Correlation between copy number variation genes (focal events) and molecular subtypes
Breast Invasive Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1R78DDP
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1R78DDP
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 69 focal events and 12 molecular subtypes across 1080 patients, 745 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  • del_1p22.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

  • del_4q35.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

  • del_6q27 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_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',  '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',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  • del_22q13.32 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 69 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, 745 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
amp 1p22 3 250 (23%) 830 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.00083
(0.00106) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05)
amp 3q26 32 340 (31%) 740 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		2e-05
(2.99e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05)
amp 6p23 299 (28%) 781 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.00013
(0.000179) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05)
amp 6q21 202 (19%) 878 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05)
amp 8q24 21 678 (63%) 402 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05)
amp 10p15 1 304 (28%) 776 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05)
amp 12p13 33 282 (26%) 798 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05)
amp 13q34 179 (17%) 901 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		2e-05
(2.99e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		4e-05
(5.85e-05)
amp 15q26 3 194 (18%) 886 1e-05
(1.56e-05) 		7e-05
(9.89e-05) 		1e-05
(1.56e-05) 		3e-05
(4.46e-05) 		0.00144
(0.0018) 		0.0101
(0.0118) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.002
(0.00248) 		6e-05
(8.57e-05)
amp 19q12 284 (26%) 796 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		2e-05
(2.99e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.00113
(0.00143)
amp 20q13 2 548 (51%) 532 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.00043
(0.000563) 		0.00038
(0.000503) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05)
del 2q37 3 317 (29%) 763 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		5e-05
(7.2e-05)
del 3p21 31 347 (32%) 733 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		8e-05
(0.000112)
del 4p16 3 339 (31%) 741 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.00035
(0.000466)
del 4q35 1 345 (32%) 735 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.0007
(0.000899)
del 5q11 2 280 (26%) 800 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05)
del 5q21 3 272 (25%) 808 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05)
del 7p22 3 137 (13%) 943 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.00144
(0.0018) 		0.00469
(0.00563) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		2e-05
(2.99e-05) 		4e-05
(5.85e-05)
del 8p23 2 558 (52%) 522 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.00394
(0.00476) 		0.00088
(0.00112) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05)
del 8p11 21 200 (19%) 880 4e-05
(5.85e-05) 		0.00017
(0.000232) 		1e-05
(1.56e-05) 		0.00116
(0.00146) 		0.0261
(0.0297) 		0.00043
(0.000563) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.00262
(0.0032) 		0.00044
(0.000576)
del 9p23 325 (30%) 755 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.0069
(0.00814) 		0.00612
(0.00727) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.00029
(0.000389) 		0.00013
(0.000179)
del 9p21 3 364 (34%) 716 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.00273
(0.00332) 		0.0273
(0.031) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		7e-05
(9.89e-05) 		1e-05
(1.56e-05)
del 9q21 11 294 (27%) 786 0.00102
(0.00129) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		2e-05
(2.99e-05) 		0.0204
(0.0234) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05)
del 9q34 2 297 (28%) 783 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05)
del 10q23 31 320 (30%) 760 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		4e-05
(5.85e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.00011
(0.000153)
del 10q26 3 319 (30%) 761 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05)
del 11p15 5 309 (29%) 771 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05)
del 12q23 1 201 (19%) 879 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05)
del 12q24 31 211 (20%) 869 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		2e-05
(2.99e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		4e-05
(5.85e-05)
del 14q24 1 353 (33%) 727 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05)
del 15q13 1 375 (35%) 705 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		5e-05
(7.2e-05) 		4e-05
(5.85e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05)
del 16q24 3 693 (64%) 387 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05)
del 17q21 31 371 (34%) 709 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.0004
(0.000527)
del 19p13 3 363 (34%) 717 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05)
del 19q13 32 216 (20%) 864 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.00018
(0.000245) 		5e-05
(7.2e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05)
del 20p13 160 (15%) 920 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.00012
(0.000166) 		0.00648
(0.00768) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05)
amp 4q13 3 163 (15%) 917 1e-05
(1.56e-05) 		2e-05
(2.99e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.0332
(0.0375) 		0.137
(0.146) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.00351
(0.00426) 		7e-05
(9.89e-05)
amp 10q22 3 150 (14%) 930 6e-05
(8.57e-05) 		5e-05
(7.2e-05) 		1e-05
(1.56e-05) 		8e-05
(0.000112) 		0.00326
(0.00396) 		0.213
(0.223) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.0001
(0.000139) 		1e-05
(1.56e-05) 		0.00174
(0.00216) 		0.00254
(0.00312)
amp 11q13 3 398 (37%) 682 0.00023
(0.000311) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.95
(0.951) 		0.00069
(0.000887) 		0.00024
(0.000324) 		5e-05
(7.2e-05) 		0.00022
(0.000298) 		0.00064
(0.000824) 		0.0142
(0.0163) 		0.00825
(0.00968)
amp 14q21 1 220 (20%) 860 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.0126
(0.0146) 		0.00748
(0.00881) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.00401
(0.00484) 		0.684
(0.693)
amp 17q12 333 (31%) 747 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.0979
(0.106) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		4e-05
(5.85e-05) 		1e-05
(1.56e-05) 		0.00051
(0.000664) 		0.00017
(0.000232)
amp 17q23 1 426 (39%) 654 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.485
(0.496) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		6e-05
(8.57e-05) 		1e-05
(1.56e-05)
amp 19p13 12 230 (21%) 850 0.00013
(0.000179) 		0.00031
(0.000415) 		1e-05
(1.56e-05) 		2e-05
(2.99e-05) 		0.00143
(0.00179) 		0.00429
(0.00516) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.0918
(0.0993)
del 1p36 13 452 (42%) 628 7e-05
(9.89e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.00184
(0.00228) 		0.0135
(0.0156) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		2e-05
(2.99e-05) 		1e-05
(1.56e-05) 		0.00228
(0.00281) 		0.164
(0.173)
del 11q25 513 (48%) 567 0.00042
(0.000552) 		0.00017
(0.000232) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.109
(0.117) 		1e-05
(1.56e-05) 		0.00147
(0.00184) 		5e-05
(7.2e-05) 		0.00385
(0.00466) 		0.00122
(0.00154) 		0.0221
(0.0252) 		0.0401
(0.045)
del 13q14 2 495 (46%) 585 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.182
(0.191) 		3e-05
(4.46e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05)
amp 1q21 3 781 (72%) 299 1e-05
(1.56e-05) 		2e-05
(2.99e-05) 		1e-05
(1.56e-05) 		2e-05
(2.99e-05) 		0.0652
(0.0716) 		0.0208
(0.0237) 		0.00082
(0.00105) 		1e-05
(1.56e-05) 		0.00036
(0.000477) 		1e-05
(1.56e-05) 		0.001
(0.00127) 		0.124
(0.132)
amp 5p15 33 394 (36%) 686 0.00864
(0.0101) 		0.00075
(0.000961) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.0746
(0.0813) 		0.795
(0.8) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		2e-05
(2.99e-05) 		2e-05
(2.99e-05) 		0.00163
(0.00203) 		0.00513
(0.00613)
amp 8p11 21 421 (39%) 659 0.0432
(0.0483) 		0.0047
(0.00563) 		1e-05
(1.56e-05) 		2e-05
(2.99e-05) 		0.771
(0.777) 		0.106
(0.114) 		4e-05
(5.85e-05) 		1e-05
(1.56e-05) 		0.00028
(0.000376) 		2e-05
(2.99e-05) 		9e-05
(0.000126) 		0.00101
(0.00128)
amp 11q14 1 267 (25%) 813 0.00571
(0.0068) 		0.00025
(0.000337) 		1e-05
(1.56e-05) 		2e-05
(2.99e-05) 		0.0702
(0.0768) 		0.384
(0.396) 		1e-05
(1.56e-05) 		2e-05
(2.99e-05) 		1e-05
(1.56e-05) 		5e-05
(7.2e-05) 		0.0295
(0.0334) 		0.0182
(0.0209)
amp 12q15 276 (26%) 804 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.287
(0.297) 		0.0131
(0.0152) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		5e-05
(7.2e-05) 		0.167
(0.176)
del 1p22 1 362 (34%) 718 0.0105
(0.0122) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.0131
(0.0152) 		0.00674
(0.00797) 		3e-05
(4.46e-05) 		1e-05
(1.56e-05) 		0.00179
(0.00222) 		1e-05
(1.56e-05) 		0.204
(0.213) 		0.967
(0.967)
del 11q23 3 547 (51%) 533 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.905
(0.907) 		2e-05
(2.99e-05) 		2e-05
(2.99e-05) 		1e-05
(1.56e-05) 		0.012
(0.0139) 		6e-05
(8.57e-05) 		0.0003
(0.000402) 		0.174
(0.184)
del 17p12 650 (60%) 430 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.0572
(0.0632) 		0.153
(0.162)
del 18q23 354 (33%) 726 9e-05
(0.000126) 		5e-05
(7.2e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.00057
(0.000737) 		0.064
(0.0704) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.00524
(0.00625) 		0.167
(0.176)
del 21q11 2 217 (20%) 863 0.00017
(0.000232) 		0.00426
(0.00513) 		1e-05
(1.56e-05) 		0.0001
(0.000139) 		0.0431
(0.0483) 		0.0821
(0.0892) 		0.00823
(0.00968) 		1e-05
(1.56e-05) 		0.00824
(0.00968) 		0.00057
(0.000737) 		0.0334
(0.0377) 		0.12
(0.129)
amp 3p25 1 198 (18%) 882 0.00062
(8e-04) 		7e-05
(9.89e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.128
(0.137) 		0.654
(0.664) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.0395
(0.0444) 		0.0697
(0.0765)
amp 11p13 223 (21%) 857 0.166
(0.176) 		0.00078
(0.000997) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.147
(0.156) 		0.0746
(0.0813) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.00021
(0.000285) 		6e-05
(8.57e-05)
amp 19q13 42 276 (26%) 804 0.00049
(0.000639) 		0.00265
(0.00324) 		1e-05
(1.56e-05) 		2e-05
(2.99e-05) 		0.00505
(0.00604) 		0.41
(0.421) 		0.0001
(0.000139) 		0.00062
(8e-04) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.177
(0.186) 		0.0741
(0.0811)
del 6q15 358 (33%) 722 1e-05
(1.56e-05) 		0.00034
(0.000453) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.719
(0.728) 		0.0855
(0.0927) 		2e-05
(2.99e-05) 		1e-05
(1.56e-05) 		0.00922
(0.0108) 		1e-05
(1.56e-05) 		0.00015
(0.000206) 		0.561
(0.572)
del 7q36 1 200 (19%) 880 0.00258
(0.00316) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.0743
(0.0812) 		0.253
(0.263) 		0.0537
(0.0596) 		2e-05
(2.99e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		7e-05
(9.89e-05) 		1e-05
(1.56e-05)
del 12p13 1 188 (17%) 892 0.035
(0.0394) 		0.112
(0.12) 		0.00036
(0.000477) 		0.0193
(0.0222) 		0.132
(0.141) 		0.447
(0.458) 		0.00034
(0.000453) 		0.00052
(0.000675) 		0.00204
(0.00252) 		3e-05
(4.46e-05) 		0.00608
(0.00723) 		0.00267
(0.00326)
amp 17p11 2 147 (14%) 933 0.0269
(0.0306) 		0.0599
(0.066) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.868
(0.871) 		0.0345
(0.0389) 		0.00012
(0.000166) 		0.0108
(0.0125) 		0.0467
(0.052) 		0.0471
(0.0524) 		0.599
(0.61) 		0.103
(0.111)
del 11q13 1 241 (22%) 839 0.00348
(0.00422) 		0.00236
(0.00291) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.605
(0.616) 		0.0394
(0.0443) 		0.00046
(0.000601) 		0.00019
(0.000258) 		0.218
(0.227) 		0.0576
(0.0635) 		0.0225
(0.0257) 		0.336
(0.346)
del 22q13 32 492 (46%) 588 0.253
(0.263) 		0.00987
(0.0115) 		1e-05
(1.56e-05) 		0.00247
(0.00304) 		0.276
(0.286) 		0.0556
(0.0615) 		0.00152
(0.0019) 		0.00675
(0.00797) 		0.00077
(0.000985) 		0.00052
(0.000675) 		0.0026
(0.00318) 		0.0777
(0.0846)
amp 8p11 23 412 (38%) 668 1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		1e-05
(1.56e-05) 		0.0545
(0.0603) 		8e-05
(0.000112) 		9e-05
(0.000126) 		0.00018
(0.000245) 		0.0859
(0.0931) 		0.166
(0.175) 		0.179
(0.188) 		0.742
(0.75)
del 6q27 375 (35%) 705 0.0227
(0.0258) 		0.0105
(0.0122) 		1e-05
(1.56e-05) 		0.00984
(0.0115) 		0.0319
(0.0361) 		0.146
(0.155) 		0.0457
(0.0509) 		0.138
(0.147) 		0.00641
(0.0076) 		0.427
(0.439) 		0.748
(0.755) 		0.61
(0.619)
amp 1q44 789 (73%) 291 4e-05
(5.85e-05) 		0.00132
(0.00166) 		1e-05
(1.56e-05) 		0.00036
(0.000477) 		0.548
(0.56) 		0.457
(0.468) 		0.852
(0.856) 		0.00042
(0.000552) 		0.496
(0.507) 		0.00027
(0.000364) 		0.112
(0.12) 		0.139
(0.148)
del 6p25 3 204 (19%) 876 0.41
(0.421) 		0.774
(0.78) 		1e-05
(1.56e-05) 		0.00088
(0.00112) 		0.25
(0.261) 		0.271
(0.281) 		0.0004
(0.000527) 		0.0544
(0.0603) 		0.0042
(0.00506) 		0.0441
(0.0492) 		0.311
(0.321) 		0.185
(0.194)
'amp_1p22.3' versus 'MRNA_CNMF'

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

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

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

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

'amp_1p22.3' versus 'MRNA_CHIERARCHICAL'

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

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

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

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

'amp_1p22.3' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
AMP PEAK 1(1P22.3) MUTATED 42 52 32 110 14
AMP PEAK 1(1P22.3) WILD-TYPE 233 355 66 147 29

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

'amp_1p22.3' versus 'METHLYATION_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
AMP PEAK 1(1P22.3) MUTATED 20 20 39 24 71 5
AMP PEAK 1(1P22.3) WILD-TYPE 124 79 174 99 64 54

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

'amp_1p22.3' versus 'RPPA_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.0011

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
AMP PEAK 1(1P22.3) MUTATED 51 18 27
AMP PEAK 1(1P22.3) WILD-TYPE 100 105 98

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

'amp_1p22.3' versus 'RPPA_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
AMP PEAK 1(1P22.3) MUTATED 15 4 45 9 18 5
AMP PEAK 1(1P22.3) WILD-TYPE 49 42 45 43 98 26

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

'amp_1p22.3' versus 'MRNASEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
AMP PEAK 1(1P22.3) MUTATED 100 129 20
AMP PEAK 1(1P22.3) WILD-TYPE 459 175 192

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

'amp_1p22.3' versus 'MRNASEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 1(1P22.3) MUTATED 48 35 7 44 99 16
AMP PEAK 1(1P22.3) WILD-TYPE 241 128 83 246 84 44

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

'amp_1p22.3' versus 'MIRSEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
AMP PEAK 1(1P22.3) MUTATED 126 32 51 38
AMP PEAK 1(1P22.3) WILD-TYPE 179 180 218 237

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

'amp_1p22.3' versus 'MIRSEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
AMP PEAK 1(1P22.3) MUTATED 53 41 39 25 9 80
AMP PEAK 1(1P22.3) WILD-TYPE 241 111 206 115 87 54

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

'amp_1p22.3' versus 'MIRSEQ_MATURE_CNMF'

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

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

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

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

'amp_1p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

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

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

'amp_1q21.3' versus 'MRNA_CNMF'

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

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

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

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

'amp_1q21.3' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3e-05

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

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

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

'amp_1q21.3' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
AMP PEAK 2(1Q21.3) MUTATED 200 249 96 204 32
AMP PEAK 2(1Q21.3) WILD-TYPE 75 158 2 53 11

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

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
AMP PEAK 2(1Q21.3) MUTATED 96 78 163 72 113 35
AMP PEAK 2(1Q21.3) WILD-TYPE 48 21 50 51 22 24

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

'amp_1q21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0208 (Fisher's exact test), Q value = 0.024

Table S17.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
AMP PEAK 2(1Q21.3) MUTATED 49 29 77 35 80 25
AMP PEAK 2(1Q21.3) WILD-TYPE 15 17 13 17 36 6

Figure S17.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 0.00082 (Fisher's exact test), Q value = 0.001

Table S18.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
AMP PEAK 2(1Q21.3) MUTATED 398 242 138
AMP PEAK 2(1Q21.3) WILD-TYPE 161 62 74

Figure S18.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S19.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 2(1Q21.3) MUTATED 193 130 53 208 159 35
AMP PEAK 2(1Q21.3) WILD-TYPE 96 33 37 82 24 25

Figure S19.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.00048

Table S20.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
AMP PEAK 2(1Q21.3) MUTATED 244 137 198 185
AMP PEAK 2(1Q21.3) WILD-TYPE 61 75 71 90

Figure S20.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S21.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
AMP PEAK 2(1Q21.3) MUTATED 211 107 159 112 54 121
AMP PEAK 2(1Q21.3) WILD-TYPE 83 45 86 28 42 13

Figure S21.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.001 (Fisher's exact test), Q value = 0.0013

Table S22.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S22.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1q44' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 5.9e-05

Table S23.  Gene #3: 'amp_1q44' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S23.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1q44' versus 'MRNA_CHIERARCHICAL'

P value = 0.00132 (Fisher's exact test), Q value = 0.0017

Table S24.  Gene #3: 'amp_1q44' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S24.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_1q44' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
AMP PEAK 3(1Q44) MUTATED 205 261 98 196 29
AMP PEAK 3(1Q44) WILD-TYPE 70 146 0 61 14

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

'amp_1q44' versus 'METHLYATION_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.00048

Table S26.  Gene #3: 'amp_1q44' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
AMP PEAK 3(1Q44) MUTATED 95 84 168 77 102 39
AMP PEAK 3(1Q44) WILD-TYPE 49 15 45 46 33 20

Figure S26.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q44' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.00055

Table S27.  Gene #3: '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 3(1Q44) MUTATED 191 133 61 221 143 37
AMP PEAK 3(1Q44) WILD-TYPE 98 30 29 69 40 23

Figure S27.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q44' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.00036

Table S28.  Gene #3: 'amp_1q44' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
AMP PEAK 3(1Q44) MUTATED 212 112 174 117 54 104
AMP PEAK 3(1Q44) WILD-TYPE 82 40 71 23 42 30

Figure S28.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3p25.1' versus 'MRNA_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 8e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 4(3P25.1) MUTATED 6 7 34 20 18 25 7 1
AMP PEAK 4(3P25.1) WILD-TYPE 15 29 85 76 91 47 13 39

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

'amp_3p25.1' versus 'MRNA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 9.9e-05

Table S30.  Gene #4: 'amp_3p25.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S30.  Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_3p25.1' versus 'CN_CNMF'

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

Table S31.  Gene #4: 'amp_3p25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
AMP PEAK 4(3P25.1) MUTATED 76 19 23 69 11
AMP PEAK 4(3P25.1) WILD-TYPE 199 388 75 188 32

Figure S31.  Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3p25.1' versus 'METHLYATION_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
AMP PEAK 4(3P25.1) MUTATED 34 19 19 12 33 3
AMP PEAK 4(3P25.1) WILD-TYPE 110 80 194 111 102 56

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

'amp_3p25.1' versus 'MRNASEQ_CNMF'

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

Table S33.  Gene #4: 'amp_3p25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
AMP PEAK 4(3P25.1) MUTATED 108 79 11
AMP PEAK 4(3P25.1) WILD-TYPE 451 225 201

Figure S33.  Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3p25.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S34.  Gene #4: 'amp_3p25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

Figure S34.  Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3p25.1' versus 'MIRSEQ_CNMF'

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

Table S35.  Gene #4: 'amp_3p25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
AMP PEAK 4(3P25.1) MUTATED 81 14 40 55
AMP PEAK 4(3P25.1) WILD-TYPE 224 198 229 220

Figure S35.  Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3p25.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S36.  Gene #4: 'amp_3p25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
AMP PEAK 4(3P25.1) MUTATED 68 37 20 20 12 33
AMP PEAK 4(3P25.1) WILD-TYPE 226 115 225 120 84 101

Figure S36.  Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3p25.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0395 (Fisher's exact test), Q value = 0.044

Table S37.  Gene #4: 'amp_3p25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 4(3P25.1) MUTATED 36 27 13 9 18
AMP PEAK 4(3P25.1) WILD-TYPE 144 112 86 102 115

Figure S37.  Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.32' versus 'MRNA_CNMF'

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

Table S38.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S38.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.32' versus 'MRNA_CHIERARCHICAL'

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

Table S39.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S39.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_3q26.32' versus 'CN_CNMF'

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

Table S40.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
AMP PEAK 5(3Q26.32) MUTATED 103 37 29 158 13
AMP PEAK 5(3Q26.32) WILD-TYPE 172 370 69 99 30

Figure S40.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.32' versus 'METHLYATION_CNMF'

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

Table S41.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
AMP PEAK 5(3Q26.32) MUTATED 44 31 29 26 86 10
AMP PEAK 5(3Q26.32) WILD-TYPE 100 68 184 97 49 49

Figure S41.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.32' versus 'RPPA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
AMP PEAK 5(3Q26.32) MUTATED 78 33 31
AMP PEAK 5(3Q26.32) WILD-TYPE 73 90 94

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

'amp_3q26.32' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3e-05

Table S43.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
AMP PEAK 5(3Q26.32) MUTATED 22 12 54 12 32 10
AMP PEAK 5(3Q26.32) WILD-TYPE 42 34 36 40 84 21

Figure S43.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_3q26.32' versus 'MRNASEQ_CNMF'

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

Table S44.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
AMP PEAK 5(3Q26.32) MUTATED 146 170 22
AMP PEAK 5(3Q26.32) WILD-TYPE 413 134 190

Figure S44.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.32' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S45.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 5(3Q26.32) MUTATED 72 67 5 52 116 26
AMP PEAK 5(3Q26.32) WILD-TYPE 217 96 85 238 67 34

Figure S45.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.32' versus 'MIRSEQ_CNMF'

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

Table S46.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
AMP PEAK 5(3Q26.32) MUTATED 162 32 52 85
AMP PEAK 5(3Q26.32) WILD-TYPE 143 180 217 190

Figure S46.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.32' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S47.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
AMP PEAK 5(3Q26.32) MUTATED 93 70 30 33 20 85
AMP PEAK 5(3Q26.32) WILD-TYPE 201 82 215 107 76 49

Figure S47.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.32' versus 'MIRSEQ_MATURE_CNMF'

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

Table S48.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S48.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S49.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S49.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q13.3' versus 'MRNA_CNMF'

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

Table S50.  Gene #6: 'amp_4q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 6(4Q13.3) MUTATED 4 3 32 18 3 18 4 3
AMP PEAK 6(4Q13.3) WILD-TYPE 17 33 87 78 106 54 16 37

Figure S50.  Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_4q13.3' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3e-05

Table S51.  Gene #6: 'amp_4q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S51.  Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_4q13.3' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
AMP PEAK 6(4Q13.3) MUTATED 75 21 2 59 6
AMP PEAK 6(4Q13.3) WILD-TYPE 200 386 96 198 37

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

'amp_4q13.3' versus 'METHLYATION_CNMF'

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

Table S53.  Gene #6: 'amp_4q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
AMP PEAK 6(4Q13.3) MUTATED 38 9 11 12 31 5
AMP PEAK 6(4Q13.3) WILD-TYPE 106 90 202 111 104 54

Figure S53.  Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_4q13.3' versus 'RPPA_CNMF'

