Correlation between copy number variation genes (focal events) and molecular subtypes
Breast Invasive Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1B857FJ
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 70 focal events and 12 molecular subtypes across 1080 patients, 731 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1q21.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_1q44 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_5p15.33 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_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',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • amp_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',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • amp_11q14.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • amp_15q26.3 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_17p11.2 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_17q12 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_17q23.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

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

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

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

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

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

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

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

  • del_7p22.3 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_7q36.1 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_8p23.2 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_8p11.21 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'.

  • del_9p23 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_9p21.3 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

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

  • del_11q23.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • del_12p13.1 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_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_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_14q32.12 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',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • del_22q13.32 cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 70 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, 731 significant findings detected.

Clinical
Features
MRNA
CNMF
MRNA
CHIERARCHICAL
CN
CNMF
METHLYATION
CNMF
RPPA
CNMF
RPPA
CHIERARCHICAL
MRNASEQ
CNMF
MRNASEQ
CHIERARCHICAL
MIRSEQ
CNMF
MIRSEQ
CHIERARCHICAL
MIRSEQ
MATURE
CNMF
MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
amp 3q26 32 339 (31%) 741 1e-05
(1.63e-05)
2e-05
(3.17e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
amp 5p15 33 394 (36%) 686 0.00151
(0.00199)
0.0147
(0.0176)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.00398
(0.00509)
0.00781
(0.00975)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
5e-05
(7.59e-05)
0.00046
(0.00065)
0.00134
(0.00178)
amp 6p23 298 (28%) 782 1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
amp 6q21 202 (19%) 878 1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
amp 8q24 21 678 (63%) 402 1e-05
(1.63e-05)
0.00037
(0.000529)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
amp 10p15 1 303 (28%) 777 1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
amp 10q22 3 149 (14%) 931 9e-05
(0.000134)
0.0238
(0.028)
1e-05
(1.63e-05)
0.00011
(0.000162)
6e-05
(9.05e-05)
0.00445
(0.00566)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.00116
(0.00155)
0.00886
(0.011)
amp 12p13 33 281 (26%) 799 1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
2e-05
(3.17e-05)
amp 13q34 178 (16%) 902 0.00056
(0.00078)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.00039
(0.000556)
amp 15q26 3 194 (18%) 886 1e-05
(1.63e-05)
0.00253
(0.00328)
1e-05
(1.63e-05)
0.001
(0.00135)
0.00142
(0.00188)
0.00054
(0.000756)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.00095
(0.00129)
0.00025
(0.000363)
amp 17q12 333 (31%) 747 5e-05
(7.59e-05)
0.00027
(0.00039)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
3e-05
(4.65e-05)
0.0043
(0.00548)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.00055
(0.000767)
0.001
(0.00135)
amp 19q12 283 (26%) 797 1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.00133
(0.00176)
del 2q37 3 318 (29%) 762 1e-05
(1.63e-05)
0.00127
(0.00169)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
del 3p21 31 347 (32%) 733 1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.00026
(0.000377)
del 4p16 3 339 (31%) 741 1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
del 4q35 2 347 (32%) 733 1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
3e-05
(4.65e-05)
del 5q11 2 280 (26%) 800 1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
del 5q21 3 273 (25%) 807 1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
del 7p22 3 139 (13%) 941 2e-05
(3.17e-05)
0.00177
(0.00231)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
2e-05
(3.17e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
del 7q36 1 200 (19%) 880 0.0001
(0.000148)
0.0221
(0.0262)
1e-05
(1.63e-05)
0.00888
(0.011)
0.00043
(0.000609)
0.0103
(0.0126)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
4e-05
(6.17e-05)
1e-05
(1.63e-05)
del 8p23 2 559 (52%) 521 9e-05
(0.000134)
0.0291
(0.0341)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
3e-05
(4.65e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.00027
(0.00039)
2e-05
(3.17e-05)
del 8p11 21 200 (19%) 880 3e-05
(4.65e-05)
0.00937
(0.0115)
1e-05
(1.63e-05)
0.0107
(0.013)
0.00043
(0.000609)
0.0008
(0.00109)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
2e-05
(3.17e-05)
1e-05
(1.63e-05)
0.0262
(0.0307)
0.00964
(0.0118)
del 9q34 2 297 (28%) 783 1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
del 10q23 31 320 (30%) 760 1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
3e-05
(4.65e-05)
del 10q26 3 318 (29%) 762 1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
del 11p15 5 309 (29%) 771 1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
5e-05
(7.59e-05)
del 12q23 1 201 (19%) 879 1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
del 12q24 31 211 (20%) 869 1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.0001
(0.000148)
del 13q14 2 498 (46%) 582 0.00011
(0.000162)
0.00055
(0.000767)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.00301
(0.00389)
0.00012
(0.000177)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
3e-05
(4.65e-05)
del 14q24 1 356 (33%) 724 1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
del 14q32 12 327 (30%) 753 0.00053
(0.000743)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
del 15q13 1 375 (35%) 705 1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
del 16q24 3 693 (64%) 387 1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
6e-05
(9.05e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
del 17q21 31 371 (34%) 709 1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.00087
(0.00118)
del 19p13 3 362 (34%) 718 1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
del 19q13 32 216 (20%) 864 1e-05
(1.63e-05)
0.00162
(0.00213)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
2e-05
(3.17e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
del 20p13 160 (15%) 920 0.002
(0.00261)
0.0151
(0.0181)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
amp 1q21 3 781 (72%) 299 0.0104
(0.0127)
3e-05
(4.65e-05)
1e-05
(1.63e-05)
4e-05
(6.17e-05)
0.00016
(0.000234)
0.00072
(0.000995)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.0465
(0.0535)
0.218
(0.233)
amp 11p13 222 (21%) 858 0.00074
(0.00102)
0.286
(0.301)
1e-05
(1.63e-05)
0.00072
(0.000995)
5e-05
(7.59e-05)
0.0113
(0.0136)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.00106
(0.00142)
2e-05
(3.17e-05)
amp 11q14 1 267 (25%) 813 0.00208
(0.00271)
0.00805
(0.01)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.00734
(0.0092)
0.00121
(0.00162)
1e-05
(1.63e-05)
5e-05
(7.59e-05)
1e-05
(1.63e-05)
6e-05
(9.05e-05)
0.0584
(0.0666)
0.0115
(0.014)
amp 17q23 1 426 (39%) 654 8e-05
(0.00012)
0.00851
(0.0106)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.00752
(0.00941)
0.0553
(0.0633)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.00023
(0.000334)
1e-05
(1.63e-05)
amp 19p13 12 229 (21%) 851 0.00057
(0.000793)
5e-05
(7.59e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.00111
(0.00149)
8e-05
(0.00012)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.116
(0.127)
amp 20q13 2 547 (51%) 533 1e-05
(1.63e-05)
0.381
(0.393)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.0127
(0.0154)
0.00152
(0.002)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.0004
(0.000569)
1e-05
(1.63e-05)
del 9p23 325 (30%) 755 0.0014
(0.00185)
0.00082
(0.00112)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.00102
(0.00138)
0.0991
(0.11)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.0183
(0.0218)
0.00015
(0.00022)
del 9q21 11 295 (27%) 785 5e-05
(7.59e-05)
0.0584
(0.0666)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.00589
(0.00745)
0.00047
(0.000664)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
6e-05
(9.05e-05)
1e-05
(1.63e-05)
del 18q23 355 (33%) 725 1e-05
(1.63e-05)
0.0029
(0.00375)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.00023
(0.000334)
0.00127
(0.00169)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.0105
(0.0128)
0.0745
(0.0839)
amp 4q13 3 163 (15%) 917 0.00173
(0.00226)
0.465
(0.476)
1e-05
(1.63e-05)
2e-05
(3.17e-05)
0.00713
(0.00897)
0.024
(0.0283)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.229
(0.244)
0.00101
(0.00136)
amp 14q21 1 220 (20%) 860 0.0234
(0.0276)
0.00133
(0.00176)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.0079
(0.00985)
5e-05
(7.59e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.0998
(0.11)
0.803
(0.807)
amp 19q13 42 275 (25%) 805 0.00029
(0.000417)
0.0216
(0.0256)
1e-05
(1.63e-05)
2e-05
(3.17e-05)
0.0353
(0.0409)
0.0374
(0.0434)
1e-05
(1.63e-05)
0.00048
(0.000675)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.0791
(0.0888)
0.19
(0.204)
del 9p21 3 365 (34%) 715 2e-05
(3.17e-05)
0.0962
(0.107)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
7e-05
(0.000105)
0.0603
(0.0686)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.0007
(0.00097)
1e-05
(1.63e-05)
del 12p13 1 188 (17%) 892 0.0189
(0.0225)
0.175
(0.188)
0.00034
(0.000487)
0.052
(0.0596)
0.00756
(0.00945)
0.00436
(0.00555)
0.00039
(0.000556)
0.00048
(0.000675)
0.00388
(0.00497)
0.00029
(0.000417)
0.0298
(0.0349)
0.0031
(0.00399)
del 17p12 650 (60%) 430 1e-05
(1.63e-05)
2e-05
(3.17e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
7e-05
(0.000105)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.313
(0.328)
0.123
(0.135)
amp 3p25 1 198 (18%) 882 0.0108
(0.0131)
0.715
(0.722)
1e-05
(1.63e-05)
0.0003
(0.000431)
0.00327
(0.00421)
0.00171
(0.00224)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.552
(0.563)
0.0656
(0.0744)
amp 8p11 23 412 (38%) 668 0.0263
(0.0309)
0.0183
(0.0218)
1e-05
(1.63e-05)
2e-05
(3.17e-05)
0.139
(0.151)
0.00051
(0.000716)
1e-05
(1.63e-05)
0.00021
(0.000307)
0.00078
(0.00107)
3e-05
(4.65e-05)
0.428
(0.438)
0.798
(0.803)
amp 8p11 21 421 (39%) 659 0.106
(0.116)
0.0697
(0.0787)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.00328
(0.00421)
0.0872
(0.0976)
1e-05
(1.63e-05)
2e-05
(3.17e-05)
0.0001
(0.000148)
0.0063
(0.00796)
0.00011
(0.000162)
0.00172
(0.00225)
amp 12q15 275 (25%) 805 1e-05
(1.63e-05)
0.0755
(0.0849)
1e-05
(1.63e-05)
3e-05
(4.65e-05)
0.08
(0.0897)
0.00368
(0.00472)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.0338
(0.0394)
0.233
(0.248)
del 1p36 13 452 (42%) 628 0.00077
(0.00106)
0.858
(0.859)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.00246
(0.0032)
0.00654
(0.00825)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
3e-05
(4.65e-05)
0.122
(0.134)
0.103
(0.114)
del 1p21 2 356 (33%) 724 0.041
(0.0475)
0.0107
(0.0131)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.0948
(0.105)
0.0166
(0.0198)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.00575
(0.00728)
2e-05
(3.17e-05)
0.632
(0.642)
0.941
(0.941)
del 6q15 358 (33%) 722 0.149
(0.162)
0.00955
(0.0117)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.165
(0.178)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.00274
(0.00355)
1e-05
(1.63e-05)
0.00309
(0.00399)
0.383
(0.395)
amp 11q13 3 397 (37%) 683 0.653
(0.662)
0.00111
(0.00149)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.597
(0.607)
0.239
(0.254)
1e-05
(1.63e-05)
3e-05
(4.65e-05)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.181
(0.195)
0.0306
(0.0357)
del 11q23 3 547 (51%) 533 0.279
(0.293)
0.1
(0.111)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.0469
(0.054)
0.0454
(0.0524)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.00013
(0.000191)
0.00022
(0.000321)
0.125
(0.137)
0.118
(0.13)
del 11q25 514 (48%) 566 0.37
(0.383)
0.424
(0.436)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.0679
(0.0768)
0.415
(0.427)
1e-05
(1.63e-05)
4e-05
(6.17e-05)
0.00076
(0.00105)
0.00876
(0.0109)
0.0256
(0.0301)
0.0144
(0.0173)
amp 1q44 789 (73%) 291 0.141
(0.154)
0.0226
(0.0268)
1e-05
(1.63e-05)
0.0346
(0.0402)
0.256
(0.271)
0.328
(0.343)
1e-05
(1.63e-05)
0.00043
(0.000609)
0.0617
(0.07)
3e-05
(4.65e-05)
0.305
(0.32)
0.0444
(0.0513)
amp 17p11 2 147 (14%) 933 0.0317
(0.0369)
0.21
(0.225)
1e-05
(1.63e-05)
0.00401
(0.00512)
0.246
(0.26)
0.278
(0.293)
0.0119
(0.0144)
0.00933
(0.0115)
0.0154
(0.0185)
0.0694
(0.0785)
0.384
(0.395)
0.0171
(0.0204)
del 21q11 2 215 (20%) 865 0.00082
(0.00112)
0.326
(0.341)
1e-05
(1.63e-05)
0.00105
(0.00141)
0.195
(0.21)
0.369
(0.383)
2e-05
(3.17e-05)
1e-05
(1.63e-05)
0.00925
(0.0114)
1e-05
(1.63e-05)
0.493
(0.503)
0.425
(0.436)
del 11q13 1 241 (22%) 839 0.207
(0.221)
0.271
(0.285)
1e-05
(1.63e-05)
1e-05
(1.63e-05)
0.352
(0.366)
0.167
(0.18)
1e-05
(1.63e-05)
0.00013
(0.000191)
0.0491
(0.0564)
0.00086
(0.00117)
0.0946
(0.105)
0.204
(0.218)
del 6p25 3 204 (19%) 876 0.835
(0.837)
0.376
(0.388)
1e-05
(1.63e-05)
0.0325
(0.0379)
0.367
(0.381)
0.0824
(0.0923)
0.00078
(0.00107)
0.0513
(0.0589)
0.00733
(0.0092)
0.00542
(0.00688)
0.622
(0.632)
0.128
(0.14)
del 22q13 32 492 (46%) 588 0.132
(0.144)
0.634
(0.644)
1e-05
(1.63e-05)
0.165
(0.178)
0.334
(0.349)
0.00819
(0.0102)
0.0189
(0.0225)
0.00698
(0.00879)
0.00058
(0.000805)
0.058
(0.0663)
0.0956
(0.106)
0.237
(0.252)
del 6q27 375 (35%) 705 0.351
(0.365)
0.69
(0.699)
1e-05
(1.63e-05)
0.146
(0.159)
0.374
(0.386)
0.239
(0.254)
0.00925
(0.0114)
0.146
(0.159)
0.159
(0.172)
0.0935
(0.104)
0.808
(0.811)
0.71
(0.717)
del 22q11 1 462 (43%) 618 0.726
(0.732)
0.781
(0.787)
1e-05
(1.63e-05)
0.0719
(0.081)
0.485
(0.496)
0.113
(0.125)
0.305
(0.32)
0.0607
(0.069)
0.0137
(0.0165)
0.0909
(0.102)
0.336
(0.35)
0.224
(0.239)
'amp_1q21.3' versus 'MRNA_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.013

Table S1.  Gene #1: 'amp_1q21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
AMP PEAK 1(1Q21.3) MUTATED 159 82 138
AMP PEAK 1(1Q21.3) WILD-TYPE 70 34 30

Figure S1.  Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1q21.3' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 4.6e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
AMP PEAK 1(1Q21.3) MUTATED 110 188 81
AMP PEAK 1(1Q21.3) WILD-TYPE 49 78 7

Figure S2.  Get High-res Image Gene #1: '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 = 1.6e-05

Table S3.  Gene #1: 'amp_1q21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
AMP PEAK 1(1Q21.3) MUTATED 229 129 167 234 22
AMP PEAK 1(1Q21.3) WILD-TYPE 101 3 128 60 7

Figure S3.  Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 6.2e-05

Table S4.  Gene #1: 'amp_1q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
AMP PEAK 1(1Q21.3) MUTATED 161 136 83 117 60
AMP PEAK 1(1Q21.3) WILD-TYPE 57 47 62 22 28

Figure S4.  Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q21.3' versus 'RPPA_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00023

Table S5.  Gene #1: 'amp_1q21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
AMP PEAK 1(1Q21.3) MUTATED 161 175 22 128 95 49 4
AMP PEAK 1(1Q21.3) WILD-TYPE 33 62 8 76 36 18 6

Figure S5.  Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_1q21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00072 (Fisher's exact test), Q value = 0.00099

Table S6.  Gene #1: 'amp_1q21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
AMP PEAK 1(1Q21.3) MUTATED 174 297 163
AMP PEAK 1(1Q21.3) WILD-TYPE 46 101 92

Figure S6.  Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S7.  Gene #1: 'amp_1q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
AMP PEAK 1(1Q21.3) MUTATED 162 121 84 191 174 34 12
AMP PEAK 1(1Q21.3) WILD-TYPE 102 48 59 34 29 17 8

Figure S7.  Get High-res Image Gene #1: '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 = 1.6e-05

Table S8.  Gene #1: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 1(1Q21.3) MUTATED 193 130 53 208 159 35
AMP PEAK 1(1Q21.3) WILD-TYPE 96 33 37 82 24 25

Figure S8.  Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S9.  Gene #1: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
AMP PEAK 1(1Q21.3) MUTATED 98 222 136 140 127 41
AMP PEAK 1(1Q21.3) WILD-TYPE 41 48 72 76 55 5

Figure S9.  Get High-res Image Gene #1: '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 = 1.6e-05

Table S10.  Gene #1: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
AMP PEAK 1(1Q21.3) MUTATED 42 90 128 109 61 87 140 48 59
AMP PEAK 1(1Q21.3) WILD-TYPE 24 33 56 77 13 26 19 25 24

Figure S10.  Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0465 (Fisher's exact test), Q value = 0.054

Table S11.  Gene #1: 'amp_1q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
AMP PEAK 1(1Q21.3) MUTATED 87 63 40 78 117 78
AMP PEAK 1(1Q21.3) WILD-TYPE 46 29 19 41 28 36

Figure S11.  Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1q44' versus 'MRNA_CHIERARCHICAL'

P value = 0.0226 (Fisher's exact test), Q value = 0.027

Table S12.  Gene #2: 'amp_1q44' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
AMP PEAK 2(1Q44) MUTATED 105 197 72
AMP PEAK 2(1Q44) WILD-TYPE 54 69 16

Figure S12.  Get High-res Image Gene #2: 'amp_1q44' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_1q44' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S13.  Gene #2: 'amp_1q44' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
AMP PEAK 2(1Q44) MUTATED 237 131 174 226 21
AMP PEAK 2(1Q44) WILD-TYPE 93 1 121 68 8

Figure S13.  Get High-res Image Gene #2: 'amp_1q44' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q44' versus 'METHLYATION_CNMF'

P value = 0.0346 (Fisher's exact test), Q value = 0.04

Table S14.  Gene #2: 'amp_1q44' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
AMP PEAK 2(1Q44) MUTATED 165 142 91 104 63
AMP PEAK 2(1Q44) WILD-TYPE 53 41 54 35 25

Figure S14.  Get High-res Image Gene #2: 'amp_1q44' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q44' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S15.  Gene #2: 'amp_1q44' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
AMP PEAK 2(1Q44) MUTATED 159 126 95 196 157 39 14
AMP PEAK 2(1Q44) WILD-TYPE 105 43 48 29 46 12 6

Figure S15.  Get High-res Image Gene #2: 'amp_1q44' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q44' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.00061

Table S16.  Gene #2: 'amp_1q44' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 2(1Q44) MUTATED 191 133 61 221 143 37
AMP PEAK 2(1Q44) WILD-TYPE 98 30 29 69 40 23

Figure S16.  Get High-res Image Gene #2: 'amp_1q44' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q44' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 4.6e-05

Table S17.  Gene #2: 'amp_1q44' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
AMP PEAK 2(1Q44) MUTATED 36 95 138 115 65 87 122 55 60
AMP PEAK 2(1Q44) WILD-TYPE 30 28 46 71 9 26 37 18 23

Figure S17.  Get High-res Image Gene #2: 'amp_1q44' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q44' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0444 (Fisher's exact test), Q value = 0.051

Table S18.  Gene #2: 'amp_1q44' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
AMP PEAK 2(1Q44) MUTATED 216 180 81
AMP PEAK 2(1Q44) WILD-TYPE 98 51 36

Figure S18.  Get High-res Image Gene #2: 'amp_1q44' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3p25.1' versus 'MRNA_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.013

Table S19.  Gene #3: 'amp_3p25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
AMP PEAK 3(3P25.1) MUTATED 51 17 50
AMP PEAK 3(3P25.1) WILD-TYPE 178 99 118

Figure S19.  Get High-res Image Gene #3: 'amp_3p25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3p25.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S20.  Gene #3: 'amp_3p25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
AMP PEAK 3(3P25.1) MUTATED 84 26 8 75 5
AMP PEAK 3(3P25.1) WILD-TYPE 246 106 287 219 24

Figure S20.  Get High-res Image Gene #3: 'amp_3p25.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3p25.1' versus 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.00043

Table S21.  Gene #3: 'amp_3p25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
AMP PEAK 3(3P25.1) MUTATED 27 39 14 33 7
AMP PEAK 3(3P25.1) WILD-TYPE 191 144 131 106 81

Figure S21.  Get High-res Image Gene #3: 'amp_3p25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3p25.1' versus 'RPPA_CNMF'

P value = 0.00327 (Fisher's exact test), Q value = 0.0042

Table S22.  Gene #3: 'amp_3p25.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
AMP PEAK 3(3P25.1) MUTATED 43 40 7 23 32 18 4
AMP PEAK 3(3P25.1) WILD-TYPE 151 197 23 181 99 49 6

Figure S22.  Get High-res Image Gene #3: 'amp_3p25.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_3p25.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00171 (Fisher's exact test), Q value = 0.0022

Table S23.  Gene #3: 'amp_3p25.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
AMP PEAK 3(3P25.1) MUTATED 58 75 34
AMP PEAK 3(3P25.1) WILD-TYPE 162 323 221

Figure S23.  Get High-res Image Gene #3: 'amp_3p25.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_3p25.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S24.  Gene #3: 'amp_3p25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
AMP PEAK 3(3P25.1) MUTATED 61 43 8 29 48 3 6
AMP PEAK 3(3P25.1) WILD-TYPE 203 126 135 196 155 48 14

Figure S24.  Get High-res Image Gene #3: '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 = 1.6e-05

Table S25.  Gene #3: 'amp_3p25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 3(3P25.1) MUTATED 57 53 4 28 43 13
AMP PEAK 3(3P25.1) WILD-TYPE 232 110 86 262 140 47

Figure S25.  Get High-res Image Gene #3: '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 = 1.6e-05

Table S26.  Gene #3: 'amp_3p25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
AMP PEAK 3(3P25.1) MUTATED 44 71 26 14 30 5
AMP PEAK 3(3P25.1) WILD-TYPE 95 199 182 202 152 41

Figure S26.  Get High-res Image Gene #3: '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 = 1.6e-05

Table S27.  Gene #3: 'amp_3p25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
AMP PEAK 3(3P25.1) MUTATED 17 33 11 22 13 25 38 10 21
AMP PEAK 3(3P25.1) WILD-TYPE 49 90 173 164 61 88 121 63 62

Figure S27.  Get High-res Image Gene #3: '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 = 1.6e-05

Table S28.  Gene #4: 'amp_3q26.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
AMP PEAK 4(3Q26.32) MUTATED 61 25 95
AMP PEAK 4(3Q26.32) WILD-TYPE 168 91 73

Figure S28.  Get High-res Image Gene #4: 'amp_3q26.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.32' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S29.  Gene #4: 'amp_3q26.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
AMP PEAK 4(3Q26.32) MUTATED 40 88 53
AMP PEAK 4(3Q26.32) WILD-TYPE 119 178 35

Figure S29.  Get High-res Image Gene #4: '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 = 1.6e-05

Table S30.  Gene #4: 'amp_3q26.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
AMP PEAK 4(3Q26.32) MUTATED 117 33 17 164 8
AMP PEAK 4(3Q26.32) WILD-TYPE 213 99 278 130 21

Figure S30.  Get High-res Image Gene #4: '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 = 1.6e-05

Table S31.  Gene #4: 'amp_3q26.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
AMP PEAK 4(3Q26.32) MUTATED 47 54 25 87 12
AMP PEAK 4(3Q26.32) WILD-TYPE 171 129 120 52 76

Figure S31.  Get High-res Image Gene #4: '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 = 1.6e-05

Table S32.  Gene #4: 'amp_3q26.32' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
AMP PEAK 4(3Q26.32) MUTATED 107 50 13 41 42 25 2
AMP PEAK 4(3Q26.32) WILD-TYPE 87 187 17 163 89 42 8

Figure S32.  Get High-res Image Gene #4: 'amp_3q26.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_3q26.32' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S33.  Gene #4: 'amp_3q26.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
AMP PEAK 4(3Q26.32) MUTATED 120 109 51
AMP PEAK 4(3Q26.32) WILD-TYPE 100 289 204

Figure S33.  Get High-res Image Gene #4: '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 = 1.6e-05

Table S34.  Gene #4: 'amp_3q26.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
AMP PEAK 4(3Q26.32) MUTATED 72 66 19 40 128 4 8
AMP PEAK 4(3Q26.32) WILD-TYPE 192 103 124 185 75 47 12

Figure S34.  Get High-res Image Gene #4: '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 = 1.6e-05

Table S35.  Gene #4: 'amp_3q26.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 4(3Q26.32) MUTATED 72 67 5 51 116 26
AMP PEAK 4(3Q26.32) WILD-TYPE 217 96 85 239 67 34

Figure S35.  Get High-res Image Gene #4: '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 = 1.6e-05

Table S36.  Gene #4: 'amp_3q26.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
AMP PEAK 4(3Q26.32) MUTATED 51 152 40 30 50 7
AMP PEAK 4(3Q26.32) WILD-TYPE 88 118 168 186 132 39

Figure S36.  Get High-res Image Gene #4: '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 = 1.6e-05

Table S37.  Gene #4: 'amp_3q26.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
AMP PEAK 4(3Q26.32) MUTATED 18 41 14 44 20 35 97 19 42
AMP PEAK 4(3Q26.32) WILD-TYPE 48 82 170 142 54 78 62 54 41

Figure S37.  Get High-res Image Gene #4: '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 = 1.6e-05

Table S38.  Gene #4: 'amp_3q26.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
AMP PEAK 4(3Q26.32) MUTATED 30 15 20 26 79 22
AMP PEAK 4(3Q26.32) WILD-TYPE 103 77 39 93 66 92

Figure S38.  Get High-res Image Gene #4: '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 = 1.6e-05

Table S39.  Gene #4: 'amp_3q26.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
AMP PEAK 4(3Q26.32) MUTATED 122 42 28
AMP PEAK 4(3Q26.32) WILD-TYPE 192 189 89

Figure S39.  Get High-res Image Gene #4: 'amp_3q26.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q13.3' versus 'MRNA_CNMF'

P value = 0.00173 (Fisher's exact test), Q value = 0.0023

Table S40.  Gene #5: 'amp_4q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
AMP PEAK 5(4Q13.3) MUTATED 31 12 42
AMP PEAK 5(4Q13.3) WILD-TYPE 198 104 126

Figure S40.  Get High-res Image Gene #5: 'amp_4q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_4q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S41.  Gene #5: 'amp_4q13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
AMP PEAK 5(4Q13.3) MUTATED 79 2 7 72 3
AMP PEAK 5(4Q13.3) WILD-TYPE 251 130 288 222 26

Figure S41.  Get High-res Image Gene #5: '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 = 3.2e-05

Table S42.  Gene #5: 'amp_4q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
AMP PEAK 5(4Q13.3) MUTATED 21 36 13 32 4
AMP PEAK 5(4Q13.3) WILD-TYPE 197 147 132 107 84

Figure S42.  Get High-res Image Gene #5: 'amp_4q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_4q13.3' versus 'RPPA_CNMF'

