Correlation between copy number variation genes (focal events) and molecular subtypes
Breast Invasive Carcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C14Q7SVX
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/C14Q7SVX
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 67 focal events and 12 molecular subtypes across 1079 patients, 644 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',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_1q44 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 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', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_5p15.33 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_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',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_8p11.21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_8q24.21 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  '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',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

  • 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',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • amp_17p11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

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

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

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

  • 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',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_20q13.2 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_1p36.13 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_1p22.1 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_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_4q35.1 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_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' and 'MRNASEQ_CNMF'.

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

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

  • 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 'MRNA_CHIERARCHICAL',  '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',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • del_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_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_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_11q23.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • 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',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_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',  'RPPA_CHIERARCHICAL',  '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_22q13.32 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 67 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, 644 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
amp 1p22 3 250 (23%) 829 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00027
(0.0545) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		2e-05
(0.00804)
amp 3q26 32 340 (32%) 739 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		3e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804)
amp 6p23 298 (28%) 781 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		4e-05
(0.0103) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804)
amp 6q21 201 (19%) 878 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804)
amp 8q24 21 677 (63%) 402 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804)
amp 10p15 1 304 (28%) 775 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804)
amp 12p13 33 281 (26%) 798 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804)
amp 13q34 179 (17%) 900 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		2e-05
(0.00804)
amp 19q12 283 (26%) 796 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00107
(0.179)
amp 20q13 2 547 (51%) 532 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00061
(0.113) 		0.00021
(0.0439) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804)
del 2q37 3 316 (29%) 763 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		7e-05
(0.0169)
del 3p21 31 347 (32%) 732 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00014
(0.0305)
del 4p16 3 339 (31%) 740 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		2e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00027
(0.0545)
del 4q35 1 345 (32%) 734 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00071
(0.129)
del 5q11 2 280 (26%) 799 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804)
del 5q21 3 272 (25%) 807 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804)
del 9q34 2 296 (27%) 783 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804)
del 10q23 31 320 (30%) 759 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00011
(0.0249)
del 10q26 3 319 (30%) 760 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804)
del 11p15 5 309 (29%) 770 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		2e-05
(0.00804)
del 12q23 1 201 (19%) 878 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804)
del 12q24 31 211 (20%) 868 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		2e-05
(0.00804) 		2e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.0001
(0.0228)
del 14q24 1 353 (33%) 726 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804)
del 15q13 1 374 (35%) 705 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		3e-05
(0.00804) 		8e-05
(0.019) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804)
del 16q24 3 692 (64%) 387 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804)
del 17q21 31 371 (34%) 708 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00041
(0.0787)
del 19p13 3 363 (34%) 716 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804)
del 19q13 32 216 (20%) 863 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00058
(0.108) 		3e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804)
del 20p13 160 (15%) 919 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00038
(0.0737) 		0.00093
(0.159) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804)
amp 17q23 1 425 (39%) 654 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.361
(1.00) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		8e-05
(0.019) 		1e-05
(0.00804)
del 8p23 2 557 (52%) 522 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00856
(0.95) 		0.00074
(0.134) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804)
del 9p23 324 (30%) 755 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.0102
(1.00) 		0.00093
(0.159) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00024
(0.049) 		8e-05
(0.019)
del 9q21 11 293 (27%) 786 0.00114
(0.188) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00777
(0.894) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804)
del 13q14 2 494 (46%) 585 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.264
(1.00) 		4e-05
(0.0103) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		3e-05
(0.00804)
amp 17q12 332 (31%) 747 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.095
(1.00) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00451
(0.586) 		1e-05
(0.00804) 		0.0003
(0.0594) 		0.00018
(0.038)
amp 19p13 12 229 (21%) 850 8e-05
(0.019) 		0.00022
(0.0451) 		1e-05
(0.00804) 		8e-05
(0.019) 		0.00091
(0.157) 		0.00215
(0.333) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.0904
(1.00)
del 7p22 3 136 (13%) 943 4e-05
(0.0103) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00221
(0.336) 		0.00491
(0.619) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		2e-05
(0.00804) 		5e-05
(0.0126)
del 9p21 3 363 (34%) 716 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00516
(0.635) 		0.00443
(0.58) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		7e-05
(0.0169) 		1e-05
(0.00804)
del 17p12 650 (60%) 429 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		2e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		2e-05
(0.00804) 		0.0581
(1.00) 		0.149
(1.00)
amp 1q21 3 781 (72%) 298 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		3e-05
(0.00804) 		0.0476
(1.00) 		0.0128
(1.00) 		0.00086
(0.151) 		1e-05
(0.00804) 		0.0005
(0.095) 		1e-05
(0.00804) 		0.00113
(0.188) 		0.121
(1.00)
amp 4q13 3 163 (15%) 916 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		2e-05
(0.00804) 		0.0673
(1.00) 		0.0427
(1.00) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00335
(0.472) 		3e-05
(0.00804)
amp 12q15 275 (25%) 804 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00021
(0.0439) 		0.29
(1.00) 		0.00486
(0.617) 		1e-05
(0.00804) 		1e-05
(0.00804) 		7e-05
(0.0169) 		1e-05
(0.00804) 		2e-05
(0.00804) 		0.168
(1.00)
amp 15q26 3 194 (18%) 885 1e-05
(0.00804) 		0.00011
(0.0249) 		1e-05
(0.00804) 		0.00117
(0.192) 		0.00216
(0.333) 		0.00719
(0.834) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00185
(0.292) 		5e-05
(0.0126)
del 8p11 21 200 (19%) 879 6e-05
(0.0148) 		0.00012
(0.0266) 		1e-05
(0.00804) 		0.00813
(0.919) 		0.0198
(1.00) 		0.00013
(0.0286) 		2e-05
(0.00804) 		1e-05
(0.00804) 		4e-05
(0.0103) 		1e-05
(0.00804) 		0.00253
(0.372) 		0.00052
(0.0983)
del 11q23 3 546 (51%) 533 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.92
(1.00) 		3e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.0337
(1.00) 		5e-05
(0.0126) 		0.0002
(0.042) 		0.175
(1.00)
amp 3p25 1 198 (18%) 881 0.0007
(0.128) 		5e-05
(0.0126) 		1e-05
(0.00804) 		0.00021
(0.0439) 		0.244
(1.00) 		0.379
(1.00) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.0389
(1.00) 		0.07
(1.00)
amp 8p11 21 420 (39%) 659 0.0427
(1.00) 		0.00463
(0.597) 		1e-05
(0.00804) 		5e-05
(0.0126) 		0.9
(1.00) 		0.0755
(1.00) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00148
(0.238) 		2e-05
(0.00804) 		6e-05
(0.0148) 		0.00088
(0.154)
amp 11p13 222 (21%) 857 0.164
(1.00) 		0.0009
(0.157) 		1e-05
(0.00804) 		0.00386
(0.533) 		0.0608
(1.00) 		0.0486
(1.00) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00013
(0.0286) 		0.00015
(0.0324)
amp 19q13 42 275 (25%) 804 0.0004
(0.0772) 		0.00242
(0.361) 		1e-05
(0.00804) 		0.00092
(0.158) 		0.00119
(0.194) 		0.245
(1.00) 		0.00021
(0.0439) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.177
(1.00) 		0.0768
(1.00)
del 1p36 13 451 (42%) 628 6e-05
(0.0148) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00375
(0.521) 		0.00414
(0.555) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00011
(0.0249) 		2e-05
(0.00804) 		0.00232
(0.35) 		0.165
(1.00)
del 6q15 358 (33%) 721 1e-05
(0.00804) 		0.00032
(0.0627) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.456
(1.00) 		0.0136
(1.00) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.028
(1.00) 		1e-05
(0.00804) 		0.00014
(0.0305) 		0.557
(1.00)
del 7q36 1 199 (18%) 880 0.00265
(0.384) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00217
(0.333) 		0.311
(1.00) 		0.0318
(1.00) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		8e-05
(0.019) 		2e-05
(0.00804)
del 18q23 354 (33%) 725 0.0001
(0.0228) 		4e-05
(0.0103) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00403
(0.549) 		0.0296
(1.00) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.005
(0.625) 		0.169
(1.00)
amp 5p15 33 393 (36%) 686 0.00847
(0.949) 		0.00085
(0.15) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.0465
(1.00) 		0.474
(1.00) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00167
(0.267) 		0.00503
(0.625)
amp 8p11 23 411 (38%) 668 1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00017
(0.036) 		0.0533
(1.00) 		8e-05
(0.019) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.552
(1.00) 		0.0924
(1.00) 		0.179
(1.00) 		0.742
(1.00)
amp 10q22 3 150 (14%) 929 7e-05
(0.0169) 		6e-05
(0.0148) 		1e-05
(0.00804) 		0.00243
(0.361) 		0.00464
(0.597) 		0.486
(1.00) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00181
(0.288) 		0.00275
(0.393)
amp 11q13 3 397 (37%) 682 0.00016
(0.0342) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.983
(1.00) 		0.0006
(0.112) 		8e-05
(0.019) 		1e-05
(0.00804) 		0.00193
(0.303) 		0.00569
(0.677) 		0.0146
(1.00) 		0.00791
(0.902)
amp 11q14 1 266 (25%) 813 0.00552
(0.662) 		0.00012
(0.0266) 		1e-05
(0.00804) 		6e-05
(0.0148) 		0.0822
(1.00) 		0.257
(1.00) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00028
(0.0557) 		0.0301
(1.00) 		0.0194
(1.00)
amp 14q21 1 220 (20%) 859 2e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		8e-05
(0.019) 		0.0716
(1.00) 		0.00271
(0.39) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.00667
(0.78) 		1e-05
(0.00804) 		0.00439
(0.579) 		0.679
(1.00)
del 1p22 1 361 (33%) 718 0.0105
(1.00) 		1e-05
(0.00804) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.0162
(1.00) 		0.00195
(0.304) 		1e-05
(0.00804) 		1e-05
(0.00804) 		0.0451
(1.00) 		1e-05
(0.00804) 		0.202
(1.00) 		0.967
(1.00)
amp 1q44 789 (73%) 290 3e-05
(0.00804) 		0.00106
(0.178) 		1e-05
(0.00804) 		0.00403
(0.549) 		0.854
(1.00) 		0.361
(1.00) 		0.894
(1.00) 		0.00015
(0.0324) 		0.758
(1.00) 		0.00016
(0.0342) 		0.113
(1.00) 		0.139
(1.00)
del 21q11 2 217 (20%) 862 0.00024
(0.049) 		0.00401
(0.549) 		1e-05
(0.00804) 		0.00027
(0.0545) 		0.0614
(1.00) 		0.00914
(1.00) 		0.00031
(0.0611) 		1e-05
(0.00804) 		0.00531
(0.643) 		0.00365
(0.511) 		0.0332
(1.00) 		0.124
(1.00)
del 12p13 1 188 (17%) 891 0.0341
(1.00) 		0.111
(1.00) 		0.00011
(0.0249) 		0.0427
(1.00) 		0.289
(1.00) 		0.313
(1.00) 		0.00083
(0.148) 		0.00054
(0.102) 		0.00236
(0.354) 		9e-05
(0.0206) 		0.00593
(0.7) 		0.00283
(0.402)
del 22q13 32 492 (46%) 587 0.255
(1.00) 		0.0097
(1.00) 		1e-05
(0.00804) 		0.0821
(1.00) 		0.174
(1.00) 		0.017
(1.00) 		0.00143
(0.232) 		0.00066
(0.121) 		0.0308
(1.00) 		0.00076
(0.136) 		0.00258
(0.377) 		0.0765
(1.00)
amp 17p11 2 146 (14%) 933 0.0273
(1.00) 		0.0598
(1.00) 		1e-05
(0.00804) 		0.00074
(0.134) 		0.712
(1.00) 		0.0184
(1.00) 		0.00045
(0.0859) 		0.0137
(1.00) 		0.667
(1.00) 		0.102
(1.00) 		0.603
(1.00) 		0.1
(1.00)
del 6p25 3 204 (19%) 875 0.406
(1.00) 		0.775
(1.00) 		1e-05
(0.00804) 		0.00414
(0.555) 		0.306
(1.00) 		0.0996
(1.00) 		0.00032
(0.0627) 		0.022
(1.00) 		0.00521
(0.636) 		0.00925
(1.00) 		0.312
(1.00) 		0.181
(1.00)
del 6q27 375 (35%) 704 0.0218
(1.00) 		0.0108
(1.00) 		1e-05
(0.00804) 		0.15
(1.00) 		0.0567
(1.00) 		0.0628
(1.00) 		0.0936
(1.00) 		0.00101
(0.171) 		0.0609
(1.00) 		0.0919
(1.00) 		0.748
(1.00) 		0.608
(1.00)
'amp_1p22.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

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 = 1e-05 (Fisher's exact test), Q value = 0.008

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 1(1P22.3) MUTATED 14 19 24 47 11
AMP PEAK 1(1P22.3) WILD-TYPE 87 133 90 41 47

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 = 1e-05 (Fisher's exact test), Q value = 0.008

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 260 412 93 265 49
AMP PEAK 1(1P22.3) MUTATED 40 54 31 111 14
AMP PEAK 1(1P22.3) WILD-TYPE 220 358 62 154 35

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 = 1e-05 (Fisher's exact test), Q value = 0.008

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
AMP PEAK 1(1P22.3) MUTATED 72 30 33 11 23
AMP PEAK 1(1P22.3) WILD-TYPE 60 167 144 77 105

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 = 0.00027 (Fisher's exact test), Q value = 0.055

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
AMP PEAK 1(1P22.3) MUTATED 52 27 17
AMP PEAK 1(1P22.3) WILD-TYPE 97 105 100

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 = 1e-05 (Fisher's exact test), Q value = 0.008

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
AMP PEAK 1(1P22.3) MUTATED 15 14 45 17 5
AMP PEAK 1(1P22.3) WILD-TYPE 49 92 45 90 26

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 = 1e-05 (Fisher's exact test), Q value = 0.008

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
AMP PEAK 1(1P22.3) MUTATED 96 130 22
AMP PEAK 1(1P22.3) WILD-TYPE 447 168 210

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 = 1e-05 (Fisher's exact test), Q value = 0.008

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
AMP PEAK 1(1P22.3) MUTATED 34 36 34 29 99 16
AMP PEAK 1(1P22.3) WILD-TYPE 185 128 272 112 84 44

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 = 1e-05 (Fisher's exact test), Q value = 0.008

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
AMP PEAK 1(1P22.3) MUTATED 126 42 79
AMP PEAK 1(1P22.3) WILD-TYPE 205 211 397

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 = 1e-05 (Fisher's exact test), Q value = 0.008

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
AMP PEAK 1(1P22.3) MUTATED 37 42 50 29 9 80
AMP PEAK 1(1P22.3) WILD-TYPE 194 118 272 98 77 54

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 = 1e-05 (Fisher's exact test), Q value = 0.008

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 1(1P22.3) MUTATED 29 73 13 12 30
AMP PEAK 1(1P22.3) WILD-TYPE 151 66 86 99 103

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 = 2e-05 (Fisher's exact test), Q value = 0.008

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
AMP PEAK 1(1P22.3) MUTATED 97 48 12
AMP PEAK 1(1P22.3) WILD-TYPE 208 199 98

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 = 1e-05 (Fisher's exact test), Q value = 0.008

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 = 1e-05 (Fisher's exact test), Q value = 0.008

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 2(1Q21.3) MUTATED 62 102 89 81 45
AMP PEAK 2(1Q21.3) WILD-TYPE 39 50 25 7 13

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 = 1e-05 (Fisher's exact test), Q value = 0.008

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 260 412 93 265 49
AMP PEAK 2(1Q21.3) MUTATED 193 250 92 210 36
AMP PEAK 2(1Q21.3) WILD-TYPE 67 162 1 55 13

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 = 3e-05 (Fisher's exact test), Q value = 0.008

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
AMP PEAK 2(1Q21.3) MUTATED 112 144 130 65 70
AMP PEAK 2(1Q21.3) WILD-TYPE 20 53 47 23 58

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 = 0.00086 (Fisher's exact test), Q value = 0.15

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
AMP PEAK 2(1Q21.3) MUTATED 390 236 150
AMP PEAK 2(1Q21.3) WILD-TYPE 153 62 82

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

'amp_1q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S18.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
AMP PEAK 2(1Q21.3) MUTATED 137 131 202 112 159 35
AMP PEAK 2(1Q21.3) WILD-TYPE 82 33 104 29 24 25

Figure S18.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.095

Table S19.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
AMP PEAK 2(1Q21.3) MUTATED 263 166 335
AMP PEAK 2(1Q21.3) WILD-TYPE 68 87 141

Figure S19.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S20.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
AMP PEAK 2(1Q21.3) MUTATED 158 113 215 109 48 121
AMP PEAK 2(1Q21.3) WILD-TYPE 73 47 107 18 38 13

Figure S20.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00113 (Fisher's exact test), Q value = 0.19

Table S21.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 2(1Q21.3) MUTATED 125 114 70 64 90
AMP PEAK 2(1Q21.3) WILD-TYPE 55 25 29 47 43

Figure S21.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1q44' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.008

Table S22.  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 S22.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1q44' versus 'MRNA_CHIERARCHICAL'

P value = 0.00106 (Fisher's exact test), Q value = 0.18

Table S23.  Gene #3: 'amp_1q44' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 3(1Q44) MUTATED 59 107 92 72 44
AMP PEAK 3(1Q44) WILD-TYPE 42 45 22 16 14

Figure S23.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_1q44' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S24.  Gene #3: 'amp_1q44' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
AMP PEAK 3(1Q44) MUTATED 197 263 93 203 33
AMP PEAK 3(1Q44) WILD-TYPE 63 149 0 62 16

Figure S24.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q44' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.032

Table S25.  Gene #3: 'amp_1q44' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
AMP PEAK 3(1Q44) MUTATED 137 134 224 109 143 37
AMP PEAK 3(1Q44) WILD-TYPE 82 30 82 32 40 23

Figure S25.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q44' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.034

Table S26.  Gene #3: 'amp_1q44' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
AMP PEAK 3(1Q44) MUTATED 157 118 235 109 50 104
AMP PEAK 3(1Q44) WILD-TYPE 74 42 87 18 36 30

Figure S26.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3p25.1' versus 'MRNA_CNMF'

P value = 7e-04 (Fisher's exact test), Q value = 0.13

Table S27.  Gene #4: 'amp_3p25.1' 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 4(3P25.1) MUTATED 6 7 34 20 18 25 7 1
AMP PEAK 4(3P25.1) WILD-TYPE 15 29 85 76 91 47 13 39

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

'amp_3p25.1' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.013

Table S28.  Gene #4: 'amp_3p25.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 4(3P25.1) MUTATED 27 18 42 18 13
AMP PEAK 4(3P25.1) WILD-TYPE 74 134 72 70 45

