21.3) MUTATED 9 12 62 33 24 38 8 6
DEL PEAK 17(9P21.3) WILD-TYPE 12 24 57 63 85 34 12 34

Figure S396.  Get High-res Image Gene #45: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p21.3' versus 'MRNA_CHIERARCHICAL'

P value = 2.64e-05 (Fisher's exact test), Q value = 0.0071

Table S397.  Gene #45: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 17(9P21.3) MUTATED 26 46 120
DEL PEAK 17(9P21.3) WILD-TYPE 96 79 146

Figure S397.  Get High-res Image Gene #45: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 8.78e-45 (Chi-square test), Q value = 7e-42

Table S398.  Gene #45: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 17(9P21.3) MUTATED 45 164 21 112 12
DEL PEAK 17(9P21.3) WILD-TYPE 332 88 83 140 36

Figure S398.  Get High-res Image Gene #45: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1.12e-16 (Chi-square test), Q value = 7e-14

Table S399.  Gene #45: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 17(9P21.3) MUTATED 48 26 44 76 10 21
DEL PEAK 17(9P21.3) WILD-TYPE 76 150 60 59 46 95

Figure S399.  Get High-res Image Gene #45: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1.17e-17 (Chi-square test), Q value = 7.5e-15

Table S400.  Gene #45: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 17(9P21.3) MUTATED 65 20 44 82 128 8
DEL PEAK 17(9P21.3) WILD-TYPE 125 75 213 87 132 40

Figure S400.  Get High-res Image Gene #45: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.48e-14 (Fisher's exact test), Q value = 2.5e-11

Table S401.  Gene #45: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 17(9P21.3) MUTATED 62 190 95
DEL PEAK 17(9P21.3) WILD-TYPE 277 243 152

Figure S401.  Get High-res Image Gene #45: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 3.11e-10 (Chi-square test), Q value = 1.4e-07

Table S402.  Gene #45: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 17(9P21.3) MUTATED 69 25 64 112 64 10
DEL PEAK 17(9P21.3) WILD-TYPE 125 145 163 139 76 22

Figure S402.  Get High-res Image Gene #45: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.56e-11 (Fisher's exact test), Q value = 7.9e-09

Table S403.  Gene #45: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 17(9P21.3) MUTATED 198 115 31
DEL PEAK 17(9P21.3) WILD-TYPE 333 158 179

Figure S403.  Get High-res Image Gene #45: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.45e-09 (Fisher's exact test), Q value = 2.3e-06

Table S404.  Gene #45: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
DEL PEAK 17(9P21.3) MUTATED 88 42 94
DEL PEAK 17(9P21.3) WILD-TYPE 160 196 124

Figure S404.  Get High-res Image Gene #45: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.35e-07 (Fisher's exact test), Q value = 0.00012

Table S405.  Gene #45: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
DEL PEAK 17(9P21.3) MUTATED 71 122 31
DEL PEAK 17(9P21.3) WILD-TYPE 94 236 150

Figure S405.  Get High-res Image Gene #45: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q21.11' versus 'MRNA_CHIERARCHICAL'

P value = 6.43e-06 (Fisher's exact test), Q value = 0.0019

Table S406.  Gene #46: 'del_9q21.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 18(9Q21.11) MUTATED 17 49 91
DEL PEAK 18(9Q21.11) WILD-TYPE 105 76 175

Figure S406.  Get High-res Image Gene #46: 'del_9q21.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9q21.11' versus 'CN_CNMF'

P value = 5.83e-27 (Chi-square test), Q value = 4.3e-24

Table S407.  Gene #46: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 18(9Q21.11) MUTATED 35 113 21 106 13
DEL PEAK 18(9Q21.11) WILD-TYPE 342 139 83 146 35

Figure S407.  Get High-res Image Gene #46: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q21.11' versus 'METHLYATION_CNMF'

P value = 1.73e-13 (Chi-square test), Q value = 9.6e-11

Table S408.  Gene #46: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 18(9Q21.11) MUTATED 52 19 25 60 7 23
DEL PEAK 18(9Q21.11) WILD-TYPE 72 157 79 75 49 93

Figure S408.  Get High-res Image Gene #46: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q21.11' versus 'RPPA_CNMF'

P value = 2.87e-06 (Fisher's exact test), Q value = 0.00091

Table S409.  Gene #46: 'del_9q21.11' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 18(9Q21.11) MUTATED 68 34 22
DEL PEAK 18(9Q21.11) WILD-TYPE 79 99 95

Figure S409.  Get High-res Image Gene #46: 'del_9q21.11' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9q21.11' versus 'MRNASEQ_CNMF'

P value = 6.93e-11 (Chi-square test), Q value = 3.4e-08

Table S410.  Gene #46: 'del_9q21.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 18(9Q21.11) MUTATED 74 12 40 53 97 9
DEL PEAK 18(9Q21.11) WILD-TYPE 116 83 217 116 163 39

Figure S410.  Get High-res Image Gene #46: 'del_9q21.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9q21.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.28e-12 (Fisher's exact test), Q value = 1.2e-09

Table S411.  Gene #46: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 18(9Q21.11) MUTATED 48 143 94
DEL PEAK 18(9Q21.11) WILD-TYPE 291 290 153

Figure S411.  Get High-res Image Gene #46: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_CNMF'

P value = 3.4e-14 (Chi-square test), Q value = 2e-11

Table S412.  Gene #46: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 18(9Q21.11) MUTATED 48 20 46 113 49 5
DEL PEAK 18(9Q21.11) WILD-TYPE 146 150 181 138 91 27

Figure S412.  Get High-res Image Gene #46: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9q21.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.99e-15 (Fisher's exact test), Q value = 1.8e-12

Table S413.  Gene #46: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 18(9Q21.11) MUTATED 139 119 23
DEL PEAK 18(9Q21.11) WILD-TYPE 392 154 187

Figure S413.  Get High-res Image Gene #46: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.89e-10 (Fisher's exact test), Q value = 3.1e-07

Table S414.  Gene #46: 'del_9q21.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
DEL PEAK 18(9Q21.11) MUTATED 59 36 91
DEL PEAK 18(9Q21.11) WILD-TYPE 189 202 127

Figure S414.  Get High-res Image Gene #46: 'del_9q21.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9q21.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.31e-10 (Fisher's exact test), Q value = 3.3e-07

Table S415.  Gene #46: 'del_9q21.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
DEL PEAK 18(9Q21.11) MUTATED 74 86 26
DEL PEAK 18(9Q21.11) WILD-TYPE 91 272 155

Figure S415.  Get High-res Image Gene #46: 'del_9q21.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q34.2' versus 'MRNA_CNMF'

P value = 3.61e-09 (Chi-square test), Q value = 1.6e-06

Table S416.  Gene #47: 'del_9q34.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 19(9Q34.2) MUTATED 6 4 40 55 23 18 7 4
DEL PEAK 19(9Q34.2) WILD-TYPE 15 32 79 41 86 54 13 36

Figure S416.  Get High-res Image Gene #47: 'del_9q34.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9q34.2' versus 'MRNA_CHIERARCHICAL'

P value = 1.75e-09 (Fisher's exact test), Q value = 7.7e-07

Table S417.  Gene #47: 'del_9q34.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 19(9Q34.2) MUTATED 15 61 81
DEL PEAK 19(9Q34.2) WILD-TYPE 107 64 185

Figure S417.  Get High-res Image Gene #47: 'del_9q34.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9q34.2' versus 'CN_CNMF'

P value = 1.2e-42 (Chi-square test), Q value = 9.5e-40

Table S418.  Gene #47: 'del_9q34.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 19(9Q34.2) MUTATED 24 101 16 138 13
DEL PEAK 19(9Q34.2) WILD-TYPE 353 151 88 114 35

Figure S418.  Get High-res Image Gene #47: 'del_9q34.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q34.2' versus 'METHLYATION_CNMF'

P value = 6.39e-21 (Chi-square test), Q value = 4.4e-18

Table S419.  Gene #47: 'del_9q34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 19(9Q34.2) MUTATED 71 18 27 48 6 18
DEL PEAK 19(9Q34.2) WILD-TYPE 53 158 77 87 50 98

Figure S419.  Get High-res Image Gene #47: 'del_9q34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q34.2' versus 'RPPA_CNMF'

P value = 1.09e-06 (Fisher's exact test), Q value = 0.00037

Table S420.  Gene #47: 'del_9q34.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 19(9Q34.2) MUTATED 68 33 21
DEL PEAK 19(9Q34.2) WILD-TYPE 79 100 96

Figure S420.  Get High-res Image Gene #47: 'del_9q34.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9q34.2' versus 'RPPA_CHIERARCHICAL'

P value = 9.56e-05 (Fisher's exact test), Q value = 0.023

Table S421.  Gene #47: 'del_9q34.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 19(9Q34.2) MUTATED 45 21 56
DEL PEAK 19(9Q34.2) WILD-TYPE 116 89 70

Figure S421.  Get High-res Image Gene #47: 'del_9q34.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9q34.2' versus 'MRNASEQ_CNMF'

P value = 1.07e-26 (Chi-square test), Q value = 8e-24

Table S422.  Gene #47: 'del_9q34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 19(9Q34.2) MUTATED 107 6 37 41 90 7
DEL PEAK 19(9Q34.2) WILD-TYPE 83 89 220 128 170 41