P value = 0.00713 (Fisher's exact test), Q value = 0.009

Table S43.  Gene #5: 'amp_4q13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
AMP PEAK 5(4Q13.3) MUTATED 37 31 7 17 27 13 1
AMP PEAK 5(4Q13.3) WILD-TYPE 157 206 23 187 104 54 9

Figure S43.  Get High-res Image Gene #5: 'amp_4q13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_4q13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.024 (Fisher's exact test), Q value = 0.028

Table S44.  Gene #5: 'amp_4q13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
AMP PEAK 5(4Q13.3) MUTATED 44 61 28
AMP PEAK 5(4Q13.3) WILD-TYPE 176 337 227

Figure S44.  Get High-res Image Gene #5: 'amp_4q13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_4q13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S45.  Gene #5: 'amp_4q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
AMP PEAK 5(4Q13.3) MUTATED 59 38 7 13 40 2 4
AMP PEAK 5(4Q13.3) WILD-TYPE 205 131 136 212 163 49 16

Figure S45.  Get High-res Image Gene #5: '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 = 1.6e-05

Table S46.  Gene #5: 'amp_4q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 5(4Q13.3) MUTATED 41 34 2 29 39 18
AMP PEAK 5(4Q13.3) WILD-TYPE 248 129 88 261 144 42

Figure S46.  Get High-res Image Gene #5: '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 = 1.6e-05

Table S47.  Gene #5: 'amp_4q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
AMP PEAK 5(4Q13.3) MUTATED 35 64 20 12 25 5
AMP PEAK 5(4Q13.3) WILD-TYPE 104 206 188 204 157 41

Figure S47.  Get High-res Image Gene #5: '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 = 1.6e-05

Table S48.  Gene #5: 'amp_4q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
AMP PEAK 5(4Q13.3) MUTATED 14 22 6 24 3 23 38 8 23
AMP PEAK 5(4Q13.3) WILD-TYPE 52 101 178 162 71 90 121 65 60

Figure S48.  Get High-res Image Gene #5: 'amp_4q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_4q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00101 (Fisher's exact test), Q value = 0.0014

Table S49.  Gene #5: 'amp_4q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
AMP PEAK 5(4Q13.3) MUTATED 63 23 11
AMP PEAK 5(4Q13.3) WILD-TYPE 251 208 106

Figure S49.  Get High-res Image Gene #5: 'amp_4q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'MRNA_CNMF'

P value = 0.00151 (Fisher's exact test), Q value = 0.002

Table S50.  Gene #6: 'amp_5p15.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
AMP PEAK 6(5P15.33) MUTATED 70 43 81
AMP PEAK 6(5P15.33) WILD-TYPE 159 73 87

Figure S50.  Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_5p15.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.0147 (Fisher's exact test), Q value = 0.018

Table S51.  Gene #6: 'amp_5p15.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
AMP PEAK 6(5P15.33) MUTATED 46 108 40
AMP PEAK 6(5P15.33) WILD-TYPE 113 158 48

Figure S51.  Get High-res Image Gene #6: '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 = 1.6e-05

Table S52.  Gene #6: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
AMP PEAK 6(5P15.33) MUTATED 140 60 36 150 8
AMP PEAK 6(5P15.33) WILD-TYPE 190 72 259 144 21

Figure S52.  Get High-res Image Gene #6: '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 = 1.6e-05

Table S53.  Gene #6: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
AMP PEAK 6(5P15.33) MUTATED 62 80 38 72 22
AMP PEAK 6(5P15.33) WILD-TYPE 156 103 107 67 66

Figure S53.  Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'RPPA_CNMF'

P value = 0.00398 (Fisher's exact test), Q value = 0.0051

Table S54.  Gene #6: 'amp_5p15.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
AMP PEAK 6(5P15.33) MUTATED 97 79 11 65 45 28 5
AMP PEAK 6(5P15.33) WILD-TYPE 97 158 19 139 86 39 5

Figure S54.  Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_5p15.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.00781 (Fisher's exact test), Q value = 0.0097

Table S55.  Gene #6: 'amp_5p15.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
AMP PEAK 6(5P15.33) MUTATED 102 144 84
AMP PEAK 6(5P15.33) WILD-TYPE 118 254 171

Figure S55.  Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S56.  Gene #6: 'amp_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
AMP PEAK 6(5P15.33) MUTATED 98 69 35 66 102 11 10
AMP PEAK 6(5P15.33) WILD-TYPE 166 100 108 159 101 40 10

Figure S56.  Get High-res Image Gene #6: '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 = 1.6e-05

Table S57.  Gene #6: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 6(5P15.33) MUTATED 97 78 20 81 89 26
AMP PEAK 6(5P15.33) WILD-TYPE 192 85 70 209 94 34

Figure S57.  Get High-res Image Gene #6: '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 = 1.6e-05

Table S58.  Gene #6: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
AMP PEAK 6(5P15.33) MUTATED 54 134 61 51 68 16
AMP PEAK 6(5P15.33) WILD-TYPE 85 136 147 165 114 30

Figure S58.  Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 7.6e-05

Table S59.  Gene #6: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
AMP PEAK 6(5P15.33) MUTATED 24 54 42 58 31 40 72 23 40
AMP PEAK 6(5P15.33) WILD-TYPE 42 69 142 128 43 73 87 50 43

Figure S59.  Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.00065

Table S60.  Gene #6: 'amp_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
AMP PEAK 6(5P15.33) MUTATED 45 34 26 41 67 23
AMP PEAK 6(5P15.33) WILD-TYPE 88 58 33 78 78 91

Figure S60.  Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00134 (Fisher's exact test), Q value = 0.0018

Table S61.  Gene #6: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
AMP PEAK 6(5P15.33) MUTATED 133 63 40
AMP PEAK 6(5P15.33) WILD-TYPE 181 168 77

Figure S61.  Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6p23' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S62.  Gene #7: 'amp_6p23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
AMP PEAK 7(6P23) MUTATED 47 18 84
AMP PEAK 7(6P23) WILD-TYPE 182 98 84

Figure S62.  Get High-res Image Gene #7: 'amp_6p23' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_6p23' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S63.  Gene #7: 'amp_6p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
AMP PEAK 7(6P23) MUTATED 28 76 45
AMP PEAK 7(6P23) WILD-TYPE 131 190 43

Figure S63.  Get High-res Image Gene #7: 'amp_6p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_6p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S64.  Gene #7: 'amp_6p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
AMP PEAK 7(6P23) MUTATED 93 22 14 158 11
AMP PEAK 7(6P23) WILD-TYPE 237 110 281 136 18

Figure S64.  Get High-res Image Gene #7: 'amp_6p23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S65.  Gene #7: 'amp_6p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
AMP PEAK 7(6P23) MUTATED 37 61 26 77 4
AMP PEAK 7(6P23) WILD-TYPE 181 122 119 62 84

Figure S65.  Get High-res Image Gene #7: 'amp_6p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6p23' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S66.  Gene #7: 'amp_6p23' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
AMP PEAK 7(6P23) MUTATED 85 41 10 34 45 20 3
AMP PEAK 7(6P23) WILD-TYPE 109 196 20 170 86 47 7

Figure S66.  Get High-res Image Gene #7: 'amp_6p23' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_6p23' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S67.  Gene #7: 'amp_6p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
AMP PEAK 7(6P23) MUTATED 94 96 48
AMP PEAK 7(6P23) WILD-TYPE 126 302 207

Figure S67.  Get High-res Image Gene #7: 'amp_6p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_6p23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S68.  Gene #7: 'amp_6p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
AMP PEAK 7(6P23) MUTATED 73 57 15 25 109 7 11
AMP PEAK 7(6P23) WILD-TYPE 191 112 128 200 94 44 9

Figure S68.  Get High-res Image Gene #7: 'amp_6p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 7(6P23) MUTATED 56 70 3 52 97 19
AMP PEAK 7(6P23) WILD-TYPE 233 93 87 238 86 41

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

'amp_6p23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S70.  Gene #7: 'amp_6p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
AMP PEAK 7(6P23) MUTATED 44 132 36 25 35 14
AMP PEAK 7(6P23) WILD-TYPE 95 138 172 191 147 32

Figure S70.  Get High-res Image Gene #7: 'amp_6p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_6p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S71.  Gene #7: 'amp_6p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
AMP PEAK 7(6P23) MUTATED 21 40 15 33 16 27 83 13 38
AMP PEAK 7(6P23) WILD-TYPE 45 83 169 153 58 86 76 60 45

Figure S71.  Get High-res Image Gene #7: 'amp_6p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S72.  Gene #7: 'amp_6p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
AMP PEAK 7(6P23) MUTATED 36 19 7 20 68 16
AMP PEAK 7(6P23) WILD-TYPE 97 73 52 99 77 98

Figure S72.  Get High-res Image Gene #7: '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 = 1.6e-05

Table S73.  Gene #7: 'amp_6p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
AMP PEAK 7(6P23) MUTATED 111 39 16
AMP PEAK 7(6P23) WILD-TYPE 203 192 101

Figure S73.  Get High-res Image Gene #7: 'amp_6p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q21' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S74.  Gene #8: 'amp_6q21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
AMP PEAK 8(6Q21) MUTATED 21 14 69
AMP PEAK 8(6Q21) WILD-TYPE 208 102 99

Figure S74.  Get High-res Image Gene #8: 'amp_6q21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_6q21' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S75.  Gene #8: 'amp_6q21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
AMP PEAK 8(6Q21) MUTATED 12 55 37
AMP PEAK 8(6Q21) WILD-TYPE 147 211 51

Figure S75.  Get High-res Image Gene #8: 'amp_6q21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_6q21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S76.  Gene #8: 'amp_6q21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
AMP PEAK 8(6Q21) MUTATED 30 13 11 145 3
AMP PEAK 8(6Q21) WILD-TYPE 300 119 284 149 26

Figure S76.  Get High-res Image Gene #8: 'amp_6q21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6q21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S77.  Gene #8: 'amp_6q21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
AMP PEAK 8(6Q21) MUTATED 12 34 21 62 4
AMP PEAK 8(6Q21) WILD-TYPE 206 149 124 77 84

Figure S77.  Get High-res Image Gene #8: 'amp_6q21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6q21' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S78.  Gene #8: 'amp_6q21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
AMP PEAK 8(6Q21) MUTATED 71 17 5 22 29 23 0
AMP PEAK 8(6Q21) WILD-TYPE 123 220 25 182 102 44 10

Figure S78.  Get High-res Image Gene #8: 'amp_6q21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_6q21' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S79.  Gene #8: 'amp_6q21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
AMP PEAK 8(6Q21) MUTATED 87 47 33
AMP PEAK 8(6Q21) WILD-TYPE 133 351 222

Figure S79.  Get High-res Image Gene #8: 'amp_6q21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_6q21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S80.  Gene #8: 'amp_6q21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
AMP PEAK 8(6Q21) MUTATED 25 47 8 17 92 4 7
AMP PEAK 8(6Q21) WILD-TYPE 239 122 135 208 111 47 13

Figure S80.  Get High-res Image Gene #8: 'amp_6q21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6q21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S81.  Gene #8: 'amp_6q21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 8(6Q21) MUTATED 25 47 2 24 82 20
AMP PEAK 8(6Q21) WILD-TYPE 264 116 88 266 101 40

Figure S81.  Get High-res Image Gene #8: 'amp_6q21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
AMP PEAK 8(6Q21) MUTATED 24 109 12 17 19 11
AMP PEAK 8(6Q21) WILD-TYPE 115 161 196 199 163 35

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

'amp_6q21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S83.  Gene #8: 'amp_6q21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
AMP PEAK 8(6Q21) MUTATED 7 30 6 8 8 18 68 10 37
AMP PEAK 8(6Q21) WILD-TYPE 59 93 178 178 66 95 91 63 46

Figure S83.  Get High-res Image Gene #8: 'amp_6q21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S84.  Gene #8: 'amp_6q21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
AMP PEAK 8(6Q21) MUTATED 14 9 4 15 67 11
AMP PEAK 8(6Q21) WILD-TYPE 119 83 55 104 78 103

Figure S84.  Get High-res Image Gene #8: '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 = 1.6e-05

Table S85.  Gene #8: 'amp_6q21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
AMP PEAK 8(6Q21) MUTATED 86 25 9
AMP PEAK 8(6Q21) WILD-TYPE 228 206 108

Figure S85.  Get High-res Image Gene #8: 'amp_6q21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p11.23' versus 'MRNA_CNMF'

P value = 0.0263 (Fisher's exact test), Q value = 0.031

Table S86.  Gene #9: 'amp_8p11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
AMP PEAK 9(8P11.23) MUTATED 108 39 62
AMP PEAK 9(8P11.23) WILD-TYPE 121 77 106

Figure S86.  Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8p11.23' versus 'MRNA_CHIERARCHICAL'

P value = 0.0183 (Fisher's exact test), Q value = 0.022

Table S87.  Gene #9: 'amp_8p11.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
AMP PEAK 9(8P11.23) MUTATED 79 100 30
AMP PEAK 9(8P11.23) WILD-TYPE 80 166 58

Figure S87.  Get High-res Image Gene #9: '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 = 1.6e-05

Table S88.  Gene #9: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
AMP PEAK 9(8P11.23) MUTATED 181 47 67 88 29
AMP PEAK 9(8P11.23) WILD-TYPE 149 85 228 206 0

Figure S88.  Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.23' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S89.  Gene #9: 'amp_8p11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
AMP PEAK 9(8P11.23) MUTATED 75 96 37 51 31
AMP PEAK 9(8P11.23) WILD-TYPE 143 87 108 88 57

Figure S89.  Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8p11.23' versus 'RPPA_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.00072

Table S90.  Gene #9: 'amp_8p11.23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
AMP PEAK 9(8P11.23) MUTATED 65 181 97
AMP PEAK 9(8P11.23) WILD-TYPE 155 217 158

Figure S90.  Get High-res Image Gene #9: '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 = 1.6e-05

Table S91.  Gene #9: 'amp_8p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
AMP PEAK 9(8P11.23) MUTATED 155 52 48 68 66 13 6
AMP PEAK 9(8P11.23) WILD-TYPE 109 117 95 157 137 38 14

Figure S91.  Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00031

Table S92.  Gene #9: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 9(8P11.23) MUTATED 137 72 29 96 59 15
AMP PEAK 9(8P11.23) WILD-TYPE 152 91 61 194 124 45

Figure S92.  Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.23' versus 'MIRSEQ_CNMF'

P value = 0.00078 (Fisher's exact test), Q value = 0.0011

Table S93.  Gene #9: 'amp_8p11.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
AMP PEAK 9(8P11.23) MUTATED 72 99 88 67 59 21
AMP PEAK 9(8P11.23) WILD-TYPE 67 171 120 149 123 25

Figure S93.  Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8p11.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 4.6e-05

Table S94.  Gene #9: 'amp_8p11.23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
AMP PEAK 9(8P11.23) MUTATED 39 31 57 75 32 50 51 36 35
AMP PEAK 9(8P11.23) WILD-TYPE 27 92 127 111 42 63 108 37 48

Figure S94.  Get High-res Image Gene #9: 'amp_8p11.23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S95.  Gene #10: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
AMP PEAK 10(8P11.21) MUTATED 157 50 65 121 28
AMP PEAK 10(8P11.21) WILD-TYPE 173 82 230 173 1

Figure S95.  Get High-res Image Gene #10: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S96.  Gene #10: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
AMP PEAK 10(8P11.21) MUTATED 72 82 40 76 27
AMP PEAK 10(8P11.21) WILD-TYPE 146 101 105 63 61

Figure S96.  Get High-res Image Gene #10: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8p11.21' versus 'RPPA_CNMF'

P value = 0.00328 (Fisher's exact test), Q value = 0.0042

Table S97.  Gene #10: 'amp_8p11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
AMP PEAK 10(8P11.21) MUTATED 98 98 12 63 49 22 2
AMP PEAK 10(8P11.21) WILD-TYPE 96 139 18 141 82 45 8

Figure S97.  Get High-res Image Gene #10: 'amp_8p11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S98.  Gene #10: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
AMP PEAK 10(8P11.21) MUTATED 134 53 39 71 102 11 7
AMP PEAK 10(8P11.21) WILD-TYPE 130 116 104 154 101 40 13

Figure S98.  Get High-res Image Gene #10: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S99.  Gene #10: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 10(8P11.21) MUTATED 126 71 24 87 93 16
AMP PEAK 10(8P11.21) WILD-TYPE 163 92 66 203 90 44

Figure S99.  Get High-res Image Gene #10: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00015

Table S100.  Gene #10: 'amp_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
AMP PEAK 10(8P11.21) MUTATED 63 126 84 59 59 21
AMP PEAK 10(8P11.21) WILD-TYPE 76 144 124 157 123 25

Figure S100.  Get High-res Image Gene #10: 'amp_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0063 (Fisher's exact test), Q value = 0.008

Table S101.  Gene #10: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
AMP PEAK 10(8P11.21) MUTATED 28 42 50 74 32 46 79 30 31
AMP PEAK 10(8P11.21) WILD-TYPE 38 81 134 112 42 67 80 43 52

Figure S101.  Get High-res Image Gene #10: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00016

Table S102.  Gene #10: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
AMP PEAK 10(8P11.21) MUTATED 54 26 12 39 74 38
AMP PEAK 10(8P11.21) WILD-TYPE 79 66 47 80 71 76

Figure S102.  Get High-res Image Gene #10: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00172 (Fisher's exact test), Q value = 0.0023

Table S103.  Gene #10: 'amp_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
AMP PEAK 10(8P11.21) MUTATED 137 73 33
AMP PEAK 10(8P11.21) WILD-TYPE 177 158 84

Figure S103.  Get High-res Image Gene #10: '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 = 1.6e-05

Table S104.  Gene #11: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
AMP PEAK 11(8Q24.21) MUTATED 143 61 146
AMP PEAK 11(8Q24.21) WILD-TYPE 86 55 22

Figure S104.  Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8q24.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.00053

Table S105.  Gene #11: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
AMP PEAK 11(8Q24.21) MUTATED 99 176 75
AMP PEAK 11(8Q24.21) WILD-TYPE 60 90 13

Figure S105.  Get High-res Image Gene #11: '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 = 1.6e-05

Table S106.  Gene #11: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
AMP PEAK 11(8Q24.21) MUTATED 245 55 89 260 29
AMP PEAK 11(8Q24.21) WILD-TYPE 85 77 206 34 0

Figure S106.  Get High-res Image Gene #11: '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 = 1.6e-05

Table S107.  Gene #11: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
AMP PEAK 11(8Q24.21) MUTATED 98 128 74 122 35
AMP PEAK 11(8Q24.21) WILD-TYPE 120 55 71 17 53

Figure S107.  Get High-res Image Gene #11: '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 = 1.6e-05

Table S108.  Gene #11: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
AMP PEAK 11(8Q24.21) MUTATED 161 126 21 97 85 48 9
AMP PEAK 11(8Q24.21) WILD-TYPE 33 111 9 107 46 19 1

Figure S108.  Get High-res Image Gene #11: '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 = 1.6e-05

Table S109.  Gene #11: 'amp_8q24.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
AMP PEAK 11(8Q24.21) MUTATED 181 240 126
AMP PEAK 11(8Q24.21) WILD-TYPE 39 158 129

Figure S109.  Get High-res Image Gene #11: '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 = 1.6e-05

Table S110.  Gene #11: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
AMP PEAK 11(8Q24.21) MUTATED 198 115 64 87 178 17 15
AMP PEAK 11(8Q24.21) WILD-TYPE 66 54 79 138 25 34 5

Figure S110.  Get High-res Image Gene #11: '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 = 1.6e-05

Table S111.  Gene #11: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 11(8Q24.21) MUTATED 168 125 27 147 162 45
AMP PEAK 11(8Q24.21) WILD-TYPE 121 38 63 143 21 15

Figure S111.  Get High-res Image Gene #11: '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 = 1.6e-05

Table S112.  Gene #11: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
AMP PEAK 11(8Q24.21) MUTATED 107 242 99 84 97 34
AMP PEAK 11(8Q24.21) WILD-TYPE 32 28 109 132 85 12

Figure S112.  Get High-res Image Gene #11: '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 = 1.6e-05

Table S113.  Gene #11: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
AMP PEAK 11(8Q24.21) MUTATED 45 91 59 96 47 72 140 44 69
AMP PEAK 11(8Q24.21) WILD-TYPE 21 32 125 90 27 41 19 29 14

Figure S113.  Get High-res Image Gene #11: '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 = 1.6e-05

Table S114.  Gene #11: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
AMP PEAK 11(8Q24.21) MUTATED 82 36 26 63 133 52
AMP PEAK 11(8Q24.21) WILD-TYPE 51 56 33 56 12 62

Figure S114.  Get High-res Image Gene #11: '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 = 1.6e-05

Table S115.  Gene #11: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
AMP PEAK 11(8Q24.21) MUTATED 234 104 54
AMP PEAK 11(8Q24.21) WILD-TYPE 80 127 63

Figure S115.  Get High-res Image Gene #11: '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 = 1.6e-05

Table S116.  Gene #12: 'amp_10p15.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
AMP PEAK 12(10P15.1) MUTATED 38 27 95
AMP PEAK 12(10P15.1) WILD-TYPE 191 89 73

Figure S116.  Get High-res Image Gene #12: '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 = 1.6e-05

Table S117.  Gene #12: 'amp_10p15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
AMP PEAK 12(10P15.1) MUTATED 21 76 63
AMP PEAK 12(10P15.1) WILD-TYPE 138 190 25

Figure S117.  Get High-res Image Gene #12: '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 = 1.6e-05

Table S118.  Gene #12: 'amp_10p15.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
AMP PEAK 12(10P15.1) MUTATED 80 24 17 175 7
AMP PEAK 12(10P15.1) WILD-TYPE 250 108 278 119 22

Figure S118.  Get High-res Image Gene #12: '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 = 1.6e-05

Table S119.  Gene #12: 'amp_10p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
AMP PEAK 12(10P15.1) MUTATED 21 50 35 90 4
AMP PEAK 12(10P15.1) WILD-TYPE 197 133 110 49 84

Figure S119.  Get High-res Image Gene #12: '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 = 1.6e-05

Table S120.  Gene #12: 'amp_10p15.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
AMP PEAK 12(10P15.1) MUTATED 110 32 10 38 37 22 4
AMP PEAK 12(10P15.1) WILD-TYPE 84 205 20 166 94 45 6

Figure S120.  Get High-res Image Gene #12: '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 = 1.6e-05

Table S121.  Gene #12: 'amp_10p15.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
AMP PEAK 12(10P15.1) MUTATED 122 90 41
AMP PEAK 12(10P15.1) WILD-TYPE 98 308 214

Figure S121.  Get High-res Image Gene #12: '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 = 1.6e-05

Table S122.  Gene #12: 'amp_10p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
AMP PEAK 12(10P15.1) MUTATED 62 58 16 21 131 7 8
AMP PEAK 12(10P15.1) WILD-TYPE 202 111 127 204 72 44 12

Figure S122.  Get High-res Image Gene #12: '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 = 1.6e-05

Table S123.  Gene #12: 'amp_10p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 12(10P15.1) MUTATED 46 55 3 47 125 27
AMP PEAK 12(10P15.1) WILD-TYPE 243 108 87 243 58 33

Figure S123.  Get High-res Image Gene #12: '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 = 1.6e-05

Table S124.  Gene #12: 'amp_10p15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
AMP PEAK 12(10P15.1) MUTATED 40 158 17 30 40 10
AMP PEAK 12(10P15.1) WILD-TYPE 99 112 191 186 142 36

Figure S124.  Get High-res Image Gene #12: '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 = 1.6e-05

Table S125.  Gene #12: 'amp_10p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
AMP PEAK 12(10P15.1) MUTATED 16 47 13 18 11 31 105 15 39
AMP PEAK 12(10P15.1) WILD-TYPE 50 76 171 168 63 82 54 58 44

Figure S125.  Get High-res Image Gene #12: '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 = 1.6e-05

Table S126.  Gene #12: 'amp_10p15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
AMP PEAK 12(10P15.1) MUTATED 27 12 8 24 86 19
AMP PEAK 12(10P15.1) WILD-TYPE 106 80 51 95 59 95

Figure S126.  Get High-res Image Gene #12: '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 = 1.6e-05

Table S127.  Gene #12: 'amp_10p15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
AMP PEAK 12(10P15.1) MUTATED 127 33 16
AMP PEAK 12(10P15.1) WILD-TYPE 187 198 101

Figure S127.  Get High-res Image Gene #12: 'amp_10p15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10q22.3' versus 'MRNA_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00013

Table S128.  Gene #13: 'amp_10q22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
AMP PEAK 13(10Q22.3) MUTATED 24 16 45
AMP PEAK 13(10Q22.3) WILD-TYPE 205 100 123

Figure S128.  Get High-res Image Gene #13: 'amp_10q22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_10q22.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0238 (Fisher's exact test), Q value = 0.028

Table S129.  Gene #13: 'amp_10q22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
AMP PEAK 13(10Q22.3) MUTATED 16 52 17
AMP PEAK 13(10Q22.3) WILD-TYPE 143 214 71

Figure S129.  Get High-res Image Gene #13: '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 = 1.6e-05

Table S130.  Gene #13: 'amp_10q22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
AMP PEAK 13(10Q22.3) MUTATED 44 19 10 74 2
AMP PEAK 13(10Q22.3) WILD-TYPE 286 113 285 220 27

Figure S130.  Get High-res Image Gene #13: 'amp_10q22.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10q22.3' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00016

Table S131.  Gene #13: 'amp_10q22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
AMP PEAK 13(10Q22.3) MUTATED 18 27 15 31 3
AMP PEAK 13(10Q22.3) WILD-TYPE 200 156 130 108 85

Figure S131.  Get High-res Image Gene #13: 'amp_10q22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_10q22.3' versus 'RPPA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 9e-05

Table S132.  Gene #13: 'amp_10q22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
AMP PEAK 13(10Q22.3) MUTATED 43 21 6 22 17 19 2
AMP PEAK 13(10Q22.3) WILD-TYPE 151 216 24 182 114 48 8

Figure S132.  Get High-res Image Gene #13: 'amp_10q22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_10q22.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00445 (Fisher's exact test), Q value = 0.0057

Table S133.  Gene #13: 'amp_10q22.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
AMP PEAK 13(10Q22.3) MUTATED 48 52 30
AMP PEAK 13(10Q22.3) WILD-TYPE 172 346 225

Figure S133.  Get High-res Image Gene #13: 'amp_10q22.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_10q22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S134.  Gene #13: 'amp_10q22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
AMP PEAK 13(10Q22.3) MUTATED 32 39 9 18 38 4 9
AMP PEAK 13(10Q22.3) WILD-TYPE 232 130 134 207 165 47 11

Figure S134.  Get High-res Image Gene #13: '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 = 1.6e-05

Table S135.  Gene #13: 'amp_10q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 13(10Q22.3) MUTATED 33 36 2 29 32 17
AMP PEAK 13(10Q22.3) WILD-TYPE 256 127 88 261 151 43

Figure S135.  Get High-res Image Gene #13: '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 = 1.6e-05

Table S136.  Gene #13: 'amp_10q22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
AMP PEAK 13(10Q22.3) MUTATED 30 49 10 20 27 9
AMP PEAK 13(10Q22.3) WILD-TYPE 109 221 198 196 155 37

Figure S136.  Get High-res Image Gene #13: '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 = 1.6e-05

Table S137.  Gene #13: 'amp_10q22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
AMP PEAK 13(10Q22.3) MUTATED 8 30 10 11 11 25 28 5 17
AMP PEAK 13(10Q22.3) WILD-TYPE 58 93 174 175 63 88 131 68 66

Figure S137.  Get High-res Image Gene #13: 'amp_10q22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_10q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00116 (Fisher's exact test), Q value = 0.0016