Figure S28.  Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_3p25.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S29.  Gene #4: 'amp_3p25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
AMP PEAK 4(3P25.1) MUTATED 75 19 23 69 12
AMP PEAK 4(3P25.1) WILD-TYPE 185 393 70 196 37

Figure S29.  Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3p25.1' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.044

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
AMP PEAK 4(3P25.1) MUTATED 34 19 38 10 14
AMP PEAK 4(3P25.1) WILD-TYPE 98 178 139 78 114

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

'amp_3p25.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S31.  Gene #4: 'amp_3p25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
AMP PEAK 4(3P25.1) MUTATED 110 77 10
AMP PEAK 4(3P25.1) WILD-TYPE 433 221 222

Figure S31.  Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3p25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S32.  Gene #4: 'amp_3p25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
AMP PEAK 4(3P25.1) MUTATED 45 53 29 14 43 13
AMP PEAK 4(3P25.1) WILD-TYPE 174 111 277 127 140 47

Figure S32.  Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3p25.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S33.  Gene #4: 'amp_3p25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
AMP PEAK 4(3P25.1) MUTATED 86 29 75
AMP PEAK 4(3P25.1) WILD-TYPE 245 224 401

Figure S33.  Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3p25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S34.  Gene #4: 'amp_3p25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
AMP PEAK 4(3P25.1) MUTATED 58 38 28 22 11 33
AMP PEAK 4(3P25.1) WILD-TYPE 173 122 294 105 75 101

Figure S34.  Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.32' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S35.  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 S35.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.32' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S36.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 5(3Q26.32) MUTATED 29 29 57 53 13
AMP PEAK 5(3Q26.32) WILD-TYPE 72 123 57 35 45

Figure S36.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_3q26.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S37.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
AMP PEAK 5(3Q26.32) MUTATED 99 37 29 161 14
AMP PEAK 5(3Q26.32) WILD-TYPE 161 375 64 104 35

Figure S37.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S38.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
AMP PEAK 5(3Q26.32) MUTATED 83 36 51 18 22
AMP PEAK 5(3Q26.32) WILD-TYPE 49 161 126 70 106

Figure S38.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.32' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
AMP PEAK 5(3Q26.32) MUTATED 76 36 30
AMP PEAK 5(3Q26.32) WILD-TYPE 73 96 87

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

'amp_3q26.32' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.008

Table S40.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
AMP PEAK 5(3Q26.32) MUTATED 22 26 54 30 10
AMP PEAK 5(3Q26.32) WILD-TYPE 42 80 36 77 21

Figure S40.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_3q26.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S41.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
AMP PEAK 5(3Q26.32) MUTATED 151 165 21
AMP PEAK 5(3Q26.32) WILD-TYPE 392 133 211

Figure S41.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S42.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
AMP PEAK 5(3Q26.32) MUTATED 62 68 50 16 116 25
AMP PEAK 5(3Q26.32) WILD-TYPE 157 96 256 125 67 35

Figure S42.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S43.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
AMP PEAK 5(3Q26.32) MUTATED 174 46 111
AMP PEAK 5(3Q26.32) WILD-TYPE 157 207 365

Figure S43.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S44.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
AMP PEAK 5(3Q26.32) MUTATED 72 71 52 32 19 85
AMP PEAK 5(3Q26.32) WILD-TYPE 159 89 270 95 67 49

Figure S44.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S45.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 5(3Q26.32) MUTATED 52 77 14 21 29
AMP PEAK 5(3Q26.32) WILD-TYPE 128 62 85 90 104

Figure S45.  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 = 1e-05 (Fisher's exact test), Q value = 0.008

Table S46.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
AMP PEAK 5(3Q26.32) MUTATED 119 49 25
AMP PEAK 5(3Q26.32) WILD-TYPE 186 198 85

Figure S46.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q13.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S47.  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 18 3 18 4 3
AMP PEAK 6(4Q13.3) WILD-TYPE 17 33 87 78 106 54 16 37

Figure S47.  Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_4q13.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S48.  Gene #6: 'amp_4q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 6(4Q13.3) MUTATED 22 12 31 18 2
AMP PEAK 6(4Q13.3) WILD-TYPE 79 140 83 70 56

Figure S48.  Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_4q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
AMP PEAK 6(4Q13.3) MUTATED 73 22 2 59 7
AMP PEAK 6(4Q13.3) WILD-TYPE 187 390 91 206 42

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

'amp_4q13.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S50.  Gene #6: 'amp_4q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
AMP PEAK 6(4Q13.3) MUTATED 32 16 37 5 11
AMP PEAK 6(4Q13.3) WILD-TYPE 100 181 140 83 117

Figure S50.  Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_4q13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S51.  Gene #6: 'amp_4q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
AMP PEAK 6(4Q13.3) MUTATED 83 68 12
AMP PEAK 6(4Q13.3) WILD-TYPE 460 230 220

Figure S51.  Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_4q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S52.  Gene #6: 'amp_4q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
AMP PEAK 6(4Q13.3) MUTATED 45 34 24 3 39 18
AMP PEAK 6(4Q13.3) WILD-TYPE 174 130 282 138 144 42

Figure S52.  Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_4q13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S53.  Gene #6: 'amp_4q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
AMP PEAK 6(4Q13.3) MUTATED 78 20 63
AMP PEAK 6(4Q13.3) WILD-TYPE 253 233 413

Figure S53.  Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_4q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S54.  Gene #6: 'amp_4q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
AMP PEAK 6(4Q13.3) MUTATED 46 42 21 10 12 30
AMP PEAK 6(4Q13.3) WILD-TYPE 185 118 301 117 74 104

Figure S54.  Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_4q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.008

Table S55.  Gene #6: 'amp_4q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
AMP PEAK 6(4Q13.3) MUTATED 65 22 10
AMP PEAK 6(4Q13.3) WILD-TYPE 240 225 100

Figure S55.  Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.00085 (Fisher's exact test), Q value = 0.15

Table S56.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 7(5P15.33) MUTATED 34 44 59 40 17
AMP PEAK 7(5P15.33) WILD-TYPE 67 108 55 48 41

Figure S56.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S57.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
AMP PEAK 7(5P15.33) MUTATED 123 65 50 137 18
AMP PEAK 7(5P15.33) WILD-TYPE 137 347 43 128 31

Figure S57.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S58.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
AMP PEAK 7(5P15.33) MUTATED 69 55 76 25 30
AMP PEAK 7(5P15.33) WILD-TYPE 63 142 101 63 98

Figure S58.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
AMP PEAK 7(5P15.33) MUTATED 190 140 60
AMP PEAK 7(5P15.33) WILD-TYPE 353 158 172

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

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S60.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
AMP PEAK 7(5P15.33) MUTATED 79 79 81 36 89 26
AMP PEAK 7(5P15.33) WILD-TYPE 140 85 225 105 94 34

Figure S60.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S61.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
AMP PEAK 7(5P15.33) MUTATED 155 69 159
AMP PEAK 7(5P15.33) WILD-TYPE 176 184 317

Figure S61.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S62.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
AMP PEAK 7(5P15.33) MUTATED 85 70 81 52 31 64
AMP PEAK 7(5P15.33) WILD-TYPE 146 90 241 75 55 70

Figure S62.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6p23' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S63.  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 S63.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_6p23' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S64.  Gene #8: 'amp_6p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 8(6P23) MUTATED 22 28 48 45 7
AMP PEAK 8(6P23) WILD-TYPE 79 124 66 43 51

Figure S64.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_6p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S65.  Gene #8: 'amp_6p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
AMP PEAK 8(6P23) MUTATED 84 29 22 147 16
AMP PEAK 8(6P23) WILD-TYPE 176 383 71 118 33

Figure S65.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S66.  Gene #8: 'amp_6p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
AMP PEAK 8(6P23) MUTATED 74 29 59 7 23
AMP PEAK 8(6P23) WILD-TYPE 58 168 118 81 105

Figure S66.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6p23' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S67.  Gene #8: 'amp_6p23' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
AMP PEAK 8(6P23) MUTATED 68 24 24
AMP PEAK 8(6P23) WILD-TYPE 81 108 93

Figure S67.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_6p23' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.01

Table S68.  Gene #8: 'amp_6p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
AMP PEAK 8(6P23) MUTATED 14 21 46 27 8
AMP PEAK 8(6P23) WILD-TYPE 50 85 44 80 23

Figure S68.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_6p23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S69.  Gene #8: 'amp_6p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
AMP PEAK 8(6P23) MUTATED 132 142 23
AMP PEAK 8(6P23) WILD-TYPE 411 156 209

Figure S69.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
AMP PEAK 8(6P23) MUTATED 46 71 50 15 97 18
AMP PEAK 8(6P23) WILD-TYPE 173 93 256 126 86 42

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

'amp_6p23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S71.  Gene #8: 'amp_6p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
AMP PEAK 8(6P23) MUTATED 159 34 93
AMP PEAK 8(6P23) WILD-TYPE 172 219 383

Figure S71.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_6p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S72.  Gene #8: 'amp_6p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
AMP PEAK 8(6P23) MUTATED 73 63 35 26 17 72
AMP PEAK 8(6P23) WILD-TYPE 158 97 287 101 69 62

Figure S72.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S73.  Gene #8: 'amp_6p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 8(6P23) MUTATED 42 67 21 12 24
AMP PEAK 8(6P23) WILD-TYPE 138 72 78 99 109

Figure S73.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_6p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S74.  Gene #8: 'amp_6p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
AMP PEAK 8(6P23) MUTATED 110 44 12
AMP PEAK 8(6P23) WILD-TYPE 195 203 98

Figure S74.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q21' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S75.  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 S75.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_6q21' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S76.  Gene #9: 'amp_6q21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 9(6Q21) MUTATED 10 14 39 37 4
AMP PEAK 9(6Q21) WILD-TYPE 91 138 75 51 54

Figure S76.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_6q21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S77.  Gene #9: 'amp_6q21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
AMP PEAK 9(6Q21) MUTATED 23 25 17 130 6
AMP PEAK 9(6Q21) WILD-TYPE 237 387 76 135 43

Figure S77.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6q21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S78.  Gene #9: 'amp_6q21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
AMP PEAK 9(6Q21) MUTATED 61 9 31 6 20
AMP PEAK 9(6Q21) WILD-TYPE 71 188 146 82 108

Figure S78.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6q21' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S79.  Gene #9: 'amp_6q21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
AMP PEAK 9(6Q21) MUTATED 55 11 16
AMP PEAK 9(6Q21) WILD-TYPE 94 121 101

Figure S79.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_6q21' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S80.  Gene #9: 'amp_6q21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
AMP PEAK 9(6Q21) MUTATED 6 15 38 16 7
AMP PEAK 9(6Q21) WILD-TYPE 58 91 52 91 24

Figure S80.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_6q21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S81.  Gene #9: 'amp_6q21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
AMP PEAK 9(6Q21) MUTATED 67 123 10
AMP PEAK 9(6Q21) WILD-TYPE 476 175 222

Figure S81.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6q21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S82.  Gene #9: 'amp_6q21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
AMP PEAK 9(6Q21) MUTATED 22 47 22 7 82 20
AMP PEAK 9(6Q21) WILD-TYPE 197 117 284 134 101 40

Figure S82.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
AMP PEAK 9(6Q21) MUTATED 129 20 42
AMP PEAK 9(6Q21) WILD-TYPE 202 233 434

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

'amp_6q21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S84.  Gene #9: 'amp_6q21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
AMP PEAK 9(6Q21) MUTATED 44 58 14 14 3 58
AMP PEAK 9(6Q21) WILD-TYPE 187 102 308 113 83 76

Figure S84.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S85.  Gene #9: 'amp_6q21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 9(6Q21) MUTATED 21 68 8 7 16
AMP PEAK 9(6Q21) WILD-TYPE 159 71 91 104 117

Figure S85.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_6q21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S86.  Gene #9: 'amp_6q21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
AMP PEAK 9(6Q21) MUTATED 85 26 9
AMP PEAK 9(6Q21) WILD-TYPE 220 221 101

Figure S86.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p11.23' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S87.  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 S87.  Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8p11.23' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S88.  Gene #10: 'amp_8p11.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 10(8P11.23) MUTATED 64 62 41 30 12
AMP PEAK 10(8P11.23) WILD-TYPE 37 90 73 58 46

Figure S88.  Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S89.  Gene #10: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
AMP PEAK 10(8P11.23) MUTATED 133 112 37 81 48
AMP PEAK 10(8P11.23) WILD-TYPE 127 300 56 184 1

Figure S89.  Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.23' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.036

Table S90.  Gene #10: 'amp_8p11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
AMP PEAK 10(8P11.23) MUTATED 47 66 92 32 35
AMP PEAK 10(8P11.23) WILD-TYPE 85 131 85 56 93

Figure S90.  Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8p11.23' versus 'RPPA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.019

Table S91.  Gene #10: 'amp_8p11.23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
AMP PEAK 10(8P11.23) MUTATED 28 47 32 54 2
AMP PEAK 10(8P11.23) WILD-TYPE 36 59 58 53 29

Figure S91.  Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8p11.23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S92.  Gene #10: 'amp_8p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
AMP PEAK 10(8P11.23) MUTATED 246 95 66
AMP PEAK 10(8P11.23) WILD-TYPE 297 203 166

Figure S92.  Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S93.  Gene #10: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
AMP PEAK 10(8P11.23) MUTATED 132 73 98 31 59 14
AMP PEAK 10(8P11.23) WILD-TYPE 87 91 208 110 124 46

Figure S93.  Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S94.  Gene #11: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
AMP PEAK 11(8P11.21) MUTATED 119 105 41 106 49
AMP PEAK 11(8P11.21) WILD-TYPE 141 307 52 159 0

Figure S94.  Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.013

Table S95.  Gene #11: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
AMP PEAK 11(8P11.21) MUTATED 71 65 81 28 38
AMP PEAK 11(8P11.21) WILD-TYPE 61 132 96 60 90

Figure S95.  Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S96.  Gene #11: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
AMP PEAK 11(8P11.21) MUTATED 226 133 57
AMP PEAK 11(8P11.21) WILD-TYPE 317 165 175

Figure S96.  Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S97.  Gene #11: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
AMP PEAK 11(8P11.21) MUTATED 119 71 86 31 93 16
AMP PEAK 11(8P11.21) WILD-TYPE 100 93 220 110 90 44

Figure S97.  Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_CNMF'

P value = 0.00148 (Fisher's exact test), Q value = 0.24

Table S98.  Gene #11: 'amp_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
AMP PEAK 11(8P11.21) MUTATED 153 81 177
AMP PEAK 11(8P11.21) WILD-TYPE 178 172 299

Figure S98.  Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S99.  Gene #11: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
AMP PEAK 11(8P11.21) MUTATED 96 53 96 52 41 73
AMP PEAK 11(8P11.21) WILD-TYPE 135 107 226 75 45 61

Figure S99.  Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.015

Table S100.  Gene #11: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 11(8P11.21) MUTATED 68 74 31 29 41
AMP PEAK 11(8P11.21) WILD-TYPE 112 65 68 82 92

Figure S100.  Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00088 (Fisher's exact test), Q value = 0.15

Table S101.  Gene #11: 'amp_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
AMP PEAK 11(8P11.21) MUTATED 134 80 29
AMP PEAK 11(8P11.21) WILD-TYPE 171 167 81

Figure S101.  Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S102.  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 S102.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8q24.21' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S103.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 12(8Q24.21) MUTATED 84 83 92 75 16
AMP PEAK 12(8Q24.21) WILD-TYPE 17 69 22 13 42

Figure S103.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S104.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
AMP PEAK 12(8Q24.21) MUTATED 200 147 43 240 47
AMP PEAK 12(8Q24.21) WILD-TYPE 60 265 50 25 2

Figure S104.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S105.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
AMP PEAK 12(8Q24.21) MUTATED 120 82 125 39 68
AMP PEAK 12(8Q24.21) WILD-TYPE 12 115 52 49 60

Figure S105.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S106.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
AMP PEAK 12(8Q24.21) MUTATED 126 71 76
AMP PEAK 12(8Q24.21) WILD-TYPE 23 61 41

Figure S106.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8q24.21' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S107.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
AMP PEAK 12(8Q24.21) MUTATED 34 57 78 79 25
AMP PEAK 12(8Q24.21) WILD-TYPE 30 49 12 28 6

Figure S107.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S108.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
AMP PEAK 12(8Q24.21) MUTATED 338 250 85
AMP PEAK 12(8Q24.21) WILD-TYPE 205 48 147

Figure S108.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S109.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
AMP PEAK 12(8Q24.21) MUTATED 168 126 140 33 162 44
AMP PEAK 12(8Q24.21) WILD-TYPE 51 38 166 108 21 16

Figure S109.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S110.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
AMP PEAK 12(8Q24.21) MUTATED 291 111 260
AMP PEAK 12(8Q24.21) WILD-TYPE 40 142 216

Figure S110.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S111.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
AMP PEAK 12(8Q24.21) MUTATED 162 124 125 77 52 122
AMP PEAK 12(8Q24.21) WILD-TYPE 69 36 197 50 34 12

Figure S111.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S112.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 12(8Q24.21) MUTATED 114 128 41 44 65
AMP PEAK 12(8Q24.21) WILD-TYPE 66 11 58 67 68

Figure S112.  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 = 1e-05 (Fisher's exact test), Q value = 0.008

Table S113.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
AMP PEAK 12(8Q24.21) MUTATED 224 116 52
AMP PEAK 12(8Q24.21) WILD-TYPE 81 131 58

Figure S113.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10p15.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S114.  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 S114.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_10p15.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S115.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 13(10P15.1) MUTATED 16 22 53 63 7
AMP PEAK 13(10P15.1) WILD-TYPE 85 130 61 25 51

Figure S115.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_10p15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S116.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
AMP PEAK 13(10P15.1) MUTATED 72 38 16 168 10
AMP PEAK 13(10P15.1) WILD-TYPE 188 374 77 97 39

Figure S116.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10p15.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S117.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
AMP PEAK 13(10P15.1) MUTATED 88 16 45 9 31
AMP PEAK 13(10P15.1) WILD-TYPE 44 181 132 79 97

Figure S117.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_10p15.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S118.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
AMP PEAK 13(10P15.1) MUTATED 78 22 29
AMP PEAK 13(10P15.1) WILD-TYPE 71 110 88

Figure S118.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_10p15.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S119.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
AMP PEAK 13(10P15.1) MUTATED 8 24 61 27 9
AMP PEAK 13(10P15.1) WILD-TYPE 56 82 29 80 22

Figure S119.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_10p15.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S120.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
AMP PEAK 13(10P15.1) MUTATED 106 172 26
AMP PEAK 13(10P15.1) WILD-TYPE 437 126 206