Figure S422.  Get High-res Image Gene #47: 'del_9q34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9q34.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.34e-19 (Fisher's exact test), Q value = 9e-17

Table S423.  Gene #47: 'del_9q34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 19(9Q34.2) MUTATED 46 122 120
DEL PEAK 19(9Q34.2) WILD-TYPE 293 311 127

Figure S423.  Get High-res Image Gene #47: 'del_9q34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q34.2' versus 'MIRSEQ_CNMF'

P value = 8.45e-23 (Chi-square test), Q value = 6e-20

Table S424.  Gene #47: 'del_9q34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 19(9Q34.2) MUTATED 44 15 45 129 45 5
DEL PEAK 19(9Q34.2) WILD-TYPE 150 155 182 122 95 27

Figure S424.  Get High-res Image Gene #47: 'del_9q34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9q34.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.29e-24 (Fisher's exact test), Q value = 9.4e-22

Table S425.  Gene #47: 'del_9q34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 19(9Q34.2) MUTATED 129 136 18
DEL PEAK 19(9Q34.2) WILD-TYPE 402 137 192

Figure S425.  Get High-res Image Gene #47: 'del_9q34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q34.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.94e-19 (Fisher's exact test), Q value = 1.3e-16

Table S426.  Gene #47: 'del_9q34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
DEL PEAK 19(9Q34.2) MUTATED 51 30 109
DEL PEAK 19(9Q34.2) WILD-TYPE 197 208 109

Figure S426.  Get High-res Image Gene #47: 'del_9q34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9q34.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.29e-19 (Fisher's exact test), Q value = 8.7e-17

Table S427.  Gene #47: 'del_9q34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
DEL PEAK 19(9Q34.2) MUTATED 91 77 22
DEL PEAK 19(9Q34.2) WILD-TYPE 74 281 159

Figure S427.  Get High-res Image Gene #47: 'del_9q34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'MRNA_CNMF'

P value = 8.49e-07 (Chi-square test), Q value = 0.00029

Table S428.  Gene #48: 'del_10q23.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 20(10Q23.31) MUTATED 7 6 36 49 20 21 7 3
DEL PEAK 20(10Q23.31) WILD-TYPE 14 30 83 47 89 51 13 37

Figure S428.  Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q23.31' versus 'MRNA_CHIERARCHICAL'

P value = 4.49e-06 (Fisher's exact test), Q value = 0.0014

Table S429.  Gene #48: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 20(10Q23.31) MUTATED 20 56 73
DEL PEAK 20(10Q23.31) WILD-TYPE 102 69 193

Figure S429.  Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 6.69e-24 (Chi-square test), Q value = 4.8e-21

Table S430.  Gene #48: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 20(10Q23.31) MUTATED 49 84 28 132 18
DEL PEAK 20(10Q23.31) WILD-TYPE 328 168 76 120 30

Figure S430.  Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 2.39e-15 (Chi-square test), Q value = 1.4e-12

Table S431.  Gene #48: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 20(10Q23.31) MUTATED 74 28 32 52 12 24
DEL PEAK 20(10Q23.31) WILD-TYPE 50 148 72 83 44 92

Figure S431.  Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CNMF'

P value = 1.98e-07 (Fisher's exact test), Q value = 7.3e-05

Table S432.  Gene #48: 'del_10q23.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 20(10Q23.31) MUTATED 68 30 20
DEL PEAK 20(10Q23.31) WILD-TYPE 79 103 97

Figure S432.  Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_10q23.31' versus 'RPPA_CHIERARCHICAL'

P value = 4.1e-05 (Fisher's exact test), Q value = 0.011

Table S433.  Gene #48: 'del_10q23.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 20(10Q23.31) MUTATED 44 19 55
DEL PEAK 20(10Q23.31) WILD-TYPE 117 91 71

Figure S433.  Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 6.08e-17 (Chi-square test), Q value = 3.8e-14

Table S434.  Gene #48: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 20(10Q23.31) MUTATED 97 17 39 63 82 6
DEL PEAK 20(10Q23.31) WILD-TYPE 93 78 218 106 178 42

Figure S434.  Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-14 (Fisher's exact test), Q value = 2.3e-11

Table S435.  Gene #48: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 20(10Q23.31) MUTATED 61 124 119
DEL PEAK 20(10Q23.31) WILD-TYPE 278 309 128

Figure S435.  Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 7.05e-12 (Chi-square test), Q value = 3.6e-09

Table S436.  Gene #48: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 20(10Q23.31) MUTATED 51 32 43 118 49 9
DEL PEAK 20(10Q23.31) WILD-TYPE 143 138 184 133 91 23

Figure S436.  Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.05e-15 (Fisher's exact test), Q value = 1.2e-12

Table S437.  Gene #48: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 20(10Q23.31) MUTATED 131 134 37
DEL PEAK 20(10Q23.31) WILD-TYPE 400 139 173

Figure S437.  Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-09 (Fisher's exact test), Q value = 8.8e-07

Table S438.  Gene #48: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
DEL PEAK 20(10Q23.31) MUTATED 59 50 101
DEL PEAK 20(10Q23.31) WILD-TYPE 189 188 117

Figure S438.  Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.42e-08 (Fisher's exact test), Q value = 5.9e-06

Table S439.  Gene #48: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
DEL PEAK 20(10Q23.31) MUTATED 81 87 42
DEL PEAK 20(10Q23.31) WILD-TYPE 84 271 139

Figure S439.  Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q26.3' versus 'MRNA_CNMF'

P value = 1.72e-10 (Chi-square test), Q value = 8.1e-08

Table S440.  Gene #49: 'del_10q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 21(10Q26.3) MUTATED 8 7 38 55 14 22 6 4
DEL PEAK 21(10Q26.3) WILD-TYPE 13 29 81 41 95 50 14 36

Figure S440.  Get High-res Image Gene #49: 'del_10q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q26.3' versus 'MRNA_CHIERARCHICAL'

P value = 2.65e-08 (Fisher's exact test), Q value = 1.1e-05

Table S441.  Gene #49: 'del_10q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 21(10Q26.3) MUTATED 18 61 75
DEL PEAK 21(10Q26.3) WILD-TYPE 104 64 191

Figure S441.  Get High-res Image Gene #49: 'del_10q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q26.3' versus 'CN_CNMF'

P value = 2.01e-28 (Chi-square test), Q value = 1.5e-25

Table S442.  Gene #49: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 21(10Q26.3) MUTATED 44 90 24 136 14
DEL PEAK 21(10Q26.3) WILD-TYPE 333 162 80 116 34

Figure S442.  Get High-res Image Gene #49: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q26.3' versus 'METHLYATION_CNMF'

P value = 6.1e-17 (Chi-square test), Q value = 3.8e-14

Table S443.  Gene #49: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 21(10Q26.3) MUTATED 73 24 37 47 11 21
DEL PEAK 21(10Q26.3) WILD-TYPE 51 152 67 88 45 95

Figure S443.  Get High-res Image Gene #49: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q26.3' versus 'RPPA_CNMF'

P value = 2.63e-08 (Fisher's exact test), Q value = 1.1e-05

Table S444.  Gene #49: 'del_10q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 21(10Q26.3) MUTATED 73 28 24
DEL PEAK 21(10Q26.3) WILD-TYPE 74 105 93

Figure S444.  Get High-res Image Gene #49: 'del_10q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_10q26.3' versus 'RPPA_CHIERARCHICAL'

P value = 1.96e-07 (Fisher's exact test), Q value = 7.3e-05

Table S445.  Gene #49: 'del_10q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 21(10Q26.3) MUTATED 45 18 62
DEL PEAK 21(10Q26.3) WILD-TYPE 116 92 64

Figure S445.  Get High-res Image Gene #49: 'del_10q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 4.19e-24 (Chi-square test), Q value = 3e-21

Table S446.  Gene #49: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 21(10Q26.3) MUTATED 103 17 30 69 80 5
DEL PEAK 21(10Q26.3) WILD-TYPE 87 78 227 100 180 43

Figure S446.  Get High-res Image Gene #49: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.1e-18 (Fisher's exact test), Q value = 1.4e-15

Table S447.  Gene #49: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 21(10Q26.3) MUTATED 52 129 123
DEL PEAK 21(10Q26.3) WILD-TYPE 287 304 124

Figure S447.  Get High-res Image Gene #49: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_CNMF'

P value = 4.7e-16 (Chi-square test), Q value = 2.9e-13

Table S448.  Gene #49: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 21(10Q26.3) MUTATED 53 28 37 122 50 7
DEL PEAK 21(10Q26.3) WILD-TYPE 141 142 190 129 90 25

Figure S448.  Get High-res Image Gene #49: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.78e-19 (Fisher's exact test), Q value = 3.1e-16

Table S449.  Gene #49: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 21(10Q26.3) MUTATED 135 135 27
DEL PEAK 21(10Q26.3) WILD-TYPE 396 138 183

Figure S449.  Get High-res Image Gene #49: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.05e-10 (Fisher's exact test), Q value = 5.1e-08

Table S450.  Gene #49: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
DEL PEAK 21(10Q26.3) MUTATED 66 42 101
DEL PEAK 21(10Q26.3) WILD-TYPE 182 196 117

Figure S450.  Get High-res Image Gene #49: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.13e-12 (Fisher's exact test), Q value = 1.6e-09