Table S138.  Gene #13: 'amp_10q22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
AMP PEAK 13(10Q22.3) MUTATED 16 5 9 14 33 8
AMP PEAK 13(10Q22.3) WILD-TYPE 117 87 50 105 112 106

Figure S138.  Get High-res Image Gene #13: 'amp_10q22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_10q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00886 (Fisher's exact test), Q value = 0.011

Table S139.  Gene #13: 'amp_10q22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
AMP PEAK 13(10Q22.3) MUTATED 52 18 15
AMP PEAK 13(10Q22.3) WILD-TYPE 262 213 102

Figure S139.  Get High-res Image Gene #13: 'amp_10q22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11p13' versus 'MRNA_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.001

Table S140.  Gene #14: 'amp_11p13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
AMP PEAK 14(11P13) MUTATED 42 19 55
AMP PEAK 14(11P13) WILD-TYPE 187 97 113

Figure S140.  Get High-res Image Gene #14: 'amp_11p13' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S141.  Gene #14: 'amp_11p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
AMP PEAK 14(11P13) MUTATED 90 18 19 95 0
AMP PEAK 14(11P13) WILD-TYPE 240 114 276 199 29

Figure S141.  Get High-res Image Gene #14: 'amp_11p13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11p13' versus 'METHLYATION_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.00099

Table S142.  Gene #14: 'amp_11p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
AMP PEAK 14(11P13) MUTATED 43 37 20 42 8
AMP PEAK 14(11P13) WILD-TYPE 175 146 125 97 80

Figure S142.  Get High-res Image Gene #14: 'amp_11p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11p13' versus 'RPPA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 7.6e-05

Table S143.  Gene #14: 'amp_11p13' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
AMP PEAK 14(11P13) MUTATED 66 34 4 33 28 18 2
AMP PEAK 14(11P13) WILD-TYPE 128 203 26 171 103 49 8

Figure S143.  Get High-res Image Gene #14: 'amp_11p13' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_11p13' versus 'RPPA_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.014

Table S144.  Gene #14: 'amp_11p13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
AMP PEAK 14(11P13) MUTATED 62 79 44
AMP PEAK 14(11P13) WILD-TYPE 158 319 211

Figure S144.  Get High-res Image Gene #14: 'amp_11p13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_11p13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S145.  Gene #14: 'amp_11p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
AMP PEAK 14(11P13) MUTATED 70 41 11 22 65 9 3
AMP PEAK 14(11P13) WILD-TYPE 194 128 132 203 138 42 17

Figure S145.  Get High-res Image Gene #14: 'amp_11p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S146.  Gene #14: 'amp_11p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 14(11P13) MUTATED 58 44 7 43 59 10
AMP PEAK 14(11P13) WILD-TYPE 231 119 83 247 124 50

Figure S146.  Get High-res Image Gene #14: 'amp_11p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11p13' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S147.  Gene #14: 'amp_11p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
AMP PEAK 14(11P13) MUTATED 35 86 32 19 34 13
AMP PEAK 14(11P13) WILD-TYPE 104 184 176 197 148 33

Figure S147.  Get High-res Image Gene #14: 'amp_11p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S148.  Gene #14: 'amp_11p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
AMP PEAK 14(11P13) MUTATED 18 29 11 31 11 31 49 8 31
AMP PEAK 14(11P13) WILD-TYPE 48 94 173 155 63 82 110 65 52

Figure S148.  Get High-res Image Gene #14: 'amp_11p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.0014

Table S149.  Gene #14: 'amp_11p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
AMP PEAK 14(11P13) MUTATED 26 10 12 20 44 13
AMP PEAK 14(11P13) WILD-TYPE 107 82 47 99 101 101

Figure S149.  Get High-res Image Gene #14: 'amp_11p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_11p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S150.  Gene #14: 'amp_11p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
AMP PEAK 14(11P13) MUTATED 80 25 20
AMP PEAK 14(11P13) WILD-TYPE 234 206 97

Figure S150.  Get High-res Image Gene #14: 'amp_11p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q13.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00111 (Fisher's exact test), Q value = 0.0015

Table S151.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
AMP PEAK 15(11Q13.3) MUTATED 61 129 24
AMP PEAK 15(11Q13.3) WILD-TYPE 98 137 64

Figure S151.  Get High-res Image Gene #15: '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 = 1.6e-05

Table S152.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
AMP PEAK 15(11Q13.3) MUTATED 205 31 39 119 3
AMP PEAK 15(11Q13.3) WILD-TYPE 125 101 256 175 26

Figure S152.  Get High-res Image Gene #15: '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 = 1.6e-05

Table S153.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
AMP PEAK 15(11Q13.3) MUTATED 69 99 25 50 21
AMP PEAK 15(11Q13.3) WILD-TYPE 149 84 120 89 67

Figure S153.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S154.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
AMP PEAK 15(11Q13.3) MUTATED 143 74 34 53 66 17 9
AMP PEAK 15(11Q13.3) WILD-TYPE 121 95 109 172 137 34 11

Figure S154.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 4.6e-05

Table S155.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 15(11Q13.3) MUTATED 120 82 19 96 58 21
AMP PEAK 15(11Q13.3) WILD-TYPE 169 81 71 194 125 39

Figure S155.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S156.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
AMP PEAK 15(11Q13.3) MUTATED 72 110 79 47 64 17
AMP PEAK 15(11Q13.3) WILD-TYPE 67 160 129 169 118 29

Figure S156.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S157.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
AMP PEAK 15(11Q13.3) MUTATED 32 48 37 69 28 55 48 33 39
AMP PEAK 15(11Q13.3) WILD-TYPE 34 75 147 117 46 58 111 40 44

Figure S157.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0306 (Fisher's exact test), Q value = 0.036

Table S158.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
AMP PEAK 15(11Q13.3) MUTATED 123 74 31
AMP PEAK 15(11Q13.3) WILD-TYPE 191 157 86

Figure S158.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q14.1' versus 'MRNA_CNMF'

P value = 0.00208 (Fisher's exact test), Q value = 0.0027

Table S159.  Gene #16: 'amp_11q14.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
AMP PEAK 16(11Q14.1) MUTATED 49 34 63
AMP PEAK 16(11Q14.1) WILD-TYPE 180 82 105

Figure S159.  Get High-res Image Gene #16: 'amp_11q14.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11q14.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00805 (Fisher's exact test), Q value = 0.01

Table S160.  Gene #16: 'amp_11q14.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
AMP PEAK 16(11Q14.1) MUTATED 31 85 30
AMP PEAK 16(11Q14.1) WILD-TYPE 128 181 58

Figure S160.  Get High-res Image Gene #16: '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 = 1.6e-05

Table S161.  Gene #16: 'amp_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
AMP PEAK 16(11Q14.1) MUTATED 107 24 23 111 2
AMP PEAK 16(11Q14.1) WILD-TYPE 223 108 272 183 27

Figure S161.  Get High-res Image Gene #16: 'amp_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q14.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S162.  Gene #16: 'amp_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
AMP PEAK 16(11Q14.1) MUTATED 36 56 17 46 18
AMP PEAK 16(11Q14.1) WILD-TYPE 182 127 128 93 70

Figure S162.  Get High-res Image Gene #16: 'amp_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q14.1' versus 'RPPA_CNMF'

P value = 0.00734 (Fisher's exact test), Q value = 0.0092

Table S163.  Gene #16: 'amp_11q14.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
AMP PEAK 16(11Q14.1) MUTATED 66 45 11 44 29 19 2
AMP PEAK 16(11Q14.1) WILD-TYPE 128 192 19 160 102 48 8

Figure S163.  Get High-res Image Gene #16: 'amp_11q14.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_11q14.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00121 (Fisher's exact test), Q value = 0.0016

Table S164.  Gene #16: 'amp_11q14.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
AMP PEAK 16(11Q14.1) MUTATED 75 86 55
AMP PEAK 16(11Q14.1) WILD-TYPE 145 312 200

Figure S164.  Get High-res Image Gene #16: 'amp_11q14.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_11q14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S165.  Gene #16: 'amp_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
AMP PEAK 16(11Q14.1) MUTATED 80 52 21 33 67 8 5
AMP PEAK 16(11Q14.1) WILD-TYPE 184 117 122 192 136 43 15

Figure S165.  Get High-res Image Gene #16: 'amp_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 7.6e-05

Table S166.  Gene #16: 'amp_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 16(11Q14.1) MUTATED 63 55 10 59 61 18
AMP PEAK 16(11Q14.1) WILD-TYPE 226 108 80 231 122 42

Figure S166.  Get High-res Image Gene #16: '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 = 1.6e-05

Table S167.  Gene #16: 'amp_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
AMP PEAK 16(11Q14.1) MUTATED 33 104 43 26 46 9
AMP PEAK 16(11Q14.1) WILD-TYPE 106 166 165 190 136 37

Figure S167.  Get High-res Image Gene #16: 'amp_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 9e-05

Table S168.  Gene #16: 'amp_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
AMP PEAK 16(11Q14.1) MUTATED 19 34 21 40 17 33 51 16 30
AMP PEAK 16(11Q14.1) WILD-TYPE 47 89 163 146 57 80 108 57 53

Figure S168.  Get High-res Image Gene #16: 'amp_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0115 (Fisher's exact test), Q value = 0.014

Table S169.  Gene #16: 'amp_11q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
AMP PEAK 16(11Q14.1) MUTATED 85 39 22
AMP PEAK 16(11Q14.1) WILD-TYPE 229 192 95

Figure S169.  Get High-res Image Gene #16: 'amp_11q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p13.33' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S170.  Gene #17: 'amp_12p13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
AMP PEAK 17(12P13.33) MUTATED 52 14 83
AMP PEAK 17(12P13.33) WILD-TYPE 177 102 85

Figure S170.  Get High-res Image Gene #17: '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 = 1.6e-05

Table S171.  Gene #17: 'amp_12p13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
AMP PEAK 17(12P13.33) MUTATED 35 65 49
AMP PEAK 17(12P13.33) WILD-TYPE 124 201 39

Figure S171.  Get High-res Image Gene #17: '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 = 1.6e-05

Table S172.  Gene #17: 'amp_12p13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
AMP PEAK 17(12P13.33) MUTATED 102 32 7 136 4
AMP PEAK 17(12P13.33) WILD-TYPE 228 100 288 158 25

Figure S172.  Get High-res Image Gene #17: '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 = 1.6e-05

Table S173.  Gene #17: 'amp_12p13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
AMP PEAK 17(12P13.33) MUTATED 43 45 17 75 5
AMP PEAK 17(12P13.33) WILD-TYPE 175 138 128 64 83

Figure S173.  Get High-res Image Gene #17: '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 = 1.6e-05

Table S174.  Gene #17: 'amp_12p13.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
AMP PEAK 17(12P13.33) MUTATED 96 49 6 30 31 14 2
AMP PEAK 17(12P13.33) WILD-TYPE 98 188 24 174 100 53 8

Figure S174.  Get High-res Image Gene #17: '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 = 1.6e-05

Table S175.  Gene #17: 'amp_12p13.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
AMP PEAK 17(12P13.33) MUTATED 98 90 40
AMP PEAK 17(12P13.33) WILD-TYPE 122 308 215

Figure S175.  Get High-res Image Gene #17: '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 = 1.6e-05

Table S176.  Gene #17: 'amp_12p13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
AMP PEAK 17(12P13.33) MUTATED 71 49 14 29 110 4 3
AMP PEAK 17(12P13.33) WILD-TYPE 193 120 129 196 93 47 17

Figure S176.  Get High-res Image Gene #17: '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 = 1.6e-05

Table S177.  Gene #17: 'amp_12p13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 17(12P13.33) MUTATED 63 57 7 36 102 15
AMP PEAK 17(12P13.33) WILD-TYPE 226 106 83 254 81 45

Figure S177.  Get High-res Image Gene #17: '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 = 1.6e-05

Table S178.  Gene #17: 'amp_12p13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
AMP PEAK 17(12P13.33) MUTATED 42 137 36 22 24 11
AMP PEAK 17(12P13.33) WILD-TYPE 97 133 172 194 158 35

Figure S178.  Get High-res Image Gene #17: '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 = 1.6e-05

Table S179.  Gene #17: 'amp_12p13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
AMP PEAK 17(12P13.33) MUTATED 16 27 18 29 21 25 86 17 33
AMP PEAK 17(12P13.33) WILD-TYPE 50 96 166 157 53 88 73 56 50

Figure S179.  Get High-res Image Gene #17: '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 = 1.6e-05

Table S180.  Gene #17: 'amp_12p13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
AMP PEAK 17(12P13.33) MUTATED 28 16 8 17 74 14
AMP PEAK 17(12P13.33) WILD-TYPE 105 76 51 102 71 100

Figure S180.  Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12p13.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S181.  Gene #17: 'amp_12p13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
AMP PEAK 17(12P13.33) MUTATED 103 39 15
AMP PEAK 17(12P13.33) WILD-TYPE 211 192 102

Figure S181.  Get High-res Image Gene #17: '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 = 1.6e-05

Table S182.  Gene #18: 'amp_12q15' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
AMP PEAK 18(12Q15) MUTATED 72 13 67
AMP PEAK 18(12Q15) WILD-TYPE 157 103 101

Figure S182.  Get High-res Image Gene #18: 'amp_12q15' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_12q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S183.  Gene #18: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
AMP PEAK 18(12Q15) MUTATED 149 33 14 75 4
AMP PEAK 18(12Q15) WILD-TYPE 181 99 281 219 25

Figure S183.  Get High-res Image Gene #18: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4.6e-05

Table S184.  Gene #18: 'amp_12q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
AMP PEAK 18(12Q15) MUTATED 62 59 21 25 9
AMP PEAK 18(12Q15) WILD-TYPE 156 124 124 114 79

Figure S184.  Get High-res Image Gene #18: 'amp_12q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q15' versus 'RPPA_CHIERARCHICAL'

P value = 0.00368 (Fisher's exact test), Q value = 0.0047

Table S185.  Gene #18: 'amp_12q15' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
AMP PEAK 18(12Q15) MUTATED 50 127 54
AMP PEAK 18(12Q15) WILD-TYPE 170 271 201

Figure S185.  Get High-res Image Gene #18: 'amp_12q15' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_12q15' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S186.  Gene #18: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
AMP PEAK 18(12Q15) MUTATED 107 63 18 37 36 9 4
AMP PEAK 18(12Q15) WILD-TYPE 157 106 125 188 167 42 16

Figure S186.  Get High-res Image Gene #18: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S187.  Gene #18: 'amp_12q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 18(12Q15) MUTATED 91 79 7 55 30 12
AMP PEAK 18(12Q15) WILD-TYPE 198 84 83 235 153 48

Figure S187.  Get High-res Image Gene #18: 'amp_12q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S188.  Gene #18: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
AMP PEAK 18(12Q15) MUTATED 59 80 48 22 46 14
AMP PEAK 18(12Q15) WILD-TYPE 80 190 160 194 136 32

Figure S188.  Get High-res Image Gene #18: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S189.  Gene #18: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
AMP PEAK 18(12Q15) MUTATED 28 40 22 45 22 32 27 24 29
AMP PEAK 18(12Q15) WILD-TYPE 38 83 162 141 52 81 132 49 54

Figure S189.  Get High-res Image Gene #18: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0338 (Fisher's exact test), Q value = 0.039

Table S190.  Gene #18: 'amp_12q15' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
AMP PEAK 18(12Q15) MUTATED 45 20 12 28 31 18
AMP PEAK 18(12Q15) WILD-TYPE 88 72 47 91 114 96

Figure S190.  Get High-res Image Gene #18: 'amp_12q15' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_13q34' versus 'MRNA_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.00078

Table S191.  Gene #19: 'amp_13q34' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
AMP PEAK 19(13Q34) MUTATED 35 15 49
AMP PEAK 19(13Q34) WILD-TYPE 194 101 119

Figure S191.  Get High-res Image Gene #19: 'amp_13q34' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_13q34' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S192.  Gene #19: 'amp_13q34' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
AMP PEAK 19(13Q34) MUTATED 22 39 38
AMP PEAK 19(13Q34) WILD-TYPE 137 227 50

Figure S192.  Get High-res Image Gene #19: 'amp_13q34' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_13q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S193.  Gene #19: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
AMP PEAK 19(13Q34) MUTATED 46 11 19 100 2
AMP PEAK 19(13Q34) WILD-TYPE 284 121 276 194 27

Figure S193.  Get High-res Image Gene #19: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q34' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S194.  Gene #19: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
AMP PEAK 19(13Q34) MUTATED 18 24 15 53 4
AMP PEAK 19(13Q34) WILD-TYPE 200 159 130 86 84

Figure S194.  Get High-res Image Gene #19: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q34' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S195.  Gene #19: 'amp_13q34' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
AMP PEAK 19(13Q34) MUTATED 56 28 5 12 26 18 2
AMP PEAK 19(13Q34) WILD-TYPE 138 209 25 192 105 49 8

Figure S195.  Get High-res Image Gene #19: 'amp_13q34' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_13q34' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S196.  Gene #19: 'amp_13q34' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
AMP PEAK 19(13Q34) MUTATED 78 51 18
AMP PEAK 19(13Q34) WILD-TYPE 142 347 237

Figure S196.  Get High-res Image Gene #19: 'amp_13q34' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_13q34' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S197.  Gene #19: 'amp_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
AMP PEAK 19(13Q34) MUTATED 34 28 7 22 80 4 3
AMP PEAK 19(13Q34) WILD-TYPE 230 141 136 203 123 47 17

Figure S197.  Get High-res Image Gene #19: 'amp_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S198.  Gene #19: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 19(13Q34) MUTATED 34 22 3 27 74 18
AMP PEAK 19(13Q34) WILD-TYPE 255 141 87 263 109 42

Figure S198.  Get High-res Image Gene #19: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q34' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S199.  Gene #19: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
AMP PEAK 19(13Q34) MUTATED 18 95 23 16 17 6
AMP PEAK 19(13Q34) WILD-TYPE 121 175 185 200 165 40

Figure S199.  Get High-res Image Gene #19: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S200.  Gene #19: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
AMP PEAK 19(13Q34) MUTATED 9 19 9 15 9 16 64 10 24
AMP PEAK 19(13Q34) WILD-TYPE 57 104 175 171 65 97 95 63 59

Figure S200.  Get High-res Image Gene #19: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_13q34' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S201.  Gene #19: 'amp_13q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
AMP PEAK 19(13Q34) MUTATED 10 6 6 16 45 14
AMP PEAK 19(13Q34) WILD-TYPE 123 86 53 103 100 100

Figure S201.  Get High-res Image Gene #19: 'amp_13q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_13q34' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.00056

Table S202.  Gene #19: 'amp_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
AMP PEAK 19(13Q34) MUTATED 64 24 9
AMP PEAK 19(13Q34) WILD-TYPE 250 207 108

Figure S202.  Get High-res Image Gene #19: 'amp_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_14q21.1' versus 'MRNA_CNMF'

P value = 0.0234 (Fisher's exact test), Q value = 0.028

Table S203.  Gene #20: 'amp_14q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
AMP PEAK 20(14Q21.1) MUTATED 47 17 47
AMP PEAK 20(14Q21.1) WILD-TYPE 182 99 121

Figure S203.  Get High-res Image Gene #20: 'amp_14q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_14q21.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00133 (Fisher's exact test), Q value = 0.0018

Table S204.  Gene #20: 'amp_14q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
AMP PEAK 20(14Q21.1) MUTATED 32 71 8
AMP PEAK 20(14Q21.1) WILD-TYPE 127 195 80

Figure S204.  Get High-res Image Gene #20: '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 = 1.6e-05

Table S205.  Gene #20: 'amp_14q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
AMP PEAK 20(14Q21.1) MUTATED 110 31 23 53 3
AMP PEAK 20(14Q21.1) WILD-TYPE 220 101 272 241 26

Figure S205.  Get High-res Image Gene #20: 'amp_14q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_14q21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S206.  Gene #20: 'amp_14q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
AMP PEAK 20(14Q21.1) MUTATED 41 60 17 19 9
AMP PEAK 20(14Q21.1) WILD-TYPE 177 123 128 120 79

Figure S206.  Get High-res Image Gene #20: 'amp_14q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_14q21.1' versus 'RPPA_CNMF'

P value = 0.0079 (Fisher's exact test), Q value = 0.0098

Table S207.  Gene #20: 'amp_14q21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
AMP PEAK 20(14Q21.1) MUTATED 45 49 9 23 32 15 3
AMP PEAK 20(14Q21.1) WILD-TYPE 149 188 21 181 99 52 7

Figure S207.  Get High-res Image Gene #20: 'amp_14q21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_14q21.1' versus 'RPPA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 7.6e-05

Table S208.  Gene #20: 'amp_14q21.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
AMP PEAK 20(14Q21.1) MUTATED 39 105 32
AMP PEAK 20(14Q21.1) WILD-TYPE 181 293 223

Figure S208.  Get High-res Image Gene #20: 'amp_14q21.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_14q21.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S209.  Gene #20: 'amp_14q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
AMP PEAK 20(14Q21.1) MUTATED 76 56 15 38 26 3 5
AMP PEAK 20(14Q21.1) WILD-TYPE 188 113 128 187 177 48 15

Figure S209.  Get High-res Image Gene #20: '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 = 1.6e-05

Table S210.  Gene #20: 'amp_14q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 20(14Q21.1) MUTATED 62 71 7 45 17 17
AMP PEAK 20(14Q21.1) WILD-TYPE 227 92 83 245 166 43

Figure S210.  Get High-res Image Gene #20: 'amp_14q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_14q21.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S211.  Gene #20: 'amp_14q21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
AMP PEAK 20(14Q21.1) MUTATED 41 61 37 18 42 15
AMP PEAK 20(14Q21.1) WILD-TYPE 98 209 171 198 140 31

Figure S211.  Get High-res Image Gene #20: 'amp_14q21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_14q21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S212.  Gene #20: 'amp_14q21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
AMP PEAK 20(14Q21.1) MUTATED 23 38 17 24 21 33 16 15 27
AMP PEAK 20(14Q21.1) WILD-TYPE 43 85 167 162 53 80 143 58 56

Figure S212.  Get High-res Image Gene #20: '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 = 1.6e-05

Table S213.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
AMP PEAK 21(15Q26.3) MUTATED 37 12 55
AMP PEAK 21(15Q26.3) WILD-TYPE 192 104 113

Figure S213.  Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_15q26.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00253 (Fisher's exact test), Q value = 0.0033

Table S214.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
AMP PEAK 21(15Q26.3) MUTATED 25 49 30
AMP PEAK 21(15Q26.3) WILD-TYPE 134 217 58

Figure S214.  Get High-res Image Gene #21: '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 = 1.6e-05

Table S215.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
AMP PEAK 21(15Q26.3) MUTATED 72 12 17 91 2
AMP PEAK 21(15Q26.3) WILD-TYPE 258 120 278 203 27

Figure S215.  Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_15q26.3' versus 'METHLYATION_CNMF'

P value = 0.001 (Fisher's exact test), Q value = 0.0014

Table S216.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
AMP PEAK 21(15Q26.3) MUTATED 25 28 18 39 13
AMP PEAK 21(15Q26.3) WILD-TYPE 193 155 127 100 75

Figure S216.  Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_15q26.3' versus 'RPPA_CNMF'

P value = 0.00142 (Fisher's exact test), Q value = 0.0019

Table S217.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
AMP PEAK 21(15Q26.3) MUTATED 55 35 5 27 27 16 0
AMP PEAK 21(15Q26.3) WILD-TYPE 139 202 25 177 104 51 10

Figure S217.  Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_15q26.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.00076

Table S218.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
AMP PEAK 21(15Q26.3) MUTATED 57 77 31
AMP PEAK 21(15Q26.3) WILD-TYPE 163 321 224

Figure S218.  Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_15q26.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S219.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
AMP PEAK 21(15Q26.3) MUTATED 59 28 15 17 67 3 4
AMP PEAK 21(15Q26.3) WILD-TYPE 205 141 128 208 136 48 16

Figure S219.  Get High-res Image Gene #21: '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 = 1.6e-05

Table S220.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 21(15Q26.3) MUTATED 52 33 6 34 62 6
AMP PEAK 21(15Q26.3) WILD-TYPE 237 130 84 256 121 54

Figure S220.  Get High-res Image Gene #21: '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 = 1.6e-05

Table S221.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
AMP PEAK 21(15Q26.3) MUTATED 33 78 26 22 24 4
AMP PEAK 21(15Q26.3) WILD-TYPE 106 192 182 194 158 42

Figure S221.  Get High-res Image Gene #21: '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 = 1.6e-05

Table S222.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
AMP PEAK 21(15Q26.3) MUTATED 16 19 8 26 10 16 51 13 28
AMP PEAK 21(15Q26.3) WILD-TYPE 50 104 176 160 64 97 108 60 55

Figure S222.  Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0013

Table S223.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
AMP PEAK 21(15Q26.3) MUTATED 22 11 5 22 42 13
AMP PEAK 21(15Q26.3) WILD-TYPE 111 81 54 97 103 101

Figure S223.  Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_15q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.00036

Table S224.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
AMP PEAK 21(15Q26.3) MUTATED 74 25 16
AMP PEAK 21(15Q26.3) WILD-TYPE 240 206 101

Figure S224.  Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17p11.2' versus 'MRNA_CNMF'

P value = 0.0317 (Fisher's exact test), Q value = 0.037

Table S225.  Gene #22: 'amp_17p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
AMP PEAK 22(17P11.2) MUTATED 36 7 21
AMP PEAK 22(17P11.2) WILD-TYPE 193 109 147

Figure S225.  Get High-res Image Gene #22: 'amp_17p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S226.  Gene #22: 'amp_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
AMP PEAK 22(17P11.2) MUTATED 74 18 12 35 8
AMP PEAK 22(17P11.2) WILD-TYPE 256 114 283 259 21

Figure S226.  Get High-res Image Gene #22: 'amp_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17p11.2' versus 'METHLYATION_CNMF'

P value = 0.00401 (Fisher's exact test), Q value = 0.0051

Table S227.  Gene #22: 'amp_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
AMP PEAK 22(17P11.2) MUTATED 35 36 9 23 9
AMP PEAK 22(17P11.2) WILD-TYPE 183 147 136 116 79

Figure S227.  Get High-res Image Gene #22: 'amp_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17p11.2' versus 'MRNASEQ_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.014

Table S228.  Gene #22: 'amp_17p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
AMP PEAK 22(17P11.2) MUTATED 52 25 13 24 24 3 4
AMP PEAK 22(17P11.2) WILD-TYPE 212 144 130 201 179 48 16

Figure S228.  Get High-res Image Gene #22: 'amp_17p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00933 (Fisher's exact test), Q value = 0.011

Table S229.  Gene #22: 'amp_17p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 22(17P11.2) MUTATED 44 32 5 35 18 11
AMP PEAK 22(17P11.2) WILD-TYPE 245 131 85 255 165 49

Figure S229.  Get High-res Image Gene #22: 'amp_17p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17p11.2' versus 'MIRSEQ_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.018

Table S230.  Gene #22: 'amp_17p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
AMP PEAK 22(17P11.2) MUTATED 25 41 36 16 21 7
AMP PEAK 22(17P11.2) WILD-TYPE 114 229 172 200 161 39

Figure S230.  Get High-res Image Gene #22: 'amp_17p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0171 (Fisher's exact test), Q value = 0.02

Table S231.  Gene #22: 'amp_17p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
AMP PEAK 22(17P11.2) MUTATED 52 26 8
AMP PEAK 22(17P11.2) WILD-TYPE 262 205 109

Figure S231.  Get High-res Image Gene #22: 'amp_17p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q12' versus 'MRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 7.6e-05

Table S232.  Gene #23: 'amp_17q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
AMP PEAK 23(17Q12) MUTATED 73 21 72
AMP PEAK 23(17Q12) WILD-TYPE 156 95 96