P value = 0.0332 (Fisher's exact test), Q value = 0.038

Table S54.  Gene #6: 'amp_4q13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
AMP PEAK 6(4Q13.3) MUTATED 33 18 13
AMP PEAK 6(4Q13.3) WILD-TYPE 118 105 112

Figure S54.  Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_4q13.3' versus 'MRNASEQ_CNMF'

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

Table S55.  Gene #6: 'amp_4q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
AMP PEAK 6(4Q13.3) MUTATED 84 68 11
AMP PEAK 6(4Q13.3) WILD-TYPE 475 236 201

Figure S55.  Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_4q13.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S56.  Gene #6: 'amp_4q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 6(4Q13.3) MUTATED 41 34 2 29 39 18
AMP PEAK 6(4Q13.3) WILD-TYPE 248 129 88 261 144 42

Figure S56.  Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_4q13.3' versus 'MIRSEQ_CNMF'

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

Table S57.  Gene #6: 'amp_4q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
AMP PEAK 6(4Q13.3) MUTATED 72 14 31 44
AMP PEAK 6(4Q13.3) WILD-TYPE 233 198 238 231

Figure S57.  Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_4q13.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S58.  Gene #6: 'amp_4q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
AMP PEAK 6(4Q13.3) MUTATED 59 38 18 5 11 30
AMP PEAK 6(4Q13.3) WILD-TYPE 235 114 227 135 85 104

Figure S58.  Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_4q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00351 (Fisher's exact test), Q value = 0.0043

Table S59.  Gene #6: 'amp_4q13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 6(4Q13.3) MUTATED 33 31 9 9 15
AMP PEAK 6(4Q13.3) WILD-TYPE 147 108 90 102 118

Figure S59.  Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_4q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 9.9e-05

Table S60.  Gene #6: 'amp_4q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S60.  Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'MRNA_CNMF'

P value = 0.00864 (Fisher's exact test), Q value = 0.01

Table S61.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 7(5P15.33) MUTATED 8 13 43 46 32 32 12 8
AMP PEAK 7(5P15.33) WILD-TYPE 13 23 76 50 77 40 8 32

Figure S61.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_5p15.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.00075 (Fisher's exact test), Q value = 0.00096

Table S62.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S62.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

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

Table S63.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
AMP PEAK 7(5P15.33) MUTATED 126 68 51 132 17
AMP PEAK 7(5P15.33) WILD-TYPE 149 339 47 125 26

Figure S63.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

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

Table S64.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
AMP PEAK 7(5P15.33) MUTATED 51 45 62 31 72 13
AMP PEAK 7(5P15.33) WILD-TYPE 93 54 151 92 63 46

Figure S64.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

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

Table S65.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
AMP PEAK 7(5P15.33) MUTATED 189 147 55
AMP PEAK 7(5P15.33) WILD-TYPE 370 157 157

Figure S65.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S66.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 7(5P15.33) MUTATED 97 78 20 81 89 26
AMP PEAK 7(5P15.33) WILD-TYPE 192 85 70 209 94 34

Figure S66.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3e-05

Table S67.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
AMP PEAK 7(5P15.33) MUTATED 136 50 88 110
AMP PEAK 7(5P15.33) WILD-TYPE 169 162 181 165

Figure S67.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3e-05

Table S68.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
AMP PEAK 7(5P15.33) MUTATED 110 68 58 52 32 64
AMP PEAK 7(5P15.33) WILD-TYPE 184 84 187 88 64 70

Figure S68.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00163 (Fisher's exact test), Q value = 0.002

Table S69.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 7(5P15.33) MUTATED 68 66 36 33 33
AMP PEAK 7(5P15.33) WILD-TYPE 112 73 63 78 100

Figure S69.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00513 (Fisher's exact test), Q value = 0.0061

Table S70.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
AMP PEAK 7(5P15.33) MUTATED 128 71 37
AMP PEAK 7(5P15.33) WILD-TYPE 177 176 73

Figure S70.  Get High-res Image Gene #7: '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 S71.  Gene #8: 'amp_6p23' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S71.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_6p23' versus 'MRNA_CHIERARCHICAL'

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

Table S72.  Gene #8: 'amp_6p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S72.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_6p23' versus 'CN_CNMF'

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

Table S73.  Gene #8: 'amp_6p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
AMP PEAK 8(6P23) MUTATED 87 30 22 145 15
AMP PEAK 8(6P23) WILD-TYPE 188 377 76 112 28

Figure S73.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p23' versus 'METHLYATION_CNMF'

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

Table S74.  Gene #8: 'amp_6p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
AMP PEAK 8(6P23) MUTATED 59 27 21 21 71 7
AMP PEAK 8(6P23) WILD-TYPE 85 72 192 102 64 52

Figure S74.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6p23' versus 'RPPA_CNMF'

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

Table S75.  Gene #8: 'amp_6p23' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
AMP PEAK 8(6P23) MUTATED 67 28 22
AMP PEAK 8(6P23) WILD-TYPE 84 95 103

Figure S75.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_6p23' versus 'RPPA_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00018

Table S76.  Gene #8: 'amp_6p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
AMP PEAK 8(6P23) MUTATED 14 9 46 12 28 8
AMP PEAK 8(6P23) WILD-TYPE 50 37 44 40 88 23

Figure S76.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_6p23' versus 'MRNASEQ_CNMF'

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

Table S77.  Gene #8: 'amp_6p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
AMP PEAK 8(6P23) MUTATED 130 147 21
AMP PEAK 8(6P23) WILD-TYPE 429 157 191

Figure S77.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6p23' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S78.  Gene #8: '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 8(6P23) MUTATED 56 70 3 53 97 19
AMP PEAK 8(6P23) WILD-TYPE 233 93 87 237 86 41

Figure S78.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6p23' versus 'MIRSEQ_CNMF'

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

Table S79.  Gene #8: 'amp_6p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
AMP PEAK 8(6P23) MUTATED 146 24 56 61
AMP PEAK 8(6P23) WILD-TYPE 159 188 213 214

Figure S79.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_6p23' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S80.  Gene #8: 'amp_6p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
AMP PEAK 8(6P23) MUTATED 83 63 28 21 20 72
AMP PEAK 8(6P23) WILD-TYPE 211 89 217 119 76 62

Figure S80.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6p23' versus 'MIRSEQ_MATURE_CNMF'

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

Table S81.  Gene #8: 'amp_6p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S81.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_6p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S82.  Gene #8: 'amp_6p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S82.  Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q21' versus 'MRNA_CNMF'

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

Table S83.  Gene #9: 'amp_6q21' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S83.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_6q21' versus 'MRNA_CHIERARCHICAL'

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

Table S84.  Gene #9: 'amp_6q21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S84.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_6q21' versus 'CN_CNMF'

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

Table S85.  Gene #9: 'amp_6q21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
AMP PEAK 9(6Q21) MUTATED 29 24 16 128 5
AMP PEAK 9(6Q21) WILD-TYPE 246 383 82 129 38

Figure S85.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6q21' versus 'METHLYATION_CNMF'

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

Table S86.  Gene #9: 'amp_6q21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
AMP PEAK 9(6Q21) MUTATED 20 19 8 20 62 4
AMP PEAK 9(6Q21) WILD-TYPE 124 80 205 103 73 55

Figure S86.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6q21' versus 'RPPA_CNMF'

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

Table S87.  Gene #9: 'amp_6q21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
AMP PEAK 9(6Q21) MUTATED 54 18 11
AMP PEAK 9(6Q21) WILD-TYPE 97 105 114

Figure S87.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_6q21' versus 'RPPA_CHIERARCHICAL'

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

Table S88.  Gene #9: 'amp_6q21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
AMP PEAK 9(6Q21) MUTATED 6 6 38 8 18 7
AMP PEAK 9(6Q21) WILD-TYPE 58 40 52 44 98 24

Figure S88.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_6q21' versus 'MRNASEQ_CNMF'

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

Table S89.  Gene #9: 'amp_6q21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
AMP PEAK 9(6Q21) MUTATED 65 123 12
AMP PEAK 9(6Q21) WILD-TYPE 494 181 200

Figure S89.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6q21' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S90.  Gene #9: '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 9(6Q21) MUTATED 25 47 2 24 82 20
AMP PEAK 9(6Q21) WILD-TYPE 264 116 88 266 101 40

Figure S90.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_CNMF'

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

Table S91.  Gene #9: 'amp_6q21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
AMP PEAK 9(6Q21) MUTATED 115 16 25 36
AMP PEAK 9(6Q21) WILD-TYPE 190 196 244 239

Figure S91.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_6q21' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S92.  Gene #9: 'amp_6q21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
AMP PEAK 9(6Q21) MUTATED 50 58 14 8 4 58
AMP PEAK 9(6Q21) WILD-TYPE 244 94 231 132 92 76

Figure S92.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_MATURE_CNMF'

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

Table S93.  Gene #9: 'amp_6q21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S93.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_6q21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S94.  Gene #9: 'amp_6q21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S94.  Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p11.23' versus 'MRNA_CNMF'

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

Table S95.  Gene #10: 'amp_8p11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S95.  Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8p11.23' versus 'MRNA_CHIERARCHICAL'

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

Table S96.  Gene #10: 'amp_8p11.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S96.  Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8p11.23' versus 'CN_CNMF'

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

Table S97.  Gene #10: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
AMP PEAK 10(8P11.23) MUTATED 147 111 36 76 42
AMP PEAK 10(8P11.23) WILD-TYPE 128 296 62 181 1

Figure S97.  Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.23' versus 'METHLYATION_CNMF'

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

Table S98.  Gene #10: 'amp_8p11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
AMP PEAK 10(8P11.23) MUTATED 91 41 57 32 47 22
AMP PEAK 10(8P11.23) WILD-TYPE 53 58 156 91 88 37

Figure S98.  Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8p11.23' versus 'RPPA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00011

Table S99.  Gene #10: 'amp_8p11.23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
AMP PEAK 10(8P11.23) MUTATED 28 17 32 28 57 2
AMP PEAK 10(8P11.23) WILD-TYPE 36 29 58 24 59 29

Figure S99.  Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8p11.23' versus 'MRNASEQ_CNMF'

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

Table S100.  Gene #10: 'amp_8p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
AMP PEAK 10(8P11.23) MUTATED 246 98 64
AMP PEAK 10(8P11.23) WILD-TYPE 313 206 148

Figure S100.  Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00025

Table S101.  Gene #10: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 10(8P11.23) MUTATED 137 72 29 96 59 15
AMP PEAK 10(8P11.23) WILD-TYPE 152 91 61 194 124 45

Figure S101.  Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MRNA_CNMF'

P value = 0.0432 (Fisher's exact test), Q value = 0.048

Table S102.  Gene #11: 'amp_8p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 11(8P11.21) MUTATED 11 13 60 44 39 27 7 9
AMP PEAK 11(8P11.21) WILD-TYPE 10 23 59 52 70 45 13 31

Figure S102.  Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8p11.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.0047 (Fisher's exact test), Q value = 0.0056

Table S103.  Gene #11: 'amp_8p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 11(8P11.21) MUTATED 54 57 45 40 14
AMP PEAK 11(8P11.21) WILD-TYPE 47 95 69 48 44

Figure S103.  Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8p11.21' versus 'CN_CNMF'

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

Table S104.  Gene #11: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
AMP PEAK 11(8P11.21) MUTATED 127 107 40 104 43
AMP PEAK 11(8P11.21) WILD-TYPE 148 300 58 153 0

Figure S104.  Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3e-05

Table S105.  Gene #11: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
AMP PEAK 11(8P11.21) MUTATED 74 37 59 37 71 19
AMP PEAK 11(8P11.21) WILD-TYPE 70 62 154 86 64 40

Figure S105.  Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 5.9e-05

Table S106.  Gene #11: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
AMP PEAK 11(8P11.21) MUTATED 226 136 55
AMP PEAK 11(8P11.21) WILD-TYPE 333 168 157

Figure S106.  Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S107.  Gene #11: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 11(8P11.21) MUTATED 126 71 24 87 93 16
AMP PEAK 11(8P11.21) WILD-TYPE 163 92 66 203 90 44

Figure S107.  Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.00038

Table S108.  Gene #11: 'amp_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
AMP PEAK 11(8P11.21) MUTATED 144 62 107 99
AMP PEAK 11(8P11.21) WILD-TYPE 161 150 162 176

Figure S108.  Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3e-05

Table S109.  Gene #11: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
AMP PEAK 11(8P11.21) MUTATED 123 51 79 42 44 73
AMP PEAK 11(8P11.21) WILD-TYPE 171 101 166 98 52 61

Figure S109.  Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_MATURE_CNMF'

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

Table S110.  Gene #11: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S110.  Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00101 (Fisher's exact test), Q value = 0.0013

Table S111.  Gene #11: 'amp_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S111.  Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNA_CNMF'

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

Table S112.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S112.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8q24.21' versus 'MRNA_CHIERARCHICAL'

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

Table S113.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S113.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

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

Table S114.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
AMP PEAK 12(8Q24.21) MUTATED 211 151 42 233 41
AMP PEAK 12(8Q24.21) WILD-TYPE 64 256 56 24 2

Figure S114.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

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

Table S115.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
AMP PEAK 12(8Q24.21) MUTATED 109 63 74 65 120 26
AMP PEAK 12(8Q24.21) WILD-TYPE 35 36 139 58 15 33

Figure S115.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'RPPA_CNMF'

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

Table S116.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
AMP PEAK 12(8Q24.21) MUTATED 126 80 68
AMP PEAK 12(8Q24.21) WILD-TYPE 25 43 57

Figure S116.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8q24.21' versus 'RPPA_CHIERARCHICAL'

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

Table S117.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
AMP PEAK 12(8Q24.21) MUTATED 34 23 78 31 83 25
AMP PEAK 12(8Q24.21) WILD-TYPE 30 23 12 21 33 6

Figure S117.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

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

Table S118.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
AMP PEAK 12(8Q24.21) MUTATED 338 255 81
AMP PEAK 12(8Q24.21) WILD-TYPE 221 49 131

Figure S118.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S119.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 12(8Q24.21) MUTATED 168 125 27 147 162 45
AMP PEAK 12(8Q24.21) WILD-TYPE 121 38 63 143 21 15

Figure S119.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

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

Table S120.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
AMP PEAK 12(8Q24.21) MUTATED 270 83 137 173
AMP PEAK 12(8Q24.21) WILD-TYPE 35 129 132 102

Figure S120.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S121.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
AMP PEAK 12(8Q24.21) MUTATED 201 118 100 68 54 122
AMP PEAK 12(8Q24.21) WILD-TYPE 93 34 145 72 42 12

Figure S121.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

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

Table S122.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S122.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S123.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S123.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10p15.1' versus 'MRNA_CNMF'

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

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

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

Figure S124.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_10p15.1' versus 'MRNA_CHIERARCHICAL'

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

Table S125.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S125.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_10p15.1' versus 'CN_CNMF'

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

Table S126.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
AMP PEAK 13(10P15.1) MUTATED 75 39 17 164 9
AMP PEAK 13(10P15.1) WILD-TYPE 200 368 81 93 34

Figure S126.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10p15.1' versus 'METHLYATION_CNMF'

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

Table S127.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
AMP PEAK 13(10P15.1) MUTATED 35 26 14 34 88 4
AMP PEAK 13(10P15.1) WILD-TYPE 109 73 199 89 47 55

Figure S127.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_10p15.1' versus 'RPPA_CNMF'

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

Table S128.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
AMP PEAK 13(10P15.1) MUTATED 78 31 20
AMP PEAK 13(10P15.1) WILD-TYPE 73 92 105

Figure S128.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_10p15.1' versus 'RPPA_CHIERARCHICAL'

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

Table S129.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
AMP PEAK 13(10P15.1) MUTATED 8 14 61 9 28 9
AMP PEAK 13(10P15.1) WILD-TYPE 56 32 29 43 88 22

Figure S129.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_10p15.1' versus 'MRNASEQ_CNMF'

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

Table S130.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
AMP PEAK 13(10P15.1) MUTATED 104 174 26
AMP PEAK 13(10P15.1) WILD-TYPE 455 130 186

Figure S130.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_10p15.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S131.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 13(10P15.1) MUTATED 46 55 3 48 125 27
AMP PEAK 13(10P15.1) WILD-TYPE 243 108 87 242 58 33

Figure S131.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10p15.1' versus 'MIRSEQ_CNMF'

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

Table S132.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
AMP PEAK 13(10P15.1) MUTATED 161 29 42 64
AMP PEAK 13(10P15.1) WILD-TYPE 144 183 227 211

Figure S132.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_10p15.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S133.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
AMP PEAK 13(10P15.1) MUTATED 85 72 22 20 7 90
AMP PEAK 13(10P15.1) WILD-TYPE 209 80 223 120 89 44

Figure S133.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_10p15.1' versus 'MIRSEQ_MATURE_CNMF'

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

Table S134.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S134.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_10p15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S135.  Gene #13: 'amp_10p15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S135.  Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10q22.3' versus 'MRNA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 8.6e-05

Table S136.  Gene #14: 'amp_10q22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S136.  Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_10q22.3' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 7.2e-05

Table S137.  Gene #14: 'amp_10q22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S137.  Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_10q22.3' versus 'CN_CNMF'

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

Table S138.  Gene #14: 'amp_10q22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
AMP PEAK 14(10Q22.3) MUTATED 43 25 12 64 6
AMP PEAK 14(10Q22.3) WILD-TYPE 232 382 86 193 37

Figure S138.  Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10q22.3' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00011

Table S139.  Gene #14: 'amp_10q22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
AMP PEAK 14(10Q22.3) MUTATED 21 16 12 16 28 2
AMP PEAK 14(10Q22.3) WILD-TYPE 123 83 201 107 107 57

Figure S139.  Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_10q22.3' versus 'RPPA_CNMF'

P value = 0.00326 (Fisher's exact test), Q value = 0.004

Table S140.  Gene #14: 'amp_10q22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
AMP PEAK 14(10Q22.3) MUTATED 39 19 13
AMP PEAK 14(10Q22.3) WILD-TYPE 112 104 112

Figure S140.  Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_10q22.3' versus 'MRNASEQ_CNMF'

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

Table S141.  Gene #14: 'amp_10q22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
AMP PEAK 14(10Q22.3) MUTATED 66 69 15
AMP PEAK 14(10Q22.3) WILD-TYPE 493 235 197

Figure S141.  Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_10q22.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S142.  Gene #14: 'amp_10q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 14(10Q22.3) MUTATED 33 36 2 30 32 17
AMP PEAK 14(10Q22.3) WILD-TYPE 256 127 88 260 151 43

Figure S142.  Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10q22.3' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00014

Table S143.  Gene #14: 'amp_10q22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
AMP PEAK 14(10Q22.3) MUTATED 58 20 21 47
AMP PEAK 14(10Q22.3) WILD-TYPE 247 192 248 228

Figure S143.  Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_10q22.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S144.  Gene #14: 'amp_10q22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
AMP PEAK 14(10Q22.3) MUTATED 51 35 13 18 5 24
AMP PEAK 14(10Q22.3) WILD-TYPE 243 117 232 122 91 110

Figure S144.  Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_10q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00174 (Fisher's exact test), Q value = 0.0022

Table S145.  Gene #14: 'amp_10q22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 14(10Q22.3) MUTATED 28 30 7 9 11
AMP PEAK 14(10Q22.3) WILD-TYPE 152 109 92 102 122

Figure S145.  Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_10q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00254 (Fisher's exact test), Q value = 0.0031

Table S146.  Gene #14: 'amp_10q22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
AMP PEAK 14(10Q22.3) MUTATED 51 18 16
AMP PEAK 14(10Q22.3) WILD-TYPE 254 229 94

Figure S146.  Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11p13' versus 'MRNA_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.001

Table S147.  Gene #15: 'amp_11p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S147.  Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11p13' versus 'CN_CNMF'

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

Table S148.  Gene #15: 'amp_11p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
AMP PEAK 15(11P13) MUTATED 85 27 17 86 8
AMP PEAK 15(11P13) WILD-TYPE 190 380 81 171 35

Figure S148.  Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11p13' versus 'METHLYATION_CNMF'

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

Table S149.  Gene #15: 'amp_11p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
AMP PEAK 15(11P13) MUTATED 44 15 27 22 39 4
AMP PEAK 15(11P13) WILD-TYPE 100 84 186 101 96 55

Figure S149.  Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11p13' versus 'MRNASEQ_CNMF'

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

Table S150.  Gene #15: 'amp_11p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
AMP PEAK 15(11P13) MUTATED 115 89 18
AMP PEAK 15(11P13) WILD-TYPE 444 215 194

Figure S150.  Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11p13' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S151.  Gene #15: '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 15(11P13) MUTATED 58 44 7 44 59 10
AMP PEAK 15(11P13) WILD-TYPE 231 119 83 246 124 50

Figure S151.  Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11p13' versus 'MIRSEQ_CNMF'

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

Table S152.  Gene #15: 'amp_11p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
AMP PEAK 15(11P13) MUTATED 100 16 47 57
AMP PEAK 15(11P13) WILD-TYPE 205 196 222 218

Figure S152.  Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11p13' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S153.  Gene #15: 'amp_11p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
AMP PEAK 15(11P13) MUTATED 80 48 20 20 14 38
AMP PEAK 15(11P13) WILD-TYPE 214 104 225 120 82 96

Figure S153.  Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00029

Table S154.  Gene #15: 'amp_11p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S154.  Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_11p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 8.6e-05

Table S155.  Gene #15: 'amp_11p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S155.  Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q13.3' versus 'MRNA_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00031

Table S156.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S156.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11q13.3' versus 'MRNA_CHIERARCHICAL'

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

Table S157.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S157.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

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

Table S158.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
AMP PEAK 16(11Q13.3) MUTATED 201 55 31 97 14
AMP PEAK 16(11Q13.3) WILD-TYPE 74 352 67 160 29

Figure S158.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

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

Table S159.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
AMP PEAK 16(11Q13.3) MUTATED 80 52 50 25 45 13
AMP PEAK 16(11Q13.3) WILD-TYPE 64 47 163 98 90 46

Figure S159.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00069 (Fisher's exact test), Q value = 0.00089

Table S160.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
AMP PEAK 16(11Q13.3) MUTATED 17 20 29 23 67 13
AMP PEAK 16(11Q13.3) WILD-TYPE 47 26 61 29 49 18

Figure S160.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00032

Table S161.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
AMP PEAK 16(11Q13.3) MUTATED 231 112 54
AMP PEAK 16(11Q13.3) WILD-TYPE 328 192 158

Figure S161.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 7.2e-05

Table S162.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 16(11Q13.3) MUTATED 120 82 19 97 58 21
AMP PEAK 16(11Q13.3) WILD-TYPE 169 81 71 193 125 39

Figure S162.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 3e-04

Table S163.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
AMP PEAK 16(11Q13.3) MUTATED 123 51 102 114
AMP PEAK 16(11Q13.3) WILD-TYPE 182 161 167 161

Figure S163.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00064 (Fisher's exact test), Q value = 0.00082

Table S164.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
AMP PEAK 16(11Q13.3) MUTATED 134 63 68 50 33 42
AMP PEAK 16(11Q13.3) WILD-TYPE 160 89 177 90 63 92

Figure S164.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.016

Table S165.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 16(11Q13.3) MUTATED 76 48 29 26 49
AMP PEAK 16(11Q13.3) WILD-TYPE 104 91 70 85 84

Figure S165.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00825 (Fisher's exact test), Q value = 0.0097

Table S166.  Gene #16: 'amp_11q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
AMP PEAK 16(11Q13.3) MUTATED 123 77 28
AMP PEAK 16(11Q13.3) WILD-TYPE 182 170 82

Figure S166.  Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q14.1' versus 'MRNA_CNMF'

P value = 0.00571 (Fisher's exact test), Q value = 0.0068

Table S167.  Gene #17: 'amp_11q14.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 17(11Q14.1) MUTATED 11 11 32 33 23 25 7 4
AMP PEAK 17(11Q14.1) WILD-TYPE 10 25 87 63 86 47 13 36