Table S451.  Gene #49: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
DEL PEAK 21(10Q26.3) MUTATED 86 91 32
DEL PEAK 21(10Q26.3) WILD-TYPE 79 267 149

Figure S451.  Get High-res Image Gene #49: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'MRNA_CNMF'

P value = 2.94e-08 (Chi-square test), Q value = 1.2e-05

Table S452.  Gene #50: 'del_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 22(11P15.5) MUTATED 3 8 33 48 14 34 7 9
DEL PEAK 22(11P15.5) WILD-TYPE 18 28 86 48 95 38 13 31

Figure S452.  Get High-res Image Gene #50: 'del_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11p15.5' versus 'MRNA_CHIERARCHICAL'

P value = 2.7e-08 (Fisher's exact test), Q value = 1.1e-05

Table S453.  Gene #50: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 22(11P15.5) MUTATED 26 65 65
DEL PEAK 22(11P15.5) WILD-TYPE 96 60 201

Figure S453.  Get High-res Image Gene #50: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 7.15e-41 (Chi-square test), Q value = 5.6e-38

Table S454.  Gene #50: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 22(11P15.5) MUTATED 36 89 19 149 8
DEL PEAK 22(11P15.5) WILD-TYPE 341 163 85 103 40

Figure S454.  Get High-res Image Gene #50: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 1.02e-14 (Chi-square test), Q value = 6e-12

Table S455.  Gene #50: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 22(11P15.5) MUTATED 64 18 34 47 12 20
DEL PEAK 22(11P15.5) WILD-TYPE 60 158 70 88 44 96

Figure S455.  Get High-res Image Gene #50: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11p15.5' versus 'RPPA_CNMF'

P value = 1.9e-09 (Fisher's exact test), Q value = 8.3e-07

Table S456.  Gene #50: 'del_11p15.5' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 22(11P15.5) MUTATED 77 27 26
DEL PEAK 22(11P15.5) WILD-TYPE 70 106 91

Figure S456.  Get High-res Image Gene #50: 'del_11p15.5' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_11p15.5' versus 'RPPA_CHIERARCHICAL'

P value = 1.86e-06 (Fisher's exact test), Q value = 0.00061

Table S457.  Gene #50: 'del_11p15.5' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 22(11P15.5) MUTATED 39 27 64
DEL PEAK 22(11P15.5) WILD-TYPE 122 83 62

Figure S457.  Get High-res Image Gene #50: 'del_11p15.5' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 1.46e-21 (Chi-square test), Q value = 1e-18

Table S458.  Gene #50: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 22(11P15.5) MUTATED 94 14 27 73 77 12
DEL PEAK 22(11P15.5) WILD-TYPE 96 81 230 96 183 36

Figure S458.  Get High-res Image Gene #50: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.91e-16 (Fisher's exact test), Q value = 1.2e-13

Table S459.  Gene #50: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 22(11P15.5) MUTATED 56 120 121
DEL PEAK 22(11P15.5) WILD-TYPE 283 313 126

Figure S459.  Get High-res Image Gene #50: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 3.44e-17 (Chi-square test), Q value = 2.2e-14

Table S460.  Gene #50: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 22(11P15.5) MUTATED 41 23 46 122 53 8
DEL PEAK 22(11P15.5) WILD-TYPE 153 147 181 129 87 24

Figure S460.  Get High-res Image Gene #50: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.67e-16 (Fisher's exact test), Q value = 2.9e-13

Table S461.  Gene #50: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 22(11P15.5) MUTATED 135 129 29
DEL PEAK 22(11P15.5) WILD-TYPE 396 144 181

Figure S461.  Get High-res Image Gene #50: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.83e-14 (Fisher's exact test), Q value = 1.1e-11

Table S462.  Gene #50: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
DEL PEAK 22(11P15.5) MUTATED 53 40 106
DEL PEAK 22(11P15.5) WILD-TYPE 195 198 112

Figure S462.  Get High-res Image Gene #50: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.26e-11 (Fisher's exact test), Q value = 1.1e-08

Table S463.  Gene #50: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
DEL PEAK 22(11P15.5) MUTATED 82 86 31
DEL PEAK 22(11P15.5) WILD-TYPE 83 272 150

Figure S463.  Get High-res Image Gene #50: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q13.1' versus 'CN_CNMF'

P value = 1.09e-12 (Chi-square test), Q value = 5.9e-10

Table S464.  Gene #51: 'del_11q13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 23(11Q13.1) MUTATED 41 94 26 56 12
DEL PEAK 23(11Q13.1) WILD-TYPE 336 158 78 196 36

Figure S464.  Get High-res Image Gene #51: 'del_11q13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q13.1' versus 'METHLYATION_CNMF'

P value = 5.95e-07 (Chi-square test), Q value = 0.00021

Table S465.  Gene #51: 'del_11q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 23(11Q13.1) MUTATED 28 24 34 47 10 12
DEL PEAK 23(11Q13.1) WILD-TYPE 96 152 70 88 46 104

Figure S465.  Get High-res Image Gene #51: 'del_11q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q13.1' versus 'MRNASEQ_CNMF'

P value = 1.38e-11 (Chi-square test), Q value = 7e-09

Table S466.  Gene #51: 'del_11q13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 23(11Q13.1) MUTATED 40 15 30 29 99 11
DEL PEAK 23(11Q13.1) WILD-TYPE 150 80 227 140 161 37

Figure S466.  Get High-res Image Gene #51: 'del_11q13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00107 (Fisher's exact test), Q value = 0.21

Table S467.  Gene #51: 'del_11q13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 23(11Q13.1) MUTATED 57 119 48
DEL PEAK 23(11Q13.1) WILD-TYPE 282 314 199

Figure S467.  Get High-res Image Gene #51: 'del_11q13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.2' versus 'MRNA_CNMF'

P value = 1.25e-07 (Chi-square test), Q value = 4.8e-05

Table S468.  Gene #52: 'del_11q23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 24(11Q23.2) MUTATED 12 21 89 41 36 38 12 22
DEL PEAK 24(11Q23.2) WILD-TYPE 9 15 30 55 73 34 8 18

Figure S468.  Get High-res Image Gene #52: 'del_11q23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11q23.2' versus 'CN_CNMF'

P value = 3.8e-33 (Chi-square test), Q value = 2.9e-30

Table S469.  Gene #52: 'del_11q23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 24(11Q23.2) MUTATED 120 207 44 135 21
DEL PEAK 24(11Q23.2) WILD-TYPE 257 45 60 117 27

Figure S469.  Get High-res Image Gene #52: 'del_11q23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q23.2' versus 'METHLYATION_CNMF'

P value = 1.3e-12 (Chi-square test), Q value = 7e-10

Table S470.  Gene #52: 'del_11q23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 24(11Q23.2) MUTATED 60 67 69 99 26 38
DEL PEAK 24(11Q23.2) WILD-TYPE 64 109 35 36 30 78

Figure S470.  Get High-res Image Gene #52: 'del_11q23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q23.2' versus 'MRNASEQ_CNMF'

P value = 5.38e-18 (Chi-square test), Q value = 3.5e-15

Table S471.  Gene #52: 'del_11q23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 24(11Q23.2) MUTATED 85 42 86 93 191 22
DEL PEAK 24(11Q23.2) WILD-TYPE 105 53 171 76 69 26

Figure S471.  Get High-res Image Gene #52: 'del_11q23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.33e-06 (Fisher's exact test), Q value = 0.001

Table S472.  Gene #52: 'del_11q23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 24(11Q23.2) MUTATED 152 260 107
DEL PEAK 24(11Q23.2) WILD-TYPE 187 173 140

Figure S472.  Get High-res Image Gene #52: 'del_11q23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.2' versus 'MIRSEQ_CNMF'

P value = 0.000152 (Chi-square test), Q value = 0.035

Table S473.  Gene #52: 'del_11q23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 24(11Q23.2) MUTATED 96 65 115 131 92 13
DEL PEAK 24(11Q23.2) WILD-TYPE 98 105 112 120 48 19

Figure S473.  Get High-res Image Gene #52: 'del_11q23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11q23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.46e-05 (Fisher's exact test), Q value = 0.0091

Table S474.  Gene #52: 'del_11q23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 24(11Q23.2) MUTATED 302 127 83
DEL PEAK 24(11Q23.2) WILD-TYPE 229 146 127

Figure S474.  Get High-res Image Gene #52: 'del_11q23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12p13.2' versus 'CN_CNMF'

P value = 0.00064 (Chi-square test), Q value = 0.13

Table S475.  Gene #53: 'del_12p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 25(12P13.2) MUTATED 44 55 16 59 6
DEL PEAK 25(12P13.2) WILD-TYPE 333 197 88 193 42

Figure S475.  Get High-res Image Gene #53: 'del_12p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_12p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000885 (Fisher's exact test), Q value = 0.18

Table S476.  Gene #53: 'del_12p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 25(12P13.2) MUTATED 43 74 61
DEL PEAK 25(12P13.2) WILD-TYPE 296 359 186

Figure S476.  Get High-res Image Gene #53: 'del_12p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.2' versus 'MIRSEQ_CNMF'

P value = 0.00111 (Chi-square test), Q value = 0.22

Table S477.  Gene #53: 'del_12p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 25(12P13.2) MUTATED 34 22 24 57 35 5
DEL PEAK 25(12P13.2) WILD-TYPE 160 148 203 194 105 27