Figure S232.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.00039

Table S233.  Gene #23: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
AMP PEAK 23(17Q12) MUTATED 44 106 16
AMP PEAK 23(17Q12) WILD-TYPE 115 160 72

Figure S233.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S234.  Gene #23: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
AMP PEAK 23(17Q12) MUTATED 188 25 30 81 9
AMP PEAK 23(17Q12) WILD-TYPE 142 107 265 213 20

Figure S234.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S235.  Gene #23: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
AMP PEAK 23(17Q12) MUTATED 55 86 33 38 17
AMP PEAK 23(17Q12) WILD-TYPE 163 97 112 101 71

Figure S235.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q12' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4.6e-05

Table S236.  Gene #23: 'amp_17q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
AMP PEAK 23(17Q12) MUTATED 56 70 16 48 50 29 8
AMP PEAK 23(17Q12) WILD-TYPE 138 167 14 156 81 38 2

Figure S236.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_17q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.0043 (Fisher's exact test), Q value = 0.0055

Table S237.  Gene #23: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
AMP PEAK 23(17Q12) MUTATED 88 123 66
AMP PEAK 23(17Q12) WILD-TYPE 132 275 189

Figure S237.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S238.  Gene #23: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
AMP PEAK 23(17Q12) MUTATED 113 106 27 35 40 5 5
AMP PEAK 23(17Q12) WILD-TYPE 151 63 116 190 163 46 15

Figure S238.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S239.  Gene #23: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 23(17Q12) MUTATED 95 85 10 68 33 40
AMP PEAK 23(17Q12) WILD-TYPE 194 78 80 222 150 20

Figure S239.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S240.  Gene #23: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
AMP PEAK 23(17Q12) MUTATED 67 88 55 42 56 18
AMP PEAK 23(17Q12) WILD-TYPE 72 182 153 174 126 28

Figure S240.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S241.  Gene #23: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
AMP PEAK 23(17Q12) MUTATED 24 65 31 56 22 34 27 30 37
AMP PEAK 23(17Q12) WILD-TYPE 42 58 153 130 52 79 132 43 46

Figure S241.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.00077

Table S242.  Gene #23: 'amp_17q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
AMP PEAK 23(17Q12) MUTATED 57 14 19 36 45 29
AMP PEAK 23(17Q12) WILD-TYPE 76 78 40 83 100 85

Figure S242.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.001 (Fisher's exact test), Q value = 0.0014

Table S243.  Gene #23: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
AMP PEAK 23(17Q12) MUTATED 117 55 28
AMP PEAK 23(17Q12) WILD-TYPE 197 176 89

Figure S243.  Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q23.1' versus 'MRNA_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00012

Table S244.  Gene #24: 'amp_17q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
AMP PEAK 24(17Q23.1) MUTATED 99 30 87
AMP PEAK 24(17Q23.1) WILD-TYPE 130 86 81

Figure S244.  Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q23.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00851 (Fisher's exact test), Q value = 0.011

Table S245.  Gene #24: 'amp_17q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
AMP PEAK 24(17Q23.1) MUTATED 66 125 25
AMP PEAK 24(17Q23.1) WILD-TYPE 93 141 63

Figure S245.  Get High-res Image Gene #24: '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 = 1.6e-05

Table S246.  Gene #24: 'amp_17q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
AMP PEAK 24(17Q23.1) MUTATED 225 29 35 126 11
AMP PEAK 24(17Q23.1) WILD-TYPE 105 103 260 168 18

Figure S246.  Get High-res Image Gene #24: '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 = 1.6e-05

Table S247.  Gene #24: 'amp_17q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
AMP PEAK 24(17Q23.1) MUTATED 69 99 44 55 24
AMP PEAK 24(17Q23.1) WILD-TYPE 149 84 101 84 64

Figure S247.  Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q23.1' versus 'RPPA_CNMF'

P value = 0.00752 (Fisher's exact test), Q value = 0.0094

Table S248.  Gene #24: 'amp_17q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
AMP PEAK 24(17Q23.1) MUTATED 81 92 16 65 58 32 8
AMP PEAK 24(17Q23.1) WILD-TYPE 113 145 14 139 73 35 2

Figure S248.  Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_17q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S249.  Gene #24: 'amp_17q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
AMP PEAK 24(17Q23.1) MUTATED 160 98 37 37 69 14 9
AMP PEAK 24(17Q23.1) WILD-TYPE 104 71 106 188 134 37 11

Figure S249.  Get High-res Image Gene #24: '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 = 1.6e-05

Table S250.  Gene #24: 'amp_17q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 24(17Q23.1) MUTATED 127 99 14 95 60 29
AMP PEAK 24(17Q23.1) WILD-TYPE 162 64 76 195 123 31

Figure S250.  Get High-res Image Gene #24: '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 = 1.6e-05

Table S251.  Gene #24: 'amp_17q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
AMP PEAK 24(17Q23.1) MUTATED 90 132 76 42 65 13
AMP PEAK 24(17Q23.1) WILD-TYPE 49 138 132 174 117 33

Figure S251.  Get High-res Image Gene #24: '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 = 1.6e-05

Table S252.  Gene #24: 'amp_17q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
AMP PEAK 24(17Q23.1) MUTATED 43 66 34 75 19 44 51 36 50
AMP PEAK 24(17Q23.1) WILD-TYPE 23 57 150 111 55 69 108 37 33

Figure S252.  Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00033

Table S253.  Gene #24: 'amp_17q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
AMP PEAK 24(17Q23.1) MUTATED 63 19 17 44 65 38
AMP PEAK 24(17Q23.1) WILD-TYPE 70 73 42 75 80 76

Figure S253.  Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S254.  Gene #24: 'amp_17q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
AMP PEAK 24(17Q23.1) MUTATED 151 64 31
AMP PEAK 24(17Q23.1) WILD-TYPE 163 167 86

Figure S254.  Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.12' versus 'MRNA_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.00079

Table S255.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
AMP PEAK 25(19P13.12) MUTATED 34 23 52
AMP PEAK 25(19P13.12) WILD-TYPE 195 93 116

Figure S255.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19p13.12' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 7.6e-05

Table S256.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
AMP PEAK 25(19P13.12) MUTATED 25 49 35
AMP PEAK 25(19P13.12) WILD-TYPE 134 217 53

Figure S256.  Get High-res Image Gene #25: '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 = 1.6e-05

Table S257.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
AMP PEAK 25(19P13.12) MUTATED 58 34 22 107 8
AMP PEAK 25(19P13.12) WILD-TYPE 272 98 273 187 21

Figure S257.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S258.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
AMP PEAK 25(19P13.12) MUTATED 28 33 29 53 14
AMP PEAK 25(19P13.12) WILD-TYPE 190 150 116 86 74

Figure S258.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.12' versus 'RPPA_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0015

Table S259.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
AMP PEAK 25(19P13.12) MUTATED 63 43 6 31 35 14 1
AMP PEAK 25(19P13.12) WILD-TYPE 131 194 24 173 96 53 9

Figure S259.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19p13.12' versus 'RPPA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00012

Table S260.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
AMP PEAK 25(19P13.12) MUTATED 72 76 45
AMP PEAK 25(19P13.12) WILD-TYPE 148 322 210

Figure S260.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_19p13.12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S261.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
AMP PEAK 25(19P13.12) MUTATED 44 32 26 28 84 6 6
AMP PEAK 25(19P13.12) WILD-TYPE 220 137 117 197 119 45 14

Figure S261.  Get High-res Image Gene #25: '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 = 1.6e-05

Table S262.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 25(19P13.12) MUTATED 47 30 14 46 74 15
AMP PEAK 25(19P13.12) WILD-TYPE 242 133 76 244 109 45

Figure S262.  Get High-res Image Gene #25: '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 = 1.6e-05

Table S263.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
AMP PEAK 25(19P13.12) MUTATED 23 93 34 36 28 9
AMP PEAK 25(19P13.12) WILD-TYPE 116 177 174 180 154 37

Figure S263.  Get High-res Image Gene #25: '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 = 1.6e-05

Table S264.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
AMP PEAK 25(19P13.12) MUTATED 9 28 30 23 12 18 62 15 26
AMP PEAK 25(19P13.12) WILD-TYPE 57 95 154 163 62 95 97 58 57

Figure S264.  Get High-res Image Gene #25: '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 = 1.6e-05

Table S265.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
AMP PEAK 25(19P13.12) MUTATED 13 19 19 19 57 14
AMP PEAK 25(19P13.12) WILD-TYPE 120 73 40 100 88 100

Figure S265.  Get High-res Image Gene #25: '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 = 1.6e-05

Table S266.  Gene #26: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
AMP PEAK 26(19Q12) MUTATED 38 29 73
AMP PEAK 26(19Q12) WILD-TYPE 191 87 95

Figure S266.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S267.  Gene #26: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
AMP PEAK 26(19Q12) MUTATED 26 64 50
AMP PEAK 26(19Q12) WILD-TYPE 133 202 38

Figure S267.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S268.  Gene #26: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
AMP PEAK 26(19Q12) MUTATED 67 39 20 147 10
AMP PEAK 26(19Q12) WILD-TYPE 263 93 275 147 19

Figure S268.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S269.  Gene #26: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
AMP PEAK 26(19Q12) MUTATED 33 47 28 75 13
AMP PEAK 26(19Q12) WILD-TYPE 185 136 117 64 75

Figure S269.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19q12' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S270.  Gene #26: 'amp_19q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
AMP PEAK 26(19Q12) MUTATED 87 41 8 40 38 23 0
AMP PEAK 26(19Q12) WILD-TYPE 107 196 22 164 93 44 10

Figure S270.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19q12' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S271.  Gene #26: 'amp_19q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
AMP PEAK 26(19Q12) MUTATED 100 82 55
AMP PEAK 26(19Q12) WILD-TYPE 120 316 200

Figure S271.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S272.  Gene #26: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
AMP PEAK 26(19Q12) MUTATED 55 48 23 28 113 6 8
AMP PEAK 26(19Q12) WILD-TYPE 209 121 120 197 90 45 12

Figure S272.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S273.  Gene #26: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 26(19Q12) MUTATED 52 44 12 46 104 23
AMP PEAK 26(19Q12) WILD-TYPE 237 119 78 244 79 37

Figure S273.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S274.  Gene #26: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
AMP PEAK 26(19Q12) MUTATED 34 126 35 34 38 12
AMP PEAK 26(19Q12) WILD-TYPE 105 144 173 182 144 34

Figure S274.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S275.  Gene #26: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
AMP PEAK 26(19Q12) MUTATED 9 44 24 27 12 25 88 18 32
AMP PEAK 26(19Q12) WILD-TYPE 57 79 160 159 62 88 71 55 51

Figure S275.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S276.  Gene #26: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
AMP PEAK 26(19Q12) MUTATED 29 15 18 18 74 21
AMP PEAK 26(19Q12) WILD-TYPE 104 77 41 101 71 93

Figure S276.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00133 (Fisher's exact test), Q value = 0.0018

Table S277.  Gene #26: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
AMP PEAK 26(19Q12) MUTATED 104 48 23
AMP PEAK 26(19Q12) WILD-TYPE 210 183 94

Figure S277.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q13.42' versus 'MRNA_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.00042

Table S278.  Gene #27: 'amp_19q13.42' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
AMP PEAK 27(19Q13.42) MUTATED 51 25 66
AMP PEAK 27(19Q13.42) WILD-TYPE 178 91 102

Figure S278.  Get High-res Image Gene #27: 'amp_19q13.42' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q13.42' versus 'MRNA_CHIERARCHICAL'

P value = 0.0216 (Fisher's exact test), Q value = 0.026

Table S279.  Gene #27: 'amp_19q13.42' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
AMP PEAK 27(19Q13.42) MUTATED 35 73 34
AMP PEAK 27(19Q13.42) WILD-TYPE 124 193 54

Figure S279.  Get High-res Image Gene #27: 'amp_19q13.42' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q13.42' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S280.  Gene #27: 'amp_19q13.42' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
AMP PEAK 27(19Q13.42) MUTATED 89 41 23 112 10
AMP PEAK 27(19Q13.42) WILD-TYPE 241 91 272 182 19

Figure S280.  Get High-res Image Gene #27: 'amp_19q13.42' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q13.42' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S281.  Gene #27: 'amp_19q13.42' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
AMP PEAK 27(19Q13.42) MUTATED 38 60 24 48 15
AMP PEAK 27(19Q13.42) WILD-TYPE 180 123 121 91 73

Figure S281.  Get High-res Image Gene #27: 'amp_19q13.42' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19q13.42' versus 'RPPA_CNMF'

P value = 0.0353 (Fisher's exact test), Q value = 0.041

Table S282.  Gene #27: 'amp_19q13.42' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
AMP PEAK 27(19Q13.42) MUTATED 65 53 8 42 39 21 1
AMP PEAK 27(19Q13.42) WILD-TYPE 129 184 22 162 92 46 9

Figure S282.  Get High-res Image Gene #27: 'amp_19q13.42' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19q13.42' versus 'RPPA_CHIERARCHICAL'

P value = 0.0374 (Fisher's exact test), Q value = 0.043

Table S283.  Gene #27: 'amp_19q13.42' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
AMP PEAK 27(19Q13.42) MUTATED 72 99 58
AMP PEAK 27(19Q13.42) WILD-TYPE 148 299 197

Figure S283.  Get High-res Image Gene #27: 'amp_19q13.42' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_19q13.42' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S284.  Gene #27: 'amp_19q13.42' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
AMP PEAK 27(19Q13.42) MUTATED 76 49 28 32 71 7 10
AMP PEAK 27(19Q13.42) WILD-TYPE 188 120 115 193 132 44 10

Figure S284.  Get High-res Image Gene #27: 'amp_19q13.42' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q13.42' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00048 (Fisher's exact test), Q value = 0.00068

Table S285.  Gene #27: 'amp_19q13.42' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 27(19Q13.42) MUTATED 67 51 13 60 63 19
AMP PEAK 27(19Q13.42) WILD-TYPE 222 112 77 230 120 41

Figure S285.  Get High-res Image Gene #27: '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 = 1.6e-05

Table S286.  Gene #27: 'amp_19q13.42' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
AMP PEAK 27(19Q13.42) MUTATED 48 96 42 30 45 10
AMP PEAK 27(19Q13.42) WILD-TYPE 91 174 166 186 137 36

Figure S286.  Get High-res Image Gene #27: '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 = 1.6e-05

Table S287.  Gene #27: 'amp_19q13.42' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
AMP PEAK 27(19Q13.42) MUTATED 11 45 29 35 11 33 54 22 31
AMP PEAK 27(19Q13.42) WILD-TYPE 55 78 155 151 63 80 105 51 52

Figure S287.  Get High-res Image Gene #27: '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 = 1.6e-05

Table S288.  Gene #28: 'amp_20q13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
AMP PEAK 28(20Q13.2) MUTATED 119 40 117
AMP PEAK 28(20Q13.2) WILD-TYPE 110 76 51

Figure S288.  Get High-res Image Gene #28: 'amp_20q13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S289.  Gene #28: 'amp_20q13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
AMP PEAK 28(20Q13.2) MUTATED 248 64 31 191 13
AMP PEAK 28(20Q13.2) WILD-TYPE 82 68 264 103 16

Figure S289.  Get High-res Image Gene #28: '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 = 1.6e-05

Table S290.  Gene #28: 'amp_20q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
AMP PEAK 28(20Q13.2) MUTATED 98 116 54 83 21
AMP PEAK 28(20Q13.2) WILD-TYPE 120 67 91 56 67

Figure S290.  Get High-res Image Gene #28: 'amp_20q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.2' versus 'RPPA_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.015

Table S291.  Gene #28: 'amp_20q13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
AMP PEAK 28(20Q13.2) MUTATED 107 120 20 83 73 39 4
AMP PEAK 28(20Q13.2) WILD-TYPE 87 117 10 121 58 28 6

Figure S291.  Get High-res Image Gene #28: 'amp_20q13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00152 (Fisher's exact test), Q value = 0.002

Table S292.  Gene #28: 'amp_20q13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
AMP PEAK 28(20Q13.2) MUTATED 124 216 106
AMP PEAK 28(20Q13.2) WILD-TYPE 96 182 149

Figure S292.  Get High-res Image Gene #28: '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 = 1.6e-05

Table S293.  Gene #28: 'amp_20q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
AMP PEAK 28(20Q13.2) MUTATED 182 109 41 72 112 16 12
AMP PEAK 28(20Q13.2) WILD-TYPE 82 60 102 153 91 35 8

Figure S293.  Get High-res Image Gene #28: '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 = 1.6e-05

Table S294.  Gene #28: 'amp_20q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 28(20Q13.2) MUTATED 160 119 9 125 97 34
AMP PEAK 28(20Q13.2) WILD-TYPE 129 44 81 165 86 26

Figure S294.  Get High-res Image Gene #28: '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 = 1.6e-05

Table S295.  Gene #28: 'amp_20q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
AMP PEAK 28(20Q13.2) MUTATED 95 169 93 65 88 29
AMP PEAK 28(20Q13.2) WILD-TYPE 44 101 115 151 94 17

Figure S295.  Get High-res Image Gene #28: '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 = 1.6e-05

Table S296.  Gene #28: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
AMP PEAK 28(20Q13.2) MUTATED 44 79 51 83 46 65 79 30 62
AMP PEAK 28(20Q13.2) WILD-TYPE 22 44 133 103 28 48 80 43 21

Figure S296.  Get High-res Image Gene #28: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.00057

Table S297.  Gene #28: 'amp_20q13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
AMP PEAK 28(20Q13.2) MUTATED 72 37 32 63 93 44
AMP PEAK 28(20Q13.2) WILD-TYPE 61 55 27 56 52 70

Figure S297.  Get High-res Image Gene #28: 'amp_20q13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S298.  Gene #28: 'amp_20q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
AMP PEAK 28(20Q13.2) MUTATED 195 94 52
AMP PEAK 28(20Q13.2) WILD-TYPE 119 137 65

Figure S298.  Get High-res Image Gene #28: 'amp_20q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.13' versus 'MRNA_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.0011

Table S299.  Gene #29: 'del_1p36.13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 1(1P36.13) MUTATED 101 33 85
DEL PEAK 1(1P36.13) WILD-TYPE 128 83 83

Figure S299.  Get High-res Image Gene #29: 'del_1p36.13' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S300.  Gene #29: 'del_1p36.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 1(1P36.13) MUTATED 191 73 31 148 9
DEL PEAK 1(1P36.13) WILD-TYPE 139 59 264 146 20

Figure S300.  Get High-res Image Gene #29: '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 = 1.6e-05

Table S301.  Gene #29: 'del_1p36.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 1(1P36.13) MUTATED 74 115 42 60 20
DEL PEAK 1(1P36.13) WILD-TYPE 144 68 103 79 68

Figure S301.  Get High-res Image Gene #29: 'del_1p36.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.13' versus 'RPPA_CNMF'

P value = 0.00246 (Fisher's exact test), Q value = 0.0032

Table S302.  Gene #29: 'del_1p36.13' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 1(1P36.13) MUTATED 101 89 14 67 56 33 6
DEL PEAK 1(1P36.13) WILD-TYPE 93 148 16 137 75 34 4

Figure S302.  Get High-res Image Gene #29: 'del_1p36.13' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p36.13' versus 'RPPA_CHIERARCHICAL'

P value = 0.00654 (Fisher's exact test), Q value = 0.0082

Table S303.  Gene #29: 'del_1p36.13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 1(1P36.13) MUTATED 99 181 86
DEL PEAK 1(1P36.13) WILD-TYPE 121 217 169

Figure S303.  Get High-res Image Gene #29: 'del_1p36.13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1p36.13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S304.  Gene #29: 'del_1p36.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 1(1P36.13) MUTATED 138 98 27 77 83 18 8
DEL PEAK 1(1P36.13) WILD-TYPE 126 71 116 148 120 33 12

Figure S304.  Get High-res Image Gene #29: '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 = 1.6e-05

Table S305.  Gene #29: 'del_1p36.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 1(1P36.13) MUTATED 130 105 9 107 80 18
DEL PEAK 1(1P36.13) WILD-TYPE 159 58 81 183 103 42

Figure S305.  Get High-res Image Gene #29: 'del_1p36.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.13' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S306.  Gene #29: 'del_1p36.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 1(1P36.13) MUTATED 61 137 84 53 82 21
DEL PEAK 1(1P36.13) WILD-TYPE 78 133 124 163 100 25

Figure S306.  Get High-res Image Gene #29: 'del_1p36.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 4.6e-05

Table S307.  Gene #29: 'del_1p36.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 1(1P36.13) MUTATED 36 56 44 66 37 55 70 31 43
DEL PEAK 1(1P36.13) WILD-TYPE 30 67 140 120 37 58 89 42 40

Figure S307.  Get High-res Image Gene #29: 'del_1p36.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p21.2' versus 'MRNA_CNMF'

P value = 0.041 (Fisher's exact test), Q value = 0.047

Table S308.  Gene #30: 'del_1p21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 2(1P21.2) MUTATED 85 29 64
DEL PEAK 2(1P21.2) WILD-TYPE 144 87 104

Figure S308.  Get High-res Image Gene #30: 'del_1p21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p21.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0107 (Fisher's exact test), Q value = 0.013

Table S309.  Gene #30: 'del_1p21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 2(1P21.2) MUTATED 52 106 20
DEL PEAK 2(1P21.2) WILD-TYPE 107 160 68

Figure S309.  Get High-res Image Gene #30: 'del_1p21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S310.  Gene #30: 'del_1p21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 2(1P21.2) MUTATED 154 71 27 96 8
DEL PEAK 2(1P21.2) WILD-TYPE 176 61 268 198 21

Figure S310.  Get High-res Image Gene #30: 'del_1p21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S311.  Gene #30: 'del_1p21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 2(1P21.2) MUTATED 65 90 31 36 19
DEL PEAK 2(1P21.2) WILD-TYPE 153 93 114 103 69

Figure S311.  Get High-res Image Gene #30: 'del_1p21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p21.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.02

Table S312.  Gene #30: 'del_1p21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 2(1P21.2) MUTATED 65 149 70
DEL PEAK 2(1P21.2) WILD-TYPE 155 249 185

Figure S312.  Get High-res Image Gene #30: 'del_1p21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1p21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S313.  Gene #30: 'del_1p21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 2(1P21.2) MUTATED 110 82 30 71 46 8 6
DEL PEAK 2(1P21.2) WILD-TYPE 154 87 113 154 157 43 14

Figure S313.  Get High-res Image Gene #30: 'del_1p21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S314.  Gene #30: 'del_1p21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 2(1P21.2) MUTATED 105 92 15 86 40 15
DEL PEAK 2(1P21.2) WILD-TYPE 184 71 75 204 143 45

Figure S314.  Get High-res Image Gene #30: 'del_1p21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p21.2' versus 'MIRSEQ_CNMF'

P value = 0.00575 (Fisher's exact test), Q value = 0.0073

Table S315.  Gene #30: 'del_1p21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 2(1P21.2) MUTATED 50 88 70 50 70 21
DEL PEAK 2(1P21.2) WILD-TYPE 89 182 138 166 112 25

Figure S315.  Get High-res Image Gene #30: 'del_1p21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S316.  Gene #30: 'del_1p21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 2(1P21.2) MUTATED 28 52 41 57 34 43 35 26 33
DEL PEAK 2(1P21.2) WILD-TYPE 38 71 143 129 40 70 124 47 50

Figure S316.  Get High-res Image Gene #30: 'del_1p21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S317.  Gene #31: 'del_2q37.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 3(2Q37.3) MUTATED 61 21 82
DEL PEAK 3(2Q37.3) WILD-TYPE 168 95 86

Figure S317.  Get High-res Image Gene #31: 'del_2q37.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_2q37.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00127 (Fisher's exact test), Q value = 0.0017

Table S318.  Gene #31: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 3(2Q37.3) MUTATED 43 78 43
DEL PEAK 3(2Q37.3) WILD-TYPE 116 188 45

Figure S318.  Get High-res Image Gene #31: '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 = 1.6e-05

Table S319.  Gene #31: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 3(2Q37.3) MUTATED 118 39 15 139 7
DEL PEAK 3(2Q37.3) WILD-TYPE 212 93 280 155 22

Figure S319.  Get High-res Image Gene #31: '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 = 1.6e-05

Table S320.  Gene #31: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 3(2Q37.3) MUTATED 54 53 21 68 10
DEL PEAK 3(2Q37.3) WILD-TYPE 164 130 124 71 78

Figure S320.  Get High-res Image Gene #31: '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 = 1.6e-05

Table S321.  Gene #31: 'del_2q37.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 3(2Q37.3) MUTATED 88 61 7 37 38 22 0
DEL PEAK 3(2Q37.3) WILD-TYPE 106 176 23 167 93 45 10

Figure S321.  Get High-res Image Gene #31: '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 = 1.6e-05

Table S322.  Gene #31: 'del_2q37.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 3(2Q37.3) MUTATED 90 124 39
DEL PEAK 3(2Q37.3) WILD-TYPE 130 274 216

Figure S322.  Get High-res Image Gene #31: '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 = 1.6e-05

Table S323.  Gene #31: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 3(2Q37.3) MUTATED 90 58 19 43 98 3 4
DEL PEAK 3(2Q37.3) WILD-TYPE 174 111 124 182 105 48 16

Figure S323.  Get High-res Image Gene #31: '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 = 1.6e-05

Table S324.  Gene #31: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 3(2Q37.3) MUTATED 87 71 10 45 88 14
DEL PEAK 3(2Q37.3) WILD-TYPE 202 92 80 245 95 46

Figure S324.  Get High-res Image Gene #31: '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 = 1.6e-05

Table S325.  Gene #31: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 3(2Q37.3) MUTATED 54 125 42 27 48 14
DEL PEAK 3(2Q37.3) WILD-TYPE 85 145 166 189 134 32

Figure S325.  Get High-res Image Gene #31: '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 = 1.6e-05

Table S326.  Gene #31: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 3(2Q37.3) MUTATED 23 47 22 44 21 30 77 16 30
DEL PEAK 3(2Q37.3) WILD-TYPE 43 76 162 142 53 83 82 57 53

Figure S326.  Get High-res Image Gene #31: '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 = 1.6e-05

Table S327.  Gene #31: 'del_2q37.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 3(2Q37.3) MUTATED 41 10 15 27 67 21
DEL PEAK 3(2Q37.3) WILD-TYPE 92 82 44 92 78 93

Figure S327.  Get High-res Image Gene #31: 'del_2q37.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_2q37.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S328.  Gene #31: 'del_2q37.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 3(2Q37.3) MUTATED 115 42 24
DEL PEAK 3(2Q37.3) WILD-TYPE 199 189 93

Figure S328.  Get High-res Image Gene #31: '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 = 1.6e-05

Table S329.  Gene #32: 'del_3p21.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 4(3P21.31) MUTATED 46 33 90
DEL PEAK 4(3P21.31) WILD-TYPE 183 83 78

Figure S329.  Get High-res Image Gene #32: '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 = 1.6e-05

Table S330.  Gene #32: 'del_3p21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 4(3P21.31) MUTATED 21 100 48
DEL PEAK 4(3P21.31) WILD-TYPE 138 166 40

Figure S330.  Get High-res Image Gene #32: '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 = 1.6e-05

Table S331.  Gene #32: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 4(3P21.31) MUTATED 117 27 30 169 4
DEL PEAK 4(3P21.31) WILD-TYPE 213 105 265 125 25

Figure S331.  Get High-res Image Gene #32: '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 = 1.6e-05

Table S332.  Gene #32: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 4(3P21.31) MUTATED 43 79 31 74 13
DEL PEAK 4(3P21.31) WILD-TYPE 175 104 114 65 75

Figure S332.  Get High-res Image Gene #32: '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 = 1.6e-05

Table S333.  Gene #32: 'del_3p21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 4(3P21.31) MUTATED 103 40 13 55 51 32 3
DEL PEAK 4(3P21.31) WILD-TYPE 91 197 17 149 80 35 7