Figure S120.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_10p15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S121.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
AMP PEAK 13(10P15.1) MUTATED 48 56 43 6 125 26
AMP PEAK 13(10P15.1) WILD-TYPE 171 108 263 135 58 34

Figure S121.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10p15.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S122.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
AMP PEAK 13(10P15.1) MUTATED 180 33 83
AMP PEAK 13(10P15.1) WILD-TYPE 151 220 393

Figure S122.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_10p15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S123.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
AMP PEAK 13(10P15.1) MUTATED 67 75 31 25 8 90
AMP PEAK 13(10P15.1) WILD-TYPE 164 85 291 102 78 44

Figure S123.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_10p15.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S124.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 13(10P15.1) MUTATED 35 89 16 11 25
AMP PEAK 13(10P15.1) WILD-TYPE 145 50 83 100 108

Figure S124.  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 = 1e-05 (Fisher's exact test), Q value = 0.008

Table S125.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
AMP PEAK 13(10P15.1) MUTATED 126 36 14
AMP PEAK 13(10P15.1) WILD-TYPE 179 211 96

Figure S125.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10q22.3' versus 'MRNA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.017

Table S126.  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 S126.  Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_10q22.3' versus 'MRNA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.015

Table S127.  Gene #14: 'amp_10q22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 14(10Q22.3) MUTATED 11 17 36 17 5
AMP PEAK 14(10Q22.3) WILD-TYPE 90 135 78 71 53

Figure S127.  Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_10q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S128.  Gene #14: 'amp_10q22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
AMP PEAK 14(10Q22.3) MUTATED 42 24 11 67 6
AMP PEAK 14(10Q22.3) WILD-TYPE 218 388 82 198 43

Figure S128.  Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10q22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S129.  Gene #14: 'amp_10q22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
AMP PEAK 14(10Q22.3) MUTATED 69 67 14
AMP PEAK 14(10Q22.3) WILD-TYPE 474 231 218

Figure S129.  Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_10q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S130.  Gene #14: 'amp_10q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
AMP PEAK 14(10Q22.3) MUTATED 30 36 31 4 32 17
AMP PEAK 14(10Q22.3) WILD-TYPE 189 128 275 137 151 43

Figure S130.  Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10q22.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S131.  Gene #14: 'amp_10q22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
AMP PEAK 14(10Q22.3) MUTATED 69 18 59
AMP PEAK 14(10Q22.3) WILD-TYPE 262 235 417

Figure S131.  Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_10q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S132.  Gene #14: 'amp_10q22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
AMP PEAK 14(10Q22.3) MUTATED 45 33 18 20 6 24
AMP PEAK 14(10Q22.3) WILD-TYPE 186 127 304 107 80 110

Figure S132.  Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11p13' versus 'MRNA_CHIERARCHICAL'

P value = 9e-04 (Fisher's exact test), Q value = 0.16

Table S133.  Gene #15: 'amp_11p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 15(11P13) MUTATED 28 26 34 25 4
AMP PEAK 15(11P13) WILD-TYPE 73 126 80 63 54

Figure S133.  Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S134.  Gene #15: 'amp_11p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
AMP PEAK 15(11P13) MUTATED 80 30 16 88 8
AMP PEAK 15(11P13) WILD-TYPE 180 382 77 177 41

Figure S134.  Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11p13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S135.  Gene #15: 'amp_11p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
AMP PEAK 15(11P13) MUTATED 114 87 21
AMP PEAK 15(11P13) WILD-TYPE 429 211 211

Figure S135.  Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S136.  Gene #15: 'amp_11p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
AMP PEAK 15(11P13) MUTATED 53 44 47 9 59 10
AMP PEAK 15(11P13) WILD-TYPE 166 120 259 132 124 50

Figure S136.  Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11p13' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S137.  Gene #15: 'amp_11p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
AMP PEAK 15(11P13) MUTATED 102 23 94
AMP PEAK 15(11P13) WILD-TYPE 229 230 382

Figure S137.  Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S138.  Gene #15: 'amp_11p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
AMP PEAK 15(11P13) MUTATED 61 53 35 19 13 38
AMP PEAK 15(11P13) WILD-TYPE 170 107 287 108 73 96

Figure S138.  Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.029

Table S139.  Gene #15: 'amp_11p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 15(11P13) MUTATED 41 42 12 16 14
AMP PEAK 15(11P13) WILD-TYPE 139 97 87 95 119

Figure S139.  Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_11p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.032

Table S140.  Gene #15: 'amp_11p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
AMP PEAK 15(11P13) MUTATED 79 29 17
AMP PEAK 15(11P13) WILD-TYPE 226 218 93

Figure S140.  Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q13.3' versus 'MRNA_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.034

Table S141.  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 S141.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11q13.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S142.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 16(11Q13.3) MUTATED 55 57 68 24 11
AMP PEAK 16(11Q13.3) WILD-TYPE 46 95 46 64 47

Figure S142.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S143.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
AMP PEAK 16(11Q13.3) MUTATED 183 67 28 101 18
AMP PEAK 16(11Q13.3) WILD-TYPE 77 345 65 164 31

Figure S143.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S144.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
AMP PEAK 16(11Q13.3) MUTATED 48 60 95 22 25
AMP PEAK 16(11Q13.3) WILD-TYPE 84 137 82 66 103

Figure S144.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'RPPA_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.11

Table S145.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
AMP PEAK 16(11Q13.3) MUTATED 17 49 29 60 13
AMP PEAK 16(11Q13.3) WILD-TYPE 47 57 61 47 18

Figure S145.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.019

Table S146.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
AMP PEAK 16(11Q13.3) MUTATED 228 109 60
AMP PEAK 16(11Q13.3) WILD-TYPE 315 189 172

Figure S146.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S147.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
AMP PEAK 16(11Q13.3) MUTATED 112 83 100 24 58 20
AMP PEAK 16(11Q13.3) WILD-TYPE 107 81 206 117 125 40

Figure S147.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q14.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.027

Table S148.  Gene #17: 'amp_11q14.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 17(11Q14.1) MUTATED 30 36 45 30 5
AMP PEAK 17(11Q14.1) WILD-TYPE 71 116 69 58 53

Figure S148.  Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S149.  Gene #17: 'amp_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
AMP PEAK 17(11Q14.1) MUTATED 102 38 19 97 10
AMP PEAK 17(11Q14.1) WILD-TYPE 158 374 74 168 39

Figure S149.  Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q14.1' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.015

Table S150.  Gene #17: 'amp_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
AMP PEAK 17(11Q14.1) MUTATED 43 32 52 18 16
AMP PEAK 17(11Q14.1) WILD-TYPE 89 165 125 70 112

Figure S150.  Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S151.  Gene #17: 'amp_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
AMP PEAK 17(11Q14.1) MUTATED 133 99 34
AMP PEAK 17(11Q14.1) WILD-TYPE 410 199 198

Figure S151.  Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S152.  Gene #17: 'amp_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
AMP PEAK 17(11Q14.1) MUTATED 55 56 60 17 61 17
AMP PEAK 17(11Q14.1) WILD-TYPE 164 108 246 124 122 43

Figure S152.  Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q14.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S153.  Gene #17: 'amp_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
AMP PEAK 17(11Q14.1) MUTATED 116 38 106
AMP PEAK 17(11Q14.1) WILD-TYPE 215 215 370

Figure S153.  Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.056

Table S154.  Gene #17: 'amp_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
AMP PEAK 17(11Q14.1) MUTATED 62 50 56 28 17 47
AMP PEAK 17(11Q14.1) WILD-TYPE 169 110 266 99 69 87

Figure S154.  Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p13.33' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S155.  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 S155.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_12p13.33' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S156.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 18(12P13.33) MUTATED 30 16 44 49 10
AMP PEAK 18(12P13.33) WILD-TYPE 71 136 70 39 48

Figure S156.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_12p13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S157.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
AMP PEAK 18(12P13.33) MUTATED 84 22 27 135 13
AMP PEAK 18(12P13.33) WILD-TYPE 176 390 66 130 36

Figure S157.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p13.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S158.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
AMP PEAK 18(12P13.33) MUTATED 71 36 44 10 16
AMP PEAK 18(12P13.33) WILD-TYPE 61 161 133 78 112

Figure S158.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12p13.33' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S159.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
AMP PEAK 18(12P13.33) MUTATED 71 30 19
AMP PEAK 18(12P13.33) WILD-TYPE 78 102 98

Figure S159.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_12p13.33' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S160.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
AMP PEAK 18(12P13.33) MUTATED 15 15 47 33 10
AMP PEAK 18(12P13.33) WILD-TYPE 49 91 43 74 21

Figure S160.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_12p13.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S161.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
AMP PEAK 18(12P13.33) MUTATED 126 135 20
AMP PEAK 18(12P13.33) WILD-TYPE 417 163 212

Figure S161.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12p13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S162.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
AMP PEAK 18(12P13.33) MUTATED 57 58 38 12 102 14
AMP PEAK 18(12P13.33) WILD-TYPE 162 106 268 129 81 46

Figure S162.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12p13.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S163.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
AMP PEAK 18(12P13.33) MUTATED 153 34 85
AMP PEAK 18(12P13.33) WILD-TYPE 178 219 391

Figure S163.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12p13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S164.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
AMP PEAK 18(12P13.33) MUTATED 63 49 41 29 13 77
AMP PEAK 18(12P13.33) WILD-TYPE 168 111 281 98 73 57

Figure S164.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p13.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S165.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 18(12P13.33) MUTATED 39 68 15 12 24
AMP PEAK 18(12P13.33) WILD-TYPE 141 71 84 99 109

Figure S165.  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 = 1e-05 (Fisher's exact test), Q value = 0.008

Table S166.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
AMP PEAK 18(12P13.33) MUTATED 99 44 15
AMP PEAK 18(12P13.33) WILD-TYPE 206 203 95

Figure S166.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q15' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S167.  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 S167.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_12q15' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S168.  Gene #19: 'amp_12q15' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 19(12Q15) MUTATED 43 24 56 18 12
AMP PEAK 19(12Q15) WILD-TYPE 58 128 58 70 46

Figure S168.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S169.  Gene #19: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
AMP PEAK 19(12Q15) MUTATED 133 31 29 70 12
AMP PEAK 19(12Q15) WILD-TYPE 127 381 64 195 37

Figure S169.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.044

Table S170.  Gene #19: 'amp_12q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
AMP PEAK 19(12Q15) MUTATED 24 50 61 13 20
AMP PEAK 19(12Q15) WILD-TYPE 108 147 116 75 108

Figure S170.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q15' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S171.  Gene #19: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
AMP PEAK 19(12Q15) MUTATED 183 62 29
AMP PEAK 19(12Q15) WILD-TYPE 360 236 203

Figure S171.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S172.  Gene #19: 'amp_12q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
AMP PEAK 19(12Q15) MUTATED 81 79 52 20 30 12
AMP PEAK 19(12Q15) WILD-TYPE 138 85 254 121 153 48

Figure S172.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.017

Table S173.  Gene #19: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
AMP PEAK 19(12Q15) MUTATED 98 39 132
AMP PEAK 19(12Q15) WILD-TYPE 233 214 344

Figure S173.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S174.  Gene #19: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
AMP PEAK 19(12Q15) MUTATED 93 43 57 32 22 22
AMP PEAK 19(12Q15) WILD-TYPE 138 117 265 95 64 112

Figure S174.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S175.  Gene #19: 'amp_12q15' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 19(12Q15) MUTATED 65 24 23 14 28
AMP PEAK 19(12Q15) WILD-TYPE 115 115 76 97 105

Figure S175.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_13q34' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S176.  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 S176.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_13q34' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S177.  Gene #20: 'amp_13q34' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 20(13Q34) MUTATED 17 14 23 38 8
AMP PEAK 20(13Q34) WILD-TYPE 84 138 91 50 50

Figure S177.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_13q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S178.  Gene #20: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
AMP PEAK 20(13Q34) MUTATED 38 23 14 97 7
AMP PEAK 20(13Q34) WILD-TYPE 222 389 79 168 42

Figure S178.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q34' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S179.  Gene #20: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
AMP PEAK 20(13Q34) MUTATED 50 17 24 5 14
AMP PEAK 20(13Q34) WILD-TYPE 82 180 153 83 114

Figure S179.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q34' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S180.  Gene #20: 'amp_13q34' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
AMP PEAK 20(13Q34) MUTATED 50 22 12
AMP PEAK 20(13Q34) WILD-TYPE 99 110 105

Figure S180.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_13q34' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S181.  Gene #20: 'amp_13q34' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
AMP PEAK 20(13Q34) MUTATED 10 9 39 17 9
AMP PEAK 20(13Q34) WILD-TYPE 54 97 51 90 22

Figure S181.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_13q34' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S182.  Gene #20: 'amp_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
AMP PEAK 20(13Q34) MUTATED 67 101 11
AMP PEAK 20(13Q34) WILD-TYPE 476 197 221

Figure S182.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S183.  Gene #20: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
AMP PEAK 20(13Q34) MUTATED 31 22 21 13 74 18
AMP PEAK 20(13Q34) WILD-TYPE 188 142 285 128 109 42

Figure S183.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q34' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S184.  Gene #20: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
AMP PEAK 20(13Q34) MUTATED 109 22 45
AMP PEAK 20(13Q34) WILD-TYPE 222 231 431

Figure S184.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S185.  Gene #20: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
AMP PEAK 20(13Q34) MUTATED 31 46 20 15 8 56
AMP PEAK 20(13Q34) WILD-TYPE 200 114 302 112 78 78

Figure S185.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_13q34' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S186.  Gene #20: 'amp_13q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 20(13Q34) MUTATED 19 47 6 8 17
AMP PEAK 20(13Q34) WILD-TYPE 161 92 93 103 116

Figure S186.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_13q34' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S187.  Gene #20: 'amp_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
AMP PEAK 20(13Q34) MUTATED 66 23 8
AMP PEAK 20(13Q34) WILD-TYPE 239 224 102

Figure S187.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_14q21.1' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S188.  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 S188.  Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_14q21.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S189.  Gene #21: 'amp_14q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 21(14Q21.1) MUTATED 29 24 42 8 8
AMP PEAK 21(14Q21.1) WILD-TYPE 72 128 72 80 50

Figure S189.  Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_14q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S190.  Gene #21: 'amp_14q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
AMP PEAK 21(14Q21.1) MUTATED 97 36 22 54 11
AMP PEAK 21(14Q21.1) WILD-TYPE 163 376 71 211 38

Figure S190.  Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_14q21.1' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.019

Table S191.  Gene #21: 'amp_14q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
AMP PEAK 21(14Q21.1) MUTATED 17 33 55 12 15
AMP PEAK 21(14Q21.1) WILD-TYPE 115 164 122 76 113

Figure S191.  Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_14q21.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S192.  Gene #21: 'amp_14q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
AMP PEAK 21(14Q21.1) MUTATED 150 47 21
AMP PEAK 21(14Q21.1) WILD-TYPE 393 251 211

Figure S192.  Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_14q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S193.  Gene #21: 'amp_14q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
AMP PEAK 21(14Q21.1) MUTATED 59 72 36 18 17 16
AMP PEAK 21(14Q21.1) WILD-TYPE 160 92 270 123 166 44

Figure S193.  Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_14q21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S194.  Gene #21: 'amp_14q21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
AMP PEAK 21(14Q21.1) MUTATED 69 53 40 32 9 11
AMP PEAK 21(14Q21.1) WILD-TYPE 162 107 282 95 77 123

Figure S194.  Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S195.  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 S195.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_15q26.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.025

Table S196.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 22(15Q26.3) MUTATED 23 23 25 30 3
AMP PEAK 22(15Q26.3) WILD-TYPE 78 129 89 58 55

Figure S196.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_15q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S197.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
AMP PEAK 22(15Q26.3) MUTATED 63 30 6 91 4
AMP PEAK 22(15Q26.3) WILD-TYPE 197 382 87 174 45

Figure S197.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_15q26.3' versus 'METHLYATION_CNMF'

P value = 0.00117 (Fisher's exact test), Q value = 0.19

Table S198.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
AMP PEAK 22(15Q26.3) MUTATED 36 19 27 14 17
AMP PEAK 22(15Q26.3) WILD-TYPE 96 178 150 74 111

Figure S198.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S199.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
AMP PEAK 22(15Q26.3) MUTATED 92 85 16
AMP PEAK 22(15Q26.3) WILD-TYPE 451 213 216

Figure S199.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S200.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
AMP PEAK 22(15Q26.3) MUTATED 50 33 29 13 62 6
AMP PEAK 22(15Q26.3) WILD-TYPE 169 131 277 128 121 54

Figure S200.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S201.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
AMP PEAK 22(15Q26.3) MUTATED 92 28 67
AMP PEAK 22(15Q26.3) WILD-TYPE 239 225 409

Figure S201.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_15q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S202.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
AMP PEAK 22(15Q26.3) MUTATED 42 44 27 16 15 43
AMP PEAK 22(15Q26.3) WILD-TYPE 189 116 295 111 71 91

Figure S202.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.013

Table S203.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
AMP PEAK 22(15Q26.3) MUTATED 75 28 12
AMP PEAK 22(15Q26.3) WILD-TYPE 230 219 98

Figure S203.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S204.  Gene #23: 'amp_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
AMP PEAK 23(17P11.2) MUTATED 62 23 13 35 13
AMP PEAK 23(17P11.2) WILD-TYPE 198 389 80 230 36

Figure S204.  Get High-res Image Gene #23: 'amp_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17p11.2' versus 'METHLYATION_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.13

Table S205.  Gene #23: 'amp_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
AMP PEAK 23(17P11.2) MUTATED 22 30 39 7 8
AMP PEAK 23(17P11.2) WILD-TYPE 110 167 138 81 120

Figure S205.  Get High-res Image Gene #23: 'amp_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17p11.2' versus 'MRNASEQ_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.086

Table S206.  Gene #23: 'amp_17p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
AMP PEAK 23(17P11.2) MUTATED 91 38 15
AMP PEAK 23(17P11.2) WILD-TYPE 452 260 217

Figure S206.  Get High-res Image Gene #23: 'amp_17p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S207.  Gene #24: '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 24(17Q12) MUTATED 9 11 53 19 14 49 7 4
AMP PEAK 24(17Q12) WILD-TYPE 12 25 66 77 95 23 13 36

Figure S207.  Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S208.  Gene #24: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 24(17Q12) MUTATED 40 28 71 16 11
AMP PEAK 24(17Q12) WILD-TYPE 61 124 43 72 47

Figure S208.  Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S209.  Gene #24: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
AMP PEAK 24(17Q12) MUTATED 171 59 21 66 15
AMP PEAK 24(17Q12) WILD-TYPE 89 353 72 199 34

Figure S209.  Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S210.  Gene #24: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
AMP PEAK 24(17Q12) MUTATED 33 46 85 23 29
AMP PEAK 24(17Q12) WILD-TYPE 99 151 92 65 99