Figure S167.  Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11q14.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.00034

Table S168.  Gene #17: 'amp_11q14.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S168.  Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11q14.1' versus 'CN_CNMF'

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

Table S169.  Gene #17: 'amp_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
AMP PEAK 17(11Q14.1) MUTATED 111 30 22 96 8
AMP PEAK 17(11Q14.1) WILD-TYPE 164 377 76 161 35

Figure S169.  Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q14.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3e-05

Table S170.  Gene #17: 'amp_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
AMP PEAK 17(11Q14.1) MUTATED 36 34 31 17 44 11
AMP PEAK 17(11Q14.1) WILD-TYPE 108 65 182 106 91 48

Figure S170.  Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q14.1' versus 'MRNASEQ_CNMF'

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

Table S171.  Gene #17: 'amp_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
AMP PEAK 17(11Q14.1) MUTATED 133 102 31
AMP PEAK 17(11Q14.1) WILD-TYPE 426 202 181

Figure S171.  Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3e-05

Table S172.  Gene #17: 'amp_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 17(11Q14.1) MUTATED 63 55 10 59 61 18
AMP PEAK 17(11Q14.1) WILD-TYPE 226 108 80 231 122 42

Figure S172.  Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q14.1' versus 'MIRSEQ_CNMF'

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

Table S173.  Gene #17: 'amp_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
AMP PEAK 17(11Q14.1) MUTATED 111 27 54 69
AMP PEAK 17(11Q14.1) WILD-TYPE 194 185 215 206

Figure S173.  Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 7.2e-05

Table S174.  Gene #17: 'amp_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
AMP PEAK 17(11Q14.1) MUTATED 79 48 36 31 20 47
AMP PEAK 17(11Q14.1) WILD-TYPE 215 104 209 109 76 87

Figure S174.  Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0295 (Fisher's exact test), Q value = 0.033

Table S175.  Gene #17: 'amp_11q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 17(11Q14.1) MUTATED 44 41 21 15 25
AMP PEAK 17(11Q14.1) WILD-TYPE 136 98 78 96 108

Figure S175.  Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_11q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0182 (Fisher's exact test), Q value = 0.021

Table S176.  Gene #17: 'amp_11q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
AMP PEAK 17(11Q14.1) MUTATED 82 42 22
AMP PEAK 17(11Q14.1) WILD-TYPE 223 205 88

Figure S176.  Get High-res Image Gene #17: '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 S177.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S177.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_12p13.33' versus 'MRNA_CHIERARCHICAL'

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

Table S178.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S178.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_12p13.33' versus 'CN_CNMF'

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

Table S179.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
AMP PEAK 18(12P13.33) MUTATED 89 22 28 132 11
AMP PEAK 18(12P13.33) WILD-TYPE 186 385 70 125 32

Figure S179.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p13.33' versus 'METHLYATION_CNMF'

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

Table S180.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
AMP PEAK 18(12P13.33) MUTATED 52 21 25 14 70 4
AMP PEAK 18(12P13.33) WILD-TYPE 92 78 188 109 65 55

Figure S180.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12p13.33' versus 'RPPA_CNMF'

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

Table S181.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
AMP PEAK 18(12P13.33) MUTATED 72 20 29
AMP PEAK 18(12P13.33) WILD-TYPE 79 103 96

Figure S181.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_12p13.33' versus 'RPPA_CHIERARCHICAL'

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

Table S182.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
AMP PEAK 18(12P13.33) MUTATED 15 8 47 6 35 10
AMP PEAK 18(12P13.33) WILD-TYPE 49 38 43 46 81 21

Figure S182.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_12p13.33' versus 'MRNASEQ_CNMF'

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

Table S183.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
AMP PEAK 18(12P13.33) MUTATED 125 137 19
AMP PEAK 18(12P13.33) WILD-TYPE 434 167 193

Figure S183.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12p13.33' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S184.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 18(12P13.33) MUTATED 63 57 7 37 102 15
AMP PEAK 18(12P13.33) WILD-TYPE 226 106 83 253 81 45

Figure S184.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12p13.33' versus 'MIRSEQ_CNMF'

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

Table S185.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
AMP PEAK 18(12P13.33) MUTATED 150 19 55 49
AMP PEAK 18(12P13.33) WILD-TYPE 155 193 214 226

Figure S185.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12p13.33' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S186.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
AMP PEAK 18(12P13.33) MUTATED 75 48 33 25 15 77
AMP PEAK 18(12P13.33) WILD-TYPE 219 104 212 115 81 57

Figure S186.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p13.33' versus 'MIRSEQ_MATURE_CNMF'

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

Table S187.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S187.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12p13.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S188.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S188.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q15' versus 'MRNA_CNMF'

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

Table S189.  Gene #19: 'amp_12q15' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S189.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_12q15' versus 'MRNA_CHIERARCHICAL'

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

Table S190.  Gene #19: 'amp_12q15' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S190.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

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

Table S191.  Gene #19: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
AMP PEAK 19(12Q15) MUTATED 141 29 30 66 10
AMP PEAK 19(12Q15) WILD-TYPE 134 378 68 191 33

Figure S191.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

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

Table S192.  Gene #19: 'amp_12q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
AMP PEAK 19(12Q15) MUTATED 75 24 35 15 20 8
AMP PEAK 19(12Q15) WILD-TYPE 69 75 178 108 115 51

Figure S192.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q15' versus 'RPPA_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 0.015

Table S193.  Gene #19: 'amp_12q15' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
AMP PEAK 19(12Q15) MUTATED 17 14 24 9 50 12
AMP PEAK 19(12Q15) WILD-TYPE 47 32 66 43 66 19

Figure S193.  Get High-res Image Gene #19: '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 S194.  Gene #19: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
AMP PEAK 19(12Q15) MUTATED 182 68 25
AMP PEAK 19(12Q15) WILD-TYPE 377 236 187

Figure S194.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S195.  Gene #19: '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 19(12Q15) MUTATED 92 79 7 55 30 12
AMP PEAK 19(12Q15) WILD-TYPE 197 84 83 235 153 48

Figure S195.  Get High-res Image Gene #19: '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 S196.  Gene #19: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
AMP PEAK 19(12Q15) MUTATED 90 21 68 91
AMP PEAK 19(12Q15) WILD-TYPE 215 191 201 184

Figure S196.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q15' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S197.  Gene #19: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
AMP PEAK 19(12Q15) MUTATED 110 40 42 33 23 22
AMP PEAK 19(12Q15) WILD-TYPE 184 112 203 107 73 112

Figure S197.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 7.2e-05

Table S198.  Gene #19: 'amp_12q15' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S198.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_13q34' versus 'MRNA_CNMF'

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

Table S199.  Gene #20: 'amp_13q34' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S199.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_13q34' versus 'MRNA_CHIERARCHICAL'

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

Table S200.  Gene #20: 'amp_13q34' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S200.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_13q34' versus 'CN_CNMF'

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

Table S201.  Gene #20: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
AMP PEAK 20(13Q34) MUTATED 41 25 13 95 5
AMP PEAK 20(13Q34) WILD-TYPE 234 382 85 162 38

Figure S201.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q34' versus 'METHLYATION_CNMF'

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

Table S202.  Gene #20: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
AMP PEAK 20(13Q34) MUTATED 23 9 16 13 52 2
AMP PEAK 20(13Q34) WILD-TYPE 121 90 197 110 83 57

Figure S202.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q34' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3e-05

Table S203.  Gene #20: 'amp_13q34' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
AMP PEAK 20(13Q34) MUTATED 50 15 19
AMP PEAK 20(13Q34) WILD-TYPE 101 108 106

Figure S203.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_13q34' versus 'RPPA_CHIERARCHICAL'

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

Table S204.  Gene #20: 'amp_13q34' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
AMP PEAK 20(13Q34) MUTATED 10 6 39 3 17 9
AMP PEAK 20(13Q34) WILD-TYPE 54 40 51 49 99 22

Figure S204.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_13q34' versus 'MRNASEQ_CNMF'

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

Table S205.  Gene #20: 'amp_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
AMP PEAK 20(13Q34) MUTATED 68 99 12
AMP PEAK 20(13Q34) WILD-TYPE 491 205 200

Figure S205.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q34' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S206.  Gene #20: '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 20(13Q34) MUTATED 34 22 3 28 74 18
AMP PEAK 20(13Q34) WILD-TYPE 255 141 87 262 109 42

Figure S206.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q34' versus 'MIRSEQ_CNMF'

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

Table S207.  Gene #20: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
AMP PEAK 20(13Q34) MUTATED 104 15 29 28
AMP PEAK 20(13Q34) WILD-TYPE 201 197 240 247

Figure S207.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q34' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S208.  Gene #20: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
AMP PEAK 20(13Q34) MUTATED 42 39 19 10 10 56
AMP PEAK 20(13Q34) WILD-TYPE 252 113 226 130 86 78

Figure S208.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_13q34' versus 'MIRSEQ_MATURE_CNMF'

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

Table S209.  Gene #20: 'amp_13q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S209.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_13q34' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 5.9e-05

Table S210.  Gene #20: 'amp_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S210.  Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_14q21.1' versus 'MRNA_CNMF'

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

Table S211.  Gene #21: 'amp_14q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S211.  Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_14q21.1' versus 'MRNA_CHIERARCHICAL'

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

Table S212.  Gene #21: 'amp_14q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S212.  Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_14q21.1' versus 'CN_CNMF'

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

Table S213.  Gene #21: 'amp_14q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
AMP PEAK 21(14Q21.1) MUTATED 102 39 22 49 8
AMP PEAK 21(14Q21.1) WILD-TYPE 173 368 76 208 35

Figure S213.  Get High-res Image Gene #21: '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 S214.  Gene #21: 'amp_14q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
AMP PEAK 21(14Q21.1) MUTATED 51 29 30 13 19 4
AMP PEAK 21(14Q21.1) WILD-TYPE 93 70 183 110 116 55

Figure S214.  Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_14q21.1' versus 'RPPA_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.015

Table S215.  Gene #21: 'amp_14q21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
AMP PEAK 21(14Q21.1) MUTATED 45 21 21
AMP PEAK 21(14Q21.1) WILD-TYPE 106 102 104

Figure S215.  Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_14q21.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00748 (Fisher's exact test), Q value = 0.0088

Table S216.  Gene #21: 'amp_14q21.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
AMP PEAK 21(14Q21.1) MUTATED 11 6 14 8 39 9
AMP PEAK 21(14Q21.1) WILD-TYPE 53 40 76 44 77 22

Figure S216.  Get High-res Image Gene #21: '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 S217.  Gene #21: 'amp_14q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
AMP PEAK 21(14Q21.1) MUTATED 148 53 18
AMP PEAK 21(14Q21.1) WILD-TYPE 411 251 194

Figure S217.  Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_14q21.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S218.  Gene #21: 'amp_14q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 21(14Q21.1) MUTATED 62 71 7 45 17 17
AMP PEAK 21(14Q21.1) WILD-TYPE 227 92 83 245 166 43

Figure S218.  Get High-res Image Gene #21: '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 S219.  Gene #21: 'amp_14q21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
AMP PEAK 21(14Q21.1) MUTATED 69 15 59 71
AMP PEAK 21(14Q21.1) WILD-TYPE 236 197 210 204

Figure S219.  Get High-res Image Gene #21: '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 S220.  Gene #21: 'amp_14q21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
AMP PEAK 21(14Q21.1) MUTATED 95 44 28 26 10 11
AMP PEAK 21(14Q21.1) WILD-TYPE 199 108 217 114 86 123

Figure S220.  Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_14q21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00401 (Fisher's exact test), Q value = 0.0048

Table S221.  Gene #21: 'amp_14q21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 21(14Q21.1) MUTATED 51 20 23 14 24
AMP PEAK 21(14Q21.1) WILD-TYPE 129 119 76 97 109

Figure S221.  Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_15q26.3' versus 'MRNA_CNMF'

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

Table S222.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 22(15Q26.3) MUTATED 3 8 31 32 4 16 8 2
AMP PEAK 22(15Q26.3) WILD-TYPE 18 28 88 64 105 56 12 38

Figure S222.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_15q26.3' versus 'MRNA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 9.9e-05

Table S223.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S223.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_15q26.3' versus 'CN_CNMF'

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

Table S224.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
AMP PEAK 22(15Q26.3) MUTATED 67 31 6 87 3
AMP PEAK 22(15Q26.3) WILD-TYPE 208 376 92 170 40

Figure S224.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_15q26.3' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4.5e-05

Table S225.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
AMP PEAK 22(15Q26.3) MUTATED 31 14 16 15 36 11
AMP PEAK 22(15Q26.3) WILD-TYPE 113 85 197 108 99 48

Figure S225.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_15q26.3' versus 'RPPA_CNMF'

P value = 0.00144 (Fisher's exact test), Q value = 0.0018

Table S226.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
AMP PEAK 22(15Q26.3) MUTATED 46 19 18
AMP PEAK 22(15Q26.3) WILD-TYPE 105 104 107

Figure S226.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_15q26.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.012

Table S227.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
AMP PEAK 22(15Q26.3) MUTATED 9 9 30 5 26 4
AMP PEAK 22(15Q26.3) WILD-TYPE 55 37 60 47 90 27

Figure S227.  Get High-res Image Gene #22: '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 S228.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
AMP PEAK 22(15Q26.3) MUTATED 93 83 17
AMP PEAK 22(15Q26.3) WILD-TYPE 466 221 195

Figure S228.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S229.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 22(15Q26.3) MUTATED 52 33 6 34 62 6
AMP PEAK 22(15Q26.3) WILD-TYPE 237 130 84 256 121 54

Figure S229.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'MIRSEQ_CNMF'

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

Table S230.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
AMP PEAK 22(15Q26.3) MUTATED 88 19 33 47
AMP PEAK 22(15Q26.3) WILD-TYPE 217 193 236 228

Figure S230.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_15q26.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S231.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
AMP PEAK 22(15Q26.3) MUTATED 56 41 20 13 14 43
AMP PEAK 22(15Q26.3) WILD-TYPE 238 111 225 127 82 91

Figure S231.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.002 (Fisher's exact test), Q value = 0.0025

Table S232.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 22(15Q26.3) MUTATED 34 39 13 14 15
AMP PEAK 22(15Q26.3) WILD-TYPE 146 100 86 97 118

Figure S232.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_15q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 8.6e-05

Table S233.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S233.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17p11.2' versus 'MRNA_CNMF'

P value = 0.0269 (Fisher's exact test), Q value = 0.031

Table S234.  Gene #23: 'amp_17p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 23(17P11.2) MUTATED 0 5 23 9 11 13 2 1
AMP PEAK 23(17P11.2) WILD-TYPE 21 31 96 87 98 59 18 39

Figure S234.  Get High-res Image Gene #23: '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 S235.  Gene #23: 'amp_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
AMP PEAK 23(17P11.2) MUTATED 63 26 14 32 12
AMP PEAK 23(17P11.2) WILD-TYPE 212 381 84 225 31

Figure S235.  Get High-res Image Gene #23: 'amp_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17p11.2' versus 'METHLYATION_CNMF'

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

Table S236.  Gene #23: 'amp_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
AMP PEAK 23(17P11.2) MUTATED 39 17 26 6 21 3
AMP PEAK 23(17P11.2) WILD-TYPE 105 82 187 117 114 56

Figure S236.  Get High-res Image Gene #23: 'amp_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0345 (Fisher's exact test), Q value = 0.039

Table S237.  Gene #23: 'amp_17p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
AMP PEAK 23(17P11.2) MUTATED 7 7 7 5 18 10
AMP PEAK 23(17P11.2) WILD-TYPE 57 39 83 47 98 21

Figure S237.  Get High-res Image Gene #23: 'amp_17p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17p11.2' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00017

Table S238.  Gene #23: 'amp_17p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
AMP PEAK 23(17P11.2) MUTATED 94 39 12
AMP PEAK 23(17P11.2) WILD-TYPE 465 265 200

Figure S238.  Get High-res Image Gene #23: 'amp_17p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.012

Table S239.  Gene #23: '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 23(17P11.2) MUTATED 44 32 5 35 18 11
AMP PEAK 23(17P11.2) WILD-TYPE 245 131 85 255 165 49

Figure S239.  Get High-res Image Gene #23: 'amp_17p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17p11.2' versus 'MIRSEQ_CNMF'

P value = 0.0467 (Fisher's exact test), Q value = 0.052

Table S240.  Gene #23: 'amp_17p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
AMP PEAK 23(17P11.2) MUTATED 49 18 43 36
AMP PEAK 23(17P11.2) WILD-TYPE 256 194 226 239

Figure S240.  Get High-res Image Gene #23: 'amp_17p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0471 (Fisher's exact test), Q value = 0.052

Table S241.  Gene #23: 'amp_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
AMP PEAK 23(17P11.2) MUTATED 50 23 24 17 19 13
AMP PEAK 23(17P11.2) WILD-TYPE 244 129 221 123 77 121

Figure S241.  Get High-res Image Gene #23: 'amp_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MRNA_CNMF'

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

Table S242.  Gene #24: 'amp_17q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 24(17Q12) MUTATED 9 11 53 19 14 49 7 4
AMP PEAK 24(17Q12) WILD-TYPE 12 25 66 77 95 23 13 36

Figure S242.  Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q12' versus 'MRNA_CHIERARCHICAL'

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

Table S243.  Gene #24: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 24(17Q12) MUTATED 40 28 71 16 11
AMP PEAK 24(17Q12) WILD-TYPE 61 124 43 72 47

Figure S243.  Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

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

Table S244.  Gene #24: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
AMP PEAK 24(17Q12) MUTATED 172 62 23 63 13
AMP PEAK 24(17Q12) WILD-TYPE 103 345 75 194 30

Figure S244.  Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

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

Table S245.  Gene #24: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
AMP PEAK 24(17Q12) MUTATED 77 37 39 30 33 13
AMP PEAK 24(17Q12) WILD-TYPE 67 62 174 93 102 46

Figure S245.  Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q12' versus 'RPPA_CHIERARCHICAL'

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

Table S246.  Gene #24: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
AMP PEAK 24(17Q12) MUTATED 9 12 20 14 44 31
AMP PEAK 24(17Q12) WILD-TYPE 55 34 70 38 72 0

Figure S246.  Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q12' versus 'MRNASEQ_CNMF'

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

Table S247.  Gene #24: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
AMP PEAK 24(17Q12) MUTATED 188 112 31
AMP PEAK 24(17Q12) WILD-TYPE 371 192 181

Figure S247.  Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S248.  Gene #24: '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 24(17Q12) MUTATED 95 85 10 68 33 40
AMP PEAK 24(17Q12) WILD-TYPE 194 78 80 222 150 20

Figure S248.  Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 5.9e-05

Table S249.  Gene #24: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
AMP PEAK 24(17Q12) MUTATED 105 45 69 107
AMP PEAK 24(17Q12) WILD-TYPE 200 167 200 168

Figure S249.  Get High-res Image Gene #24: '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 S250.  Gene #24: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
AMP PEAK 24(17Q12) MUTATED 119 66 49 40 30 22
AMP PEAK 24(17Q12) WILD-TYPE 175 86 196 100 66 112

Figure S250.  Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.00066

Table S251.  Gene #24: 'amp_17q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 24(17Q12) MUTATED 77 38 19 29 37
AMP PEAK 24(17Q12) WILD-TYPE 103 101 80 82 96

Figure S251.  Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00023

Table S252.  Gene #24: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
AMP PEAK 24(17Q12) MUTATED 117 58 25
AMP PEAK 24(17Q12) WILD-TYPE 188 189 85

Figure S252.  Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q23.1' versus 'MRNA_CNMF'

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

Table S253.  Gene #25: 'amp_17q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 25(17Q23.1) MUTATED 9 17 81 29 16 44 11 9
AMP PEAK 25(17Q23.1) WILD-TYPE 12 19 38 67 93 28 9 31

Figure S253.  Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q23.1' versus 'MRNA_CHIERARCHICAL'

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

Table S254.  Gene #25: 'amp_17q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 25(17Q23.1) MUTATED 62 45 71 25 13
AMP PEAK 25(17Q23.1) WILD-TYPE 39 107 43 63 45

Figure S254.  Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q23.1' versus 'CN_CNMF'

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

Table S255.  Gene #25: 'amp_17q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
AMP PEAK 25(17Q23.1) MUTATED 201 72 25 110 18
AMP PEAK 25(17Q23.1) WILD-TYPE 74 335 73 147 25

Figure S255.  Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q23.1' versus 'METHLYATION_CNMF'

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

Table S256.  Gene #25: 'amp_17q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
AMP PEAK 25(17Q23.1) MUTATED 97 42 46 36 53 17
AMP PEAK 25(17Q23.1) WILD-TYPE 47 57 167 87 82 42

Figure S256.  Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q23.1' versus 'RPPA_CHIERARCHICAL'

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

Table S257.  Gene #25: 'amp_17q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
AMP PEAK 25(17Q23.1) MUTATED 13 18 26 20 71 19
AMP PEAK 25(17Q23.1) WILD-TYPE 51 28 64 32 45 12

Figure S257.  Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q23.1' versus 'MRNASEQ_CNMF'

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

Table S258.  Gene #25: 'amp_17q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
AMP PEAK 25(17Q23.1) MUTATED 247 128 49
AMP PEAK 25(17Q23.1) WILD-TYPE 312 176 163

Figure S258.  Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q23.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S259.  Gene #25: 'amp_17q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 25(17Q23.1) MUTATED 127 99 14 95 60 29
AMP PEAK 25(17Q23.1) WILD-TYPE 162 64 76 195 123 31

Figure S259.  Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q23.1' versus 'MIRSEQ_CNMF'

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

Table S260.  Gene #25: 'amp_17q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
AMP PEAK 25(17Q23.1) MUTATED 150 47 92 129
AMP PEAK 25(17Q23.1) WILD-TYPE 155 165 177 146

Figure S260.  Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q23.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S261.  Gene #25: 'amp_17q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
AMP PEAK 25(17Q23.1) MUTATED 154 77 61 42 40 44
AMP PEAK 25(17Q23.1) WILD-TYPE 140 75 184 98 56 90

Figure S261.  Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 8.6e-05

Table S262.  Gene #25: 'amp_17q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 25(17Q23.1) MUTATED 88 58 26 27 47
AMP PEAK 25(17Q23.1) WILD-TYPE 92 81 73 84 86

Figure S262.  Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S263.  Gene #25: 'amp_17q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
AMP PEAK 25(17Q23.1) MUTATED 150 67 29
AMP PEAK 25(17Q23.1) WILD-TYPE 155 180 81

Figure S263.  Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.12' versus 'MRNA_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00018

Table S264.  Gene #26: 'amp_19p13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 26(19P13.12) MUTATED 5 6 22 40 16 11 5 4
AMP PEAK 26(19P13.12) WILD-TYPE 16 30 97 56 93 61 15 36

Figure S264.  Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19p13.12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.00041

Table S265.  Gene #26: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 26(19P13.12) MUTATED 19 21 23 35 11
AMP PEAK 26(19P13.12) WILD-TYPE 82 131 91 53 47

Figure S265.  Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19p13.12' versus 'CN_CNMF'

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

Table S266.  Gene #26: 'amp_19p13.12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
AMP PEAK 26(19P13.12) MUTATED 51 43 28 96 12
AMP PEAK 26(19P13.12) WILD-TYPE 224 364 70 161 31

Figure S266.  Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.12' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3e-05

Table S267.  Gene #26: 'amp_19p13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
AMP PEAK 26(19P13.12) MUTATED 25 20 27 27 51 8
AMP PEAK 26(19P13.12) WILD-TYPE 119 79 186 96 84 51

Figure S267.  Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.12' versus 'RPPA_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.0018

Table S268.  Gene #26: 'amp_19p13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
AMP PEAK 26(19P13.12) MUTATED 49 18 25
AMP PEAK 26(19P13.12) WILD-TYPE 102 105 100

Figure S268.  Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19p13.12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00429 (Fisher's exact test), Q value = 0.0052