Figure S333.  Get High-res Image Gene #32: '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 = 1.6e-05

Table S334.  Gene #32: 'del_3p21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 4(3P21.31) MUTATED 119 103 75
DEL PEAK 4(3P21.31) WILD-TYPE 101 295 180

Figure S334.  Get High-res Image Gene #32: '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 = 1.6e-05

Table S335.  Gene #32: 'del_3p21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 4(3P21.31) MUTATED 86 79 30 22 109 13 7
DEL PEAK 4(3P21.31) WILD-TYPE 178 90 113 203 94 38 13

Figure S335.  Get High-res Image Gene #32: '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 = 1.6e-05

Table S336.  Gene #32: 'del_3p21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 4(3P21.31) MUTATED 53 84 12 74 100 23
DEL PEAK 4(3P21.31) WILD-TYPE 236 79 78 216 83 37

Figure S336.  Get High-res Image Gene #32: '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 = 1.6e-05

Table S337.  Gene #32: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 4(3P21.31) MUTATED 55 143 49 32 49 12
DEL PEAK 4(3P21.31) WILD-TYPE 84 127 159 184 133 34

Figure S337.  Get High-res Image Gene #32: '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 = 1.6e-05

Table S338.  Gene #32: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 4(3P21.31) MUTATED 18 52 27 40 10 41 86 24 42
DEL PEAK 4(3P21.31) WILD-TYPE 48 71 157 146 64 72 73 49 41

Figure S338.  Get High-res Image Gene #32: '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 = 1.6e-05

Table S339.  Gene #32: 'del_3p21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 4(3P21.31) MUTATED 43 21 13 25 83 28
DEL PEAK 4(3P21.31) WILD-TYPE 90 71 46 94 62 86

Figure S339.  Get High-res Image Gene #32: 'del_3p21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.00038

Table S340.  Gene #32: 'del_3p21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 4(3P21.31) MUTATED 125 63 25
DEL PEAK 4(3P21.31) WILD-TYPE 189 168 92

Figure S340.  Get High-res Image Gene #32: '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 = 1.6e-05

Table S341.  Gene #33: 'del_4p16.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 5(4P16.3) MUTATED 51 31 87
DEL PEAK 5(4P16.3) WILD-TYPE 178 85 81

Figure S341.  Get High-res Image Gene #33: '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 = 1.6e-05

Table S342.  Gene #33: 'del_4p16.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 5(4P16.3) MUTATED 32 85 52
DEL PEAK 5(4P16.3) WILD-TYPE 127 181 36

Figure S342.  Get High-res Image Gene #33: '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 = 1.6e-05

Table S343.  Gene #33: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 5(4P16.3) MUTATED 76 54 23 180 6
DEL PEAK 5(4P16.3) WILD-TYPE 254 78 272 114 23

Figure S343.  Get High-res Image Gene #33: '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 = 1.6e-05

Table S344.  Gene #33: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 5(4P16.3) MUTATED 49 50 35 88 12
DEL PEAK 5(4P16.3) WILD-TYPE 169 133 110 51 76

Figure S344.  Get High-res Image Gene #33: '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 = 1.6e-05

Table S345.  Gene #33: 'del_4p16.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 5(4P16.3) MUTATED 109 53 7 44 38 29 2
DEL PEAK 5(4P16.3) WILD-TYPE 85 184 23 160 93 38 8

Figure S345.  Get High-res Image Gene #33: 'del_4p16.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4p16.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S346.  Gene #33: 'del_4p16.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 5(4P16.3) MUTATED 123 101 58
DEL PEAK 5(4P16.3) WILD-TYPE 97 297 197

Figure S346.  Get High-res Image Gene #33: '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 = 1.6e-05

Table S347.  Gene #33: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 5(4P16.3) MUTATED 59 72 18 51 122 7 9
DEL PEAK 5(4P16.3) WILD-TYPE 205 97 125 174 81 44 11

Figure S347.  Get High-res Image Gene #33: '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 = 1.6e-05

Table S348.  Gene #33: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 5(4P16.3) MUTATED 66 66 10 55 112 29
DEL PEAK 5(4P16.3) WILD-TYPE 223 97 80 235 71 31

Figure S348.  Get High-res Image Gene #33: '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 = 1.6e-05

Table S349.  Gene #33: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 5(4P16.3) MUTATED 35 150 37 39 54 13
DEL PEAK 5(4P16.3) WILD-TYPE 104 120 171 177 128 33

Figure S349.  Get High-res Image Gene #33: '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 = 1.6e-05

Table S350.  Gene #33: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 5(4P16.3) MUTATED 15 52 28 36 26 30 95 10 36
DEL PEAK 5(4P16.3) WILD-TYPE 51 71 156 150 48 83 64 63 47

Figure S350.  Get High-res Image Gene #33: '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 = 1.6e-05

Table S351.  Gene #33: 'del_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 5(4P16.3) MUTATED 25 24 18 29 86 20
DEL PEAK 5(4P16.3) WILD-TYPE 108 68 41 90 59 94

Figure S351.  Get High-res Image Gene #33: 'del_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S352.  Gene #33: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 5(4P16.3) MUTATED 121 46 35
DEL PEAK 5(4P16.3) WILD-TYPE 193 185 82

Figure S352.  Get High-res Image Gene #33: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q35.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S353.  Gene #34: 'del_4q35.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 6(4Q35.2) MUTATED 55 29 86
DEL PEAK 6(4Q35.2) WILD-TYPE 174 87 82

Figure S353.  Get High-res Image Gene #34: 'del_4q35.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q35.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S354.  Gene #34: 'del_4q35.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 6(4Q35.2) MUTATED 37 86 47
DEL PEAK 6(4Q35.2) WILD-TYPE 122 180 41

Figure S354.  Get High-res Image Gene #34: 'del_4q35.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q35.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S355.  Gene #34: 'del_4q35.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 6(4Q35.2) MUTATED 73 62 18 187 7
DEL PEAK 6(4Q35.2) WILD-TYPE 257 70 277 107 22

Figure S355.  Get High-res Image Gene #34: 'del_4q35.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q35.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S356.  Gene #34: 'del_4q35.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 6(4Q35.2) MUTATED 47 45 42 89 16
DEL PEAK 6(4Q35.2) WILD-TYPE 171 138 103 50 72

Figure S356.  Get High-res Image Gene #34: 'del_4q35.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q35.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S357.  Gene #34: 'del_4q35.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 6(4Q35.2) MUTATED 107 47 11 39 46 36 1
DEL PEAK 6(4Q35.2) WILD-TYPE 87 190 19 165 85 31 9

Figure S357.  Get High-res Image Gene #34: 'del_4q35.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4q35.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S358.  Gene #34: 'del_4q35.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 6(4Q35.2) MUTATED 122 109 56
DEL PEAK 6(4Q35.2) WILD-TYPE 98 289 199

Figure S358.  Get High-res Image Gene #34: 'del_4q35.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4q35.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S359.  Gene #34: 'del_4q35.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 6(4Q35.2) MUTATED 56 71 20 58 125 7 9
DEL PEAK 6(4Q35.2) WILD-TYPE 208 98 123 167 78 44 11

Figure S359.  Get High-res Image Gene #34: 'del_4q35.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q35.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S360.  Gene #34: 'del_4q35.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 6(4Q35.2) MUTATED 60 69 10 67 116 24
DEL PEAK 6(4Q35.2) WILD-TYPE 229 94 80 223 67 36

Figure S360.  Get High-res Image Gene #34: 'del_4q35.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S361.  Gene #34: 'del_4q35.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 6(4Q35.2) MUTATED 35 150 34 39 61 15
DEL PEAK 6(4Q35.2) WILD-TYPE 104 120 174 177 121 31

Figure S361.  Get High-res Image Gene #34: 'del_4q35.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q35.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S362.  Gene #34: 'del_4q35.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 6(4Q35.2) MUTATED 14 42 27 36 29 34 99 10 43
DEL PEAK 6(4Q35.2) WILD-TYPE 52 81 157 150 45 79 60 63 40

Figure S362.  Get High-res Image Gene #34: 'del_4q35.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q35.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S363.  Gene #34: 'del_4q35.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 6(4Q35.2) MUTATED 28 21 19 31 85 23
DEL PEAK 6(4Q35.2) WILD-TYPE 105 71 40 88 60 91

Figure S363.  Get High-res Image Gene #34: 'del_4q35.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q35.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 4.6e-05

Table S364.  Gene #34: 'del_4q35.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 6(4Q35.2) MUTATED 124 47 36
DEL PEAK 6(4Q35.2) WILD-TYPE 190 184 81

Figure S364.  Get High-res Image Gene #34: 'del_4q35.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q11.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S365.  Gene #35: 'del_5q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 7(5Q11.2) MUTATED 23 23 90
DEL PEAK 7(5Q11.2) WILD-TYPE 206 93 78

Figure S365.  Get High-res Image Gene #35: '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 = 1.6e-05

Table S366.  Gene #35: 'del_5q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 7(5Q11.2) MUTATED 12 61 63
DEL PEAK 7(5Q11.2) WILD-TYPE 147 205 25

Figure S366.  Get High-res Image Gene #35: '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 = 1.6e-05

Table S367.  Gene #35: 'del_5q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 7(5Q11.2) MUTATED 49 10 15 202 4
DEL PEAK 7(5Q11.2) WILD-TYPE 281 122 280 92 25

Figure S367.  Get High-res Image Gene #35: '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 = 1.6e-05

Table S368.  Gene #35: 'del_5q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 7(5Q11.2) MUTATED 22 29 37 102 7
DEL PEAK 7(5Q11.2) WILD-TYPE 196 154 108 37 81

Figure S368.  Get High-res Image Gene #35: '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 = 1.6e-05

Table S369.  Gene #35: 'del_5q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 7(5Q11.2) MUTATED 112 26 9 26 39 24 3
DEL PEAK 7(5Q11.2) WILD-TYPE 82 211 21 178 92 43 7

Figure S369.  Get High-res Image Gene #35: '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 = 1.6e-05

Table S370.  Gene #35: 'del_5q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 7(5Q11.2) MUTATED 134 72 33
DEL PEAK 7(5Q11.2) WILD-TYPE 86 326 222

Figure S370.  Get High-res Image Gene #35: '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 = 1.6e-05

Table S371.  Gene #35: 'del_5q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 7(5Q11.2) MUTATED 47 51 10 18 143 4 5
DEL PEAK 7(5Q11.2) WILD-TYPE 217 118 133 207 60 47 15

Figure S371.  Get High-res Image Gene #35: '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 = 1.6e-05

Table S372.  Gene #35: 'del_5q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 7(5Q11.2) MUTATED 36 44 2 33 137 26
DEL PEAK 7(5Q11.2) WILD-TYPE 253 119 88 257 46 34

Figure S372.  Get High-res Image Gene #35: '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 = 1.6e-05

Table S373.  Gene #35: 'del_5q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 7(5Q11.2) MUTATED 35 160 13 25 28 7
DEL PEAK 7(5Q11.2) WILD-TYPE 104 110 195 191 154 39

Figure S373.  Get High-res Image Gene #35: '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 = 1.6e-05

Table S374.  Gene #35: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 7(5Q11.2) MUTATED 9 42 8 20 7 19 120 11 32
DEL PEAK 7(5Q11.2) WILD-TYPE 57 81 176 166 67 94 39 62 51

Figure S374.  Get High-res Image Gene #35: '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 = 1.6e-05

Table S375.  Gene #35: 'del_5q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 7(5Q11.2) MUTATED 19 13 8 16 101 14
DEL PEAK 7(5Q11.2) WILD-TYPE 114 79 51 103 44 100

Figure S375.  Get High-res Image Gene #35: 'del_5q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S376.  Gene #35: 'del_5q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 7(5Q11.2) MUTATED 128 28 15
DEL PEAK 7(5Q11.2) WILD-TYPE 186 203 102

Figure S376.  Get High-res Image Gene #35: '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 = 1.6e-05

Table S377.  Gene #36: 'del_5q21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 8(5Q21.3) MUTATED 20 22 93
DEL PEAK 8(5Q21.3) WILD-TYPE 209 94 75

Figure S377.  Get High-res Image Gene #36: '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 = 1.6e-05

Table S378.  Gene #36: 'del_5q21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 8(5Q21.3) MUTATED 10 59 66
DEL PEAK 8(5Q21.3) WILD-TYPE 149 207 22

Figure S378.  Get High-res Image Gene #36: '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 = 1.6e-05

Table S379.  Gene #36: 'del_5q21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 8(5Q21.3) MUTATED 43 10 8 208 4
DEL PEAK 8(5Q21.3) WILD-TYPE 287 122 287 86 25

Figure S379.  Get High-res Image Gene #36: '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 = 1.6e-05

Table S380.  Gene #36: 'del_5q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 8(5Q21.3) MUTATED 19 27 34 109 4
DEL PEAK 8(5Q21.3) WILD-TYPE 199 156 111 30 84

Figure S380.  Get High-res Image Gene #36: '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 = 1.6e-05

Table S381.  Gene #36: 'del_5q21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 8(5Q21.3) MUTATED 111 18 7 27 42 24 3
DEL PEAK 8(5Q21.3) WILD-TYPE 83 219 23 177 89 43 7

Figure S381.  Get High-res Image Gene #36: '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 = 1.6e-05

Table S382.  Gene #36: 'del_5q21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 8(5Q21.3) MUTATED 135 60 37
DEL PEAK 8(5Q21.3) WILD-TYPE 85 338 218

Figure S382.  Get High-res Image Gene #36: '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 = 1.6e-05

Table S383.  Gene #36: 'del_5q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 8(5Q21.3) MUTATED 43 47 8 12 151 4 6
DEL PEAK 8(5Q21.3) WILD-TYPE 221 122 135 213 52 47 14

Figure S383.  Get High-res Image Gene #36: '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 = 1.6e-05

Table S384.  Gene #36: 'del_5q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 8(5Q21.3) MUTATED 34 40 1 29 143 24
DEL PEAK 8(5Q21.3) WILD-TYPE 255 123 89 261 40 36

Figure S384.  Get High-res Image Gene #36: '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 = 1.6e-05

Table S385.  Gene #36: 'del_5q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 8(5Q21.3) MUTATED 33 164 10 23 26 7
DEL PEAK 8(5Q21.3) WILD-TYPE 106 106 198 193 156 39

Figure S385.  Get High-res Image Gene #36: '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 = 1.6e-05

Table S386.  Gene #36: 'del_5q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 8(5Q21.3) MUTATED 10 43 7 14 6 17 122 9 35
DEL PEAK 8(5Q21.3) WILD-TYPE 56 80 177 172 68 96 37 64 48

Figure S386.  Get High-res Image Gene #36: '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 = 1.6e-05

Table S387.  Gene #36: 'del_5q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 8(5Q21.3) MUTATED 16 13 6 13 104 14
DEL PEAK 8(5Q21.3) WILD-TYPE 117 79 53 106 41 100

Figure S387.  Get High-res Image Gene #36: 'del_5q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S388.  Gene #36: 'del_5q21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 8(5Q21.3) MUTATED 132 24 10
DEL PEAK 8(5Q21.3) WILD-TYPE 182 207 107

Figure S388.  Get High-res Image Gene #36: '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 = 1.6e-05

Table S389.  Gene #37: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 9(6P25.3) MUTATED 87 28 24 59 6
DEL PEAK 9(6P25.3) WILD-TYPE 243 104 271 235 23

Figure S389.  Get High-res Image Gene #37: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 0.0325 (Fisher's exact test), Q value = 0.038

Table S390.  Gene #37: 'del_6p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 9(6P25.3) MUTATED 42 41 19 35 11
DEL PEAK 9(6P25.3) WILD-TYPE 176 142 126 104 77

Figure S390.  Get High-res Image Gene #37: 'del_6p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 0.00078 (Fisher's exact test), Q value = 0.0011

Table S391.  Gene #37: 'del_6p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 9(6P25.3) MUTATED 65 34 12 40 45 6 1
DEL PEAK 9(6P25.3) WILD-TYPE 199 135 131 185 158 45 19

Figure S391.  Get High-res Image Gene #37: 'del_6p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6p25.3' versus 'MIRSEQ_CNMF'

P value = 0.00733 (Fisher's exact test), Q value = 0.0092

Table S392.  Gene #37: 'del_6p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 9(6P25.3) MUTATED 30 61 42 22 37 8
DEL PEAK 9(6P25.3) WILD-TYPE 109 209 166 194 145 38

Figure S392.  Get High-res Image Gene #37: 'del_6p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00542 (Fisher's exact test), Q value = 0.0069

Table S393.  Gene #37: 'del_6p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 9(6P25.3) MUTATED 16 25 21 36 17 28 35 5 17
DEL PEAK 9(6P25.3) WILD-TYPE 50 98 163 150 57 85 124 68 66

Figure S393.  Get High-res Image Gene #37: 'del_6p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q15' versus 'MRNA_CHIERARCHICAL'

P value = 0.00955 (Fisher's exact test), Q value = 0.012

Table S394.  Gene #38: 'del_6q15' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 10(6Q15) MUTATED 58 99 18
DEL PEAK 10(6Q15) WILD-TYPE 101 167 70

Figure S394.  Get High-res Image Gene #38: 'del_6q15' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_6q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S395.  Gene #38: 'del_6q15' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 10(6Q15) MUTATED 202 47 52 45 12
DEL PEAK 10(6Q15) WILD-TYPE 128 85 243 249 17

Figure S395.  Get High-res Image Gene #38: 'del_6q15' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q15' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S396.  Gene #38: 'del_6q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 10(6Q15) MUTATED 93 74 31 29 20
DEL PEAK 10(6Q15) WILD-TYPE 125 109 114 110 68

Figure S396.  Get High-res Image Gene #38: 'del_6q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q15' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S397.  Gene #38: 'del_6q15' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 10(6Q15) MUTATED 52 165 78
DEL PEAK 10(6Q15) WILD-TYPE 168 233 177

Figure S397.  Get High-res Image Gene #38: 'del_6q15' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_6q15' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S398.  Gene #38: 'del_6q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 10(6Q15) MUTATED 134 61 39 68 38 12 5
DEL PEAK 10(6Q15) WILD-TYPE 130 108 104 157 165 39 15

Figure S398.  Get High-res Image Gene #38: 'del_6q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S399.  Gene #38: 'del_6q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 10(6Q15) MUTATED 123 64 26 93 30 21
DEL PEAK 10(6Q15) WILD-TYPE 166 99 64 197 153 39

Figure S399.  Get High-res Image Gene #38: 'del_6q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q15' versus 'MIRSEQ_CNMF'

P value = 0.00274 (Fisher's exact test), Q value = 0.0036

Table S400.  Gene #38: 'del_6q15' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 10(6Q15) MUTATED 56 73 81 57 71 17
DEL PEAK 10(6Q15) WILD-TYPE 83 197 127 159 111 29

Figure S400.  Get High-res Image Gene #38: 'del_6q15' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S401.  Gene #38: 'del_6q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 10(6Q15) MUTATED 34 41 50 83 29 42 26 27 23
DEL PEAK 10(6Q15) WILD-TYPE 32 82 134 103 45 71 133 46 60

Figure S401.  Get High-res Image Gene #38: 'del_6q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q15' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00309 (Fisher's exact test), Q value = 0.004

Table S402.  Gene #38: 'del_6q15' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 10(6Q15) MUTATED 52 28 24 46 29 40
DEL PEAK 10(6Q15) WILD-TYPE 81 64 35 73 116 74

Figure S402.  Get High-res Image Gene #38: 'del_6q15' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6q27' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S403.  Gene #39: 'del_6q27' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 11(6Q27) MUTATED 177 46 54 87 11
DEL PEAK 11(6Q27) WILD-TYPE 153 86 241 207 18

Figure S403.  Get High-res Image Gene #39: 'del_6q27' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q27' versus 'MRNASEQ_CNMF'

P value = 0.00925 (Fisher's exact test), Q value = 0.011

Table S404.  Gene #39: 'del_6q27' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 11(6Q27) MUTATED 114 64 43 63 70 13 6
DEL PEAK 11(6Q27) WILD-TYPE 150 105 100 162 133 38 14

Figure S404.  Get High-res Image Gene #39: 'del_6q27' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7p22.3' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S405.  Gene #40: 'del_7p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 12(7P22.3) MUTATED 24 10 43
DEL PEAK 12(7P22.3) WILD-TYPE 205 106 125

Figure S405.  Get High-res Image Gene #40: 'del_7p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_7p22.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00177 (Fisher's exact test), Q value = 0.0023

Table S406.  Gene #40: 'del_7p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 12(7P22.3) MUTATED 16 37 24
DEL PEAK 12(7P22.3) WILD-TYPE 143 229 64

Figure S406.  Get High-res Image Gene #40: '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 = 1.6e-05

Table S407.  Gene #40: 'del_7p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 12(7P22.3) MUTATED 59 6 7 67 0
DEL PEAK 12(7P22.3) WILD-TYPE 271 126 288 227 29

Figure S407.  Get High-res Image Gene #40: '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 = 1.6e-05

Table S408.  Gene #40: 'del_7p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 12(7P22.3) MUTATED 16 27 4 33 3
DEL PEAK 12(7P22.3) WILD-TYPE 202 156 141 106 85

Figure S408.  Get High-res Image Gene #40: 'del_7p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_7p22.3' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S409.  Gene #40: 'del_7p22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 12(7P22.3) MUTATED 47 23 4 11 15 12 0
DEL PEAK 12(7P22.3) WILD-TYPE 147 214 26 193 116 55 10

Figure S409.  Get High-res Image Gene #40: 'del_7p22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_7p22.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S410.  Gene #40: 'del_7p22.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 12(7P22.3) MUTATED 52 44 16
DEL PEAK 12(7P22.3) WILD-TYPE 168 354 239

Figure S410.  Get High-res Image Gene #40: 'del_7p22.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_7p22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S411.  Gene #40: 'del_7p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 12(7P22.3) MUTATED 40 27 6 12 50 1 1
DEL PEAK 12(7P22.3) WILD-TYPE 224 142 137 213 153 50 19

Figure S411.  Get High-res Image Gene #40: '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 = 1.6e-05

Table S412.  Gene #40: 'del_7p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 12(7P22.3) MUTATED 38 27 0 19 48 5
DEL PEAK 12(7P22.3) WILD-TYPE 251 136 90 271 135 55

Figure S412.  Get High-res Image Gene #40: '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 = 1.6e-05

Table S413.  Gene #40: 'del_7p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 12(7P22.3) MUTATED 23 62 18 4 22 5
DEL PEAK 12(7P22.3) WILD-TYPE 116 208 190 212 160 41

Figure S413.  Get High-res Image Gene #40: '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 = 1.6e-05

Table S414.  Gene #40: 'del_7p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 12(7P22.3) MUTATED 11 17 2 12 6 19 43 6 18
DEL PEAK 12(7P22.3) WILD-TYPE 55 106 182 174 68 94 116 67 65

Figure S414.  Get High-res Image Gene #40: 'del_7p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7p22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S415.  Gene #40: 'del_7p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 12(7P22.3) MUTATED 17 4 4 9 36 4
DEL PEAK 12(7P22.3) WILD-TYPE 116 88 55 110 109 110

Figure S415.  Get High-res Image Gene #40: 'del_7p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S416.  Gene #40: 'del_7p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 12(7P22.3) MUTATED 55 13 6
DEL PEAK 12(7P22.3) WILD-TYPE 259 218 111

Figure S416.  Get High-res Image Gene #40: 'del_7p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q36.1' versus 'MRNA_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00015

Table S417.  Gene #41: 'del_7q36.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 13(7Q36.1) MUTATED 34 16 52
DEL PEAK 13(7Q36.1) WILD-TYPE 195 100 116

Figure S417.  Get High-res Image Gene #41: 'del_7q36.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_7q36.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0221 (Fisher's exact test), Q value = 0.026

Table S418.  Gene #41: 'del_7q36.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 13(7Q36.1) MUTATED 21 64 17
DEL PEAK 13(7Q36.1) WILD-TYPE 138 202 71

Figure S418.  Get High-res Image Gene #41: '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 = 1.6e-05

Table S419.  Gene #41: 'del_7q36.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 13(7Q36.1) MUTATED 83 19 18 78 2
DEL PEAK 13(7Q36.1) WILD-TYPE 247 113 277 216 27

Figure S419.  Get High-res Image Gene #41: 'del_7q36.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_7q36.1' versus 'METHLYATION_CNMF'

P value = 0.00888 (Fisher's exact test), Q value = 0.011

Table S420.  Gene #41: 'del_7q36.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 13(7Q36.1) MUTATED 28 40 15 31 13
DEL PEAK 13(7Q36.1) WILD-TYPE 190 143 130 108 75

Figure S420.  Get High-res Image Gene #41: 'del_7q36.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_7q36.1' versus 'RPPA_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.00061

Table S421.  Gene #41: 'del_7q36.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 13(7Q36.1) MUTATED 47 35 5 27 26 25 1
DEL PEAK 13(7Q36.1) WILD-TYPE 147 202 25 177 105 42 9

Figure S421.  Get High-res Image Gene #41: 'del_7q36.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_7q36.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.013

Table S422.  Gene #41: 'del_7q36.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 13(7Q36.1) MUTATED 56 73 37
DEL PEAK 13(7Q36.1) WILD-TYPE 164 325 218

Figure S422.  Get High-res Image Gene #41: 'del_7q36.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_7q36.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S423.  Gene #41: 'del_7q36.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 13(7Q36.1) MUTATED 47 53 14 28 49 4 3
DEL PEAK 13(7Q36.1) WILD-TYPE 217 116 129 197 154 47 17

Figure S423.  Get High-res Image Gene #41: '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 = 1.6e-05

Table S424.  Gene #41: 'del_7q36.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 13(7Q36.1) MUTATED 53 46 5 36 40 18
DEL PEAK 13(7Q36.1) WILD-TYPE 236 117 85 254 143 42

Figure S424.  Get High-res Image Gene #41: '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 = 1.6e-05

Table S425.  Gene #41: 'del_7q36.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 13(7Q36.1) MUTATED 30 79 28 17 35 6
DEL PEAK 13(7Q36.1) WILD-TYPE 109 191 180 199 147 40

Figure S425.  Get High-res Image Gene #41: '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 = 1.6e-05

Table S426.  Gene #41: 'del_7q36.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 13(7Q36.1) MUTATED 14 38 9 28 12 21 35 11 27
DEL PEAK 13(7Q36.1) WILD-TYPE 52 85 175 158 62 92 124 62 56

Figure S426.  Get High-res Image Gene #41: 'del_7q36.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7q36.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 6.2e-05

Table S427.  Gene #41: 'del_7q36.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 13(7Q36.1) MUTATED 23 6 11 20 45 12
DEL PEAK 13(7Q36.1) WILD-TYPE 110 86 48 99 100 102

Figure S427.  Get High-res Image Gene #41: 'del_7q36.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7q36.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S428.  Gene #41: 'del_7q36.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 13(7Q36.1) MUTATED 74 20 23
DEL PEAK 13(7Q36.1) WILD-TYPE 240 211 94

Figure S428.  Get High-res Image Gene #41: 'del_7q36.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'MRNA_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00013

Table S429.  Gene #42: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 14(8P23.2) MUTATED 112 51 113
DEL PEAK 14(8P23.2) WILD-TYPE 117 65 55

Figure S429.  Get High-res Image Gene #42: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p23.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0291 (Fisher's exact test), Q value = 0.034

Table S430.  Gene #42: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 14(8P23.2) MUTATED 75 144 57
DEL PEAK 14(8P23.2) WILD-TYPE 84 122 31

Figure S430.  Get High-res Image Gene #42: '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 = 1.6e-05

Table S431.  Gene #42: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 14(8P23.2) MUTATED 223 27 84 208 17
DEL PEAK 14(8P23.2) WILD-TYPE 107 105 211 86 12