Figure S477.  Get High-res Image Gene #53: 'del_12p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_12p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.84e-05 (Fisher's exact test), Q value = 0.0051

Table S478.  Gene #53: 'del_12p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 25(12P13.2) MUTATED 82 72 23
DEL PEAK 25(12P13.2) WILD-TYPE 449 201 187

Figure S478.  Get High-res Image Gene #53: 'del_12p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q23.1' versus 'MRNA_CNMF'

P value = 8.74e-14 (Chi-square test), Q value = 4.9e-11

Table S479.  Gene #54: 'del_12q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 26(12Q23.1) MUTATED 2 1 14 43 6 23 4 4
DEL PEAK 26(12Q23.1) WILD-TYPE 19 35 105 53 103 49 16 36

Figure S479.  Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12q23.1' versus 'MRNA_CHIERARCHICAL'

P value = 9.86e-13 (Fisher's exact test), Q value = 5.3e-10

Table S480.  Gene #54: 'del_12q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 26(12Q23.1) MUTATED 9 53 35
DEL PEAK 26(12Q23.1) WILD-TYPE 113 72 231

Figure S480.  Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12q23.1' versus 'CN_CNMF'

P value = 1.2e-29 (Chi-square test), Q value = 9.1e-27

Table S481.  Gene #54: 'del_12q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 26(12Q23.1) MUTATED 30 34 17 111 4
DEL PEAK 26(12Q23.1) WILD-TYPE 347 218 87 141 44

Figure S481.  Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q23.1' versus 'METHLYATION_CNMF'

P value = 5.89e-23 (Chi-square test), Q value = 4.2e-20

Table S482.  Gene #54: 'del_12q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 26(12Q23.1) MUTATED 64 11 22 22 5 12
DEL PEAK 26(12Q23.1) WILD-TYPE 60 165 82 113 51 104

Figure S482.  Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12q23.1' versus 'RPPA_CNMF'

P value = 3.98e-07 (Fisher's exact test), Q value = 0.00014

Table S483.  Gene #54: 'del_12q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 26(12Q23.1) MUTATED 49 11 18
DEL PEAK 26(12Q23.1) WILD-TYPE 98 122 99

Figure S483.  Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_12q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 3.66e-08 (Fisher's exact test), Q value = 1.5e-05

Table S484.  Gene #54: 'del_12q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 26(12Q23.1) MUTATED 20 11 47
DEL PEAK 26(12Q23.1) WILD-TYPE 141 99 79

Figure S484.  Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_12q23.1' versus 'MRNASEQ_CNMF'

P value = 4.39e-23 (Chi-square test), Q value = 3.2e-20

Table S485.  Gene #54: 'del_12q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 26(12Q23.1) MUTATED 85 8 23 36 32 8
DEL PEAK 26(12Q23.1) WILD-TYPE 105 87 234 133 228 40

Figure S485.  Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.92e-22 (Fisher's exact test), Q value = 1.4e-19

Table S486.  Gene #54: 'del_12q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 26(12Q23.1) MUTATED 30 60 102
DEL PEAK 26(12Q23.1) WILD-TYPE 309 373 145

Figure S486.  Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q23.1' versus 'MIRSEQ_CNMF'

P value = 2.26e-16 (Chi-square test), Q value = 1.4e-13

Table S487.  Gene #54: 'del_12q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 26(12Q23.1) MUTATED 25 23 15 92 29 8
DEL PEAK 26(12Q23.1) WILD-TYPE 169 147 212 159 111 24

Figure S487.  Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_12q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.27e-18 (Fisher's exact test), Q value = 8.3e-16

Table S488.  Gene #54: 'del_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 26(12Q23.1) MUTATED 72 103 17
DEL PEAK 26(12Q23.1) WILD-TYPE 459 170 193

Figure S488.  Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.7e-13 (Fisher's exact test), Q value = 4.2e-10

Table S489.  Gene #54: 'del_12q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
DEL PEAK 26(12Q23.1) MUTATED 32 28 82
DEL PEAK 26(12Q23.1) WILD-TYPE 216 210 136

Figure S489.  Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_12q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.86e-14 (Fisher's exact test), Q value = 3.3e-11

Table S490.  Gene #54: 'del_12q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
DEL PEAK 26(12Q23.1) MUTATED 70 53 19
DEL PEAK 26(12Q23.1) WILD-TYPE 95 305 162

Figure S490.  Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q24.31' versus 'MRNA_CNMF'

P value = 1.46e-10 (Chi-square test), Q value = 7e-08

Table S491.  Gene #55: 'del_12q24.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 27(12Q24.31) MUTATED 4 6 12 42 6 20 5 6
DEL PEAK 27(12Q24.31) WILD-TYPE 17 30 107 54 103 52 15 34

Figure S491.  Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12q24.31' versus 'MRNA_CHIERARCHICAL'

P value = 1.68e-10 (Fisher's exact test), Q value = 8e-08

Table S492.  Gene #55: 'del_12q24.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 27(12Q24.31) MUTATED 14 52 35
DEL PEAK 27(12Q24.31) WILD-TYPE 108 73 231

Figure S492.  Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12q24.31' versus 'CN_CNMF'

P value = 6.84e-26 (Chi-square test), Q value = 5e-23

Table S493.  Gene #55: 'del_12q24.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 27(12Q24.31) MUTATED 39 31 18 110 5
DEL PEAK 27(12Q24.31) WILD-TYPE 338 221 86 142 43

Figure S493.  Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q24.31' versus 'METHLYATION_CNMF'

P value = 9.27e-21 (Chi-square test), Q value = 6.4e-18

Table S494.  Gene #55: 'del_12q24.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 27(12Q24.31) MUTATED 64 15 22 18 6 15
DEL PEAK 27(12Q24.31) WILD-TYPE 60 161 82 117 50 101

Figure S494.  Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12q24.31' versus 'RPPA_CNMF'

P value = 7.73e-06 (Fisher's exact test), Q value = 0.0022

Table S495.  Gene #55: 'del_12q24.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 27(12Q24.31) MUTATED 48 13 20
DEL PEAK 27(12Q24.31) WILD-TYPE 99 120 97

Figure S495.  Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_12q24.31' versus 'RPPA_CHIERARCHICAL'

P value = 2.47e-07 (Fisher's exact test), Q value = 9.1e-05

Table S496.  Gene #55: 'del_12q24.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 27(12Q24.31) MUTATED 21 13 47
DEL PEAK 27(12Q24.31) WILD-TYPE 140 97 79

Figure S496.  Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_12q24.31' versus 'MRNASEQ_CNMF'

P value = 1.31e-20 (Chi-square test), Q value = 9e-18

Table S497.  Gene #55: 'del_12q24.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 27(12Q24.31) MUTATED 83 15 26 41 27 7
DEL PEAK 27(12Q24.31) WILD-TYPE 107 80 231 128 233 41

Figure S497.  Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q24.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.82e-20 (Fisher's exact test), Q value = 1.2e-17

Table S498.  Gene #55: 'del_12q24.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 27(12Q24.31) MUTATED 41 55 103
DEL PEAK 27(12Q24.31) WILD-TYPE 298 378 144

Figure S498.  Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q24.31' versus 'MIRSEQ_CNMF'

P value = 7.42e-12 (Chi-square test), Q value = 3.8e-09

Table S499.  Gene #55: 'del_12q24.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 27(12Q24.31) MUTATED 31 30 17 88 27 7
DEL PEAK 27(12Q24.31) WILD-TYPE 163 140 210 163 113 25

Figure S499.  Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_12q24.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.36e-15 (Fisher's exact test), Q value = 3.7e-12

Table S500.  Gene #55: 'del_12q24.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 27(12Q24.31) MUTATED 75 101 24
DEL PEAK 27(12Q24.31) WILD-TYPE 456 172 186

Figure S500.  Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q24.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.17e-09 (Fisher's exact test), Q value = 5.2e-07

Table S501.  Gene #55: 'del_12q24.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
DEL PEAK 27(12Q24.31) MUTATED 34 32 77
DEL PEAK 27(12Q24.31) WILD-TYPE 214 206 141

Figure S501.  Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_12q24.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.14e-10 (Fisher's exact test), Q value = 1.5e-07

Table S502.  Gene #55: 'del_12q24.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
DEL PEAK 27(12Q24.31) MUTATED 65 53 25
DEL PEAK 27(12Q24.31) WILD-TYPE 100 305 156

Figure S502.  Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q14.2' versus 'MRNA_CNMF'

P value = 6.78e-06 (Chi-square test), Q value = 0.002

Table S503.  Gene #56: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 28(13Q14.2) MUTATED 8 12 70 60 34 41 9 13
DEL PEAK 28(13Q14.2) WILD-TYPE 13 24 49 36 75 31 11 27

Figure S503.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

P value = 2.41e-06 (Fisher's exact test), Q value = 0.00079

Table S504.  Gene #56: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 28(13Q14.2) MUTATED 38 79 130
DEL PEAK 28(13Q14.2) WILD-TYPE 84 46 136

Figure S504.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 9.2e-32 (Chi-square test), Q value = 7e-29

Table S505.  Gene #56: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 28(13Q14.2) MUTATED 81 161 60 151 28
DEL PEAK 28(13Q14.2) WILD-TYPE 296 91 44 101 20

Figure S505.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 6.86e-09 (Chi-square test), Q value = 2.9e-06

Table S506.  Gene #56: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 28(13Q14.2) MUTATED 79 58 56 75 16 42
DEL PEAK 28(13Q14.2) WILD-TYPE 45 118 48 60 40 74