Figure S210.  Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q12' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S211.  Gene #24: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
AMP PEAK 24(17Q12) MUTATED 9 28 20 41 31
AMP PEAK 24(17Q12) WILD-TYPE 55 78 70 66 0

Figure S211.  Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S212.  Gene #24: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
AMP PEAK 24(17Q12) MUTATED 191 104 35
AMP PEAK 24(17Q12) WILD-TYPE 352 194 197

Figure S212.  Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S213.  Gene #24: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
AMP PEAK 24(17Q12) MUTATED 94 86 58 19 33 40
AMP PEAK 24(17Q12) WILD-TYPE 125 78 248 122 150 20

Figure S213.  Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S214.  Gene #24: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
AMP PEAK 24(17Q12) MUTATED 101 71 73 32 26 22
AMP PEAK 24(17Q12) WILD-TYPE 130 89 249 95 60 112

Figure S214.  Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.059

Table S215.  Gene #24: 'amp_17q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 24(17Q12) MUTATED 77 38 19 29 37
AMP PEAK 24(17Q12) WILD-TYPE 103 101 80 82 96

Figure S215.  Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.038

Table S216.  Gene #24: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
AMP PEAK 24(17Q12) MUTATED 117 58 25
AMP PEAK 24(17Q12) WILD-TYPE 188 189 85

Figure S216.  Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q23.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S217.  Gene #25: '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 25(17Q23.1) MUTATED 9 17 81 29 16 44 11 9
AMP PEAK 25(17Q23.1) WILD-TYPE 12 19 38 67 93 28 9 31

Figure S217.  Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q23.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S218.  Gene #25: 'amp_17q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 25(17Q23.1) MUTATED 62 45 71 25 13
AMP PEAK 25(17Q23.1) WILD-TYPE 39 107 43 63 45

Figure S218.  Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S219.  Gene #25: 'amp_17q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
AMP PEAK 25(17Q23.1) MUTATED 201 68 23 113 20
AMP PEAK 25(17Q23.1) WILD-TYPE 59 344 70 152 29

Figure S219.  Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S220.  Gene #25: 'amp_17q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
AMP PEAK 25(17Q23.1) MUTATED 52 61 99 28 40
AMP PEAK 25(17Q23.1) WILD-TYPE 80 136 78 60 88

Figure S220.  Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S221.  Gene #25: 'amp_17q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
AMP PEAK 25(17Q23.1) MUTATED 13 40 26 68 19
AMP PEAK 25(17Q23.1) WILD-TYPE 51 66 64 39 12

Figure S221.  Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S222.  Gene #25: 'amp_17q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
AMP PEAK 25(17Q23.1) MUTATED 249 122 52
AMP PEAK 25(17Q23.1) WILD-TYPE 294 176 180

Figure S222.  Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S223.  Gene #25: 'amp_17q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
AMP PEAK 25(17Q23.1) MUTATED 126 100 88 20 60 29
AMP PEAK 25(17Q23.1) WILD-TYPE 93 64 218 121 123 31

Figure S223.  Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q23.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S224.  Gene #25: 'amp_17q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
AMP PEAK 25(17Q23.1) MUTATED 166 64 187
AMP PEAK 25(17Q23.1) WILD-TYPE 165 189 289

Figure S224.  Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S225.  Gene #25: 'amp_17q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
AMP PEAK 25(17Q23.1) MUTATED 126 84 93 34 36 44
AMP PEAK 25(17Q23.1) WILD-TYPE 105 76 229 93 50 90

Figure S225.  Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.019

Table S226.  Gene #25: 'amp_17q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 25(17Q23.1) MUTATED 88 58 26 27 47
AMP PEAK 25(17Q23.1) WILD-TYPE 92 81 73 84 86

Figure S226.  Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S227.  Gene #25: 'amp_17q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
AMP PEAK 25(17Q23.1) MUTATED 150 67 29
AMP PEAK 25(17Q23.1) WILD-TYPE 155 180 81

Figure S227.  Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.12' versus 'MRNA_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.019

Table S228.  Gene #26: '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 26(19P13.12) MUTATED 5 6 22 40 16 11 5 4
AMP PEAK 26(19P13.12) WILD-TYPE 16 30 97 56 93 61 15 36

Figure S228.  Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19p13.12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.045

Table S229.  Gene #26: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 26(19P13.12) MUTATED 19 21 23 35 11
AMP PEAK 26(19P13.12) WILD-TYPE 82 131 91 53 47

Figure S229.  Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19p13.12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S230.  Gene #26: 'amp_19p13.12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
AMP PEAK 26(19P13.12) MUTATED 49 38 29 100 13
AMP PEAK 26(19P13.12) WILD-TYPE 211 374 64 165 36

Figure S230.  Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.12' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.019

Table S231.  Gene #26: 'amp_19p13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
AMP PEAK 26(19P13.12) MUTATED 47 25 31 16 26
AMP PEAK 26(19P13.12) WILD-TYPE 85 172 146 72 102

Figure S231.  Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.12' versus 'RPPA_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.16

Table S232.  Gene #26: 'amp_19p13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
AMP PEAK 26(19P13.12) MUTATED 49 25 17
AMP PEAK 26(19P13.12) WILD-TYPE 100 107 100

Figure S232.  Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19p13.12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S233.  Gene #26: 'amp_19p13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
AMP PEAK 26(19P13.12) MUTATED 88 102 37
AMP PEAK 26(19P13.12) WILD-TYPE 455 196 195

Figure S233.  Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19p13.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S234.  Gene #26: 'amp_19p13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
AMP PEAK 26(19P13.12) MUTATED 39 30 54 15 74 15
AMP PEAK 26(19P13.12) WILD-TYPE 180 134 252 126 109 45

Figure S234.  Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S235.  Gene #26: 'amp_19p13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
AMP PEAK 26(19P13.12) MUTATED 105 48 70
AMP PEAK 26(19P13.12) WILD-TYPE 226 205 406

Figure S235.  Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19p13.12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S236.  Gene #26: 'amp_19p13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
AMP PEAK 26(19P13.12) MUTATED 44 42 53 18 10 56
AMP PEAK 26(19P13.12) WILD-TYPE 187 118 269 109 76 78

Figure S236.  Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19p13.12' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S237.  Gene #26: 'amp_19p13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 26(19P13.12) MUTATED 27 54 16 27 18
AMP PEAK 26(19P13.12) WILD-TYPE 153 85 83 84 115

Figure S237.  Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S238.  Gene #27: '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 27(19Q12) MUTATED 4 5 29 55 15 20 7 5
AMP PEAK 27(19Q12) WILD-TYPE 17 31 90 41 94 52 13 35

Figure S238.  Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S239.  Gene #27: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 27(19Q12) MUTATED 20 24 35 50 11
AMP PEAK 27(19Q12) WILD-TYPE 81 128 79 38 47

Figure S239.  Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S240.  Gene #27: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
AMP PEAK 27(19Q12) MUTATED 55 39 30 143 16
AMP PEAK 27(19Q12) WILD-TYPE 205 373 63 122 33

Figure S240.  Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S241.  Gene #27: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
AMP PEAK 27(19Q12) MUTATED 69 29 43 15 25
AMP PEAK 27(19Q12) WILD-TYPE 63 168 134 73 103

Figure S241.  Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19q12' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S242.  Gene #27: 'amp_19q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
AMP PEAK 27(19Q12) MUTATED 64 22 24
AMP PEAK 27(19Q12) WILD-TYPE 85 110 93

Figure S242.  Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19q12' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S243.  Gene #27: 'amp_19q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
AMP PEAK 27(19Q12) MUTATED 15 21 46 18 10
AMP PEAK 27(19Q12) WILD-TYPE 49 85 44 89 21

Figure S243.  Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S244.  Gene #27: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
AMP PEAK 27(19Q12) MUTATED 107 140 35
AMP PEAK 27(19Q12) WILD-TYPE 436 158 197

Figure S244.  Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S245.  Gene #27: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
AMP PEAK 27(19Q12) MUTATED 45 44 51 15 104 23
AMP PEAK 27(19Q12) WILD-TYPE 174 120 255 126 79 37

Figure S245.  Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S246.  Gene #27: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
AMP PEAK 27(19Q12) MUTATED 153 46 80
AMP PEAK 27(19Q12) WILD-TYPE 178 207 396

Figure S246.  Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S247.  Gene #27: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
AMP PEAK 27(19Q12) MUTATED 61 61 51 19 12 75
AMP PEAK 27(19Q12) WILD-TYPE 170 99 271 108 74 59

Figure S247.  Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S248.  Gene #27: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 27(19Q12) MUTATED 37 72 16 25 26
AMP PEAK 27(19Q12) WILD-TYPE 143 67 83 86 107

Figure S248.  Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00107 (Fisher's exact test), Q value = 0.18

Table S249.  Gene #27: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
AMP PEAK 27(19Q12) MUTATED 102 52 22
AMP PEAK 27(19Q12) WILD-TYPE 203 195 88

Figure S249.  Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q13.42' versus 'MRNA_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.077

Table S250.  Gene #28: '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 28(19Q13.42) MUTATED 5 8 36 40 17 20 10 6
AMP PEAK 28(19Q13.42) WILD-TYPE 16 28 83 56 92 52 10 34

Figure S250.  Get High-res Image Gene #28: 'amp_19q13.42' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q13.42' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S251.  Gene #28: 'amp_19q13.42' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
AMP PEAK 28(19Q13.42) MUTATED 74 42 30 109 20
AMP PEAK 28(19Q13.42) WILD-TYPE 186 370 63 156 29

Figure S251.  Get High-res Image Gene #28: 'amp_19q13.42' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q13.42' versus 'METHLYATION_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.16

Table S252.  Gene #28: 'amp_19q13.42' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
AMP PEAK 28(19Q13.42) MUTATED 42 35 56 19 21
AMP PEAK 28(19Q13.42) WILD-TYPE 90 162 121 69 107

Figure S252.  Get High-res Image Gene #28: 'amp_19q13.42' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19q13.42' versus 'RPPA_CNMF'

P value = 0.00119 (Fisher's exact test), Q value = 0.19

Table S253.  Gene #28: 'amp_19q13.42' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
AMP PEAK 28(19Q13.42) MUTATED 57 26 27
AMP PEAK 28(19Q13.42) WILD-TYPE 92 106 90

Figure S253.  Get High-res Image Gene #28: 'amp_19q13.42' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19q13.42' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.044

Table S254.  Gene #28: 'amp_19q13.42' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
AMP PEAK 28(19Q13.42) MUTATED 136 98 40
AMP PEAK 28(19Q13.42) WILD-TYPE 407 200 192

Figure S254.  Get High-res Image Gene #28: 'amp_19q13.42' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q13.42' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S255.  Gene #28: 'amp_19q13.42' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
AMP PEAK 28(19Q13.42) MUTATED 62 51 63 16 63 19
AMP PEAK 28(19Q13.42) WILD-TYPE 157 113 243 125 120 41

Figure S255.  Get High-res Image Gene #28: 'amp_19q13.42' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q13.42' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S256.  Gene #28: 'amp_19q13.42' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
AMP PEAK 28(19Q13.42) MUTATED 119 49 103
AMP PEAK 28(19Q13.42) WILD-TYPE 212 204 373

Figure S256.  Get High-res Image Gene #28: 'amp_19q13.42' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19q13.42' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S257.  Gene #28: 'amp_19q13.42' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
AMP PEAK 28(19Q13.42) MUTATED 71 59 61 20 16 44
AMP PEAK 28(19Q13.42) WILD-TYPE 160 101 261 107 70 90

Figure S257.  Get High-res Image Gene #28: 'amp_19q13.42' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S258.  Gene #29: '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 29(20Q13.2) MUTATED 12 18 85 52 35 49 15 10
AMP PEAK 29(20Q13.2) WILD-TYPE 9 18 34 44 74 23 5 30

Figure S258.  Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q13.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S259.  Gene #29: 'amp_20q13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 29(20Q13.2) MUTATED 73 56 86 44 17
AMP PEAK 29(20Q13.2) WILD-TYPE 28 96 28 44 41

Figure S259.  Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S260.  Gene #29: 'amp_20q13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
AMP PEAK 29(20Q13.2) MUTATED 210 75 57 177 28
AMP PEAK 29(20Q13.2) WILD-TYPE 50 337 36 88 21

Figure S260.  Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S261.  Gene #29: 'amp_20q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
AMP PEAK 29(20Q13.2) MUTATED 83 78 113 29 49
AMP PEAK 29(20Q13.2) WILD-TYPE 49 119 64 59 79

Figure S261.  Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.2' versus 'RPPA_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.11

Table S262.  Gene #29: 'amp_20q13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
AMP PEAK 29(20Q13.2) MUTATED 101 66 54
AMP PEAK 29(20Q13.2) WILD-TYPE 48 66 63

Figure S262.  Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.044

Table S263.  Gene #29: 'amp_20q13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
AMP PEAK 29(20Q13.2) MUTATED 29 44 53 73 22
AMP PEAK 29(20Q13.2) WILD-TYPE 35 62 37 34 9

Figure S263.  Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20q13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S264.  Gene #29: 'amp_20q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
AMP PEAK 29(20Q13.2) MUTATED 309 172 63
AMP PEAK 29(20Q13.2) WILD-TYPE 234 126 169

Figure S264.  Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S265.  Gene #29: 'amp_20q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
AMP PEAK 29(20Q13.2) MUTATED 153 120 104 36 98 33
AMP PEAK 29(20Q13.2) WILD-TYPE 66 44 202 105 85 27

Figure S265.  Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S266.  Gene #29: 'amp_20q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
AMP PEAK 29(20Q13.2) MUTATED 211 83 245
AMP PEAK 29(20Q13.2) WILD-TYPE 120 170 231

Figure S266.  Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S267.  Gene #29: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
AMP PEAK 29(20Q13.2) MUTATED 156 104 101 65 42 71
AMP PEAK 29(20Q13.2) WILD-TYPE 75 56 221 62 44 63

Figure S267.  Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S268.  Gene #29: 'amp_20q13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 29(20Q13.2) MUTATED 117 87 42 45 51
AMP PEAK 29(20Q13.2) WILD-TYPE 63 52 57 66 82

Figure S268.  Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S269.  Gene #29: 'amp_20q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
AMP PEAK 29(20Q13.2) MUTATED 188 103 51
AMP PEAK 29(20Q13.2) WILD-TYPE 117 144 59

Figure S269.  Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.13' versus 'MRNA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.015

Table S270.  Gene #30: '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 S270.  Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.13' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S271.  Gene #30: 'del_1p36.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 1(1P36.13) MUTATED 57 39 67 39 17
DEL PEAK 1(1P36.13) WILD-TYPE 44 113 47 49 41

Figure S271.  Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S272.  Gene #30: 'del_1p36.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 1(1P36.13) MUTATED 168 66 60 135 22
DEL PEAK 1(1P36.13) WILD-TYPE 92 346 33 130 27

Figure S272.  Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S273.  Gene #30: 'del_1p36.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 1(1P36.13) MUTATED 58 64 110 24 36
DEL PEAK 1(1P36.13) WILD-TYPE 74 133 67 64 92

Figure S273.  Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S274.  Gene #30: 'del_1p36.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 1(1P36.13) MUTATED 263 127 58
DEL PEAK 1(1P36.13) WILD-TYPE 280 171 174

Figure S274.  Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S275.  Gene #30: 'del_1p36.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 1(1P36.13) MUTATED 112 106 99 33 80 18
DEL PEAK 1(1P36.13) WILD-TYPE 107 58 207 108 103 42

Figure S275.  Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.13' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.025

Table S276.  Gene #30: 'del_1p36.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 1(1P36.13) MUTATED 162 80 195
DEL PEAK 1(1P36.13) WILD-TYPE 169 173 281

Figure S276.  Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S277.  Gene #30: 'del_1p36.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 1(1P36.13) MUTATED 116 75 92 60 34 60
DEL PEAK 1(1P36.13) WILD-TYPE 115 85 230 67 52 74

Figure S277.  Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p22.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S278.  Gene #31: 'del_1p22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 2(1P22.1) MUTATED 49 40 62 18 14
DEL PEAK 2(1P22.1) WILD-TYPE 52 112 52 70 44

Figure S278.  Get High-res Image Gene #31: 'del_1p22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S279.  Gene #31: 'del_1p22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 2(1P22.1) MUTATED 143 64 58 81 15
DEL PEAK 2(1P22.1) WILD-TYPE 117 348 35 184 34

Figure S279.  Get High-res Image Gene #31: 'del_1p22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S280.  Gene #31: 'del_1p22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 2(1P22.1) MUTATED 32 55 87 25 29
DEL PEAK 2(1P22.1) WILD-TYPE 100 142 90 63 99

Figure S280.  Get High-res Image Gene #31: 'del_1p22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S281.  Gene #31: 'del_1p22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 2(1P22.1) MUTATED 222 80 56
DEL PEAK 2(1P22.1) WILD-TYPE 321 218 176

Figure S281.  Get High-res Image Gene #31: 'del_1p22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S282.  Gene #31: 'del_1p22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 2(1P22.1) MUTATED 89 96 86 32 38 17
DEL PEAK 2(1P22.1) WILD-TYPE 130 68 220 109 145 43

Figure S282.  Get High-res Image Gene #31: 'del_1p22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S283.  Gene #31: 'del_1p22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 2(1P22.1) MUTATED 99 56 84 58 29 26
DEL PEAK 2(1P22.1) WILD-TYPE 132 104 238 69 57 108

Figure S283.  Get High-res Image Gene #31: 'del_1p22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S284.  Gene #32: '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 S284.  Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_2q37.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S285.  Gene #32: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 3(2Q37.3) MUTATED 40 22 48 43 10
DEL PEAK 3(2Q37.3) WILD-TYPE 61 130 66 45 48

Figure S285.  Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S286.  Gene #32: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 3(2Q37.3) MUTATED 99 43 28 128 18
DEL PEAK 3(2Q37.3) WILD-TYPE 161 369 65 137 31

Figure S286.  Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S287.  Gene #32: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 3(2Q37.3) MUTATED 64 46 49 15 19
DEL PEAK 3(2Q37.3) WILD-TYPE 68 151 128 73 109

Figure S287.  Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q37.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S288.  Gene #32: 'del_2q37.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
DEL PEAK 3(2Q37.3) MUTATED 73 40 14
DEL PEAK 3(2Q37.3) WILD-TYPE 76 92 103

Figure S288.  Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_2q37.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S289.  Gene #32: 'del_2q37.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
DEL PEAK 3(2Q37.3) MUTATED 19 10 41 45 12
DEL PEAK 3(2Q37.3) WILD-TYPE 45 96 49 62 19

Figure S289.  Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S290.  Gene #32: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 3(2Q37.3) MUTATED 157 132 24
DEL PEAK 3(2Q37.3) WILD-TYPE 386 166 208

Figure S290.  Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S291.  Gene #32: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 3(2Q37.3) MUTATED 76 72 44 19 88 14
DEL PEAK 3(2Q37.3) WILD-TYPE 143 92 262 122 95 46