Figure S431.  Get High-res Image Gene #42: '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 = 1.6e-05

Table S432.  Gene #42: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 14(8P23.2) MUTATED 98 103 67 89 25
DEL PEAK 14(8P23.2) WILD-TYPE 120 80 78 50 63

Figure S432.  Get High-res Image Gene #42: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S433.  Gene #42: 'del_8p23.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 14(8P23.2) MUTATED 127 107 19 82 72 46 6
DEL PEAK 14(8P23.2) WILD-TYPE 67 130 11 122 59 21 4

Figure S433.  Get High-res Image Gene #42: 'del_8p23.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_8p23.2' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 4.6e-05

Table S434.  Gene #42: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 14(8P23.2) MUTATED 145 201 113
DEL PEAK 14(8P23.2) WILD-TYPE 75 197 142

Figure S434.  Get High-res Image Gene #42: '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 = 1.6e-05

Table S435.  Gene #42: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 14(8P23.2) MUTATED 162 112 52 70 123 22 14
DEL PEAK 14(8P23.2) WILD-TYPE 102 57 91 155 80 29 6

Figure S435.  Get High-res Image Gene #42: '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 = 1.6e-05

Table S436.  Gene #42: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 14(8P23.2) MUTATED 147 109 25 114 113 47
DEL PEAK 14(8P23.2) WILD-TYPE 142 54 65 176 70 13

Figure S436.  Get High-res Image Gene #42: '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 = 1.6e-05

Table S437.  Gene #42: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 14(8P23.2) MUTATED 90 180 90 73 91 23
DEL PEAK 14(8P23.2) WILD-TYPE 49 90 118 143 91 23

Figure S437.  Get High-res Image Gene #42: '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 = 1.6e-05

Table S438.  Gene #42: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 14(8P23.2) MUTATED 37 74 54 85 29 61 99 46 62
DEL PEAK 14(8P23.2) WILD-TYPE 29 49 130 101 45 52 60 27 21

Figure S438.  Get High-res Image Gene #42: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.00039

Table S439.  Gene #42: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 14(8P23.2) MUTATED 70 38 28 50 96 51
DEL PEAK 14(8P23.2) WILD-TYPE 63 54 31 69 49 63

Figure S439.  Get High-res Image Gene #42: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S440.  Gene #42: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 14(8P23.2) MUTATED 188 102 43
DEL PEAK 14(8P23.2) WILD-TYPE 126 129 74

Figure S440.  Get High-res Image Gene #42: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p11.21' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4.6e-05

Table S441.  Gene #43: 'del_8p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 15(8P11.21) MUTATED 33 15 53
DEL PEAK 15(8P11.21) WILD-TYPE 196 101 115

Figure S441.  Get High-res Image Gene #43: 'del_8p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p11.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.00937 (Fisher's exact test), Q value = 0.012

Table S442.  Gene #43: 'del_8p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 15(8P11.21) MUTATED 19 61 21
DEL PEAK 15(8P11.21) WILD-TYPE 140 205 67

Figure S442.  Get High-res Image Gene #43: '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 = 1.6e-05

Table S443.  Gene #43: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 15(8P11.21) MUTATED 66 13 29 92 0
DEL PEAK 15(8P11.21) WILD-TYPE 264 119 266 202 29

Figure S443.  Get High-res Image Gene #43: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p11.21' versus 'METHLYATION_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.013

Table S444.  Gene #43: 'del_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 15(8P11.21) MUTATED 25 39 26 29 8
DEL PEAK 15(8P11.21) WILD-TYPE 193 144 119 110 80

Figure S444.  Get High-res Image Gene #43: 'del_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p11.21' versus 'RPPA_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.00061

Table S445.  Gene #43: 'del_8p11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 15(8P11.21) MUTATED 37 32 10 31 31 24 3
DEL PEAK 15(8P11.21) WILD-TYPE 157 205 20 173 100 43 7

Figure S445.  Get High-res Image Gene #43: 'del_8p11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_8p11.21' versus 'RPPA_CHIERARCHICAL'

P value = 8e-04 (Fisher's exact test), Q value = 0.0011

Table S446.  Gene #43: 'del_8p11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 15(8P11.21) MUTATED 62 64 42
DEL PEAK 15(8P11.21) WILD-TYPE 158 334 213

Figure S446.  Get High-res Image Gene #43: 'del_8p11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_8p11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S447.  Gene #43: 'del_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 15(8P11.21) MUTATED 39 64 18 23 42 8 6
DEL PEAK 15(8P11.21) WILD-TYPE 225 105 125 202 161 43 14

Figure S447.  Get High-res Image Gene #43: '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 = 1.6e-05

Table S448.  Gene #43: 'del_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 15(8P11.21) MUTATED 42 54 3 41 35 25
DEL PEAK 15(8P11.21) WILD-TYPE 247 109 87 249 148 35

Figure S448.  Get High-res Image Gene #43: 'del_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p11.21' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S449.  Gene #43: 'del_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 15(8P11.21) MUTATED 29 72 24 23 40 10
DEL PEAK 15(8P11.21) WILD-TYPE 110 198 184 193 142 36

Figure S449.  Get High-res Image Gene #43: '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 = 1.6e-05

Table S450.  Gene #43: 'del_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 15(8P11.21) MUTATED 16 43 13 20 16 22 28 7 33
DEL PEAK 15(8P11.21) WILD-TYPE 50 80 171 166 58 91 131 66 50

Figure S450.  Get High-res Image Gene #43: 'del_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0262 (Fisher's exact test), Q value = 0.031

Table S451.  Gene #43: 'del_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 15(8P11.21) MUTATED 27 15 12 26 35 10
DEL PEAK 15(8P11.21) WILD-TYPE 106 77 47 93 110 104

Figure S451.  Get High-res Image Gene #43: 'del_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00964 (Fisher's exact test), Q value = 0.012

Table S452.  Gene #43: 'del_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 15(8P11.21) MUTATED 74 31 20
DEL PEAK 15(8P11.21) WILD-TYPE 240 200 97

Figure S452.  Get High-res Image Gene #43: 'del_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'MRNA_CNMF'

P value = 0.0014 (Fisher's exact test), Q value = 0.0019

Table S453.  Gene #44: 'del_9p23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 16(9P23) MUTATED 77 25 71
DEL PEAK 16(9P23) WILD-TYPE 152 91 97

Figure S453.  Get High-res Image Gene #44: 'del_9p23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p23' versus 'MRNA_CHIERARCHICAL'

P value = 0.00082 (Fisher's exact test), Q value = 0.0011

Table S454.  Gene #44: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 16(9P23) MUTATED 49 107 17
DEL PEAK 16(9P23) WILD-TYPE 110 159 71

Figure S454.  Get High-res Image Gene #44: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S455.  Gene #44: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 16(9P23) MUTATED 186 15 22 95 7
DEL PEAK 16(9P23) WILD-TYPE 144 117 273 199 22

Figure S455.  Get High-res Image Gene #44: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S456.  Gene #44: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 16(9P23) MUTATED 54 87 24 41 11
DEL PEAK 16(9P23) WILD-TYPE 164 96 121 98 77

Figure S456.  Get High-res Image Gene #44: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p23' versus 'RPPA_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.0014

Table S457.  Gene #44: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 16(9P23) MUTATED 68 64 14 51 44 25 8
DEL PEAK 16(9P23) WILD-TYPE 126 173 16 153 87 42 2

Figure S457.  Get High-res Image Gene #44: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S458.  Gene #44: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 16(9P23) MUTATED 123 78 24 39 44 7 9
DEL PEAK 16(9P23) WILD-TYPE 141 91 119 186 159 44 11

Figure S458.  Get High-res Image Gene #44: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S459.  Gene #44: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 16(9P23) MUTATED 104 83 8 65 35 29
DEL PEAK 16(9P23) WILD-TYPE 185 80 82 225 148 31

Figure S459.  Get High-res Image Gene #44: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S460.  Gene #44: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 16(9P23) MUTATED 71 97 51 32 54 13
DEL PEAK 16(9P23) WILD-TYPE 68 173 157 184 128 33

Figure S460.  Get High-res Image Gene #44: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S461.  Gene #44: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 16(9P23) MUTATED 32 54 20 54 19 45 27 21 46
DEL PEAK 16(9P23) WILD-TYPE 34 69 164 132 55 68 132 52 37

Figure S461.  Get High-res Image Gene #44: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0183 (Fisher's exact test), Q value = 0.022

Table S462.  Gene #44: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 16(9P23) MUTATED 54 23 14 27 44 27
DEL PEAK 16(9P23) WILD-TYPE 79 69 45 92 101 87

Figure S462.  Get High-res Image Gene #44: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00022

Table S463.  Gene #44: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 16(9P23) MUTATED 114 53 22
DEL PEAK 16(9P23) WILD-TYPE 200 178 95

Figure S463.  Get High-res Image Gene #44: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S464.  Gene #45: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 17(9P21.3) MUTATED 83 25 85
DEL PEAK 17(9P21.3) WILD-TYPE 146 91 83

Figure S464.  Get High-res Image Gene #45: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S465.  Gene #45: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 17(9P21.3) MUTATED 191 19 29 119 7
DEL PEAK 17(9P21.3) WILD-TYPE 139 113 266 175 22

Figure S465.  Get High-res Image Gene #45: '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 = 1.6e-05

Table S466.  Gene #45: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 17(9P21.3) MUTATED 61 83 30 53 11
DEL PEAK 17(9P21.3) WILD-TYPE 157 100 115 86 77

Figure S466.  Get High-res Image Gene #45: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00011

Table S467.  Gene #45: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 17(9P21.3) MUTATED 81 69 14 54 48 30 8
DEL PEAK 17(9P21.3) WILD-TYPE 113 168 16 150 83 37 2

Figure S467.  Get High-res Image Gene #45: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S468.  Gene #45: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 17(9P21.3) MUTATED 127 83 23 44 69 7 8
DEL PEAK 17(9P21.3) WILD-TYPE 137 86 120 181 134 44 12

Figure S468.  Get High-res Image Gene #45: '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 = 1.6e-05

Table S469.  Gene #45: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 17(9P21.3) MUTATED 113 88 6 63 60 31
DEL PEAK 17(9P21.3) WILD-TYPE 176 75 84 227 123 29

Figure S469.  Get High-res Image Gene #45: '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 = 1.6e-05

Table S470.  Gene #45: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 17(9P21.3) MUTATED 68 121 57 34 61 14
DEL PEAK 17(9P21.3) WILD-TYPE 71 149 151 182 121 32

Figure S470.  Get High-res Image Gene #45: '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 = 1.6e-05

Table S471.  Gene #45: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 17(9P21.3) MUTATED 32 62 22 56 22 45 47 21 48
DEL PEAK 17(9P21.3) WILD-TYPE 34 61 162 130 52 68 112 52 35

Figure S471.  Get High-res Image Gene #45: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-04 (Fisher's exact test), Q value = 0.00097

Table S472.  Gene #45: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 17(9P21.3) MUTATED 55 21 19 30 59 25
DEL PEAK 17(9P21.3) WILD-TYPE 78 71 40 89 86 89

Figure S472.  Get High-res Image Gene #45: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S473.  Gene #45: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 17(9P21.3) MUTATED 131 55 23
DEL PEAK 17(9P21.3) WILD-TYPE 183 176 94

Figure S473.  Get High-res Image Gene #45: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q21.11' versus 'MRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 7.6e-05

Table S474.  Gene #46: 'del_9q21.11' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 18(9Q21.11) MUTATED 64 22 72
DEL PEAK 18(9Q21.11) WILD-TYPE 165 94 96

Figure S474.  Get High-res Image Gene #46: 'del_9q21.11' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9q21.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S475.  Gene #46: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 18(9Q21.11) MUTATED 131 16 19 121 8
DEL PEAK 18(9Q21.11) WILD-TYPE 199 116 276 173 21

Figure S475.  Get High-res Image Gene #46: '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 = 1.6e-05

Table S476.  Gene #46: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 18(9Q21.11) MUTATED 49 51 28 57 8
DEL PEAK 18(9Q21.11) WILD-TYPE 169 132 117 82 80

Figure S476.  Get High-res Image Gene #46: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q21.11' versus 'RPPA_CNMF'

P value = 0.00589 (Fisher's exact test), Q value = 0.0075

Table S477.  Gene #46: 'del_9q21.11' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 18(9Q21.11) MUTATED 74 55 7 43 38 21 3
DEL PEAK 18(9Q21.11) WILD-TYPE 120 182 23 161 93 46 7

Figure S477.  Get High-res Image Gene #46: 'del_9q21.11' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9q21.11' versus 'RPPA_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.00066

Table S478.  Gene #46: 'del_9q21.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 18(9Q21.11) MUTATED 81 108 52
DEL PEAK 18(9Q21.11) WILD-TYPE 139 290 203

Figure S478.  Get High-res Image Gene #46: 'del_9q21.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9q21.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S479.  Gene #46: 'del_9q21.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 18(9Q21.11) MUTATED 96 49 15 43 77 6 8
DEL PEAK 18(9Q21.11) WILD-TYPE 168 120 128 182 126 45 12

Figure S479.  Get High-res Image Gene #46: '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 = 1.6e-05

Table S480.  Gene #46: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 18(9Q21.11) MUTATED 85 59 5 53 69 23
DEL PEAK 18(9Q21.11) WILD-TYPE 204 104 85 237 114 37

Figure S480.  Get High-res Image Gene #46: '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 = 1.6e-05

Table S481.  Gene #46: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 18(9Q21.11) MUTATED 51 120 40 26 42 9
DEL PEAK 18(9Q21.11) WILD-TYPE 88 150 168 190 140 37

Figure S481.  Get High-res Image Gene #46: '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 = 1.6e-05

Table S482.  Gene #46: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 18(9Q21.11) MUTATED 20 47 16 37 18 35 63 15 37
DEL PEAK 18(9Q21.11) WILD-TYPE 46 76 168 149 56 78 96 58 46

Figure S482.  Get High-res Image Gene #46: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 9e-05

Table S483.  Gene #46: 'del_9q21.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 18(9Q21.11) MUTATED 40 17 11 21 59 21
DEL PEAK 18(9Q21.11) WILD-TYPE 93 75 48 98 86 93

Figure S483.  Get High-res Image Gene #46: 'del_9q21.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9q21.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S484.  Gene #46: 'del_9q21.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 18(9Q21.11) MUTATED 110 43 16
DEL PEAK 18(9Q21.11) WILD-TYPE 204 188 101

Figure S484.  Get High-res Image Gene #46: '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 = 1.6e-05

Table S485.  Gene #47: 'del_9q34.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 19(9Q34.2) MUTATED 62 18 77
DEL PEAK 19(9Q34.2) WILD-TYPE 167 98 91

Figure S485.  Get High-res Image Gene #47: '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 = 1.6e-05

Table S486.  Gene #47: 'del_9q34.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 19(9Q34.2) MUTATED 39 68 50
DEL PEAK 19(9Q34.2) WILD-TYPE 120 198 38

Figure S486.  Get High-res Image Gene #47: '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 = 1.6e-05

Table S487.  Gene #47: 'del_9q34.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 19(9Q34.2) MUTATED 119 12 10 148 8
DEL PEAK 19(9Q34.2) WILD-TYPE 211 120 285 146 21

Figure S487.  Get High-res Image Gene #47: '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 = 1.6e-05

Table S488.  Gene #47: 'del_9q34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 19(9Q34.2) MUTATED 42 46 24 75 7
DEL PEAK 19(9Q34.2) WILD-TYPE 176 137 121 64 81

Figure S488.  Get High-res Image Gene #47: '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 = 1.6e-05

Table S489.  Gene #47: 'del_9q34.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 19(9Q34.2) MUTATED 84 44 11 39 30 24 2
DEL PEAK 19(9Q34.2) WILD-TYPE 110 193 19 165 101 43 8

Figure S489.  Get High-res Image Gene #47: '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 = 1.6e-05

Table S490.  Gene #47: 'del_9q34.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 19(9Q34.2) MUTATED 91 96 47
DEL PEAK 19(9Q34.2) WILD-TYPE 129 302 208

Figure S490.  Get High-res Image Gene #47: '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 = 1.6e-05

Table S491.  Gene #47: 'del_9q34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 19(9Q34.2) MUTATED 87 37 8 42 110 3 8
DEL PEAK 19(9Q34.2) WILD-TYPE 177 132 135 183 93 48 12

Figure S491.  Get High-res Image Gene #47: '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 = 1.6e-05

Table S492.  Gene #47: 'del_9q34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 19(9Q34.2) MUTATED 76 50 2 50 102 15
DEL PEAK 19(9Q34.2) WILD-TYPE 213 113 88 240 81 45

Figure S492.  Get High-res Image Gene #47: '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 = 1.6e-05

Table S493.  Gene #47: 'del_9q34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 19(9Q34.2) MUTATED 45 136 41 18 40 8
DEL PEAK 19(9Q34.2) WILD-TYPE 94 134 167 198 142 38

Figure S493.  Get High-res Image Gene #47: '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 = 1.6e-05

Table S494.  Gene #47: 'del_9q34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 19(9Q34.2) MUTATED 18 36 13 37 16 35 88 13 32
DEL PEAK 19(9Q34.2) WILD-TYPE 48 87 171 149 58 78 71 60 51

Figure S494.  Get High-res Image Gene #47: '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 = 1.6e-05

Table S495.  Gene #47: 'del_9q34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 19(9Q34.2) MUTATED 33 15 10 18 78 21
DEL PEAK 19(9Q34.2) WILD-TYPE 100 77 49 101 67 93

Figure S495.  Get High-res Image Gene #47: 'del_9q34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9q34.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S496.  Gene #47: 'del_9q34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 19(9Q34.2) MUTATED 124 39 12
DEL PEAK 19(9Q34.2) WILD-TYPE 190 192 105

Figure S496.  Get High-res Image Gene #47: '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 = 1.6e-05

Table S497.  Gene #48: 'del_10q23.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 20(10Q23.31) MUTATED 48 25 76
DEL PEAK 20(10Q23.31) WILD-TYPE 181 91 92

Figure S497.  Get High-res Image Gene #48: '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 = 1.6e-05

Table S498.  Gene #48: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 20(10Q23.31) MUTATED 33 71 45
DEL PEAK 20(10Q23.31) WILD-TYPE 126 195 43

Figure S498.  Get High-res Image Gene #48: '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 = 1.6e-05

Table S499.  Gene #48: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 20(10Q23.31) MUTATED 112 30 22 148 8
DEL PEAK 20(10Q23.31) WILD-TYPE 218 102 273 146 21

Figure S499.  Get High-res Image Gene #48: '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 = 1.6e-05

Table S500.  Gene #48: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 20(10Q23.31) MUTATED 50 62 32 74 16
DEL PEAK 20(10Q23.31) WILD-TYPE 168 121 113 65 72

Figure S500.  Get High-res Image Gene #48: '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 = 1.6e-05

Table S501.  Gene #48: 'del_10q23.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 20(10Q23.31) MUTATED 86 50 15 38 46 25 2
DEL PEAK 20(10Q23.31) WILD-TYPE 108 187 15 166 85 42 8

Figure S501.  Get High-res Image Gene #48: '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 = 1.6e-05

Table S502.  Gene #48: 'del_10q23.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 20(10Q23.31) MUTATED 99 110 53
DEL PEAK 20(10Q23.31) WILD-TYPE 121 288 202

Figure S502.  Get High-res Image Gene #48: '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 = 1.6e-05

Table S503.  Gene #48: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 20(10Q23.31) MUTATED 85 67 23 35 102 3 4
DEL PEAK 20(10Q23.31) WILD-TYPE 179 102 120 190 101 48 16

Figure S503.  Get High-res Image Gene #48: '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 = 1.6e-05

Table S504.  Gene #48: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 20(10Q23.31) MUTATED 71 65 10 55 96 22
DEL PEAK 20(10Q23.31) WILD-TYPE 218 98 80 235 87 38

Figure S504.  Get High-res Image Gene #48: '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 = 1.6e-05

Table S505.  Gene #48: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 20(10Q23.31) MUTATED 48 125 45 34 47 12
DEL PEAK 20(10Q23.31) WILD-TYPE 91 145 163 182 135 34

Figure S505.  Get High-res Image Gene #48: '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 = 1.6e-05

Table S506.  Gene #48: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 20(10Q23.31) MUTATED 21 45 32 37 11 30 81 19 35
DEL PEAK 20(10Q23.31) WILD-TYPE 45 78 152 149 63 83 78 54 48

Figure S506.  Get High-res Image Gene #48: '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 = 1.6e-05

Table S507.  Gene #48: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 20(10Q23.31) MUTATED 38 21 12 23 78 26
DEL PEAK 20(10Q23.31) WILD-TYPE 95 71 47 96 67 88

Figure S507.  Get High-res Image Gene #48: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 4.6e-05

Table S508.  Gene #48: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 20(10Q23.31) MUTATED 120 55 23
DEL PEAK 20(10Q23.31) WILD-TYPE 194 176 94

Figure S508.  Get High-res Image Gene #48: '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 = 1.6e-05

Table S509.  Gene #49: 'del_10q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 21(10Q26.3) MUTATED 46 24 84
DEL PEAK 21(10Q26.3) WILD-TYPE 183 92 84

Figure S509.  Get High-res Image Gene #49: '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 = 1.6e-05

Table S510.  Gene #49: 'del_10q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 21(10Q26.3) MUTATED 30 75 49
DEL PEAK 21(10Q26.3) WILD-TYPE 129 191 39

Figure S510.  Get High-res Image Gene #49: '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 = 1.6e-05

Table S511.  Gene #49: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 21(10Q26.3) MUTATED 114 27 20 152 5
DEL PEAK 21(10Q26.3) WILD-TYPE 216 105 275 142 24

Figure S511.  Get High-res Image Gene #49: '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 = 1.6e-05

Table S512.  Gene #49: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 21(10Q26.3) MUTATED 45 68 28 73 12
DEL PEAK 21(10Q26.3) WILD-TYPE 173 115 117 66 76

Figure S512.  Get High-res Image Gene #49: '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 = 1.6e-05

Table S513.  Gene #49: 'del_10q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 21(10Q26.3) MUTATED 89 53 14 34 48 28 4
DEL PEAK 21(10Q26.3) WILD-TYPE 105 184 16 170 83 39 6

Figure S513.  Get High-res Image Gene #49: '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 = 1.6e-05

Table S514.  Gene #49: 'del_10q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 21(10Q26.3) MUTATED 108 113 49
DEL PEAK 21(10Q26.3) WILD-TYPE 112 285 206

Figure S514.  Get High-res Image Gene #49: '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 = 1.6e-05

Table S515.  Gene #49: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 21(10Q26.3) MUTATED 85 71 16 30 108 5 3
DEL PEAK 21(10Q26.3) WILD-TYPE 179 98 127 195 95 46 17

Figure S515.  Get High-res Image Gene #49: '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 = 1.6e-05

Table S516.  Gene #49: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 21(10Q26.3) MUTATED 67 71 6 50 98 26
DEL PEAK 21(10Q26.3) WILD-TYPE 222 92 84 240 85 34

Figure S516.  Get High-res Image Gene #49: '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 = 1.6e-05

Table S517.  Gene #49: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 21(10Q26.3) MUTATED 48 130 40 31 50 8
DEL PEAK 21(10Q26.3) WILD-TYPE 91 140 168 185 132 38

Figure S517.  Get High-res Image Gene #49: '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 = 1.6e-05

Table S518.  Gene #49: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 21(10Q26.3) MUTATED 22 52 21 36 8 29 81 19 39
DEL PEAK 21(10Q26.3) WILD-TYPE 44 71 163 150 66 84 78 54 44

Figure S518.  Get High-res Image Gene #49: '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 = 1.6e-05

Table S519.  Gene #49: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 21(10Q26.3) MUTATED 42 21 12 26 74 22
DEL PEAK 21(10Q26.3) WILD-TYPE 91 71 47 93 71 92

Figure S519.  Get High-res Image Gene #49: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S520.  Gene #49: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 21(10Q26.3) MUTATED 128 48 21
DEL PEAK 21(10Q26.3) WILD-TYPE 186 183 96

Figure S520.  Get High-res Image Gene #49: '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 = 1.6e-05

Table S521.  Gene #50: 'del_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 22(11P15.5) MUTATED 42 31 83
DEL PEAK 22(11P15.5) WILD-TYPE 187 85 85

Figure S521.  Get High-res Image Gene #50: '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 = 1.6e-05

Table S522.  Gene #50: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 22(11P15.5) MUTATED 27 87 42
DEL PEAK 22(11P15.5) WILD-TYPE 132 179 46

Figure S522.  Get High-res Image Gene #50: '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 = 1.6e-05

Table S523.  Gene #50: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 22(11P15.5) MUTATED 110 19 19 157 4
DEL PEAK 22(11P15.5) WILD-TYPE 220 113 276 137 25

Figure S523.  Get High-res Image Gene #50: '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 = 1.6e-05

Table S524.  Gene #50: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 22(11P15.5) MUTATED 41 59 24 74 9
DEL PEAK 22(11P15.5) WILD-TYPE 177 124 121 65 79

Figure S524.  Get High-res Image Gene #50: '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 = 1.6e-05

Table S525.  Gene #50: 'del_11p15.5' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 22(11P15.5) MUTATED 91 50 13 38 44 21 4
DEL PEAK 22(11P15.5) WILD-TYPE 103 187 17 166 87 46 6

Figure S525.  Get High-res Image Gene #50: '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 = 1.6e-05

Table S526.  Gene #50: 'del_11p15.5' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 22(11P15.5) MUTATED 106 103 52
DEL PEAK 22(11P15.5) WILD-TYPE 114 295 203

Figure S526.  Get High-res Image Gene #50: '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 = 1.6e-05

Table S527.  Gene #50: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 22(11P15.5) MUTATED 75 69 19 29 100 10 6
DEL PEAK 22(11P15.5) WILD-TYPE 189 100 124 196 103 41 14

Figure S527.  Get High-res Image Gene #50: '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 = 1.6e-05

Table S528.  Gene #50: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 22(11P15.5) MUTATED 60 62 9 57 91 29
DEL PEAK 22(11P15.5) WILD-TYPE 229 101 81 233 92 31

Figure S528.  Get High-res Image Gene #50: '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 = 1.6e-05

Table S529.  Gene #50: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 22(11P15.5) MUTATED 49 131 41 30 37 13
DEL PEAK 22(11P15.5) WILD-TYPE 90 139 167 186 145 33

Figure S529.  Get High-res Image Gene #50: '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 = 1.6e-05

Table S530.  Gene #50: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 22(11P15.5) MUTATED 20 44 21 33 18 31 78 19 37
DEL PEAK 22(11P15.5) WILD-TYPE 46 79 163 153 56 82 81 54 46

Figure S530.  Get High-res Image Gene #50: '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 = 1.6e-05

Table S531.  Gene #50: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 22(11P15.5) MUTATED 35 18 11 25 69 23
DEL PEAK 22(11P15.5) WILD-TYPE 98 74 48 94 76 91

Figure S531.  Get High-res Image Gene #50: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 7.6e-05

Table S532.  Gene #50: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 22(11P15.5) MUTATED 112 48 21
DEL PEAK 22(11P15.5) WILD-TYPE 202 183 96

Figure S532.  Get High-res Image Gene #50: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S533.  Gene #51: 'del_11q13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 23(11Q13.1) MUTATED 127 28 21 61 4
DEL PEAK 23(11Q13.1) WILD-TYPE 203 104 274 233 25

Figure S533.  Get High-res Image Gene #51: 'del_11q13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S534.  Gene #51: 'del_11q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 23(11Q13.1) MUTATED 45 62 16 37 8
DEL PEAK 23(11Q13.1) WILD-TYPE 173 121 129 102 80