Figure S506.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 2.45e-14 (Chi-square test), Q value = 1.4e-11

Table S507.  Gene #56: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 28(13Q14.2) MUTATED 119 26 83 92 139 12
DEL PEAK 28(13Q14.2) WILD-TYPE 71 69 174 77 121 36

Figure S507.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.13e-12 (Fisher's exact test), Q value = 6.1e-10

Table S508.  Gene #56: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 28(13Q14.2) MUTATED 105 217 149
DEL PEAK 28(13Q14.2) WILD-TYPE 234 216 98

Figure S508.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 1.72e-10 (Chi-square test), Q value = 8.1e-08

Table S509.  Gene #56: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 28(13Q14.2) MUTATED 87 41 105 149 75 13
DEL PEAK 28(13Q14.2) WILD-TYPE 107 129 122 102 65 19

Figure S509.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.74e-10 (Fisher's exact test), Q value = 8.2e-08

Table S510.  Gene #56: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 28(13Q14.2) MUTATED 252 159 59
DEL PEAK 28(13Q14.2) WILD-TYPE 279 114 151

Figure S510.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.09e-09 (Fisher's exact test), Q value = 2.6e-06

Table S511.  Gene #56: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
DEL PEAK 28(13Q14.2) MUTATED 110 73 129
DEL PEAK 28(13Q14.2) WILD-TYPE 138 165 89

Figure S511.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.5e-07 (Fisher's exact test), Q value = 0.00032

Table S512.  Gene #56: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
DEL PEAK 28(13Q14.2) MUTATED 99 155 58
DEL PEAK 28(13Q14.2) WILD-TYPE 66 203 123

Figure S512.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q24.1' versus 'MRNA_CNMF'

P value = 5.85e-16 (Chi-square test), Q value = 3.6e-13

Table S513.  Gene #57: 'del_14q24.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 29(14Q24.1) MUTATED 4 7 47 63 10 22 10 8
DEL PEAK 29(14Q24.1) WILD-TYPE 17 29 72 33 99 50 10 32

Figure S513.  Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q24.1' versus 'MRNA_CHIERARCHICAL'

P value = 4.83e-10 (Fisher's exact test), Q value = 2.2e-07

Table S514.  Gene #57: 'del_14q24.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 29(14Q24.1) MUTATED 27 72 72
DEL PEAK 29(14Q24.1) WILD-TYPE 95 53 194

Figure S514.  Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q24.1' versus 'CN_CNMF'

P value = 2.05e-44 (Chi-square test), Q value = 1.6e-41

Table S515.  Gene #57: 'del_14q24.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 29(14Q24.1) MUTATED 41 89 24 165 18
DEL PEAK 29(14Q24.1) WILD-TYPE 336 163 80 87 30

Figure S515.  Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q24.1' versus 'METHLYATION_CNMF'

P value = 1.85e-22 (Chi-square test), Q value = 1.3e-19

Table S516.  Gene #57: 'del_14q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 29(14Q24.1) MUTATED 82 23 32 56 11 24
DEL PEAK 29(14Q24.1) WILD-TYPE 42 153 72 79 45 92

Figure S516.  Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q24.1' versus 'RPPA_CNMF'

P value = 3.27e-08 (Fisher's exact test), Q value = 1.3e-05

Table S517.  Gene #57: 'del_14q24.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 29(14Q24.1) MUTATED 77 27 33
DEL PEAK 29(14Q24.1) WILD-TYPE 70 106 84

Figure S517.  Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_14q24.1' versus 'RPPA_CHIERARCHICAL'

P value = 2.82e-07 (Fisher's exact test), Q value = 1e-04

Table S518.  Gene #57: 'del_14q24.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 29(14Q24.1) MUTATED 42 27 68
DEL PEAK 29(14Q24.1) WILD-TYPE 119 83 58

Figure S518.  Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_14q24.1' versus 'MRNASEQ_CNMF'

P value = 2.04e-34 (Chi-square test), Q value = 1.6e-31

Table S519.  Gene #57: 'del_14q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 29(14Q24.1) MUTATED 125 14 32 59 95 6
DEL PEAK 29(14Q24.1) WILD-TYPE 65 81 225 110 165 42

Figure S519.  Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.41e-23 (Fisher's exact test), Q value = 1e-20

Table S520.  Gene #57: 'del_14q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 29(14Q24.1) MUTATED 59 130 142
DEL PEAK 29(14Q24.1) WILD-TYPE 280 303 105

Figure S520.  Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q24.1' versus 'MIRSEQ_CNMF'

P value = 1.06e-22 (Chi-square test), Q value = 7.5e-20

Table S521.  Gene #57: 'del_14q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 29(14Q24.1) MUTATED 46 33 46 144 53 5
DEL PEAK 29(14Q24.1) WILD-TYPE 148 137 181 107 87 27

Figure S521.  Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_14q24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.65e-23 (Fisher's exact test), Q value = 5.4e-20

Table S522.  Gene #57: 'del_14q24.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 29(14Q24.1) MUTATED 143 152 32
DEL PEAK 29(14Q24.1) WILD-TYPE 388 121 178

Figure S522.  Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.96e-20 (Fisher's exact test), Q value = 2e-17

Table S523.  Gene #57: 'del_14q24.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
DEL PEAK 29(14Q24.1) MUTATED 70 39 125
DEL PEAK 29(14Q24.1) WILD-TYPE 178 199 93

Figure S523.  Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_14q24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.25e-16 (Fisher's exact test), Q value = 1.4e-13

Table S524.  Gene #57: 'del_14q24.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
DEL PEAK 29(14Q24.1) MUTATED 99 101 34
DEL PEAK 29(14Q24.1) WILD-TYPE 66 257 147

Figure S524.  Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q13.1' versus 'MRNA_CNMF'

P value = 1.29e-07 (Chi-square test), Q value = 4.9e-05

Table S525.  Gene #58: 'del_15q13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 30(15Q13.1) MUTATED 5 11 41 58 24 34 10 8
DEL PEAK 30(15Q13.1) WILD-TYPE 16 25 78 38 85 38 10 32

Figure S525.  Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q13.1' versus 'MRNA_CHIERARCHICAL'

P value = 4.27e-08 (Fisher's exact test), Q value = 1.7e-05

Table S526.  Gene #58: 'del_15q13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 30(15Q13.1) MUTATED 25 70 96
DEL PEAK 30(15Q13.1) WILD-TYPE 97 55 170

Figure S526.  Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q13.1' versus 'CN_CNMF'

P value = 5.3e-45 (Chi-square test), Q value = 4.2e-42

Table S527.  Gene #58: 'del_15q13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 30(15Q13.1) MUTATED 42 89 46 169 14
DEL PEAK 30(15Q13.1) WILD-TYPE 335 163 58 83 34

Figure S527.  Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q13.1' versus 'METHLYATION_CNMF'

P value = 3.53e-18 (Chi-square test), Q value = 2.3e-15

Table S528.  Gene #58: 'del_15q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 30(15Q13.1) MUTATED 81 28 38 54 13 27
DEL PEAK 30(15Q13.1) WILD-TYPE 43 148 66 81 43 89

Figure S528.  Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q13.1' versus 'RPPA_CNMF'

P value = 9.66e-05 (Fisher's exact test), Q value = 0.024

Table S529.  Gene #58: 'del_15q13.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 30(15Q13.1) MUTATED 78 40 38
DEL PEAK 30(15Q13.1) WILD-TYPE 69 93 79

Figure S529.  Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_15q13.1' versus 'RPPA_CHIERARCHICAL'

P value = 7.54e-06 (Fisher's exact test), Q value = 0.0022

Table S530.  Gene #58: 'del_15q13.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 30(15Q13.1) MUTATED 55 30 71
DEL PEAK 30(15Q13.1) WILD-TYPE 106 80 55

Figure S530.  Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_15q13.1' versus 'MRNASEQ_CNMF'

P value = 5.23e-25 (Chi-square test), Q value = 3.8e-22

Table S531.  Gene #58: 'del_15q13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 30(15Q13.1) MUTATED 122 16 57 78 79 7
DEL PEAK 30(15Q13.1) WILD-TYPE 68 79 200 91 181 41

Figure S531.  Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.39e-20 (Fisher's exact test), Q value = 9.5e-18

Table S532.  Gene #58: 'del_15q13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 30(15Q13.1) MUTATED 67 149 143
DEL PEAK 30(15Q13.1) WILD-TYPE 272 284 104

Figure S532.  Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q13.1' versus 'MIRSEQ_CNMF'

P value = 2.72e-22 (Chi-square test), Q value = 1.9e-19

Table S533.  Gene #58: 'del_15q13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 30(15Q13.1) MUTATED 68 26 49 148 49 11
DEL PEAK 30(15Q13.1) WILD-TYPE 126 144 178 103 91 21

Figure S533.  Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.11e-24 (Fisher's exact test), Q value = 1.5e-21

Table S534.  Gene #58: 'del_15q13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 30(15Q13.1) MUTATED 171 154 26
DEL PEAK 30(15Q13.1) WILD-TYPE 360 119 184

Figure S534.  Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_15q13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.55e-19 (Fisher's exact test), Q value = 1e-16

Table S535.  Gene #58: 'del_15q13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
DEL PEAK 30(15Q13.1) MUTATED 82 37 123
DEL PEAK 30(15Q13.1) WILD-TYPE 166 201 95