Figure S291.  Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S292.  Gene #32: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 3(2Q37.3) MUTATED 147 40 121
DEL PEAK 3(2Q37.3) WILD-TYPE 184 213 355

Figure S292.  Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S293.  Gene #32: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 3(2Q37.3) MUTATED 74 53 52 36 25 68
DEL PEAK 3(2Q37.3) WILD-TYPE 157 107 270 91 61 66

Figure S293.  Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S294.  Gene #32: 'del_2q37.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 3(2Q37.3) MUTATED 59 61 14 20 27
DEL PEAK 3(2Q37.3) WILD-TYPE 121 78 85 91 106

Figure S294.  Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_2q37.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.017

Table S295.  Gene #32: 'del_2q37.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 3(2Q37.3) MUTATED 108 48 25
DEL PEAK 3(2Q37.3) WILD-TYPE 197 199 85

Figure S295.  Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p21.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S296.  Gene #33: '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 S296.  Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p21.31' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S297.  Gene #33: 'del_3p21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 4(3P21.31) MUTATED 29 36 55 48 1
DEL PEAK 4(3P21.31) WILD-TYPE 72 116 59 40 57

Figure S297.  Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p21.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S298.  Gene #33: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 4(3P21.31) MUTATED 99 60 18 164 6
DEL PEAK 4(3P21.31) WILD-TYPE 161 352 75 101 43

Figure S298.  Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p21.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S299.  Gene #33: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 4(3P21.31) MUTATED 70 31 74 23 27
DEL PEAK 4(3P21.31) WILD-TYPE 62 166 103 65 101

Figure S299.  Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p21.31' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S300.  Gene #33: 'del_3p21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
DEL PEAK 4(3P21.31) MUTATED 81 27 36
DEL PEAK 4(3P21.31) WILD-TYPE 68 105 81

Figure S300.  Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p21.31' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S301.  Gene #33: 'del_3p21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
DEL PEAK 4(3P21.31) MUTATED 5 32 55 41 11
DEL PEAK 4(3P21.31) WILD-TYPE 59 74 35 66 20

Figure S301.  Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p21.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S302.  Gene #33: 'del_3p21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 4(3P21.31) MUTATED 144 158 44
DEL PEAK 4(3P21.31) WILD-TYPE 399 140 188

Figure S302.  Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S303.  Gene #33: 'del_3p21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 4(3P21.31) MUTATED 60 85 72 7 100 22
DEL PEAK 4(3P21.31) WILD-TYPE 159 79 234 134 83 38

Figure S303.  Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S304.  Gene #33: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 4(3P21.31) MUTATED 171 54 115
DEL PEAK 4(3P21.31) WILD-TYPE 160 199 361

Figure S304.  Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S305.  Gene #33: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 4(3P21.31) MUTATED 98 69 66 23 11 73
DEL PEAK 4(3P21.31) WILD-TYPE 133 91 256 104 75 61

Figure S305.  Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S306.  Gene #33: 'del_3p21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 4(3P21.31) MUTATED 54 80 22 21 36
DEL PEAK 4(3P21.31) WILD-TYPE 126 59 77 90 97

Figure S306.  Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.031

Table S307.  Gene #33: 'del_3p21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 4(3P21.31) MUTATED 123 67 23
DEL PEAK 4(3P21.31) WILD-TYPE 182 180 87

Figure S307.  Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p16.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S308.  Gene #34: '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 S308.  Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4p16.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S309.  Gene #34: 'del_4p16.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 5(4P16.3) MUTATED 27 28 51 52 11
DEL PEAK 5(4P16.3) WILD-TYPE 74 124 63 36 47

Figure S309.  Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4p16.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S310.  Gene #34: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 5(4P16.3) MUTATED 75 50 44 156 14
DEL PEAK 5(4P16.3) WILD-TYPE 185 362 49 109 35

Figure S310.  Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S311.  Gene #34: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 5(4P16.3) MUTATED 84 40 50 15 29
DEL PEAK 5(4P16.3) WILD-TYPE 48 157 127 73 99

Figure S311.  Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p16.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S312.  Gene #34: 'del_4p16.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
DEL PEAK 5(4P16.3) MUTATED 77 38 25
DEL PEAK 5(4P16.3) WILD-TYPE 72 94 92

Figure S312.  Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4p16.3' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S313.  Gene #34: 'del_4p16.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
DEL PEAK 5(4P16.3) MUTATED 18 25 54 32 11
DEL PEAK 5(4P16.3) WILD-TYPE 46 81 36 75 20

Figure S313.  Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4p16.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S314.  Gene #34: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 5(4P16.3) MUTATED 137 169 31
DEL PEAK 5(4P16.3) WILD-TYPE 406 129 201

Figure S314.  Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S315.  Gene #34: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 5(4P16.3) MUTATED 49 67 57 24 112 28
DEL PEAK 5(4P16.3) WILD-TYPE 170 97 249 117 71 32

Figure S315.  Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S316.  Gene #34: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 5(4P16.3) MUTATED 167 47 114
DEL PEAK 5(4P16.3) WILD-TYPE 164 206 362

Figure S316.  Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S317.  Gene #34: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 5(4P16.3) MUTATED 70 67 53 38 16 84
DEL PEAK 5(4P16.3) WILD-TYPE 161 93 269 89 70 50

Figure S317.  Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S318.  Gene #34: 'del_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 5(4P16.3) MUTATED 48 83 21 27 23
DEL PEAK 5(4P16.3) WILD-TYPE 132 56 78 84 110

Figure S318.  Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.055

Table S319.  Gene #34: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 5(4P16.3) MUTATED 115 54 33
DEL PEAK 5(4P16.3) WILD-TYPE 190 193 77

Figure S319.  Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q35.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S320.  Gene #35: 'del_4q35.1' 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 6(4Q35.1) MUTATED 6 9 25 54 24 34 9 9
DEL PEAK 6(4Q35.1) WILD-TYPE 15 27 94 42 85 38 11 31

Figure S320.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q35.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S321.  Gene #35: 'del_4q35.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 6(4Q35.1) MUTATED 25 31 52 49 13
DEL PEAK 6(4Q35.1) WILD-TYPE 76 121 62 39 45

Figure S321.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q35.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S322.  Gene #35: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 6(4Q35.1) MUTATED 65 53 49 164 14
DEL PEAK 6(4Q35.1) WILD-TYPE 195 359 44 101 35

Figure S322.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q35.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S323.  Gene #35: 'del_4q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 6(4Q35.1) MUTATED 82 38 41 19 38
DEL PEAK 6(4Q35.1) WILD-TYPE 50 159 136 69 90

Figure S323.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q35.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S324.  Gene #35: 'del_4q35.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
DEL PEAK 6(4Q35.1) MUTATED 80 33 27
DEL PEAK 6(4Q35.1) WILD-TYPE 69 99 90

Figure S324.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4q35.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S325.  Gene #35: 'del_4q35.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
DEL PEAK 6(4Q35.1) MUTATED 15 26 54 34 11
DEL PEAK 6(4Q35.1) WILD-TYPE 49 80 36 73 20

Figure S325.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4q35.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S326.  Gene #35: 'del_4q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 6(4Q35.1) MUTATED 146 166 31
DEL PEAK 6(4Q35.1) WILD-TYPE 397 132 201

Figure S326.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S327.  Gene #35: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 6(4Q35.1) MUTATED 44 68 65 27 116 23
DEL PEAK 6(4Q35.1) WILD-TYPE 175 96 241 114 67 37

Figure S327.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S328.  Gene #35: 'del_4q35.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 6(4Q35.1) MUTATED 167 52 114
DEL PEAK 6(4Q35.1) WILD-TYPE 164 201 362

Figure S328.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q35.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S329.  Gene #35: 'del_4q35.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 6(4Q35.1) MUTATED 65 69 54 43 15 87
DEL PEAK 6(4Q35.1) WILD-TYPE 166 91 268 84 71 47

Figure S329.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S330.  Gene #35: 'del_4q35.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 6(4Q35.1) MUTATED 50 86 23 26 22
DEL PEAK 6(4Q35.1) WILD-TYPE 130 53 76 85 111

Figure S330.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q35.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00071 (Fisher's exact test), Q value = 0.13

Table S331.  Gene #35: 'del_4q35.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 6(4Q35.1) MUTATED 116 57 34
DEL PEAK 6(4Q35.1) WILD-TYPE 189 190 76

Figure S331.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q11.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S332.  Gene #36: '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 S332.  Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S333.  Gene #36: 'del_5q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 7(5Q11.2) MUTATED 18 15 38 63 2
DEL PEAK 7(5Q11.2) WILD-TYPE 83 137 76 25 56

Figure S333.  Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S334.  Gene #36: 'del_5q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 7(5Q11.2) MUTATED 39 32 8 189 12
DEL PEAK 7(5Q11.2) WILD-TYPE 221 380 85 76 37

Figure S334.  Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S335.  Gene #36: 'del_5q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 7(5Q11.2) MUTATED 99 16 30 9 32
DEL PEAK 7(5Q11.2) WILD-TYPE 33 181 147 79 96

Figure S335.  Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q11.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S336.  Gene #36: 'del_5q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
DEL PEAK 7(5Q11.2) MUTATED 80 12 23
DEL PEAK 7(5Q11.2) WILD-TYPE 69 120 94

Figure S336.  Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_5q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S337.  Gene #36: 'del_5q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
DEL PEAK 7(5Q11.2) MUTATED 4 14 64 23 10
DEL PEAK 7(5Q11.2) WILD-TYPE 60 92 26 84 21

Figure S337.  Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_5q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S338.  Gene #36: 'del_5q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 7(5Q11.2) MUTATED 81 181 16
DEL PEAK 7(5Q11.2) WILD-TYPE 462 117 216

Figure S338.  Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S339.  Gene #36: 'del_5q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 7(5Q11.2) MUTATED 35 44 31 5 137 26
DEL PEAK 7(5Q11.2) WILD-TYPE 184 120 275 136 46 34

Figure S339.  Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S340.  Gene #36: 'del_5q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 7(5Q11.2) MUTATED 184 29 55
DEL PEAK 7(5Q11.2) WILD-TYPE 147 224 421

Figure S340.  Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S341.  Gene #36: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 7(5Q11.2) MUTATED 53 64 26 11 8 106
DEL PEAK 7(5Q11.2) WILD-TYPE 178 96 296 116 78 28

Figure S341.  Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S342.  Gene #36: 'del_5q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 7(5Q11.2) MUTATED 26 98 12 15 20
DEL PEAK 7(5Q11.2) WILD-TYPE 154 41 87 96 113

Figure S342.  Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S343.  Gene #36: 'del_5q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 7(5Q11.2) MUTATED 125 31 15
DEL PEAK 7(5Q11.2) WILD-TYPE 180 216 95

Figure S343.  Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q21.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S344.  Gene #37: '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 S344.  Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q21.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S345.  Gene #37: 'del_5q21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 8(5Q21.3) MUTATED 18 13 36 66 2
DEL PEAK 8(5Q21.3) WILD-TYPE 83 139 78 22 56

Figure S345.  Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S346.  Gene #37: 'del_5q21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 8(5Q21.3) MUTATED 38 23 8 193 10
DEL PEAK 8(5Q21.3) WILD-TYPE 222 389 85 72 39

Figure S346.  Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S347.  Gene #37: 'del_5q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 8(5Q21.3) MUTATED 106 10 28 6 30
DEL PEAK 8(5Q21.3) WILD-TYPE 26 187 149 82 98

Figure S347.  Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q21.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S348.  Gene #37: 'del_5q21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
DEL PEAK 8(5Q21.3) MUTATED 78 12 23
DEL PEAK 8(5Q21.3) WILD-TYPE 71 120 94

Figure S348.  Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_5q21.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S349.  Gene #37: 'del_5q21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
DEL PEAK 8(5Q21.3) MUTATED 5 16 62 21 9
DEL PEAK 8(5Q21.3) WILD-TYPE 59 90 28 86 22

Figure S349.  Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_5q21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S350.  Gene #37: 'del_5q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 8(5Q21.3) MUTATED 71 188 11
DEL PEAK 8(5Q21.3) WILD-TYPE 472 110 221

Figure S350.  Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S351.  Gene #37: 'del_5q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 8(5Q21.3) MUTATED 31 40 29 4 142 24
DEL PEAK 8(5Q21.3) WILD-TYPE 188 124 277 137 41 36

Figure S351.  Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S352.  Gene #37: 'del_5q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 8(5Q21.3) MUTATED 186 24 52
DEL PEAK 8(5Q21.3) WILD-TYPE 145 229 424

Figure S352.  Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S353.  Gene #37: 'del_5q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 8(5Q21.3) MUTATED 52 67 20 8 6 109
DEL PEAK 8(5Q21.3) WILD-TYPE 179 93 302 119 80 25

Figure S353.  Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S354.  Gene #37: 'del_5q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 8(5Q21.3) MUTATED 22 101 12 12 18
DEL PEAK 8(5Q21.3) WILD-TYPE 158 38 87 99 115

Figure S354.  Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S355.  Gene #37: 'del_5q21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 8(5Q21.3) MUTATED 124 30 11
DEL PEAK 8(5Q21.3) WILD-TYPE 181 217 99

Figure S355.  Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S356.  Gene #38: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 9(6P25.3) MUTATED 78 42 17 57 10
DEL PEAK 9(6P25.3) WILD-TYPE 182 370 76 208 39

Figure S356.  Get High-res Image Gene #38: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.063

Table S357.  Gene #38: 'del_6p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 9(6P25.3) MUTATED 118 61 24
DEL PEAK 9(6P25.3) WILD-TYPE 425 237 208

Figure S357.  Get High-res Image Gene #38: 'del_6p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q15' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S358.  Gene #39: '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 S358.  Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_6q15' versus 'MRNA_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.063

Table S359.  Gene #39: 'del_6q15' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 10(6Q15) MUTATED 50 51 42 18 14
DEL PEAK 10(6Q15) WILD-TYPE 51 101 72 70 44

Figure S359.  Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_6q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S360.  Gene #39: 'del_6q15' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 10(6Q15) MUTATED 161 91 27 53 26
DEL PEAK 10(6Q15) WILD-TYPE 99 321 66 212 23

Figure S360.  Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q15' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S361.  Gene #39: 'del_6q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 10(6Q15) MUTATED 26 81 73 21 25
DEL PEAK 10(6Q15) WILD-TYPE 106 116 104 67 103

Figure S361.  Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q15' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S362.  Gene #39: 'del_6q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 10(6Q15) MUTATED 221 68 66
DEL PEAK 10(6Q15) WILD-TYPE 322 230 166

Figure S362.  Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S363.  Gene #39: 'del_6q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 10(6Q15) MUTATED 109 65 94 37 30 20
DEL PEAK 10(6Q15) WILD-TYPE 110 99 212 104 153 40

Figure S363.  Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S364.  Gene #39: 'del_6q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 10(6Q15) MUTATED 90 49 100 50 43 23
DEL PEAK 10(6Q15) WILD-TYPE 141 111 222 77 43 111

Figure S364.  Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q15' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.031

Table S365.  Gene #39: 'del_6q15' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 10(6Q15) MUTATED 76 25 33 38 47
DEL PEAK 10(6Q15) WILD-TYPE 104 114 66 73 86

Figure S365.  Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6q27' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S366.  Gene #40: 'del_6q27' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 11(6Q27) MUTATED 135 97 26 89 28
DEL PEAK 11(6Q27) WILD-TYPE 125 315 67 176 21

Figure S366.  Get High-res Image Gene #40: 'del_6q27' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q27' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00101 (Fisher's exact test), Q value = 0.17

Table S367.  Gene #40: 'del_6q27' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 11(6Q27) MUTATED 91 59 100 30 63 28
DEL PEAK 11(6Q27) WILD-TYPE 128 105 206 111 120 32

Figure S367.  Get High-res Image Gene #40: 'del_6q27' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7p22.3' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.01

Table S368.  Gene #41: '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 S368.  Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_7p22.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S369.  Gene #41: 'del_7p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 12(7P22.3) MUTATED 20 8 22 24 2
DEL PEAK 12(7P22.3) WILD-TYPE 81 144 92 64 56

Figure S369.  Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_7p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S370.  Gene #41: 'del_7p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 12(7P22.3) MUTATED 53 12 3 65 3
DEL PEAK 12(7P22.3) WILD-TYPE 207 400 90 200 46

Figure S370.  Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_7p22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S371.  Gene #41: 'del_7p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 12(7P22.3) MUTATED 30 12 25 6 4
DEL PEAK 12(7P22.3) WILD-TYPE 102 185 152 82 124

Figure S371.  Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_7p22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S372.  Gene #41: 'del_7p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 12(7P22.3) MUTATED 63 67 4
DEL PEAK 12(7P22.3) WILD-TYPE 480 231 228

Figure S372.  Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7p22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S373.  Gene #41: 'del_7p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 12(7P22.3) MUTATED 32 28 13 8 48 5
DEL PEAK 12(7P22.3) WILD-TYPE 187 136 293 133 135 55

Figure S373.  Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7p22.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S374.  Gene #41: 'del_7p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 12(7P22.3) MUTATED 71 7 54
DEL PEAK 12(7P22.3) WILD-TYPE 260 246 422

Figure S374.  Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_7p22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S375.  Gene #41: 'del_7p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 12(7P22.3) MUTATED 42 24 5 14 8 39
DEL PEAK 12(7P22.3) WILD-TYPE 189 136 317 113 78 95

Figure S375.  Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7p22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S376.  Gene #41: 'del_7p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 12(7P22.3) MUTATED 18 34 6 6 11
DEL PEAK 12(7P22.3) WILD-TYPE 162 105 93 105 122

Figure S376.  Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.013

Table S377.  Gene #41: 'del_7p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 12(7P22.3) MUTATED 53 16 6
DEL PEAK 12(7P22.3) WILD-TYPE 252 231 104

Figure S377.  Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q36.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S378.  Gene #42: 'del_7q36.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 13(7Q36.1) MUTATED 16 17 45 17 7
DEL PEAK 13(7Q36.1) WILD-TYPE 85 135 69 71 51

Figure S378.  Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_7q36.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S379.  Gene #42: 'del_7q36.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 13(7Q36.1) MUTATED 66 38 14 74 7
DEL PEAK 13(7Q36.1) WILD-TYPE 194 374 79 191 42

Figure S379.  Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_7q36.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S380.  Gene #42: 'del_7q36.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 13(7Q36.1) MUTATED 100 77 20
DEL PEAK 13(7Q36.1) WILD-TYPE 443 221 212

Figure S380.  Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7q36.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S381.  Gene #42: 'del_7q36.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 13(7Q36.1) MUTATED 44 46 33 16 40 18
DEL PEAK 13(7Q36.1) WILD-TYPE 175 118 273 125 143 42