Figure S534.  Get High-res Image Gene #51: 'del_11q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S535.  Gene #51: 'del_11q13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 23(11Q13.1) MUTATED 100 34 17 30 44 10 4
DEL PEAK 23(11Q13.1) WILD-TYPE 164 135 126 195 159 41 16

Figure S535.  Get High-res Image Gene #51: 'del_11q13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00019

Table S536.  Gene #51: 'del_11q13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 23(11Q13.1) MUTATED 88 39 8 55 39 10
DEL PEAK 23(11Q13.1) WILD-TYPE 201 124 82 235 144 50

Figure S536.  Get High-res Image Gene #51: 'del_11q13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q13.1' versus 'MIRSEQ_CNMF'

P value = 0.0491 (Fisher's exact test), Q value = 0.056

Table S537.  Gene #51: 'del_11q13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 23(11Q13.1) MUTATED 43 67 44 36 39 9
DEL PEAK 23(11Q13.1) WILD-TYPE 96 203 164 180 143 37

Figure S537.  Get High-res Image Gene #51: 'del_11q13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11q13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00086 (Fisher's exact test), Q value = 0.0012

Table S538.  Gene #51: 'del_11q13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 23(11Q13.1) MUTATED 24 26 21 44 19 29 35 23 17
DEL PEAK 23(11Q13.1) WILD-TYPE 42 97 163 142 55 84 124 50 66

Figure S538.  Get High-res Image Gene #51: 'del_11q13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S539.  Gene #52: 'del_11q23.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 24(11Q23.3) MUTATED 269 50 71 150 7
DEL PEAK 24(11Q23.3) WILD-TYPE 61 82 224 144 22

Figure S539.  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 = 1.6e-05

Table S540.  Gene #52: 'del_11q23.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 24(11Q23.3) MUTATED 111 127 49 72 32
DEL PEAK 24(11Q23.3) WILD-TYPE 107 56 96 67 56

Figure S540.  Get High-res Image Gene #52: 'del_11q23.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q23.3' versus 'RPPA_CNMF'

P value = 0.0469 (Fisher's exact test), Q value = 0.054

Table S541.  Gene #52: 'del_11q23.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 24(11Q23.3) MUTATED 100 129 20 96 73 24 5
DEL PEAK 24(11Q23.3) WILD-TYPE 94 108 10 108 58 43 5

Figure S541.  Get High-res Image Gene #52: 'del_11q23.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_11q23.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0454 (Fisher's exact test), Q value = 0.052

Table S542.  Gene #52: 'del_11q23.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 24(11Q23.3) MUTATED 98 219 130
DEL PEAK 24(11Q23.3) WILD-TYPE 122 179 125

Figure S542.  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 = 1.6e-05

Table S543.  Gene #52: 'del_11q23.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 24(11Q23.3) MUTATED 196 88 57 82 88 24 9
DEL PEAK 24(11Q23.3) WILD-TYPE 68 81 86 143 115 27 11

Figure S543.  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 = 1.6e-05

Table S544.  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 289 163 90 290 183 60
DEL PEAK 24(11Q23.3) MUTATED 167 100 26 149 78 24
DEL PEAK 24(11Q23.3) WILD-TYPE 122 63 64 141 105 36

Figure S544.  Get High-res Image Gene #52: 'del_11q23.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.3' versus 'MIRSEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00019

Table S545.  Gene #52: 'del_11q23.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 24(11Q23.3) MUTATED 91 136 111 85 89 20
DEL PEAK 24(11Q23.3) WILD-TYPE 48 134 97 131 93 26

Figure S545.  Get High-res Image Gene #52: 'del_11q23.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.00032

Table S546.  Gene #52: 'del_11q23.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 24(11Q23.3) MUTATED 42 61 70 103 33 66 67 43 47
DEL PEAK 24(11Q23.3) WILD-TYPE 24 62 114 83 41 47 92 30 36

Figure S546.  Get High-res Image Gene #52: 'del_11q23.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11q25' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S547.  Gene #53: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 25(11Q25) MUTATED 252 42 59 156 5
DEL PEAK 25(11Q25) WILD-TYPE 78 90 236 138 24

Figure S547.  Get High-res Image Gene #53: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q25' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S548.  Gene #53: 'del_11q25' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 25(11Q25) MUTATED 99 112 47 77 26
DEL PEAK 25(11Q25) WILD-TYPE 119 71 98 62 62

Figure S548.  Get High-res Image Gene #53: 'del_11q25' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q25' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S549.  Gene #53: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 25(11Q25) MUTATED 172 82 53 71 103 23 7
DEL PEAK 25(11Q25) WILD-TYPE 92 87 90 154 100 28 13

Figure S549.  Get High-res Image Gene #53: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q25' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 6.2e-05

Table S550.  Gene #53: 'del_11q25' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 25(11Q25) MUTATED 144 91 23 137 94 22
DEL PEAK 25(11Q25) WILD-TYPE 145 72 67 153 89 38

Figure S550.  Get High-res Image Gene #53: 'del_11q25' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q25' versus 'MIRSEQ_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.001

Table S551.  Gene #53: 'del_11q25' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 25(11Q25) MUTATED 81 144 98 80 79 19
DEL PEAK 25(11Q25) WILD-TYPE 58 126 110 136 103 27

Figure S551.  Get High-res Image Gene #53: 'del_11q25' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11q25' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00876 (Fisher's exact test), Q value = 0.011

Table S552.  Gene #53: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 25(11Q25) MUTATED 37 60 62 91 31 56 81 39 44
DEL PEAK 25(11Q25) WILD-TYPE 29 63 122 95 43 57 78 34 39

Figure S552.  Get High-res Image Gene #53: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11q25' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0256 (Fisher's exact test), Q value = 0.03

Table S553.  Gene #53: 'del_11q25' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 25(11Q25) MUTATED 72 36 21 47 77 53
DEL PEAK 25(11Q25) WILD-TYPE 61 56 38 72 68 61

Figure S553.  Get High-res Image Gene #53: 'del_11q25' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11q25' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.017

Table S554.  Gene #53: 'del_11q25' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 25(11Q25) MUTATED 161 103 42
DEL PEAK 25(11Q25) WILD-TYPE 153 128 75

Figure S554.  Get High-res Image Gene #53: 'del_11q25' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12p13.1' versus 'MRNA_CNMF'

P value = 0.0189 (Fisher's exact test), Q value = 0.022

Table S555.  Gene #54: 'del_12p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 26(12P13.1) MUTATED 35 17 43
DEL PEAK 26(12P13.1) WILD-TYPE 194 99 125

Figure S555.  Get High-res Image Gene #54: 'del_12p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12p13.1' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.00049

Table S556.  Gene #54: 'del_12p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 26(12P13.1) MUTATED 67 22 31 66 2
DEL PEAK 26(12P13.1) WILD-TYPE 263 110 264 228 27

Figure S556.  Get High-res Image Gene #54: 'del_12p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_12p13.1' versus 'RPPA_CNMF'

P value = 0.00756 (Fisher's exact test), Q value = 0.0094

Table S557.  Gene #54: 'del_12p13.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 26(12P13.1) MUTATED 40 34 6 29 24 23 3
DEL PEAK 26(12P13.1) WILD-TYPE 154 203 24 175 107 44 7

Figure S557.  Get High-res Image Gene #54: 'del_12p13.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_12p13.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00436 (Fisher's exact test), Q value = 0.0055

Table S558.  Gene #54: 'del_12p13.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 26(12P13.1) MUTATED 57 63 39
DEL PEAK 26(12P13.1) WILD-TYPE 163 335 216

Figure S558.  Get High-res Image Gene #54: 'del_12p13.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_12p13.1' versus 'MRNASEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.00056

Table S559.  Gene #54: 'del_12p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 26(12P13.1) MUTATED 47 40 19 25 49 3 4
DEL PEAK 26(12P13.1) WILD-TYPE 217 129 124 200 154 48 16

Figure S559.  Get High-res Image Gene #54: 'del_12p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00048 (Fisher's exact test), Q value = 0.00068

Table S560.  Gene #54: 'del_12p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 26(12P13.1) MUTATED 43 36 7 41 42 18
DEL PEAK 26(12P13.1) WILD-TYPE 246 127 83 249 141 42

Figure S560.  Get High-res Image Gene #54: 'del_12p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_CNMF'

P value = 0.00388 (Fisher's exact test), Q value = 0.005

Table S561.  Gene #54: 'del_12p13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 26(12P13.1) MUTATED 31 62 23 28 33 8
DEL PEAK 26(12P13.1) WILD-TYPE 108 208 185 188 149 38

Figure S561.  Get High-res Image Gene #54: 'del_12p13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_12p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.00042

Table S562.  Gene #54: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 26(12P13.1) MUTATED 11 30 15 34 9 14 34 14 24
DEL PEAK 26(12P13.1) WILD-TYPE 55 93 169 152 65 99 125 59 59

Figure S562.  Get High-res Image Gene #54: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.035

Table S563.  Gene #54: 'del_12p13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 26(12P13.1) MUTATED 21 11 8 19 39 15
DEL PEAK 26(12P13.1) WILD-TYPE 112 81 51 100 106 99

Figure S563.  Get High-res Image Gene #54: 'del_12p13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_12p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0031 (Fisher's exact test), Q value = 0.004

Table S564.  Gene #54: 'del_12p13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 26(12P13.1) MUTATED 70 28 15
DEL PEAK 26(12P13.1) WILD-TYPE 244 203 102

Figure S564.  Get High-res Image Gene #54: 'del_12p13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q23.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S565.  Gene #55: 'del_12q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 27(12Q23.1) MUTATED 18 21 57
DEL PEAK 27(12Q23.1) WILD-TYPE 211 95 111

Figure S565.  Get High-res Image Gene #55: '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 = 1.6e-05

Table S566.  Gene #55: 'del_12q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 27(12Q23.1) MUTATED 9 50 37
DEL PEAK 27(12Q23.1) WILD-TYPE 150 216 51

Figure S566.  Get High-res Image Gene #55: '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 = 1.6e-05

Table S567.  Gene #55: 'del_12q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 27(12Q23.1) MUTATED 41 21 18 118 3
DEL PEAK 27(12Q23.1) WILD-TYPE 289 111 277 176 26

Figure S567.  Get High-res Image Gene #55: '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 = 1.6e-05

Table S568.  Gene #55: 'del_12q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 27(12Q23.1) MUTATED 18 33 17 67 8
DEL PEAK 27(12Q23.1) WILD-TYPE 200 150 128 72 80

Figure S568.  Get High-res Image Gene #55: '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 = 1.6e-05

Table S569.  Gene #55: 'del_12q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 27(12Q23.1) MUTATED 64 19 6 22 36 17 2
DEL PEAK 27(12Q23.1) WILD-TYPE 130 218 24 182 95 50 8

Figure S569.  Get High-res Image Gene #55: '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 = 1.6e-05

Table S570.  Gene #55: 'del_12q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 27(12Q23.1) MUTATED 78 55 33
DEL PEAK 27(12Q23.1) WILD-TYPE 142 343 222

Figure S570.  Get High-res Image Gene #55: '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 = 1.6e-05

Table S571.  Gene #55: 'del_12q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 27(12Q23.1) MUTATED 36 35 9 20 91 5 3
DEL PEAK 27(12Q23.1) WILD-TYPE 228 134 134 205 112 46 17

Figure S571.  Get High-res Image Gene #55: '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 = 1.6e-05

Table S572.  Gene #55: 'del_12q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 27(12Q23.1) MUTATED 28 41 6 25 80 19
DEL PEAK 27(12Q23.1) WILD-TYPE 261 122 84 265 103 41

Figure S572.  Get High-res Image Gene #55: '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 = 1.6e-05

Table S573.  Gene #55: 'del_12q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 27(12Q23.1) MUTATED 29 97 13 24 23 11
DEL PEAK 27(12Q23.1) WILD-TYPE 110 173 195 192 159 35

Figure S573.  Get High-res Image Gene #55: '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 = 1.6e-05

Table S574.  Gene #55: 'del_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 27(12Q23.1) MUTATED 15 29 16 11 10 13 66 11 26
DEL PEAK 27(12Q23.1) WILD-TYPE 51 94 168 175 64 100 93 62 57

Figure S574.  Get High-res Image Gene #55: '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 = 1.6e-05

Table S575.  Gene #55: 'del_12q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 27(12Q23.1) MUTATED 19 7 11 13 65 16
DEL PEAK 27(12Q23.1) WILD-TYPE 114 85 48 106 80 98

Figure S575.  Get High-res Image Gene #55: '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 = 1.6e-05

Table S576.  Gene #55: 'del_12q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 27(12Q23.1) MUTATED 91 27 13
DEL PEAK 27(12Q23.1) WILD-TYPE 223 204 104

Figure S576.  Get High-res Image Gene #55: '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 = 1.6e-05

Table S577.  Gene #56: 'del_12q24.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 28(12Q24.31) MUTATED 18 25 58
DEL PEAK 28(12Q24.31) WILD-TYPE 211 91 110

Figure S577.  Get High-res Image Gene #56: '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 = 1.6e-05

Table S578.  Gene #56: 'del_12q24.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 28(12Q24.31) MUTATED 9 55 37
DEL PEAK 28(12Q24.31) WILD-TYPE 150 211 51

Figure S578.  Get High-res Image Gene #56: '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 = 1.6e-05

Table S579.  Gene #56: 'del_12q24.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 28(12Q24.31) MUTATED 42 24 23 117 5
DEL PEAK 28(12Q24.31) WILD-TYPE 288 108 272 177 24

Figure S579.  Get High-res Image Gene #56: '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 = 1.6e-05

Table S580.  Gene #56: 'del_12q24.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 28(12Q24.31) MUTATED 23 32 19 67 10
DEL PEAK 28(12Q24.31) WILD-TYPE 195 151 126 72 78

Figure S580.  Get High-res Image Gene #56: 'del_12q24.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12q24.31' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S581.  Gene #56: 'del_12q24.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 28(12Q24.31) MUTATED 62 20 7 25 39 18 2
DEL PEAK 28(12Q24.31) WILD-TYPE 132 217 23 179 92 49 8

Figure S581.  Get High-res Image Gene #56: 'del_12q24.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_12q24.31' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S582.  Gene #56: 'del_12q24.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 28(12Q24.31) MUTATED 78 58 37
DEL PEAK 28(12Q24.31) WILD-TYPE 142 340 218

Figure S582.  Get High-res Image Gene #56: '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 = 1.6e-05

Table S583.  Gene #56: 'del_12q24.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 28(12Q24.31) MUTATED 29 42 18 23 88 7 3
DEL PEAK 28(12Q24.31) WILD-TYPE 235 127 125 202 115 44 17

Figure S583.  Get High-res Image Gene #56: '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 = 1.6e-05

Table S584.  Gene #56: 'del_12q24.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 28(12Q24.31) MUTATED 26 37 15 31 79 22
DEL PEAK 28(12Q24.31) WILD-TYPE 263 126 75 259 104 38

Figure S584.  Get High-res Image Gene #56: '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 = 1.6e-05

Table S585.  Gene #56: 'del_12q24.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 28(12Q24.31) MUTATED 26 92 15 31 31 13
DEL PEAK 28(12Q24.31) WILD-TYPE 113 178 193 185 151 33

Figure S585.  Get High-res Image Gene #56: '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 = 1.6e-05

Table S586.  Gene #56: 'del_12q24.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 28(12Q24.31) MUTATED 13 30 21 13 14 15 65 12 25
DEL PEAK 28(12Q24.31) WILD-TYPE 53 93 163 173 60 98 94 61 58

Figure S586.  Get High-res Image Gene #56: '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 = 1.6e-05

Table S587.  Gene #56: 'del_12q24.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 28(12Q24.31) MUTATED 20 13 12 16 61 18
DEL PEAK 28(12Q24.31) WILD-TYPE 113 79 47 103 84 96

Figure S587.  Get High-res Image Gene #56: '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 = 0.00015

Table S588.  Gene #56: 'del_12q24.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 28(12Q24.31) MUTATED 89 34 17
DEL PEAK 28(12Q24.31) WILD-TYPE 225 197 100

Figure S588.  Get High-res Image Gene #56: 'del_12q24.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q14.2' versus 'MRNA_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00016

Table S589.  Gene #57: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 29(13Q14.2) MUTATED 106 41 102
DEL PEAK 29(13Q14.2) WILD-TYPE 123 75 66

Figure S589.  Get High-res Image Gene #57: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.00077

Table S590.  Gene #57: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 29(13Q14.2) MUTATED 70 120 59
DEL PEAK 29(13Q14.2) WILD-TYPE 89 146 29

Figure S590.  Get High-res Image Gene #57: '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 = 1.6e-05

Table S591.  Gene #57: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 29(13Q14.2) MUTATED 194 70 44 176 14
DEL PEAK 29(13Q14.2) WILD-TYPE 136 62 251 118 15

Figure S591.  Get High-res Image Gene #57: '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 = 1.6e-05

Table S592.  Gene #57: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 29(13Q14.2) MUTATED 97 97 48 89 17
DEL PEAK 29(13Q14.2) WILD-TYPE 121 86 97 50 71

Figure S592.  Get High-res Image Gene #57: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'RPPA_CNMF'

P value = 0.00301 (Fisher's exact test), Q value = 0.0039

Table S593.  Gene #57: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 29(13Q14.2) MUTATED 116 103 15 81 61 30 3
DEL PEAK 29(13Q14.2) WILD-TYPE 78 134 15 123 70 37 7

Figure S593.  Get High-res Image Gene #57: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q14.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00018

Table S594.  Gene #57: 'del_13q14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 29(13Q14.2) MUTATED 130 171 108
DEL PEAK 29(13Q14.2) WILD-TYPE 90 227 147

Figure S594.  Get High-res Image Gene #57: '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 = 1.6e-05

Table S595.  Gene #57: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 29(13Q14.2) MUTATED 137 88 41 77 127 16 10
DEL PEAK 29(13Q14.2) WILD-TYPE 127 81 102 148 76 35 10

Figure S595.  Get High-res Image Gene #57: '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 = 1.6e-05

Table S596.  Gene #57: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 29(13Q14.2) MUTATED 130 96 19 110 117 24
DEL PEAK 29(13Q14.2) WILD-TYPE 159 67 71 180 66 36

Figure S596.  Get High-res Image Gene #57: '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 = 1.6e-05

Table S597.  Gene #57: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 29(13Q14.2) MUTATED 75 159 95 60 79 19
DEL PEAK 29(13Q14.2) WILD-TYPE 64 111 113 156 103 27

Figure S597.  Get High-res Image Gene #57: '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 = 1.6e-05

Table S598.  Gene #57: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 29(13Q14.2) MUTATED 30 62 47 85 25 63 101 32 42
DEL PEAK 29(13Q14.2) WILD-TYPE 36 61 137 101 49 50 58 41 41

Figure S598.  Get High-res Image Gene #57: '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 = 1.6e-05

Table S599.  Gene #57: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 29(13Q14.2) MUTATED 66 31 17 44 91 37
DEL PEAK 29(13Q14.2) WILD-TYPE 67 61 42 75 54 77

Figure S599.  Get High-res Image Gene #57: '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 = 4.6e-05

Table S600.  Gene #57: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 29(13Q14.2) MUTATED 167 77 42
DEL PEAK 29(13Q14.2) WILD-TYPE 147 154 75

Figure S600.  Get High-res Image Gene #57: '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 = 1.6e-05

Table S601.  Gene #58: 'del_14q24.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 30(14Q24.1) MUTATED 56 31 85
DEL PEAK 30(14Q24.1) WILD-TYPE 173 85 83

Figure S601.  Get High-res Image Gene #58: '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 = 1.6e-05

Table S602.  Gene #58: 'del_14q24.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 30(14Q24.1) MUTATED 33 80 59
DEL PEAK 30(14Q24.1) WILD-TYPE 126 186 29

Figure S602.  Get High-res Image Gene #58: '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 = 1.6e-05

Table S603.  Gene #58: 'del_14q24.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 30(14Q24.1) MUTATED 118 26 20 182 10
DEL PEAK 30(14Q24.1) WILD-TYPE 212 106 275 112 19

Figure S603.  Get High-res Image Gene #58: '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 = 1.6e-05

Table S604.  Gene #58: 'del_14q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 30(14Q24.1) MUTATED 48 61 33 96 11
DEL PEAK 30(14Q24.1) WILD-TYPE 170 122 112 43 77

Figure S604.  Get High-res Image Gene #58: '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 = 1.6e-05

Table S605.  Gene #58: 'del_14q24.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 30(14Q24.1) MUTATED 117 47 11 54 40 20 2
DEL PEAK 30(14Q24.1) WILD-TYPE 77 190 19 150 91 47 8

Figure S605.  Get High-res Image Gene #58: '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 = 1.6e-05

Table S606.  Gene #58: 'del_14q24.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 30(14Q24.1) MUTATED 113 105 73
DEL PEAK 30(14Q24.1) WILD-TYPE 107 293 182

Figure S606.  Get High-res Image Gene #58: '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 = 1.6e-05

Table S607.  Gene #58: 'del_14q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 30(14Q24.1) MUTATED 105 55 21 24 132 8 9
DEL PEAK 30(14Q24.1) WILD-TYPE 159 114 122 201 71 43 11

Figure S607.  Get High-res Image Gene #58: '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 = 1.6e-05

Table S608.  Gene #58: 'del_14q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 30(14Q24.1) MUTATED 69 69 6 70 124 16
DEL PEAK 30(14Q24.1) WILD-TYPE 220 94 84 220 59 44

Figure S608.  Get High-res Image Gene #58: '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 = 1.6e-05

Table S609.  Gene #58: 'del_14q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 30(14Q24.1) MUTATED 52 157 45 41 43 8
DEL PEAK 30(14Q24.1) WILD-TYPE 87 113 163 175 139 38

Figure S609.  Get High-res Image Gene #58: '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 = 1.6e-05

Table S610.  Gene #58: 'del_14q24.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 30(14Q24.1) MUTATED 27 44 23 43 16 32 106 17 38
DEL PEAK 30(14Q24.1) WILD-TYPE 39 79 161 143 58 81 53 56 45

Figure S610.  Get High-res Image Gene #58: '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 = 1.6e-05

Table S611.  Gene #58: 'del_14q24.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 30(14Q24.1) MUTATED 39 19 16 29 94 24
DEL PEAK 30(14Q24.1) WILD-TYPE 94 73 43 90 51 90

Figure S611.  Get High-res Image Gene #58: '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 = 1.6e-05

Table S612.  Gene #58: 'del_14q24.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 30(14Q24.1) MUTATED 146 48 27
DEL PEAK 30(14Q24.1) WILD-TYPE 168 183 90

Figure S612.  Get High-res Image Gene #58: 'del_14q24.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q32.12' versus 'MRNA_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.00074

Table S613.  Gene #59: 'del_14q32.12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 31(14Q32.12) MUTATED 52 30 68
DEL PEAK 31(14Q32.12) WILD-TYPE 177 86 100

Figure S613.  Get High-res Image Gene #59: 'del_14q32.12' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q32.12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S614.  Gene #59: 'del_14q32.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 31(14Q32.12) MUTATED 32 70 48
DEL PEAK 31(14Q32.12) WILD-TYPE 127 196 40

Figure S614.  Get High-res Image Gene #59: 'del_14q32.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q32.12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S615.  Gene #59: 'del_14q32.12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 31(14Q32.12) MUTATED 106 25 19 168 9
DEL PEAK 31(14Q32.12) WILD-TYPE 224 107 276 126 20

Figure S615.  Get High-res Image Gene #59: 'del_14q32.12' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q32.12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S616.  Gene #59: 'del_14q32.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 31(14Q32.12) MUTATED 47 57 37 84 13
DEL PEAK 31(14Q32.12) WILD-TYPE 171 126 108 55 75

Figure S616.  Get High-res Image Gene #59: 'del_14q32.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q32.12' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S617.  Gene #59: 'del_14q32.12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 31(14Q32.12) MUTATED 98 45 9 53 36 22 2
DEL PEAK 31(14Q32.12) WILD-TYPE 96 192 21 151 95 45 8

Figure S617.  Get High-res Image Gene #59: 'del_14q32.12' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_14q32.12' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S618.  Gene #59: 'del_14q32.12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 31(14Q32.12) MUTATED 95 98 72
DEL PEAK 31(14Q32.12) WILD-TYPE 125 300 183

Figure S618.  Get High-res Image Gene #59: 'del_14q32.12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_14q32.12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S619.  Gene #59: 'del_14q32.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 31(14Q32.12) MUTATED 96 51 21 25 114 8 10
DEL PEAK 31(14Q32.12) WILD-TYPE 168 118 122 200 89 43 10

Figure S619.  Get High-res Image Gene #59: 'del_14q32.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q32.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S620.  Gene #59: 'del_14q32.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 31(14Q32.12) MUTATED 60 66 8 68 109 14
DEL PEAK 31(14Q32.12) WILD-TYPE 229 97 82 222 74 46

Figure S620.  Get High-res Image Gene #59: 'del_14q32.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S621.  Gene #59: 'del_14q32.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 31(14Q32.12) MUTATED 45 141 44 41 39 7
DEL PEAK 31(14Q32.12) WILD-TYPE 94 129 164 175 143 39

Figure S621.  Get High-res Image Gene #59: 'del_14q32.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_14q32.12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S622.  Gene #59: 'del_14q32.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 31(14Q32.12) MUTATED 23 41 23 40 17 31 97 14 31
DEL PEAK 31(14Q32.12) WILD-TYPE 43 82 161 146 57 82 62 59 52

Figure S622.  Get High-res Image Gene #59: 'del_14q32.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q32.12' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S623.  Gene #59: 'del_14q32.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 31(14Q32.12) MUTATED 31 23 16 31 86 22
DEL PEAK 31(14Q32.12) WILD-TYPE 102 69 43 88 59 92

Figure S623.  Get High-res Image Gene #59: 'del_14q32.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_14q32.12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S624.  Gene #59: 'del_14q32.12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 31(14Q32.12) MUTATED 133 48 28
DEL PEAK 31(14Q32.12) WILD-TYPE 181 183 89

Figure S624.  Get High-res Image Gene #59: 'del_14q32.12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q13.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S625.  Gene #60: 'del_15q13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 32(15Q13.1) MUTATED 71 28 92
DEL PEAK 32(15Q13.1) WILD-TYPE 158 88 76

Figure S625.  Get High-res Image Gene #60: '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 = 1.6e-05

Table S626.  Gene #60: 'del_15q13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 32(15Q13.1) MUTATED 43 94 54
DEL PEAK 32(15Q13.1) WILD-TYPE 116 172 34

Figure S626.  Get High-res Image Gene #60: '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 = 1.6e-05

Table S627.  Gene #60: 'del_15q13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 32(15Q13.1) MUTATED 105 57 17 188 8
DEL PEAK 32(15Q13.1) WILD-TYPE 225 75 278 106 21

Figure S627.  Get High-res Image Gene #60: '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 = 1.6e-05

Table S628.  Gene #60: 'del_15q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 32(15Q13.1) MUTATED 54 67 32 91 16
DEL PEAK 32(15Q13.1) WILD-TYPE 164 116 113 48 72

Figure S628.  Get High-res Image Gene #60: 'del_15q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q13.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S629.  Gene #60: 'del_15q13.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 32(15Q13.1) MUTATED 104 63 14 43 54 34 2
DEL PEAK 32(15Q13.1) WILD-TYPE 90 174 16 161 77 33 8

Figure S629.  Get High-res Image Gene #60: 'del_15q13.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_15q13.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S630.  Gene #60: 'del_15q13.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 32(15Q13.1) MUTATED 122 127 65
DEL PEAK 32(15Q13.1) WILD-TYPE 98 271 190

Figure S630.  Get High-res Image Gene #60: '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 = 1.6e-05

Table S631.  Gene #60: 'del_15q13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 32(15Q13.1) MUTATED 84 74 23 51 127 6 7
DEL PEAK 32(15Q13.1) WILD-TYPE 180 95 120 174 76 45 13