Table S269.  Gene #26: 'amp_19p13.12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
AMP PEAK 26(19P13.12) MUTATED 12 10 35 6 22 7
AMP PEAK 26(19P13.12) WILD-TYPE 52 36 55 46 94 24

Figure S269.  Get High-res Image Gene #26: '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 S270.  Gene #26: 'amp_19p13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
AMP PEAK 26(19P13.12) MUTATED 91 103 33
AMP PEAK 26(19P13.12) WILD-TYPE 468 201 179

Figure S270.  Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19p13.12' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S271.  Gene #26: 'amp_19p13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 26(19P13.12) MUTATED 47 30 14 47 74 15
AMP PEAK 26(19P13.12) WILD-TYPE 242 133 76 243 109 45

Figure S271.  Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.12' versus 'MIRSEQ_CNMF'

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

Table S272.  Gene #26: 'amp_19p13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
AMP PEAK 26(19P13.12) MUTATED 99 35 47 43
AMP PEAK 26(19P13.12) WILD-TYPE 206 177 222 232

Figure S272.  Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19p13.12' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S273.  Gene #26: 'amp_19p13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
AMP PEAK 26(19P13.12) MUTATED 52 42 38 23 13 56
AMP PEAK 26(19P13.12) WILD-TYPE 242 110 207 117 83 78

Figure S273.  Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19p13.12' versus 'MIRSEQ_MATURE_CNMF'

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

Table S274.  Gene #26: 'amp_19p13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 26(19P13.12) MUTATED 27 54 16 27 18
AMP PEAK 26(19P13.12) WILD-TYPE 153 85 83 84 115

Figure S274.  Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'MRNA_CNMF'

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

Table S275.  Gene #27: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 27(19Q12) MUTATED 4 5 29 55 15 20 7 5
AMP PEAK 27(19Q12) WILD-TYPE 17 31 90 41 94 52 13 35

Figure S275.  Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q12' versus 'MRNA_CHIERARCHICAL'

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

Table S276.  Gene #27: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 27(19Q12) MUTATED 20 24 35 50 11
AMP PEAK 27(19Q12) WILD-TYPE 81 128 79 38 47

Figure S276.  Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

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

Table S277.  Gene #27: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
AMP PEAK 27(19Q12) MUTATED 57 45 29 139 14
AMP PEAK 27(19Q12) WILD-TYPE 218 362 69 118 29

Figure S277.  Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

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

Table S278.  Gene #27: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
AMP PEAK 27(19Q12) MUTATED 40 23 30 28 70 6
AMP PEAK 27(19Q12) WILD-TYPE 104 76 183 95 65 53

Figure S278.  Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19q12' versus 'RPPA_CNMF'

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

Table S279.  Gene #27: 'amp_19q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
AMP PEAK 27(19Q12) MUTATED 65 26 20
AMP PEAK 27(19Q12) WILD-TYPE 86 97 105

Figure S279.  Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19q12' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3e-05

Table S280.  Gene #27: 'amp_19q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
AMP PEAK 27(19Q12) MUTATED 15 11 46 10 19 10
AMP PEAK 27(19Q12) WILD-TYPE 49 35 44 42 97 21

Figure S280.  Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_19q12' versus 'MRNASEQ_CNMF'

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

Table S281.  Gene #27: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
AMP PEAK 27(19Q12) MUTATED 108 143 31
AMP PEAK 27(19Q12) WILD-TYPE 451 161 181

Figure S281.  Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S282.  Gene #27: '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 27(19Q12) MUTATED 52 44 12 47 104 23
AMP PEAK 27(19Q12) WILD-TYPE 237 119 78 243 79 37

Figure S282.  Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

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

Table S283.  Gene #27: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
AMP PEAK 27(19Q12) MUTATED 139 32 50 59
AMP PEAK 27(19Q12) WILD-TYPE 166 180 219 216

Figure S283.  Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S284.  Gene #27: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
AMP PEAK 27(19Q12) MUTATED 75 59 35 22 14 75
AMP PEAK 27(19Q12) WILD-TYPE 219 93 210 118 82 59

Figure S284.  Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CNMF'

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

Table S285.  Gene #27: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 27(19Q12) MUTATED 37 72 16 25 26
AMP PEAK 27(19Q12) WILD-TYPE 143 67 83 86 107

Figure S285.  Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00113 (Fisher's exact test), Q value = 0.0014

Table S286.  Gene #27: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
AMP PEAK 27(19Q12) MUTATED 102 52 22
AMP PEAK 27(19Q12) WILD-TYPE 203 195 88

Figure S286.  Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q13.42' versus 'MRNA_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.00064

Table S287.  Gene #28: 'amp_19q13.42' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 28(19Q13.42) MUTATED 5 8 36 40 17 20 10 6
AMP PEAK 28(19Q13.42) WILD-TYPE 16 28 83 56 92 52 10 34

Figure S287.  Get High-res Image Gene #28: 'amp_19q13.42' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q13.42' versus 'MRNA_CHIERARCHICAL'

P value = 0.00265 (Fisher's exact test), Q value = 0.0032

Table S288.  Gene #28: 'amp_19q13.42' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 28(19Q13.42) MUTATED 23 31 42 34 12
AMP PEAK 28(19Q13.42) WILD-TYPE 78 121 72 54 46

Figure S288.  Get High-res Image Gene #28: '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 S289.  Gene #28: 'amp_19q13.42' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
AMP PEAK 28(19Q13.42) MUTATED 79 45 29 105 18
AMP PEAK 28(19Q13.42) WILD-TYPE 196 362 69 152 25

Figure S289.  Get High-res Image Gene #28: '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 = 3e-05

Table S290.  Gene #28: 'amp_19q13.42' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
AMP PEAK 28(19Q13.42) MUTATED 52 26 34 22 44 8
AMP PEAK 28(19Q13.42) WILD-TYPE 92 73 179 101 91 51

Figure S290.  Get High-res Image Gene #28: 'amp_19q13.42' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19q13.42' versus 'RPPA_CNMF'

P value = 0.00505 (Fisher's exact test), Q value = 0.006

Table S291.  Gene #28: 'amp_19q13.42' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
AMP PEAK 28(19Q13.42) MUTATED 56 30 25
AMP PEAK 28(19Q13.42) WILD-TYPE 95 93 100

Figure S291.  Get High-res Image Gene #28: 'amp_19q13.42' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19q13.42' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00014

Table S292.  Gene #28: 'amp_19q13.42' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
AMP PEAK 28(19Q13.42) MUTATED 138 101 35
AMP PEAK 28(19Q13.42) WILD-TYPE 421 203 177

Figure S292.  Get High-res Image Gene #28: 'amp_19q13.42' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q13.42' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 8e-04

Table S293.  Gene #28: 'amp_19q13.42' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 28(19Q13.42) MUTATED 67 51 13 61 63 19
AMP PEAK 28(19Q13.42) WILD-TYPE 222 112 77 229 120 41

Figure S293.  Get High-res Image Gene #28: 'amp_19q13.42' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q13.42' versus 'MIRSEQ_CNMF'

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

Table S294.  Gene #28: 'amp_19q13.42' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
AMP PEAK 28(19Q13.42) MUTATED 108 35 61 68
AMP PEAK 28(19Q13.42) WILD-TYPE 197 177 208 207

Figure S294.  Get High-res Image Gene #28: 'amp_19q13.42' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19q13.42' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S295.  Gene #28: 'amp_19q13.42' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
AMP PEAK 28(19Q13.42) MUTATED 87 55 45 23 18 44
AMP PEAK 28(19Q13.42) WILD-TYPE 207 97 200 117 78 90

Figure S295.  Get High-res Image Gene #28: 'amp_19q13.42' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MRNA_CNMF'

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

Table S296.  Gene #29: 'amp_20q13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 29(20Q13.2) MUTATED 12 18 85 52 35 49 15 10
AMP PEAK 29(20Q13.2) WILD-TYPE 9 18 34 44 74 23 5 30

Figure S296.  Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q13.2' versus 'MRNA_CHIERARCHICAL'

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

Table S297.  Gene #29: 'amp_20q13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
AMP PEAK 29(20Q13.2) MUTATED 73 56 86 44 17
AMP PEAK 29(20Q13.2) WILD-TYPE 28 96 28 44 41

Figure S297.  Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q13.2' versus 'CN_CNMF'

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

Table S298.  Gene #29: 'amp_20q13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
AMP PEAK 29(20Q13.2) MUTATED 219 77 57 169 26
AMP PEAK 29(20Q13.2) WILD-TYPE 56 330 41 88 17

Figure S298.  Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.2' versus 'METHLYATION_CNMF'

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

Table S299.  Gene #29: 'amp_20q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
AMP PEAK 29(20Q13.2) MUTATED 112 56 63 46 80 16
AMP PEAK 29(20Q13.2) WILD-TYPE 32 43 150 77 55 43

Figure S299.  Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.2' versus 'RPPA_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.00056

Table S300.  Gene #29: 'amp_20q13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
AMP PEAK 29(20Q13.2) MUTATED 103 58 61
AMP PEAK 29(20Q13.2) WILD-TYPE 48 65 64

Figure S300.  Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 5e-04

Table S301.  Gene #29: 'amp_20q13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
AMP PEAK 29(20Q13.2) MUTATED 29 21 53 19 78 22
AMP PEAK 29(20Q13.2) WILD-TYPE 35 25 37 33 38 9

Figure S301.  Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20q13.2' versus 'MRNASEQ_CNMF'

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

Table S302.  Gene #29: 'amp_20q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
AMP PEAK 29(20Q13.2) MUTATED 310 178 57
AMP PEAK 29(20Q13.2) WILD-TYPE 249 126 155

Figure S302.  Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q13.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S303.  Gene #29: 'amp_20q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
AMP PEAK 29(20Q13.2) MUTATED 160 119 9 125 98 34
AMP PEAK 29(20Q13.2) WILD-TYPE 129 44 81 165 85 26

Figure S303.  Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_CNMF'

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

Table S304.  Gene #29: 'amp_20q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
AMP PEAK 29(20Q13.2) MUTATED 193 61 124 162
AMP PEAK 29(20Q13.2) WILD-TYPE 112 151 145 113

Figure S304.  Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q13.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S305.  Gene #29: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
AMP PEAK 29(20Q13.2) MUTATED 190 97 78 61 43 71
AMP PEAK 29(20Q13.2) WILD-TYPE 104 55 167 79 53 63

Figure S305.  Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_MATURE_CNMF'

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

Table S306.  Gene #29: 'amp_20q13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
AMP PEAK 29(20Q13.2) MUTATED 117 87 42 45 51
AMP PEAK 29(20Q13.2) WILD-TYPE 63 52 57 66 82

Figure S306.  Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S307.  Gene #29: 'amp_20q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
AMP PEAK 29(20Q13.2) MUTATED 188 103 51
AMP PEAK 29(20Q13.2) WILD-TYPE 117 144 59

Figure S307.  Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.13' versus 'MRNA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 9.9e-05

Table S308.  Gene #30: 'del_1p36.13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 1(1P36.13) MUTATED 9 11 61 42 31 46 7 12
DEL PEAK 1(1P36.13) WILD-TYPE 12 25 58 54 78 26 13 28

Figure S308.  Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.13' versus 'MRNA_CHIERARCHICAL'

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

Table S309.  Gene #30: 'del_1p36.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 1(1P36.13) MUTATED 57 39 67 39 17
DEL PEAK 1(1P36.13) WILD-TYPE 44 113 47 49 41

Figure S309.  Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.13' versus 'CN_CNMF'

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

Table S310.  Gene #30: 'del_1p36.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 1(1P36.13) MUTATED 172 65 63 134 18
DEL PEAK 1(1P36.13) WILD-TYPE 103 342 35 123 25

Figure S310.  Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.13' versus 'METHLYATION_CNMF'

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

Table S311.  Gene #30: 'del_1p36.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 1(1P36.13) MUTATED 85 60 54 36 57 19
DEL PEAK 1(1P36.13) WILD-TYPE 59 39 159 87 78 40

Figure S311.  Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.13' versus 'RPPA_CNMF'

P value = 0.00184 (Fisher's exact test), Q value = 0.0023

Table S312.  Gene #30: 'del_1p36.13' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 1(1P36.13) MUTATED 81 40 54
DEL PEAK 1(1P36.13) WILD-TYPE 70 83 71

Figure S312.  Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p36.13' versus 'RPPA_CHIERARCHICAL'

P value = 0.0135 (Fisher's exact test), Q value = 0.016

Table S313.  Gene #30: 'del_1p36.13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 1(1P36.13) MUTATED 24 12 41 19 61 18
DEL PEAK 1(1P36.13) WILD-TYPE 40 34 49 33 55 13

Figure S313.  Get High-res Image Gene #30: '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 S314.  Gene #30: 'del_1p36.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 1(1P36.13) MUTATED 261 134 54
DEL PEAK 1(1P36.13) WILD-TYPE 298 170 158

Figure S314.  Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.13' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S315.  Gene #30: 'del_1p36.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 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 S315.  Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.13' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3e-05

Table S316.  Gene #30: 'del_1p36.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 1(1P36.13) MUTATED 150 56 110 122
DEL PEAK 1(1P36.13) WILD-TYPE 155 156 159 153

Figure S316.  Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.13' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S317.  Gene #30: 'del_1p36.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 1(1P36.13) MUTATED 154 66 66 56 36 60
DEL PEAK 1(1P36.13) WILD-TYPE 140 86 179 84 60 74

Figure S317.  Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00228 (Fisher's exact test), Q value = 0.0028

Table S318.  Gene #30: 'del_1p36.13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 1(1P36.13) MUTATED 82 57 42 28 41
DEL PEAK 1(1P36.13) WILD-TYPE 98 82 57 83 92

Figure S318.  Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p22.1' versus 'MRNA_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.012

Table S319.  Gene #31: 'del_1p22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 2(1P22.1) MUTATED 8 12 49 23 35 38 7 11
DEL PEAK 2(1P22.1) WILD-TYPE 13 24 70 73 74 34 13 29

Figure S319.  Get High-res Image Gene #31: 'del_1p22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p22.1' versus 'MRNA_CHIERARCHICAL'

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

Table S320.  Gene #31: 'del_1p22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 2(1P22.1) MUTATED 49 40 62 18 14
DEL PEAK 2(1P22.1) WILD-TYPE 52 112 52 70 44

Figure S320.  Get High-res Image Gene #31: 'del_1p22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p22.1' versus 'CN_CNMF'

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

Table S321.  Gene #31: 'del_1p22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 2(1P22.1) MUTATED 146 64 59 81 12
DEL PEAK 2(1P22.1) WILD-TYPE 129 343 39 176 31

Figure S321.  Get High-res Image Gene #31: 'del_1p22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p22.1' versus 'METHLYATION_CNMF'

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

Table S322.  Gene #31: 'del_1p22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 2(1P22.1) MUTATED 70 47 49 28 33 17
DEL PEAK 2(1P22.1) WILD-TYPE 74 52 164 95 102 42

Figure S322.  Get High-res Image Gene #31: 'del_1p22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p22.1' versus 'RPPA_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.015

Table S323.  Gene #31: 'del_1p22.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 2(1P22.1) MUTATED 61 30 47
DEL PEAK 2(1P22.1) WILD-TYPE 90 93 78

Figure S323.  Get High-res Image Gene #31: 'del_1p22.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p22.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00674 (Fisher's exact test), Q value = 0.008

Table S324.  Gene #31: 'del_1p22.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 2(1P22.1) MUTATED 21 13 23 13 51 17
DEL PEAK 2(1P22.1) WILD-TYPE 43 33 67 39 65 14

Figure S324.  Get High-res Image Gene #31: 'del_1p22.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1p22.1' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4.5e-05

Table S325.  Gene #31: 'del_1p22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 2(1P22.1) MUTATED 221 87 51
DEL PEAK 2(1P22.1) WILD-TYPE 338 217 161

Figure S325.  Get High-res Image Gene #31: 'del_1p22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p22.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S326.  Gene #31: 'del_1p22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 2(1P22.1) MUTATED 104 96 15 90 38 16
DEL PEAK 2(1P22.1) WILD-TYPE 185 67 75 200 145 44

Figure S326.  Get High-res Image Gene #31: 'del_1p22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p22.1' versus 'MIRSEQ_CNMF'

P value = 0.00179 (Fisher's exact test), Q value = 0.0022

Table S327.  Gene #31: 'del_1p22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 2(1P22.1) MUTATED 98 50 96 109
DEL PEAK 2(1P22.1) WILD-TYPE 207 162 173 166

Figure S327.  Get High-res Image Gene #31: 'del_1p22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p22.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S328.  Gene #31: 'del_1p22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 2(1P22.1) MUTATED 135 50 63 51 28 26
DEL PEAK 2(1P22.1) WILD-TYPE 159 102 182 89 68 108

Figure S328.  Get High-res Image Gene #31: 'del_1p22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MRNA_CNMF'

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

Table S329.  Gene #32: 'del_2q37.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 3(2Q37.3) MUTATED 5 9 42 49 24 28 6 0
DEL PEAK 3(2Q37.3) WILD-TYPE 16 27 77 47 85 44 14 40

Figure S329.  Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_2q37.3' versus 'MRNA_CHIERARCHICAL'

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

Table S330.  Gene #32: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 3(2Q37.3) MUTATED 40 22 48 43 10
DEL PEAK 3(2Q37.3) WILD-TYPE 61 130 66 45 48

Figure S330.  Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

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

Table S331.  Gene #32: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 3(2Q37.3) MUTATED 105 46 26 126 14
DEL PEAK 3(2Q37.3) WILD-TYPE 170 361 72 131 29

Figure S331.  Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

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

Table S332.  Gene #32: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 3(2Q37.3) MUTATED 57 23 38 16 63 8
DEL PEAK 3(2Q37.3) WILD-TYPE 87 76 175 107 72 51

Figure S332.  Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q37.3' versus 'RPPA_CNMF'

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

Table S333.  Gene #32: 'del_2q37.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 3(2Q37.3) MUTATED 73 17 38
DEL PEAK 3(2Q37.3) WILD-TYPE 78 106 87

Figure S333.  Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_2q37.3' versus 'RPPA_CHIERARCHICAL'

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

Table S334.  Gene #32: 'del_2q37.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 3(2Q37.3) MUTATED 19 5 41 4 47 12
DEL PEAK 3(2Q37.3) WILD-TYPE 45 41 49 48 69 19

Figure S334.  Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_2q37.3' versus 'MRNASEQ_CNMF'

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

Table S335.  Gene #32: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 3(2Q37.3) MUTATED 156 136 22
DEL PEAK 3(2Q37.3) WILD-TYPE 403 168 190

Figure S335.  Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S336.  Gene #32: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 3(2Q37.3) MUTATED 87 71 10 44 88 14
DEL PEAK 3(2Q37.3) WILD-TYPE 202 92 80 246 95 46

Figure S336.  Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

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

Table S337.  Gene #32: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 3(2Q37.3) MUTATED 136 31 57 85
DEL PEAK 3(2Q37.3) WILD-TYPE 169 181 212 190

Figure S337.  Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S338.  Gene #32: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 3(2Q37.3) MUTATED 94 52 34 34 27 68
DEL PEAK 3(2Q37.3) WILD-TYPE 200 100 211 106 69 66

Figure S338.  Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_MATURE_CNMF'

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

Table S339.  Gene #32: 'del_2q37.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 3(2Q37.3) MUTATED 59 61 14 20 27
DEL PEAK 3(2Q37.3) WILD-TYPE 121 78 85 91 106

Figure S339.  Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_2q37.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 7.2e-05

Table S340.  Gene #32: 'del_2q37.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 3(2Q37.3) MUTATED 108 48 25
DEL PEAK 3(2Q37.3) WILD-TYPE 197 199 85

Figure S340.  Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p21.31' versus 'MRNA_CNMF'

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

Table S341.  Gene #33: 'del_3p21.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 4(3P21.31) MUTATED 5 15 38 52 8 35 9 7
DEL PEAK 4(3P21.31) WILD-TYPE 16 21 81 44 101 37 11 33

Figure S341.  Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p21.31' versus 'MRNA_CHIERARCHICAL'

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

Table S342.  Gene #33: 'del_3p21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 4(3P21.31) MUTATED 29 36 55 48 1
DEL PEAK 4(3P21.31) WILD-TYPE 72 116 59 40 57

Figure S342.  Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p21.31' versus 'CN_CNMF'

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

Table S343.  Gene #33: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 4(3P21.31) MUTATED 102 58 21 161 5
DEL PEAK 4(3P21.31) WILD-TYPE 173 349 77 96 38

Figure S343.  Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p21.31' versus 'METHLYATION_CNMF'

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

Table S344.  Gene #33: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 4(3P21.31) MUTATED 60 45 21 26 70 18
DEL PEAK 4(3P21.31) WILD-TYPE 84 54 192 97 65 41

Figure S344.  Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p21.31' versus 'RPPA_CNMF'

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

Table S345.  Gene #33: 'del_3p21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 4(3P21.31) MUTATED 82 38 24
DEL PEAK 4(3P21.31) WILD-TYPE 69 85 101

Figure S345.  Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p21.31' versus 'RPPA_CHIERARCHICAL'

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

Table S346.  Gene #33: 'del_3p21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 4(3P21.31) MUTATED 5 12 55 19 42 11
DEL PEAK 4(3P21.31) WILD-TYPE 59 34 35 33 74 20

Figure S346.  Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p21.31' versus 'MRNASEQ_CNMF'

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

Table S347.  Gene #33: 'del_3p21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 4(3P21.31) MUTATED 142 163 41
DEL PEAK 4(3P21.31) WILD-TYPE 417 141 171

Figure S347.  Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p21.31' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S348.  Gene #33: 'del_3p21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 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 S348.  Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_CNMF'

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

Table S349.  Gene #33: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 4(3P21.31) MUTATED 154 34 66 86
DEL PEAK 4(3P21.31) WILD-TYPE 151 178 203 189

Figure S349.  Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p21.31' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S350.  Gene #33: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 4(3P21.31) MUTATED 119 68 45 24 11 73
DEL PEAK 4(3P21.31) WILD-TYPE 175 84 200 116 85 61

Figure S350.  Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_MATURE_CNMF'

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

Table S351.  Gene #33: 'del_3p21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 4(3P21.31) MUTATED 54 80 22 21 36
DEL PEAK 4(3P21.31) WILD-TYPE 126 59 77 90 97

Figure S351.  Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00011

Table S352.  Gene #33: 'del_3p21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 4(3P21.31) MUTATED 123 67 23
DEL PEAK 4(3P21.31) WILD-TYPE 182 180 87

Figure S352.  Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p16.3' versus 'MRNA_CNMF'

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

Table S353.  Gene #34: 'del_4p16.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 5(4P16.3) MUTATED 3 10 25 58 22 38 7 6
DEL PEAK 5(4P16.3) WILD-TYPE 18 26 94 38 87 34 13 34

Figure S353.  Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4p16.3' versus 'MRNA_CHIERARCHICAL'

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

Table S354.  Gene #34: 'del_4p16.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 5(4P16.3) MUTATED 27 28 51 52 11
DEL PEAK 5(4P16.3) WILD-TYPE 74 124 63 36 47

Figure S354.  Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4p16.3' versus 'CN_CNMF'

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

Table S355.  Gene #34: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 5(4P16.3) MUTATED 74 52 44 158 11
DEL PEAK 5(4P16.3) WILD-TYPE 201 355 54 99 32

Figure S355.  Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

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

Table S356.  Gene #34: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 5(4P16.3) MUTATED 40 25 43 33 86 7
DEL PEAK 5(4P16.3) WILD-TYPE 104 74 170 90 49 52

Figure S356.  Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p16.3' versus 'RPPA_CNMF'

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

Table S357.  Gene #34: 'del_4p16.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 5(4P16.3) MUTATED 80 26 34
DEL PEAK 5(4P16.3) WILD-TYPE 71 97 91

Figure S357.  Get High-res Image Gene #34: '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 S358.  Gene #34: 'del_4p16.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 5(4P16.3) MUTATED 18 8 54 17 32 11
DEL PEAK 5(4P16.3) WILD-TYPE 46 38 36 35 84 20