Figure S381.  Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7q36.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S382.  Gene #42: 'del_7q36.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 13(7Q36.1) MUTATED 92 20 82
DEL PEAK 13(7Q36.1) WILD-TYPE 239 233 394

Figure S382.  Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_7q36.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S383.  Gene #42: 'del_7q36.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 13(7Q36.1) MUTATED 54 46 24 24 15 31
DEL PEAK 13(7Q36.1) WILD-TYPE 177 114 298 103 71 103

Figure S383.  Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7q36.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.019

Table S384.  Gene #42: 'del_7q36.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 13(7Q36.1) MUTATED 41 39 9 11 17
DEL PEAK 13(7Q36.1) WILD-TYPE 139 100 90 100 116

Figure S384.  Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7q36.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S385.  Gene #42: 'del_7q36.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 13(7Q36.1) MUTATED 76 21 20
DEL PEAK 13(7Q36.1) WILD-TYPE 229 226 90

Figure S385.  Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S386.  Gene #43: '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 S386.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p23.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S387.  Gene #43: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 14(8P23.2) MUTATED 67 59 78 57 15
DEL PEAK 14(8P23.2) WILD-TYPE 34 93 36 31 43

Figure S387.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S388.  Gene #43: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 14(8P23.2) MUTATED 175 133 22 187 40
DEL PEAK 14(8P23.2) WILD-TYPE 85 279 71 78 9

Figure S388.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S389.  Gene #43: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 14(8P23.2) MUTATED 87 81 102 26 63
DEL PEAK 14(8P23.2) WILD-TYPE 45 116 75 62 65

Figure S389.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00074 (Fisher's exact test), Q value = 0.13

Table S390.  Gene #43: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
DEL PEAK 14(8P23.2) MUTATED 22 57 58 66 22
DEL PEAK 14(8P23.2) WILD-TYPE 42 49 32 41 9

Figure S390.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S391.  Gene #43: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 14(8P23.2) MUTATED 283 193 77
DEL PEAK 14(8P23.2) WILD-TYPE 260 105 155

Figure S391.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S392.  Gene #43: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 14(8P23.2) MUTATED 138 110 122 23 113 47
DEL PEAK 14(8P23.2) WILD-TYPE 81 54 184 118 70 13

Figure S392.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S393.  Gene #43: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 14(8P23.2) MUTATED 215 104 226
DEL PEAK 14(8P23.2) WILD-TYPE 116 149 250

Figure S393.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S394.  Gene #43: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 14(8P23.2) MUTATED 131 110 127 51 43 83
DEL PEAK 14(8P23.2) WILD-TYPE 100 50 195 76 43 51

Figure S394.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S395.  Gene #43: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 14(8P23.2) MUTATED 100 92 43 39 58
DEL PEAK 14(8P23.2) WILD-TYPE 80 47 56 72 75

Figure S395.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S396.  Gene #43: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 14(8P23.2) MUTATED 187 105 40
DEL PEAK 14(8P23.2) WILD-TYPE 118 142 70

Figure S396.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p11.21' versus 'MRNA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.015

Table S397.  Gene #44: '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 3 22 24 8 26 7 7
DEL PEAK 15(8P11.21) WILD-TYPE 17 33 97 72 101 46 13 33

Figure S397.  Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p11.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.027

Table S398.  Gene #44: 'del_8p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 15(8P11.21) MUTATED 20 18 37 21 5
DEL PEAK 15(8P11.21) WILD-TYPE 81 134 77 67 53

Figure S398.  Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S399.  Gene #44: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 15(8P11.21) MUTATED 56 44 14 85 1
DEL PEAK 15(8P11.21) WILD-TYPE 204 368 79 180 48

Figure S399.  Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p11.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.029

Table S400.  Gene #44: 'del_8p11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
DEL PEAK 15(8P11.21) MUTATED 5 21 21 23 16
DEL PEAK 15(8P11.21) WILD-TYPE 59 85 69 84 15

Figure S400.  Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_8p11.21' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S401.  Gene #44: 'del_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 15(8P11.21) MUTATED 97 78 25
DEL PEAK 15(8P11.21) WILD-TYPE 446 220 207

Figure S401.  Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S402.  Gene #44: 'del_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 15(8P11.21) MUTATED 37 54 38 10 35 26
DEL PEAK 15(8P11.21) WILD-TYPE 182 110 268 131 148 34

Figure S402.  Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p11.21' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.01

Table S403.  Gene #44: 'del_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 15(8P11.21) MUTATED 87 27 84
DEL PEAK 15(8P11.21) WILD-TYPE 244 226 392

Figure S403.  Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S404.  Gene #44: 'del_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 15(8P11.21) MUTATED 52 61 29 23 11 22
DEL PEAK 15(8P11.21) WILD-TYPE 179 99 293 104 75 112

Figure S404.  Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.098

Table S405.  Gene #44: 'del_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 15(8P11.21) MUTATED 77 31 17
DEL PEAK 15(8P11.21) WILD-TYPE 228 216 93

Figure S405.  Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S406.  Gene #45: '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 S406.  Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p23' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S407.  Gene #45: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 16(9P23) MUTATED 49 36 61 17 10
DEL PEAK 16(9P23) WILD-TYPE 52 116 53 71 48

Figure S407.  Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S408.  Gene #45: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 16(9P23) MUTATED 159 46 15 93 11
DEL PEAK 16(9P23) WILD-TYPE 101 366 78 172 38

Figure S408.  Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S409.  Gene #45: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 16(9P23) MUTATED 37 43 90 14 25
DEL PEAK 16(9P23) WILD-TYPE 95 154 87 74 103

Figure S409.  Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p23' versus 'RPPA_CHIERARCHICAL'

P value = 0.00093 (Fisher's exact test), Q value = 0.16

Table S410.  Gene #45: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
DEL PEAK 16(9P23) MUTATED 15 31 26 53 15
DEL PEAK 16(9P23) WILD-TYPE 49 75 64 54 16

Figure S410.  Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S411.  Gene #45: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 16(9P23) MUTATED 200 90 34
DEL PEAK 16(9P23) WILD-TYPE 343 208 198

Figure S411.  Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S412.  Gene #45: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 16(9P23) MUTATED 101 84 60 16 35 28
DEL PEAK 16(9P23) WILD-TYPE 118 80 246 125 148 32

Figure S412.  Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S413.  Gene #45: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 16(9P23) MUTATED 124 41 152
DEL PEAK 16(9P23) WILD-TYPE 207 212 324

Figure S413.  Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S414.  Gene #45: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 16(9P23) MUTATED 104 76 54 37 24 22
DEL PEAK 16(9P23) WILD-TYPE 127 84 268 90 62 112

Figure S414.  Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.049

Table S415.  Gene #45: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 16(9P23) MUTATED 74 39 23 20 33
DEL PEAK 16(9P23) WILD-TYPE 106 100 76 91 100

Figure S415.  Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.019

Table S416.  Gene #45: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 16(9P23) MUTATED 112 56 21
DEL PEAK 16(9P23) WILD-TYPE 193 191 89

Figure S416.  Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S417.  Gene #46: '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 S417.  Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p21.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S418.  Gene #46: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 17(9P21.3) MUTATED 53 34 65 28 12
DEL PEAK 17(9P21.3) WILD-TYPE 48 118 49 60 46

Figure S418.  Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S419.  Gene #46: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 17(9P21.3) MUTATED 164 52 18 117 12
DEL PEAK 17(9P21.3) WILD-TYPE 96 360 75 148 37

Figure S419.  Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S420.  Gene #46: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 17(9P21.3) MUTATED 51 49 86 14 28
DEL PEAK 17(9P21.3) WILD-TYPE 81 148 91 74 100

Figure S420.  Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S421.  Gene #46: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 17(9P21.3) MUTATED 210 117 33
DEL PEAK 17(9P21.3) WILD-TYPE 333 181 199

Figure S421.  Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S422.  Gene #46: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 17(9P21.3) MUTATED 104 89 56 21 60 30
DEL PEAK 17(9P21.3) WILD-TYPE 115 75 250 120 123 30

Figure S422.  Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S423.  Gene #46: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 17(9P21.3) MUTATED 146 45 162
DEL PEAK 17(9P21.3) WILD-TYPE 185 208 314

Figure S423.  Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S424.  Gene #46: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 17(9P21.3) MUTATED 108 84 53 41 28 39
DEL PEAK 17(9P21.3) WILD-TYPE 123 76 269 86 58 95

Figure S424.  Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.017

Table S425.  Gene #46: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 17(9P21.3) MUTATED 76 54 24 25 30
DEL PEAK 17(9P21.3) WILD-TYPE 104 85 75 86 103

Figure S425.  Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S426.  Gene #46: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 17(9P21.3) MUTATED 128 58 23
DEL PEAK 17(9P21.3) WILD-TYPE 177 189 87

Figure S426.  Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q21.11' versus 'MRNA_CNMF'

P value = 0.00114 (Fisher's exact test), Q value = 0.19

Table S427.  Gene #47: 'del_9q21.11' 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 18(9Q21.11) MUTATED 5 6 42 41 24 27 7 5
DEL PEAK 18(9Q21.11) WILD-TYPE 16 30 77 55 85 45 13 35

Figure S427.  Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9q21.11' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S428.  Gene #47: 'del_9q21.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 18(9Q21.11) MUTATED 37 25 50 35 10
DEL PEAK 18(9Q21.11) WILD-TYPE 64 127 64 53 48

Figure S428.  Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9q21.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S429.  Gene #47: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 18(9Q21.11) MUTATED 110 43 18 108 14
DEL PEAK 18(9Q21.11) WILD-TYPE 150 369 75 157 35

Figure S429.  Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q21.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S430.  Gene #47: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 18(9Q21.11) MUTATED 55 40 54 12 26
DEL PEAK 18(9Q21.11) WILD-TYPE 77 157 123 76 102

Figure S430.  Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q21.11' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S431.  Gene #47: 'del_9q21.11' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
DEL PEAK 18(9Q21.11) MUTATED 69 33 22
DEL PEAK 18(9Q21.11) WILD-TYPE 80 99 95

Figure S431.  Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9q21.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S432.  Gene #47: 'del_9q21.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 18(9Q21.11) MUTATED 158 107 28
DEL PEAK 18(9Q21.11) WILD-TYPE 385 191 204

Figure S432.  Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9q21.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S433.  Gene #47: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 18(9Q21.11) MUTATED 79 60 48 15 69 22
DEL PEAK 18(9Q21.11) WILD-TYPE 140 104 258 126 114 38

Figure S433.  Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S434.  Gene #47: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 18(9Q21.11) MUTATED 139 33 114
DEL PEAK 18(9Q21.11) WILD-TYPE 192 220 362

Figure S434.  Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9q21.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S435.  Gene #47: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 18(9Q21.11) MUTATED 77 67 38 30 19 55
DEL PEAK 18(9Q21.11) WILD-TYPE 154 93 284 97 67 79

Figure S435.  Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S436.  Gene #47: 'del_9q21.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 18(9Q21.11) MUTATED 55 56 21 15 22
DEL PEAK 18(9Q21.11) WILD-TYPE 125 83 78 96 111

Figure S436.  Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9q21.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S437.  Gene #47: 'del_9q21.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 18(9Q21.11) MUTATED 107 45 17
DEL PEAK 18(9Q21.11) WILD-TYPE 198 202 93

Figure S437.  Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q34.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S438.  Gene #48: '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 S438.  Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9q34.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S439.  Gene #48: 'del_9q34.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 19(9Q34.2) MUTATED 36 23 38 50 10
DEL PEAK 19(9Q34.2) WILD-TYPE 65 129 76 38 48

Figure S439.  Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9q34.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S440.  Gene #48: 'del_9q34.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 19(9Q34.2) MUTATED 98 30 14 140 14
DEL PEAK 19(9Q34.2) WILD-TYPE 162 382 79 125 35

Figure S440.  Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q34.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S441.  Gene #48: 'del_9q34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 19(9Q34.2) MUTATED 74 37 47 10 21
DEL PEAK 19(9Q34.2) WILD-TYPE 58 160 130 78 107

Figure S441.  Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q34.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S442.  Gene #48: 'del_9q34.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
DEL PEAK 19(9Q34.2) MUTATED 68 33 21
DEL PEAK 19(9Q34.2) WILD-TYPE 81 99 96

Figure S442.  Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9q34.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S443.  Gene #48: 'del_9q34.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
DEL PEAK 19(9Q34.2) MUTATED 12 20 50 37 3
DEL PEAK 19(9Q34.2) WILD-TYPE 52 86 40 70 28

Figure S443.  Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9q34.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S444.  Gene #48: 'del_9q34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 19(9Q34.2) MUTATED 144 133 18
DEL PEAK 19(9Q34.2) WILD-TYPE 399 165 214

Figure S444.  Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9q34.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S445.  Gene #48: 'del_9q34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 19(9Q34.2) MUTATED 75 51 39 14 102 14
DEL PEAK 19(9Q34.2) WILD-TYPE 144 113 267 127 81 46

Figure S445.  Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q34.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S446.  Gene #48: 'del_9q34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 19(9Q34.2) MUTATED 155 31 101
DEL PEAK 19(9Q34.2) WILD-TYPE 176 222 375

Figure S446.  Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9q34.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S447.  Gene #48: 'del_9q34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 19(9Q34.2) MUTATED 69 61 33 29 17 78
DEL PEAK 19(9Q34.2) WILD-TYPE 162 99 289 98 69 56

Figure S447.  Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q34.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S448.  Gene #48: 'del_9q34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 19(9Q34.2) MUTATED 48 77 17 13 20
DEL PEAK 19(9Q34.2) WILD-TYPE 132 62 82 98 113

Figure S448.  Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9q34.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S449.  Gene #48: 'del_9q34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 19(9Q34.2) MUTATED 118 43 14
DEL PEAK 19(9Q34.2) WILD-TYPE 187 204 96

Figure S449.  Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S450.  Gene #49: '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 S450.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q23.31' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S451.  Gene #49: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 20(10Q23.31) MUTATED 28 29 39 45 8
DEL PEAK 20(10Q23.31) WILD-TYPE 73 123 75 43 50

Figure S451.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S452.  Gene #49: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 20(10Q23.31) MUTATED 88 53 24 137 18
DEL PEAK 20(10Q23.31) WILD-TYPE 172 359 69 128 31

Figure S452.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S453.  Gene #49: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 20(10Q23.31) MUTATED 76 40 65 17 26
DEL PEAK 20(10Q23.31) WILD-TYPE 56 157 112 71 102

Figure S453.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S454.  Gene #49: 'del_10q23.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
DEL PEAK 20(10Q23.31) MUTATED 68 30 20
DEL PEAK 20(10Q23.31) WILD-TYPE 81 102 97

Figure S454.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_10q23.31' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S455.  Gene #49: 'del_10q23.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
DEL PEAK 20(10Q23.31) MUTATED 12 17 45 34 10
DEL PEAK 20(10Q23.31) WILD-TYPE 52 89 45 73 21

Figure S455.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S456.  Gene #49: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 20(10Q23.31) MUTATED 145 142 31
DEL PEAK 20(10Q23.31) WILD-TYPE 398 156 201

Figure S456.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S457.  Gene #49: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 20(10Q23.31) MUTATED 69 65 49 17 96 22
DEL PEAK 20(10Q23.31) WILD-TYPE 150 99 257 124 87 38

Figure S457.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S458.  Gene #49: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 20(10Q23.31) MUTATED 144 56 111
DEL PEAK 20(10Q23.31) WILD-TYPE 187 197 365

Figure S458.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S459.  Gene #49: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 20(10Q23.31) MUTATED 66 71 57 26 18 73
DEL PEAK 20(10Q23.31) WILD-TYPE 165 89 265 101 68 61

Figure S459.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S460.  Gene #49: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 20(10Q23.31) MUTATED 53 74 22 17 32
DEL PEAK 20(10Q23.31) WILD-TYPE 127 65 77 94 101

Figure S460.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.025

Table S461.  Gene #49: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 20(10Q23.31) MUTATED 116 61 21
DEL PEAK 20(10Q23.31) WILD-TYPE 189 186 89

Figure S461.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q26.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S462.  Gene #50: '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 S462.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q26.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S463.  Gene #50: 'del_10q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 21(10Q26.3) MUTATED 31 23 44 49 7
DEL PEAK 21(10Q26.3) WILD-TYPE 70 129 70 39 51

Figure S463.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S464.  Gene #50: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 21(10Q26.3) MUTATED 95 50 21 140 13
DEL PEAK 21(10Q26.3) WILD-TYPE 165 362 72 125 36

Figure S464.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q26.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S465.  Gene #50: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 21(10Q26.3) MUTATED 75 37 68 12 24
DEL PEAK 21(10Q26.3) WILD-TYPE 57 160 109 76 104

Figure S465.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q26.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S466.  Gene #50: 'del_10q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
DEL PEAK 21(10Q26.3) MUTATED 73 28 24
DEL PEAK 21(10Q26.3) WILD-TYPE 76 104 93

Figure S466.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_10q26.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S467.  Gene #50: 'del_10q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
DEL PEAK 21(10Q26.3) MUTATED 11 16 48 36 14
DEL PEAK 21(10Q26.3) WILD-TYPE 53 90 42 71 17

Figure S467.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S468.  Gene #50: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 21(10Q26.3) MUTATED 145 150 23
DEL PEAK 21(10Q26.3) WILD-TYPE 398 148 209

Figure S468.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S469.  Gene #50: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 21(10Q26.3) MUTATED 64 71 43 16 98 26
DEL PEAK 21(10Q26.3) WILD-TYPE 155 93 263 125 85 34

Figure S469.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S470.  Gene #50: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 21(10Q26.3) MUTATED 147 48 113
DEL PEAK 21(10Q26.3) WILD-TYPE 184 205 363

Figure S470.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S471.  Gene #50: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 21(10Q26.3) MUTATED 76 73 48 21 18 72
DEL PEAK 21(10Q26.3) WILD-TYPE 155 87 274 106 68 62

Figure S471.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S472.  Gene #50: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 21(10Q26.3) MUTATED 60 72 20 13 33
DEL PEAK 21(10Q26.3) WILD-TYPE 120 67 79 98 100

Figure S472.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S473.  Gene #50: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 21(10Q26.3) MUTATED 125 54 19
DEL PEAK 21(10Q26.3) WILD-TYPE 180 193 91

Figure S473.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S474.  Gene #51: '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 S474.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11p15.5' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S475.  Gene #51: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 22(11P15.5) MUTATED 24 32 50 42 8
DEL PEAK 22(11P15.5) WILD-TYPE 77 120 64 46 50

Figure S475.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S476.  Gene #51: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 22(11P15.5) MUTATED 89 36 17 159 8
DEL PEAK 22(11P15.5) WILD-TYPE 171 376 76 106 41

Figure S476.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S477.  Gene #51: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 22(11P15.5) MUTATED 69 33 57 15 22
DEL PEAK 22(11P15.5) WILD-TYPE 63 164 120 73 106