Figure S535.  Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.31e-17 (Fisher's exact test), Q value = 2.7e-14

Table S536.  Gene #58: 'del_15q13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
DEL PEAK 30(15Q13.1) MUTATED 100 111 31
DEL PEAK 30(15Q13.1) WILD-TYPE 65 247 150

Figure S536.  Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q24.3' versus 'MRNA_CNMF'

P value = 9.32e-17 (Chi-square test), Q value = 5.8e-14

Table S537.  Gene #59: 'del_16q24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 31(16Q24.3) MUTATED 16 25 81 27 94 45 13 35
DEL PEAK 31(16Q24.3) WILD-TYPE 5 11 38 69 15 27 7 5

Figure S537.  Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_16q24.3' versus 'MRNA_CHIERARCHICAL'

P value = 2.85e-14 (Fisher's exact test), Q value = 1.6e-11

Table S538.  Gene #59: 'del_16q24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 31(16Q24.3) MUTATED 96 45 195
DEL PEAK 31(16Q24.3) WILD-TYPE 26 80 71

Figure S538.  Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_16q24.3' versus 'CN_CNMF'

P value = 1.15e-13 (Chi-square test), Q value = 6.4e-11

Table S539.  Gene #59: 'del_16q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 31(16Q24.3) MUTATED 269 159 85 114 38
DEL PEAK 31(16Q24.3) WILD-TYPE 108 93 19 138 10

Figure S539.  Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q24.3' versus 'METHLYATION_CNMF'

P value = 4.58e-12 (Chi-square test), Q value = 2.4e-09

Table S540.  Gene #59: 'del_16q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 31(16Q24.3) MUTATED 51 142 80 77 32 67
DEL PEAK 31(16Q24.3) WILD-TYPE 73 34 24 58 24 49

Figure S540.  Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q24.3' versus 'RPPA_CNMF'

P value = 1.21e-09 (Fisher's exact test), Q value = 5.4e-07

Table S541.  Gene #59: 'del_16q24.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 31(16Q24.3) MUTATED 63 103 84
DEL PEAK 31(16Q24.3) WILD-TYPE 84 30 33

Figure S541.  Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_16q24.3' versus 'RPPA_CHIERARCHICAL'

P value = 3.55e-11 (Fisher's exact test), Q value = 1.8e-08

Table S542.  Gene #59: 'del_16q24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 31(16Q24.3) MUTATED 119 83 48
DEL PEAK 31(16Q24.3) WILD-TYPE 42 27 78

Figure S542.  Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_16q24.3' versus 'MRNASEQ_CNMF'

P value = 6.73e-32 (Chi-square test), Q value = 5.2e-29

Table S543.  Gene #59: 'del_16q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 31(16Q24.3) MUTATED 62 70 222 94 166 41
DEL PEAK 31(16Q24.3) WILD-TYPE 128 25 35 75 94 7

Figure S543.  Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.16e-26 (Fisher's exact test), Q value = 8.6e-24

Table S544.  Gene #59: 'del_16q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 31(16Q24.3) MUTATED 272 292 91
DEL PEAK 31(16Q24.3) WILD-TYPE 67 141 156

Figure S544.  Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16q24.3' versus 'MIRSEQ_CNMF'

P value = 6.07e-16 (Chi-square test), Q value = 3.7e-13

Table S545.  Gene #59: 'del_16q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 31(16Q24.3) MUTATED 141 119 174 109 82 28
DEL PEAK 31(16Q24.3) WILD-TYPE 53 51 53 142 58 4

Figure S545.  Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.46e-17 (Fisher's exact test), Q value = 5.9e-14

Table S546.  Gene #59: 'del_16q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 31(16Q24.3) MUTATED 374 118 161
DEL PEAK 31(16Q24.3) WILD-TYPE 157 155 49

Figure S546.  Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.08e-11 (Fisher's exact test), Q value = 1e-08

Table S547.  Gene #59: 'del_16q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
DEL PEAK 31(16Q24.3) MUTATED 169 180 98
DEL PEAK 31(16Q24.3) WILD-TYPE 79 58 120

Figure S547.  Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.86e-13 (Fisher's exact test), Q value = 1.6e-10

Table S548.  Gene #59: 'del_16q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
DEL PEAK 31(16Q24.3) MUTATED 66 239 142
DEL PEAK 31(16Q24.3) WILD-TYPE 99 119 39

Figure S548.  Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p12' versus 'MRNA_CNMF'

P value = 1.14e-12 (Chi-square test), Q value = 6.1e-10

Table S549.  Gene #60: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 32(17P12) MUTATED 14 27 78 65 33 62 15 24
DEL PEAK 32(17P12) WILD-TYPE 7 9 41 31 76 10 5 16

Figure S549.  Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p12' versus 'CN_CNMF'

P value = 4.31e-30 (Chi-square test), Q value = 3.3e-27

Table S550.  Gene #60: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 32(17P12) MUTATED 150 200 50 196 26
DEL PEAK 32(17P12) WILD-TYPE 227 52 54 56 22

Figure S550.  Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 1.17e-10 (Chi-square test), Q value = 5.7e-08

Table S551.  Gene #60: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 32(17P12) MUTATED 80 73 72 106 32 56
DEL PEAK 32(17P12) WILD-TYPE 44 103 32 29 24 60

Figure S551.  Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p12' versus 'RPPA_CNMF'

P value = 3.52e-06 (Fisher's exact test), Q value = 0.0011

Table S552.  Gene #60: 'del_17p12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 32(17P12) MUTATED 114 67 66
DEL PEAK 32(17P12) WILD-TYPE 33 66 51

Figure S552.  Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_17p12' versus 'RPPA_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.14

Table S553.  Gene #60: 'del_17p12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 32(17P12) MUTATED 93 59 95
DEL PEAK 32(17P12) WILD-TYPE 68 51 31

Figure S553.  Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 4.35e-21 (Chi-square test), Q value = 3e-18

Table S554.  Gene #60: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 32(17P12) MUTATED 121 54 96 144 171 27
DEL PEAK 32(17P12) WILD-TYPE 69 41 161 25 89 21

Figure S554.  Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.33e-05 (Fisher's exact test), Q value = 0.0063

Table S555.  Gene #60: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 32(17P12) MUTATED 171 274 168
DEL PEAK 32(17P12) WILD-TYPE 168 159 79

Figure S555.  Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_CNMF'

P value = 1.08e-10 (Chi-square test), Q value = 5.2e-08

Table S556.  Gene #60: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 32(17P12) MUTATED 120 79 109 175 109 19
DEL PEAK 32(17P12) WILD-TYPE 74 91 118 76 31 13

Figure S556.  Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.32e-07 (Fisher's exact test), Q value = 0.00032

Table S557.  Gene #60: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 32(17P12) MUTATED 326 189 96
DEL PEAK 32(17P12) WILD-TYPE 205 84 114

Figure S557.  Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.01e-05 (Fisher's exact test), Q value = 0.015

Table S558.  Gene #60: 'del_17p12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
DEL PEAK 32(17P12) MUTATED 146 119 153
DEL PEAK 32(17P12) WILD-TYPE 102 119 65

Figure S558.  Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17q21.31' versus 'MRNA_CNMF'

P value = 5.96e-16 (Chi-square test), Q value = 3.6e-13

Table S559.  Gene #61: 'del_17q21.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 33(17Q21.31) MUTATED 7 17 28 53 13 50 9 15
DEL PEAK 33(17Q21.31) WILD-TYPE 14 19 91 43 96 22 11 25

Figure S559.  Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17q21.31' versus 'MRNA_CHIERARCHICAL'

P value = 4.27e-08 (Fisher's exact test), Q value = 1.7e-05

Table S560.  Gene #61: 'del_17q21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 33(17Q21.31) MUTATED 42 74 76
DEL PEAK 33(17Q21.31) WILD-TYPE 80 51 190

Figure S560.  Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17q21.31' versus 'CN_CNMF'

P value = 6.83e-31 (Chi-square test), Q value = 5.2e-28

Table S561.  Gene #61: 'del_17q21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 33(17Q21.31) MUTATED 76 89 23 163 9
DEL PEAK 33(17Q21.31) WILD-TYPE 301 163 81 89 39

Figure S561.  Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_17q21.31' versus 'METHLYATION_CNMF'

P value = 7.01e-18 (Chi-square test), Q value = 4.5e-15

Table S562.  Gene #61: 'del_17q21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 33(17Q21.31) MUTATED 78 20 37 45 15 35
DEL PEAK 33(17Q21.31) WILD-TYPE 46 156 67 90 41 81

Figure S562.  Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17q21.31' versus 'RPPA_CNMF'

P value = 3.71e-12 (Fisher's exact test), Q value = 1.9e-09

Table S563.  Gene #61: 'del_17q21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 33(17Q21.31) MUTATED 89 25 44
DEL PEAK 33(17Q21.31) WILD-TYPE 58 108 73

Figure S563.  Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_17q21.31' versus 'RPPA_CHIERARCHICAL'

P value = 3.98e-12 (Fisher's exact test), Q value = 2.1e-09

Table S564.  Gene #61: 'del_17q21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 33(17Q21.31) MUTATED 42 33 83
DEL PEAK 33(17Q21.31) WILD-TYPE 119 77 43

Figure S564.  Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_17q21.31' versus 'MRNASEQ_CNMF'

P value = 5.57e-36 (Chi-square test), Q value = 4.3e-33

Table S565.  Gene #61: 'del_17q21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 33(17Q21.31) MUTATED 102 28 39 115 58 14
DEL PEAK 33(17Q21.31) WILD-TYPE 88 67 218 54 202 34

Figure S565.  Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17q21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.26e-18 (Fisher's exact test), Q value = 5.9e-15

Table S566.  Gene #61: 'del_17q21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 33(17Q21.31) MUTATED 89 122 145
DEL PEAK 33(17Q21.31) WILD-TYPE 250 311 102

Figure S566.  Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17q21.31' versus 'MIRSEQ_CNMF'

P value = 1.66e-16 (Chi-square test), Q value = 1e-13

Table S567.  Gene #61: 'del_17q21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 33(17Q21.31) MUTATED 63 38 44 138 55 14
DEL PEAK 33(17Q21.31) WILD-TYPE 131 132 183 113 85 18

Figure S567.  Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17q21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-13 (Fisher's exact test), Q value = 1.7e-10

Table S568.  Gene #61: 'del_17q21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 33(17Q21.31) MUTATED 165 143 44
DEL PEAK 33(17Q21.31) WILD-TYPE 366 130 166

Figure S568.  Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17q21.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.02e-13 (Fisher's exact test), Q value = 5.7e-11

Table S569.  Gene #61: 'del_17q21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
DEL PEAK 33(17Q21.31) MUTATED 78 50 120
DEL PEAK 33(17Q21.31) WILD-TYPE 170 188 98

Figure S569.  Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17q21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.79e-09 (Fisher's exact test), Q value = 3.3e-06

Table S570.  Gene #61: 'del_17q21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
DEL PEAK 33(17Q21.31) MUTATED 90 114 44
DEL PEAK 33(17Q21.31) WILD-TYPE 75 244 137

Figure S570.  Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q23' versus 'MRNA_CNMF'

P value = 0.000145 (Chi-square test), Q value = 0.033

Table S571.  Gene #62: 'del_18q23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 34(18Q23) MUTATED 6 13 38 38 18 37 6 9
DEL PEAK 34(18Q23) WILD-TYPE 15 23 81 58 91 35 14 31

Figure S571.  Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q23' versus 'CN_CNMF'

P value = 3.17e-17 (Chi-square test), Q value = 2e-14

Table S572.  Gene #62: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 34(18Q23) MUTATED 63 106 37 122 12
DEL PEAK 34(18Q23) WILD-TYPE 314 146 67 130 36

Figure S572.  Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q23' versus 'METHLYATION_CNMF'

P value = 6.68e-10 (Chi-square test), Q value = 3e-07

Table S573.  Gene #62: 'del_18q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 34(18Q23) MUTATED 55 33 51 60 14 25
DEL PEAK 34(18Q23) WILD-TYPE 69 143 53 75 42 91

Figure S573.  Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q23' versus 'MRNASEQ_CNMF'

P value = 1.65e-10 (Chi-square test), Q value = 7.9e-08

Table S574.  Gene #62: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 34(18Q23) MUTATED 76 25 52 87 85 10
DEL PEAK 34(18Q23) WILD-TYPE 114 70 205 82 175 38

Figure S574.  Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000286 (Fisher's exact test), Q value = 0.063

Table S575.  Gene #62: 'del_18q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 34(18Q23) MUTATED 86 148 101
DEL PEAK 34(18Q23) WILD-TYPE 253 285 146

Figure S575.  Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_CNMF'

P value = 2.38e-08 (Chi-square test), Q value = 9.7e-06

Table S576.  Gene #62: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 34(18Q23) MUTATED 69 34 55 118 49 11
DEL PEAK 34(18Q23) WILD-TYPE 125 136 172 133 91 21

Figure S576.  Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18q23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.83e-06 (Fisher's exact test), Q value = 9e-04

Table S577.  Gene #62: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 34(18Q23) MUTATED 164 122 50
DEL PEAK 34(18Q23) WILD-TYPE 367 151 160

Figure S577.  Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.21e-07 (Fisher's exact test), Q value = 0.00015

Table S578.  Gene #62: 'del_18q23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
DEL PEAK 34(18Q23) MUTATED 75 52 99
DEL PEAK 34(18Q23) WILD-TYPE 173 186 119

Figure S578.  Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.03

Table S579.  Gene #62: 'del_18q23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
DEL PEAK 34(18Q23) MUTATED 75 105 46
DEL PEAK 34(18Q23) WILD-TYPE 90 253 135

Figure S579.  Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'MRNA_CNMF'

P value = 1.15e-11 (Chi-square test), Q value = 5.9e-09

Table S580.  Gene #63: 'del_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 35(19P13.3) MUTATED 7 10 48 57 13 35 6 6
DEL PEAK 35(19P13.3) WILD-TYPE 14 26 71 39 96 37 14 34

Figure S580.  Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19p13.3' versus 'MRNA_CHIERARCHICAL'

P value = 4.92e-09 (Fisher's exact test), Q value = 2.1e-06

Table S581.  Gene #63: 'del_19p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 35(19P13.3) MUTATED 21 68 93
DEL PEAK 35(19P13.3) WILD-TYPE 101 57 173

Figure S581.  Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 3.35e-55 (Chi-square test), Q value = 2.7e-52

Table S582.  Gene #63: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 35(19P13.3) MUTATED 30 129 13 157 16
DEL PEAK 35(19P13.3) WILD-TYPE 347 123 91 95 32

Figure S582.  Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 6.13e-24 (Chi-square test), Q value = 4.4e-21

Table S583.  Gene #63: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 35(19P13.3) MUTATED 68 14 28 71 8 27
DEL PEAK 35(19P13.3) WILD-TYPE 56 162 76 64 48 89

Figure S583.  Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p13.3' versus 'RPPA_CNMF'

P value = 8.17e-07 (Fisher's exact test), Q value = 0.00028

Table S584.  Gene #63: 'del_19p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 35(19P13.3) MUTATED 80 37 32
DEL PEAK 35(19P13.3) WILD-TYPE 67 96 85

Figure S584.  Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 3.6e-06 (Fisher's exact test), Q value = 0.0011

Table S585.  Gene #63: 'del_19p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 35(19P13.3) MUTATED 47 32 70
DEL PEAK 35(19P13.3) WILD-TYPE 114 78 56

Figure S585.  Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 7.24e-27 (Chi-square test), Q value = 5.4e-24

Table S586.  Gene #63: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 35(19P13.3) MUTATED 109 16 28 77 96 14
DEL PEAK 35(19P13.3) WILD-TYPE 81 79 229 92 164 34

Figure S586.  Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.26e-19 (Fisher's exact test), Q value = 3.5e-16

Table S587.  Gene #63: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 35(19P13.3) MUTATED 56 157 127
DEL PEAK 35(19P13.3) WILD-TYPE 283 276 120

Figure S587.  Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 2.84e-25 (Chi-square test), Q value = 2.1e-22

Table S588.  Gene #63: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 35(19P13.3) MUTATED 46 26 45 139 70 9
DEL PEAK 35(19P13.3) WILD-TYPE 148 144 182 112 70 23

Figure S588.  Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.61e-21 (Fisher's exact test), Q value = 1.8e-18

Table S589.  Gene #63: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 35(19P13.3) MUTATED 156 149 30
DEL PEAK 35(19P13.3) WILD-TYPE 375 124 180

Figure S589.  Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.57e-19 (Fisher's exact test), Q value = 4.3e-16

Table S590.  Gene #63: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
DEL PEAK 35(19P13.3) MUTATED 71 39 122
DEL PEAK 35(19P13.3) WILD-TYPE 177 199 96

Figure S590.  Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.62e-12 (Fisher's exact test), Q value = 8.6e-10

Table S591.  Gene #63: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
DEL PEAK 35(19P13.3) MUTATED 90 110 32
DEL PEAK 35(19P13.3) WILD-TYPE 75 248 149

Figure S591.  Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.32' versus 'MRNA_CNMF'

P value = 1.72e-06 (Chi-square test), Q value = 0.00057

Table S592.  Gene #64: 'del_19q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 36(19Q13.32) MUTATED 4 7 23 26 7 28 1 3
DEL PEAK 36(19Q13.32) WILD-TYPE 17 29 96 70 102 44 19 37

Figure S592.  Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19q13.32' versus 'MRNA_CHIERARCHICAL'

P value = 4.65e-06 (Fisher's exact test), Q value = 0.0014

Table S593.  Gene #64: 'del_19q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 36(19Q13.32) MUTATED 8 38 53
DEL PEAK 36(19Q13.32) WILD-TYPE 114 87 213

Figure S593.  Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19q13.32' versus 'CN_CNMF'

P value = 3.51e-27 (Chi-square test), Q value = 2.6e-24

Table S594.  Gene #64: 'del_19q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 36(19Q13.32) MUTATED 18 86 8 86 6
DEL PEAK 36(19Q13.32) WILD-TYPE 359 166 96 166 42

Figure S594.  Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.32' versus 'METHLYATION_CNMF'

P value = 4.2e-14 (Chi-square test), Q value = 2.4e-11

Table S595.  Gene #64: 'del_19q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 36(19Q13.32) MUTATED 45 7 21 44 5 15
DEL PEAK 36(19Q13.32) WILD-TYPE 79 169 83 91 51 101

Figure S595.  Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.32' versus 'RPPA_CNMF'

P value = 0.000458 (Fisher's exact test), Q value = 0.099

Table S596.  Gene #64: 'del_19q13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 36(19Q13.32) MUTATED 45 20 15
DEL PEAK 36(19Q13.32) WILD-TYPE 102 113 102

Figure S596.  Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19q13.32' versus 'RPPA_CHIERARCHICAL'

P value = 2.51e-05 (Fisher's exact test), Q value = 0.0068

Table S597.  Gene #64: 'del_19q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 36(19Q13.32) MUTATED 27 11 42
DEL PEAK 36(19Q13.32) WILD-TYPE 134 99 84

Figure S597.  Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_19q13.32' versus 'MRNASEQ_CNMF'

P value = 3.86e-15 (Chi-square test), Q value = 2.3e-12

Table S598.  Gene #64: 'del_19q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 36(19Q13.32) MUTATED 59 7 17 56 60 4
DEL PEAK 36(19Q13.32) WILD-TYPE 131 88 240 113 200 44

Figure S598.  Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.52e-14 (Fisher's exact test), Q value = 8.8e-12

Table S599.  Gene #64: 'del_19q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 36(19Q13.32) MUTATED 25 99 79
DEL PEAK 36(19Q13.32) WILD-TYPE 314 334 168

Figure S599.  Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.32' versus 'MIRSEQ_CNMF'

P value = 3.92e-12 (Chi-square test), Q value = 2e-09

Table S600.  Gene #64: 'del_19q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 36(19Q13.32) MUTATED 33 13 23 81 40 7
DEL PEAK 36(19Q13.32) WILD-TYPE 161 157 204 170 100 25

Figure S600.  Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.02e-10 (Fisher's exact test), Q value = 5e-08

Table S601.  Gene #64: 'del_19q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 36(19Q13.32) MUTATED 100 83 14
DEL PEAK 36(19Q13.32) WILD-TYPE 431 190 196

Figure S601.  Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.36e-15 (Fisher's exact test), Q value = 8.2e-13

Table S602.  Gene #64: 'del_19q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
DEL PEAK 36(19Q13.32) MUTATED 50 13 77
DEL PEAK 36(19Q13.32) WILD-TYPE 198 225 141

Figure S602.  Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19q13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.8e-08 (Fisher's exact test), Q value = 1.1e-05

Table S603.  Gene #64: 'del_19q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
DEL PEAK 36(19Q13.32) MUTATED 55 70 15
DEL PEAK 36(19Q13.32) WILD-TYPE 110 288 166

Figure S603.  Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p13' versus 'MRNA_CNMF'

P value = 2.72e-06 (Chi-square test), Q value = 0.00088

Table S604.  Gene #65: 'del_20p13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 37(20P13) MUTATED 1 3 28 25 3 16 3 1
DEL PEAK 37(20P13) WILD-TYPE 20 33 91 71 106 56 17 39

Figure S604.  Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_20p13' versus 'MRNA_CHIERARCHICAL'

P value = 1.15e-05 (Fisher's exact test), Q value = 0.0033

Table S605.  Gene #65: 'del_20p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 37(20P13) MUTATED 6 33 41
DEL PEAK 37(20P13) WILD-TYPE 116 92 225

Figure S605.  Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_20p13' versus 'CN_CNMF'

P value = 1.98e-20 (Chi-square test), Q value = 1.3e-17

Table S606.  Gene #65: 'del_20p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 37(20P13) MUTATED 15 45 5 78 10
DEL PEAK 37(20P13) WILD-TYPE 362 207 99 174 38

Figure S606.  Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #3: 'CN_CNMF'

'del_20p13' versus 'METHLYATION_CNMF'

P value = 1.96e-12 (Chi-square test), Q value = 1e-09

Table S607.  Gene #65: 'del_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 37(20P13) MUTATED 41 7 14 26 4 7
DEL PEAK 37(20P13) WILD-TYPE 83 169 90 109 52 109

Figure S607.  Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_20p13' versus 'RPPA_CNMF'

P value = 0.000985 (Fisher's exact test), Q value = 0.2

Table S608.  Gene #65: 'del_20p13' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 37(20P13) MUTATED 36 11 17
DEL PEAK 37(20P13) WILD-TYPE 111 122 100

Figure S608.  Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_20p13' versus 'MRNASEQ_CNMF'

P value = 9.71e-14 (Chi-square test), Q value = 5.5e-11

Table S609.  Gene #65: 'del_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 37(20P13) MUTATED 55 4 11 33 46 2
DEL PEAK 37(20P13) WILD-TYPE 135 91 246 136 214 46

Figure S609.  Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_20p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.43e-12 (Fisher's exact test), Q value = 7.6e-10

Table S610.  Gene #65: 'del_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 37(20P13) MUTATED 20 62 69
DEL PEAK 37(20P13) WILD-TYPE 319 371 178

Figure S610.  Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_20p13' versus 'MIRSEQ_CNMF'

P value = 1.99e-17 (Chi-square test), Q value = 1.3e-14

Table S611.  Gene #65: 'del_20p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 194 170 227 251 140 32
DEL PEAK 37(20P13) MUTATED 16 7 15 75 29 2
DEL PEAK 37(20P13) WILD-TYPE 178 163 212 176 111 30

Figure S611.  Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_20p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.8e-14 (Fisher's exact test), Q value = 2.2e-11

Table S612.  Gene #65: 'del_20p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 531 273 210
DEL PEAK 37(20P13) MUTATED 55 78 11
DEL PEAK 37(20P13) WILD-TYPE 476 195 199

Figure S612.  Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_20p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.82e-11 (Fisher's exact test), Q value = 4.3e-08

Table S613.  Gene #65: 'del_20p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 248 238 218
DEL PEAK 37(20P13) MUTATED 28 13 60
DEL PEAK 37(20P13) WILD-TYPE 220 225 158

Figure S613.  Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_20p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.75e-11 (Fisher's exact test), Q value = 3.3e-08

Table S614.  Gene #65: 'del_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 358 181
DEL PEAK 37(20P13) MUTATED 52 37 12
DEL PEAK 37(20P13) WILD-TYPE 113 321 169

Figure S614.  Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q11.2' versus 'MRNA_CNMF'

P value = 0.000299 (Chi-square test), Q value = 0.066

Table S615.  Gene #66: 'del_21q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 38(21Q11.2) MUTATED 3 11 37 16 11 23 3 4
DEL PEAK 38(21Q11.2) WILD-TYPE 18 25 82 80 98 49 17 36

Figure S615.  Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_21q11.2' versus 'CN_CNMF'

P value = 5.97e-15 (Chi-square test), Q value = 3.5e-12

Table S616.  Gene #66: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 38(21Q11.2) MUTATED 27 84 19 65 10
DEL PEAK 38(21Q11.2) WILD-TYPE 350 168 85 187 38

Figure S616.  Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 1.92e-05 (Chi-square test), Q value = 0.0052

Table S617.  Gene #66: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 38(21Q11.2) MUTATED 20 22 27 44 8 14
DEL PEAK 38(21Q11.2) WILD-TYPE 104 154 77 91 48 102

Figure S617.  Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

P value = 1.89e-05 (Chi-square test), Q value = 0.0052

Table S618.  Gene #66: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 190 95 257 169 260 48
DEL PEAK 38(21Q11.2) MUTATED 31 14 30 48 69 8
DEL PEAK 38(21Q11.2) WILD-TYPE 159 81 227 121 191 40

Figure S618.  Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_21q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.73e-05 (Fisher's exact test), Q value = 0.012

Table S619.  Gene #66: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 339 433 247
DEL PEAK 38(21Q11.2) MUTATED 44 111 45
DEL PEAK 38(21Q11.2) WILD-TYPE 295 322 202

Figure S619.  Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q11.1' versus 'CN_CNMF'

P value = 2.38e-10 (Chi-square test), Q value = 1.1e-07

Table S620.  Gene #67: 'del_22q11.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 39(22Q11.1) MUTATED 117 129 67 118 17
DEL PEAK 39(22Q11.1) WILD-TYPE 260 123 37 134 31

Figure S620.  Get High-res Image Gene #67: 'del_22q11.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q11.1' versus 'METHLYATION_CNMF'

P value = 1.04e-05 (Chi-square test), Q value = 0.003

Table S621.  Gene #67: 'del_22q11.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 39(22Q11.1) MUTATED 59 62 51 79 13 43
DEL PEAK 39(22Q11.1) WILD-TYPE 65 114 53 56 43 73

Figure S621.  Get High-res Image Gene #67: 'del_22q11.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q13.32' versus 'CN_CNMF'

P value = 9.53e-12 (Chi-square test), Q value = 4.9e-09

Table S622.  Gene #68: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 377 252 104 252 48
DEL PEAK 40(22Q13.32) MUTATED 123 140 71 121 22
DEL PEAK 40(22Q13.32) WILD-TYPE 254 112 33 131 26

Figure S622.  Get High-res Image Gene #68: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 0.000417 (Chi-square test), Q value = 0.091

Table S623.  Gene #68: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 124 176 104 135 56 116
DEL PEAK 40(22Q13.32) MUTATED 63 70 49 82 18 45
DEL PEAK 40(22Q13.32) WILD-TYPE 61 106 55 53 38 71

Figure S623.  Get High-res Image Gene #68: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Molecular subtype file = BRCA-TP.transferedmergedcluster.txt

  • Number of patients = 1033

  • Number of significantly focal cnvs = 68

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have alterations, K = 3

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[2] 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)
[3] 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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