Figure S358.  Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4p16.3' versus 'MRNASEQ_CNMF'

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

Table S359.  Gene #34: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 5(4P16.3) MUTATED 137 171 30
DEL PEAK 5(4P16.3) WILD-TYPE 422 133 182

Figure S359.  Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S360.  Gene #34: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 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 S360.  Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_CNMF'

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

Table S361.  Gene #34: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 5(4P16.3) MUTATED 157 38 49 84
DEL PEAK 5(4P16.3) WILD-TYPE 148 174 220 191

Figure S361.  Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S362.  Gene #34: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 5(4P16.3) MUTATED 89 64 34 42 15 84
DEL PEAK 5(4P16.3) WILD-TYPE 205 88 211 98 81 50

Figure S362.  Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

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

Table S363.  Gene #34: 'del_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 5(4P16.3) MUTATED 48 83 21 27 23
DEL PEAK 5(4P16.3) WILD-TYPE 132 56 78 84 110

Figure S363.  Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.00047

Table S364.  Gene #34: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 5(4P16.3) MUTATED 115 54 33
DEL PEAK 5(4P16.3) WILD-TYPE 190 193 77

Figure S364.  Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q35.1' versus 'MRNA_CNMF'

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

Table S365.  Gene #35: 'del_4q35.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 6(4Q35.1) MUTATED 6 9 25 54 24 34 9 9
DEL PEAK 6(4Q35.1) WILD-TYPE 15 27 94 42 85 38 11 31

Figure S365.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q35.1' versus 'MRNA_CHIERARCHICAL'

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

Table S366.  Gene #35: 'del_4q35.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 6(4Q35.1) MUTATED 25 31 52 49 13
DEL PEAK 6(4Q35.1) WILD-TYPE 76 121 62 39 45

Figure S366.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q35.1' versus 'CN_CNMF'

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

Table S367.  Gene #35: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 6(4Q35.1) MUTATED 66 53 48 165 13
DEL PEAK 6(4Q35.1) WILD-TYPE 209 354 50 92 30

Figure S367.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q35.1' versus 'METHLYATION_CNMF'

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

Table S368.  Gene #35: 'del_4q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 6(4Q35.1) MUTATED 31 24 44 44 84 8
DEL PEAK 6(4Q35.1) WILD-TYPE 113 75 169 79 51 51

Figure S368.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q35.1' versus 'RPPA_CNMF'

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

Table S369.  Gene #35: 'del_4q35.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 6(4Q35.1) MUTATED 82 28 30
DEL PEAK 6(4Q35.1) WILD-TYPE 69 95 95

Figure S369.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4q35.1' versus 'RPPA_CHIERARCHICAL'

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

Table S370.  Gene #35: 'del_4q35.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 6(4Q35.1) MUTATED 15 11 54 15 34 11
DEL PEAK 6(4Q35.1) WILD-TYPE 49 35 36 37 82 20

Figure S370.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4q35.1' versus 'MRNASEQ_CNMF'

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

Table S371.  Gene #35: 'del_4q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 6(4Q35.1) MUTATED 143 171 30
DEL PEAK 6(4Q35.1) WILD-TYPE 416 133 182

Figure S371.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q35.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S372.  Gene #35: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 6(4Q35.1) MUTATED 61 67 9 67 116 24
DEL PEAK 6(4Q35.1) WILD-TYPE 228 96 81 223 67 36

Figure S372.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MIRSEQ_CNMF'

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

Table S373.  Gene #35: 'del_4q35.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 6(4Q35.1) MUTATED 159 38 51 85
DEL PEAK 6(4Q35.1) WILD-TYPE 146 174 218 190

Figure S373.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q35.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S374.  Gene #35: 'del_4q35.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 6(4Q35.1) MUTATED 82 69 36 45 14 87
DEL PEAK 6(4Q35.1) WILD-TYPE 212 83 209 95 82 47

Figure S374.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MIRSEQ_MATURE_CNMF'

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

Table S375.  Gene #35: 'del_4q35.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 6(4Q35.1) MUTATED 50 86 23 26 22
DEL PEAK 6(4Q35.1) WILD-TYPE 130 53 76 85 111

Figure S375.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q35.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 9e-04

Table S376.  Gene #35: 'del_4q35.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 6(4Q35.1) MUTATED 116 57 34
DEL PEAK 6(4Q35.1) WILD-TYPE 189 190 76

Figure S376.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q11.2' versus 'MRNA_CNMF'

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

Table S377.  Gene #36: 'del_5q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 7(5Q11.2) MUTATED 3 5 19 69 7 26 3 4
DEL PEAK 7(5Q11.2) WILD-TYPE 18 31 100 27 102 46 17 36

Figure S377.  Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q11.2' versus 'MRNA_CHIERARCHICAL'

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

Table S378.  Gene #36: 'del_5q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 7(5Q11.2) MUTATED 18 15 38 63 2
DEL PEAK 7(5Q11.2) WILD-TYPE 83 137 76 25 56

Figure S378.  Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q11.2' versus 'CN_CNMF'

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

Table S379.  Gene #36: 'del_5q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 7(5Q11.2) MUTATED 43 35 8 185 9
DEL PEAK 7(5Q11.2) WILD-TYPE 232 372 90 72 34

Figure S379.  Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q11.2' versus 'METHLYATION_CNMF'

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

Table S380.  Gene #36: 'del_5q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 7(5Q11.2) MUTATED 31 13 11 34 101 7
DEL PEAK 7(5Q11.2) WILD-TYPE 113 86 202 89 34 52

Figure S380.  Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q11.2' versus 'RPPA_CNMF'

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

Table S381.  Gene #36: 'del_5q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 7(5Q11.2) MUTATED 79 25 11
DEL PEAK 7(5Q11.2) WILD-TYPE 72 98 114

Figure S381.  Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_5q11.2' versus 'RPPA_CHIERARCHICAL'

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

Table S382.  Gene #36: 'del_5q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 7(5Q11.2) MUTATED 4 3 64 10 24 10
DEL PEAK 7(5Q11.2) WILD-TYPE 60 43 26 42 92 21

Figure S382.  Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_5q11.2' versus 'MRNASEQ_CNMF'

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

Table S383.  Gene #36: 'del_5q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 7(5Q11.2) MUTATED 80 182 16
DEL PEAK 7(5Q11.2) WILD-TYPE 479 122 196

Figure S383.  Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q11.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S384.  Gene #36: 'del_5q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 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 S384.  Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_CNMF'

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

Table S385.  Gene #36: 'del_5q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 7(5Q11.2) MUTATED 166 24 24 54
DEL PEAK 7(5Q11.2) WILD-TYPE 139 188 245 221

Figure S385.  Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q11.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S386.  Gene #36: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 7(5Q11.2) MUTATED 64 65 20 7 6 106
DEL PEAK 7(5Q11.2) WILD-TYPE 230 87 225 133 90 28

Figure S386.  Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_MATURE_CNMF'

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

Table S387.  Gene #36: 'del_5q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 7(5Q11.2) MUTATED 26 98 12 15 20
DEL PEAK 7(5Q11.2) WILD-TYPE 154 41 87 96 113

Figure S387.  Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S388.  Gene #36: 'del_5q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 7(5Q11.2) MUTATED 125 31 15
DEL PEAK 7(5Q11.2) WILD-TYPE 180 216 95

Figure S388.  Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q21.3' versus 'MRNA_CNMF'

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

Table S389.  Gene #37: 'del_5q21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 8(5Q21.3) MUTATED 2 5 19 71 7 24 5 2
DEL PEAK 8(5Q21.3) WILD-TYPE 19 31 100 25 102 48 15 38

Figure S389.  Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q21.3' versus 'MRNA_CHIERARCHICAL'

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

Table S390.  Gene #37: 'del_5q21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 8(5Q21.3) MUTATED 18 13 36 66 2
DEL PEAK 8(5Q21.3) WILD-TYPE 83 139 78 22 56

Figure S390.  Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q21.3' versus 'CN_CNMF'

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

Table S391.  Gene #37: 'del_5q21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 8(5Q21.3) MUTATED 38 26 8 192 8
DEL PEAK 8(5Q21.3) WILD-TYPE 237 381 90 65 35

Figure S391.  Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q21.3' versus 'METHLYATION_CNMF'

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

Table S392.  Gene #37: 'del_5q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 8(5Q21.3) MUTATED 27 13 7 31 108 6
DEL PEAK 8(5Q21.3) WILD-TYPE 117 86 206 92 27 53

Figure S392.  Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q21.3' versus 'RPPA_CNMF'

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

Table S393.  Gene #37: 'del_5q21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 8(5Q21.3) MUTATED 77 25 11
DEL PEAK 8(5Q21.3) WILD-TYPE 74 98 114

Figure S393.  Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_5q21.3' versus 'RPPA_CHIERARCHICAL'

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

Table S394.  Gene #37: 'del_5q21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 8(5Q21.3) MUTATED 5 4 62 11 22 9
DEL PEAK 8(5Q21.3) WILD-TYPE 59 42 28 41 94 22

Figure S394.  Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_5q21.3' versus 'MRNASEQ_CNMF'

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

Table S395.  Gene #37: 'del_5q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 8(5Q21.3) MUTATED 69 188 13
DEL PEAK 8(5Q21.3) WILD-TYPE 490 116 199

Figure S395.  Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q21.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S396.  Gene #37: 'del_5q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 8(5Q21.3) MUTATED 34 40 1 29 142 24
DEL PEAK 8(5Q21.3) WILD-TYPE 255 123 89 261 41 36

Figure S396.  Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q21.3' versus 'MIRSEQ_CNMF'

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

Table S397.  Gene #37: 'del_5q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 8(5Q21.3) MUTATED 171 21 23 47
DEL PEAK 8(5Q21.3) WILD-TYPE 134 191 246 228

Figure S397.  Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q21.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S398.  Gene #37: 'del_5q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 8(5Q21.3) MUTATED 61 67 13 8 4 109
DEL PEAK 8(5Q21.3) WILD-TYPE 233 85 232 132 92 25

Figure S398.  Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q21.3' versus 'MIRSEQ_MATURE_CNMF'

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

Table S399.  Gene #37: 'del_5q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 8(5Q21.3) MUTATED 22 101 12 12 18
DEL PEAK 8(5Q21.3) WILD-TYPE 158 38 87 99 115

Figure S399.  Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S400.  Gene #37: 'del_5q21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 8(5Q21.3) MUTATED 124 30 11
DEL PEAK 8(5Q21.3) WILD-TYPE 181 217 99

Figure S400.  Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

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

Table S401.  Gene #38: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 9(6P25.3) MUTATED 81 40 15 57 11
DEL PEAK 9(6P25.3) WILD-TYPE 194 367 83 200 32

Figure S401.  Get High-res Image Gene #38: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 0.00088 (Fisher's exact test), Q value = 0.0011

Table S402.  Gene #38: 'del_6p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 9(6P25.3) MUTATED 40 18 30 16 37 7
DEL PEAK 9(6P25.3) WILD-TYPE 104 81 183 107 98 52

Figure S402.  Get High-res Image Gene #38: 'del_6p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.00053

Table S403.  Gene #38: 'del_6p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 9(6P25.3) MUTATED 119 63 21
DEL PEAK 9(6P25.3) WILD-TYPE 440 241 191

Figure S403.  Get High-res Image Gene #38: 'del_6p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6p25.3' versus 'MIRSEQ_CNMF'

P value = 0.0042 (Fisher's exact test), Q value = 0.0051

Table S404.  Gene #38: 'del_6p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 9(6P25.3) MUTATED 66 24 47 63
DEL PEAK 9(6P25.3) WILD-TYPE 239 188 222 212

Figure S404.  Get High-res Image Gene #38: 'del_6p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0441 (Fisher's exact test), Q value = 0.049

Table S405.  Gene #38: 'del_6p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 9(6P25.3) MUTATED 65 31 31 24 17 32
DEL PEAK 9(6P25.3) WILD-TYPE 229 121 214 116 79 102

Figure S405.  Get High-res Image Gene #38: 'del_6p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q15' versus 'MRNA_CNMF'

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

Table S406.  Gene #39: 'del_6q15' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 10(6Q15) MUTATED 6 13 63 20 24 29 4 16
DEL PEAK 10(6Q15) WILD-TYPE 15 23 56 76 85 43 16 24

Figure S406.  Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_6q15' versus 'MRNA_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.00045

Table S407.  Gene #39: 'del_6q15' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 10(6Q15) MUTATED 50 51 42 18 14
DEL PEAK 10(6Q15) WILD-TYPE 51 101 72 70 44

Figure S407.  Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_6q15' versus 'CN_CNMF'

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

Table S408.  Gene #39: 'del_6q15' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 10(6Q15) MUTATED 169 90 25 50 24
DEL PEAK 10(6Q15) WILD-TYPE 106 317 73 207 19

Figure S408.  Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q15' versus 'METHLYATION_CNMF'

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

Table S409.  Gene #39: 'del_6q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 10(6Q15) MUTATED 76 33 75 22 25 16
DEL PEAK 10(6Q15) WILD-TYPE 68 66 138 101 110 43

Figure S409.  Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q15' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3e-05

Table S410.  Gene #39: 'del_6q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 10(6Q15) MUTATED 225 74 58
DEL PEAK 10(6Q15) WILD-TYPE 334 230 154

Figure S410.  Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q15' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S411.  Gene #39: '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 S411.  Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q15' versus 'MIRSEQ_CNMF'

P value = 0.00922 (Fisher's exact test), Q value = 0.011

Table S412.  Gene #39: 'del_6q15' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 10(6Q15) MUTATED 97 56 90 112
DEL PEAK 10(6Q15) WILD-TYPE 208 156 179 163

Figure S412.  Get High-res Image Gene #39: '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 S413.  Gene #39: 'del_6q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 10(6Q15) MUTATED 119 41 72 57 43 23
DEL PEAK 10(6Q15) WILD-TYPE 175 111 173 83 53 111

Figure S413.  Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q15' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00021

Table S414.  Gene #39: 'del_6q15' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 10(6Q15) MUTATED 76 25 33 38 47
DEL PEAK 10(6Q15) WILD-TYPE 104 114 66 73 86

Figure S414.  Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6q27' versus 'MRNA_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.026

Table S415.  Gene #40: 'del_6q27' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 11(6Q27) MUTATED 9 13 57 34 25 27 7 14
DEL PEAK 11(6Q27) WILD-TYPE 12 23 62 62 84 45 13 26

Figure S415.  Get High-res Image Gene #40: 'del_6q27' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_6q27' versus 'MRNA_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.012

Table S416.  Gene #40: 'del_6q27' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 11(6Q27) MUTATED 48 47 46 32 13
DEL PEAK 11(6Q27) WILD-TYPE 53 105 68 56 45

Figure S416.  Get High-res Image Gene #40: 'del_6q27' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_6q27' versus 'CN_CNMF'

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

Table S417.  Gene #40: 'del_6q27' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 11(6Q27) MUTATED 141 98 25 87 24
DEL PEAK 11(6Q27) WILD-TYPE 134 309 73 170 19

Figure S417.  Get High-res Image Gene #40: 'del_6q27' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q27' versus 'METHLYATION_CNMF'

P value = 0.00984 (Fisher's exact test), Q value = 0.011

Table S418.  Gene #40: 'del_6q27' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 11(6Q27) MUTATED 66 27 65 35 53 19
DEL PEAK 11(6Q27) WILD-TYPE 78 72 148 88 82 40

Figure S418.  Get High-res Image Gene #40: 'del_6q27' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q27' versus 'RPPA_CNMF'

P value = 0.0319 (Fisher's exact test), Q value = 0.036

Table S419.  Gene #40: 'del_6q27' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 11(6Q27) MUTATED 68 39 40
DEL PEAK 11(6Q27) WILD-TYPE 83 84 85

Figure S419.  Get High-res Image Gene #40: 'del_6q27' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_6q27' versus 'MRNASEQ_CNMF'

P value = 0.0457 (Fisher's exact test), Q value = 0.051

Table S420.  Gene #40: 'del_6q27' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 11(6Q27) MUTATED 198 116 59
DEL PEAK 11(6Q27) WILD-TYPE 361 188 153

Figure S420.  Get High-res Image Gene #40: 'del_6q27' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q27' versus 'MIRSEQ_CNMF'

P value = 0.00641 (Fisher's exact test), Q value = 0.0076

Table S421.  Gene #40: 'del_6q27' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 11(6Q27) MUTATED 128 58 89 94
DEL PEAK 11(6Q27) WILD-TYPE 177 154 180 181

Figure S421.  Get High-res Image Gene #40: 'del_6q27' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_7p22.3' versus 'MRNA_CNMF'

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

Table S422.  Gene #41: 'del_7p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 12(7P22.3) MUTATED 4 3 24 25 2 12 2 4
DEL PEAK 12(7P22.3) WILD-TYPE 17 33 95 71 107 60 18 36

Figure S422.  Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_7p22.3' versus 'MRNA_CHIERARCHICAL'

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

Table S423.  Gene #41: 'del_7p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 12(7P22.3) MUTATED 20 8 22 24 2
DEL PEAK 12(7P22.3) WILD-TYPE 81 144 92 64 56

Figure S423.  Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_7p22.3' versus 'CN_CNMF'

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

Table S424.  Gene #41: 'del_7p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 12(7P22.3) MUTATED 55 12 3 65 2
DEL PEAK 12(7P22.3) WILD-TYPE 220 395 95 192 41

Figure S424.  Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_7p22.3' versus 'METHLYATION_CNMF'

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

Table S425.  Gene #41: 'del_7p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 12(7P22.3) MUTATED 17 15 11 5 31 2
DEL PEAK 12(7P22.3) WILD-TYPE 127 84 202 118 104 57

Figure S425.  Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_7p22.3' versus 'RPPA_CNMF'

P value = 0.00144 (Fisher's exact test), Q value = 0.0018

Table S426.  Gene #41: 'del_7p22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 12(7P22.3) MUTATED 34 10 13
DEL PEAK 12(7P22.3) WILD-TYPE 117 113 112

Figure S426.  Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_7p22.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00469 (Fisher's exact test), Q value = 0.0056

Table S427.  Gene #41: 'del_7p22.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 12(7P22.3) MUTATED 5 2 23 4 19 4
DEL PEAK 12(7P22.3) WILD-TYPE 59 44 67 48 97 27

Figure S427.  Get High-res Image Gene #41: '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 S428.  Gene #41: 'del_7p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 12(7P22.3) MUTATED 63 68 4
DEL PEAK 12(7P22.3) WILD-TYPE 496 236 208

Figure S428.  Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7p22.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S429.  Gene #41: 'del_7p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 12(7P22.3) MUTATED 35 28 0 19 48 5
DEL PEAK 12(7P22.3) WILD-TYPE 254 135 90 271 135 55

Figure S429.  Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7p22.3' versus 'MIRSEQ_CNMF'

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

Table S430.  Gene #41: 'del_7p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 12(7P22.3) MUTATED 68 4 26 35
DEL PEAK 12(7P22.3) WILD-TYPE 237 208 243 240

Figure S430.  Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_7p22.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S431.  Gene #41: 'del_7p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 12(7P22.3) MUTATED 47 25 4 9 9 39
DEL PEAK 12(7P22.3) WILD-TYPE 247 127 241 131 87 95

Figure S431.  Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7p22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3e-05

Table S432.  Gene #41: 'del_7p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 12(7P22.3) MUTATED 18 34 6 6 11
DEL PEAK 12(7P22.3) WILD-TYPE 162 105 93 105 122

Figure S432.  Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 5.9e-05

Table S433.  Gene #41: 'del_7p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 12(7P22.3) MUTATED 53 16 6
DEL PEAK 12(7P22.3) WILD-TYPE 252 231 104

Figure S433.  Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q36.1' versus 'MRNA_CNMF'

P value = 0.00258 (Fisher's exact test), Q value = 0.0032

Table S434.  Gene #42: 'del_7q36.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 13(7Q36.1) MUTATED 6 7 22 21 10 26 4 6
DEL PEAK 13(7Q36.1) WILD-TYPE 15 29 97 75 99 46 16 34

Figure S434.  Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_7q36.1' versus 'MRNA_CHIERARCHICAL'

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

Table S435.  Gene #42: 'del_7q36.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 13(7Q36.1) MUTATED 16 17 45 17 7
DEL PEAK 13(7Q36.1) WILD-TYPE 85 135 69 71 51

Figure S435.  Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_7q36.1' versus 'CN_CNMF'

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

Table S436.  Gene #42: 'del_7q36.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 13(7Q36.1) MUTATED 72 33 15 74 6
DEL PEAK 13(7Q36.1) WILD-TYPE 203 374 83 183 37

Figure S436.  Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_7q36.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3e-05

Table S437.  Gene #42: 'del_7q36.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 13(7Q36.1) MUTATED 99 81 18
DEL PEAK 13(7Q36.1) WILD-TYPE 460 223 194

Figure S437.  Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7q36.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S438.  Gene #42: 'del_7q36.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 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 S438.  Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7q36.1' versus 'MIRSEQ_CNMF'

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

Table S439.  Gene #42: 'del_7q36.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 13(7Q36.1) MUTATED 83 17 37 58
DEL PEAK 13(7Q36.1) WILD-TYPE 222 195 232 217

Figure S439.  Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_7q36.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S440.  Gene #42: 'del_7q36.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 13(7Q36.1) MUTATED 66 46 19 18 15 31
DEL PEAK 13(7Q36.1) WILD-TYPE 228 106 226 122 81 103

Figure S440.  Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7q36.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 9.9e-05

Table S441.  Gene #42: 'del_7q36.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 13(7Q36.1) MUTATED 41 39 9 11 17
DEL PEAK 13(7Q36.1) WILD-TYPE 139 100 90 100 116

Figure S441.  Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7q36.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S442.  Gene #42: 'del_7q36.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 13(7Q36.1) MUTATED 76 21 20
DEL PEAK 13(7Q36.1) WILD-TYPE 229 226 90

Figure S442.  Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'MRNA_CNMF'

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

Table S443.  Gene #43: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 14(8P23.2) MUTATED 12 15 78 64 29 47 13 18
DEL PEAK 14(8P23.2) WILD-TYPE 9 21 41 32 80 25 7 22

Figure S443.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p23.2' versus 'MRNA_CHIERARCHICAL'

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

Table S444.  Gene #43: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 14(8P23.2) MUTATED 67 59 78 57 15
DEL PEAK 14(8P23.2) WILD-TYPE 34 93 36 31 43

Figure S444.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

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

Table S445.  Gene #43: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 14(8P23.2) MUTATED 188 134 22 180 34
DEL PEAK 14(8P23.2) WILD-TYPE 87 273 76 77 9

Figure S445.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

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

Table S446.  Gene #43: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 14(8P23.2) MUTATED 92 51 72 57 86 23
DEL PEAK 14(8P23.2) WILD-TYPE 52 48 141 66 49 36

Figure S446.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.2' versus 'RPPA_CNMF'

P value = 0.00394 (Fisher's exact test), Q value = 0.0048

Table S447.  Gene #43: 'del_8p23.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 14(8P23.2) MUTATED 99 70 57
DEL PEAK 14(8P23.2) WILD-TYPE 52 53 68

Figure S447.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_8p23.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00088 (Fisher's exact test), Q value = 0.0011

Table S448.  Gene #43: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 14(8P23.2) MUTATED 22 21 58 32 71 22
DEL PEAK 14(8P23.2) WILD-TYPE 42 25 32 20 45 9

Figure S448.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_8p23.2' versus 'MRNASEQ_CNMF'

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

Table S449.  Gene #43: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 14(8P23.2) MUTATED 280 201 73
DEL PEAK 14(8P23.2) WILD-TYPE 279 103 139

Figure S449.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S450.  Gene #43: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 14(8P23.2) MUTATED 146 109 25 114 113 47
DEL PEAK 14(8P23.2) WILD-TYPE 143 54 65 176 70 13

Figure S450.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

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

Table S451.  Gene #43: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 14(8P23.2) MUTATED 200 79 116 151
DEL PEAK 14(8P23.2) WILD-TYPE 105 133 153 124