Figure S477.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11p15.5' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S478.  Gene #51: 'del_11p15.5' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
DEL PEAK 22(11P15.5) MUTATED 77 27 26
DEL PEAK 22(11P15.5) WILD-TYPE 72 105 91

Figure S478.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_11p15.5' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S479.  Gene #51: 'del_11p15.5' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
DEL PEAK 22(11P15.5) MUTATED 11 20 48 36 15
DEL PEAK 22(11P15.5) WILD-TYPE 53 86 42 71 16

Figure S479.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S480.  Gene #51: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 22(11P15.5) MUTATED 133 147 28
DEL PEAK 22(11P15.5) WILD-TYPE 410 151 204

Figure S480.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S481.  Gene #51: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 22(11P15.5) MUTATED 57 63 54 15 91 28
DEL PEAK 22(11P15.5) WILD-TYPE 162 101 252 126 92 32

Figure S481.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S482.  Gene #51: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 22(11P15.5) MUTATED 157 43 101
DEL PEAK 22(11P15.5) WILD-TYPE 174 210 375

Figure S482.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S483.  Gene #51: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 22(11P15.5) MUTATED 76 68 49 27 12 69
DEL PEAK 22(11P15.5) WILD-TYPE 155 92 273 100 74 65

Figure S483.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S484.  Gene #51: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 22(11P15.5) MUTATED 47 69 20 15 30
DEL PEAK 22(11P15.5) WILD-TYPE 133 70 79 96 103

Figure S484.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S485.  Gene #51: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 22(11P15.5) MUTATED 110 51 20
DEL PEAK 22(11P15.5) WILD-TYPE 195 196 90

Figure S485.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q23.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S486.  Gene #52: 'del_11q23.3' 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 23(11Q23.3) MUTATED 12 21 89 40 36 37 12 22
DEL PEAK 23(11Q23.3) WILD-TYPE 9 15 30 56 73 35 8 18

Figure S486.  Get High-res Image Gene #52: 'del_11q23.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11q23.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S487.  Gene #52: 'del_11q23.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 23(11Q23.3) MUTATED 77 74 64 37 17
DEL PEAK 23(11Q23.3) WILD-TYPE 24 78 50 51 41

Figure S487.  Get High-res Image Gene #52: 'del_11q23.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S488.  Gene #52: 'del_11q23.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 23(11Q23.3) MUTATED 212 134 39 140 21
DEL PEAK 23(11Q23.3) WILD-TYPE 48 278 54 125 28

Figure S488.  Get High-res Image Gene #52: 'del_11q23.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q23.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S489.  Gene #52: 'del_11q23.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 23(11Q23.3) MUTATED 66 98 123 33 44
DEL PEAK 23(11Q23.3) WILD-TYPE 66 99 54 55 84

Figure S489.  Get High-res Image Gene #52: 'del_11q23.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q23.3' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.008

Table S490.  Gene #52: 'del_11q23.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
DEL PEAK 23(11Q23.3) MUTATED 20 54 41 75 17
DEL PEAK 23(11Q23.3) WILD-TYPE 44 52 49 32 14

Figure S490.  Get High-res Image Gene #52: 'del_11q23.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_11q23.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S491.  Gene #52: 'del_11q23.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 23(11Q23.3) MUTATED 313 138 93
DEL PEAK 23(11Q23.3) WILD-TYPE 230 160 139

Figure S491.  Get High-res Image Gene #52: 'del_11q23.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S492.  Gene #52: 'del_11q23.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 23(11Q23.3) MUTATED 158 100 151 33 78 24
DEL PEAK 23(11Q23.3) WILD-TYPE 61 64 155 108 105 36

Figure S492.  Get High-res Image Gene #52: 'del_11q23.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.013

Table S493.  Gene #52: 'del_11q23.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 23(11Q23.3) MUTATED 149 79 139 59 45 60
DEL PEAK 23(11Q23.3) WILD-TYPE 82 81 183 68 41 74

Figure S493.  Get High-res Image Gene #52: 'del_11q23.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.042

Table S494.  Gene #52: 'del_11q23.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 23(11Q23.3) MUTATED 106 63 57 37 64
DEL PEAK 23(11Q23.3) WILD-TYPE 74 76 42 74 69

Figure S494.  Get High-res Image Gene #52: 'del_11q23.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_12p13.1' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.025

Table S495.  Gene #53: 'del_12p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 24(12P13.1) MUTATED 55 47 14 65 7
DEL PEAK 24(12P13.1) WILD-TYPE 205 365 79 200 42

Figure S495.  Get High-res Image Gene #53: 'del_12p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_12p13.1' versus 'MRNASEQ_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.15

Table S496.  Gene #53: 'del_12p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 24(12P13.1) MUTATED 83 73 31
DEL PEAK 24(12P13.1) WILD-TYPE 460 225 201

Figure S496.  Get High-res Image Gene #53: 'del_12p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.1

Table S497.  Gene #53: 'del_12p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 24(12P13.1) MUTATED 37 36 40 14 42 18
DEL PEAK 24(12P13.1) WILD-TYPE 182 128 266 127 141 42

Figure S497.  Get High-res Image Gene #53: 'del_12p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.021

Table S498.  Gene #53: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 24(12P13.1) MUTATED 44 46 41 12 14 28
DEL PEAK 24(12P13.1) WILD-TYPE 187 114 281 115 72 106

Figure S498.  Get High-res Image Gene #53: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q23.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S499.  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 25(12Q23.1) MUTATED 2 1 14 43 6 22 4 4
DEL PEAK 25(12Q23.1) WILD-TYPE 19 35 105 53 103 50 16 36

Figure S499.  Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12q23.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S500.  Gene #54: 'del_12q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 25(12Q23.1) MUTATED 12 10 34 37 3
DEL PEAK 25(12Q23.1) WILD-TYPE 89 142 80 51 55

Figure S500.  Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S501.  Gene #54: 'del_12q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 25(12Q23.1) MUTATED 33 32 16 115 5
DEL PEAK 25(12Q23.1) WILD-TYPE 227 380 77 150 44

Figure S501.  Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S502.  Gene #54: 'del_12q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 25(12Q23.1) MUTATED 68 14 30 12 14
DEL PEAK 25(12Q23.1) WILD-TYPE 64 183 147 76 114

Figure S502.  Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12q23.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S503.  Gene #54: 'del_12q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
DEL PEAK 25(12Q23.1) MUTATED 49 11 18
DEL PEAK 25(12Q23.1) WILD-TYPE 100 121 99

Figure S503.  Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_12q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S504.  Gene #54: 'del_12q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
DEL PEAK 25(12Q23.1) MUTATED 5 11 40 15 7
DEL PEAK 25(12Q23.1) WILD-TYPE 59 95 50 92 24

Figure S504.  Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_12q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S505.  Gene #54: 'del_12q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 25(12Q23.1) MUTATED 66 114 19
DEL PEAK 25(12Q23.1) WILD-TYPE 477 184 213

Figure S505.  Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S506.  Gene #54: 'del_12q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 25(12Q23.1) MUTATED 26 42 26 7 80 18
DEL PEAK 25(12Q23.1) WILD-TYPE 193 122 280 134 103 42

Figure S506.  Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q23.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S507.  Gene #54: 'del_12q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 25(12Q23.1) MUTATED 117 25 55
DEL PEAK 25(12Q23.1) WILD-TYPE 214 228 421

Figure S507.  Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_12q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S508.  Gene #54: 'del_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 25(12Q23.1) MUTATED 46 45 28 12 7 59
DEL PEAK 25(12Q23.1) WILD-TYPE 185 115 294 115 79 75

Figure S508.  Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S509.  Gene #54: 'del_12q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 25(12Q23.1) MUTATED 27 62 7 14 21
DEL PEAK 25(12Q23.1) WILD-TYPE 153 77 92 97 112

Figure S509.  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 = 1e-05 (Fisher's exact test), Q value = 0.008

Table S510.  Gene #54: 'del_12q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 25(12Q23.1) MUTATED 90 30 11
DEL PEAK 25(12Q23.1) WILD-TYPE 215 217 99

Figure S510.  Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q24.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S511.  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 26(12Q24.31) MUTATED 4 6 12 42 6 20 5 6
DEL PEAK 26(12Q24.31) WILD-TYPE 17 30 107 54 103 52 15 34

Figure S511.  Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12q24.31' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S512.  Gene #55: 'del_12q24.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 26(12Q24.31) MUTATED 10 15 35 37 4
DEL PEAK 26(12Q24.31) WILD-TYPE 91 137 79 51 54

Figure S512.  Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12q24.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S513.  Gene #55: 'del_12q24.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 26(12Q24.31) MUTATED 33 40 17 115 6
DEL PEAK 26(12Q24.31) WILD-TYPE 227 372 76 150 43

Figure S513.  Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q24.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S514.  Gene #55: 'del_12q24.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 26(12Q24.31) MUTATED 68 18 26 14 16
DEL PEAK 26(12Q24.31) WILD-TYPE 64 179 151 74 112

Figure S514.  Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12q24.31' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S515.  Gene #55: 'del_12q24.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
DEL PEAK 26(12Q24.31) MUTATED 49 13 20
DEL PEAK 26(12Q24.31) WILD-TYPE 100 119 97

Figure S515.  Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_12q24.31' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S516.  Gene #55: 'del_12q24.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
DEL PEAK 26(12Q24.31) MUTATED 7 13 36 16 10
DEL PEAK 26(12Q24.31) WILD-TYPE 57 93 54 91 21

Figure S516.  Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_12q24.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S517.  Gene #55: 'del_12q24.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 26(12Q24.31) MUTATED 63 118 29
DEL PEAK 26(12Q24.31) WILD-TYPE 480 180 203

Figure S517.  Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q24.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S518.  Gene #55: 'del_12q24.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 26(12Q24.31) MUTATED 25 37 41 6 79 22
DEL PEAK 26(12Q24.31) WILD-TYPE 194 127 265 135 104 38

Figure S518.  Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q24.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S519.  Gene #55: 'del_12q24.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 26(12Q24.31) MUTATED 108 37 63
DEL PEAK 26(12Q24.31) WILD-TYPE 223 216 413

Figure S519.  Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_12q24.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S520.  Gene #55: 'del_12q24.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 26(12Q24.31) MUTATED 49 44 38 14 5 58
DEL PEAK 26(12Q24.31) WILD-TYPE 182 116 284 113 81 76

Figure S520.  Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q24.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S521.  Gene #55: 'del_12q24.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 26(12Q24.31) MUTATED 29 60 12 16 23
DEL PEAK 26(12Q24.31) WILD-TYPE 151 79 87 95 110

Figure S521.  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 = 1e-04 (Fisher's exact test), Q value = 0.023

Table S522.  Gene #55: 'del_12q24.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 26(12Q24.31) MUTATED 88 37 15
DEL PEAK 26(12Q24.31) WILD-TYPE 217 210 95

Figure S522.  Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q14.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S523.  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 27(13Q14.2) MUTATED 8 12 70 60 34 41 9 13
DEL PEAK 27(13Q14.2) WILD-TYPE 13 24 49 36 75 31 11 27

Figure S523.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S524.  Gene #56: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 27(13Q14.2) MUTATED 64 47 67 56 13
DEL PEAK 27(13Q14.2) WILD-TYPE 37 105 47 32 45

Figure S524.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S525.  Gene #56: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 27(13Q14.2) MUTATED 164 90 54 159 27
DEL PEAK 27(13Q14.2) WILD-TYPE 96 322 39 106 22

Figure S525.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S526.  Gene #56: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 27(13Q14.2) MUTATED 84 81 97 24 44
DEL PEAK 27(13Q14.2) WILD-TYPE 48 116 80 64 84

Figure S526.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.01

Table S527.  Gene #56: 'del_13q14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
DEL PEAK 27(13Q14.2) MUTATED 19 44 58 61 10
DEL PEAK 27(13Q14.2) WILD-TYPE 45 62 32 46 21

Figure S527.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S528.  Gene #56: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 27(13Q14.2) MUTATED 257 172 63
DEL PEAK 27(13Q14.2) WILD-TYPE 286 126 169

Figure S528.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S529.  Gene #56: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 27(13Q14.2) MUTATED 112 96 109 37 114 24
DEL PEAK 27(13Q14.2) WILD-TYPE 107 68 197 104 69 36

Figure S529.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S530.  Gene #56: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 27(13Q14.2) MUTATED 188 83 212
DEL PEAK 27(13Q14.2) WILD-TYPE 143 170 264

Figure S530.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S531.  Gene #56: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 27(13Q14.2) MUTATED 130 72 107 49 37 88
DEL PEAK 27(13Q14.2) WILD-TYPE 101 88 215 78 49 46

Figure S531.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S532.  Gene #56: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 27(13Q14.2) MUTATED 92 87 35 25 46
DEL PEAK 27(13Q14.2) WILD-TYPE 88 52 64 86 87

Figure S532.  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 = 3e-05 (Fisher's exact test), Q value = 0.008

Table S533.  Gene #56: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 27(13Q14.2) MUTATED 163 84 38
DEL PEAK 27(13Q14.2) WILD-TYPE 142 163 72

Figure S533.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q24.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S534.  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 28(14Q24.1) MUTATED 4 7 47 63 10 22 10 8
DEL PEAK 28(14Q24.1) WILD-TYPE 17 29 72 33 99 50 10 32

Figure S534.  Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q24.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S535.  Gene #57: 'del_14q24.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 28(14Q24.1) MUTATED 37 30 41 59 4
DEL PEAK 28(14Q24.1) WILD-TYPE 64 122 73 29 54

Figure S535.  Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S536.  Gene #57: 'del_14q24.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 28(14Q24.1) MUTATED 96 48 22 170 17
DEL PEAK 28(14Q24.1) WILD-TYPE 164 364 71 95 32

Figure S536.  Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q24.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S537.  Gene #57: 'del_14q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 28(14Q24.1) MUTATED 88 38 58 17 31
DEL PEAK 28(14Q24.1) WILD-TYPE 44 159 119 71 97

Figure S537.  Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q24.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S538.  Gene #57: 'del_14q24.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
DEL PEAK 28(14Q24.1) MUTATED 77 27 33
DEL PEAK 28(14Q24.1) WILD-TYPE 72 105 84

Figure S538.  Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_14q24.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S539.  Gene #57: 'del_14q24.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
DEL PEAK 28(14Q24.1) MUTATED 6 27 58 38 8
DEL PEAK 28(14Q24.1) WILD-TYPE 58 79 32 69 23

Figure S539.  Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_14q24.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S540.  Gene #57: 'del_14q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 28(14Q24.1) MUTATED 151 166 34
DEL PEAK 28(14Q24.1) WILD-TYPE 392 132 198

Figure S540.  Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S541.  Gene #57: 'del_14q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 28(14Q24.1) MUTATED 71 68 57 15 124 16
DEL PEAK 28(14Q24.1) WILD-TYPE 148 96 249 126 59 44

Figure S541.  Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q24.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S542.  Gene #57: 'del_14q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 28(14Q24.1) MUTATED 177 50 116
DEL PEAK 28(14Q24.1) WILD-TYPE 154 203 360

Figure S542.  Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_14q24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S543.  Gene #57: 'del_14q24.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 28(14Q24.1) MUTATED 82 68 54 26 17 96
DEL PEAK 28(14Q24.1) WILD-TYPE 149 92 268 101 69 38

Figure S543.  Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S544.  Gene #57: 'del_14q24.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 28(14Q24.1) MUTATED 56 89 19 24 31
DEL PEAK 28(14Q24.1) WILD-TYPE 124 50 80 87 102

Figure S544.  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 = 1e-05 (Fisher's exact test), Q value = 0.008

Table S545.  Gene #57: 'del_14q24.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 28(14Q24.1) MUTATED 145 52 22
DEL PEAK 28(14Q24.1) WILD-TYPE 160 195 88

Figure S545.  Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q13.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S546.  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 29(15Q13.1) MUTATED 5 11 41 58 24 34 10 8
DEL PEAK 29(15Q13.1) WILD-TYPE 16 25 78 38 85 38 10 32

Figure S546.  Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q13.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S547.  Gene #58: 'del_15q13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 29(15Q13.1) MUTATED 36 35 54 54 12
DEL PEAK 29(15Q13.1) WILD-TYPE 65 117 60 34 46

Figure S547.  Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S548.  Gene #58: 'del_15q13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 29(15Q13.1) MUTATED 92 49 44 175 14
DEL PEAK 29(15Q13.1) WILD-TYPE 168 363 49 90 35

Figure S548.  Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S549.  Gene #58: 'del_15q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 29(15Q13.1) MUTATED 86 45 65 20 29
DEL PEAK 29(15Q13.1) WILD-TYPE 46 152 112 68 99

Figure S549.  Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q13.1' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.008

Table S550.  Gene #58: 'del_15q13.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
DEL PEAK 29(15Q13.1) MUTATED 80 39 38
DEL PEAK 29(15Q13.1) WILD-TYPE 69 93 79

Figure S550.  Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_15q13.1' versus 'RPPA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.019

Table S551.  Gene #58: 'del_15q13.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
DEL PEAK 29(15Q13.1) MUTATED 18 29 54 43 13
DEL PEAK 29(15Q13.1) WILD-TYPE 46 77 36 64 18

Figure S551.  Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_15q13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S552.  Gene #58: 'del_15q13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 29(15Q13.1) MUTATED 175 166 31
DEL PEAK 29(15Q13.1) WILD-TYPE 368 132 201

Figure S552.  Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S553.  Gene #58: 'del_15q13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 29(15Q13.1) MUTATED 70 75 62 24 120 21
DEL PEAK 29(15Q13.1) WILD-TYPE 149 89 244 117 63 39

Figure S553.  Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q13.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S554.  Gene #58: 'del_15q13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 29(15Q13.1) MUTATED 185 45 135
DEL PEAK 29(15Q13.1) WILD-TYPE 146 208 341

Figure S554.  Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S555.  Gene #58: 'del_15q13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 29(15Q13.1) MUTATED 89 70 48 46 17 95
DEL PEAK 29(15Q13.1) WILD-TYPE 142 90 274 81 69 39

Figure S555.  Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_15q13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S556.  Gene #58: 'del_15q13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 29(15Q13.1) MUTATED 65 90 21 28 26
DEL PEAK 29(15Q13.1) WILD-TYPE 115 49 78 83 107

Figure S556.  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 = 1e-05 (Fisher's exact test), Q value = 0.008

Table S557.  Gene #58: 'del_15q13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 29(15Q13.1) MUTATED 139 54 37
DEL PEAK 29(15Q13.1) WILD-TYPE 166 193 73

Figure S557.  Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q24.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S558.  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 30(16Q24.3) MUTATED 16 25 81 27 94 45 13 35
DEL PEAK 30(16Q24.3) WILD-TYPE 5 11 38 69 15 27 7 5

Figure S558.  Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_16q24.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S559.  Gene #59: 'del_16q24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 30(16Q24.3) MUTATED 74 124 71 22 45
DEL PEAK 30(16Q24.3) WILD-TYPE 27 28 43 66 13