Figure S631.  Get High-res Image Gene #60: '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 = 1.6e-05

Table S632.  Gene #60: 'del_15q13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 32(15Q13.1) MUTATED 77 74 12 67 120 22
DEL PEAK 32(15Q13.1) WILD-TYPE 212 89 78 223 63 38

Figure S632.  Get High-res Image Gene #60: '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 = 1.6e-05

Table S633.  Gene #60: 'del_15q13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 32(15Q13.1) MUTATED 47 161 42 33 63 20
DEL PEAK 32(15Q13.1) WILD-TYPE 92 109 166 183 119 26

Figure S633.  Get High-res Image Gene #60: '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 = 1.6e-05

Table S634.  Gene #60: 'del_15q13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 32(15Q13.1) MUTATED 19 54 27 37 30 43 104 9 43
DEL PEAK 32(15Q13.1) WILD-TYPE 47 69 157 149 44 70 55 64 40

Figure S634.  Get High-res Image Gene #60: '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 = 1.6e-05

Table S635.  Gene #60: 'del_15q13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 32(15Q13.1) MUTATED 42 23 23 30 93 19
DEL PEAK 32(15Q13.1) WILD-TYPE 91 69 36 89 52 95

Figure S635.  Get High-res Image Gene #60: '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 = 1.6e-05

Table S636.  Gene #60: 'del_15q13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 32(15Q13.1) MUTATED 146 47 37
DEL PEAK 32(15Q13.1) WILD-TYPE 168 184 80

Figure S636.  Get High-res Image Gene #60: '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 = 1.6e-05

Table S637.  Gene #61: 'del_16q24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 33(16Q24.3) MUTATED 179 82 75
DEL PEAK 33(16Q24.3) WILD-TYPE 50 34 93

Figure S637.  Get High-res Image Gene #61: '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 = 1.6e-05

Table S638.  Gene #61: 'del_16q24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 33(16Q24.3) MUTATED 125 189 22
DEL PEAK 33(16Q24.3) WILD-TYPE 34 77 66

Figure S638.  Get High-res Image Gene #61: '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 = 1.6e-05

Table S639.  Gene #61: 'del_16q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 33(16Q24.3) MUTATED 210 107 209 143 24
DEL PEAK 33(16Q24.3) WILD-TYPE 120 25 86 151 5

Figure S639.  Get High-res Image Gene #61: '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 = 1.6e-05

Table S640.  Gene #61: 'del_16q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 33(16Q24.3) MUTATED 163 125 86 57 57
DEL PEAK 33(16Q24.3) WILD-TYPE 55 58 59 82 31

Figure S640.  Get High-res Image Gene #61: 'del_16q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q24.3' versus 'RPPA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 9e-05

Table S641.  Gene #61: 'del_16q24.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 33(16Q24.3) MUTATED 98 170 18 142 78 35 5
DEL PEAK 33(16Q24.3) WILD-TYPE 96 67 12 62 53 32 5

Figure S641.  Get High-res Image Gene #61: '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 = 1.6e-05

Table S642.  Gene #61: 'del_16q24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 33(16Q24.3) MUTATED 88 271 187
DEL PEAK 33(16Q24.3) WILD-TYPE 132 127 68

Figure S642.  Get High-res Image Gene #61: '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 = 1.6e-05

Table S643.  Gene #61: 'del_16q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 33(16Q24.3) MUTATED 162 97 112 192 69 42 16
DEL PEAK 33(16Q24.3) WILD-TYPE 102 72 31 33 134 9 4

Figure S643.  Get High-res Image Gene #61: '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 = 1.6e-05

Table S644.  Gene #61: 'del_16q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 33(16Q24.3) MUTATED 194 99 77 231 60 29
DEL PEAK 33(16Q24.3) WILD-TYPE 95 64 13 59 123 31

Figure S644.  Get High-res Image Gene #61: '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 = 1.6e-05

Table S645.  Gene #61: 'del_16q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 33(16Q24.3) MUTATED 80 119 150 155 136 41
DEL PEAK 33(16Q24.3) WILD-TYPE 59 151 58 61 46 5

Figure S645.  Get High-res Image Gene #61: '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 = 1.6e-05

Table S646.  Gene #61: 'del_16q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 33(16Q24.3) MUTATED 29 67 148 133 67 94 56 45 42
DEL PEAK 33(16Q24.3) WILD-TYPE 37 56 36 53 7 19 103 28 41

Figure S646.  Get High-res Image Gene #61: '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 = 1.6e-05

Table S647.  Gene #61: 'del_16q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 33(16Q24.3) MUTATED 77 65 40 84 63 87
DEL PEAK 33(16Q24.3) WILD-TYPE 56 27 19 35 82 27

Figure S647.  Get High-res Image Gene #61: '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 = 1.6e-05

Table S648.  Gene #61: 'del_16q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 33(16Q24.3) MUTATED 157 172 87
DEL PEAK 33(16Q24.3) WILD-TYPE 157 59 30

Figure S648.  Get High-res Image Gene #61: '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 = 1.6e-05

Table S649.  Gene #62: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 34(17P12) MUTATED 114 72 132
DEL PEAK 34(17P12) WILD-TYPE 115 44 36

Figure S649.  Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p12' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S650.  Gene #62: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 34(17P12) MUTATED 74 186 58
DEL PEAK 34(17P12) WILD-TYPE 85 80 30

Figure S650.  Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S651.  Gene #62: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 34(17P12) MUTATED 240 71 99 226 14
DEL PEAK 34(17P12) WILD-TYPE 90 61 196 68 15

Figure S651.  Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S652.  Gene #62: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 34(17P12) MUTATED 111 141 73 94 41
DEL PEAK 34(17P12) WILD-TYPE 107 42 72 45 47

Figure S652.  Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p12' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S653.  Gene #62: 'del_17p12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 34(17P12) MUTATED 141 118 22 106 89 51 8
DEL PEAK 34(17P12) WILD-TYPE 53 119 8 98 42 16 2

Figure S653.  Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_17p12' versus 'RPPA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00011

Table S654.  Gene #62: 'del_17p12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 34(17P12) MUTATED 161 232 142
DEL PEAK 34(17P12) WILD-TYPE 59 166 113

Figure S654.  Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S655.  Gene #62: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 34(17P12) MUTATED 182 140 74 79 129 28 15
DEL PEAK 34(17P12) WILD-TYPE 82 29 69 146 74 23 5

Figure S655.  Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S656.  Gene #62: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 34(17P12) MUTATED 152 134 43 154 116 48
DEL PEAK 34(17P12) WILD-TYPE 137 29 47 136 67 12

Figure S656.  Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S657.  Gene #62: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 34(17P12) MUTATED 107 193 103 105 104 27
DEL PEAK 34(17P12) WILD-TYPE 32 77 105 111 78 19

Figure S657.  Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S658.  Gene #62: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 34(17P12) MUTATED 42 98 78 96 44 67 100 51 63
DEL PEAK 34(17P12) WILD-TYPE 24 25 106 90 30 46 59 22 20

Figure S658.  Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17q21.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S659.  Gene #63: 'del_17q21.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 35(17Q21.31) MUTATED 49 45 98
DEL PEAK 35(17Q21.31) WILD-TYPE 180 71 70

Figure S659.  Get High-res Image Gene #63: '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 = 1.6e-05

Table S660.  Gene #63: 'del_17q21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 35(17Q21.31) MUTATED 26 120 46
DEL PEAK 35(17Q21.31) WILD-TYPE 133 146 42

Figure S660.  Get High-res Image Gene #63: '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 = 1.6e-05

Table S661.  Gene #63: 'del_17q21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 35(17Q21.31) MUTATED 103 43 47 178 0
DEL PEAK 35(17Q21.31) WILD-TYPE 227 89 248 116 29

Figure S661.  Get High-res Image Gene #63: '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 = 1.6e-05

Table S662.  Gene #63: 'del_17q21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 35(17Q21.31) MUTATED 37 69 44 84 15
DEL PEAK 35(17Q21.31) WILD-TYPE 181 114 101 55 73

Figure S662.  Get High-res Image Gene #63: '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 = 1.6e-05

Table S663.  Gene #63: 'del_17q21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 35(17Q21.31) MUTATED 99 48 13 56 55 33 5
DEL PEAK 35(17Q21.31) WILD-TYPE 95 189 17 148 76 34 5

Figure S663.  Get High-res Image Gene #63: '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 = 1.6e-05

Table S664.  Gene #63: 'del_17q21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 35(17Q21.31) MUTATED 138 101 70
DEL PEAK 35(17Q21.31) WILD-TYPE 82 297 185

Figure S664.  Get High-res Image Gene #63: '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 = 1.6e-05

Table S665.  Gene #63: 'del_17q21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 35(17Q21.31) MUTATED 60 119 33 31 105 14 8
DEL PEAK 35(17Q21.31) WILD-TYPE 204 50 110 194 98 37 12

Figure S665.  Get High-res Image Gene #63: '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 = 1.6e-05

Table S666.  Gene #63: 'del_17q21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 35(17Q21.31) MUTATED 44 90 21 79 96 40
DEL PEAK 35(17Q21.31) WILD-TYPE 245 73 69 211 87 20

Figure S666.  Get High-res Image Gene #63: '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 = 1.6e-05

Table S667.  Gene #63: 'del_17q21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 35(17Q21.31) MUTATED 55 147 40 50 55 16
DEL PEAK 35(17Q21.31) WILD-TYPE 84 123 168 166 127 30

Figure S667.  Get High-res Image Gene #63: '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 = 1.6e-05

Table S668.  Gene #63: 'del_17q21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 35(17Q21.31) MUTATED 21 86 39 32 25 22 84 22 32
DEL PEAK 35(17Q21.31) WILD-TYPE 45 37 145 154 49 91 75 51 51

Figure S668.  Get High-res Image Gene #63: '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 = 1.6e-05

Table S669.  Gene #63: 'del_17q21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 35(17Q21.31) MUTATED 40 21 21 28 80 36
DEL PEAK 35(17Q21.31) WILD-TYPE 93 71 38 91 65 78

Figure S669.  Get High-res Image Gene #63: 'del_17q21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17q21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00087 (Fisher's exact test), Q value = 0.0012

Table S670.  Gene #63: 'del_17q21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 35(17Q21.31) MUTATED 130 64 32
DEL PEAK 35(17Q21.31) WILD-TYPE 184 167 85

Figure S670.  Get High-res Image Gene #63: 'del_17q21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q23' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S671.  Gene #64: 'del_18q23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 36(18Q23) MUTATED 57 30 78
DEL PEAK 36(18Q23) WILD-TYPE 172 86 90

Figure S671.  Get High-res Image Gene #64: 'del_18q23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q23' versus 'MRNA_CHIERARCHICAL'

P value = 0.0029 (Fisher's exact test), Q value = 0.0038

Table S672.  Gene #64: 'del_18q23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 36(18Q23) MUTATED 35 95 35
DEL PEAK 36(18Q23) WILD-TYPE 124 171 53

Figure S672.  Get High-res Image Gene #64: 'del_18q23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18q23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S673.  Gene #64: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 36(18Q23) MUTATED 125 46 46 133 5
DEL PEAK 36(18Q23) WILD-TYPE 205 86 249 161 24

Figure S673.  Get High-res Image Gene #64: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S674.  Gene #64: 'del_18q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 36(18Q23) MUTATED 58 89 38 61 15
DEL PEAK 36(18Q23) WILD-TYPE 160 94 107 78 73

Figure S674.  Get High-res Image Gene #64: 'del_18q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q23' versus 'RPPA_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00033

Table S675.  Gene #64: 'del_18q23' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 36(18Q23) MUTATED 86 57 14 58 44 25 4
DEL PEAK 36(18Q23) WILD-TYPE 108 180 16 146 87 42 6

Figure S675.  Get High-res Image Gene #64: 'del_18q23' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_18q23' versus 'RPPA_CHIERARCHICAL'

P value = 0.00127 (Fisher's exact test), Q value = 0.0017

Table S676.  Gene #64: 'del_18q23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 36(18Q23) MUTATED 92 130 66
DEL PEAK 36(18Q23) WILD-TYPE 128 268 189

Figure S676.  Get High-res Image Gene #64: 'del_18q23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_18q23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S677.  Gene #64: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 36(18Q23) MUTATED 92 89 30 40 84 14 5
DEL PEAK 36(18Q23) WILD-TYPE 172 80 113 185 119 37 15

Figure S677.  Get High-res Image Gene #64: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S678.  Gene #64: 'del_18q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 36(18Q23) MUTATED 61 94 19 75 77 28
DEL PEAK 36(18Q23) WILD-TYPE 228 69 71 215 106 32

Figure S678.  Get High-res Image Gene #64: 'del_18q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S679.  Gene #64: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 36(18Q23) MUTATED 47 129 54 51 58 12
DEL PEAK 36(18Q23) WILD-TYPE 92 141 154 165 124 34

Figure S679.  Get High-res Image Gene #64: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18q23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S680.  Gene #64: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 36(18Q23) MUTATED 23 54 41 46 19 37 63 24 44
DEL PEAK 36(18Q23) WILD-TYPE 43 69 143 140 55 76 96 49 39

Figure S680.  Get High-res Image Gene #64: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.013

Table S681.  Gene #64: 'del_18q23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 36(18Q23) MUTATED 44 30 20 29 64 29
DEL PEAK 36(18Q23) WILD-TYPE 89 62 39 90 81 85

Figure S681.  Get High-res Image Gene #64: 'del_18q23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S682.  Gene #65: 'del_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 37(19P13.3) MUTATED 58 28 95
DEL PEAK 37(19P13.3) WILD-TYPE 171 88 73

Figure S682.  Get High-res Image Gene #65: '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 = 1.6e-05

Table S683.  Gene #65: 'del_19p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 37(19P13.3) MUTATED 36 93 52
DEL PEAK 37(19P13.3) WILD-TYPE 123 173 36

Figure S683.  Get High-res Image Gene #65: '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 = 1.6e-05

Table S684.  Gene #65: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 37(19P13.3) MUTATED 151 19 15 171 6
DEL PEAK 37(19P13.3) WILD-TYPE 179 113 280 123 23

Figure S684.  Get High-res Image Gene #65: '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 = 1.6e-05

Table S685.  Gene #65: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 37(19P13.3) MUTATED 46 69 38 78 7
DEL PEAK 37(19P13.3) WILD-TYPE 172 114 107 61 81

Figure S685.  Get High-res Image Gene #65: '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 = 1.6e-05

Table S686.  Gene #65: 'del_19p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 37(19P13.3) MUTATED 111 60 10 41 47 29 2
DEL PEAK 37(19P13.3) WILD-TYPE 83 177 20 163 84 38 8

Figure S686.  Get High-res Image Gene #65: '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 = 1.6e-05

Table S687.  Gene #65: 'del_19p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 37(19P13.3) MUTATED 114 129 57
DEL PEAK 37(19P13.3) WILD-TYPE 106 269 198

Figure S687.  Get High-res Image Gene #65: '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 = 1.6e-05

Table S688.  Gene #65: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 37(19P13.3) MUTATED 110 72 21 23 115 9 10
DEL PEAK 37(19P13.3) WILD-TYPE 154 97 122 202 88 42 10

Figure S688.  Get High-res Image Gene #65: '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 = 1.6e-05

Table S689.  Gene #65: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 37(19P13.3) MUTATED 80 88 4 62 107 19
DEL PEAK 37(19P13.3) WILD-TYPE 209 75 86 228 76 41

Figure S689.  Get High-res Image Gene #65: '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 = 1.6e-05

Table S690.  Gene #65: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 37(19P13.3) MUTATED 69 153 41 35 42 12
DEL PEAK 37(19P13.3) WILD-TYPE 70 117 167 181 140 34

Figure S690.  Get High-res Image Gene #65: '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 = 1.6e-05

Table S691.  Gene #65: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 37(19P13.3) MUTATED 26 48 13 44 14 37 94 28 48
DEL PEAK 37(19P13.3) WILD-TYPE 40 75 171 142 60 76 65 45 35

Figure S691.  Get High-res Image Gene #65: '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 = 1.6e-05

Table S692.  Gene #65: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 37(19P13.3) MUTATED 50 16 9 25 88 27
DEL PEAK 37(19P13.3) WILD-TYPE 83 76 50 94 57 87

Figure S692.  Get High-res Image Gene #65: '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 = 1.6e-05

Table S693.  Gene #65: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 37(19P13.3) MUTATED 143 55 17
DEL PEAK 37(19P13.3) WILD-TYPE 171 176 100

Figure S693.  Get High-res Image Gene #65: '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 = 1.6e-05

Table S694.  Gene #66: 'del_19q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 38(19Q13.32) MUTATED 31 14 54
DEL PEAK 38(19Q13.32) WILD-TYPE 198 102 114

Figure S694.  Get High-res Image Gene #66: 'del_19q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19q13.32' versus 'MRNA_CHIERARCHICAL'

P value = 0.00162 (Fisher's exact test), Q value = 0.0021

Table S695.  Gene #66: 'del_19q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 38(19Q13.32) MUTATED 17 58 24
DEL PEAK 38(19Q13.32) WILD-TYPE 142 208 64

Figure S695.  Get High-res Image Gene #66: '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 = 1.6e-05

Table S696.  Gene #66: 'del_19q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 38(19Q13.32) MUTATED 96 14 10 95 1
DEL PEAK 38(19Q13.32) WILD-TYPE 234 118 285 199 28

Figure S696.  Get High-res Image Gene #66: '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 = 1.6e-05

Table S697.  Gene #66: 'del_19q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 38(19Q13.32) MUTATED 30 46 21 51 6
DEL PEAK 38(19Q13.32) WILD-TYPE 188 137 124 88 82

Figure S697.  Get High-res Image Gene #66: 'del_19q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.32' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S698.  Gene #66: 'del_19q13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 38(19Q13.32) MUTATED 62 34 4 25 32 21 1
DEL PEAK 38(19Q13.32) WILD-TYPE 132 203 26 179 99 46 9

Figure S698.  Get High-res Image Gene #66: 'del_19q13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19q13.32' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S699.  Gene #66: 'del_19q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 38(19Q13.32) MUTATED 70 76 33
DEL PEAK 38(19Q13.32) WILD-TYPE 150 322 222

Figure S699.  Get High-res Image Gene #66: '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 = 1.6e-05

Table S700.  Gene #66: 'del_19q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 38(19Q13.32) MUTATED 66 59 9 16 61 3 1
DEL PEAK 38(19Q13.32) WILD-TYPE 198 110 134 209 142 48 19

Figure S700.  Get High-res Image Gene #66: '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 = 1.6e-05

Table S701.  Gene #66: 'del_19q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 38(19Q13.32) MUTATED 56 55 3 24 58 19
DEL PEAK 38(19Q13.32) WILD-TYPE 233 108 87 266 125 41

Figure S701.  Get High-res Image Gene #66: '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 = 1.6e-05

Table S702.  Gene #66: 'del_19q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 38(19Q13.32) MUTATED 39 89 25 20 27 9
DEL PEAK 38(19Q13.32) WILD-TYPE 100 181 183 196 155 37

Figure S702.  Get High-res Image Gene #66: '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 = 1.6e-05

Table S703.  Gene #66: 'del_19q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 38(19Q13.32) MUTATED 20 34 8 27 12 19 49 12 28
DEL PEAK 38(19Q13.32) WILD-TYPE 46 89 176 159 62 94 110 61 55

Figure S703.  Get High-res Image Gene #66: '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 = 1.6e-05

Table S704.  Gene #66: 'del_19q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 38(19Q13.32) MUTATED 29 13 3 21 55 13
DEL PEAK 38(19Q13.32) WILD-TYPE 104 79 56 98 90 101

Figure S704.  Get High-res Image Gene #66: '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 = 1.6e-05

Table S705.  Gene #66: 'del_19q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 38(19Q13.32) MUTATED 97 30 7
DEL PEAK 38(19Q13.32) WILD-TYPE 217 201 110

Figure S705.  Get High-res Image Gene #66: 'del_19q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p13' versus 'MRNA_CNMF'

P value = 0.002 (Fisher's exact test), Q value = 0.0026

Table S706.  Gene #67: 'del_20p13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 39(20P13) MUTATED 28 12 40
DEL PEAK 39(20P13) WILD-TYPE 201 104 128

Figure S706.  Get High-res Image Gene #67: 'del_20p13' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_20p13' versus 'MRNA_CHIERARCHICAL'

P value = 0.0151 (Fisher's exact test), Q value = 0.018

Table S707.  Gene #67: 'del_20p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
DEL PEAK 39(20P13) MUTATED 20 37 23
DEL PEAK 39(20P13) WILD-TYPE 139 229 65

Figure S707.  Get High-res Image Gene #67: 'del_20p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_20p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S708.  Gene #67: 'del_20p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 39(20P13) MUTATED 58 7 11 81 3
DEL PEAK 39(20P13) WILD-TYPE 272 125 284 213 26

Figure S708.  Get High-res Image Gene #67: 'del_20p13' versus Molecular Subtype #3: 'CN_CNMF'

'del_20p13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S709.  Gene #67: 'del_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 39(20P13) MUTATED 12 30 11 47 6
DEL PEAK 39(20P13) WILD-TYPE 206 153 134 92 82

Figure S709.  Get High-res Image Gene #67: 'del_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_20p13' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S710.  Gene #67: 'del_20p13' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
DEL PEAK 39(20P13) MUTATED 56 21 6 19 20 11 3
DEL PEAK 39(20P13) WILD-TYPE 138 216 24 185 111 56 7

Figure S710.  Get High-res Image Gene #67: 'del_20p13' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_20p13' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S711.  Gene #67: 'del_20p13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 39(20P13) MUTATED 61 50 25
DEL PEAK 39(20P13) WILD-TYPE 159 348 230

Figure S711.  Get High-res Image Gene #67: 'del_20p13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_20p13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S712.  Gene #67: 'del_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 39(20P13) MUTATED 54 29 7 8 58 2 1
DEL PEAK 39(20P13) WILD-TYPE 210 140 136 217 145 49 19

Figure S712.  Get High-res Image Gene #67: 'del_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_20p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S713.  Gene #67: 'del_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 39(20P13) MUTATED 37 33 2 20 56 11
DEL PEAK 39(20P13) WILD-TYPE 252 130 88 270 127 49

Figure S713.  Get High-res Image Gene #67: 'del_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_20p13' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S714.  Gene #67: 'del_20p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 39(20P13) MUTATED 24 80 16 13 15 3
DEL PEAK 39(20P13) WILD-TYPE 115 190 192 203 167 43

Figure S714.  Get High-res Image Gene #67: 'del_20p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_20p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S715.  Gene #67: 'del_20p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 39(20P13) MUTATED 9 18 6 18 3 18 49 6 24
DEL PEAK 39(20P13) WILD-TYPE 57 105 178 168 71 95 110 67 59

Figure S715.  Get High-res Image Gene #67: 'del_20p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_20p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S716.  Gene #67: 'del_20p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
DEL PEAK 39(20P13) MUTATED 13 7 3 13 47 10
DEL PEAK 39(20P13) WILD-TYPE 120 85 56 106 98 104

Figure S716.  Get High-res Image Gene #67: '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 = 1.6e-05

Table S717.  Gene #67: 'del_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
DEL PEAK 39(20P13) MUTATED 70 19 4
DEL PEAK 39(20P13) WILD-TYPE 244 212 113

Figure S717.  Get High-res Image Gene #67: 'del_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q11.2' versus 'MRNA_CNMF'

P value = 0.00082 (Fisher's exact test), Q value = 0.0011

Table S718.  Gene #68: 'del_21q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
DEL PEAK 40(21Q11.2) MUTATED 42 14 50
DEL PEAK 40(21Q11.2) WILD-TYPE 187 102 118

Figure S718.  Get High-res Image Gene #68: '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 = 1.6e-05

Table S719.  Gene #68: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 40(21Q11.2) MUTATED 105 18 17 67 8
DEL PEAK 40(21Q11.2) WILD-TYPE 225 114 278 227 21

Figure S719.  Get High-res Image Gene #68: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.0014

Table S720.  Gene #68: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
DEL PEAK 40(21Q11.2) MUTATED 46 51 20 24 8
DEL PEAK 40(21Q11.2) WILD-TYPE 172 132 125 115 80

Figure S720.  Get High-res Image Gene #68: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S721.  Gene #68: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 40(21Q11.2) MUTATED 75 47 21 30 31 6 4
DEL PEAK 40(21Q11.2) WILD-TYPE 189 122 122 195 172 45 16

Figure S721.  Get High-res Image Gene #68: '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 = 1.6e-05

Table S722.  Gene #68: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 40(21Q11.2) MUTATED 57 57 6 52 28 14
DEL PEAK 40(21Q11.2) WILD-TYPE 232 106 84 238 155 46

Figure S722.  Get High-res Image Gene #68: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00925 (Fisher's exact test), Q value = 0.011

Table S723.  Gene #68: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 40(21Q11.2) MUTATED 40 58 33 30 41 8
DEL PEAK 40(21Q11.2) WILD-TYPE 99 212 175 186 141 38

Figure S723.  Get High-res Image Gene #68: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_21q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S724.  Gene #68: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
DEL PEAK 40(21Q11.2) MUTATED 24 30 15 28 15 28 23 20 27
DEL PEAK 40(21Q11.2) WILD-TYPE 42 93 169 158 59 85 136 53 56

Figure S724.  Get High-res Image Gene #68: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_22q11.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S725.  Gene #69: 'del_22q11.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 41(22Q11.1) MUTATED 164 80 77 134 7
DEL PEAK 41(22Q11.1) WILD-TYPE 166 52 218 160 22

Figure S725.  Get High-res Image Gene #69: 'del_22q11.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q11.1' versus 'MIRSEQ_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.017

Table S726.  Gene #69: 'del_22q11.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 41(22Q11.1) MUTATED 70 121 93 71 73 23
DEL PEAK 41(22Q11.1) WILD-TYPE 69 149 115 145 109 23

Figure S726.  Get High-res Image Gene #69: 'del_22q11.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S727.  Gene #70: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
DEL PEAK 42(22Q13.32) MUTATED 182 84 79 139 8
DEL PEAK 42(22Q13.32) WILD-TYPE 148 48 216 155 21

Figure S727.  Get High-res Image Gene #70: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.32' versus 'RPPA_CHIERARCHICAL'

P value = 0.00819 (Fisher's exact test), Q value = 0.01

Table S728.  Gene #70: 'del_22q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
DEL PEAK 42(22Q13.32) MUTATED 84 203 118
DEL PEAK 42(22Q13.32) WILD-TYPE 136 195 137

Figure S728.  Get High-res Image Gene #70: 'del_22q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 0.0189 (Fisher's exact test), Q value = 0.022

Table S729.  Gene #70: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
DEL PEAK 42(22Q13.32) MUTATED 141 73 58 108 84 16 11
DEL PEAK 42(22Q13.32) WILD-TYPE 123 96 85 117 119 35 9

Figure S729.  Get High-res Image Gene #70: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00698 (Fisher's exact test), Q value = 0.0088

Table S730.  Gene #70: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 42(22Q13.32) MUTATED 140 89 33 134 77 18
DEL PEAK 42(22Q13.32) WILD-TYPE 149 74 57 156 106 42

Figure S730.  Get High-res Image Gene #70: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.00081

Table S731.  Gene #70: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
DEL PEAK 42(22Q13.32) MUTATED 78 120 102 79 75 29
DEL PEAK 42(22Q13.32) WILD-TYPE 61 150 106 137 107 17

Figure S731.  Get High-res Image Gene #70: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

Methods & Data
Input
  • Copy number data file = all_lesions.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BRCA-TP/22531239/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BRCA-TP/22595637/BRCA-TP.transferedmergedcluster.txt

  • Number of patients = 1080

  • Number of significantly focal cnvs = 70

  • 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)