Figure S451.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S452.  Gene #43: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 14(8P23.2) MUTATED 168 103 97 50 45 83
DEL PEAK 14(8P23.2) WILD-TYPE 126 49 148 90 51 51

Figure S452.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

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

Table S453.  Gene #43: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 14(8P23.2) MUTATED 100 92 43 39 58
DEL PEAK 14(8P23.2) WILD-TYPE 80 47 56 72 75

Figure S453.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S454.  Gene #43: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 14(8P23.2) MUTATED 187 105 40
DEL PEAK 14(8P23.2) WILD-TYPE 118 142 70

Figure S454.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p11.21' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 5.9e-05

Table S455.  Gene #44: 'del_8p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 15(8P11.21) MUTATED 4 3 22 24 8 26 7 7
DEL PEAK 15(8P11.21) WILD-TYPE 17 33 97 72 101 46 13 33

Figure S455.  Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p11.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00023

Table S456.  Gene #44: 'del_8p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 15(8P11.21) MUTATED 20 18 37 21 5
DEL PEAK 15(8P11.21) WILD-TYPE 81 134 77 67 53

Figure S456.  Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p11.21' versus 'CN_CNMF'

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

Table S457.  Gene #44: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 15(8P11.21) MUTATED 62 45 14 79 0
DEL PEAK 15(8P11.21) WILD-TYPE 213 362 84 178 43

Figure S457.  Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p11.21' versus 'METHLYATION_CNMF'

P value = 0.00116 (Fisher's exact test), Q value = 0.0015

Table S458.  Gene #44: 'del_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 15(8P11.21) MUTATED 32 20 18 22 29 6
DEL PEAK 15(8P11.21) WILD-TYPE 112 79 195 101 106 53

Figure S458.  Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p11.21' versus 'RPPA_CNMF'

P value = 0.0261 (Fisher's exact test), Q value = 0.03

Table S459.  Gene #44: 'del_8p11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 15(8P11.21) MUTATED 42 26 18
DEL PEAK 15(8P11.21) WILD-TYPE 109 97 107

Figure S459.  Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_8p11.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.00056

Table S460.  Gene #44: 'del_8p11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 15(8P11.21) MUTATED 5 9 21 10 25 16
DEL PEAK 15(8P11.21) WILD-TYPE 59 37 69 42 91 15

Figure S460.  Get High-res Image Gene #44: '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 S461.  Gene #44: 'del_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 15(8P11.21) MUTATED 93 83 24
DEL PEAK 15(8P11.21) WILD-TYPE 466 221 188

Figure S461.  Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p11.21' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S462.  Gene #44: 'del_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 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 S462.  Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p11.21' versus 'MIRSEQ_CNMF'

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

Table S463.  Gene #44: 'del_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 15(8P11.21) MUTATED 78 21 33 66
DEL PEAK 15(8P11.21) WILD-TYPE 227 191 236 209

Figure S463.  Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p11.21' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S464.  Gene #44: 'del_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 15(8P11.21) MUTATED 64 57 19 24 12 22
DEL PEAK 15(8P11.21) WILD-TYPE 230 95 226 116 84 112

Figure S464.  Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00262 (Fisher's exact test), Q value = 0.0032

Table S465.  Gene #44: 'del_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 15(8P11.21) MUTATED 48 32 15 14 16
DEL PEAK 15(8P11.21) WILD-TYPE 132 107 84 97 117

Figure S465.  Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.00058

Table S466.  Gene #44: 'del_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 15(8P11.21) MUTATED 77 31 17
DEL PEAK 15(8P11.21) WILD-TYPE 228 216 93

Figure S466.  Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'MRNA_CNMF'

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

Table S467.  Gene #45: 'del_9p23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 16(9P23) MUTATED 9 15 57 21 22 34 10 5
DEL PEAK 16(9P23) WILD-TYPE 12 21 62 75 87 38 10 35

Figure S467.  Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p23' versus 'MRNA_CHIERARCHICAL'

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

Table S468.  Gene #45: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 16(9P23) MUTATED 49 36 61 17 10
DEL PEAK 16(9P23) WILD-TYPE 52 116 53 71 48

Figure S468.  Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

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

Table S469.  Gene #45: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 16(9P23) MUTATED 167 46 15 88 9
DEL PEAK 16(9P23) WILD-TYPE 108 361 83 169 34

Figure S469.  Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

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

Table S470.  Gene #45: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 16(9P23) MUTATED 80 42 28 22 36 9
DEL PEAK 16(9P23) WILD-TYPE 64 57 185 101 99 50

Figure S470.  Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p23' versus 'RPPA_CNMF'

P value = 0.0069 (Fisher's exact test), Q value = 0.0081

Table S471.  Gene #45: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 16(9P23) MUTATED 68 35 38
DEL PEAK 16(9P23) WILD-TYPE 83 88 87

Figure S471.  Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p23' versus 'RPPA_CHIERARCHICAL'

P value = 0.00612 (Fisher's exact test), Q value = 0.0073

Table S472.  Gene #45: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 16(9P23) MUTATED 15 15 26 15 55 15
DEL PEAK 16(9P23) WILD-TYPE 49 31 64 37 61 16

Figure S472.  Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p23' versus 'MRNASEQ_CNMF'

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

Table S473.  Gene #45: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 16(9P23) MUTATED 195 95 34
DEL PEAK 16(9P23) WILD-TYPE 364 209 178

Figure S473.  Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S474.  Gene #45: '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 S474.  Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

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

Table S475.  Gene #45: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 16(9P23) MUTATED 112 31 68 107
DEL PEAK 16(9P23) WILD-TYPE 193 181 201 168

Figure S475.  Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S476.  Gene #45: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 16(9P23) MUTATED 132 69 39 32 24 22
DEL PEAK 16(9P23) WILD-TYPE 162 83 206 108 72 112

Figure S476.  Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.00039

Table S477.  Gene #45: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 16(9P23) MUTATED 74 39 23 20 33
DEL PEAK 16(9P23) WILD-TYPE 106 100 76 91 100

Figure S477.  Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00018

Table S478.  Gene #45: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 16(9P23) MUTATED 112 56 21
DEL PEAK 16(9P23) WILD-TYPE 193 191 89

Figure S478.  Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'MRNA_CNMF'

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

Table S479.  Gene #46: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 17(9P21.3) MUTATED 9 12 62 33 24 38 8 6
DEL PEAK 17(9P21.3) WILD-TYPE 12 24 57 63 85 34 12 34

Figure S479.  Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p21.3' versus 'MRNA_CHIERARCHICAL'

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

Table S480.  Gene #46: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 17(9P21.3) MUTATED 53 34 65 28 12
DEL PEAK 17(9P21.3) WILD-TYPE 48 118 49 60 46

Figure S480.  Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

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

Table S481.  Gene #46: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 17(9P21.3) MUTATED 170 54 19 112 9
DEL PEAK 17(9P21.3) WILD-TYPE 105 353 79 145 34

Figure S481.  Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

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

Table S482.  Gene #46: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 17(9P21.3) MUTATED 77 42 33 25 51 9
DEL PEAK 17(9P21.3) WILD-TYPE 67 57 180 98 84 50

Figure S482.  Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 0.00273 (Fisher's exact test), Q value = 0.0033

Table S483.  Gene #46: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 17(9P21.3) MUTATED 75 40 40
DEL PEAK 17(9P21.3) WILD-TYPE 76 83 85

Figure S483.  Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0273 (Fisher's exact test), Q value = 0.031

Table S484.  Gene #46: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 17(9P21.3) MUTATED 17 15 34 17 55 17
DEL PEAK 17(9P21.3) WILD-TYPE 47 31 56 35 61 14

Figure S484.  Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

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

Table S485.  Gene #46: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 17(9P21.3) MUTATED 205 123 32
DEL PEAK 17(9P21.3) WILD-TYPE 354 181 180

Figure S485.  Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S486.  Gene #46: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 17(9P21.3) MUTATED 113 88 6 62 60 31
DEL PEAK 17(9P21.3) WILD-TYPE 176 75 84 228 123 29

Figure S486.  Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

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

Table S487.  Gene #46: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 17(9P21.3) MUTATED 132 34 73 115
DEL PEAK 17(9P21.3) WILD-TYPE 173 178 196 160

Figure S487.  Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S488.  Gene #46: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 17(9P21.3) MUTATED 137 80 36 34 28 39
DEL PEAK 17(9P21.3) WILD-TYPE 157 72 209 106 68 95

Figure S488.  Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 9.9e-05

Table S489.  Gene #46: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 17(9P21.3) MUTATED 76 54 24 25 30
DEL PEAK 17(9P21.3) WILD-TYPE 104 85 75 86 103

Figure S489.  Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S490.  Gene #46: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 17(9P21.3) MUTATED 128 58 23
DEL PEAK 17(9P21.3) WILD-TYPE 177 189 87

Figure S490.  Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q21.11' versus 'MRNA_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.0013

Table S491.  Gene #47: 'del_9q21.11' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 18(9Q21.11) MUTATED 5 6 42 41 24 27 7 5
DEL PEAK 18(9Q21.11) WILD-TYPE 16 30 77 55 85 45 13 35

Figure S491.  Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9q21.11' versus 'MRNA_CHIERARCHICAL'

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

Table S492.  Gene #47: 'del_9q21.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 18(9Q21.11) MUTATED 37 25 50 35 10
DEL PEAK 18(9Q21.11) WILD-TYPE 64 127 64 53 48

Figure S492.  Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9q21.11' versus 'CN_CNMF'

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

Table S493.  Gene #47: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 18(9Q21.11) MUTATED 115 44 18 105 12
DEL PEAK 18(9Q21.11) WILD-TYPE 160 363 80 152 31

Figure S493.  Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q21.11' versus 'METHLYATION_CNMF'

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

Table S494.  Gene #47: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 18(9Q21.11) MUTATED 58 23 27 26 53 5
DEL PEAK 18(9Q21.11) WILD-TYPE 86 76 186 97 82 54

Figure S494.  Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q21.11' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3e-05

Table S495.  Gene #47: 'del_9q21.11' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 18(9Q21.11) MUTATED 70 26 29
DEL PEAK 18(9Q21.11) WILD-TYPE 81 97 96

Figure S495.  Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9q21.11' versus 'RPPA_CHIERARCHICAL'

P value = 0.0204 (Fisher's exact test), Q value = 0.023

Table S496.  Gene #47: 'del_9q21.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 18(9Q21.11) MUTATED 15 12 38 9 39 12
DEL PEAK 18(9Q21.11) WILD-TYPE 49 34 52 43 77 19

Figure S496.  Get High-res Image Gene #47: '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 S497.  Gene #47: 'del_9q21.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 18(9Q21.11) MUTATED 157 110 26
DEL PEAK 18(9Q21.11) WILD-TYPE 402 194 186

Figure S497.  Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9q21.11' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S498.  Gene #47: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 18(9Q21.11) MUTATED 85 59 5 52 69 23
DEL PEAK 18(9Q21.11) WILD-TYPE 204 104 85 238 114 37

Figure S498.  Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_CNMF'

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

Table S499.  Gene #47: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 18(9Q21.11) MUTATED 128 25 53 81
DEL PEAK 18(9Q21.11) WILD-TYPE 177 187 216 194

Figure S499.  Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9q21.11' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S500.  Gene #47: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 18(9Q21.11) MUTATED 101 61 25 25 20 55
DEL PEAK 18(9Q21.11) WILD-TYPE 193 91 220 115 76 79

Figure S500.  Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_MATURE_CNMF'

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

Table S501.  Gene #47: 'del_9q21.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 18(9Q21.11) MUTATED 55 56 21 15 22
DEL PEAK 18(9Q21.11) WILD-TYPE 125 83 78 96 111

Figure S501.  Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9q21.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S502.  Gene #47: 'del_9q21.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 18(9Q21.11) MUTATED 107 45 17
DEL PEAK 18(9Q21.11) WILD-TYPE 198 202 93

Figure S502.  Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q34.2' versus 'MRNA_CNMF'

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

Table S503.  Gene #48: 'del_9q34.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 19(9Q34.2) MUTATED 6 4 40 55 23 18 7 4
DEL PEAK 19(9Q34.2) WILD-TYPE 15 32 79 41 86 54 13 36

Figure S503.  Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9q34.2' versus 'MRNA_CHIERARCHICAL'

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

Table S504.  Gene #48: 'del_9q34.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 19(9Q34.2) MUTATED 36 23 38 50 10
DEL PEAK 19(9Q34.2) WILD-TYPE 65 129 76 38 48

Figure S504.  Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9q34.2' versus 'CN_CNMF'

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

Table S505.  Gene #48: 'del_9q34.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 19(9Q34.2) MUTATED 103 30 14 138 12
DEL PEAK 19(9Q34.2) WILD-TYPE 172 377 84 119 31

Figure S505.  Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q34.2' versus 'METHLYATION_CNMF'

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

Table S506.  Gene #48: 'del_9q34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 19(9Q34.2) MUTATED 47 25 24 21 72 5
DEL PEAK 19(9Q34.2) WILD-TYPE 97 74 189 102 63 54

Figure S506.  Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q34.2' versus 'RPPA_CNMF'

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

Table S507.  Gene #48: 'del_9q34.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 19(9Q34.2) MUTATED 68 25 30
DEL PEAK 19(9Q34.2) WILD-TYPE 83 98 95

Figure S507.  Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9q34.2' versus 'RPPA_CHIERARCHICAL'

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

Table S508.  Gene #48: 'del_9q34.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 19(9Q34.2) MUTATED 12 12 50 7 39 3
DEL PEAK 19(9Q34.2) WILD-TYPE 52 34 40 45 77 28

Figure S508.  Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9q34.2' versus 'MRNASEQ_CNMF'

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

Table S509.  Gene #48: 'del_9q34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 19(9Q34.2) MUTATED 141 137 17
DEL PEAK 19(9Q34.2) WILD-TYPE 418 167 195

Figure S509.  Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9q34.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S510.  Gene #48: 'del_9q34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 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 S510.  Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q34.2' versus 'MIRSEQ_CNMF'

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

Table S511.  Gene #48: 'del_9q34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 19(9Q34.2) MUTATED 144 19 53 72
DEL PEAK 19(9Q34.2) WILD-TYPE 161 193 216 203

Figure S511.  Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9q34.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S512.  Gene #48: 'del_9q34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 19(9Q34.2) MUTATED 90 58 20 24 18 78
DEL PEAK 19(9Q34.2) WILD-TYPE 204 94 225 116 78 56

Figure S512.  Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q34.2' versus 'MIRSEQ_MATURE_CNMF'

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

Table S513.  Gene #48: 'del_9q34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 19(9Q34.2) MUTATED 48 77 17 13 20
DEL PEAK 19(9Q34.2) WILD-TYPE 132 62 82 98 113

Figure S513.  Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9q34.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S514.  Gene #48: 'del_9q34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 19(9Q34.2) MUTATED 118 43 14
DEL PEAK 19(9Q34.2) WILD-TYPE 187 204 96

Figure S514.  Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'MRNA_CNMF'

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

Table S515.  Gene #49: 'del_10q23.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 20(10Q23.31) MUTATED 7 6 36 49 20 21 7 3
DEL PEAK 20(10Q23.31) WILD-TYPE 14 30 83 47 89 51 13 37

Figure S515.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q23.31' versus 'MRNA_CHIERARCHICAL'

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

Table S516.  Gene #49: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 20(10Q23.31) MUTATED 28 29 39 45 8
DEL PEAK 20(10Q23.31) WILD-TYPE 73 123 75 43 50

Figure S516.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

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

Table S517.  Gene #49: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 20(10Q23.31) MUTATED 91 54 25 134 16
DEL PEAK 20(10Q23.31) WILD-TYPE 184 353 73 123 27

Figure S517.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

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

Table S518.  Gene #49: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 20(10Q23.31) MUTATED 56 29 35 27 76 11
DEL PEAK 20(10Q23.31) WILD-TYPE 88 70 178 96 59 48

Figure S518.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CNMF'

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

Table S519.  Gene #49: 'del_10q23.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 20(10Q23.31) MUTATED 68 24 26
DEL PEAK 20(10Q23.31) WILD-TYPE 83 99 99

Figure S519.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_10q23.31' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 5.9e-05

Table S520.  Gene #49: 'del_10q23.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 20(10Q23.31) MUTATED 12 8 45 9 34 10
DEL PEAK 20(10Q23.31) WILD-TYPE 52 38 45 43 82 21

Figure S520.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_10q23.31' versus 'MRNASEQ_CNMF'

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

Table S521.  Gene #49: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 20(10Q23.31) MUTATED 146 145 28
DEL PEAK 20(10Q23.31) WILD-TYPE 413 159 184

Figure S521.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S522.  Gene #49: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 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 S522.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

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

Table S523.  Gene #49: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 20(10Q23.31) MUTATED 135 38 61 77
DEL PEAK 20(10Q23.31) WILD-TYPE 170 174 208 198

Figure S523.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S524.  Gene #49: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 20(10Q23.31) MUTATED 92 64 41 21 20 73
DEL PEAK 20(10Q23.31) WILD-TYPE 202 88 204 119 76 61

Figure S524.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

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

Table S525.  Gene #49: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 20(10Q23.31) MUTATED 53 74 22 17 32
DEL PEAK 20(10Q23.31) WILD-TYPE 127 65 77 94 101

Figure S525.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00015

Table S526.  Gene #49: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 20(10Q23.31) MUTATED 116 61 21
DEL PEAK 20(10Q23.31) WILD-TYPE 189 186 89

Figure S526.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q26.3' versus 'MRNA_CNMF'

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

Table S527.  Gene #50: 'del_10q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 21(10Q26.3) MUTATED 8 7 38 55 14 22 6 4
DEL PEAK 21(10Q26.3) WILD-TYPE 13 29 81 41 95 50 14 36

Figure S527.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q26.3' versus 'MRNA_CHIERARCHICAL'

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

Table S528.  Gene #50: 'del_10q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 21(10Q26.3) MUTATED 31 23 44 49 7
DEL PEAK 21(10Q26.3) WILD-TYPE 70 129 70 39 51

Figure S528.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q26.3' versus 'CN_CNMF'

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

Table S529.  Gene #50: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 21(10Q26.3) MUTATED 98 50 22 138 11
DEL PEAK 21(10Q26.3) WILD-TYPE 177 357 76 119 32

Figure S529.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q26.3' versus 'METHLYATION_CNMF'

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

Table S530.  Gene #50: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 21(10Q26.3) MUTATED 53 35 29 24 76 10
DEL PEAK 21(10Q26.3) WILD-TYPE 91 64 184 99 59 49

Figure S530.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q26.3' versus 'RPPA_CNMF'

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

Table S531.  Gene #50: 'del_10q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 21(10Q26.3) MUTATED 75 25 25
DEL PEAK 21(10Q26.3) WILD-TYPE 76 98 100

Figure S531.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_10q26.3' versus 'RPPA_CHIERARCHICAL'

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

Table S532.  Gene #50: 'del_10q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 21(10Q26.3) MUTATED 11 6 48 10 36 14
DEL PEAK 21(10Q26.3) WILD-TYPE 53 40 42 42 80 17

Figure S532.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_10q26.3' versus 'MRNASEQ_CNMF'

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

Table S533.  Gene #50: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 21(10Q26.3) MUTATED 145 153 21
DEL PEAK 21(10Q26.3) WILD-TYPE 414 151 191

Figure S533.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S534.  Gene #50: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
DEL PEAK 21(10Q26.3) MUTATED 67 71 6 51 98 26
DEL PEAK 21(10Q26.3) WILD-TYPE 222 92 84 239 85 34

Figure S534.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_CNMF'

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

Table S535.  Gene #50: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 21(10Q26.3) MUTATED 142 32 52 82
DEL PEAK 21(10Q26.3) WILD-TYPE 163 180 217 193

Figure S535.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q26.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S536.  Gene #50: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 21(10Q26.3) MUTATED 100 68 33 15 20 72
DEL PEAK 21(10Q26.3) WILD-TYPE 194 84 212 125 76 62

Figure S536.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_MATURE_CNMF'

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

Table S537.  Gene #50: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 21(10Q26.3) MUTATED 60 72 20 13 33
DEL PEAK 21(10Q26.3) WILD-TYPE 120 67 79 98 100

Figure S537.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S538.  Gene #50: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 21(10Q26.3) MUTATED 125 54 19
DEL PEAK 21(10Q26.3) WILD-TYPE 180 193 91

Figure S538.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'MRNA_CNMF'

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

Table S539.  Gene #51: 'del_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 22(11P15.5) MUTATED 3 8 33 48 14 34 7 9
DEL PEAK 22(11P15.5) WILD-TYPE 18 28 86 48 95 38 13 31

Figure S539.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11p15.5' versus 'MRNA_CHIERARCHICAL'

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

Table S540.  Gene #51: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 22(11P15.5) MUTATED 24 32 50 42 8
DEL PEAK 22(11P15.5) WILD-TYPE 77 120 64 46 50

Figure S540.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

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

Table S541.  Gene #51: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 22(11P15.5) MUTATED 94 34 20 155 6
DEL PEAK 22(11P15.5) WILD-TYPE 181 373 78 102 37

Figure S541.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

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

Table S542.  Gene #51: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 22(11P15.5) MUTATED 54 29 23 21 68 12
DEL PEAK 22(11P15.5) WILD-TYPE 90 70 190 102 67 47

Figure S542.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11p15.5' versus 'RPPA_CNMF'

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

Table S543.  Gene #51: 'del_11p15.5' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 22(11P15.5) MUTATED 76 29 25
DEL PEAK 22(11P15.5) WILD-TYPE 75 94 100

Figure S543.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_11p15.5' versus 'RPPA_CHIERARCHICAL'

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

Table S544.  Gene #51: 'del_11p15.5' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 22(11P15.5) MUTATED 11 9 48 11 36 15
DEL PEAK 22(11P15.5) WILD-TYPE 53 37 42 41 80 16

Figure S544.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_11p15.5' versus 'MRNASEQ_CNMF'

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

Table S545.  Gene #51: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 22(11P15.5) MUTATED 129 153 26
DEL PEAK 22(11P15.5) WILD-TYPE 430 151 186

Figure S545.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S546.  Gene #51: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 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 S546.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

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

Table S547.  Gene #51: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 22(11P15.5) MUTATED 147 26 61 67
DEL PEAK 22(11P15.5) WILD-TYPE 158 186 208 208

Figure S547.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S548.  Gene #51: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 22(11P15.5) MUTATED 91 68 38 24 11 69
DEL PEAK 22(11P15.5) WILD-TYPE 203 84 207 116 85 65

Figure S548.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

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

Table S549.  Gene #51: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 22(11P15.5) MUTATED 47 69 20 15 30
DEL PEAK 22(11P15.5) WILD-TYPE 133 70 79 96 103

Figure S549.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S550.  Gene #51: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 22(11P15.5) MUTATED 110 51 20
DEL PEAK 22(11P15.5) WILD-TYPE 195 196 90

Figure S550.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q13.1' versus 'MRNA_CNMF'

P value = 0.00348 (Fisher's exact test), Q value = 0.0042

Table S551.  Gene #52: 'del_11q13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 23(11Q13.1) MUTATED 3 7 45 21 16 19 2 9
DEL PEAK 23(11Q13.1) WILD-TYPE 18 29 74 75 93 53 18 31

Figure S551.  Get High-res Image Gene #52: 'del_11q13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11q13.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00236 (Fisher's exact test), Q value = 0.0029

Table S552.  Gene #52: 'del_11q13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 23(11Q13.1) MUTATED 39 29 26 20 8
DEL PEAK 23(11Q13.1) WILD-TYPE 62 123 88 68 50

Figure S552.  Get High-res Image Gene #52: 'del_11q13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11q13.1' versus 'CN_CNMF'

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

Table S553.  Gene #52: 'del_11q13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 23(11Q13.1) MUTATED 110 37 28 57 9
DEL PEAK 23(11Q13.1) WILD-TYPE 165 370 70 200 34

Figure S553.  Get High-res Image Gene #52: '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 S554.  Gene #52: 'del_11q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 23(11Q13.1) MUTATED 54 28 31 13 32 10
DEL PEAK 23(11Q13.1) WILD-TYPE 90 71 182 110 103 49

Figure S554.  Get High-res Image Gene #52: 'del_11q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q13.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0394 (Fisher's exact test), Q value = 0.044

Table S555.  Gene #52: 'del_11q13.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 23(11Q13.1) MUTATED 9 8 20 9 39 8
DEL PEAK 23(11Q13.1) WILD-TYPE 55 38 70 43 77 23

Figure S555.  Get High-res Image Gene #52: 'del_11q13.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_11q13.1' versus 'MRNASEQ_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 6e-04

Table S556.  Gene #52: 'del_11q13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 23(11Q13.1) MUTATED 146 65 28
DEL PEAK 23(11Q13.1) WILD-TYPE 413 239 184

Figure S556.  Get High-res Image Gene #52: 'del_11q13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00026

Table S557.  Gene #52: '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 S557.  Get High-res Image Gene #52: 'del_11q13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.026

Table S558.  Gene #52: 'del_11q13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 23(11Q13.1) MUTATED 55 33 15 19 31
DEL PEAK 23(11Q13.1) WILD-TYPE 125 106 84 92 102

Figure S558.  Get High-res Image Gene #52: 'del_11q13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11q23.3' versus 'MRNA_CNMF'

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

Table S559.  Gene #53: 'del_11q23.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 24(11Q23.3) MUTATED 12 21 89 40 36 37 12 22
DEL PEAK 24(11Q23.3) WILD-TYPE 9 15 30 56 73 35 8 18

Figure S559.  Get High-res Image Gene #53: 'del_11q23.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11q23.3' versus 'MRNA_CHIERARCHICAL'

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

Table S560.  Gene #53: 'del_11q23.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 24(11Q23.3) MUTATED 77 74 64 37 17
DEL PEAK 24(11Q23.3) WILD-TYPE 24 78 50 51 41

Figure S560.  Get High-res Image Gene #53: 'del_11q23.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11q23.3' versus 'CN_CNMF'

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

Table S561.  Gene #53: 'del_11q23.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 24(11Q23.3) MUTATED 234 116 48 132 17
DEL PEAK 24(11Q23.3) WILD-TYPE 41 291 50 125 26

Figure S561.  Get High-res Image Gene #53: '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 S562.  Gene #53: 'del_11q23.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 24(11Q23.3) MUTATED 108 68 83 42 65 25
DEL PEAK 24(11Q23.3) WILD-TYPE 36 31 130 81 70 34

Figure S562.  Get High-res Image Gene #53: 'del_11q23.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q23.3' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3e-05

Table S563.  Gene #53: 'del_11q23.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 24(11Q23.3) MUTATED 20 23 41 24 83 17
DEL PEAK 24(11Q23.3) WILD-TYPE 44 23 49 28 33 14

Figure S563.  Get High-res Image Gene #53: 'del_11q23.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_11q23.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3e-05

Table S564.  Gene #53: 'del_11q23.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 24(11Q23.3) MUTATED 318 144 82
DEL PEAK 24(11Q23.3) WILD-TYPE 241 160 130

Figure S564.  Get High-res Image Gene #53: '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 S565.  Gene #53: '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 S565.  Get High-res Image Gene #53: 'del_11q23.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.3' versus 'MIRSEQ_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.014

Table S566.  Gene #53: 'del_11q23.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 24(11Q23.3) MUTATED 155 87 136 154
DEL PEAK 24(11Q23.3) WILD-TYPE 150 125 133 121

Figure S566.  Get High-res Image Gene #53: 'del_11q23.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 8.6e-05

Table S567.  Gene #53: 'del_11q23.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 24(11Q23.3) MUTATED 183 75 103 63 48 60
DEL PEAK 24(11Q23.3) WILD-TYPE 111 77 142 77 48 74

Figure S567.  Get High-res Image Gene #53: 'del_11q23.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 4e-04

Table S568.  Gene #53: 'del_11q23.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 24(11Q23.3) MUTATED 106 63 57 37 64
DEL PEAK 24(11Q23.3) WILD-TYPE 74 76 42 74 69

Figure S568.  Get High-res Image Gene #53: 'del_11q23.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11q25' versus 'MRNA_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.00055

Table S569.  Gene #54: 'del_11q25' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 25(11Q25) MUTATED 10 20 76 47 34 38 12 20
DEL PEAK 25(11Q25) WILD-TYPE 11 16 43 49 75 34 8 20

Figure S569.  Get High-res Image Gene #54: 'del_11q25' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11q25' versus 'MRNA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00023

Table S570.  Gene #54: 'del_11q25' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 25(11Q25) MUTATED 65 69 62 45 16
DEL PEAK 25(11Q25) WILD-TYPE 36 83 52 43 42

Figure S570.  Get High-res Image Gene #54: 'del_11q25' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11q25' versus 'CN_CNMF'

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

Table S571.  Gene #54: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 25(11Q25) MUTATED 216 101 41 140 15
DEL PEAK 25(11Q25) WILD-TYPE 59 306 57 117 28

Figure S571.  Get High-res Image Gene #54: '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 S572.  Gene #54: 'del_11q25' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 25(11Q25) MUTATED 97 61 71 41 69 21
DEL PEAK 25(11Q25) WILD-TYPE 47 38 142 82 66 38

Figure S572.  Get High-res Image Gene #54: 'del_11q25' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q25' versus 'RPPA_CHIERARCHICAL'

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

Table S573.  Gene #54: 'del_11q25' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 25(11Q25) MUTATED 16 19 46 24 77 17
DEL PEAK 25(11Q25) WILD-TYPE 48 27 44 28 39 14

Figure S573.  Get High-res Image Gene #54: 'del_11q25' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_11q25' versus 'MRNASEQ_CNMF'

P value = 0.00147 (Fisher's exact test), Q value = 0.0018

Table S574.  Gene #54: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 25(11Q25) MUTATED 280 153 77
DEL PEAK 25(11Q25) WILD-TYPE 279 151 135

Figure S574.  Get High-res Image Gene #54: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q25' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 7.2e-05

Table S575.  Gene #54: '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 93 22
DEL PEAK 25(11Q25) WILD-TYPE 145 72 67 153 90 38

Figure S575.  Get High-res Image Gene #54: 'del_11q25' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q25' versus 'MIRSEQ_CNMF'

P value = 0.00385 (Fisher's exact test), Q value = 0.0047

Table S576.  Gene #54: 'del_11q25' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 25(11Q25) MUTATED 162 79 124 136
DEL PEAK 25(11Q25) WILD-TYPE 143 133 145 139

Figure S576.  Get High-res Image Gene #54: 'del_11q25' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11q25' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00122 (Fisher's exact test), Q value = 0.0015

Table S577.  Gene #54: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 25(11Q25) MUTATED 160 74 95 57 41 74
DEL PEAK 25(11Q25) WILD-TYPE 134 78 150 83 55 60

Figure S577.  Get High-res Image Gene #54: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11q25' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.025

Table S578.  Gene #54: 'del_11q25' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 25(11Q25) MUTATED 91 71 47 36 61
DEL PEAK 25(11Q25) WILD-TYPE 89 68 52 75 72

Figure S578.  Get High-res Image Gene #54: 'del_11q25' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11q25' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0401 (Fisher's exact test), Q value = 0.045

Table S579.  Gene #54: 'del_11q25' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 25(11Q25) MUTATED 156 108 42
DEL PEAK 25(11Q25) WILD-TYPE 149 139 68

Figure S579.  Get High-res Image Gene #54: 'del_11q25' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12p13.1' versus 'MRNA_CNMF'

P value = 0.035 (Fisher's exact test), Q value = 0.039

Table S580.  Gene #55: 'del_12p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 26(12P13.1) MUTATED 5 8 26 24 9 13 5 5
DEL PEAK 26(12P13.1) WILD-TYPE 16 28 93 72 100 59 15 35

Figure S580.  Get High-res Image Gene #55: 'del_12p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12p13.1' versus 'CN_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.00048

Table S581.  Gene #55: 'del_12p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 26(12P13.1) MUTATED 58 49 14 62 5
DEL PEAK 26(12P13.1) WILD-TYPE 217 358 84 195 38

Figure S581.  Get High-res Image Gene #55: 'del_12p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 0.0193 (Fisher's exact test), Q value = 0.022

Table S582.  Gene #55: 'del_12p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 26(12P13.1) MUTATED 29 14 27 15 35 9
DEL PEAK 26(12P13.1) WILD-TYPE 115 85 186 108 100 50

Figure S582.  Get High-res Image Gene #55: 'del_12p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12p13.1' versus 'MRNASEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.00045

Table S583.  Gene #55: 'del_12p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 26(12P13.1) MUTATED 86 75 26
DEL PEAK 26(12P13.1) WILD-TYPE 473 229 186

Figure S583.  Get High-res Image Gene #55: 'del_12p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.00067

Table S584.  Gene #55: '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 S584.  Get High-res Image Gene #55: 'del_12p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_CNMF'

P value = 0.00204 (Fisher's exact test), Q value = 0.0025

Table S585.  Gene #55: 'del_12p13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 26(12P13.1) MUTATED 69 28 33 55
DEL PEAK 26(12P13.1) WILD-TYPE 236 184 236 220

Figure S585.  Get High-res Image Gene #55: 'del_12p13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_12p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 4.5e-05

Table S586.  Gene #55: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 26(12P13.1) MUTATED 56 45 25 20 11 28
DEL PEAK 26(12P13.1) WILD-TYPE 238 107 220 120 85 106

Figure S586.  Get High-res Image Gene #55: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00608 (Fisher's exact test), Q value = 0.0072

Table S587.  Gene #55: 'del_12p13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 26(12P13.1) MUTATED 31 38 11 13 20
DEL PEAK 26(12P13.1) WILD-TYPE 149 101 88 98 113

Figure S587.  Get High-res Image Gene #55: 'del_12p13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_12p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00267 (Fisher's exact test), Q value = 0.0033

Table S588.  Gene #55: 'del_12p13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 26(12P13.1) MUTATED 68 28 17
DEL PEAK 26(12P13.1) WILD-TYPE 237 219 93

Figure S588.  Get High-res Image Gene #55: '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 S589.  Gene #56: 'del_12q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 27(12Q23.1) MUTATED 2 1 14 43 6 22 4 4
DEL PEAK 27(12Q23.1) WILD-TYPE 19 35 105 53 103 50 16 36

Figure S589.  Get High-res Image Gene #56: '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 S590.  Gene #56: 'del_12q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 27(12Q23.1) MUTATED 12 10 34 37 3
DEL PEAK 27(12Q23.1) WILD-TYPE 89 142 80 51 55

Figure S590.  Get High-res Image Gene #56: '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 S591.  Gene #56: 'del_12q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 27(12Q23.1) MUTATED 37 32 17 112 3
DEL PEAK 27(12Q23.1) WILD-TYPE 238 375 81 145 40

Figure S591.  Get High-res Image Gene #56: '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 S592.  Gene #56: 'del_12q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 27(12Q23.1) MUTATED 24 18 16 14 67 4
DEL PEAK 27(12Q23.1) WILD-TYPE 120 81 197 109 68 55

Figure S592.  Get High-res Image Gene #56: '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 S593.  Gene #56: 'del_12q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 27(12Q23.1) MUTATED 49 19 10
DEL PEAK 27(12Q23.1) WILD-TYPE 102 104 115

Figure S593.  Get High-res Image Gene #56: '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 S594.  Gene #56: 'del_12q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 27(12Q23.1) MUTATED 5 5 40 6 15 7
DEL PEAK 27(12Q23.1) WILD-TYPE 59 41 50 46 101 24

Figure S594.  Get High-res Image Gene #56: '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 S595.  Gene #56: 'del_12q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 27(12Q23.1) MUTATED 63 116 20
DEL PEAK 27(12Q23.1) WILD-TYPE 496 188 192

Figure S595.  Get High-res Image Gene #56: '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 S596.  Gene #56: '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 S596.  Get High-res Image Gene #56: '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 S597.  Gene #56: 'del_12q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 27(12Q23.1) MUTATED 109 22 20 46
DEL PEAK 27(12Q23.1) WILD-TYPE 196 190 249 229

Figure S597.  Get High-res Image Gene #56: '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 S598.  Gene #56: 'del_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 27(12Q23.1) MUTATED 54 43 23 13 5 59
DEL PEAK 27(12Q23.1) WILD-TYPE 240 109 222 127 91 75

Figure S598.  Get High-res Image Gene #56: '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 S599.  Gene #56: 'del_12q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 27(12Q23.1) MUTATED 27 62 7 14 21
DEL PEAK 27(12Q23.1) WILD-TYPE 153 77 92 97 112

Figure S599.  Get High-res Image Gene #56: '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 S600.  Gene #56: 'del_12q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 27(12Q23.1) MUTATED 90 30 11
DEL PEAK 27(12Q23.1) WILD-TYPE 215 217 99

Figure S600.  Get High-res Image Gene #56: '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 S601.  Gene #57: 'del_12q24.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 28(12Q24.31) MUTATED 4 6 12 42 6 20 5 6
DEL PEAK 28(12Q24.31) WILD-TYPE 17 30 107 54 103 52 15 34

Figure S601.  Get High-res Image Gene #57: '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 S602.  Gene #57: 'del_12q24.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 28(12Q24.31) MUTATED 10 15 35 37 4
DEL PEAK 28(12Q24.31) WILD-TYPE 91 137 79 51 54

Figure S602.  Get High-res Image Gene #57: '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 S603.  Gene #57: 'del_12q24.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 28(12Q24.31) MUTATED 38 40 17 112 4
DEL PEAK 28(12Q24.31) WILD-TYPE 237 367 81 145 39

Figure S603.  Get High-res Image Gene #57: '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 S604.  Gene #57: 'del_12q24.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 28(12Q24.31) MUTATED 19 21 21 17 67 6
DEL PEAK 28(12Q24.31) WILD-TYPE 125 78 192 106 68 53

Figure S604.  Get High-res Image Gene #57: '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 S605.  Gene #57: 'del_12q24.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 28(12Q24.31) MUTATED 50 20 12
DEL PEAK 28(12Q24.31) WILD-TYPE 101 103 113

Figure S605.  Get High-res Image Gene #57: 'del_12q24.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_12q24.31' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3e-05

Table S606.  Gene #57: 'del_12q24.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 28(12Q24.31) MUTATED 7 6 36 7 16 10
DEL PEAK 28(12Q24.31) WILD-TYPE 57 40 54 45 100 21

Figure S606.  Get High-res Image Gene #57: '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 S607.  Gene #57: 'del_12q24.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 28(12Q24.31) MUTATED 64 118 28
DEL PEAK 28(12Q24.31) WILD-TYPE 495 186 184

Figure S607.  Get High-res Image Gene #57: '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 S608.  Gene #57: '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 S608.  Get High-res Image Gene #57: '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 S609.  Gene #57: 'del_12q24.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 28(12Q24.31) MUTATED 104 28 27 49
DEL PEAK 28(12Q24.31) WILD-TYPE 201 184 242 226

Figure S609.  Get High-res Image Gene #57: '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 S610.  Gene #57: 'del_12q24.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 28(12Q24.31) MUTATED 55 46 31 15 3 58
DEL PEAK 28(12Q24.31) WILD-TYPE 239 106 214 125 93 76

Figure S610.  Get High-res Image Gene #57: '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 S611.  Gene #57: 'del_12q24.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 28(12Q24.31) MUTATED 29 60 12 16 23
DEL PEAK 28(12Q24.31) WILD-TYPE 151 79 87 95 110

Figure S611.  Get High-res Image Gene #57: 'del_12q24.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_12q24.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 5.9e-05

Table S612.  Gene #57: 'del_12q24.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 28(12Q24.31) MUTATED 88 37 15
DEL PEAK 28(12Q24.31) WILD-TYPE 217 210 95

Figure S612.  Get High-res Image Gene #57: 'del_12q24.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q14.2' versus 'MRNA_CNMF'

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

Table S613.  Gene #58: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 29(13Q14.2) MUTATED 8 12 70 60 34 41 9 13
DEL PEAK 29(13Q14.2) WILD-TYPE 13 24 49 36 75 31 11 27

Figure S613.  Get High-res Image Gene #58: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

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

Table S614.  Gene #58: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 29(13Q14.2) MUTATED 64 47 67 56 13
DEL PEAK 29(13Q14.2) WILD-TYPE 37 105 47 32 45

Figure S614.  Get High-res Image Gene #58: '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 S615.  Gene #58: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 29(13Q14.2) MUTATED 172 86 57 154 26
DEL PEAK 29(13Q14.2) WILD-TYPE 103 321 41 103 17

Figure S615.  Get High-res Image Gene #58: '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 S616.  Gene #58: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 29(13Q14.2) MUTATED 77 53 73 44 83 16
DEL PEAK 29(13Q14.2) WILD-TYPE 67 46 140 79 52 43

Figure S616.  Get High-res Image Gene #58: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 4.5e-05

Table S617.  Gene #58: 'del_13q14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 29(13Q14.2) MUTATED 19 22 58 18 66 10
DEL PEAK 29(13Q14.2) WILD-TYPE 45 24 32 34 50 21

Figure S617.  Get High-res Image Gene #58: '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 S618.  Gene #58: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 29(13Q14.2) MUTATED 261 176 56
DEL PEAK 29(13Q14.2) WILD-TYPE 298 128 156

Figure S618.  Get High-res Image Gene #58: '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 S619.  Gene #58: '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 95 19 110 114 25
DEL PEAK 29(13Q14.2) WILD-TYPE 159 68 71 180 69 35

Figure S619.  Get High-res Image Gene #58: '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 S620.  Gene #58: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 29(13Q14.2) MUTATED 177 57 110 140
DEL PEAK 29(13Q14.2) WILD-TYPE 128 155 159 135

Figure S620.  Get High-res Image Gene #58: '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 S621.  Gene #58: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 29(13Q14.2) MUTATED 168 68 76 49 35 88
DEL PEAK 29(13Q14.2) WILD-TYPE 126 84 169 91 61 46

Figure S621.  Get High-res Image Gene #58: '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 S622.  Gene #58: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 29(13Q14.2) MUTATED 92 87 35 25 46
DEL PEAK 29(13Q14.2) WILD-TYPE 88 52 64 86 87

Figure S622.  Get High-res Image Gene #58: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S623.  Gene #58: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 29(13Q14.2) MUTATED 163 84 38
DEL PEAK 29(13Q14.2) WILD-TYPE 142 163 72

Figure S623.  Get High-res Image Gene #58: '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 S624.  Gene #59: 'del_14q24.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 30(14Q24.1) MUTATED 4 7 47 63 10 22 10 8
DEL PEAK 30(14Q24.1) WILD-TYPE 17 29 72 33 99 50 10 32

Figure S624.  Get High-res Image Gene #59: '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 S625.  Gene #59: 'del_14q24.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 30(14Q24.1) MUTATED 37 30 41 59 4
DEL PEAK 30(14Q24.1) WILD-TYPE 64 122 73 29 54

Figure S625.  Get High-res Image Gene #59: '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 S626.  Gene #59: 'del_14q24.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 30(14Q24.1) MUTATED 99 49 24 167 14
DEL PEAK 30(14Q24.1) WILD-TYPE 176 358 74 90 29

Figure S626.  Get High-res Image Gene #59: '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 S627.  Gene #59: 'del_14q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 30(14Q24.1) MUTATED 59 32 28 28 88 11
DEL PEAK 30(14Q24.1) WILD-TYPE 85 67 185 95 47 48

Figure S627.  Get High-res Image Gene #59: '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 S628.  Gene #59: 'del_14q24.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 30(14Q24.1) MUTATED 79 32 26
DEL PEAK 30(14Q24.1) WILD-TYPE 72 91 99

Figure S628.  Get High-res Image Gene #59: '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 S629.  Gene #59: 'del_14q24.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 30(14Q24.1) MUTATED 6 12 58 13 40 8
DEL PEAK 30(14Q24.1) WILD-TYPE 58 34 32 39 76 23

Figure S629.  Get High-res Image Gene #59: '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 S630.  Gene #59: 'del_14q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 30(14Q24.1) MUTATED 151 169 31
DEL PEAK 30(14Q24.1) WILD-TYPE 408 135 181

Figure S630.  Get High-res Image Gene #59: '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 S631.  Gene #59: '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 68 6 68 124 16
DEL PEAK 30(14Q24.1) WILD-TYPE 220 95 84 222 59 44

Figure S631.  Get High-res Image Gene #59: '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 S632.  Gene #59: 'del_14q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 30(14Q24.1) MUTATED 170 39 55 79
DEL PEAK 30(14Q24.1) WILD-TYPE 135 173 214 196

Figure S632.  Get High-res Image Gene #59: '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 S633.  Gene #59: 'del_14q24.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 30(14Q24.1) MUTATED 98 64 40 27 18 96
DEL PEAK 30(14Q24.1) WILD-TYPE 196 88 205 113 78 38

Figure S633.  Get High-res Image Gene #59: '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 S634.  Gene #59: 'del_14q24.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 30(14Q24.1) MUTATED 56 89 19 24 31
DEL PEAK 30(14Q24.1) WILD-TYPE 124 50 80 87 102

Figure S634.  Get High-res Image Gene #59: '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 S635.  Gene #59: 'del_14q24.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 30(14Q24.1) MUTATED 145 52 22
DEL PEAK 30(14Q24.1) WILD-TYPE 160 195 88

Figure S635.  Get High-res Image Gene #59: 'del_14q24.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q13.1' versus 'MRNA_CNMF'

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

Table S636.  Gene #60: 'del_15q13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 31(15Q13.1) MUTATED 5 11 41 58 24 34 10 8
DEL PEAK 31(15Q13.1) WILD-TYPE 16 25 78 38 85 38 10 32

Figure S636.  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 S637.  Gene #60: 'del_15q13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 31(15Q13.1) MUTATED 36 35 54 54 12
DEL PEAK 31(15Q13.1) WILD-TYPE 65 117 60 34 46

Figure S637.  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 S638.  Gene #60: 'del_15q13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 31(15Q13.1) MUTATED 95 51 44 172 13
DEL PEAK 31(15Q13.1) WILD-TYPE 180 356 54 85 30

Figure S638.  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 S639.  Gene #60: 'del_15q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 31(15Q13.1) MUTATED 57 35 39 29 88 12
DEL PEAK 31(15Q13.1) WILD-TYPE 87 64 174 94 47 47

Figure S639.  Get High-res Image Gene #60: 'del_15q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q13.1' versus 'RPPA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 7.2e-05

Table S640.  Gene #60: 'del_15q13.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 31(15Q13.1) MUTATED 81 39 38
DEL PEAK 31(15Q13.1) WILD-TYPE 70 84 87

Figure S640.  Get High-res Image Gene #60: 'del_15q13.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_15q13.1' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 5.9e-05

Table S641.  Gene #60: 'del_15q13.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 31(15Q13.1) MUTATED 18 9 54 18 46 13
DEL PEAK 31(15Q13.1) WILD-TYPE 46 37 36 34 70 18

Figure S641.  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 S642.  Gene #60: 'del_15q13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 31(15Q13.1) MUTATED 170 170 32
DEL PEAK 31(15Q13.1) WILD-TYPE 389 134 180

Figure S642.  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 S643.  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 31(15Q13.1) MUTATED 77 74 12 67 120 22
DEL PEAK 31(15Q13.1) WILD-TYPE 212 89 78 223 63 38

Figure S643.  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 S644.  Gene #60: 'del_15q13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 31(15Q13.1) MUTATED 172 28 63 103
DEL PEAK 31(15Q13.1) WILD-TYPE 133 184 206 172

Figure S644.  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 S645.  Gene #60: 'del_15q13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 31(15Q13.1) MUTATED 109 71 30 44 17 95
DEL PEAK 31(15Q13.1) WILD-TYPE 185 81 215 96 79 39

Figure S645.  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 S646.  Gene #60: 'del_15q13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 31(15Q13.1) MUTATED 65 90 21 28 26
DEL PEAK 31(15Q13.1) WILD-TYPE 115 49 78 83 107

Figure S646.  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 S647.  Gene #60: 'del_15q13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 31(15Q13.1) MUTATED 139 54 37
DEL PEAK 31(15Q13.1) WILD-TYPE 166 193 73

Figure S647.  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 S648.  Gene #61: 'del_16q24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 32(16Q24.3) MUTATED 16 25 81 27 94 45 13 35
DEL PEAK 32(16Q24.3) WILD-TYPE 5 11 38 69 15 27 7 5

Figure S648.  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 S649.  Gene #61: 'del_16q24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 32(16Q24.3) MUTATED 74 124 71 22 45
DEL PEAK 32(16Q24.3) WILD-TYPE 27 28 43 66 13

Figure S649.  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 S650.  Gene #61: 'del_16q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 32(16Q24.3) MUTATED 176 289 80 116 32
DEL PEAK 32(16Q24.3) WILD-TYPE 99 118 18 141 11

Figure S650.  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 S651.  Gene #61: 'del_16q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 32(16Q24.3) MUTATED 77 75 172 71 58 35
DEL PEAK 32(16Q24.3) WILD-TYPE 67 24 41 52 77 24

Figure S651.  Get High-res Image Gene #61: 'del_16q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q24.3' versus 'RPPA_CNMF'

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

Table S652.  Gene #61: 'del_16q24.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 32(16Q24.3) MUTATED 67 87 98
DEL PEAK 32(16Q24.3) WILD-TYPE 84 36 27

Figure S652.  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 S653.  Gene #61: 'del_16q24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 32(16Q24.3) MUTATED 54 36 28 36 83 15
DEL PEAK 32(16Q24.3) WILD-TYPE 10 10 62 16 33 16

Figure S653.  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 S654.  Gene #61: 'del_16q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 32(16Q24.3) MUTATED 398 125 167
DEL PEAK 32(16Q24.3) WILD-TYPE 161 179 45

Figure S654.  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 S655.  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 32(16Q24.3) MUTATED 194 99 77 231 60 29
DEL PEAK 32(16Q24.3) WILD-TYPE 95 64 13 59 123 31

Figure S655.  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 S656.  Gene #61: 'del_16q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 32(16Q24.3) MUTATED 131 151 205 194
DEL PEAK 32(16Q24.3) WILD-TYPE 174 61 64 81

Figure S656.  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 S657.  Gene #61: 'del_16q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 32(16Q24.3) MUTATED 192 71 186 120 62 50
DEL PEAK 32(16Q24.3) WILD-TYPE 102 81 59 20 34 84

Figure S657.  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 S658.  Gene #61: 'del_16q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 32(16Q24.3) MUTATED 119 59 68 78 92
DEL PEAK 32(16Q24.3) WILD-TYPE 61 80 31 33 41

Figure S658.  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 S659.  Gene #61: 'del_16q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 32(16Q24.3) MUTATED 154 177 85
DEL PEAK 32(16Q24.3) WILD-TYPE 151 70 25

Figure S659.  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 S660.  Gene #62: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 33(17P12) MUTATED 14 27 78 65 33 62 15 24
DEL PEAK 33(17P12) WILD-TYPE 7 9 41 31 76 10 5 16

Figure S660.  Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p12' versus 'MRNA_CHIERARCHICAL'

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

Table S661.  Gene #62: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 33(17P12) MUTATED 69 86 93 58 12
DEL PEAK 33(17P12) WILD-TYPE 32 66 21 30 46

Figure S661.  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 S662.  Gene #62: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 33(17P12) MUTATED 217 163 45 201 24
DEL PEAK 33(17P12) WILD-TYPE 58 244 53 56 19

Figure S662.  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 S663.  Gene #62: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 33(17P12) MUTATED 116 72 91 63 88 30
DEL PEAK 33(17P12) WILD-TYPE 28 27 122 60 47 29

Figure S663.  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 S664.  Gene #62: 'del_17p12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 33(17P12) MUTATED 118 71 59
DEL PEAK 33(17P12) WILD-TYPE 33 52 66

Figure S664.  Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_17p12' versus 'RPPA_CHIERARCHICAL'

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

Table S665.  Gene #62: 'del_17p12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 33(17P12) MUTATED 23 22 65 32 80 26
DEL PEAK 33(17P12) WILD-TYPE 41 24 25 20 36 5

Figure S665.  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 S666.  Gene #62: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 33(17P12) MUTATED 322 219 106
DEL PEAK 33(17P12) WILD-TYPE 237 85 106

Figure S666.  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 S667.  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 33(17P12) MUTATED 152 134 43 154 116 48
DEL PEAK 33(17P12) WILD-TYPE 137 29 47 136 67 12

Figure S667.  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 S668.  Gene #62: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 33(17P12) MUTATED 216 103 146 174
DEL PEAK 33(17P12) WILD-TYPE 89 109 123 101

Figure S668.  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 S669.  Gene #62: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 33(17P12) MUTATED 204 104 118 82 38 93
DEL PEAK 33(17P12) WILD-TYPE 90 48 127 58 58 41

Figure S669.  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 S670.  Gene #63: 'del_17q21.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 34(17Q21.31) MUTATED 7 17 28 53 13 50 9 15
DEL PEAK 34(17Q21.31) WILD-TYPE 14 19 91 43 96 22 11 25

Figure S670.  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 S671.  Gene #63: 'del_17q21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 34(17Q21.31) MUTATED 24 49 70 46 3
DEL PEAK 34(17Q21.31) WILD-TYPE 77 103 44 42 55

Figure S671.  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 S672.  Gene #63: 'del_17q21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 34(17Q21.31) MUTATED 92 83 24 165 7
DEL PEAK 34(17Q21.31) WILD-TYPE 183 324 74 92 36

Figure S672.  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 S673.  Gene #63: 'del_17q21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 34(17Q21.31) MUTATED 51 35 26 40 83 14
DEL PEAK 34(17Q21.31) WILD-TYPE 93 64 187 83 52 45

Figure S673.  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 S674.  Gene #63: 'del_17q21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 34(17Q21.31) MUTATED 91 45 22
DEL PEAK 34(17Q21.31) WILD-TYPE 60 78 103

Figure S674.  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 S675.  Gene #63: 'del_17q21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 34(17Q21.31) MUTATED 10 13 52 18 39 26
DEL PEAK 34(17Q21.31) WILD-TYPE 54 33 38 34 77 5

Figure S675.  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 S676.  Gene #63: 'del_17q21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 34(17Q21.31) MUTATED 136 182 52
DEL PEAK 34(17Q21.31) WILD-TYPE 423 122 160

Figure S676.  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 S677.  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 34(17Q21.31) MUTATED 44 90 21 79 96 40
DEL PEAK 34(17Q21.31) WILD-TYPE 245 73 69 211 87 20

Figure S677.  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 S678.  Gene #63: 'del_17q21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 34(17Q21.31) MUTATED 161 46 61 95
DEL PEAK 34(17Q21.31) WILD-TYPE 144 166 208 180

Figure S678.  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 S679.  Gene #63: 'del_17q21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 34(17Q21.31) MUTATED 109 73 57 34 11 79
DEL PEAK 34(17Q21.31) WILD-TYPE 185 79 188 106 85 55

Figure S679.  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 S680.  Gene #63: 'del_17q21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 34(17Q21.31) MUTATED 55 76 19 30 46
DEL PEAK 34(17Q21.31) WILD-TYPE 125 63 80 81 87

Figure S680.  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 = 4e-04 (Fisher's exact test), Q value = 0.00053

Table S681.  Gene #63: 'del_17q21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 34(17Q21.31) MUTATED 128 70 28
DEL PEAK 34(17Q21.31) WILD-TYPE 177 177 82

Figure S681.  Get High-res Image Gene #63: 'del_17q21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q23' versus 'MRNA_CNMF'

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

Table S682.  Gene #64: 'del_18q23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 35(18Q23) MUTATED 6 13 38 38 18 37 6 9
DEL PEAK 35(18Q23) WILD-TYPE 15 23 81 58 91 35 14 31

Figure S682.  Get High-res Image Gene #64: 'del_18q23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q23' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 7.2e-05

Table S683.  Gene #64: 'del_18q23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 35(18Q23) MUTATED 31 35 54 35 10
DEL PEAK 35(18Q23) WILD-TYPE 70 117 60 53 48

Figure S683.  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 S684.  Gene #64: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 35(18Q23) MUTATED 112 68 36 127 11
DEL PEAK 35(18Q23) WILD-TYPE 163 339 62 130 32

Figure S684.  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 S685.  Gene #64: 'del_18q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 35(18Q23) MUTATED 65 47 47 31 59 11
DEL PEAK 35(18Q23) WILD-TYPE 79 52 166 92 76 48

Figure S685.  Get High-res Image Gene #64: 'del_18q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q23' versus 'RPPA_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.00074

Table S686.  Gene #64: 'del_18q23' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 35(18Q23) MUTATED 66 31 31
DEL PEAK 35(18Q23) WILD-TYPE 85 92 94

Figure S686.  Get High-res Image Gene #64: 'del_18q23' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_18q23' versus 'MRNASEQ_CNMF'

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

Table S687.  Gene #64: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 35(18Q23) MUTATED 168 139 46
DEL PEAK 35(18Q23) WILD-TYPE 391 165 166

Figure S687.  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 S688.  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 35(18Q23) MUTATED 61 94 19 74 77 28
DEL PEAK 35(18Q23) WILD-TYPE 228 69 71 216 106 32

Figure S688.  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 S689.  Gene #64: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 35(18Q23) MUTATED 137 48 73 92
DEL PEAK 35(18Q23) WILD-TYPE 168 164 196 183

Figure S689.  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 S690.  Gene #64: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 35(18Q23) MUTATED 112 70 59 38 17 54
DEL PEAK 35(18Q23) WILD-TYPE 182 82 186 102 79 80

Figure S690.  Get High-res Image Gene #64: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00524 (Fisher's exact test), Q value = 0.0063

Table S691.  Gene #64: 'del_18q23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 35(18Q23) MUTATED 61 62 26 27 39
DEL PEAK 35(18Q23) WILD-TYPE 119 77 73 84 94

Figure S691.  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 S692.  Gene #65: 'del_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 36(19P13.3) MUTATED 7 10 48 57 13 35 6 6
DEL PEAK 36(19P13.3) WILD-TYPE 14 26 71 39 96 37 14 34

Figure S692.  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 S693.  Gene #65: 'del_19p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 36(19P13.3) MUTATED 44 28 54 53 3
DEL PEAK 36(19P13.3) WILD-TYPE 57 124 60 35 55

Figure S693.  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 S694.  Gene #65: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 36(19P13.3) MUTATED 137 38 15 159 14
DEL PEAK 36(19P13.3) WILD-TYPE 138 369 83 98 29

Figure S694.  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 S695.  Gene #65: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 36(19P13.3) MUTATED 75 27 22 36 72 7
DEL PEAK 36(19P13.3) WILD-TYPE 69 72 191 87 63 52

Figure S695.  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 S696.  Gene #65: 'del_19p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 36(19P13.3) MUTATED 83 34 32
DEL PEAK 36(19P13.3) WILD-TYPE 68 89 93

Figure S696.  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 S697.  Gene #65: 'del_19p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 36(19P13.3) MUTATED 6 16 50 13 47 17
DEL PEAK 36(19P13.3) WILD-TYPE 58 30 40 39 69 14

Figure S697.  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 S698.  Gene #65: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 36(19P13.3) MUTATED 170 164 27
DEL PEAK 36(19P13.3) WILD-TYPE 389 140 185

Figure S698.  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 S699.  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 36(19P13.3) MUTATED 81 88 4 61 108 19
DEL PEAK 36(19P13.3) WILD-TYPE 208 75 86 229 75 41

Figure S699.  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 S700.  Gene #65: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 36(19P13.3) MUTATED 170 31 64 88
DEL PEAK 36(19P13.3) WILD-TYPE 135 181 205 187

Figure S700.  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 S701.  Gene #65: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 36(19P13.3) MUTATED 113 73 34 25 23 85
DEL PEAK 36(19P13.3) WILD-TYPE 181 79 211 115 73 49

Figure S701.  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 S702.  Gene #65: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 36(19P13.3) MUTATED 62 82 17 18 37
DEL PEAK 36(19P13.3) WILD-TYPE 118 57 82 93 96

Figure S702.  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 S703.  Gene #65: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 36(19P13.3) MUTATED 139 60 17
DEL PEAK 36(19P13.3) WILD-TYPE 166 187 93

Figure S703.  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 S704.  Gene #66: 'del_19q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 37(19Q13.32) MUTATED 4 7 23 26 7 28 1 3
DEL PEAK 37(19Q13.32) WILD-TYPE 17 29 96 70 102 44 19 37

Figure S704.  Get High-res Image Gene #66: 'del_19q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19q13.32' versus 'MRNA_CHIERARCHICAL'

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

Table S705.  Gene #66: 'del_19q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 37(19Q13.32) MUTATED 26 11 36 24 2
DEL PEAK 37(19Q13.32) WILD-TYPE 75 141 78 64 56

Figure S705.  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 S706.  Gene #66: 'del_19q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 37(19Q13.32) MUTATED 92 22 8 88 6
DEL PEAK 37(19Q13.32) WILD-TYPE 183 385 90 169 37

Figure S706.  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 S707.  Gene #66: 'del_19q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 37(19Q13.32) MUTATED 48 21 13 19 48 5
DEL PEAK 37(19Q13.32) WILD-TYPE 96 78 200 104 87 54

Figure S707.  Get High-res Image Gene #66: 'del_19q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.32' versus 'RPPA_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00025

Table S708.  Gene #66: 'del_19q13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 37(19Q13.32) MUTATED 47 16 17
DEL PEAK 37(19Q13.32) WILD-TYPE 104 107 108

Figure S708.  Get High-res Image Gene #66: 'del_19q13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19q13.32' versus 'RPPA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 7.2e-05

Table S709.  Gene #66: 'del_19q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 37(19Q13.32) MUTATED 4 6 30 5 24 11
DEL PEAK 37(19Q13.32) WILD-TYPE 60 40 60 47 92 20

Figure S709.  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 S710.  Gene #66: 'del_19q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 37(19Q13.32) MUTATED 101 103 11
DEL PEAK 37(19Q13.32) WILD-TYPE 458 201 201

Figure S710.  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 S711.  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 37(19Q13.32) MUTATED 56 55 3 24 58 19
DEL PEAK 37(19Q13.32) WILD-TYPE 233 108 87 266 125 41

Figure S711.  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 S712.  Gene #66: 'del_19q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 37(19Q13.32) MUTATED 102 16 37 54
DEL PEAK 37(19Q13.32) WILD-TYPE 203 196 232 221

Figure S712.  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 S713.  Gene #66: 'del_19q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 37(19Q13.32) MUTATED 71 44 16 16 16 46
DEL PEAK 37(19Q13.32) WILD-TYPE 223 108 229 124 80 88

Figure S713.  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 S714.  Gene #66: 'del_19q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 37(19Q13.32) MUTATED 43 50 16 7 18
DEL PEAK 37(19Q13.32) WILD-TYPE 137 89 83 104 115

Figure S714.  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 S715.  Gene #66: 'del_19q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 37(19Q13.32) MUTATED 92 36 6
DEL PEAK 37(19Q13.32) WILD-TYPE 213 211 104

Figure S715.  Get High-res Image Gene #66: 'del_19q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p13' versus 'MRNA_CNMF'

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

Table S716.  Gene #67: 'del_20p13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 38(20P13) MUTATED 1 3 28 25 3 16 3 1
DEL PEAK 38(20P13) WILD-TYPE 20 33 91 71 106 56 17 39

Figure S716.  Get High-res Image Gene #67: 'del_20p13' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_20p13' versus 'MRNA_CHIERARCHICAL'

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

Table S717.  Gene #67: 'del_20p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 38(20P13) MUTATED 23 9 25 23 0
DEL PEAK 38(20P13) WILD-TYPE 78 143 89 65 58

Figure S717.  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 S718.  Gene #67: 'del_20p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 38(20P13) MUTATED 49 18 7 78 8
DEL PEAK 38(20P13) WILD-TYPE 226 389 91 179 35

Figure S718.  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 S719.  Gene #67: 'del_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 38(20P13) MUTATED 29 12 13 7 43 2
DEL PEAK 38(20P13) WILD-TYPE 115 87 200 116 92 57

Figure S719.  Get High-res Image Gene #67: 'del_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_20p13' versus 'RPPA_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00017

Table S720.  Gene #67: 'del_20p13' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 38(20P13) MUTATED 38 17 9
DEL PEAK 38(20P13) WILD-TYPE 113 106 116

Figure S720.  Get High-res Image Gene #67: 'del_20p13' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_20p13' versus 'RPPA_CHIERARCHICAL'

P value = 0.00648 (Fisher's exact test), Q value = 0.0077

Table S721.  Gene #67: 'del_20p13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
DEL PEAK 38(20P13) MUTATED 5 4 24 4 20 7
DEL PEAK 38(20P13) WILD-TYPE 59 42 66 48 96 24

Figure S721.  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 S722.  Gene #67: 'del_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 38(20P13) MUTATED 67 83 9
DEL PEAK 38(20P13) WILD-TYPE 492 221 203

Figure S722.  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 S723.  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 38(20P13) MUTATED 37 33 2 20 56 11
DEL PEAK 38(20P13) WILD-TYPE 252 130 88 270 127 49

Figure S723.  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 S724.  Gene #67: 'del_20p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 38(20P13) MUTATED 85 11 22 33
DEL PEAK 38(20P13) WILD-TYPE 220 201 247 242

Figure S724.  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 S725.  Gene #67: 'del_20p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 38(20P13) MUTATED 46 36 11 5 10 43
DEL PEAK 38(20P13) WILD-TYPE 248 116 234 135 86 91

Figure S725.  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 S726.  Gene #67: 'del_20p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 38(20P13) MUTATED 21 46 9 6 11
DEL PEAK 38(20P13) WILD-TYPE 159 93 90 105 122

Figure S726.  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 S727.  Gene #67: 'del_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
DEL PEAK 38(20P13) MUTATED 72 20 1
DEL PEAK 38(20P13) WILD-TYPE 233 227 109

Figure S727.  Get High-res Image Gene #67: 'del_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q11.2' versus 'MRNA_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00023

Table S728.  Gene #68: 'del_21q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 39(21Q11.2) MUTATED 3 11 37 16 11 23 3 4
DEL PEAK 39(21Q11.2) WILD-TYPE 18 25 82 80 98 49 17 36

Figure S728.  Get High-res Image Gene #68: 'del_21q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_21q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00426 (Fisher's exact test), Q value = 0.0051

Table S729.  Gene #68: 'del_21q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 39(21Q11.2) MUTATED 31 22 32 15 8
DEL PEAK 39(21Q11.2) WILD-TYPE 70 130 82 73 50

Figure S729.  Get High-res Image Gene #68: 'del_21q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_21q11.2' versus 'CN_CNMF'

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

Table S730.  Gene #68: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 39(21Q11.2) MUTATED 93 31 17 66 10
DEL PEAK 39(21Q11.2) WILD-TYPE 182 376 81 191 33

Figure S730.  Get High-res Image Gene #68: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00014

Table S731.  Gene #68: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 39(21Q11.2) MUTATED 47 26 28 18 22 8
DEL PEAK 39(21Q11.2) WILD-TYPE 97 73 185 105 113 51

Figure S731.  Get High-res Image Gene #68: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_21q11.2' versus 'RPPA_CNMF'

P value = 0.0431 (Fisher's exact test), Q value = 0.048

Table S732.  Gene #68: 'del_21q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
DEL PEAK 39(21Q11.2) MUTATED 44 23 22
DEL PEAK 39(21Q11.2) WILD-TYPE 107 100 103

Figure S732.  Get High-res Image Gene #68: 'del_21q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00823 (Fisher's exact test), Q value = 0.0097

Table S733.  Gene #68: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 39(21Q11.2) MUTATED 125 64 27
DEL PEAK 39(21Q11.2) WILD-TYPE 434 240 185

Figure S733.  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 S734.  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 39(21Q11.2) MUTATED 57 57 6 51 31 14
DEL PEAK 39(21Q11.2) WILD-TYPE 232 106 84 239 152 46

Figure S734.  Get High-res Image Gene #68: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00824 (Fisher's exact test), Q value = 0.0097

Table S735.  Gene #68: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 39(21Q11.2) MUTATED 74 28 48 62
DEL PEAK 39(21Q11.2) WILD-TYPE 231 184 221 213

Figure S735.  Get High-res Image Gene #68: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_21q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00057 (Fisher's exact test), Q value = 0.00074

Table S736.  Gene #68: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 39(21Q11.2) MUTATED 75 42 33 28 12 22
DEL PEAK 39(21Q11.2) WILD-TYPE 219 110 212 112 84 112

Figure S736.  Get High-res Image Gene #68: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0334 (Fisher's exact test), Q value = 0.038

Table S737.  Gene #68: 'del_21q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 39(21Q11.2) MUTATED 47 28 15 13 26
DEL PEAK 39(21Q11.2) WILD-TYPE 133 111 84 98 107

Figure S737.  Get High-res Image Gene #68: 'del_21q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_22q13.32' versus 'MRNA_CHIERARCHICAL'

P value = 0.00987 (Fisher's exact test), Q value = 0.012

Table S738.  Gene #69: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
DEL PEAK 40(22Q13.32) MUTATED 62 68 46 37 22
DEL PEAK 40(22Q13.32) WILD-TYPE 39 84 68 51 36

Figure S738.  Get High-res Image Gene #69: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

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

Table S739.  Gene #69: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
DEL PEAK 40(22Q13.32) MUTATED 147 144 60 122 19
DEL PEAK 40(22Q13.32) WILD-TYPE 128 263 38 135 24

Figure S739.  Get High-res Image Gene #69: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 0.00247 (Fisher's exact test), Q value = 0.003

Table S740.  Gene #69: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
DEL PEAK 40(22Q13.32) MUTATED 85 43 88 48 67 20
DEL PEAK 40(22Q13.32) WILD-TYPE 59 56 125 75 68 39

Figure S740.  Get High-res Image Gene #69: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 0.00152 (Fisher's exact test), Q value = 0.0019

Table S741.  Gene #69: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
DEL PEAK 40(22Q13.32) MUTATED 284 126 81
DEL PEAK 40(22Q13.32) WILD-TYPE 275 178 131

Figure S741.  Get High-res Image Gene #69: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00675 (Fisher's exact test), Q value = 0.008

Table S742.  Gene #69: '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 40(22Q13.32) MUTATED 140 89 33 134 77 18
DEL PEAK 40(22Q13.32) WILD-TYPE 149 74 57 156 106 42

Figure S742.  Get High-res Image Gene #69: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.00099

Table S743.  Gene #69: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
DEL PEAK 40(22Q13.32) MUTATED 139 72 139 133
DEL PEAK 40(22Q13.32) WILD-TYPE 166 140 130 142

Figure S743.  Get High-res Image Gene #69: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_22q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.00067

Table S744.  Gene #69: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
DEL PEAK 40(22Q13.32) MUTATED 163 68 90 68 38 56
DEL PEAK 40(22Q13.32) WILD-TYPE 131 84 155 72 58 78

Figure S744.  Get High-res Image Gene #69: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0026 (Fisher's exact test), Q value = 0.0032

Table S745.  Gene #69: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
DEL PEAK 40(22Q13.32) MUTATED 103 63 47 38 56
DEL PEAK 40(22Q13.32) WILD-TYPE 77 76 52 73 77

Figure S745.  Get High-res Image Gene #69: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_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/19785968/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BRCA-TP/20125499/BRCA-TP.transferedmergedcluster.txt

  • Number of patients = 1080

  • Number of significantly focal cnvs = 69

  • 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)
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