Figure S559.  Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_16q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S560.  Gene #59: 'del_16q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 30(16Q24.3) MUTATED 166 292 75 121 38
DEL PEAK 30(16Q24.3) WILD-TYPE 94 120 18 144 11

Figure S560.  Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q24.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S561.  Gene #59: 'del_16q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 30(16Q24.3) MUTATED 53 152 118 61 72
DEL PEAK 30(16Q24.3) WILD-TYPE 79 45 59 27 56

Figure S561.  Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q24.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S562.  Gene #59: 'del_16q24.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
DEL PEAK 30(16Q24.3) MUTATED 64 103 84
DEL PEAK 30(16Q24.3) WILD-TYPE 85 29 33

Figure S562.  Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_16q24.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S563.  Gene #59: 'del_16q24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
DEL PEAK 30(16Q24.3) MUTATED 54 80 28 74 15
DEL PEAK 30(16Q24.3) WILD-TYPE 10 26 62 33 16

Figure S563.  Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_16q24.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S564.  Gene #59: 'del_16q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 30(16Q24.3) MUTATED 383 119 186
DEL PEAK 30(16Q24.3) WILD-TYPE 160 179 46

Figure S564.  Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S565.  Gene #59: 'del_16q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 30(16Q24.3) MUTATED 156 100 246 98 60 28
DEL PEAK 30(16Q24.3) WILD-TYPE 63 64 60 43 123 32

Figure S565.  Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16q24.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S566.  Gene #59: 'del_16q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 30(16Q24.3) MUTATED 151 181 348
DEL PEAK 30(16Q24.3) WILD-TYPE 180 72 128

Figure S566.  Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S567.  Gene #59: 'del_16q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 30(16Q24.3) MUTATED 139 78 240 111 62 50
DEL PEAK 30(16Q24.3) WILD-TYPE 92 82 82 16 24 84

Figure S567.  Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S568.  Gene #59: 'del_16q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 30(16Q24.3) MUTATED 119 59 68 78 92
DEL PEAK 30(16Q24.3) WILD-TYPE 61 80 31 33 41

Figure S568.  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 = 1e-05 (Fisher's exact test), Q value = 0.008

Table S569.  Gene #59: 'del_16q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 30(16Q24.3) MUTATED 154 177 85
DEL PEAK 30(16Q24.3) WILD-TYPE 151 70 25

Figure S569.  Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S570.  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 31(17P12) MUTATED 14 27 78 65 33 62 15 24
DEL PEAK 31(17P12) WILD-TYPE 7 9 41 31 76 10 5 16

Figure S570.  Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S571.  Gene #60: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 31(17P12) MUTATED 69 86 93 58 12
DEL PEAK 31(17P12) WILD-TYPE 32 66 21 30 46

Figure S571.  Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S572.  Gene #60: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 31(17P12) MUTATED 208 161 42 209 30
DEL PEAK 31(17P12) WILD-TYPE 52 251 51 56 19

Figure S572.  Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S573.  Gene #60: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 31(17P12) MUTATED 87 98 133 43 65
DEL PEAK 31(17P12) WILD-TYPE 45 99 44 45 63

Figure S573.  Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p12' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S574.  Gene #60: 'del_17p12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
DEL PEAK 31(17P12) MUTATED 116 66 66
DEL PEAK 31(17P12) WILD-TYPE 33 66 51

Figure S574.  Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_17p12' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S575.  Gene #60: 'del_17p12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
DEL PEAK 31(17P12) MUTATED 23 57 65 77 26
DEL PEAK 31(17P12) WILD-TYPE 41 49 25 30 5

Figure S575.  Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S576.  Gene #60: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 31(17P12) MUTATED 316 214 116
DEL PEAK 31(17P12) WILD-TYPE 227 84 116

Figure S576.  Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S577.  Gene #60: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 31(17P12) MUTATED 146 135 173 28 116 48
DEL PEAK 31(17P12) WILD-TYPE 73 29 133 113 67 12

Figure S577.  Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S578.  Gene #60: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 31(17P12) MUTATED 238 130 271
DEL PEAK 31(17P12) WILD-TYPE 93 123 205

Figure S578.  Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S579.  Gene #60: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 31(17P12) MUTATED 160 108 168 70 40 93
DEL PEAK 31(17P12) WILD-TYPE 71 52 154 57 46 41

Figure S579.  Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17q21.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S580.  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 32(17Q21.31) MUTATED 7 17 28 53 13 50 9 15
DEL PEAK 32(17Q21.31) WILD-TYPE 14 19 91 43 96 22 11 25

Figure S580.  Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17q21.31' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S581.  Gene #61: 'del_17q21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 32(17Q21.31) MUTATED 24 49 70 46 3
DEL PEAK 32(17Q21.31) WILD-TYPE 77 103 44 42 55

Figure S581.  Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17q21.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S582.  Gene #61: 'del_17q21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 32(17Q21.31) MUTATED 85 84 23 170 9
DEL PEAK 32(17Q21.31) WILD-TYPE 175 328 70 95 40

Figure S582.  Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_17q21.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S583.  Gene #61: 'del_17q21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 32(17Q21.31) MUTATED 81 30 63 18 40
DEL PEAK 32(17Q21.31) WILD-TYPE 51 167 114 70 88

Figure S583.  Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17q21.31' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S584.  Gene #61: 'del_17q21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
DEL PEAK 32(17Q21.31) MUTATED 90 24 44
DEL PEAK 32(17Q21.31) WILD-TYPE 59 108 73

Figure S584.  Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_17q21.31' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S585.  Gene #61: 'del_17q21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
DEL PEAK 32(17Q21.31) MUTATED 10 34 52 36 26
DEL PEAK 32(17Q21.31) WILD-TYPE 54 72 38 71 5

Figure S585.  Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_17q21.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S586.  Gene #61: 'del_17q21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 32(17Q21.31) MUTATED 142 174 54
DEL PEAK 32(17Q21.31) WILD-TYPE 401 124 178

Figure S586.  Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17q21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S587.  Gene #61: 'del_17q21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 32(17Q21.31) MUTATED 46 91 89 9 96 39
DEL PEAK 32(17Q21.31) WILD-TYPE 173 73 217 132 87 21

Figure S587.  Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17q21.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S588.  Gene #61: 'del_17q21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 32(17Q21.31) MUTATED 177 61 125
DEL PEAK 32(17Q21.31) WILD-TYPE 154 192 351

Figure S588.  Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17q21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S589.  Gene #61: 'del_17q21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 32(17Q21.31) MUTATED 103 70 68 32 11 79
DEL PEAK 32(17Q21.31) WILD-TYPE 128 90 254 95 75 55

Figure S589.  Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17q21.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S590.  Gene #61: 'del_17q21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 32(17Q21.31) MUTATED 55 76 19 30 46
DEL PEAK 32(17Q21.31) WILD-TYPE 125 63 80 81 87

Figure S590.  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 = 0.00041 (Fisher's exact test), Q value = 0.079

Table S591.  Gene #61: 'del_17q21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 32(17Q21.31) MUTATED 128 70 28
DEL PEAK 32(17Q21.31) WILD-TYPE 177 177 82

Figure S591.  Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q23' versus 'MRNA_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.023

Table S592.  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 33(18Q23) MUTATED 6 13 38 38 18 37 6 9
DEL PEAK 33(18Q23) WILD-TYPE 15 23 81 58 91 35 14 31

Figure S592.  Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q23' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.01

Table S593.  Gene #62: 'del_18q23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 33(18Q23) MUTATED 31 35 54 35 10
DEL PEAK 33(18Q23) WILD-TYPE 70 117 60 53 48

Figure S593.  Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18q23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S594.  Gene #62: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 33(18Q23) MUTATED 110 68 32 131 13
DEL PEAK 33(18Q23) WILD-TYPE 150 344 61 134 36

Figure S594.  Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S595.  Gene #62: 'del_18q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 33(18Q23) MUTATED 59 47 88 17 30
DEL PEAK 33(18Q23) WILD-TYPE 73 150 89 71 98

Figure S595.  Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S596.  Gene #62: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 33(18Q23) MUTATED 171 133 47
DEL PEAK 33(18Q23) WILD-TYPE 372 165 185

Figure S596.  Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S597.  Gene #62: 'del_18q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 33(18Q23) MUTATED 52 95 81 19 77 27
DEL PEAK 33(18Q23) WILD-TYPE 167 69 225 122 106 33

Figure S597.  Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S598.  Gene #62: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 33(18Q23) MUTATED 144 63 143
DEL PEAK 33(18Q23) WILD-TYPE 187 190 333

Figure S598.  Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18q23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S599.  Gene #62: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 33(18Q23) MUTATED 89 76 81 32 18 54
DEL PEAK 33(18Q23) WILD-TYPE 142 84 241 95 68 80

Figure S599.  Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S600.  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 34(19P13.3) MUTATED 7 10 48 57 13 35 6 6
DEL PEAK 34(19P13.3) WILD-TYPE 14 26 71 39 96 37 14 34

Figure S600.  Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19p13.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S601.  Gene #63: 'del_19p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 34(19P13.3) MUTATED 44 28 54 53 3
DEL PEAK 34(19P13.3) WILD-TYPE 57 124 60 35 55

Figure S601.  Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S602.  Gene #63: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 34(19P13.3) MUTATED 133 37 14 162 17
DEL PEAK 34(19P13.3) WILD-TYPE 127 375 79 103 32

Figure S602.  Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S603.  Gene #63: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 34(19P13.3) MUTATED 74 34 68 12 34
DEL PEAK 34(19P13.3) WILD-TYPE 58 163 109 76 94

Figure S603.  Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p13.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S604.  Gene #63: 'del_19p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
DEL PEAK 34(19P13.3) MUTATED 81 36 32
DEL PEAK 34(19P13.3) WILD-TYPE 68 96 85

Figure S604.  Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S605.  Gene #63: 'del_19p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
DEL PEAK 34(19P13.3) MUTATED 6 31 50 45 17
DEL PEAK 34(19P13.3) WILD-TYPE 58 75 40 62 14

Figure S605.  Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S606.  Gene #63: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 34(19P13.3) MUTATED 175 157 29
DEL PEAK 34(19P13.3) WILD-TYPE 368 141 203

Figure S606.  Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S607.  Gene #63: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 34(19P13.3) MUTATED 77 88 58 10 108 20
DEL PEAK 34(19P13.3) WILD-TYPE 142 76 248 131 75 40

Figure S607.  Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S608.  Gene #63: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 34(19P13.3) MUTATED 187 47 119
DEL PEAK 34(19P13.3) WILD-TYPE 144 206 357

Figure S608.  Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S609.  Gene #63: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 34(19P13.3) MUTATED 96 74 49 26 23 85
DEL PEAK 34(19P13.3) WILD-TYPE 135 86 273 101 63 49

Figure S609.  Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S610.  Gene #63: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 34(19P13.3) MUTATED 62 82 17 18 37
DEL PEAK 34(19P13.3) WILD-TYPE 118 57 82 93 96

Figure S610.  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 = 1e-05 (Fisher's exact test), Q value = 0.008

Table S611.  Gene #63: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 34(19P13.3) MUTATED 139 60 17
DEL PEAK 34(19P13.3) WILD-TYPE 166 187 93

Figure S611.  Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.32' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S612.  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 35(19Q13.32) MUTATED 4 7 23 26 7 28 1 3
DEL PEAK 35(19Q13.32) WILD-TYPE 17 29 96 70 102 44 19 37

Figure S612.  Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19q13.32' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S613.  Gene #64: 'del_19q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 35(19Q13.32) MUTATED 26 11 36 24 2
DEL PEAK 35(19Q13.32) WILD-TYPE 75 141 78 64 56

Figure S613.  Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S614.  Gene #64: 'del_19q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 35(19Q13.32) MUTATED 88 23 8 89 8
DEL PEAK 35(19Q13.32) WILD-TYPE 172 389 85 176 41

Figure S614.  Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S615.  Gene #64: 'del_19q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 35(19Q13.32) MUTATED 47 19 47 8 18
DEL PEAK 35(19Q13.32) WILD-TYPE 85 178 130 80 110

Figure S615.  Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.32' versus 'RPPA_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.11

Table S616.  Gene #64: 'del_19q13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
DEL PEAK 35(19Q13.32) MUTATED 45 20 15
DEL PEAK 35(19Q13.32) WILD-TYPE 104 112 102

Figure S616.  Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19q13.32' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.008

Table S617.  Gene #64: 'del_19q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
DEL PEAK 35(19Q13.32) MUTATED 4 12 30 23 11
DEL PEAK 35(19Q13.32) WILD-TYPE 60 94 60 84 20

Figure S617.  Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_19q13.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S618.  Gene #64: 'del_19q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 35(19Q13.32) MUTATED 103 99 13
DEL PEAK 35(19Q13.32) WILD-TYPE 440 199 219

Figure S618.  Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S619.  Gene #64: 'del_19q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 35(19Q13.32) MUTATED 50 56 25 8 58 18
DEL PEAK 35(19Q13.32) WILD-TYPE 169 108 281 133 125 42

Figure S619.  Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S620.  Gene #64: 'del_19q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 35(19Q13.32) MUTATED 109 27 73
DEL PEAK 35(19Q13.32) WILD-TYPE 222 226 403

Figure S620.  Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S621.  Gene #64: 'del_19q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 35(19Q13.32) MUTATED 62 44 21 20 16 46
DEL PEAK 35(19Q13.32) WILD-TYPE 169 116 301 107 70 88

Figure S621.  Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S622.  Gene #64: 'del_19q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 35(19Q13.32) MUTATED 43 50 16 7 18
DEL PEAK 35(19Q13.32) WILD-TYPE 137 89 83 104 115

Figure S622.  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 = 1e-05 (Fisher's exact test), Q value = 0.008

Table S623.  Gene #64: 'del_19q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 35(19Q13.32) MUTATED 92 36 6
DEL PEAK 35(19Q13.32) WILD-TYPE 213 211 104

Figure S623.  Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p13' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S624.  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 36(20P13) MUTATED 1 3 28 25 3 16 3 1
DEL PEAK 36(20P13) WILD-TYPE 20 33 91 71 106 56 17 39

Figure S624.  Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_20p13' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S625.  Gene #65: 'del_20p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 36(20P13) MUTATED 23 9 25 23 0
DEL PEAK 36(20P13) WILD-TYPE 78 143 89 65 58

Figure S625.  Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_20p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S626.  Gene #65: 'del_20p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 36(20P13) MUTATED 46 20 7 78 9
DEL PEAK 36(20P13) WILD-TYPE 214 392 86 187 40

Figure S626.  Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #3: 'CN_CNMF'

'del_20p13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S627.  Gene #65: 'del_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 36(20P13) MUTATED 44 11 29 8 10
DEL PEAK 36(20P13) WILD-TYPE 88 186 148 80 118

Figure S627.  Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_20p13' versus 'RPPA_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.074

Table S628.  Gene #65: 'del_20p13' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
DEL PEAK 36(20P13) MUTATED 37 10 17
DEL PEAK 36(20P13) WILD-TYPE 112 122 100

Figure S628.  Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_20p13' versus 'RPPA_CHIERARCHICAL'

P value = 0.00093 (Fisher's exact test), Q value = 0.16

Table S629.  Gene #65: 'del_20p13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
DEL PEAK 36(20P13) MUTATED 5 8 24 20 7
DEL PEAK 36(20P13) WILD-TYPE 59 98 66 87 24

Figure S629.  Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_20p13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S630.  Gene #65: 'del_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 36(20P13) MUTATED 69 81 9
DEL PEAK 36(20P13) WILD-TYPE 474 217 223

Figure S630.  Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_20p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S631.  Gene #65: 'del_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 36(20P13) MUTATED 35 33 21 3 56 11
DEL PEAK 36(20P13) WILD-TYPE 184 131 285 138 127 49

Figure S631.  Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_20p13' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S632.  Gene #65: 'del_20p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
DEL PEAK 36(20P13) MUTATED 88 16 47
DEL PEAK 36(20P13) WILD-TYPE 243 237 429

Figure S632.  Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_20p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S633.  Gene #65: 'del_20p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 36(20P13) MUTATED 36 36 16 7 13 43
DEL PEAK 36(20P13) WILD-TYPE 195 124 306 120 73 91

Figure S633.  Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_20p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S634.  Gene #65: 'del_20p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 36(20P13) MUTATED 21 46 9 6 11
DEL PEAK 36(20P13) WILD-TYPE 159 93 90 105 122

Figure S634.  Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_20p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S635.  Gene #65: 'del_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 36(20P13) MUTATED 72 20 1
DEL PEAK 36(20P13) WILD-TYPE 233 227 109

Figure S635.  Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q11.2' versus 'MRNA_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.049

Table S636.  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 37(21Q11.2) MUTATED 3 11 37 16 11 23 3 4
DEL PEAK 37(21Q11.2) WILD-TYPE 18 25 82 80 98 49 17 36

Figure S636.  Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_21q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S637.  Gene #66: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 37(21Q11.2) MUTATED 89 33 17 68 10
DEL PEAK 37(21Q11.2) WILD-TYPE 171 379 76 197 39

Figure S637.  Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.055

Table S638.  Gene #66: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
DEL PEAK 37(21Q11.2) MUTATED 22 38 53 8 18
DEL PEAK 37(21Q11.2) WILD-TYPE 110 159 124 80 110

Figure S638.  Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.061

Table S639.  Gene #66: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 37(21Q11.2) MUTATED 126 63 26
DEL PEAK 37(21Q11.2) WILD-TYPE 417 235 206

Figure S639.  Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_21q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S640.  Gene #66: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 37(21Q11.2) MUTATED 51 57 48 14 31 14
DEL PEAK 37(21Q11.2) WILD-TYPE 168 107 258 127 152 46

Figure S640.  Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S641.  Gene #67: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
DEL PEAK 38(22Q13.32) MUTATED 145 141 58 126 22
DEL PEAK 38(22Q13.32) WILD-TYPE 115 271 35 139 27

Figure S641.  Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.23

Table S642.  Gene #67: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
DEL PEAK 38(22Q13.32) MUTATED 277 123 89
DEL PEAK 38(22Q13.32) WILD-TYPE 266 175 143

Figure S642.  Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.12

Table S643.  Gene #67: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
DEL PEAK 38(22Q13.32) MUTATED 119 89 131 54 77 19
DEL PEAK 38(22Q13.32) WILD-TYPE 100 75 175 87 106 41

Figure S643.  Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00076 (Fisher's exact test), Q value = 0.14

Table S644.  Gene #67: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
DEL PEAK 38(22Q13.32) MUTATED 117 76 122 75 37 56
DEL PEAK 38(22Q13.32) WILD-TYPE 114 84 200 52 49 78

Figure S644.  Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Molecular subtype file = BRCA-TP.transferedmergedcluster.txt

  • Number of patients = 1079

  • Number of significantly focal cnvs = 67

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
Copyright © 2015 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle