Correlation between copy number variation genes (focal events) and molecular subtypes
Lung Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1RN3782
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1RN3782
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 75 focal events and 12 molecular subtypes across 516 patients, 613 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1p34.3 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_3q26.2 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'.

  • amp_4q12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • amp_5q35.1 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_7p21.1 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_7q31.2 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • amp_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_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_12p12.1 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_12q14.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_13q33.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_16p11.2 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

  • 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', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_20p11.21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_20q13.33 cnv correlated to '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_22q11.22 cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • del_1p13.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

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

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

  • del_3q29 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • del_4q22.1 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_4q34.3 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_5q12.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_5q31.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_6q14.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_6q26 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_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 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • del_9p23 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_9p21.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_10p15.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • del_11q23.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

  • del_12p13.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_12q12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_12q24.33 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_13q12.11 cnv correlated to '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_13q34 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_14q32.33 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_15q11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_15q15.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • del_17p13.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_18q21.32 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • del_19p13.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_19q13.33 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_20q13.12 cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • del_xp22.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 75 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, 613 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
amp 3q26 2 169 (33%) 347 0.00058
(0.00138) 		0.00163
(0.00348) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.00273
(0.00547) 		0.00148
(0.0032) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.00016
(0.000435) 		1e-05
(3.95e-05)
amp 10p15 1 142 (28%) 374 0.0208
(0.0346) 		0.0166
(0.029) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.00025
(0.00065) 		0.00054
(0.0013) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		2e-05
(7e-05) 		1e-05
(3.95e-05) 		0.00012
(0.000339) 		0.00046
(0.00113)
del 4q22 1 158 (31%) 358 0.00194
(0.00407) 		0.00294
(0.00585) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.0205
(0.0343) 		0.00262
(0.00529) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.00333
(0.00659) 		0.00035
(0.000887)
del 4q34 3 187 (36%) 329 0.00197
(0.0041) 		0.00307
(0.00609) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.037
(0.0565) 		0.002
(0.00416) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		4e-05
(0.000124) 		2e-05
(7e-05)
del 8p23 2 254 (49%) 262 0.021
(0.0348) 		0.00945
(0.0172) 		1e-05
(3.95e-05) 		0.00551
(0.0104) 		0.0114
(0.0204) 		0.00147
(0.00319) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		9e-05
(0.000259) 		0.00019
(0.000507) 		0.00022
(0.000577) 		0.00383
(0.00749)
del 11p15 5 143 (28%) 373 0.0225
(0.0368) 		0.0317
(0.0493) 		1e-05
(3.95e-05) 		0.00042
(0.00104) 		0.022
(0.0362) 		0.00259
(0.00524) 		6e-05
(0.000181) 		1e-05
(3.95e-05) 		0.00057
(0.00136) 		2e-05
(7e-05) 		2e-05
(7e-05) 		0.0255
(0.0411)
amp 11q13 3 172 (33%) 344 0.00107
(0.00241) 		0.00116
(0.00261) 		1e-05
(3.95e-05) 		0.00016
(0.000435) 		0.18
(0.23) 		0.00381
(0.00747) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		4e-05
(0.000124)
amp 12p12 1 178 (34%) 338 0.0244
(0.0397) 		0.0382
(0.058) 		1e-05
(3.95e-05) 		0.00242
(0.00495) 		0.0567
(0.0819) 		0.0155
(0.0271) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.00076
(0.00176) 		4e-05
(0.000124)
amp 17q12 227 (44%) 289 0.0968
(0.131) 		0.0474
(0.0702) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.00136
(0.00298) 		0.00026
(0.000672) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		2e-05
(7e-05) 		1e-05
(3.95e-05) 		2e-05
(7e-05) 		1e-05
(3.95e-05)
amp 19q12 139 (27%) 377 0.0222
(0.0365) 		0.0409
(0.0614) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.00013
(0.000362) 		0.00258
(0.00523) 		0.00067
(0.00158) 		4e-05
(0.000124) 		1e-05
(3.95e-05) 		4e-05
(0.000124) 		0.0643
(0.0916) 		0.00103
(0.00233)
amp 20q13 33 251 (49%) 265 0.0664
(0.094) 		0.0433
(0.0647) 		1e-05
(3.95e-05) 		0.00019
(0.000507) 		0.0491
(0.0724) 		0.0016
(0.00343) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		3e-05
(9.75e-05) 		1e-05
(3.95e-05)
del 13q12 11 293 (57%) 223 0.105
(0.141) 		0.038
(0.0578) 		1e-05
(3.95e-05) 		0.0204
(0.0343) 		0.00033
(0.000841) 		0.0488
(0.0721) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.00174
(0.00369) 		0.00119
(0.00266) 		0.00196
(0.0041) 		0.00924
(0.0168)
amp 8q24 21 325 (63%) 191 0.163
(0.21) 		0.0876
(0.119) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.00566
(0.0107) 		0.037
(0.0565) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		4e-05
(0.000124) 		1e-05
(3.95e-05) 		2e-05
(7e-05)
amp 12q14 1 169 (33%) 347 0.229
(0.285) 		0.287
(0.345) 		1e-05
(3.95e-05) 		0.00013
(0.000362) 		0.00058
(0.00138) 		0.0463
(0.0686) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		8e-05
(0.000234) 		1e-05
(3.95e-05)
amp 12q15 169 (33%) 347 0.0585
(0.0842) 		0.0626
(0.0894) 		1e-05
(3.95e-05) 		0.00011
(0.000311) 		0.00057
(0.00136) 		0.01
(0.0181) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		3e-05
(9.75e-05) 		1e-05
(3.95e-05)
amp 14q13 3 233 (45%) 283 0.434
(0.49) 		0.536
(0.584) 		1e-05
(3.95e-05) 		4e-05
(0.000124) 		0.0246
(0.0398) 		0.0248
(0.04) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		2e-05
(7e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05)
amp 17q23 1 249 (48%) 267 0.458
(0.513) 		0.298
(0.355) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.0394
(0.0595) 		0.00272
(0.00546) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		4e-05
(0.000124) 		1e-05
(3.95e-05) 		0.00025
(0.00065) 		1e-05
(3.95e-05)
amp 18q11 2 105 (20%) 411 0.0336
(0.052) 		0.0201
(0.0338) 		2e-05
(7e-05) 		1e-05
(3.95e-05) 		0.603
(0.647) 		0.256
(0.312) 		0.00014
(0.000386) 		5e-05
(0.000152) 		3e-05
(9.75e-05) 		3e-05
(9.75e-05) 		1e-05
(3.95e-05) 		3e-05
(9.75e-05)
del 3p21 31 248 (48%) 268 0.204
(0.257) 		0.342
(0.396) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.0365
(0.056) 		0.0023
(0.00473) 		0.00715
(0.0133) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		2e-05
(7e-05) 		0.0113
(0.0202) 		2e-05
(7e-05)
del 4p16 3 130 (25%) 386 0.297
(0.355) 		0.308
(0.365) 		1e-05
(3.95e-05) 		0.00137
(0.00299) 		0.0211
(0.0348) 		0.0279
(0.0442) 		2e-05
(7e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.00533
(0.0101) 		0.00018
(0.000484)
del 5q12 1 179 (35%) 337 0.33
(0.386) 		0.184
(0.235) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		3e-05
(9.75e-05) 		3e-05
(9.75e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05)
del 5q31 1 211 (41%) 305 0.148
(0.192) 		0.242
(0.298) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		7e-05
(0.000207) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05)
del 9q21 11 258 (50%) 258 0.431
(0.489) 		0.484
(0.537) 		1e-05
(3.95e-05) 		0.00157
(0.00337) 		0.0196
(0.0331) 		0.00086
(0.00197) 		0.00128
(0.00283) 		7e-05
(0.000207) 		0.0001
(0.000286) 		1e-05
(3.95e-05) 		0.0172
(0.0298) 		0.00073
(0.00169)
del 16p13 3 111 (22%) 405 0.075
(0.104) 		0.0877
(0.119) 		1e-05
(3.95e-05) 		0.0001
(0.000286) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		4e-05
(0.000124) 		1e-05
(3.95e-05) 		0.00064
(0.00151)
del 16q23 1 169 (33%) 347 1
(1.00) 		0.878
(0.905) 		1e-05
(3.95e-05) 		4e-05
(0.000124) 		5e-05
(0.000152) 		0.00391
(0.0076) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.00759
(0.0141) 		0.00131
(0.00288) 		3e-05
(9.75e-05) 		0.00099
(0.00226)
del 16q24 3 188 (36%) 328 0.899
(0.92) 		0.894
(0.92) 		1e-05
(3.95e-05) 		0.00021
(0.000553) 		0.0233
(0.0379) 		0.0224
(0.0368) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.00882
(0.0162) 		0.00045
(0.00111) 		3e-05
(9.75e-05) 		9e-05
(0.000259)
del 19p13 3 276 (53%) 240 0.807
(0.835) 		0.813
(0.84) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.00101
(0.0023) 		0.036
(0.0554) 		2e-05
(7e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.00125
(0.00278) 		0.00045
(0.00111)
del 22q13 32 250 (48%) 266 0.432
(0.489) 		0.206
(0.26) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.00824
(0.0152) 		0.00038
(0.000955) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.00033
(0.000841) 		5e-05
(0.000152)
amp 5q35 1 126 (24%) 390 0.36
(0.415) 		0.287
(0.345) 		0.00069
(0.00162) 		0.0874
(0.119) 		0.00013
(0.000362) 		3e-05
(9.75e-05) 		0.00071
(0.00165) 		0.00197
(0.0041) 		0.0002
(0.000533) 		1e-05
(3.95e-05) 		0.0245
(0.0397) 		0.0171
(0.0297)
amp 8p11 21 175 (34%) 341 0.332
(0.388) 		0.441
(0.497) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.118
(0.156) 		0.00892
(0.0163) 		1e-05
(3.95e-05) 		2e-05
(7e-05) 		0.00037
(0.000933) 		2e-05
(7e-05) 		0.00252
(0.00513) 		0.00216
(0.00448)
amp 20p11 21 201 (39%) 315 0.0839
(0.115) 		0.0969
(0.131) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.384
(0.44) 		0.00573
(0.0108) 		2e-05
(7e-05) 		1e-05
(3.95e-05) 		2e-05
(7e-05) 		2e-05
(7e-05) 		0.00305
(0.00606) 		0.0007
(0.00164)
del 10q26 3 148 (29%) 368 0.554
(0.601) 		0.335
(0.391) 		1e-05
(3.95e-05) 		0.026
(0.0416) 		0.0301
(0.0471) 		0.569
(0.616) 		2e-05
(7e-05) 		1e-05
(3.95e-05) 		0.0132
(0.0233) 		1e-05
(3.95e-05) 		0.0104
(0.0188) 		0.00231
(0.00474)
del 15q11 2 263 (51%) 253 0.655
(0.699) 		0.469
(0.523) 		1e-05
(3.95e-05) 		4e-05
(0.000124) 		0.0177
(0.0303) 		0.488
(0.541) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		7e-05
(0.000207) 		0.00046
(0.00113) 		0.00407
(0.00784) 		0.00036
(0.00091)
del 15q15 1 275 (53%) 241 0.203
(0.256) 		0.16
(0.206) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.0294
(0.0464) 		0.327
(0.383) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		9e-05
(0.000259) 		0.00229
(0.00472) 		0.0005
(0.00121)
del 17p13 3 281 (54%) 235 0.661
(0.703) 		0.581
(0.625) 		1e-05
(3.95e-05) 		4e-05
(0.000124) 		0.0186
(0.0315) 		0.874
(0.902) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.0186
(0.0315) 		0.0313
(0.0489) 		3e-05
(9.75e-05) 		0.00343
(0.00677)
del 19p13 2 269 (52%) 247 0.9
(0.92) 		1
(1.00) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.00083
(0.00192) 		0.203
(0.257) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		2e-05
(7e-05) 		0.0003
(0.000769)
del 19q13 33 195 (38%) 321 0.0863
(0.118) 		0.253
(0.309) 		1e-05
(3.95e-05) 		2e-05
(7e-05) 		0.0173
(0.0298) 		0.00151
(0.00326) 		0.00129
(0.00285) 		1e-05
(3.95e-05) 		2e-05
(7e-05) 		3e-05
(9.75e-05) 		0.0652
(0.0927) 		0.0135
(0.0239)
del 21q11 2 179 (35%) 337 0.0932
(0.127) 		0.145
(0.188) 		1e-05
(3.95e-05) 		0.00039
(0.000978) 		0.00401
(0.00774) 		0.0513
(0.075) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		3e-05
(9.75e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05)
amp 1q21 3 377 (73%) 139 0.288
(0.346) 		0.516
(0.569) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.00011
(0.000311) 		0.0806
(0.111) 		0.00014
(0.000386) 		0.00023
(0.000602) 		0.00514
(0.00982) 		2e-05
(7e-05) 		0.0142
(0.025) 		0.192
(0.244)
amp 4q12 96 (19%) 420 0.294
(0.352) 		0.252
(0.309) 		1e-05
(3.95e-05) 		0.00173
(0.00369) 		0.753
(0.787) 		0.0216
(0.0357) 		0.00042
(0.00104) 		0.00014
(0.000386) 		0.00101
(0.0023) 		0.00071
(0.00165) 		0.792
(0.824) 		0.00251
(0.00512)
amp 5p15 33 333 (65%) 183 0.638
(0.682) 		0.805
(0.834) 		1e-05
(3.95e-05) 		0.00378
(0.00743) 		0.132
(0.173) 		0.7
(0.742) 		1e-05
(3.95e-05) 		5e-05
(0.000152) 		0.00385
(0.00752) 		0.00128
(0.00283) 		0.00015
(0.00041) 		1e-05
(3.95e-05)
amp 5p13 1 304 (59%) 212 1
(1.00) 		1
(1.00) 		1e-05
(3.95e-05) 		0.00029
(0.000748) 		0.236
(0.292) 		0.602
(0.646) 		1e-05
(3.95e-05) 		2e-05
(7e-05) 		0.0003
(0.000769) 		0.0005
(0.00121) 		7e-05
(0.000207) 		1e-05
(3.95e-05)
amp 7p21 1 284 (55%) 232 0.735
(0.77) 		0.9
(0.92) 		1e-05
(3.95e-05) 		0.0712
(0.0999) 		0.0295
(0.0464) 		0.115
(0.153) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		7e-05
(0.000207) 		3e-05
(9.75e-05) 		0.0269
(0.0428) 		4e-05
(0.000124)
amp 7p11 2 274 (53%) 242 0.731
(0.769) 		0.901
(0.92) 		1e-05
(3.95e-05) 		0.0518
(0.0755) 		0.0676
(0.0955) 		0.0174
(0.03) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.00021
(0.000553) 		1e-05
(3.95e-05)
amp 7q31 2 218 (42%) 298 0.53
(0.579) 		0.39
(0.446) 		1e-05
(3.95e-05) 		0.44
(0.496) 		0.0378
(0.0576) 		0.157
(0.203) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.00178
(0.00376) 		0.00126
(0.0028) 		0.00857
(0.0157) 		1e-05
(3.95e-05)
amp xq28 159 (31%) 357 0.148
(0.192) 		0.242
(0.298) 		3e-05
(9.75e-05) 		0.018
(0.0307) 		0.0279
(0.0443) 		0.213
(0.267) 		5e-05
(0.000152) 		0.00015
(0.00041) 		0.0109
(0.0195) 		0.11
(0.147) 		0.0295
(0.0464) 		0.00013
(0.000362)
del 3p26 2 233 (45%) 283 0.192
(0.244) 		0.244
(0.299) 		1e-05
(3.95e-05) 		0.00047
(0.00115) 		0.0497
(0.0731) 		0.012
(0.0214) 		0.0532
(0.0773) 		1e-05
(3.95e-05) 		0.00026
(0.000672) 		7e-05
(0.000207) 		0.0787
(0.109) 		0.00015
(0.00041)
del 12q12 99 (19%) 417 1
(1.00) 		0.75
(0.785) 		1e-05
(3.95e-05) 		0.00392
(0.0076) 		0.00089
(0.00204) 		0.455
(0.51) 		0.00184
(0.00387) 		0.0408
(0.0614) 		0.0569
(0.082) 		0.0215
(0.0355) 		0.0423
(0.0633) 		0.0366
(0.0561)
del 18q21 32 255 (49%) 261 0.0357
(0.0549) 		0.0776
(0.108) 		1e-05
(3.95e-05) 		0.608
(0.652) 		0.00106
(0.0024) 		0.018
(0.0307) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.00222
(0.00458) 		0.308
(0.365) 		0.0509
(0.0746) 		0.0172
(0.0298)
del 18q23 249 (48%) 267 0.00705
(0.0131) 		0.026
(0.0416) 		1e-05
(3.95e-05) 		0.381
(0.438) 		0.00049
(0.0012) 		0.0109
(0.0195) 		1e-05
(3.95e-05) 		4e-05
(0.000124) 		0.00141
(0.00307) 		0.298
(0.355) 		0.0713
(0.1) 		0.0564
(0.0816)
amp 1p34 3 137 (27%) 379 0.731
(0.769) 		0.521
(0.571) 		1e-05
(3.95e-05) 		0.281
(0.339) 		0.00011
(0.000311) 		0.0066
(0.0123) 		0.00256
(0.0052) 		0.00887
(0.0162) 		0.267
(0.324) 		0.0141
(0.0248) 		0.541
(0.588) 		0.0229
(0.0374)
amp 6p21 1 189 (37%) 327 0.276
(0.335) 		0.223
(0.278) 		3e-05
(9.75e-05) 		1e-05
(3.95e-05) 		0.188
(0.239) 		0.362
(0.417) 		0.00393
(0.00761) 		0.0148
(0.026) 		0.0355
(0.0548) 		0.00639
(0.0119) 		0.00174
(0.00369) 		0.0604
(0.0868)
del 1p36 13 122 (24%) 394 0.24
(0.297) 		0.316
(0.372) 		1e-05
(3.95e-05) 		0.00018
(0.000484) 		0.135
(0.177) 		0.201
(0.254) 		1e-05
(3.95e-05) 		1e-05
(3.95e-05) 		0.0208
(0.0346) 		0.0111
(0.0199) 		0.00218
(0.00451) 		0.0805
(0.111)
del 2q22 1 46 (9%) 470 0.531
(0.58) 		0.518
(0.57) 		0.00125
(0.00278) 		0.00145
(0.00315) 		0.102
(0.137) 		0.00175
(0.00371) 		0.182
(0.233) 		0.00574
(0.0108) 		0.017
(0.0295) 		0.0229
(0.0374) 		0.498
(0.551) 		0.0385
(0.0583)
del 3q29 136 (26%) 380 0.732
(0.769) 		0.614
(0.657) 		0.0264
(0.0422) 		0.011
(0.0198) 		0.109
(0.146) 		0.0258
(0.0415) 		0.00048
(0.00117) 		1e-05
(3.95e-05) 		0.574
(0.62) 		0.00134
(0.00294) 		0.00279
(0.00558) 		0.898
(0.92)
del 10p15 3 131 (25%) 385 1
(1.00) 		1
(1.00) 		1e-05
(3.95e-05) 		0.0198
(0.0334) 		0.499
(0.551) 		0.987
(1.00) 		0.00056
(0.00134) 		0.00119
(0.00266) 		0.00387
(0.00754) 		0.00017
(0.000459) 		0.0127
(0.0225) 		0.129
(0.17)
del 11q23 1 120 (23%) 396 1
(1.00) 		1
(1.00) 		1e-05
(3.95e-05) 		8e-05
(0.000234) 		0.0302
(0.0472) 		0.0797
(0.11) 		2e-05
(7e-05) 		0.00055
(0.00132) 		0.005
(0.00959) 		0.056
(0.0811) 		0.00156
(0.00336) 		0.654
(0.698)
del 11q25 115 (22%) 401 0.466
(0.521) 		0.483
(0.536) 		3e-05
(9.75e-05) 		0.00035
(0.000887) 		0.014
(0.0247) 		0.0533
(0.0773) 		9e-05
(0.000259) 		0.00287
(0.00573) 		0.0495
(0.0729) 		0.268
(0.326) 		0.00068
(0.0016) 		0.799
(0.83)
del 20p13 130 (25%) 386 0.466
(0.521) 		0.314
(0.37) 		0.00017
(0.000459) 		0.00085
(0.00196) 		0.0281
(0.0445) 		0.243
(0.298) 		2e-05
(7e-05) 		1e-05
(3.95e-05) 		0.938
(0.956) 		0.587
(0.632) 		0.0174
(0.0299) 		0.0288
(0.0455)
del 1p13 1 151 (29%) 365 0.238
(0.294) 		0.451
(0.507) 		1e-05
(3.95e-05) 		0.00541
(0.0103) 		0.0528
(0.0769) 		0.524
(0.575) 		1e-05
(3.95e-05) 		7e-05
(0.000207) 		0.0772
(0.107) 		2e-05
(7e-05) 		0.00509
(0.00975) 		0.574
(0.62)
del 13q34 241 (47%) 275 0.0766
(0.107) 		0.113
(0.15) 		1e-05
(3.95e-05) 		0.0791
(0.109) 		0.00272
(0.00546) 		0.328
(0.384) 		3e-05
(9.75e-05) 		1e-05
(3.95e-05) 		0.00949
(0.0172) 		0.00606
(0.0113) 		0.132
(0.173) 		0.0735
(0.103)
amp 16p11 2 167 (32%) 349 0.727
(0.768) 		0.532
(0.581) 		1e-05
(3.95e-05) 		0.48
(0.534) 		0.0196
(0.0331) 		0.762
(0.796) 		0.0685
(0.0965) 		0.0332
(0.0516) 		0.0456
(0.0678) 		0.0159
(0.0277) 		0.517
(0.57) 		0.348
(0.404)
del 9p21 3 294 (57%) 222 0.897
(0.92) 		1
(1.00) 		1e-05
(3.95e-05) 		0.0979
(0.132) 		0.314
(0.37) 		0.222
(0.277) 		0.00021
(0.000553) 		2e-05
(7e-05) 		0.143
(0.187) 		0.00823
(0.0152) 		0.379
(0.435) 		0.0441
(0.0658)
del 12p13 2 140 (27%) 376 1
(1.00) 		0.897
(0.92) 		1e-05
(3.95e-05) 		0.0451
(0.0672) 		0.0117
(0.0208) 		0.241
(0.297) 		0.00053
(0.00128) 		0.0056
(0.0106) 		0.983
(0.999) 		0.959
(0.977) 		0.434
(0.49) 		0.102
(0.137)
del xp22 2 145 (28%) 371 1
(1.00) 		1
(1.00) 		3e-05
(9.75e-05) 		0.0176
(0.0301) 		0.0207
(0.0345) 		0.0973
(0.131) 		2e-05
(7e-05) 		9e-05
(0.000259) 		0.554
(0.601) 		0.453
(0.508) 		0.398
(0.454) 		0.0635
(0.0906)
amp 13q33 3 76 (15%) 440 0.733
(0.769) 		0.52
(0.571) 		0.0498
(0.0732) 		0.00021
(0.000553) 		0.138
(0.181) 		0.43
(0.488) 		0.308
(0.365) 		0.0321
(0.05) 		0.283
(0.341) 		0.169
(0.217) 		0.0612
(0.0877) 		0.0403
(0.0607)
amp 22q11 22 90 (17%) 426 0.403
(0.459) 		0.123
(0.163) 		0.00775
(0.0143) 		0.338
(0.393) 		0.283
(0.341) 		0.0608
(0.0873) 		0.159
(0.205) 		0.0662
(0.0939) 		0.0417
(0.0625) 		0.0659
(0.0936) 		0.0353
(0.0545) 		0.0268
(0.0427)
del 3q11 1 141 (27%) 375 0.679
(0.72) 		0.686
(0.727) 		5e-05
(0.000152) 		0.0206
(0.0345) 		0.148
(0.192) 		0.721
(0.763) 		0.325
(0.381) 		0.0387
(0.0586) 		0.171
(0.219) 		0.0258
(0.0415) 		0.66
(0.703) 		0.474
(0.528)
del 6q14 3 253 (49%) 263 0.901
(0.92) 		0.73
(0.769) 		0.0302
(0.0472) 		1e-05
(3.95e-05) 		0.417
(0.474) 		0.207
(0.26) 		0.221
(0.276) 		0.00042
(0.00104) 		0.307
(0.365) 		0.00179
(0.00377) 		0.314
(0.37) 		0.0779
(0.108)
del 12q24 33 133 (26%) 383 0.0723
(0.101) 		0.0696
(0.0979) 		1e-05
(3.95e-05) 		0.406
(0.462) 		0.00442
(0.0085) 		0.15
(0.194) 		3e-05
(9.75e-05) 		8e-05
(0.000234) 		0.278
(0.337) 		0.0512
(0.0749) 		0.0683
(0.0964) 		0.775
(0.807)
del 14q32 33 150 (29%) 366 0.23
(0.286) 		0.289
(0.346) 		1e-05
(3.95e-05) 		0.00578
(0.0108) 		0.392
(0.448) 		0.3
(0.357) 		0.727
(0.768) 		0.0277
(0.0441) 		0.0209
(0.0348) 		0.11
(0.147) 		0.801
(0.832) 		0.222
(0.277)
del 6q26 258 (50%) 258 0.22
(0.276) 		0.333
(0.389) 		0.0975
(0.132) 		1e-05
(3.95e-05) 		0.247
(0.302) 		0.206
(0.259) 		0.339
(0.394) 		0.00519
(0.0099) 		0.675
(0.717) 		0.0152
(0.0266) 		0.387
(0.443) 		0.144
(0.188)
del 9p23 287 (56%) 229 1
(1.00) 		0.804
(0.834) 		1e-05
(3.95e-05) 		0.116
(0.154) 		0.363
(0.418) 		0.356
(0.412) 		0.046
(0.0684) 		0.00061
(0.00144) 		0.196
(0.249) 		0.062
(0.0887) 		0.765
(0.797) 		0.0806
(0.111)
del 8p11 21 125 (24%) 391 0.569
(0.616) 		0.508
(0.561) 		1e-05
(3.95e-05) 		0.243
(0.298) 		0.569
(0.616) 		0.444
(0.5) 		0.0182
(0.031) 		0.111
(0.148) 		0.295
(0.353) 		0.529
(0.579) 		0.276
(0.335) 		0.109
(0.146)
del 20q13 12 82 (16%) 434 0.213
(0.267) 		0.578
(0.623) 		0.352
(0.407) 		0.327
(0.383) 		0.0867
(0.118) 		0.152
(0.197) 		0.255
(0.311) 		0.00369
(0.00727) 		0.111
(0.148) 		0.0351
(0.0543) 		0.0741
(0.103) 		0.123
(0.163)
'amp_1p34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S1.  Gene #1: 'amp_1p34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
AMP PEAK 1(1P34.3) MUTATED 78 27 17 15
AMP PEAK 1(1P34.3) WILD-TYPE 94 111 115 59

Figure S1.  Get High-res Image Gene #1: 'amp_1p34.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1p34.3' versus 'RPPA_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00031

Table S2.  Gene #1: 'amp_1p34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
AMP PEAK 1(1P34.3) MUTATED 38 4 24 22 15
AMP PEAK 1(1P34.3) WILD-TYPE 53 18 42 53 94

Figure S2.  Get High-res Image Gene #1: 'amp_1p34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_1p34.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0066 (Fisher's exact test), Q value = 0.012

Table S3.  Gene #1: 'amp_1p34.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
AMP PEAK 1(1P34.3) MUTATED 52 43 8
AMP PEAK 1(1P34.3) WILD-TYPE 115 90 55

Figure S3.  Get High-res Image Gene #1: 'amp_1p34.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_1p34.3' versus 'MRNASEQ_CNMF'

P value = 0.00256 (Fisher's exact test), Q value = 0.0052

Table S4.  Gene #1: 'amp_1p34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
AMP PEAK 1(1P34.3) MUTATED 47 31 13 34 10
AMP PEAK 1(1P34.3) WILD-TYPE 83 88 77 81 48

Figure S4.  Get High-res Image Gene #1: 'amp_1p34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1p34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00887 (Fisher's exact test), Q value = 0.016

Table S5.  Gene #1: 'amp_1p34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 1(1P34.3) MUTATED 23 29 40 8 11 9 15
AMP PEAK 1(1P34.3) WILD-TYPE 55 81 57 40 42 40 62

Figure S5.  Get High-res Image Gene #1: 'amp_1p34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1p34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0141 (Fisher's exact test), Q value = 0.025

Table S6.  Gene #1: 'amp_1p34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
AMP PEAK 1(1P34.3) MUTATED 14 8 37 28 39 10
AMP PEAK 1(1P34.3) WILD-TYPE 57 31 108 102 57 19

Figure S6.  Get High-res Image Gene #1: 'amp_1p34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1p34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0229 (Fisher's exact test), Q value = 0.037

Table S7.  Gene #1: 'amp_1p34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
AMP PEAK 1(1P34.3) MUTATED 20 66 34
AMP PEAK 1(1P34.3) WILD-TYPE 84 172 58

Figure S7.  Get High-res Image Gene #1: 'amp_1p34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S8.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
AMP PEAK 2(1Q21.3) MUTATED 141 98 71 67
AMP PEAK 2(1Q21.3) WILD-TYPE 31 40 61 7

Figure S8.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S9.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
AMP PEAK 2(1Q21.3) MUTATED 131 134 71
AMP PEAK 2(1Q21.3) WILD-TYPE 25 36 58

Figure S9.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q21.3' versus 'RPPA_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00031

Table S10.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
AMP PEAK 2(1Q21.3) MUTATED 74 17 60 58 66
AMP PEAK 2(1Q21.3) WILD-TYPE 17 5 6 17 43

Figure S10.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00039

Table S11.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
AMP PEAK 2(1Q21.3) MUTATED 106 82 54 95 37
AMP PEAK 2(1Q21.3) WILD-TYPE 24 37 36 20 21

Figure S11.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 6e-04

Table S12.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 2(1Q21.3) MUTATED 54 78 69 45 45 38 45
AMP PEAK 2(1Q21.3) WILD-TYPE 24 32 28 3 8 11 32

Figure S12.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 0.00514 (Fisher's exact test), Q value = 0.0098

Table S13.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
AMP PEAK 2(1Q21.3) MUTATED 124 177 71
AMP PEAK 2(1Q21.3) WILD-TYPE 62 44 32

Figure S13.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S14.  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 71 39 145 130 96 29
AMP PEAK 2(1Q21.3) MUTATED 55 37 112 75 76 17
AMP PEAK 2(1Q21.3) WILD-TYPE 16 2 33 55 20 12

Figure S14.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.025

Table S15.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
AMP PEAK 2(1Q21.3) MUTATED 38 78 68 27 52 55
AMP PEAK 2(1Q21.3) WILD-TYPE 21 12 27 16 18 22

Figure S15.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'MRNA_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.0014

Table S16.  Gene #3: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 10 7
AMP PEAK 3(3Q26.2) MUTATED 0 6 4
AMP PEAK 3(3Q26.2) WILD-TYPE 15 4 3

Figure S16.  Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00163 (Fisher's exact test), Q value = 0.0035

Table S17.  Gene #3: 'amp_3q26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
AMP PEAK 3(3Q26.2) MUTATED 0 6 4
AMP PEAK 3(3Q26.2) WILD-TYPE 14 5 3

Figure S17.  Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S18.  Gene #3: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
AMP PEAK 3(3Q26.2) MUTATED 52 80 14 23
AMP PEAK 3(3Q26.2) WILD-TYPE 120 58 118 51

Figure S18.  Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S19.  Gene #3: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
AMP PEAK 3(3Q26.2) MUTATED 71 51 23
AMP PEAK 3(3Q26.2) WILD-TYPE 85 119 106

Figure S19.  Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'RPPA_CNMF'

P value = 0.00273 (Fisher's exact test), Q value = 0.0055

Table S20.  Gene #3: 'amp_3q26.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
AMP PEAK 3(3Q26.2) MUTATED 28 7 17 40 30
AMP PEAK 3(3Q26.2) WILD-TYPE 63 15 49 35 79

Figure S20.  Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_3q26.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00148 (Fisher's exact test), Q value = 0.0032

Table S21.  Gene #3: 'amp_3q26.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
AMP PEAK 3(3Q26.2) MUTATED 43 60 19
AMP PEAK 3(3Q26.2) WILD-TYPE 124 73 44

Figure S21.  Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_3q26.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S22.  Gene #3: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
AMP PEAK 3(3Q26.2) MUTATED 51 7 41 55 15
AMP PEAK 3(3Q26.2) WILD-TYPE 79 112 49 60 43

Figure S22.  Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S23.  Gene #3: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 3(3Q26.2) MUTATED 8 39 64 5 17 19 17
AMP PEAK 3(3Q26.2) WILD-TYPE 70 71 33 43 36 30 60

Figure S23.  Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S24.  Gene #3: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
AMP PEAK 3(3Q26.2) MUTATED 39 102 26
AMP PEAK 3(3Q26.2) WILD-TYPE 147 119 77

Figure S24.  Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S25.  Gene #3: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
AMP PEAK 3(3Q26.2) MUTATED 11 14 53 34 52 3
AMP PEAK 3(3Q26.2) WILD-TYPE 60 25 92 96 44 26

Figure S25.  Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00044

Table S26.  Gene #3: 'amp_3q26.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
AMP PEAK 3(3Q26.2) MUTATED 6 35 42 10 21 26
AMP PEAK 3(3Q26.2) WILD-TYPE 53 55 53 33 49 51

Figure S26.  Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S27.  Gene #3: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
AMP PEAK 3(3Q26.2) MUTATED 16 94 30
AMP PEAK 3(3Q26.2) WILD-TYPE 88 144 62

Figure S27.  Get High-res Image Gene #3: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S28.  Gene #4: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
AMP PEAK 4(4Q12) MUTATED 46 34 7 9
AMP PEAK 4(4Q12) WILD-TYPE 126 104 125 65

Figure S28.  Get High-res Image Gene #4: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_4q12' versus 'METHLYATION_CNMF'

P value = 0.00173 (Fisher's exact test), Q value = 0.0037

Table S29.  Gene #4: 'amp_4q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
AMP PEAK 4(4Q12) MUTATED 37 34 11
AMP PEAK 4(4Q12) WILD-TYPE 119 136 118

Figure S29.  Get High-res Image Gene #4: 'amp_4q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_4q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.0216 (Fisher's exact test), Q value = 0.036

Table S30.  Gene #4: 'amp_4q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
AMP PEAK 4(4Q12) MUTATED 24 36 11
AMP PEAK 4(4Q12) WILD-TYPE 143 97 52

Figure S30.  Get High-res Image Gene #4: 'amp_4q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_4q12' versus 'MRNASEQ_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.001

Table S31.  Gene #4: 'amp_4q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
AMP PEAK 4(4Q12) MUTATED 38 11 15 26 6
AMP PEAK 4(4Q12) WILD-TYPE 92 108 75 89 52

Figure S31.  Get High-res Image Gene #4: 'amp_4q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_4q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00039

Table S32.  Gene #4: 'amp_4q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 4(4Q12) MUTATED 8 29 29 5 9 11 5
AMP PEAK 4(4Q12) WILD-TYPE 70 81 68 43 44 38 72

Figure S32.  Get High-res Image Gene #4: 'amp_4q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_4q12' versus 'MIRSEQ_CNMF'

P value = 0.00101 (Fisher's exact test), Q value = 0.0023

Table S33.  Gene #4: 'amp_4q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
AMP PEAK 4(4Q12) MUTATED 20 54 22
AMP PEAK 4(4Q12) WILD-TYPE 166 167 81

Figure S33.  Get High-res Image Gene #4: 'amp_4q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_4q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00071 (Fisher's exact test), Q value = 0.0017

Table S34.  Gene #4: 'amp_4q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
AMP PEAK 4(4Q12) MUTATED 8 7 39 12 21 9
AMP PEAK 4(4Q12) WILD-TYPE 63 32 106 118 75 20

Figure S34.  Get High-res Image Gene #4: 'amp_4q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_4q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00251 (Fisher's exact test), Q value = 0.0051

Table S35.  Gene #4: 'amp_4q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
AMP PEAK 4(4Q12) MUTATED 8 54 17
AMP PEAK 4(4Q12) WILD-TYPE 96 184 75

Figure S35.  Get High-res Image Gene #4: 'amp_4q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S36.  Gene #5: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
AMP PEAK 5(5P15.33) MUTATED 157 78 45 53
AMP PEAK 5(5P15.33) WILD-TYPE 15 60 87 21

Figure S36.  Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 0.00378 (Fisher's exact test), Q value = 0.0074

Table S37.  Gene #5: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
AMP PEAK 5(5P15.33) MUTATED 114 113 70
AMP PEAK 5(5P15.33) WILD-TYPE 42 57 59

Figure S37.  Get High-res Image Gene #5: '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 = 3.9e-05

Table S38.  Gene #5: 'amp_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
AMP PEAK 5(5P15.33) MUTATED 111 63 38 81 37
AMP PEAK 5(5P15.33) WILD-TYPE 19 56 52 34 21

Figure S38.  Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00015

Table S39.  Gene #5: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 5(5P15.33) MUTATED 48 81 77 22 35 29 38
AMP PEAK 5(5P15.33) WILD-TYPE 30 29 20 26 18 20 39

Figure S39.  Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 0.00385 (Fisher's exact test), Q value = 0.0075

Table S40.  Gene #5: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
AMP PEAK 5(5P15.33) MUTATED 105 160 67
AMP PEAK 5(5P15.33) WILD-TYPE 81 61 36

Figure S40.  Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00128 (Fisher's exact test), Q value = 0.0028

Table S41.  Gene #5: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
AMP PEAK 5(5P15.33) MUTATED 45 26 104 66 73 18
AMP PEAK 5(5P15.33) WILD-TYPE 26 13 41 64 23 11

Figure S41.  Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00041

Table S42.  Gene #5: 'amp_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
AMP PEAK 5(5P15.33) MUTATED 25 72 65 26 42 56
AMP PEAK 5(5P15.33) WILD-TYPE 34 18 30 17 28 21

Figure S42.  Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S43.  Gene #5: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
AMP PEAK 5(5P15.33) MUTATED 46 179 61
AMP PEAK 5(5P15.33) WILD-TYPE 58 59 31

Figure S43.  Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S44.  Gene #6: 'amp_5p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
AMP PEAK 6(5P13.1) MUTATED 142 69 40 53
AMP PEAK 6(5P13.1) WILD-TYPE 30 69 92 21

Figure S44.  Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p13.1' versus 'METHLYATION_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.00075

Table S45.  Gene #6: 'amp_5p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
AMP PEAK 6(5P13.1) MUTATED 111 101 62
AMP PEAK 6(5P13.1) WILD-TYPE 45 69 67

Figure S45.  Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_5p13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S46.  Gene #6: 'amp_5p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
AMP PEAK 6(5P13.1) MUTATED 93 56 33 83 36
AMP PEAK 6(5P13.1) WILD-TYPE 37 63 57 32 22

Figure S46.  Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S47.  Gene #6: 'amp_5p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 6(5P13.1) MUTATED 42 71 74 18 37 25 34
AMP PEAK 6(5P13.1) WILD-TYPE 36 39 23 30 16 24 43

Figure S47.  Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5p13.1' versus 'MIRSEQ_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.00077

Table S48.  Gene #6: 'amp_5p13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
AMP PEAK 6(5P13.1) MUTATED 91 151 61
AMP PEAK 6(5P13.1) WILD-TYPE 95 70 42

Figure S48.  Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_5p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.0012

Table S49.  Gene #6: 'amp_5p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
AMP PEAK 6(5P13.1) MUTATED 39 26 96 57 68 17
AMP PEAK 6(5P13.1) WILD-TYPE 32 13 49 73 28 12

Figure S49.  Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5p13.1' versus 'MIRSEQ_MATURE_CNMF'

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

Table S50.  Gene #6: 'amp_5p13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
AMP PEAK 6(5P13.1) MUTATED 23 71 54 25 39 50
AMP PEAK 6(5P13.1) WILD-TYPE 36 19 41 18 31 27

Figure S50.  Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_5p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S51.  Gene #6: 'amp_5p13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
AMP PEAK 6(5P13.1) MUTATED 40 169 53
AMP PEAK 6(5P13.1) WILD-TYPE 64 69 39

Figure S51.  Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5q35.1' versus 'CN_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0016

Table S52.  Gene #7: 'amp_5q35.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
AMP PEAK 7(5Q35.1) MUTATED 59 22 33 12
AMP PEAK 7(5Q35.1) WILD-TYPE 113 116 99 62

Figure S52.  Get High-res Image Gene #7: 'amp_5q35.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5q35.1' versus 'RPPA_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00036

Table S53.  Gene #7: 'amp_5q35.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
AMP PEAK 7(5Q35.1) MUTATED 27 4 26 6 24
AMP PEAK 7(5Q35.1) WILD-TYPE 64 18 40 69 85

Figure S53.  Get High-res Image Gene #7: 'amp_5q35.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_5q35.1' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S54.  Gene #7: 'amp_5q35.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
AMP PEAK 7(5Q35.1) MUTATED 56 14 17
AMP PEAK 7(5Q35.1) WILD-TYPE 111 119 46

Figure S54.  Get High-res Image Gene #7: 'amp_5q35.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_5q35.1' versus 'MRNASEQ_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0017

Table S55.  Gene #7: 'amp_5q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
AMP PEAK 7(5Q35.1) MUTATED 31 44 11 22 16
AMP PEAK 7(5Q35.1) WILD-TYPE 99 75 79 93 42

Figure S55.  Get High-res Image Gene #7: 'amp_5q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00197 (Fisher's exact test), Q value = 0.0041

Table S56.  Gene #7: 'amp_5q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 7(5Q35.1) MUTATED 33 23 24 13 9 5 17
AMP PEAK 7(5Q35.1) WILD-TYPE 45 87 73 35 44 44 60

Figure S56.  Get High-res Image Gene #7: 'amp_5q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5q35.1' versus 'MIRSEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.00053

Table S57.  Gene #7: 'amp_5q35.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
AMP PEAK 7(5Q35.1) MUTATED 61 36 29
AMP PEAK 7(5Q35.1) WILD-TYPE 125 185 74

Figure S57.  Get High-res Image Gene #7: 'amp_5q35.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_5q35.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S58.  Gene #7: 'amp_5q35.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
AMP PEAK 7(5Q35.1) MUTATED 35 11 24 32 12 12
AMP PEAK 7(5Q35.1) WILD-TYPE 36 28 121 98 84 17

Figure S58.  Get High-res Image Gene #7: 'amp_5q35.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5q35.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0245 (Fisher's exact test), Q value = 0.04

Table S59.  Gene #7: 'amp_5q35.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
AMP PEAK 7(5Q35.1) MUTATED 20 12 21 15 20 19
AMP PEAK 7(5Q35.1) WILD-TYPE 39 78 74 28 50 58

Figure S59.  Get High-res Image Gene #7: 'amp_5q35.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_5q35.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0171 (Fisher's exact test), Q value = 0.03

Table S60.  Gene #7: 'amp_5q35.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
AMP PEAK 7(5Q35.1) MUTATED 33 46 28
AMP PEAK 7(5Q35.1) WILD-TYPE 71 192 64

Figure S60.  Get High-res Image Gene #7: 'amp_5q35.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6p21.1' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S61.  Gene #8: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
AMP PEAK 8(6P21.1) MUTATED 69 49 30 41
AMP PEAK 8(6P21.1) WILD-TYPE 103 89 102 33

Figure S61.  Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S62.  Gene #8: 'amp_6p21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
AMP PEAK 8(6P21.1) MUTATED 75 68 26
AMP PEAK 8(6P21.1) WILD-TYPE 81 102 103

Figure S62.  Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CNMF'

P value = 0.00393 (Fisher's exact test), Q value = 0.0076

Table S63.  Gene #8: 'amp_6p21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
AMP PEAK 8(6P21.1) MUTATED 49 41 21 57 20
AMP PEAK 8(6P21.1) WILD-TYPE 81 78 69 58 38

Figure S63.  Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0148 (Fisher's exact test), Q value = 0.026

Table S64.  Gene #8: 'amp_6p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 8(6P21.1) MUTATED 25 36 44 23 25 17 18
AMP PEAK 8(6P21.1) WILD-TYPE 53 74 53 25 28 32 59

Figure S64.  Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_CNMF'

P value = 0.0355 (Fisher's exact test), Q value = 0.055

Table S65.  Gene #8: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
AMP PEAK 8(6P21.1) MUTATED 57 94 34
AMP PEAK 8(6P21.1) WILD-TYPE 129 127 69

Figure S65.  Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_6p21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00639 (Fisher's exact test), Q value = 0.012

Table S66.  Gene #8: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
AMP PEAK 8(6P21.1) MUTATED 22 15 65 32 42 9
AMP PEAK 8(6P21.1) WILD-TYPE 49 24 80 98 54 20

Figure S66.  Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00174 (Fisher's exact test), Q value = 0.0037

Table S67.  Gene #8: 'amp_6p21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
AMP PEAK 8(6P21.1) MUTATED 16 50 32 17 19 25
AMP PEAK 8(6P21.1) WILD-TYPE 43 40 63 26 51 52

Figure S67.  Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S68.  Gene #9: 'amp_7p21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
AMP PEAK 9(7P21.1) MUTATED 146 84 26 28
AMP PEAK 9(7P21.1) WILD-TYPE 26 54 106 46

Figure S68.  Get High-res Image Gene #9: 'amp_7p21.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7p21.1' versus 'RPPA_CNMF'

P value = 0.0295 (Fisher's exact test), Q value = 0.046

Table S69.  Gene #9: 'amp_7p21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
AMP PEAK 9(7P21.1) MUTATED 63 13 31 42 54
AMP PEAK 9(7P21.1) WILD-TYPE 28 9 35 33 55

Figure S69.  Get High-res Image Gene #9: 'amp_7p21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_7p21.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S70.  Gene #9: 'amp_7p21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
AMP PEAK 9(7P21.1) MUTATED 106 43 45 54 32
AMP PEAK 9(7P21.1) WILD-TYPE 24 76 45 61 26

Figure S70.  Get High-res Image Gene #9: 'amp_7p21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S71.  Gene #9: 'amp_7p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 9(7P21.1) MUTATED 37 82 60 11 26 29 35
AMP PEAK 9(7P21.1) WILD-TYPE 41 28 37 37 27 20 42

Figure S71.  Get High-res Image Gene #9: 'amp_7p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7p21.1' versus 'MIRSEQ_CNMF'

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

Table S72.  Gene #9: 'amp_7p21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
AMP PEAK 9(7P21.1) MUTATED 81 128 71
AMP PEAK 9(7P21.1) WILD-TYPE 105 93 32

Figure S72.  Get High-res Image Gene #9: 'amp_7p21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7p21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S73.  Gene #9: 'amp_7p21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
AMP PEAK 9(7P21.1) MUTATED 25 20 98 61 56 20
AMP PEAK 9(7P21.1) WILD-TYPE 46 19 47 69 40 9

Figure S73.  Get High-res Image Gene #9: 'amp_7p21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7p21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0269 (Fisher's exact test), Q value = 0.043

Table S74.  Gene #9: 'amp_7p21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
AMP PEAK 9(7P21.1) MUTATED 22 48 55 27 39 51
AMP PEAK 9(7P21.1) WILD-TYPE 37 42 40 16 31 26

Figure S74.  Get High-res Image Gene #9: 'amp_7p21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7p21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S75.  Gene #9: 'amp_7p21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
AMP PEAK 9(7P21.1) MUTATED 39 141 62
AMP PEAK 9(7P21.1) WILD-TYPE 65 97 30

Figure S75.  Get High-res Image Gene #9: 'amp_7p21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S76.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
AMP PEAK 10(7P11.2) MUTATED 140 85 23 26
AMP PEAK 10(7P11.2) WILD-TYPE 32 53 109 48

Figure S76.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0174 (Fisher's exact test), Q value = 0.03

Table S77.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
AMP PEAK 10(7P11.2) MUTATED 83 85 29
AMP PEAK 10(7P11.2) WILD-TYPE 84 48 34

Figure S77.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S78.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
AMP PEAK 10(7P11.2) MUTATED 105 36 49 49 31
AMP PEAK 10(7P11.2) WILD-TYPE 25 83 41 66 27

Figure S78.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S79.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 10(7P11.2) MUTATED 31 82 57 9 24 32 35
AMP PEAK 10(7P11.2) WILD-TYPE 47 28 40 39 29 17 42

Figure S79.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S80.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
AMP PEAK 10(7P11.2) MUTATED 70 130 70
AMP PEAK 10(7P11.2) WILD-TYPE 116 91 33

Figure S80.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S81.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
AMP PEAK 10(7P11.2) MUTATED 19 22 101 55 54 19
AMP PEAK 10(7P11.2) WILD-TYPE 52 17 44 75 42 10

Figure S81.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00055

Table S82.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
AMP PEAK 10(7P11.2) MUTATED 17 47 53 25 38 54
AMP PEAK 10(7P11.2) WILD-TYPE 42 43 42 18 32 23

Figure S82.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S83.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
AMP PEAK 10(7P11.2) MUTATED 33 143 58
AMP PEAK 10(7P11.2) WILD-TYPE 71 95 34

Figure S83.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S84.  Gene #11: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
AMP PEAK 11(7Q31.2) MUTATED 112 62 17 27
AMP PEAK 11(7Q31.2) WILD-TYPE 60 76 115 47

Figure S84.  Get High-res Image Gene #11: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q31.2' versus 'RPPA_CNMF'

P value = 0.0378 (Fisher's exact test), Q value = 0.058

Table S85.  Gene #11: 'amp_7q31.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
AMP PEAK 11(7Q31.2) MUTATED 44 8 21 42 44
AMP PEAK 11(7Q31.2) WILD-TYPE 47 14 45 33 65

Figure S85.  Get High-res Image Gene #11: 'amp_7q31.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S86.  Gene #11: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
AMP PEAK 11(7Q31.2) MUTATED 88 25 38 37 26
AMP PEAK 11(7Q31.2) WILD-TYPE 42 94 52 78 32

Figure S86.  Get High-res Image Gene #11: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S87.  Gene #11: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 11(7Q31.2) MUTATED 22 74 46 5 16 22 29
AMP PEAK 11(7Q31.2) WILD-TYPE 56 36 51 43 37 27 48

Figure S87.  Get High-res Image Gene #11: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_CNMF'

P value = 0.00178 (Fisher's exact test), Q value = 0.0038

Table S88.  Gene #11: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
AMP PEAK 11(7Q31.2) MUTATED 59 105 50
AMP PEAK 11(7Q31.2) WILD-TYPE 127 116 53

Figure S88.  Get High-res Image Gene #11: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00126 (Fisher's exact test), Q value = 0.0028

Table S89.  Gene #11: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
AMP PEAK 11(7Q31.2) MUTATED 17 16 77 47 43 14
AMP PEAK 11(7Q31.2) WILD-TYPE 54 23 68 83 53 15

Figure S89.  Get High-res Image Gene #11: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00857 (Fisher's exact test), Q value = 0.016

Table S90.  Gene #11: 'amp_7q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
AMP PEAK 11(7Q31.2) MUTATED 15 38 43 20 24 43
AMP PEAK 11(7Q31.2) WILD-TYPE 44 52 52 23 46 34

Figure S90.  Get High-res Image Gene #11: 'amp_7q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S91.  Gene #11: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
AMP PEAK 11(7Q31.2) MUTATED 23 115 45
AMP PEAK 11(7Q31.2) WILD-TYPE 81 123 47

Figure S91.  Get High-res Image Gene #11: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S92.  Gene #12: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
AMP PEAK 12(8P11.21) MUTATED 44 60 18 53
AMP PEAK 12(8P11.21) WILD-TYPE 128 78 114 21

Figure S92.  Get High-res Image Gene #12: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S93.  Gene #12: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
AMP PEAK 12(8P11.21) MUTATED 72 59 24
AMP PEAK 12(8P11.21) WILD-TYPE 84 111 105

Figure S93.  Get High-res Image Gene #12: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8p11.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.00892 (Fisher's exact test), Q value = 0.016

Table S94.  Gene #12: 'amp_8p11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
AMP PEAK 12(8P11.21) MUTATED 50 60 17
AMP PEAK 12(8P11.21) WILD-TYPE 117 73 46

Figure S94.  Get High-res Image Gene #12: 'amp_8p11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8p11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S95.  Gene #12: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
AMP PEAK 12(8P11.21) MUTATED 41 23 27 65 16
AMP PEAK 12(8P11.21) WILD-TYPE 89 96 63 50 42

Figure S95.  Get High-res Image Gene #12: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S96.  Gene #12: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 12(8P11.21) MUTATED 17 38 39 15 32 18 13
AMP PEAK 12(8P11.21) WILD-TYPE 61 72 58 33 21 31 64

Figure S96.  Get High-res Image Gene #12: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.00093

Table S97.  Gene #12: 'amp_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
AMP PEAK 12(8P11.21) MUTATED 44 94 35
AMP PEAK 12(8P11.21) WILD-TYPE 142 127 68

Figure S97.  Get High-res Image Gene #12: '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 = 7e-05

Table S98.  Gene #12: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
AMP PEAK 12(8P11.21) MUTATED 16 18 57 29 47 6
AMP PEAK 12(8P11.21) WILD-TYPE 55 21 88 101 49 23

Figure S98.  Get High-res Image Gene #12: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00252 (Fisher's exact test), Q value = 0.0051

Table S99.  Gene #12: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
AMP PEAK 12(8P11.21) MUTATED 10 45 32 14 22 25
AMP PEAK 12(8P11.21) WILD-TYPE 49 45 63 29 48 52

Figure S99.  Get High-res Image Gene #12: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00216 (Fisher's exact test), Q value = 0.0045

Table S100.  Gene #12: 'amp_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
AMP PEAK 12(8P11.21) MUTATED 22 96 30
AMP PEAK 12(8P11.21) WILD-TYPE 82 142 62

Figure S100.  Get High-res Image Gene #12: 'amp_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S101.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
AMP PEAK 13(8Q24.21) MUTATED 117 97 47 64
AMP PEAK 13(8Q24.21) WILD-TYPE 55 41 85 10

Figure S101.  Get High-res Image Gene #13: '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 = 3.9e-05

Table S102.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
AMP PEAK 13(8Q24.21) MUTATED 104 126 55
AMP PEAK 13(8Q24.21) WILD-TYPE 52 44 74

Figure S102.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'RPPA_CNMF'

P value = 0.00566 (Fisher's exact test), Q value = 0.011

Table S103.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
AMP PEAK 13(8Q24.21) MUTATED 59 11 49 58 60
AMP PEAK 13(8Q24.21) WILD-TYPE 32 11 17 17 49

Figure S103.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8q24.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.037 (Fisher's exact test), Q value = 0.056

Table S104.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
AMP PEAK 13(8Q24.21) MUTATED 101 98 38
AMP PEAK 13(8Q24.21) WILD-TYPE 66 35 25

Figure S104.  Get High-res Image Gene #13: '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 = 3.9e-05

Table S105.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
AMP PEAK 13(8Q24.21) MUTATED 98 51 52 92 28
AMP PEAK 13(8Q24.21) WILD-TYPE 32 68 38 23 30

Figure S105.  Get High-res Image Gene #13: '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 = 3.9e-05

Table S106.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 13(8Q24.21) MUTATED 39 80 67 28 47 31 29
AMP PEAK 13(8Q24.21) WILD-TYPE 39 30 30 20 6 18 48

Figure S106.  Get High-res Image Gene #13: '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 = 3.9e-05

Table S107.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
AMP PEAK 13(8Q24.21) MUTATED 91 161 69
AMP PEAK 13(8Q24.21) WILD-TYPE 95 60 34

Figure S107.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S108.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
AMP PEAK 13(8Q24.21) MUTATED 37 32 104 67 67 14
AMP PEAK 13(8Q24.21) WILD-TYPE 34 7 41 63 29 15

Figure S108.  Get High-res Image Gene #13: '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 = 3.9e-05

Table S109.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
AMP PEAK 13(8Q24.21) MUTATED 16 74 64 21 47 49
AMP PEAK 13(8Q24.21) WILD-TYPE 43 16 31 22 23 28

Figure S109.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S110.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
AMP PEAK 13(8Q24.21) MUTATED 45 169 57
AMP PEAK 13(8Q24.21) WILD-TYPE 59 69 35

Figure S110.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10p15.1' versus 'MRNA_CNMF'

P value = 0.0208 (Fisher's exact test), Q value = 0.035

Table S111.  Gene #14: 'amp_10p15.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 10 7
AMP PEAK 14(10P15.1) MUTATED 0 2 3
AMP PEAK 14(10P15.1) WILD-TYPE 15 8 4

Figure S111.  Get High-res Image Gene #14: 'amp_10p15.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_10p15.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.029

Table S112.  Gene #14: 'amp_10p15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
AMP PEAK 14(10P15.1) MUTATED 0 2 3
AMP PEAK 14(10P15.1) WILD-TYPE 14 9 4

Figure S112.  Get High-res Image Gene #14: '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 = 3.9e-05

Table S113.  Gene #14: 'amp_10p15.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
AMP PEAK 14(10P15.1) MUTATED 39 52 10 41
AMP PEAK 14(10P15.1) WILD-TYPE 133 86 122 33

Figure S113.  Get High-res Image Gene #14: '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 = 3.9e-05

Table S114.  Gene #14: 'amp_10p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
AMP PEAK 14(10P15.1) MUTATED 56 55 13
AMP PEAK 14(10P15.1) WILD-TYPE 100 115 116

Figure S114.  Get High-res Image Gene #14: 'amp_10p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_10p15.1' versus 'RPPA_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.00065

Table S115.  Gene #14: 'amp_10p15.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
AMP PEAK 14(10P15.1) MUTATED 15 2 18 33 40
AMP PEAK 14(10P15.1) WILD-TYPE 76 20 48 42 69

Figure S115.  Get High-res Image Gene #14: 'amp_10p15.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_10p15.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.0013

Table S116.  Gene #14: 'amp_10p15.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
AMP PEAK 14(10P15.1) MUTATED 33 50 25
AMP PEAK 14(10P15.1) WILD-TYPE 134 83 38

Figure S116.  Get High-res Image Gene #14: '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 = 3.9e-05

Table S117.  Gene #14: 'amp_10p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
AMP PEAK 14(10P15.1) MUTATED 37 16 28 51 8
AMP PEAK 14(10P15.1) WILD-TYPE 93 103 62 64 50

Figure S117.  Get High-res Image Gene #14: '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 = 3.9e-05

Table S118.  Gene #14: 'amp_10p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 14(10P15.1) MUTATED 8 31 27 16 25 23 10
AMP PEAK 14(10P15.1) WILD-TYPE 70 79 70 32 28 26 67

Figure S118.  Get High-res Image Gene #14: 'amp_10p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10p15.1' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S119.  Gene #14: 'amp_10p15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
AMP PEAK 14(10P15.1) MUTATED 32 83 23
AMP PEAK 14(10P15.1) WILD-TYPE 154 138 80

Figure S119.  Get High-res Image Gene #14: '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 = 3.9e-05

Table S120.  Gene #14: 'amp_10p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
AMP PEAK 14(10P15.1) MUTATED 17 17 54 14 34 2
AMP PEAK 14(10P15.1) WILD-TYPE 54 22 91 116 62 27

Figure S120.  Get High-res Image Gene #14: 'amp_10p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_10p15.1' versus 'MIRSEQ_MATURE_CNMF'

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

Table S121.  Gene #14: 'amp_10p15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
AMP PEAK 14(10P15.1) MUTATED 4 36 33 8 19 20
AMP PEAK 14(10P15.1) WILD-TYPE 55 54 62 35 51 57

Figure S121.  Get High-res Image Gene #14: 'amp_10p15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_10p15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0011

Table S122.  Gene #14: 'amp_10p15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
AMP PEAK 14(10P15.1) MUTATED 16 83 21
AMP PEAK 14(10P15.1) WILD-TYPE 88 155 71

Figure S122.  Get High-res Image Gene #14: 'amp_10p15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q13.3' versus 'MRNA_CNMF'

P value = 0.00107 (Fisher's exact test), Q value = 0.0024

Table S123.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 10 7
AMP PEAK 15(11Q13.3) MUTATED 3 3 7
AMP PEAK 15(11Q13.3) WILD-TYPE 12 7 0

Figure S123.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11q13.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00116 (Fisher's exact test), Q value = 0.0026

Table S124.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
AMP PEAK 15(11Q13.3) MUTATED 3 3 7
AMP PEAK 15(11Q13.3) WILD-TYPE 11 8 0

Figure S124.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S125.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
AMP PEAK 15(11Q13.3) MUTATED 74 52 17 29
AMP PEAK 15(11Q13.3) WILD-TYPE 98 86 115 45

Figure S125.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00044

Table S126.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
AMP PEAK 15(11Q13.3) MUTATED 59 67 24
AMP PEAK 15(11Q13.3) WILD-TYPE 97 103 105

Figure S126.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00381 (Fisher's exact test), Q value = 0.0075

Table S127.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
AMP PEAK 15(11Q13.3) MUTATED 44 59 19
AMP PEAK 15(11Q13.3) WILD-TYPE 123 74 44

Figure S127.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S128.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
AMP PEAK 15(11Q13.3) MUTATED 56 21 24 58 13
AMP PEAK 15(11Q13.3) WILD-TYPE 74 98 66 57 45

Figure S128.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S129.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 15(11Q13.3) MUTATED 20 45 39 3 35 16 14
AMP PEAK 15(11Q13.3) WILD-TYPE 58 65 58 45 18 33 63

Figure S129.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S130.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
AMP PEAK 15(11Q13.3) MUTATED 32 101 36
AMP PEAK 15(11Q13.3) WILD-TYPE 154 120 67

Figure S130.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S131.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
AMP PEAK 15(11Q13.3) MUTATED 10 20 62 25 43 9
AMP PEAK 15(11Q13.3) WILD-TYPE 61 19 83 105 53 20

Figure S131.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S132.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
AMP PEAK 15(11Q13.3) MUTATED 7 51 31 16 20 20
AMP PEAK 15(11Q13.3) WILD-TYPE 52 39 64 27 50 57

Figure S132.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S133.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
AMP PEAK 15(11Q13.3) MUTATED 17 94 34
AMP PEAK 15(11Q13.3) WILD-TYPE 87 144 58

Figure S133.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p12.1' versus 'MRNA_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 0.04

Table S134.  Gene #16: 'amp_12p12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 10 7
AMP PEAK 16(12P12.1) MUTATED 2 3 5
AMP PEAK 16(12P12.1) WILD-TYPE 13 7 2

Figure S134.  Get High-res Image Gene #16: 'amp_12p12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_12p12.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0382 (Fisher's exact test), Q value = 0.058

Table S135.  Gene #16: 'amp_12p12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
AMP PEAK 16(12P12.1) MUTATED 2 3 5
AMP PEAK 16(12P12.1) WILD-TYPE 12 8 2

Figure S135.  Get High-res Image Gene #16: 'amp_12p12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_12p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S136.  Gene #16: 'amp_12p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
AMP PEAK 16(12P12.1) MUTATED 44 95 20 19
AMP PEAK 16(12P12.1) WILD-TYPE 128 43 112 55

Figure S136.  Get High-res Image Gene #16: 'amp_12p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p12.1' versus 'METHLYATION_CNMF'

P value = 0.00242 (Fisher's exact test), Q value = 0.0049

Table S137.  Gene #16: 'amp_12p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
AMP PEAK 16(12P12.1) MUTATED 63 61 28
AMP PEAK 16(12P12.1) WILD-TYPE 93 109 101

Figure S137.  Get High-res Image Gene #16: 'amp_12p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12p12.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0155 (Fisher's exact test), Q value = 0.027

Table S138.  Gene #16: 'amp_12p12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
AMP PEAK 16(12P12.1) MUTATED 43 55 21
AMP PEAK 16(12P12.1) WILD-TYPE 124 78 42

Figure S138.  Get High-res Image Gene #16: 'amp_12p12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_12p12.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S139.  Gene #16: 'amp_12p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
AMP PEAK 16(12P12.1) MUTATED 50 10 50 53 15
AMP PEAK 16(12P12.1) WILD-TYPE 80 109 40 62 43

Figure S139.  Get High-res Image Gene #16: 'amp_12p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S140.  Gene #16: 'amp_12p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 16(12P12.1) MUTATED 12 43 35 5 32 30 21
AMP PEAK 16(12P12.1) WILD-TYPE 66 67 62 43 21 19 56

Figure S140.  Get High-res Image Gene #16: 'amp_12p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S141.  Gene #16: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
AMP PEAK 16(12P12.1) MUTATED 39 103 33
AMP PEAK 16(12P12.1) WILD-TYPE 147 118 70

Figure S141.  Get High-res Image Gene #16: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S142.  Gene #16: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
AMP PEAK 16(12P12.1) MUTATED 12 22 57 33 45 6
AMP PEAK 16(12P12.1) WILD-TYPE 59 17 88 97 51 23

Figure S142.  Get High-res Image Gene #16: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0018

Table S143.  Gene #16: 'amp_12p12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
AMP PEAK 16(12P12.1) MUTATED 9 41 38 13 17 30
AMP PEAK 16(12P12.1) WILD-TYPE 50 49 57 30 53 47

Figure S143.  Get High-res Image Gene #16: 'amp_12p12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S144.  Gene #16: 'amp_12p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
AMP PEAK 16(12P12.1) MUTATED 19 101 28
AMP PEAK 16(12P12.1) WILD-TYPE 85 137 64

Figure S144.  Get High-res Image Gene #16: 'amp_12p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S145.  Gene #17: 'amp_12q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
AMP PEAK 17(12Q14.1) MUTATED 34 93 18 24
AMP PEAK 17(12Q14.1) WILD-TYPE 138 45 114 50

Figure S145.  Get High-res Image Gene #17: 'amp_12q14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q14.1' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00036

Table S146.  Gene #17: 'amp_12q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
AMP PEAK 17(12Q14.1) MUTATED 69 53 26
AMP PEAK 17(12Q14.1) WILD-TYPE 87 117 103

Figure S146.  Get High-res Image Gene #17: 'amp_12q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q14.1' versus 'RPPA_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.0014

Table S147.  Gene #17: 'amp_12q14.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
AMP PEAK 17(12Q14.1) MUTATED 25 5 23 42 31
AMP PEAK 17(12Q14.1) WILD-TYPE 66 17 43 33 78

Figure S147.  Get High-res Image Gene #17: 'amp_12q14.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_12q14.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0463 (Fisher's exact test), Q value = 0.069

Table S148.  Gene #17: 'amp_12q14.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
AMP PEAK 17(12Q14.1) MUTATED 50 57 19
AMP PEAK 17(12Q14.1) WILD-TYPE 117 76 44

Figure S148.  Get High-res Image Gene #17: 'amp_12q14.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_12q14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S149.  Gene #17: 'amp_12q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
AMP PEAK 17(12Q14.1) MUTATED 38 14 43 62 12
AMP PEAK 17(12Q14.1) WILD-TYPE 92 105 47 53 46

Figure S149.  Get High-res Image Gene #17: 'amp_12q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S150.  Gene #17: 'amp_12q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 17(12Q14.1) MUTATED 13 33 37 6 36 31 13
AMP PEAK 17(12Q14.1) WILD-TYPE 65 77 60 42 17 18 64

Figure S150.  Get High-res Image Gene #17: 'amp_12q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S151.  Gene #17: 'amp_12q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
AMP PEAK 17(12Q14.1) MUTATED 31 105 31
AMP PEAK 17(12Q14.1) WILD-TYPE 155 116 72

Figure S151.  Get High-res Image Gene #17: 'amp_12q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S152.  Gene #17: 'amp_12q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
AMP PEAK 17(12Q14.1) MUTATED 12 25 49 23 49 9
AMP PEAK 17(12Q14.1) WILD-TYPE 59 14 96 107 47 20

Figure S152.  Get High-res Image Gene #17: 'amp_12q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00023

Table S153.  Gene #17: 'amp_12q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
AMP PEAK 17(12Q14.1) MUTATED 6 44 33 14 22 23
AMP PEAK 17(12Q14.1) WILD-TYPE 53 46 62 29 48 54

Figure S153.  Get High-res Image Gene #17: 'amp_12q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S154.  Gene #17: 'amp_12q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
AMP PEAK 17(12Q14.1) MUTATED 13 106 23
AMP PEAK 17(12Q14.1) WILD-TYPE 91 132 69

Figure S154.  Get High-res Image Gene #17: 'amp_12q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S155.  Gene #18: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
AMP PEAK 18(12Q15) MUTATED 35 90 19 25
AMP PEAK 18(12Q15) WILD-TYPE 137 48 113 49

Figure S155.  Get High-res Image Gene #18: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00031

Table S156.  Gene #18: 'amp_12q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
AMP PEAK 18(12Q15) MUTATED 69 53 26
AMP PEAK 18(12Q15) WILD-TYPE 87 117 103

Figure S156.  Get High-res Image Gene #18: 'amp_12q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q15' versus 'RPPA_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0014

Table S157.  Gene #18: 'amp_12q15' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
AMP PEAK 18(12Q15) MUTATED 25 7 24 41 27
AMP PEAK 18(12Q15) WILD-TYPE 66 15 42 34 82

Figure S157.  Get High-res Image Gene #18: 'amp_12q15' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_12q15' versus 'RPPA_CHIERARCHICAL'

P value = 0.01 (Fisher's exact test), Q value = 0.018

Table S158.  Gene #18: 'amp_12q15' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
AMP PEAK 18(12Q15) MUTATED 51 58 15
AMP PEAK 18(12Q15) WILD-TYPE 116 75 48

Figure S158.  Get High-res Image Gene #18: 'amp_12q15' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_12q15' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S159.  Gene #18: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
AMP PEAK 18(12Q15) MUTATED 39 13 43 63 11
AMP PEAK 18(12Q15) WILD-TYPE 91 106 47 52 47

Figure S159.  Get High-res Image Gene #18: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S160.  Gene #18: 'amp_12q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 18(12Q15) MUTATED 16 29 37 6 36 31 14
AMP PEAK 18(12Q15) WILD-TYPE 62 81 60 42 17 18 63

Figure S160.  Get High-res Image Gene #18: 'amp_12q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S161.  Gene #18: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
AMP PEAK 18(12Q15) MUTATED 32 106 30
AMP PEAK 18(12Q15) WILD-TYPE 154 115 73

Figure S161.  Get High-res Image Gene #18: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S162.  Gene #18: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
AMP PEAK 18(12Q15) MUTATED 12 25 44 26 51 10
AMP PEAK 18(12Q15) WILD-TYPE 59 14 101 104 45 19

Figure S162.  Get High-res Image Gene #18: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S163.  Gene #18: 'amp_12q15' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
AMP PEAK 18(12Q15) MUTATED 5 43 34 16 21 25
AMP PEAK 18(12Q15) WILD-TYPE 54 47 61 27 49 52

Figure S163.  Get High-res Image Gene #18: 'amp_12q15' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12q15' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S164.  Gene #18: 'amp_12q15' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
AMP PEAK 18(12Q15) MUTATED 15 104 25
AMP PEAK 18(12Q15) WILD-TYPE 89 134 67

Figure S164.  Get High-res Image Gene #18: 'amp_12q15' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q33.3' versus 'CN_CNMF'

P value = 0.0498 (Fisher's exact test), Q value = 0.073

Table S165.  Gene #19: 'amp_13q33.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
AMP PEAK 19(13Q33.3) MUTATED 28 19 12 17
AMP PEAK 19(13Q33.3) WILD-TYPE 144 119 120 57

Figure S165.  Get High-res Image Gene #19: 'amp_13q33.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q33.3' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00055

Table S166.  Gene #19: 'amp_13q33.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
AMP PEAK 19(13Q33.3) MUTATED 36 21 8
AMP PEAK 19(13Q33.3) WILD-TYPE 120 149 121

Figure S166.  Get High-res Image Gene #19: 'amp_13q33.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q33.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0321 (Fisher's exact test), Q value = 0.05

Table S167.  Gene #19: 'amp_13q33.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 19(13Q33.3) MUTATED 12 11 25 8 7 7 6
AMP PEAK 19(13Q33.3) WILD-TYPE 66 99 72 40 46 42 71

Figure S167.  Get High-res Image Gene #19: 'amp_13q33.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q33.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0403 (Fisher's exact test), Q value = 0.061

Table S168.  Gene #19: 'amp_13q33.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
AMP PEAK 19(13Q33.3) MUTATED 8 43 14
AMP PEAK 19(13Q33.3) WILD-TYPE 96 195 78

Figure S168.  Get High-res Image Gene #19: 'amp_13q33.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_14q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S169.  Gene #20: 'amp_14q13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
AMP PEAK 20(14Q13.3) MUTATED 96 68 23 46
AMP PEAK 20(14Q13.3) WILD-TYPE 76 70 109 28

Figure S169.  Get High-res Image Gene #20: 'amp_14q13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_14q13.3' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S170.  Gene #20: 'amp_14q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
AMP PEAK 20(14Q13.3) MUTATED 85 84 37
AMP PEAK 20(14Q13.3) WILD-TYPE 71 86 92

Figure S170.  Get High-res Image Gene #20: 'amp_14q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_14q13.3' versus 'RPPA_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 0.04

Table S171.  Gene #20: 'amp_14q13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
AMP PEAK 20(14Q13.3) MUTATED 40 5 27 44 45
AMP PEAK 20(14Q13.3) WILD-TYPE 51 17 39 31 64

Figure S171.  Get High-res Image Gene #20: 'amp_14q13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_14q13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0248 (Fisher's exact test), Q value = 0.04

Table S172.  Gene #20: 'amp_14q13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
AMP PEAK 20(14Q13.3) MUTATED 63 71 27
AMP PEAK 20(14Q13.3) WILD-TYPE 104 62 36

Figure S172.  Get High-res Image Gene #20: 'amp_14q13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_14q13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S173.  Gene #20: 'amp_14q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
AMP PEAK 20(14Q13.3) MUTATED 78 40 20 78 16
AMP PEAK 20(14Q13.3) WILD-TYPE 52 79 70 37 42

Figure S173.  Get High-res Image Gene #20: 'amp_14q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_14q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S174.  Gene #20: 'amp_14q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 20(14Q13.3) MUTATED 34 60 63 10 42 8 15
AMP PEAK 20(14Q13.3) WILD-TYPE 44 50 34 38 11 41 62

Figure S174.  Get High-res Image Gene #20: 'amp_14q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_14q13.3' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S175.  Gene #20: 'amp_14q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
AMP PEAK 20(14Q13.3) MUTATED 56 118 55
AMP PEAK 20(14Q13.3) WILD-TYPE 130 103 48

Figure S175.  Get High-res Image Gene #20: 'amp_14q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_14q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S176.  Gene #20: 'amp_14q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
AMP PEAK 20(14Q13.3) MUTATED 28 32 74 29 52 14
AMP PEAK 20(14Q13.3) WILD-TYPE 43 7 71 101 44 15

Figure S176.  Get High-res Image Gene #20: 'amp_14q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_14q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S177.  Gene #20: 'amp_14q13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
AMP PEAK 20(14Q13.3) MUTATED 13 58 43 24 29 29
AMP PEAK 20(14Q13.3) WILD-TYPE 46 32 52 19 41 48

Figure S177.  Get High-res Image Gene #20: 'amp_14q13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_14q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S178.  Gene #20: 'amp_14q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
AMP PEAK 20(14Q13.3) MUTATED 27 125 44
AMP PEAK 20(14Q13.3) WILD-TYPE 77 113 48

Figure S178.  Get High-res Image Gene #20: 'amp_14q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_16p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S179.  Gene #21: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
AMP PEAK 21(16P11.2) MUTATED 79 46 25 17
AMP PEAK 21(16P11.2) WILD-TYPE 93 92 107 57

Figure S179.  Get High-res Image Gene #21: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_16p11.2' versus 'RPPA_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.033

Table S180.  Gene #21: 'amp_16p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
AMP PEAK 21(16P11.2) MUTATED 40 7 23 28 24
AMP PEAK 21(16P11.2) WILD-TYPE 51 15 43 47 85

Figure S180.  Get High-res Image Gene #21: 'amp_16p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_16p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0332 (Fisher's exact test), Q value = 0.052

Table S181.  Gene #21: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 21(16P11.2) MUTATED 31 41 38 9 18 11 19
AMP PEAK 21(16P11.2) WILD-TYPE 47 69 59 39 35 38 58

Figure S181.  Get High-res Image Gene #21: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'MIRSEQ_CNMF'

P value = 0.0456 (Fisher's exact test), Q value = 0.068

Table S182.  Gene #21: 'amp_16p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
AMP PEAK 21(16P11.2) MUTATED 48 80 38
AMP PEAK 21(16P11.2) WILD-TYPE 138 141 65

Figure S182.  Get High-res Image Gene #21: 'amp_16p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_16p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0159 (Fisher's exact test), Q value = 0.028

Table S183.  Gene #21: 'amp_16p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
AMP PEAK 21(16P11.2) MUTATED 19 17 48 32 34 16
AMP PEAK 21(16P11.2) WILD-TYPE 52 22 97 98 62 13

Figure S183.  Get High-res Image Gene #21: 'amp_16p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.0474 (Fisher's exact test), Q value = 0.07

Table S184.  Gene #22: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
AMP PEAK 22(17Q12) MUTATED 4 6 6
AMP PEAK 22(17Q12) WILD-TYPE 10 5 1

Figure S184.  Get High-res Image Gene #22: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S185.  Gene #22: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
AMP PEAK 22(17Q12) MUTATED 105 71 17 34
AMP PEAK 22(17Q12) WILD-TYPE 67 67 115 40

Figure S185.  Get High-res Image Gene #22: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S186.  Gene #22: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
AMP PEAK 22(17Q12) MUTATED 74 89 29
AMP PEAK 22(17Q12) WILD-TYPE 82 81 100

Figure S186.  Get High-res Image Gene #22: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q12' versus 'RPPA_CNMF'

P value = 0.00136 (Fisher's exact test), Q value = 0.003

Table S187.  Gene #22: 'amp_17q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
AMP PEAK 22(17Q12) MUTATED 45 10 28 44 32
AMP PEAK 22(17Q12) WILD-TYPE 46 12 38 31 77

Figure S187.  Get High-res Image Gene #22: 'amp_17q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_17q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.00067

Table S188.  Gene #22: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
AMP PEAK 22(17Q12) MUTATED 66 75 18
AMP PEAK 22(17Q12) WILD-TYPE 101 58 45

Figure S188.  Get High-res Image Gene #22: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S189.  Gene #22: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
AMP PEAK 22(17Q12) MUTATED 80 31 32 60 22
AMP PEAK 22(17Q12) WILD-TYPE 50 88 58 55 36

Figure S189.  Get High-res Image Gene #22: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S190.  Gene #22: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 22(17Q12) MUTATED 30 62 57 8 29 17 22
AMP PEAK 22(17Q12) WILD-TYPE 48 48 40 40 24 32 55

Figure S190.  Get High-res Image Gene #22: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S191.  Gene #22: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
AMP PEAK 22(17Q12) MUTATED 57 124 43
AMP PEAK 22(17Q12) WILD-TYPE 129 97 60

Figure S191.  Get High-res Image Gene #22: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S192.  Gene #22: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
AMP PEAK 22(17Q12) MUTATED 19 25 72 37 60 11
AMP PEAK 22(17Q12) WILD-TYPE 52 14 73 93 36 18

Figure S192.  Get High-res Image Gene #22: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S193.  Gene #22: 'amp_17q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
AMP PEAK 22(17Q12) MUTATED 9 51 46 16 29 36
AMP PEAK 22(17Q12) WILD-TYPE 50 39 49 27 41 41

Figure S193.  Get High-res Image Gene #22: 'amp_17q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S194.  Gene #22: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
AMP PEAK 22(17Q12) MUTATED 24 121 42
AMP PEAK 22(17Q12) WILD-TYPE 80 117 50

Figure S194.  Get High-res Image Gene #22: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S195.  Gene #23: 'amp_17q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
AMP PEAK 23(17Q23.1) MUTATED 113 77 23 36
AMP PEAK 23(17Q23.1) WILD-TYPE 59 61 109 38

Figure S195.  Get High-res Image Gene #23: '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 = 3.9e-05

Table S196.  Gene #23: 'amp_17q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
AMP PEAK 23(17Q23.1) MUTATED 73 103 37
AMP PEAK 23(17Q23.1) WILD-TYPE 83 67 92

Figure S196.  Get High-res Image Gene #23: 'amp_17q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q23.1' versus 'RPPA_CNMF'

P value = 0.0394 (Fisher's exact test), Q value = 0.059

Table S197.  Gene #23: 'amp_17q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
AMP PEAK 23(17Q23.1) MUTATED 50 11 30 45 42
AMP PEAK 23(17Q23.1) WILD-TYPE 41 11 36 30 67

Figure S197.  Get High-res Image Gene #23: 'amp_17q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_17q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00272 (Fisher's exact test), Q value = 0.0055

Table S198.  Gene #23: 'amp_17q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
AMP PEAK 23(17Q23.1) MUTATED 75 80 23
AMP PEAK 23(17Q23.1) WILD-TYPE 92 53 40

Figure S198.  Get High-res Image Gene #23: '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 = 3.9e-05

Table S199.  Gene #23: 'amp_17q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
AMP PEAK 23(17Q23.1) MUTATED 90 38 41 56 23
AMP PEAK 23(17Q23.1) WILD-TYPE 40 81 49 59 35

Figure S199.  Get High-res Image Gene #23: '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 = 3.9e-05

Table S200.  Gene #23: 'amp_17q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 23(17Q23.1) MUTATED 36 74 55 7 29 22 25
AMP PEAK 23(17Q23.1) WILD-TYPE 42 36 42 41 24 27 52

Figure S200.  Get High-res Image Gene #23: 'amp_17q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q23.1' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S201.  Gene #23: 'amp_17q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
AMP PEAK 23(17Q23.1) MUTATED 67 130 50
AMP PEAK 23(17Q23.1) WILD-TYPE 119 91 53

Figure S201.  Get High-res Image Gene #23: '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 = 3.9e-05

Table S202.  Gene #23: 'amp_17q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
AMP PEAK 23(17Q23.1) MUTATED 25 22 84 44 60 12
AMP PEAK 23(17Q23.1) WILD-TYPE 46 17 61 86 36 17

Figure S202.  Get High-res Image Gene #23: 'amp_17q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.00065

Table S203.  Gene #23: 'amp_17q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
AMP PEAK 23(17Q23.1) MUTATED 12 51 51 19 35 37
AMP PEAK 23(17Q23.1) WILD-TYPE 47 39 44 24 35 40

Figure S203.  Get High-res Image Gene #23: '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 = 3.9e-05

Table S204.  Gene #23: 'amp_17q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
AMP PEAK 23(17Q23.1) MUTATED 28 130 47
AMP PEAK 23(17Q23.1) WILD-TYPE 76 108 45

Figure S204.  Get High-res Image Gene #23: 'amp_17q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18q11.2' versus 'MRNA_CNMF'

P value = 0.0336 (Fisher's exact test), Q value = 0.052

Table S205.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 10 7
AMP PEAK 24(18Q11.2) MUTATED 1 1 4
AMP PEAK 24(18Q11.2) WILD-TYPE 14 9 3

Figure S205.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_18q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0201 (Fisher's exact test), Q value = 0.034

Table S206.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
AMP PEAK 24(18Q11.2) MUTATED 1 1 4
AMP PEAK 24(18Q11.2) WILD-TYPE 13 10 3

Figure S206.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_18q11.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S207.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
AMP PEAK 24(18Q11.2) MUTATED 35 30 12 28
AMP PEAK 24(18Q11.2) WILD-TYPE 137 108 120 46

Figure S207.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S208.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
AMP PEAK 24(18Q11.2) MUTATED 52 34 9
AMP PEAK 24(18Q11.2) WILD-TYPE 104 136 120

Figure S208.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00039

Table S209.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
AMP PEAK 24(18Q11.2) MUTATED 25 14 16 41 7
AMP PEAK 24(18Q11.2) WILD-TYPE 105 105 74 74 51

Figure S209.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00015

Table S210.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 24(18Q11.2) MUTATED 7 17 30 7 22 9 11
AMP PEAK 24(18Q11.2) WILD-TYPE 71 93 67 41 31 40 66

Figure S210.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S211.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
AMP PEAK 24(18Q11.2) MUTATED 19 62 22
AMP PEAK 24(18Q11.2) WILD-TYPE 167 159 81

Figure S211.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S212.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
AMP PEAK 24(18Q11.2) MUTATED 7 12 30 16 35 3
AMP PEAK 24(18Q11.2) WILD-TYPE 64 27 115 114 61 26

Figure S212.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S213.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
AMP PEAK 24(18Q11.2) MUTATED 7 37 19 8 4 17
AMP PEAK 24(18Q11.2) WILD-TYPE 52 53 76 35 66 60

Figure S213.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S214.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
AMP PEAK 24(18Q11.2) MUTATED 9 68 15
AMP PEAK 24(18Q11.2) WILD-TYPE 95 170 77

Figure S214.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q12' versus 'MRNA_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 0.037

Table S215.  Gene #25: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 10 7
AMP PEAK 25(19Q12) MUTATED 0 4 2
AMP PEAK 25(19Q12) WILD-TYPE 15 6 5

Figure S215.  Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.0409 (Fisher's exact test), Q value = 0.061

Table S216.  Gene #25: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
AMP PEAK 25(19Q12) MUTATED 0 4 2
AMP PEAK 25(19Q12) WILD-TYPE 14 7 5

Figure S216.  Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S217.  Gene #25: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
AMP PEAK 25(19Q12) MUTATED 42 56 12 29
AMP PEAK 25(19Q12) WILD-TYPE 130 82 120 45

Figure S217.  Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S218.  Gene #25: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
AMP PEAK 25(19Q12) MUTATED 66 38 22
AMP PEAK 25(19Q12) WILD-TYPE 90 132 107

Figure S218.  Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19q12' versus 'RPPA_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00036

Table S219.  Gene #25: 'amp_19q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
AMP PEAK 25(19Q12) MUTATED 17 7 17 37 22
AMP PEAK 25(19Q12) WILD-TYPE 74 15 49 38 87

Figure S219.  Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00258 (Fisher's exact test), Q value = 0.0052

Table S220.  Gene #25: 'amp_19q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
AMP PEAK 25(19Q12) MUTATED 36 51 13
AMP PEAK 25(19Q12) WILD-TYPE 131 82 50

Figure S220.  Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0016

Table S221.  Gene #25: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
AMP PEAK 25(19Q12) MUTATED 40 18 28 41 9
AMP PEAK 25(19Q12) WILD-TYPE 90 101 62 74 49

Figure S221.  Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S222.  Gene #25: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 25(19Q12) MUTATED 8 30 36 13 17 21 11
AMP PEAK 25(19Q12) WILD-TYPE 70 80 61 35 36 28 66

Figure S222.  Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S223.  Gene #25: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
AMP PEAK 25(19Q12) MUTATED 28 86 24
AMP PEAK 25(19Q12) WILD-TYPE 158 135 79

Figure S223.  Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S224.  Gene #25: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
AMP PEAK 25(19Q12) MUTATED 16 13 47 21 39 2
AMP PEAK 25(19Q12) WILD-TYPE 55 26 98 109 57 27

Figure S224.  Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00103 (Fisher's exact test), Q value = 0.0023

Table S225.  Gene #25: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
AMP PEAK 25(19Q12) MUTATED 23 83 15
AMP PEAK 25(19Q12) WILD-TYPE 81 155 77

Figure S225.  Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S226.  Gene #26: 'amp_20p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
AMP PEAK 26(20P11.21) MUTATED 77 64 16 44
AMP PEAK 26(20P11.21) WILD-TYPE 95 74 116 30

Figure S226.  Get High-res Image Gene #26: 'amp_20p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S227.  Gene #26: 'amp_20p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
AMP PEAK 26(20P11.21) MUTATED 85 54 36
AMP PEAK 26(20P11.21) WILD-TYPE 71 116 93

Figure S227.  Get High-res Image Gene #26: 'amp_20p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20p11.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.00573 (Fisher's exact test), Q value = 0.011

Table S228.  Gene #26: 'amp_20p11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
AMP PEAK 26(20P11.21) MUTATED 53 66 22
AMP PEAK 26(20P11.21) WILD-TYPE 114 67 41

Figure S228.  Get High-res Image Gene #26: 'amp_20p11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20p11.21' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S229.  Gene #26: 'amp_20p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
AMP PEAK 26(20P11.21) MUTATED 46 33 32 67 19
AMP PEAK 26(20P11.21) WILD-TYPE 84 86 58 48 39

Figure S229.  Get High-res Image Gene #26: 'amp_20p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S230.  Gene #26: 'amp_20p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 26(20P11.21) MUTATED 19 32 62 17 31 17 19
AMP PEAK 26(20P11.21) WILD-TYPE 59 78 35 31 22 32 58

Figure S230.  Get High-res Image Gene #26: 'amp_20p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20p11.21' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S231.  Gene #26: 'amp_20p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
AMP PEAK 26(20P11.21) MUTATED 49 107 42
AMP PEAK 26(20P11.21) WILD-TYPE 137 114 61

Figure S231.  Get High-res Image Gene #26: 'amp_20p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S232.  Gene #26: 'amp_20p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
AMP PEAK 26(20P11.21) MUTATED 19 18 58 36 56 11
AMP PEAK 26(20P11.21) WILD-TYPE 52 21 87 94 40 18

Figure S232.  Get High-res Image Gene #26: 'amp_20p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00305 (Fisher's exact test), Q value = 0.0061

Table S233.  Gene #26: 'amp_20p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
AMP PEAK 26(20P11.21) MUTATED 16 49 28 21 26 29
AMP PEAK 26(20P11.21) WILD-TYPE 43 41 67 22 44 48

Figure S233.  Get High-res Image Gene #26: 'amp_20p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.0016

Table S234.  Gene #26: 'amp_20p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
AMP PEAK 26(20P11.21) MUTATED 29 112 28
AMP PEAK 26(20P11.21) WILD-TYPE 75 126 64

Figure S234.  Get High-res Image Gene #26: 'amp_20p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.0433 (Fisher's exact test), Q value = 0.065

Table S235.  Gene #27: 'amp_20q13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
AMP PEAK 27(20Q13.33) MUTATED 4 5 6
AMP PEAK 27(20Q13.33) WILD-TYPE 10 6 1

Figure S235.  Get High-res Image Gene #27: 'amp_20q13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S236.  Gene #27: 'amp_20q13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
AMP PEAK 27(20Q13.33) MUTATED 98 77 24 52
AMP PEAK 27(20Q13.33) WILD-TYPE 74 61 108 22

Figure S236.  Get High-res Image Gene #27: 'amp_20q13.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.33' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00051

Table S237.  Gene #27: 'amp_20q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
AMP PEAK 27(20Q13.33) MUTATED 94 78 47
AMP PEAK 27(20Q13.33) WILD-TYPE 62 92 82

Figure S237.  Get High-res Image Gene #27: 'amp_20q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.33' versus 'RPPA_CNMF'

P value = 0.0491 (Fisher's exact test), Q value = 0.072

Table S238.  Gene #27: 'amp_20q13.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
AMP PEAK 27(20Q13.33) MUTATED 48 9 28 48 49
AMP PEAK 27(20Q13.33) WILD-TYPE 43 13 38 27 60

Figure S238.  Get High-res Image Gene #27: 'amp_20q13.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q13.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.0016 (Fisher's exact test), Q value = 0.0034

Table S239.  Gene #27: 'amp_20q13.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
AMP PEAK 27(20Q13.33) MUTATED 68 82 32
AMP PEAK 27(20Q13.33) WILD-TYPE 99 51 31

Figure S239.  Get High-res Image Gene #27: 'amp_20q13.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20q13.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S240.  Gene #27: 'amp_20q13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
AMP PEAK 27(20Q13.33) MUTATED 68 41 34 82 22
AMP PEAK 27(20Q13.33) WILD-TYPE 62 78 56 33 36

Figure S240.  Get High-res Image Gene #27: 'amp_20q13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S241.  Gene #27: 'amp_20q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 27(20Q13.33) MUTATED 27 51 68 22 38 18 23
AMP PEAK 27(20Q13.33) WILD-TYPE 51 59 29 26 15 31 54

Figure S241.  Get High-res Image Gene #27: 'amp_20q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S242.  Gene #27: 'amp_20q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
AMP PEAK 27(20Q13.33) MUTATED 64 136 46
AMP PEAK 27(20Q13.33) WILD-TYPE 122 85 57

Figure S242.  Get High-res Image Gene #27: 'amp_20q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S243.  Gene #27: 'amp_20q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
AMP PEAK 27(20Q13.33) MUTATED 25 26 77 43 62 13
AMP PEAK 27(20Q13.33) WILD-TYPE 46 13 68 87 34 16

Figure S243.  Get High-res Image Gene #27: 'amp_20q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S244.  Gene #27: 'amp_20q13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
AMP PEAK 27(20Q13.33) MUTATED 18 62 37 21 30 39
AMP PEAK 27(20Q13.33) WILD-TYPE 41 28 58 22 40 38

Figure S244.  Get High-res Image Gene #27: 'amp_20q13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S245.  Gene #27: 'amp_20q13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
AMP PEAK 27(20Q13.33) MUTATED 32 137 38
AMP PEAK 27(20Q13.33) WILD-TYPE 72 101 54

Figure S245.  Get High-res Image Gene #27: 'amp_20q13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_22q11.22' versus 'CN_CNMF'

P value = 0.00775 (Fisher's exact test), Q value = 0.014

Table S246.  Gene #28: 'amp_22q11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
AMP PEAK 28(22Q11.22) MUTATED 41 25 12 12
AMP PEAK 28(22Q11.22) WILD-TYPE 131 113 120 62

Figure S246.  Get High-res Image Gene #28: 'amp_22q11.22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_22q11.22' versus 'MIRSEQ_CNMF'

P value = 0.0417 (Fisher's exact test), Q value = 0.063

Table S247.  Gene #28: 'amp_22q11.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
AMP PEAK 28(22Q11.22) MUTATED 23 48 19
AMP PEAK 28(22Q11.22) WILD-TYPE 163 173 84

Figure S247.  Get High-res Image Gene #28: 'amp_22q11.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_22q11.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0353 (Fisher's exact test), Q value = 0.055

Table S248.  Gene #28: 'amp_22q11.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
AMP PEAK 28(22Q11.22) MUTATED 6 24 22 4 9 13
AMP PEAK 28(22Q11.22) WILD-TYPE 53 66 73 39 61 64

Figure S248.  Get High-res Image Gene #28: 'amp_22q11.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_22q11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 0.043

Table S249.  Gene #28: 'amp_22q11.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
AMP PEAK 28(22Q11.22) MUTATED 10 51 17
AMP PEAK 28(22Q11.22) WILD-TYPE 94 187 75

Figure S249.  Get High-res Image Gene #28: 'amp_22q11.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xq28' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S250.  Gene #29: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
AMP PEAK 29(XQ28) MUTATED 70 42 21 26
AMP PEAK 29(XQ28) WILD-TYPE 102 96 111 48

Figure S250.  Get High-res Image Gene #29: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xq28' versus 'METHLYATION_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.031

Table S251.  Gene #29: 'amp_xq28' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
AMP PEAK 29(XQ28) MUTATED 48 61 27
AMP PEAK 29(XQ28) WILD-TYPE 108 109 102

Figure S251.  Get High-res Image Gene #29: 'amp_xq28' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xq28' versus 'RPPA_CNMF'

P value = 0.0279 (Fisher's exact test), Q value = 0.044

Table S252.  Gene #29: 'amp_xq28' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
AMP PEAK 29(XQ28) MUTATED 38 4 15 29 30
AMP PEAK 29(XQ28) WILD-TYPE 53 18 51 46 79

Figure S252.  Get High-res Image Gene #29: 'amp_xq28' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_xq28' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00015

Table S253.  Gene #29: 'amp_xq28' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
AMP PEAK 29(XQ28) MUTATED 62 26 24 34 12
AMP PEAK 29(XQ28) WILD-TYPE 68 93 66 81 46

Figure S253.  Get High-res Image Gene #29: 'amp_xq28' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xq28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00041

Table S254.  Gene #29: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
AMP PEAK 29(XQ28) MUTATED 20 50 38 6 14 14 16
AMP PEAK 29(XQ28) WILD-TYPE 58 60 59 42 39 35 61

Figure S254.  Get High-res Image Gene #29: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.02

Table S255.  Gene #29: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
AMP PEAK 29(XQ28) MUTATED 43 73 40
AMP PEAK 29(XQ28) WILD-TYPE 143 148 63

Figure S255.  Get High-res Image Gene #29: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_xq28' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0295 (Fisher's exact test), Q value = 0.046

Table S256.  Gene #29: 'amp_xq28' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
AMP PEAK 29(XQ28) MUTATED 9 32 36 9 21 24
AMP PEAK 29(XQ28) WILD-TYPE 50 58 59 34 49 53

Figure S256.  Get High-res Image Gene #29: 'amp_xq28' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_xq28' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00036

Table S257.  Gene #29: 'amp_xq28' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
AMP PEAK 29(XQ28) MUTATED 15 82 34
AMP PEAK 29(XQ28) WILD-TYPE 89 156 58

Figure S257.  Get High-res Image Gene #29: 'amp_xq28' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S258.  Gene #30: 'del_1p36.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 1(1P36.13) MUTATED 16 51 18 37
DEL PEAK 1(1P36.13) WILD-TYPE 156 87 114 37

Figure S258.  Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.13' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00048

Table S259.  Gene #30: 'del_1p36.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 1(1P36.13) MUTATED 44 47 13
DEL PEAK 1(1P36.13) WILD-TYPE 112 123 116

Figure S259.  Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S260.  Gene #30: 'del_1p36.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 1(1P36.13) MUTATED 24 16 32 41 6
DEL PEAK 1(1P36.13) WILD-TYPE 106 103 58 74 52

Figure S260.  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 = 3.9e-05

Table S261.  Gene #30: 'del_1p36.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 1(1P36.13) MUTATED 11 27 20 11 26 18 6
DEL PEAK 1(1P36.13) WILD-TYPE 67 83 77 37 27 31 71

Figure S261.  Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.13' versus 'MIRSEQ_CNMF'

P value = 0.0208 (Fisher's exact test), Q value = 0.035

Table S262.  Gene #30: 'del_1p36.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 1(1P36.13) MUTATED 37 64 17
DEL PEAK 1(1P36.13) WILD-TYPE 149 157 86

Figure S262.  Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0111 (Fisher's exact test), Q value = 0.02

Table S263.  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 71 39 145 130 96 29
DEL PEAK 1(1P36.13) MUTATED 17 18 33 24 23 3
DEL PEAK 1(1P36.13) WILD-TYPE 54 21 112 106 73 26

Figure S263.  Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00218 (Fisher's exact test), Q value = 0.0045

Table S264.  Gene #30: 'del_1p36.13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
DEL PEAK 1(1P36.13) MUTATED 4 29 25 8 19 12
DEL PEAK 1(1P36.13) WILD-TYPE 55 61 70 35 51 65

Figure S264.  Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S265.  Gene #31: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 2(1P13.1) MUTATED 33 52 27 39
DEL PEAK 2(1P13.1) WILD-TYPE 139 86 105 35

Figure S265.  Get High-res Image Gene #31: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p13.1' versus 'METHLYATION_CNMF'

P value = 0.00541 (Fisher's exact test), Q value = 0.01

Table S266.  Gene #31: 'del_1p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 2(1P13.1) MUTATED 50 53 22
DEL PEAK 2(1P13.1) WILD-TYPE 106 117 107

Figure S266.  Get High-res Image Gene #31: 'del_1p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S267.  Gene #31: 'del_1p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 2(1P13.1) MUTATED 30 25 30 54 10
DEL PEAK 2(1P13.1) WILD-TYPE 100 94 60 61 48

Figure S267.  Get High-res Image Gene #31: 'del_1p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p13.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S268.  Gene #31: 'del_1p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 2(1P13.1) MUTATED 21 28 27 20 27 17 9
DEL PEAK 2(1P13.1) WILD-TYPE 57 82 70 28 26 32 68

Figure S268.  Get High-res Image Gene #31: 'del_1p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S269.  Gene #31: 'del_1p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 2(1P13.1) MUTATED 14 25 37 30 29 13
DEL PEAK 2(1P13.1) WILD-TYPE 57 14 108 100 67 16

Figure S269.  Get High-res Image Gene #31: 'del_1p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00509 (Fisher's exact test), Q value = 0.0097

Table S270.  Gene #31: 'del_1p13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
DEL PEAK 2(1P13.1) MUTATED 11 33 24 19 17 13
DEL PEAK 2(1P13.1) WILD-TYPE 48 57 71 24 53 64

Figure S270.  Get High-res Image Gene #31: 'del_1p13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_2q22.1' versus 'CN_CNMF'

P value = 0.00125 (Fisher's exact test), Q value = 0.0028

Table S271.  Gene #32: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 3(2Q22.1) MUTATED 14 17 3 12
DEL PEAK 3(2Q22.1) WILD-TYPE 158 121 129 62

Figure S271.  Get High-res Image Gene #32: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 0.00145 (Fisher's exact test), Q value = 0.0032

Table S272.  Gene #32: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 3(2Q22.1) MUTATED 22 15 3
DEL PEAK 3(2Q22.1) WILD-TYPE 134 155 126

Figure S272.  Get High-res Image Gene #32: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q22.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00175 (Fisher's exact test), Q value = 0.0037

Table S273.  Gene #32: 'del_2q22.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
DEL PEAK 3(2Q22.1) MUTATED 7 21 4
DEL PEAK 3(2Q22.1) WILD-TYPE 160 112 59

Figure S273.  Get High-res Image Gene #32: 'del_2q22.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_2q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00574 (Fisher's exact test), Q value = 0.011

Table S274.  Gene #32: 'del_2q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 3(2Q22.1) MUTATED 6 9 10 2 8 10 1
DEL PEAK 3(2Q22.1) WILD-TYPE 72 101 87 46 45 39 76

Figure S274.  Get High-res Image Gene #32: 'del_2q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.029

Table S275.  Gene #32: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 3(2Q22.1) MUTATED 8 26 11
DEL PEAK 3(2Q22.1) WILD-TYPE 178 195 92

Figure S275.  Get High-res Image Gene #32: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0229 (Fisher's exact test), Q value = 0.037

Table S276.  Gene #32: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 3(2Q22.1) MUTATED 4 4 13 6 17 1
DEL PEAK 3(2Q22.1) WILD-TYPE 67 35 132 124 79 28

Figure S276.  Get High-res Image Gene #32: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0385 (Fisher's exact test), Q value = 0.058

Table S277.  Gene #32: 'del_2q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
DEL PEAK 3(2Q22.1) MUTATED 3 26 7
DEL PEAK 3(2Q22.1) WILD-TYPE 101 212 85

Figure S277.  Get High-res Image Gene #32: 'del_2q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S278.  Gene #33: 'del_3p26.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 4(3P26.2) MUTATED 93 74 23 43
DEL PEAK 4(3P26.2) WILD-TYPE 79 64 109 31

Figure S278.  Get High-res Image Gene #33: 'del_3p26.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p26.2' versus 'METHLYATION_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0012

Table S279.  Gene #33: 'del_3p26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 4(3P26.2) MUTATED 89 71 45
DEL PEAK 4(3P26.2) WILD-TYPE 67 99 84

Figure S279.  Get High-res Image Gene #33: 'del_3p26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p26.2' versus 'RPPA_CNMF'

P value = 0.0497 (Fisher's exact test), Q value = 0.073

Table S280.  Gene #33: 'del_3p26.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 4(3P26.2) MUTATED 40 9 26 47 51
DEL PEAK 4(3P26.2) WILD-TYPE 51 13 40 28 58

Figure S280.  Get High-res Image Gene #33: 'del_3p26.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p26.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.021

Table S281.  Gene #33: 'del_3p26.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
DEL PEAK 4(3P26.2) MUTATED 66 75 32
DEL PEAK 4(3P26.2) WILD-TYPE 101 58 31

Figure S281.  Get High-res Image Gene #33: 'del_3p26.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S282.  Gene #33: 'del_3p26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 4(3P26.2) MUTATED 30 40 65 15 35 26 19
DEL PEAK 4(3P26.2) WILD-TYPE 48 70 32 33 18 23 58

Figure S282.  Get High-res Image Gene #33: 'del_3p26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.00067

Table S283.  Gene #33: 'del_3p26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 4(3P26.2) MUTATED 61 112 55
DEL PEAK 4(3P26.2) WILD-TYPE 125 109 48

Figure S283.  Get High-res Image Gene #33: 'del_3p26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p26.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S284.  Gene #33: 'del_3p26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 4(3P26.2) MUTATED 30 24 59 45 61 9
DEL PEAK 4(3P26.2) WILD-TYPE 41 15 86 85 35 20

Figure S284.  Get High-res Image Gene #33: 'del_3p26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00041

Table S285.  Gene #33: 'del_3p26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
DEL PEAK 4(3P26.2) MUTATED 31 128 39
DEL PEAK 4(3P26.2) WILD-TYPE 73 110 53

Figure S285.  Get High-res Image Gene #33: 'del_3p26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p21.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S286.  Gene #34: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 5(3P21.31) MUTATED 97 83 25 43
DEL PEAK 5(3P21.31) WILD-TYPE 75 55 107 31

Figure S286.  Get High-res Image Gene #34: '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 = 3.9e-05

Table S287.  Gene #34: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 5(3P21.31) MUTATED 102 74 43
DEL PEAK 5(3P21.31) WILD-TYPE 54 96 86

Figure S287.  Get High-res Image Gene #34: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p21.31' versus 'RPPA_CNMF'

P value = 0.0365 (Fisher's exact test), Q value = 0.056

Table S288.  Gene #34: 'del_3p21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 5(3P21.31) MUTATED 41 9 28 49 55
DEL PEAK 5(3P21.31) WILD-TYPE 50 13 38 26 54

Figure S288.  Get High-res Image Gene #34: 'del_3p21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p21.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0023 (Fisher's exact test), Q value = 0.0047

Table S289.  Gene #34: 'del_3p21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
DEL PEAK 5(3P21.31) MUTATED 68 81 33
DEL PEAK 5(3P21.31) WILD-TYPE 99 52 30

Figure S289.  Get High-res Image Gene #34: 'del_3p21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p21.31' versus 'MRNASEQ_CNMF'

P value = 0.00715 (Fisher's exact test), Q value = 0.013

Table S290.  Gene #34: 'del_3p21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 5(3P21.31) MUTATED 58 44 49 68 25
DEL PEAK 5(3P21.31) WILD-TYPE 72 75 41 47 33

Figure S290.  Get High-res Image Gene #34: '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 = 3.9e-05

Table S291.  Gene #34: 'del_3p21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 5(3P21.31) MUTATED 28 45 70 15 37 29 20
DEL PEAK 5(3P21.31) WILD-TYPE 50 65 27 33 16 20 57

Figure S291.  Get High-res Image Gene #34: '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 = 3.9e-05

Table S292.  Gene #34: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 5(3P21.31) MUTATED 63 123 57
DEL PEAK 5(3P21.31) WILD-TYPE 123 98 46

Figure S292.  Get High-res Image Gene #34: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S293.  Gene #34: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 5(3P21.31) MUTATED 32 27 63 45 65 11
DEL PEAK 5(3P21.31) WILD-TYPE 39 12 82 85 31 18

Figure S293.  Get High-res Image Gene #34: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.02

Table S294.  Gene #34: 'del_3p21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
DEL PEAK 5(3P21.31) MUTATED 21 56 48 24 32 30
DEL PEAK 5(3P21.31) WILD-TYPE 38 34 47 19 38 47

Figure S294.  Get High-res Image Gene #34: 'del_3p21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S295.  Gene #34: 'del_3p21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
DEL PEAK 5(3P21.31) MUTATED 32 137 42
DEL PEAK 5(3P21.31) WILD-TYPE 72 101 50

Figure S295.  Get High-res Image Gene #34: 'del_3p21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q11.1' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00015

Table S296.  Gene #35: 'del_3q11.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 6(3Q11.1) MUTATED 59 38 17 27
DEL PEAK 6(3Q11.1) WILD-TYPE 113 100 115 47

Figure S296.  Get High-res Image Gene #35: 'del_3q11.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q11.1' versus 'METHLYATION_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.034

Table S297.  Gene #35: 'del_3q11.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 6(3Q11.1) MUTATED 56 49 27
DEL PEAK 6(3Q11.1) WILD-TYPE 100 121 102

Figure S297.  Get High-res Image Gene #35: 'del_3q11.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3q11.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0387 (Fisher's exact test), Q value = 0.059

Table S298.  Gene #35: 'del_3q11.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 6(3Q11.1) MUTATED 20 25 23 17 22 17 14
DEL PEAK 6(3Q11.1) WILD-TYPE 58 85 74 31 31 32 63

Figure S298.  Get High-res Image Gene #35: 'del_3q11.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3q11.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0258 (Fisher's exact test), Q value = 0.042

Table S299.  Gene #35: 'del_3q11.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 6(3Q11.1) MUTATED 22 19 35 32 27 4
DEL PEAK 6(3Q11.1) WILD-TYPE 49 20 110 98 69 25

Figure S299.  Get High-res Image Gene #35: 'del_3q11.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3q29' versus 'CN_CNMF'

P value = 0.0264 (Fisher's exact test), Q value = 0.042

Table S300.  Gene #36: 'del_3q29' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 7(3Q29) MUTATED 50 35 24 27
DEL PEAK 7(3Q29) WILD-TYPE 122 103 108 47

Figure S300.  Get High-res Image Gene #36: 'del_3q29' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q29' versus 'METHLYATION_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.02

Table S301.  Gene #36: 'del_3q29' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 7(3Q29) MUTATED 51 51 23
DEL PEAK 7(3Q29) WILD-TYPE 105 119 106

Figure S301.  Get High-res Image Gene #36: 'del_3q29' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3q29' versus 'RPPA_CHIERARCHICAL'

P value = 0.0258 (Fisher's exact test), Q value = 0.042

Table S302.  Gene #36: 'del_3q29' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
DEL PEAK 7(3Q29) MUTATED 52 24 19
DEL PEAK 7(3Q29) WILD-TYPE 115 109 44

Figure S302.  Get High-res Image Gene #36: 'del_3q29' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3q29' versus 'MRNASEQ_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.0012

Table S303.  Gene #36: 'del_3q29' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 7(3Q29) MUTATED 23 39 14 43 14
DEL PEAK 7(3Q29) WILD-TYPE 107 80 76 72 44

Figure S303.  Get High-res Image Gene #36: 'del_3q29' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3q29' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S304.  Gene #36: 'del_3q29' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 7(3Q29) MUTATED 24 20 13 23 29 13 11
DEL PEAK 7(3Q29) WILD-TYPE 54 90 84 25 24 36 66

Figure S304.  Get High-res Image Gene #36: 'del_3q29' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3q29' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00134 (Fisher's exact test), Q value = 0.0029

Table S305.  Gene #36: 'del_3q29' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 7(3Q29) MUTATED 26 20 35 29 18 6
DEL PEAK 7(3Q29) WILD-TYPE 45 19 110 101 78 23

Figure S305.  Get High-res Image Gene #36: 'del_3q29' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3q29' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00279 (Fisher's exact test), Q value = 0.0056

Table S306.  Gene #36: 'del_3q29' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
DEL PEAK 7(3Q29) MUTATED 20 37 19 13 18 12
DEL PEAK 7(3Q29) WILD-TYPE 39 53 76 30 52 65

Figure S306.  Get High-res Image Gene #36: 'del_3q29' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4p16.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S307.  Gene #37: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 8(4P16.3) MUTATED 41 47 9 33
DEL PEAK 8(4P16.3) WILD-TYPE 131 91 123 41

Figure S307.  Get High-res Image Gene #37: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

P value = 0.00137 (Fisher's exact test), Q value = 0.003

Table S308.  Gene #37: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 8(4P16.3) MUTATED 55 36 23
DEL PEAK 8(4P16.3) WILD-TYPE 101 134 106

Figure S308.  Get High-res Image Gene #37: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p16.3' versus 'RPPA_CNMF'

P value = 0.0211 (Fisher's exact test), Q value = 0.035

Table S309.  Gene #37: 'del_4p16.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 8(4P16.3) MUTATED 20 8 14 31 25
DEL PEAK 8(4P16.3) WILD-TYPE 71 14 52 44 84

Figure S309.  Get High-res Image Gene #37: 'del_4p16.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4p16.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0279 (Fisher's exact test), Q value = 0.044

Table S310.  Gene #37: 'del_4p16.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
DEL PEAK 8(4P16.3) MUTATED 43 45 10
DEL PEAK 8(4P16.3) WILD-TYPE 124 88 53

Figure S310.  Get High-res Image Gene #37: 'del_4p16.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4p16.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S311.  Gene #37: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 8(4P16.3) MUTATED 33 13 21 46 16
DEL PEAK 8(4P16.3) WILD-TYPE 97 106 69 69 42

Figure S311.  Get High-res Image Gene #37: '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 = 3.9e-05

Table S312.  Gene #37: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 8(4P16.3) MUTATED 13 22 43 5 23 11 12
DEL PEAK 8(4P16.3) WILD-TYPE 65 88 54 43 30 38 65

Figure S312.  Get High-res Image Gene #37: '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 = 3.9e-05

Table S313.  Gene #37: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 8(4P16.3) MUTATED 24 80 25
DEL PEAK 8(4P16.3) WILD-TYPE 162 141 78

Figure S313.  Get High-res Image Gene #37: '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 = 3.9e-05

Table S314.  Gene #37: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 8(4P16.3) MUTATED 6 15 42 21 41 4
DEL PEAK 8(4P16.3) WILD-TYPE 65 24 103 109 55 25

Figure S314.  Get High-res Image Gene #37: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00533 (Fisher's exact test), Q value = 0.01

Table S315.  Gene #37: 'del_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
DEL PEAK 8(4P16.3) MUTATED 5 31 30 11 17 17
DEL PEAK 8(4P16.3) WILD-TYPE 54 59 65 32 53 60

Figure S315.  Get High-res Image Gene #37: 'del_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00048

Table S316.  Gene #37: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
DEL PEAK 8(4P16.3) MUTATED 13 78 20
DEL PEAK 8(4P16.3) WILD-TYPE 91 160 72

Figure S316.  Get High-res Image Gene #37: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.1' versus 'MRNA_CNMF'

P value = 0.00194 (Fisher's exact test), Q value = 0.0041

Table S317.  Gene #38: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 10 7
DEL PEAK 9(4Q22.1) MUTATED 2 2 6
DEL PEAK 9(4Q22.1) WILD-TYPE 13 8 1

Figure S317.  Get High-res Image Gene #38: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00294 (Fisher's exact test), Q value = 0.0059

Table S318.  Gene #38: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
DEL PEAK 9(4Q22.1) MUTATED 2 2 6
DEL PEAK 9(4Q22.1) WILD-TYPE 12 9 1

Figure S318.  Get High-res Image Gene #38: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S319.  Gene #38: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 9(4Q22.1) MUTATED 50 65 9 34
DEL PEAK 9(4Q22.1) WILD-TYPE 122 73 123 40

Figure S319.  Get High-res Image Gene #38: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S320.  Gene #38: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 9(4Q22.1) MUTATED 71 40 23
DEL PEAK 9(4Q22.1) WILD-TYPE 85 130 106

Figure S320.  Get High-res Image Gene #38: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q22.1' versus 'RPPA_CNMF'

P value = 0.0205 (Fisher's exact test), Q value = 0.034

Table S321.  Gene #38: 'del_4q22.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 9(4Q22.1) MUTATED 27 6 16 36 30
DEL PEAK 9(4Q22.1) WILD-TYPE 64 16 50 39 79

Figure S321.  Get High-res Image Gene #38: 'del_4q22.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4q22.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00262 (Fisher's exact test), Q value = 0.0053

Table S322.  Gene #38: 'del_4q22.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
DEL PEAK 9(4Q22.1) MUTATED 52 53 10
DEL PEAK 9(4Q22.1) WILD-TYPE 115 80 53

Figure S322.  Get High-res Image Gene #38: 'del_4q22.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S323.  Gene #38: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 9(4Q22.1) MUTATED 41 13 33 54 16
DEL PEAK 9(4Q22.1) WILD-TYPE 89 106 57 61 42

Figure S323.  Get High-res Image Gene #38: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S324.  Gene #38: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 9(4Q22.1) MUTATED 13 22 47 6 29 26 14
DEL PEAK 9(4Q22.1) WILD-TYPE 65 88 50 42 24 23 63

Figure S324.  Get High-res Image Gene #38: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S325.  Gene #38: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 9(4Q22.1) MUTATED 30 93 34
DEL PEAK 9(4Q22.1) WILD-TYPE 156 128 69

Figure S325.  Get High-res Image Gene #38: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S326.  Gene #38: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 9(4Q22.1) MUTATED 12 16 52 24 47 6
DEL PEAK 9(4Q22.1) WILD-TYPE 59 23 93 106 49 23

Figure S326.  Get High-res Image Gene #38: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00333 (Fisher's exact test), Q value = 0.0066

Table S327.  Gene #38: 'del_4q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
DEL PEAK 9(4Q22.1) MUTATED 7 38 28 15 22 20
DEL PEAK 9(4Q22.1) WILD-TYPE 52 52 67 28 48 57

Figure S327.  Get High-res Image Gene #38: 'del_4q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.00089

Table S328.  Gene #38: 'del_4q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
DEL PEAK 9(4Q22.1) MUTATED 20 90 20
DEL PEAK 9(4Q22.1) WILD-TYPE 84 148 72

Figure S328.  Get High-res Image Gene #38: 'del_4q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'MRNA_CNMF'

P value = 0.00197 (Fisher's exact test), Q value = 0.0041

Table S329.  Gene #39: 'del_4q34.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 10 7
DEL PEAK 10(4Q34.3) MUTATED 2 2 6
DEL PEAK 10(4Q34.3) WILD-TYPE 13 8 1

Figure S329.  Get High-res Image Gene #39: 'del_4q34.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q34.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00307 (Fisher's exact test), Q value = 0.0061

Table S330.  Gene #39: 'del_4q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
DEL PEAK 10(4Q34.3) MUTATED 2 2 6
DEL PEAK 10(4Q34.3) WILD-TYPE 12 9 1

Figure S330.  Get High-res Image Gene #39: 'del_4q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S331.  Gene #39: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 10(4Q34.3) MUTATED 57 77 13 40
DEL PEAK 10(4Q34.3) WILD-TYPE 115 61 119 34

Figure S331.  Get High-res Image Gene #39: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S332.  Gene #39: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 10(4Q34.3) MUTATED 86 50 26
DEL PEAK 10(4Q34.3) WILD-TYPE 70 120 103

Figure S332.  Get High-res Image Gene #39: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q34.3' versus 'RPPA_CNMF'

P value = 0.037 (Fisher's exact test), Q value = 0.056

Table S333.  Gene #39: 'del_4q34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 10(4Q34.3) MUTATED 31 7 20 40 38
DEL PEAK 10(4Q34.3) WILD-TYPE 60 15 46 35 71

Figure S333.  Get High-res Image Gene #39: 'del_4q34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4q34.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.002 (Fisher's exact test), Q value = 0.0042

Table S334.  Gene #39: 'del_4q34.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
DEL PEAK 10(4Q34.3) MUTATED 55 65 16
DEL PEAK 10(4Q34.3) WILD-TYPE 112 68 47

Figure S334.  Get High-res Image Gene #39: 'del_4q34.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S335.  Gene #39: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 10(4Q34.3) MUTATED 46 16 40 67 16
DEL PEAK 10(4Q34.3) WILD-TYPE 84 103 50 48 42

Figure S335.  Get High-res Image Gene #39: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S336.  Gene #39: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 10(4Q34.3) MUTATED 15 25 56 8 36 29 16
DEL PEAK 10(4Q34.3) WILD-TYPE 63 85 41 40 17 20 61

Figure S336.  Get High-res Image Gene #39: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S337.  Gene #39: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 10(4Q34.3) MUTATED 38 113 34
DEL PEAK 10(4Q34.3) WILD-TYPE 148 108 69

Figure S337.  Get High-res Image Gene #39: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S338.  Gene #39: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 10(4Q34.3) MUTATED 13 21 61 26 60 4
DEL PEAK 10(4Q34.3) WILD-TYPE 58 18 84 104 36 25

Figure S338.  Get High-res Image Gene #39: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S339.  Gene #39: 'del_4q34.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
DEL PEAK 10(4Q34.3) MUTATED 7 48 37 15 28 24
DEL PEAK 10(4Q34.3) WILD-TYPE 52 42 58 28 42 53

Figure S339.  Get High-res Image Gene #39: 'del_4q34.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S340.  Gene #39: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
DEL PEAK 10(4Q34.3) MUTATED 22 115 22
DEL PEAK 10(4Q34.3) WILD-TYPE 82 123 70

Figure S340.  Get High-res Image Gene #39: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S341.  Gene #40: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 11(5Q12.1) MUTATED 78 59 5 37
DEL PEAK 11(5Q12.1) WILD-TYPE 94 79 127 37

Figure S341.  Get High-res Image Gene #40: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S342.  Gene #40: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 11(5Q12.1) MUTATED 74 57 21
DEL PEAK 11(5Q12.1) WILD-TYPE 82 113 108

Figure S342.  Get High-res Image Gene #40: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q12.1' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S343.  Gene #40: 'del_5q12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 11(5Q12.1) MUTATED 32 8 13 44 28
DEL PEAK 11(5Q12.1) WILD-TYPE 59 14 53 31 81

Figure S343.  Get High-res Image Gene #40: 'del_5q12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_5q12.1' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S344.  Gene #40: 'del_5q12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
DEL PEAK 11(5Q12.1) MUTATED 40 66 19
DEL PEAK 11(5Q12.1) WILD-TYPE 127 67 44

Figure S344.  Get High-res Image Gene #40: 'del_5q12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_5q12.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S345.  Gene #40: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 11(5Q12.1) MUTATED 58 20 28 56 15
DEL PEAK 11(5Q12.1) WILD-TYPE 72 99 62 59 43

Figure S345.  Get High-res Image Gene #40: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S346.  Gene #40: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 11(5Q12.1) MUTATED 13 40 51 7 25 24 17
DEL PEAK 11(5Q12.1) WILD-TYPE 65 70 46 41 28 25 60

Figure S346.  Get High-res Image Gene #40: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S347.  Gene #40: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 11(5Q12.1) MUTATED 36 108 31
DEL PEAK 11(5Q12.1) WILD-TYPE 150 113 72

Figure S347.  Get High-res Image Gene #40: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S348.  Gene #40: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 11(5Q12.1) MUTATED 10 18 57 30 55 5
DEL PEAK 11(5Q12.1) WILD-TYPE 61 21 88 100 41 24

Figure S348.  Get High-res Image Gene #40: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S349.  Gene #40: 'del_5q12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
DEL PEAK 11(5Q12.1) MUTATED 5 50 31 12 22 28
DEL PEAK 11(5Q12.1) WILD-TYPE 54 40 64 31 48 49

Figure S349.  Get High-res Image Gene #40: 'del_5q12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S350.  Gene #40: 'del_5q12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
DEL PEAK 11(5Q12.1) MUTATED 15 109 24
DEL PEAK 11(5Q12.1) WILD-TYPE 89 129 68

Figure S350.  Get High-res Image Gene #40: 'del_5q12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S351.  Gene #41: 'del_5q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 12(5Q31.1) MUTATED 82 74 12 43
DEL PEAK 12(5Q31.1) WILD-TYPE 90 64 120 31

Figure S351.  Get High-res Image Gene #41: 'del_5q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q31.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S352.  Gene #41: 'del_5q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 12(5Q31.1) MUTATED 85 75 24
DEL PEAK 12(5Q31.1) WILD-TYPE 71 95 105

Figure S352.  Get High-res Image Gene #41: 'del_5q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q31.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S353.  Gene #41: 'del_5q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 12(5Q31.1) MUTATED 39 9 18 50 35
DEL PEAK 12(5Q31.1) WILD-TYPE 52 13 48 25 74

Figure S353.  Get High-res Image Gene #41: 'del_5q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_5q31.1' versus 'RPPA_CHIERARCHICAL'

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

Table S354.  Gene #41: 'del_5q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
DEL PEAK 12(5Q31.1) MUTATED 51 74 26
DEL PEAK 12(5Q31.1) WILD-TYPE 116 59 37

Figure S354.  Get High-res Image Gene #41: 'del_5q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_5q31.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S355.  Gene #41: 'del_5q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 12(5Q31.1) MUTATED 65 25 36 65 18
DEL PEAK 12(5Q31.1) WILD-TYPE 65 94 54 50 40

Figure S355.  Get High-res Image Gene #41: 'del_5q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S356.  Gene #41: 'del_5q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 12(5Q31.1) MUTATED 14 52 53 11 31 27 21
DEL PEAK 12(5Q31.1) WILD-TYPE 64 58 44 37 22 22 56

Figure S356.  Get High-res Image Gene #41: 'del_5q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q31.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S357.  Gene #41: 'del_5q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 12(5Q31.1) MUTATED 47 123 37
DEL PEAK 12(5Q31.1) WILD-TYPE 139 98 66

Figure S357.  Get High-res Image Gene #41: 'del_5q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S358.  Gene #41: 'del_5q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 12(5Q31.1) MUTATED 16 17 72 33 63 6
DEL PEAK 12(5Q31.1) WILD-TYPE 55 22 73 97 33 23

Figure S358.  Get High-res Image Gene #41: 'del_5q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q31.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S359.  Gene #41: 'del_5q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
DEL PEAK 12(5Q31.1) MUTATED 8 56 44 15 21 35
DEL PEAK 12(5Q31.1) WILD-TYPE 51 34 51 28 49 42

Figure S359.  Get High-res Image Gene #41: 'del_5q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S360.  Gene #41: 'del_5q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
DEL PEAK 12(5Q31.1) MUTATED 21 124 34
DEL PEAK 12(5Q31.1) WILD-TYPE 83 114 58

Figure S360.  Get High-res Image Gene #41: 'del_5q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q14.3' versus 'CN_CNMF'

P value = 0.0302 (Fisher's exact test), Q value = 0.047

Table S361.  Gene #42: 'del_6q14.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 13(6Q14.3) MUTATED 82 64 59 48
DEL PEAK 13(6Q14.3) WILD-TYPE 90 74 73 26

Figure S361.  Get High-res Image Gene #42: 'del_6q14.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q14.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S362.  Gene #42: 'del_6q14.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 13(6Q14.3) MUTATED 73 109 45
DEL PEAK 13(6Q14.3) WILD-TYPE 83 61 84

Figure S362.  Get High-res Image Gene #42: 'del_6q14.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q14.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.001

Table S363.  Gene #42: 'del_6q14.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 13(6Q14.3) MUTATED 32 58 38 35 34 21 32
DEL PEAK 13(6Q14.3) WILD-TYPE 46 52 59 13 19 28 45

Figure S363.  Get High-res Image Gene #42: 'del_6q14.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q14.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00179 (Fisher's exact test), Q value = 0.0038

Table S364.  Gene #42: 'del_6q14.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 13(6Q14.3) MUTATED 35 22 88 50 38 17
DEL PEAK 13(6Q14.3) WILD-TYPE 36 17 57 80 58 12

Figure S364.  Get High-res Image Gene #42: 'del_6q14.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S365.  Gene #43: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 14(6Q26) MUTATED 72 108 46
DEL PEAK 14(6Q26) WILD-TYPE 84 62 83

Figure S365.  Get High-res Image Gene #43: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00519 (Fisher's exact test), Q value = 0.0099

Table S366.  Gene #43: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 14(6Q26) MUTATED 31 63 40 32 32 25 32
DEL PEAK 14(6Q26) WILD-TYPE 47 47 57 16 21 24 45

Figure S366.  Get High-res Image Gene #43: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0152 (Fisher's exact test), Q value = 0.027

Table S367.  Gene #43: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 14(6Q26) MUTATED 33 20 88 57 39 18
DEL PEAK 14(6Q26) WILD-TYPE 38 19 57 73 57 11

Figure S367.  Get High-res Image Gene #43: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MRNA_CNMF'

P value = 0.021 (Fisher's exact test), Q value = 0.035

Table S368.  Gene #44: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 10 7
DEL PEAK 15(8P23.2) MUTATED 6 7 7
DEL PEAK 15(8P23.2) WILD-TYPE 9 3 0

Figure S368.  Get High-res Image Gene #44: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p23.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00945 (Fisher's exact test), Q value = 0.017

Table S369.  Gene #44: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
DEL PEAK 15(8P23.2) MUTATED 5 8 7
DEL PEAK 15(8P23.2) WILD-TYPE 9 3 0

Figure S369.  Get High-res Image Gene #44: '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 = 3.9e-05

Table S370.  Gene #44: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 15(8P23.2) MUTATED 115 77 27 35
DEL PEAK 15(8P23.2) WILD-TYPE 57 61 105 39

Figure S370.  Get High-res Image Gene #44: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 0.00551 (Fisher's exact test), Q value = 0.01

Table S371.  Gene #44: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 15(8P23.2) MUTATED 78 95 48
DEL PEAK 15(8P23.2) WILD-TYPE 78 75 81

Figure S371.  Get High-res Image Gene #44: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.2' versus 'RPPA_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.02

Table S372.  Gene #44: 'del_8p23.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 15(8P23.2) MUTATED 52 11 25 46 45
DEL PEAK 15(8P23.2) WILD-TYPE 39 11 41 29 64

Figure S372.  Get High-res Image Gene #44: 'del_8p23.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_8p23.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00147 (Fisher's exact test), Q value = 0.0032

Table S373.  Gene #44: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
DEL PEAK 15(8P23.2) MUTATED 68 82 29
DEL PEAK 15(8P23.2) WILD-TYPE 99 51 34

Figure S373.  Get High-res Image Gene #44: '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 = 3.9e-05

Table S374.  Gene #44: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 15(8P23.2) MUTATED 94 39 40 54 25
DEL PEAK 15(8P23.2) WILD-TYPE 36 80 50 61 33

Figure S374.  Get High-res Image Gene #44: '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 = 3.9e-05

Table S375.  Gene #44: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 15(8P23.2) MUTATED 34 70 64 11 20 24 29
DEL PEAK 15(8P23.2) WILD-TYPE 44 40 33 37 33 25 48

Figure S375.  Get High-res Image Gene #44: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00026

Table S376.  Gene #44: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 15(8P23.2) MUTATED 68 123 59
DEL PEAK 15(8P23.2) WILD-TYPE 118 98 44

Figure S376.  Get High-res Image Gene #44: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00051

Table S377.  Gene #44: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 15(8P23.2) MUTATED 27 17 92 49 54 11
DEL PEAK 15(8P23.2) WILD-TYPE 44 22 53 81 42 18

Figure S377.  Get High-res Image Gene #44: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00058

Table S378.  Gene #44: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
DEL PEAK 15(8P23.2) MUTATED 15 41 52 16 39 48
DEL PEAK 15(8P23.2) WILD-TYPE 44 49 43 27 31 29

Figure S378.  Get High-res Image Gene #44: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00383 (Fisher's exact test), Q value = 0.0075

Table S379.  Gene #44: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
DEL PEAK 15(8P23.2) MUTATED 36 128 47
DEL PEAK 15(8P23.2) WILD-TYPE 68 110 45

Figure S379.  Get High-res Image Gene #44: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S380.  Gene #45: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 16(8P11.21) MUTATED 68 37 14 6
DEL PEAK 16(8P11.21) WILD-TYPE 104 101 118 68

Figure S380.  Get High-res Image Gene #45: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p11.21' versus 'MRNASEQ_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.031

Table S381.  Gene #45: 'del_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 16(8P11.21) MUTATED 46 24 21 23 10
DEL PEAK 16(8P11.21) WILD-TYPE 84 95 69 92 48

Figure S381.  Get High-res Image Gene #45: 'del_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S382.  Gene #46: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 17(9P23) MUTATED 109 98 54 26
DEL PEAK 17(9P23) WILD-TYPE 63 40 78 48

Figure S382.  Get High-res Image Gene #46: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 0.046 (Fisher's exact test), Q value = 0.068

Table S383.  Gene #46: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 17(9P23) MUTATED 66 62 63 62 32
DEL PEAK 17(9P23) WILD-TYPE 64 57 27 53 26

Figure S383.  Get High-res Image Gene #46: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.0014

Table S384.  Gene #46: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 17(9P23) MUTATED 42 53 63 24 27 40 36
DEL PEAK 17(9P23) WILD-TYPE 36 57 34 24 26 9 41

Figure S384.  Get High-res Image Gene #46: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S385.  Gene #47: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 18(9P21.3) MUTATED 112 103 54 25
DEL PEAK 18(9P21.3) WILD-TYPE 60 35 78 49

Figure S385.  Get High-res Image Gene #47: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00055

Table S386.  Gene #47: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 18(9P21.3) MUTATED 72 62 70 56 32
DEL PEAK 18(9P21.3) WILD-TYPE 58 57 20 59 26

Figure S386.  Get High-res Image Gene #47: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S387.  Gene #47: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 18(9P21.3) MUTATED 45 57 63 23 25 43 36
DEL PEAK 18(9P21.3) WILD-TYPE 33 53 34 25 28 6 41

Figure S387.  Get High-res Image Gene #47: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00823 (Fisher's exact test), Q value = 0.015

Table S388.  Gene #47: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 18(9P21.3) MUTATED 33 22 78 68 69 20
DEL PEAK 18(9P21.3) WILD-TYPE 38 17 67 62 27 9

Figure S388.  Get High-res Image Gene #47: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0441 (Fisher's exact test), Q value = 0.066

Table S389.  Gene #47: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
DEL PEAK 18(9P21.3) MUTATED 47 142 53
DEL PEAK 18(9P21.3) WILD-TYPE 57 96 39

Figure S389.  Get High-res Image Gene #47: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q21.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S390.  Gene #48: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 19(9Q21.11) MUTATED 94 96 30 38
DEL PEAK 19(9Q21.11) WILD-TYPE 78 42 102 36

Figure S390.  Get High-res Image Gene #48: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q21.11' versus 'METHLYATION_CNMF'

P value = 0.00157 (Fisher's exact test), Q value = 0.0034

Table S391.  Gene #48: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 19(9Q21.11) MUTATED 94 77 52
DEL PEAK 19(9Q21.11) WILD-TYPE 62 93 77

Figure S391.  Get High-res Image Gene #48: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q21.11' versus 'RPPA_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.033

Table S392.  Gene #48: 'del_9q21.11' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 19(9Q21.11) MUTATED 48 10 30 48 43
DEL PEAK 19(9Q21.11) WILD-TYPE 43 12 36 27 66

Figure S392.  Get High-res Image Gene #48: 'del_9q21.11' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9q21.11' versus 'RPPA_CHIERARCHICAL'

P value = 0.00086 (Fisher's exact test), Q value = 0.002

Table S393.  Gene #48: 'del_9q21.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
DEL PEAK 19(9Q21.11) MUTATED 82 78 19
DEL PEAK 19(9Q21.11) WILD-TYPE 85 55 44

Figure S393.  Get High-res Image Gene #48: 'del_9q21.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9q21.11' versus 'MRNASEQ_CNMF'

P value = 0.00128 (Fisher's exact test), Q value = 0.0028

Table S394.  Gene #48: 'del_9q21.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 19(9Q21.11) MUTATED 62 45 44 75 30
DEL PEAK 19(9Q21.11) WILD-TYPE 68 74 46 40 28

Figure S394.  Get High-res Image Gene #48: 'del_9q21.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9q21.11' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S395.  Gene #48: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 19(9Q21.11) MUTATED 35 48 59 16 38 31 29
DEL PEAK 19(9Q21.11) WILD-TYPE 43 62 38 32 15 18 48

Figure S395.  Get High-res Image Gene #48: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_CNMF'

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

Table S396.  Gene #48: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 19(9Q21.11) MUTATED 70 123 61
DEL PEAK 19(9Q21.11) WILD-TYPE 116 98 42

Figure S396.  Get High-res Image Gene #48: '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 = 3.9e-05

Table S397.  Gene #48: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 19(9Q21.11) MUTATED 25 26 70 48 68 17
DEL PEAK 19(9Q21.11) WILD-TYPE 46 13 75 82 28 12

Figure S397.  Get High-res Image Gene #48: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0172 (Fisher's exact test), Q value = 0.03

Table S398.  Gene #48: 'del_9q21.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
DEL PEAK 19(9Q21.11) MUTATED 20 56 48 25 32 35
DEL PEAK 19(9Q21.11) WILD-TYPE 39 34 47 18 38 42

Figure S398.  Get High-res Image Gene #48: 'del_9q21.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9q21.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.0017

Table S399.  Gene #48: 'del_9q21.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
DEL PEAK 19(9Q21.11) MUTATED 36 135 45
DEL PEAK 19(9Q21.11) WILD-TYPE 68 103 47

Figure S399.  Get High-res Image Gene #48: 'del_9q21.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S400.  Gene #49: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 20(10P15.3) MUTATED 67 33 16 15
DEL PEAK 20(10P15.3) WILD-TYPE 105 105 116 59

Figure S400.  Get High-res Image Gene #49: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 0.0198 (Fisher's exact test), Q value = 0.033

Table S401.  Gene #49: 'del_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 20(10P15.3) MUTATED 47 45 21
DEL PEAK 20(10P15.3) WILD-TYPE 109 125 108

Figure S401.  Get High-res Image Gene #49: 'del_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0013

Table S402.  Gene #49: 'del_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 20(10P15.3) MUTATED 41 19 13 38 19
DEL PEAK 20(10P15.3) WILD-TYPE 89 100 77 77 39

Figure S402.  Get High-res Image Gene #49: 'del_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00119 (Fisher's exact test), Q value = 0.0027

Table S403.  Gene #49: 'del_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 20(10P15.3) MUTATED 16 28 40 6 17 9 14
DEL PEAK 20(10P15.3) WILD-TYPE 62 82 57 42 36 40 63

Figure S403.  Get High-res Image Gene #49: 'del_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_CNMF'

P value = 0.00387 (Fisher's exact test), Q value = 0.0075

Table S404.  Gene #49: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 20(10P15.3) MUTATED 34 59 37
DEL PEAK 20(10P15.3) WILD-TYPE 152 162 66

Figure S404.  Get High-res Image Gene #49: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10p15.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00046

Table S405.  Gene #49: 'del_10p15.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 20(10P15.3) MUTATED 10 12 29 29 35 15
DEL PEAK 20(10P15.3) WILD-TYPE 61 27 116 101 61 14

Figure S405.  Get High-res Image Gene #49: 'del_10p15.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.023

Table S406.  Gene #49: 'del_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
DEL PEAK 20(10P15.3) MUTATED 10 33 21 17 13 18
DEL PEAK 20(10P15.3) WILD-TYPE 49 57 74 26 57 59

Figure S406.  Get High-res Image Gene #49: 'del_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S407.  Gene #50: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 21(10Q26.3) MUTATED 78 40 12 18
DEL PEAK 21(10Q26.3) WILD-TYPE 94 98 120 56

Figure S407.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q26.3' versus 'METHLYATION_CNMF'

P value = 0.026 (Fisher's exact test), Q value = 0.042

Table S408.  Gene #50: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 21(10Q26.3) MUTATED 52 50 25
DEL PEAK 21(10Q26.3) WILD-TYPE 104 120 104

Figure S408.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q26.3' versus 'RPPA_CNMF'

P value = 0.0301 (Fisher's exact test), Q value = 0.047

Table S409.  Gene #50: 'del_10q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 21(10Q26.3) MUTATED 35 7 15 26 22
DEL PEAK 21(10Q26.3) WILD-TYPE 56 15 51 49 87

Figure S409.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S410.  Gene #50: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 21(10Q26.3) MUTATED 56 20 15 38 17
DEL PEAK 21(10Q26.3) WILD-TYPE 74 99 75 77 41

Figure S410.  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 = 3.9e-05

Table S411.  Gene #50: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 21(10Q26.3) MUTATED 22 40 48 1 11 9 15
DEL PEAK 21(10Q26.3) WILD-TYPE 56 70 49 47 42 40 62

Figure S411.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_CNMF'

P value = 0.0132 (Fisher's exact test), Q value = 0.023

Table S412.  Gene #50: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 21(10Q26.3) MUTATED 39 70 36
DEL PEAK 21(10Q26.3) WILD-TYPE 147 151 67

Figure S412.  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 = 3.9e-05

Table S413.  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 71 39 145 130 96 29
DEL PEAK 21(10Q26.3) MUTATED 8 9 41 30 43 14
DEL PEAK 21(10Q26.3) WILD-TYPE 63 30 104 100 53 15

Figure S413.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.019

Table S414.  Gene #50: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
DEL PEAK 21(10Q26.3) MUTATED 7 32 22 16 22 25
DEL PEAK 21(10Q26.3) WILD-TYPE 52 58 73 27 48 52

Figure S414.  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 = 0.00231 (Fisher's exact test), Q value = 0.0047

Table S415.  Gene #50: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
DEL PEAK 21(10Q26.3) MUTATED 17 82 25
DEL PEAK 21(10Q26.3) WILD-TYPE 87 156 67

Figure S415.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'MRNA_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.037

Table S416.  Gene #51: 'del_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 10 7
DEL PEAK 22(11P15.5) MUTATED 1 2 4
DEL PEAK 22(11P15.5) WILD-TYPE 14 8 3

Figure S416.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11p15.5' versus 'MRNA_CHIERARCHICAL'

P value = 0.0317 (Fisher's exact test), Q value = 0.049

Table S417.  Gene #51: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
DEL PEAK 22(11P15.5) MUTATED 1 2 4
DEL PEAK 22(11P15.5) WILD-TYPE 13 9 3

Figure S417.  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 = 3.9e-05

Table S418.  Gene #51: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 22(11P15.5) MUTATED 60 54 10 19
DEL PEAK 22(11P15.5) WILD-TYPE 112 84 122 55

Figure S418.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.001

Table S419.  Gene #51: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 22(11P15.5) MUTATED 59 44 22
DEL PEAK 22(11P15.5) WILD-TYPE 97 126 107

Figure S419.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11p15.5' versus 'RPPA_CNMF'

P value = 0.022 (Fisher's exact test), Q value = 0.036

Table S420.  Gene #51: 'del_11p15.5' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 22(11P15.5) MUTATED 20 6 13 32 30
DEL PEAK 22(11P15.5) WILD-TYPE 71 16 53 43 79

Figure S420.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_11p15.5' versus 'RPPA_CHIERARCHICAL'

P value = 0.00259 (Fisher's exact test), Q value = 0.0052

Table S421.  Gene #51: 'del_11p15.5' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
DEL PEAK 22(11P15.5) MUTATED 34 51 16
DEL PEAK 22(11P15.5) WILD-TYPE 133 82 47

Figure S421.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_11p15.5' versus 'MRNASEQ_CNMF'

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

Table S422.  Gene #51: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 22(11P15.5) MUTATED 47 14 29 36 14
DEL PEAK 22(11P15.5) WILD-TYPE 83 105 61 79 44

Figure S422.  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 = 3.9e-05

Table S423.  Gene #51: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 22(11P15.5) MUTATED 8 36 38 8 14 23 13
DEL PEAK 22(11P15.5) WILD-TYPE 70 74 59 40 39 26 64

Figure S423.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0014

Table S424.  Gene #51: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 22(11P15.5) MUTATED 37 80 23
DEL PEAK 22(11P15.5) WILD-TYPE 149 141 80

Figure S424.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S425.  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 71 39 145 130 96 29
DEL PEAK 22(11P15.5) MUTATED 13 8 58 25 35 1
DEL PEAK 22(11P15.5) WILD-TYPE 58 31 87 105 61 28

Figure S425.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S426.  Gene #51: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
DEL PEAK 22(11P15.5) MUTATED 8 40 32 4 17 20
DEL PEAK 22(11P15.5) WILD-TYPE 51 50 63 39 53 57

Figure S426.  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 = 0.0255 (Fisher's exact test), Q value = 0.041

Table S427.  Gene #51: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
DEL PEAK 22(11P15.5) MUTATED 19 77 25
DEL PEAK 22(11P15.5) WILD-TYPE 85 161 67

Figure S427.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S428.  Gene #52: 'del_11q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 23(11Q23.1) MUTATED 28 48 14 30
DEL PEAK 23(11Q23.1) WILD-TYPE 144 90 118 44

Figure S428.  Get High-res Image Gene #52: 'del_11q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q23.1' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00023

Table S429.  Gene #52: 'del_11q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 23(11Q23.1) MUTATED 54 32 18
DEL PEAK 23(11Q23.1) WILD-TYPE 102 138 111

Figure S429.  Get High-res Image Gene #52: 'del_11q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q23.1' versus 'RPPA_CNMF'

P value = 0.0302 (Fisher's exact test), Q value = 0.047

Table S430.  Gene #52: 'del_11q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 23(11Q23.1) MUTATED 13 3 14 26 26
DEL PEAK 23(11Q23.1) WILD-TYPE 78 19 52 49 83

Figure S430.  Get High-res Image Gene #52: 'del_11q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_11q23.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S431.  Gene #52: 'del_11q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 23(11Q23.1) MUTATED 26 13 25 43 11
DEL PEAK 23(11Q23.1) WILD-TYPE 104 106 65 72 47

Figure S431.  Get High-res Image Gene #52: 'del_11q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.0013

Table S432.  Gene #52: 'del_11q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 23(11Q23.1) MUTATED 10 26 22 16 20 16 8
DEL PEAK 23(11Q23.1) WILD-TYPE 68 84 75 32 33 33 69

Figure S432.  Get High-res Image Gene #52: 'del_11q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.1' versus 'MIRSEQ_CNMF'

P value = 0.005 (Fisher's exact test), Q value = 0.0096

Table S433.  Gene #52: 'del_11q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 23(11Q23.1) MUTATED 35 67 17
DEL PEAK 23(11Q23.1) WILD-TYPE 151 154 86

Figure S433.  Get High-res Image Gene #52: 'del_11q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00156 (Fisher's exact test), Q value = 0.0034

Table S434.  Gene #52: 'del_11q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
DEL PEAK 23(11Q23.1) MUTATED 9 33 24 3 14 14
DEL PEAK 23(11Q23.1) WILD-TYPE 50 57 71 40 56 63

Figure S434.  Get High-res Image Gene #52: 'del_11q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11q25' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S435.  Gene #53: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 24(11Q25) MUTATED 31 43 14 27
DEL PEAK 24(11Q25) WILD-TYPE 141 95 118 47

Figure S435.  Get High-res Image Gene #53: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q25' versus 'METHLYATION_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.00089

Table S436.  Gene #53: 'del_11q25' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 24(11Q25) MUTATED 51 35 17
DEL PEAK 24(11Q25) WILD-TYPE 105 135 112

Figure S436.  Get High-res Image Gene #53: 'del_11q25' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q25' versus 'RPPA_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.025

Table S437.  Gene #53: 'del_11q25' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 24(11Q25) MUTATED 11 3 13 25 27
DEL PEAK 24(11Q25) WILD-TYPE 80 19 53 50 82

Figure S437.  Get High-res Image Gene #53: 'del_11q25' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_11q25' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00026

Table S438.  Gene #53: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 24(11Q25) MUTATED 25 12 26 39 11
DEL PEAK 24(11Q25) WILD-TYPE 105 107 64 76 47

Figure S438.  Get High-res Image Gene #53: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q25' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00287 (Fisher's exact test), Q value = 0.0057

Table S439.  Gene #53: 'del_11q25' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 24(11Q25) MUTATED 11 25 20 14 19 16 8
DEL PEAK 24(11Q25) WILD-TYPE 67 85 77 34 34 33 69

Figure S439.  Get High-res Image Gene #53: 'del_11q25' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q25' versus 'MIRSEQ_CNMF'

P value = 0.0495 (Fisher's exact test), Q value = 0.073

Table S440.  Gene #53: 'del_11q25' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 24(11Q25) MUTATED 34 61 19
DEL PEAK 24(11Q25) WILD-TYPE 152 160 84

Figure S440.  Get High-res Image Gene #53: 'del_11q25' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11q25' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.0016

Table S441.  Gene #53: 'del_11q25' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
DEL PEAK 24(11Q25) MUTATED 9 30 29 2 14 14
DEL PEAK 24(11Q25) WILD-TYPE 50 60 66 41 56 63

Figure S441.  Get High-res Image Gene #53: 'del_11q25' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_12p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S442.  Gene #54: 'del_12p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 25(12P13.2) MUTATED 75 17 27 21
DEL PEAK 25(12P13.2) WILD-TYPE 97 121 105 53

Figure S442.  Get High-res Image Gene #54: 'del_12p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_12p13.2' versus 'METHLYATION_CNMF'

P value = 0.0451 (Fisher's exact test), Q value = 0.067

Table S443.  Gene #54: 'del_12p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 25(12P13.2) MUTATED 40 56 26
DEL PEAK 25(12P13.2) WILD-TYPE 116 114 103

Figure S443.  Get High-res Image Gene #54: 'del_12p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12p13.2' versus 'RPPA_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.021

Table S444.  Gene #54: 'del_12p13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 25(12P13.2) MUTATED 31 11 16 17 20
DEL PEAK 25(12P13.2) WILD-TYPE 60 11 50 58 89

Figure S444.  Get High-res Image Gene #54: 'del_12p13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_12p13.2' versus 'MRNASEQ_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.0013

Table S445.  Gene #54: 'del_12p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 25(12P13.2) MUTATED 48 37 11 25 18
DEL PEAK 25(12P13.2) WILD-TYPE 82 82 79 90 40

Figure S445.  Get High-res Image Gene #54: 'del_12p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0056 (Fisher's exact test), Q value = 0.011

Table S446.  Gene #54: 'del_12p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 25(12P13.2) MUTATED 23 36 35 11 8 5 21
DEL PEAK 25(12P13.2) WILD-TYPE 55 74 62 37 45 44 56

Figure S446.  Get High-res Image Gene #54: 'del_12p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S447.  Gene #55: 'del_12q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 26(12Q12) MUTATED 60 9 19 11
DEL PEAK 26(12Q12) WILD-TYPE 112 129 113 63

Figure S447.  Get High-res Image Gene #55: 'del_12q12' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q12' versus 'METHLYATION_CNMF'

P value = 0.00392 (Fisher's exact test), Q value = 0.0076

Table S448.  Gene #55: 'del_12q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 26(12Q12) MUTATED 22 47 20
DEL PEAK 26(12Q12) WILD-TYPE 134 123 109

Figure S448.  Get High-res Image Gene #55: 'del_12q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12q12' versus 'RPPA_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.002

Table S449.  Gene #55: 'del_12q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 26(12Q12) MUTATED 28 3 18 7 14
DEL PEAK 26(12Q12) WILD-TYPE 63 19 48 68 95

Figure S449.  Get High-res Image Gene #55: 'del_12q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_12q12' versus 'MRNASEQ_CNMF'

P value = 0.00184 (Fisher's exact test), Q value = 0.0039

Table S450.  Gene #55: 'del_12q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 26(12Q12) MUTATED 34 29 11 11 13
DEL PEAK 26(12Q12) WILD-TYPE 96 90 79 104 45

Figure S450.  Get High-res Image Gene #55: 'del_12q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0408 (Fisher's exact test), Q value = 0.061

Table S451.  Gene #55: 'del_12q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 26(12Q12) MUTATED 16 26 20 10 2 7 17
DEL PEAK 26(12Q12) WILD-TYPE 62 84 77 38 51 42 60

Figure S451.  Get High-res Image Gene #55: 'del_12q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0215 (Fisher's exact test), Q value = 0.036

Table S452.  Gene #55: 'del_12q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 26(12Q12) MUTATED 15 1 32 30 13 6
DEL PEAK 26(12Q12) WILD-TYPE 56 38 113 100 83 23

Figure S452.  Get High-res Image Gene #55: 'del_12q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0423 (Fisher's exact test), Q value = 0.063

Table S453.  Gene #55: 'del_12q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
DEL PEAK 26(12Q12) MUTATED 14 8 18 12 14 19
DEL PEAK 26(12Q12) WILD-TYPE 45 82 77 31 56 58

Figure S453.  Get High-res Image Gene #55: 'del_12q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_12q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0366 (Fisher's exact test), Q value = 0.056

Table S454.  Gene #55: 'del_12q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
DEL PEAK 26(12Q12) MUTATED 18 40 27
DEL PEAK 26(12Q12) WILD-TYPE 86 198 65

Figure S454.  Get High-res Image Gene #55: 'del_12q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q24.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S455.  Gene #56: 'del_12q24.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 27(12Q24.33) MUTATED 80 10 29 14
DEL PEAK 27(12Q24.33) WILD-TYPE 92 128 103 60

Figure S455.  Get High-res Image Gene #56: 'del_12q24.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q24.33' versus 'RPPA_CNMF'

P value = 0.00442 (Fisher's exact test), Q value = 0.0085

Table S456.  Gene #56: 'del_12q24.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 27(12Q24.33) MUTATED 31 8 20 10 20
DEL PEAK 27(12Q24.33) WILD-TYPE 60 14 46 65 89

Figure S456.  Get High-res Image Gene #56: 'del_12q24.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_12q24.33' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S457.  Gene #56: 'del_12q24.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 27(12Q24.33) MUTATED 46 37 11 18 20
DEL PEAK 27(12Q24.33) WILD-TYPE 84 82 79 97 38

Figure S457.  Get High-res Image Gene #56: 'del_12q24.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q24.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00023

Table S458.  Gene #56: 'del_12q24.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 27(12Q24.33) MUTATED 21 31 32 16 2 6 24
DEL PEAK 27(12Q24.33) WILD-TYPE 57 79 65 32 51 43 53

Figure S458.  Get High-res Image Gene #56: 'del_12q24.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q12.11' versus 'MRNA_CHIERARCHICAL'

P value = 0.038 (Fisher's exact test), Q value = 0.058

Table S459.  Gene #57: 'del_13q12.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
DEL PEAK 28(13Q12.11) MUTATED 3 7 5
DEL PEAK 28(13Q12.11) WILD-TYPE 11 4 2

Figure S459.  Get High-res Image Gene #57: 'del_13q12.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q12.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S460.  Gene #57: 'del_13q12.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 28(13Q12.11) MUTATED 125 97 31 40
DEL PEAK 28(13Q12.11) WILD-TYPE 47 41 101 34

Figure S460.  Get High-res Image Gene #57: 'del_13q12.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q12.11' versus 'METHLYATION_CNMF'

P value = 0.0204 (Fisher's exact test), Q value = 0.034

Table S461.  Gene #57: 'del_13q12.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 28(13Q12.11) MUTATED 93 107 61
DEL PEAK 28(13Q12.11) WILD-TYPE 63 63 68

Figure S461.  Get High-res Image Gene #57: 'del_13q12.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q12.11' versus 'RPPA_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.00084

Table S462.  Gene #57: 'del_13q12.11' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 28(13Q12.11) MUTATED 64 12 34 53 48
DEL PEAK 28(13Q12.11) WILD-TYPE 27 10 32 22 61

Figure S462.  Get High-res Image Gene #57: 'del_13q12.11' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q12.11' versus 'RPPA_CHIERARCHICAL'

P value = 0.0488 (Fisher's exact test), Q value = 0.072

Table S463.  Gene #57: 'del_13q12.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
DEL PEAK 28(13Q12.11) MUTATED 94 87 30
DEL PEAK 28(13Q12.11) WILD-TYPE 73 46 33

Figure S463.  Get High-res Image Gene #57: 'del_13q12.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_13q12.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S464.  Gene #57: 'del_13q12.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 28(13Q12.11) MUTATED 99 43 40 79 29
DEL PEAK 28(13Q12.11) WILD-TYPE 31 76 50 36 29

Figure S464.  Get High-res Image Gene #57: 'del_13q12.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q12.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S465.  Gene #57: 'del_13q12.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 28(13Q12.11) MUTATED 38 79 66 15 39 22 31
DEL PEAK 28(13Q12.11) WILD-TYPE 40 31 31 33 14 27 46

Figure S465.  Get High-res Image Gene #57: 'del_13q12.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q12.11' versus 'MIRSEQ_CNMF'

P value = 0.00174 (Fisher's exact test), Q value = 0.0037

Table S466.  Gene #57: 'del_13q12.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 28(13Q12.11) MUTATED 87 140 64
DEL PEAK 28(13Q12.11) WILD-TYPE 99 81 39

Figure S466.  Get High-res Image Gene #57: 'del_13q12.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q12.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00119 (Fisher's exact test), Q value = 0.0027

Table S467.  Gene #57: 'del_13q12.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 28(13Q12.11) MUTATED 36 26 93 57 65 14
DEL PEAK 28(13Q12.11) WILD-TYPE 35 13 52 73 31 15

Figure S467.  Get High-res Image Gene #57: 'del_13q12.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q12.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00196 (Fisher's exact test), Q value = 0.0041

Table S468.  Gene #57: 'del_13q12.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
DEL PEAK 28(13Q12.11) MUTATED 21 62 54 24 40 51
DEL PEAK 28(13Q12.11) WILD-TYPE 38 28 41 19 30 26

Figure S468.  Get High-res Image Gene #57: 'del_13q12.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_13q12.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00924 (Fisher's exact test), Q value = 0.017

Table S469.  Gene #57: 'del_13q12.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
DEL PEAK 28(13Q12.11) MUTATED 48 152 52
DEL PEAK 28(13Q12.11) WILD-TYPE 56 86 40

Figure S469.  Get High-res Image Gene #57: 'del_13q12.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S470.  Gene #58: 'del_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 29(13Q34) MUTATED 96 82 25 38
DEL PEAK 29(13Q34) WILD-TYPE 76 56 107 36

Figure S470.  Get High-res Image Gene #58: 'del_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q34' versus 'RPPA_CNMF'

P value = 0.00272 (Fisher's exact test), Q value = 0.0055

Table S471.  Gene #58: 'del_13q34' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 29(13Q34) MUTATED 52 8 26 45 40
DEL PEAK 29(13Q34) WILD-TYPE 39 14 40 30 69

Figure S471.  Get High-res Image Gene #58: 'del_13q34' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q34' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S472.  Gene #58: 'del_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 29(13Q34) MUTATED 76 38 35 66 23
DEL PEAK 29(13Q34) WILD-TYPE 54 81 55 49 35

Figure S472.  Get High-res Image Gene #58: 'del_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S473.  Gene #58: 'del_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 29(13Q34) MUTATED 31 69 48 14 34 19 23
DEL PEAK 29(13Q34) WILD-TYPE 47 41 49 34 19 30 54

Figure S473.  Get High-res Image Gene #58: 'del_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q34' versus 'MIRSEQ_CNMF'

P value = 0.00949 (Fisher's exact test), Q value = 0.017

Table S474.  Gene #58: 'del_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 29(13Q34) MUTATED 70 112 55
DEL PEAK 29(13Q34) WILD-TYPE 116 109 48

Figure S474.  Get High-res Image Gene #58: 'del_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00606 (Fisher's exact test), Q value = 0.011

Table S475.  Gene #58: 'del_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 29(13Q34) MUTATED 30 26 78 47 45 11
DEL PEAK 29(13Q34) WILD-TYPE 41 13 67 83 51 18

Figure S475.  Get High-res Image Gene #58: 'del_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q32.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S476.  Gene #59: 'del_14q32.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 30(14Q32.33) MUTATED 54 58 20 18
DEL PEAK 30(14Q32.33) WILD-TYPE 118 80 112 56

Figure S476.  Get High-res Image Gene #59: 'del_14q32.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q32.33' versus 'METHLYATION_CNMF'

P value = 0.00578 (Fisher's exact test), Q value = 0.011

Table S477.  Gene #59: 'del_14q32.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 30(14Q32.33) MUTATED 57 49 25
DEL PEAK 30(14Q32.33) WILD-TYPE 99 121 104

Figure S477.  Get High-res Image Gene #59: 'del_14q32.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q32.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0277 (Fisher's exact test), Q value = 0.044

Table S478.  Gene #59: 'del_14q32.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 30(14Q32.33) MUTATED 18 31 30 12 16 25 17
DEL PEAK 30(14Q32.33) WILD-TYPE 60 79 67 36 37 24 60

Figure S478.  Get High-res Image Gene #59: 'del_14q32.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.33' versus 'MIRSEQ_CNMF'

P value = 0.0209 (Fisher's exact test), Q value = 0.035

Table S479.  Gene #59: 'del_14q32.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 30(14Q32.33) MUTATED 48 79 23
DEL PEAK 30(14Q32.33) WILD-TYPE 138 142 80

Figure S479.  Get High-res Image Gene #59: 'del_14q32.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S480.  Gene #60: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 31(15Q11.2) MUTATED 124 65 25 49
DEL PEAK 31(15Q11.2) WILD-TYPE 48 73 107 25

Figure S480.  Get High-res Image Gene #60: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q11.2' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S481.  Gene #60: 'del_15q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 31(15Q11.2) MUTATED 81 102 45
DEL PEAK 31(15Q11.2) WILD-TYPE 75 68 84

Figure S481.  Get High-res Image Gene #60: 'del_15q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q11.2' versus 'RPPA_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.03

Table S482.  Gene #60: 'del_15q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 31(15Q11.2) MUTATED 59 11 31 41 45
DEL PEAK 31(15Q11.2) WILD-TYPE 32 11 35 34 64

Figure S482.  Get High-res Image Gene #60: 'del_15q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_15q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S483.  Gene #60: 'del_15q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 31(15Q11.2) MUTATED 96 40 21 74 28
DEL PEAK 31(15Q11.2) WILD-TYPE 34 79 69 41 30

Figure S483.  Get High-res Image Gene #60: 'del_15q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S484.  Gene #60: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 31(15Q11.2) MUTATED 39 73 62 12 36 9 28
DEL PEAK 31(15Q11.2) WILD-TYPE 39 37 35 36 17 40 49

Figure S484.  Get High-res Image Gene #60: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_CNMF'

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

Table S485.  Gene #60: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 31(15Q11.2) MUTATED 71 130 59
DEL PEAK 31(15Q11.2) WILD-TYPE 115 91 44

Figure S485.  Get High-res Image Gene #60: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0011

Table S486.  Gene #60: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 31(15Q11.2) MUTATED 29 29 84 51 53 14
DEL PEAK 31(15Q11.2) WILD-TYPE 42 10 61 79 43 15

Figure S486.  Get High-res Image Gene #60: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00407 (Fisher's exact test), Q value = 0.0078

Table S487.  Gene #60: 'del_15q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
DEL PEAK 31(15Q11.2) MUTATED 16 51 53 20 40 41
DEL PEAK 31(15Q11.2) WILD-TYPE 43 39 42 23 30 36

Figure S487.  Get High-res Image Gene #60: 'del_15q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.00091

Table S488.  Gene #60: 'del_15q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
DEL PEAK 31(15Q11.2) MUTATED 36 130 55
DEL PEAK 31(15Q11.2) WILD-TYPE 68 108 37

Figure S488.  Get High-res Image Gene #60: 'del_15q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S489.  Gene #61: 'del_15q15.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 32(15Q15.1) MUTATED 125 73 25 52
DEL PEAK 32(15Q15.1) WILD-TYPE 47 65 107 22

Figure S489.  Get High-res Image Gene #61: 'del_15q15.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q15.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S490.  Gene #61: 'del_15q15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 32(15Q15.1) MUTATED 82 108 45
DEL PEAK 32(15Q15.1) WILD-TYPE 74 62 84

Figure S490.  Get High-res Image Gene #61: 'del_15q15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q15.1' versus 'RPPA_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 0.046

Table S491.  Gene #61: 'del_15q15.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 32(15Q15.1) MUTATED 62 11 31 41 52
DEL PEAK 32(15Q15.1) WILD-TYPE 29 11 35 34 57

Figure S491.  Get High-res Image Gene #61: 'del_15q15.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_15q15.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S492.  Gene #61: 'del_15q15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 32(15Q15.1) MUTATED 101 40 25 74 31
DEL PEAK 32(15Q15.1) WILD-TYPE 29 79 65 41 27

Figure S492.  Get High-res Image Gene #61: 'del_15q15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S493.  Gene #61: 'del_15q15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 32(15Q15.1) MUTATED 39 76 65 12 37 11 31
DEL PEAK 32(15Q15.1) WILD-TYPE 39 34 32 36 16 38 46

Figure S493.  Get High-res Image Gene #61: 'del_15q15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S494.  Gene #61: 'del_15q15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 32(15Q15.1) MUTATED 73 137 62
DEL PEAK 32(15Q15.1) WILD-TYPE 113 84 41

Figure S494.  Get High-res Image Gene #61: 'del_15q15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00026

Table S495.  Gene #61: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 32(15Q15.1) MUTATED 29 29 89 52 58 15
DEL PEAK 32(15Q15.1) WILD-TYPE 42 10 56 78 38 14

Figure S495.  Get High-res Image Gene #61: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00229 (Fisher's exact test), Q value = 0.0047

Table S496.  Gene #61: 'del_15q15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
DEL PEAK 32(15Q15.1) MUTATED 16 52 54 23 41 41
DEL PEAK 32(15Q15.1) WILD-TYPE 43 38 41 20 29 36

Figure S496.  Get High-res Image Gene #61: 'del_15q15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.0012

Table S497.  Gene #61: 'del_15q15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
DEL PEAK 32(15Q15.1) MUTATED 37 137 53
DEL PEAK 32(15Q15.1) WILD-TYPE 67 101 39

Figure S497.  Get High-res Image Gene #61: 'del_15q15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S498.  Gene #62: 'del_16p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 33(16P13.3) MUTATED 23 46 10 32
DEL PEAK 33(16P13.3) WILD-TYPE 149 92 122 42

Figure S498.  Get High-res Image Gene #62: 'del_16p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_16p13.3' versus 'METHLYATION_CNMF'

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

Table S499.  Gene #62: 'del_16p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 33(16P13.3) MUTATED 45 42 12
DEL PEAK 33(16P13.3) WILD-TYPE 111 128 117

Figure S499.  Get High-res Image Gene #62: 'del_16p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16p13.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S500.  Gene #62: 'del_16p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 33(16P13.3) MUTATED 11 4 10 34 21
DEL PEAK 33(16P13.3) WILD-TYPE 80 18 56 41 88

Figure S500.  Get High-res Image Gene #62: 'del_16p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_16p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S501.  Gene #62: 'del_16p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
DEL PEAK 33(16P13.3) MUTATED 22 49 9
DEL PEAK 33(16P13.3) WILD-TYPE 145 84 54

Figure S501.  Get High-res Image Gene #62: 'del_16p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_16p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S502.  Gene #62: 'del_16p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 33(16P13.3) MUTATED 29 6 23 43 9
DEL PEAK 33(16P13.3) WILD-TYPE 101 113 67 72 49

Figure S502.  Get High-res Image Gene #62: 'del_16p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S503.  Gene #62: 'del_16p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 33(16P13.3) MUTATED 4 32 23 6 23 15 7
DEL PEAK 33(16P13.3) WILD-TYPE 74 78 74 42 30 34 70

Figure S503.  Get High-res Image Gene #62: 'del_16p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S504.  Gene #62: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 33(16P13.3) MUTATED 24 71 14
DEL PEAK 33(16P13.3) WILD-TYPE 162 150 89

Figure S504.  Get High-res Image Gene #62: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S505.  Gene #62: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 33(16P13.3) MUTATED 11 9 46 13 28 2
DEL PEAK 33(16P13.3) WILD-TYPE 60 30 99 117 68 27

Figure S505.  Get High-res Image Gene #62: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S506.  Gene #62: 'del_16p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
DEL PEAK 33(16P13.3) MUTATED 3 41 18 3 14 17
DEL PEAK 33(16P13.3) WILD-TYPE 56 49 77 40 56 60

Figure S506.  Get High-res Image Gene #62: 'del_16p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00064 (Fisher's exact test), Q value = 0.0015

Table S507.  Gene #62: 'del_16p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
DEL PEAK 33(16P13.3) MUTATED 13 69 14
DEL PEAK 33(16P13.3) WILD-TYPE 91 169 78

Figure S507.  Get High-res Image Gene #62: 'del_16p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S508.  Gene #63: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 34(16Q23.1) MUTATED 66 54 16 33
DEL PEAK 34(16Q23.1) WILD-TYPE 106 84 116 41

Figure S508.  Get High-res Image Gene #63: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S509.  Gene #63: 'del_16q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 34(16Q23.1) MUTATED 57 67 22
DEL PEAK 34(16Q23.1) WILD-TYPE 99 103 107

Figure S509.  Get High-res Image Gene #63: 'del_16q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q23.1' versus 'RPPA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00015

Table S510.  Gene #63: 'del_16q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 34(16Q23.1) MUTATED 34 8 14 40 23
DEL PEAK 34(16Q23.1) WILD-TYPE 57 14 52 35 86

Figure S510.  Get High-res Image Gene #63: 'del_16q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_16q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00391 (Fisher's exact test), Q value = 0.0076

Table S511.  Gene #63: 'del_16q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
DEL PEAK 34(16Q23.1) MUTATED 46 58 15
DEL PEAK 34(16Q23.1) WILD-TYPE 121 75 48

Figure S511.  Get High-res Image Gene #63: 'del_16q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S512.  Gene #63: 'del_16q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 34(16Q23.1) MUTATED 68 19 33 39 10
DEL PEAK 34(16Q23.1) WILD-TYPE 62 100 57 76 48

Figure S512.  Get High-res Image Gene #63: 'del_16q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S513.  Gene #63: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 34(16Q23.1) MUTATED 20 59 37 9 17 17 10
DEL PEAK 34(16Q23.1) WILD-TYPE 58 51 60 39 36 32 67

Figure S513.  Get High-res Image Gene #63: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 0.00759 (Fisher's exact test), Q value = 0.014

Table S514.  Gene #63: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 34(16Q23.1) MUTATED 46 86 37
DEL PEAK 34(16Q23.1) WILD-TYPE 140 135 66

Figure S514.  Get High-res Image Gene #63: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00131 (Fisher's exact test), Q value = 0.0029

Table S515.  Gene #63: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 34(16Q23.1) MUTATED 19 10 64 29 39 8
DEL PEAK 34(16Q23.1) WILD-TYPE 52 29 81 101 57 21

Figure S515.  Get High-res Image Gene #63: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S516.  Gene #63: 'del_16q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
DEL PEAK 34(16Q23.1) MUTATED 5 42 37 12 22 23
DEL PEAK 34(16Q23.1) WILD-TYPE 54 48 58 31 48 54

Figure S516.  Get High-res Image Gene #63: 'del_16q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00099 (Fisher's exact test), Q value = 0.0023

Table S517.  Gene #63: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
DEL PEAK 34(16Q23.1) MUTATED 19 90 32
DEL PEAK 34(16Q23.1) WILD-TYPE 85 148 60

Figure S517.  Get High-res Image Gene #63: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S518.  Gene #64: 'del_16q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 35(16Q24.3) MUTATED 73 57 22 36
DEL PEAK 35(16Q24.3) WILD-TYPE 99 81 110 38

Figure S518.  Get High-res Image Gene #64: 'del_16q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q24.3' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00055

Table S519.  Gene #64: 'del_16q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 35(16Q24.3) MUTATED 64 71 28
DEL PEAK 35(16Q24.3) WILD-TYPE 92 99 101

Figure S519.  Get High-res Image Gene #64: 'del_16q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q24.3' versus 'RPPA_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 0.038

Table S520.  Gene #64: 'del_16q24.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 35(16Q24.3) MUTATED 36 8 17 37 32
DEL PEAK 35(16Q24.3) WILD-TYPE 55 14 49 38 77

Figure S520.  Get High-res Image Gene #64: 'del_16q24.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_16q24.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0224 (Fisher's exact test), Q value = 0.037

Table S521.  Gene #64: 'del_16q24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
DEL PEAK 35(16Q24.3) MUTATED 51 60 19
DEL PEAK 35(16Q24.3) WILD-TYPE 116 73 44

Figure S521.  Get High-res Image Gene #64: '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 = 3.9e-05

Table S522.  Gene #64: 'del_16q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 35(16Q24.3) MUTATED 71 24 31 48 14
DEL PEAK 35(16Q24.3) WILD-TYPE 59 95 59 67 44

Figure S522.  Get High-res Image Gene #64: '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 = 3.9e-05

Table S523.  Gene #64: 'del_16q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 35(16Q24.3) MUTATED 24 60 42 10 24 15 13
DEL PEAK 35(16Q24.3) WILD-TYPE 54 50 55 38 29 34 64

Figure S523.  Get High-res Image Gene #64: 'del_16q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16q24.3' versus 'MIRSEQ_CNMF'

P value = 0.00882 (Fisher's exact test), Q value = 0.016

Table S524.  Gene #64: 'del_16q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 35(16Q24.3) MUTATED 53 95 40
DEL PEAK 35(16Q24.3) WILD-TYPE 133 126 63

Figure S524.  Get High-res Image Gene #64: 'del_16q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0011

Table S525.  Gene #64: 'del_16q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 35(16Q24.3) MUTATED 21 12 70 32 44 9
DEL PEAK 35(16Q24.3) WILD-TYPE 50 27 75 98 52 20

Figure S525.  Get High-res Image Gene #64: 'del_16q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S526.  Gene #64: 'del_16q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
DEL PEAK 35(16Q24.3) MUTATED 8 49 40 13 22 26
DEL PEAK 35(16Q24.3) WILD-TYPE 51 41 55 30 48 51

Figure S526.  Get High-res Image Gene #64: 'del_16q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00026

Table S527.  Gene #64: 'del_16q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
DEL PEAK 35(16Q24.3) MUTATED 20 100 38
DEL PEAK 35(16Q24.3) WILD-TYPE 84 138 54

Figure S527.  Get High-res Image Gene #64: 'del_16q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S528.  Gene #65: 'del_17p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 36(17P13.3) MUTATED 125 84 32 40
DEL PEAK 36(17P13.3) WILD-TYPE 47 54 100 34

Figure S528.  Get High-res Image Gene #65: 'del_17p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p13.3' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S529.  Gene #65: 'del_17p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 36(17P13.3) MUTATED 85 111 50
DEL PEAK 36(17P13.3) WILD-TYPE 71 59 79

Figure S529.  Get High-res Image Gene #65: 'del_17p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p13.3' versus 'RPPA_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.032

Table S530.  Gene #65: 'del_17p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 36(17P13.3) MUTATED 63 12 30 46 55
DEL PEAK 36(17P13.3) WILD-TYPE 28 10 36 29 54

Figure S530.  Get High-res Image Gene #65: 'del_17p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_17p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S531.  Gene #65: 'del_17p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 36(17P13.3) MUTATED 93 42 47 68 29
DEL PEAK 36(17P13.3) WILD-TYPE 37 77 43 47 29

Figure S531.  Get High-res Image Gene #65: 'del_17p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S532.  Gene #65: 'del_17p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 36(17P13.3) MUTATED 37 77 61 10 34 24 36
DEL PEAK 36(17P13.3) WILD-TYPE 41 33 36 38 19 25 41

Figure S532.  Get High-res Image Gene #65: 'del_17p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.3' versus 'MIRSEQ_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.032

Table S533.  Gene #65: 'del_17p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 36(17P13.3) MUTATED 88 135 54
DEL PEAK 36(17P13.3) WILD-TYPE 98 86 49

Figure S533.  Get High-res Image Gene #65: 'del_17p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0313 (Fisher's exact test), Q value = 0.049

Table S534.  Gene #65: 'del_17p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 36(17P13.3) MUTATED 30 23 90 63 58 13
DEL PEAK 36(17P13.3) WILD-TYPE 41 16 55 67 38 16

Figure S534.  Get High-res Image Gene #65: 'del_17p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S535.  Gene #65: 'del_17p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
DEL PEAK 36(17P13.3) MUTATED 14 53 63 18 38 47
DEL PEAK 36(17P13.3) WILD-TYPE 45 37 32 25 32 30

Figure S535.  Get High-res Image Gene #65: 'del_17p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00343 (Fisher's exact test), Q value = 0.0068

Table S536.  Gene #65: 'del_17p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
DEL PEAK 36(17P13.3) MUTATED 41 140 52
DEL PEAK 36(17P13.3) WILD-TYPE 63 98 40

Figure S536.  Get High-res Image Gene #65: 'del_17p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q21.32' versus 'MRNA_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 0.055

Table S537.  Gene #66: 'del_18q21.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 10 7
DEL PEAK 37(18Q21.32) MUTATED 4 8 4
DEL PEAK 37(18Q21.32) WILD-TYPE 11 2 3

Figure S537.  Get High-res Image Gene #66: 'del_18q21.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q21.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S538.  Gene #66: 'del_18q21.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 37(18Q21.32) MUTATED 113 79 41 22
DEL PEAK 37(18Q21.32) WILD-TYPE 59 59 91 52

Figure S538.  Get High-res Image Gene #66: 'del_18q21.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q21.32' versus 'RPPA_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.0024

Table S539.  Gene #66: 'del_18q21.32' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 37(18Q21.32) MUTATED 51 12 30 50 40
DEL PEAK 37(18Q21.32) WILD-TYPE 40 10 36 25 69

Figure S539.  Get High-res Image Gene #66: 'del_18q21.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_18q21.32' versus 'RPPA_CHIERARCHICAL'

P value = 0.018 (Fisher's exact test), Q value = 0.031

Table S540.  Gene #66: 'del_18q21.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
DEL PEAK 37(18Q21.32) MUTATED 74 80 29
DEL PEAK 37(18Q21.32) WILD-TYPE 93 53 34

Figure S540.  Get High-res Image Gene #66: 'del_18q21.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_18q21.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S541.  Gene #66: 'del_18q21.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 37(18Q21.32) MUTATED 88 42 50 45 27
DEL PEAK 37(18Q21.32) WILD-TYPE 42 77 40 70 31

Figure S541.  Get High-res Image Gene #66: 'del_18q21.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q21.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S542.  Gene #66: 'del_18q21.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 37(18Q21.32) MUTATED 39 65 58 10 17 29 34
DEL PEAK 37(18Q21.32) WILD-TYPE 39 45 39 38 36 20 43

Figure S542.  Get High-res Image Gene #66: 'del_18q21.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.32' versus 'MIRSEQ_CNMF'

P value = 0.00222 (Fisher's exact test), Q value = 0.0046

Table S543.  Gene #66: 'del_18q21.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 37(18Q21.32) MUTATED 74 115 62
DEL PEAK 37(18Q21.32) WILD-TYPE 112 106 41

Figure S543.  Get High-res Image Gene #66: 'del_18q21.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18q21.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0172 (Fisher's exact test), Q value = 0.03

Table S544.  Gene #66: 'del_18q21.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
DEL PEAK 37(18Q21.32) MUTATED 40 124 53
DEL PEAK 37(18Q21.32) WILD-TYPE 64 114 39

Figure S544.  Get High-res Image Gene #66: 'del_18q21.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q23' versus 'MRNA_CNMF'

P value = 0.00705 (Fisher's exact test), Q value = 0.013

Table S545.  Gene #67: 'del_18q23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 10 7
DEL PEAK 38(18Q23) MUTATED 4 9 4
DEL PEAK 38(18Q23) WILD-TYPE 11 1 3

Figure S545.  Get High-res Image Gene #67: 'del_18q23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q23' versus 'MRNA_CHIERARCHICAL'

P value = 0.026 (Fisher's exact test), Q value = 0.042

Table S546.  Gene #67: 'del_18q23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
DEL PEAK 38(18Q23) MUTATED 4 9 4
DEL PEAK 38(18Q23) WILD-TYPE 10 2 3

Figure S546.  Get High-res Image Gene #67: 'del_18q23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18q23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S547.  Gene #67: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 38(18Q23) MUTATED 112 78 40 19
DEL PEAK 38(18Q23) WILD-TYPE 60 60 92 55

Figure S547.  Get High-res Image Gene #67: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q23' versus 'RPPA_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0012

Table S548.  Gene #67: 'del_18q23' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 38(18Q23) MUTATED 52 13 27 48 38
DEL PEAK 38(18Q23) WILD-TYPE 39 9 39 27 71

Figure S548.  Get High-res Image Gene #67: 'del_18q23' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_18q23' versus 'RPPA_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.02

Table S549.  Gene #67: 'del_18q23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
DEL PEAK 38(18Q23) MUTATED 71 79 28
DEL PEAK 38(18Q23) WILD-TYPE 96 54 35

Figure S549.  Get High-res Image Gene #67: 'del_18q23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_18q23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S550.  Gene #67: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 38(18Q23) MUTATED 88 42 49 41 27
DEL PEAK 38(18Q23) WILD-TYPE 42 77 41 74 31

Figure S550.  Get High-res Image Gene #67: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S551.  Gene #67: 'del_18q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 38(18Q23) MUTATED 36 66 56 10 17 28 34
DEL PEAK 38(18Q23) WILD-TYPE 42 44 41 38 36 21 43

Figure S551.  Get High-res Image Gene #67: 'del_18q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_CNMF'

P value = 0.00141 (Fisher's exact test), Q value = 0.0031

Table S552.  Gene #67: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 38(18Q23) MUTATED 72 112 62
DEL PEAK 38(18Q23) WILD-TYPE 114 109 41

Figure S552.  Get High-res Image Gene #67: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S553.  Gene #68: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 39(19P13.3) MUTATED 85 99 43 49
DEL PEAK 39(19P13.3) WILD-TYPE 87 39 89 25

Figure S553.  Get High-res Image Gene #68: '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 = 3.9e-05

Table S554.  Gene #68: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 39(19P13.3) MUTATED 122 79 41
DEL PEAK 39(19P13.3) WILD-TYPE 34 91 88

Figure S554.  Get High-res Image Gene #68: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p13.3' versus 'RPPA_CNMF'

P value = 0.00101 (Fisher's exact test), Q value = 0.0023

Table S555.  Gene #68: 'del_19p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 39(19P13.3) MUTATED 41 12 44 53 50
DEL PEAK 39(19P13.3) WILD-TYPE 50 10 22 22 59

Figure S555.  Get High-res Image Gene #68: 'del_19p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.036 (Fisher's exact test), Q value = 0.055

Table S556.  Gene #68: 'del_19p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
DEL PEAK 39(19P13.3) MUTATED 88 84 28
DEL PEAK 39(19P13.3) WILD-TYPE 79 49 35

Figure S556.  Get High-res Image Gene #68: 'del_19p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S557.  Gene #68: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 39(19P13.3) MUTATED 65 50 55 83 20
DEL PEAK 39(19P13.3) WILD-TYPE 65 69 35 32 38

Figure S557.  Get High-res Image Gene #68: '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 = 3.9e-05

Table S558.  Gene #68: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 39(19P13.3) MUTATED 25 49 63 39 34 42 21
DEL PEAK 39(19P13.3) WILD-TYPE 53 61 34 9 19 7 56

Figure S558.  Get High-res Image Gene #68: '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 = 3.9e-05

Table S559.  Gene #68: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 39(19P13.3) MUTATED 78 147 45
DEL PEAK 39(19P13.3) WILD-TYPE 108 74 58

Figure S559.  Get High-res Image Gene #68: '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 = 3.9e-05

Table S560.  Gene #68: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 39(19P13.3) MUTATED 34 25 86 46 68 11
DEL PEAK 39(19P13.3) WILD-TYPE 37 14 59 84 28 18

Figure S560.  Get High-res Image Gene #68: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00125 (Fisher's exact test), Q value = 0.0028

Table S561.  Gene #68: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
DEL PEAK 39(19P13.3) MUTATED 26 65 52 18 36 35
DEL PEAK 39(19P13.3) WILD-TYPE 33 25 43 25 34 42

Figure S561.  Get High-res Image Gene #68: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0011

Table S562.  Gene #68: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
DEL PEAK 39(19P13.3) MUTATED 47 147 38
DEL PEAK 39(19P13.3) WILD-TYPE 57 91 54

Figure S562.  Get High-res Image Gene #68: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S563.  Gene #69: 'del_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 40(19P13.2) MUTATED 83 93 40 53
DEL PEAK 40(19P13.2) WILD-TYPE 89 45 92 21

Figure S563.  Get High-res Image Gene #69: 'del_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S564.  Gene #69: 'del_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 40(19P13.2) MUTATED 120 82 34
DEL PEAK 40(19P13.2) WILD-TYPE 36 88 95

Figure S564.  Get High-res Image Gene #69: 'del_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p13.2' versus 'RPPA_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.0019

Table S565.  Gene #69: 'del_19p13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 40(19P13.2) MUTATED 39 12 44 50 47
DEL PEAK 40(19P13.2) WILD-TYPE 52 10 22 25 62

Figure S565.  Get High-res Image Gene #69: 'del_19p13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19p13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S566.  Gene #69: 'del_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 40(19P13.2) MUTATED 66 47 50 83 20
DEL PEAK 40(19P13.2) WILD-TYPE 64 72 40 32 38

Figure S566.  Get High-res Image Gene #69: 'del_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S567.  Gene #69: 'del_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 40(19P13.2) MUTATED 22 52 54 38 40 38 22
DEL PEAK 40(19P13.2) WILD-TYPE 56 58 43 10 13 11 55

Figure S567.  Get High-res Image Gene #69: 'del_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S568.  Gene #69: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 40(19P13.2) MUTATED 76 144 43
DEL PEAK 40(19P13.2) WILD-TYPE 110 77 60

Figure S568.  Get High-res Image Gene #69: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S569.  Gene #69: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 40(19P13.2) MUTATED 34 26 81 45 66 11
DEL PEAK 40(19P13.2) WILD-TYPE 37 13 64 85 30 18

Figure S569.  Get High-res Image Gene #69: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S570.  Gene #69: 'del_19p13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
DEL PEAK 40(19P13.2) MUTATED 22 66 51 16 39 33
DEL PEAK 40(19P13.2) WILD-TYPE 37 24 44 27 31 44

Figure S570.  Get High-res Image Gene #69: 'del_19p13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.00077

Table S571.  Gene #69: 'del_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
DEL PEAK 40(19P13.2) MUTATED 44 145 38
DEL PEAK 40(19P13.2) WILD-TYPE 60 93 54

Figure S571.  Get High-res Image Gene #69: 'del_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S572.  Gene #70: 'del_19q13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 41(19Q13.33) MUTATED 77 62 27 29
DEL PEAK 41(19Q13.33) WILD-TYPE 95 76 105 45

Figure S572.  Get High-res Image Gene #70: 'del_19q13.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.33' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S573.  Gene #70: 'del_19q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 41(19Q13.33) MUTATED 72 68 24
DEL PEAK 41(19Q13.33) WILD-TYPE 84 102 105

Figure S573.  Get High-res Image Gene #70: 'del_19q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.33' versus 'RPPA_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 0.03

Table S574.  Gene #70: 'del_19q13.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 41(19Q13.33) MUTATED 31 9 35 34 32
DEL PEAK 41(19Q13.33) WILD-TYPE 60 13 31 41 77

Figure S574.  Get High-res Image Gene #70: 'del_19q13.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19q13.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.00151 (Fisher's exact test), Q value = 0.0033

Table S575.  Gene #70: 'del_19q13.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
DEL PEAK 41(19Q13.33) MUTATED 65 63 13
DEL PEAK 41(19Q13.33) WILD-TYPE 102 70 50

Figure S575.  Get High-res Image Gene #70: 'del_19q13.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_19q13.33' versus 'MRNASEQ_CNMF'

P value = 0.00129 (Fisher's exact test), Q value = 0.0028

Table S576.  Gene #70: 'del_19q13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 41(19Q13.33) MUTATED 59 32 33 54 14
DEL PEAK 41(19Q13.33) WILD-TYPE 71 87 57 61 44

Figure S576.  Get High-res Image Gene #70: 'del_19q13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S577.  Gene #70: 'del_19q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 41(19Q13.33) MUTATED 19 47 45 23 24 23 11
DEL PEAK 41(19Q13.33) WILD-TYPE 59 63 52 25 29 26 66

Figure S577.  Get High-res Image Gene #70: 'del_19q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.33' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S578.  Gene #70: 'del_19q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 41(19Q13.33) MUTATED 46 105 39
DEL PEAK 41(19Q13.33) WILD-TYPE 140 116 64

Figure S578.  Get High-res Image Gene #70: 'del_19q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19q13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S579.  Gene #70: 'del_19q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 41(19Q13.33) MUTATED 21 22 57 28 48 14
DEL PEAK 41(19Q13.33) WILD-TYPE 50 17 88 102 48 15

Figure S579.  Get High-res Image Gene #70: 'del_19q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0135 (Fisher's exact test), Q value = 0.024

Table S580.  Gene #70: 'del_19q13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
DEL PEAK 41(19Q13.33) MUTATED 27 99 29
DEL PEAK 41(19Q13.33) WILD-TYPE 77 139 63

Figure S580.  Get High-res Image Gene #70: 'del_19q13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p13' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00046

Table S581.  Gene #71: 'del_20p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 42(20P13) MUTATED 61 37 22 10
DEL PEAK 42(20P13) WILD-TYPE 111 101 110 64

Figure S581.  Get High-res Image Gene #71: 'del_20p13' versus Molecular Subtype #3: 'CN_CNMF'

'del_20p13' versus 'METHLYATION_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.002

Table S582.  Gene #71: 'del_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 42(20P13) MUTATED 26 59 30
DEL PEAK 42(20P13) WILD-TYPE 130 111 99

Figure S582.  Get High-res Image Gene #71: 'del_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_20p13' versus 'RPPA_CNMF'

P value = 0.0281 (Fisher's exact test), Q value = 0.045

Table S583.  Gene #71: 'del_20p13' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 42(20P13) MUTATED 33 2 15 22 22
DEL PEAK 42(20P13) WILD-TYPE 58 20 51 53 87

Figure S583.  Get High-res Image Gene #71: 'del_20p13' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_20p13' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S584.  Gene #71: 'del_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 42(20P13) MUTATED 52 21 26 15 15
DEL PEAK 42(20P13) WILD-TYPE 78 98 64 100 43

Figure S584.  Get High-res Image Gene #71: 'del_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_20p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S585.  Gene #71: 'del_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 42(20P13) MUTATED 23 43 20 0 10 16 17
DEL PEAK 42(20P13) WILD-TYPE 55 67 77 48 43 33 60

Figure S585.  Get High-res Image Gene #71: 'del_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_20p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.03

Table S586.  Gene #71: 'del_20p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
DEL PEAK 42(20P13) MUTATED 8 22 33 5 20 18
DEL PEAK 42(20P13) WILD-TYPE 51 68 62 38 50 59

Figure S586.  Get High-res Image Gene #71: 'del_20p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_20p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0288 (Fisher's exact test), Q value = 0.045

Table S587.  Gene #71: 'del_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
DEL PEAK 42(20P13) MUTATED 17 59 30
DEL PEAK 42(20P13) WILD-TYPE 87 179 62

Figure S587.  Get High-res Image Gene #71: 'del_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20q13.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00369 (Fisher's exact test), Q value = 0.0073

Table S588.  Gene #72: 'del_20q13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 43(20Q13.12) MUTATED 18 17 6 12 8 13 8
DEL PEAK 43(20Q13.12) WILD-TYPE 60 93 91 36 45 36 69

Figure S588.  Get High-res Image Gene #72: 'del_20q13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_20q13.12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0351 (Fisher's exact test), Q value = 0.054

Table S589.  Gene #72: 'del_20q13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 43(20Q13.12) MUTATED 18 11 20 20 11 2
DEL PEAK 43(20Q13.12) WILD-TYPE 53 28 125 110 85 27

Figure S589.  Get High-res Image Gene #72: 'del_20q13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_21q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S590.  Gene #73: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 44(21Q11.2) MUTATED 41 81 18 39
DEL PEAK 44(21Q11.2) WILD-TYPE 131 57 114 35

Figure S590.  Get High-res Image Gene #73: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.00098

Table S591.  Gene #73: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 44(21Q11.2) MUTATED 65 61 26
DEL PEAK 44(21Q11.2) WILD-TYPE 91 109 103

Figure S591.  Get High-res Image Gene #73: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_21q11.2' versus 'RPPA_CNMF'

P value = 0.00401 (Fisher's exact test), Q value = 0.0077

Table S592.  Gene #73: 'del_21q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 44(21Q11.2) MUTATED 21 5 21 38 38
DEL PEAK 44(21Q11.2) WILD-TYPE 70 17 45 37 71

Figure S592.  Get High-res Image Gene #73: 'del_21q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S593.  Gene #73: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 44(21Q11.2) MUTATED 41 14 42 65 14
DEL PEAK 44(21Q11.2) WILD-TYPE 89 105 48 50 44

Figure S593.  Get High-res Image Gene #73: '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 = 3.9e-05

Table S594.  Gene #73: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 44(21Q11.2) MUTATED 10 38 41 12 36 22 17
DEL PEAK 44(21Q11.2) WILD-TYPE 68 72 56 36 17 27 60

Figure S594.  Get High-res Image Gene #73: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S595.  Gene #73: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 44(21Q11.2) MUTATED 40 104 31
DEL PEAK 44(21Q11.2) WILD-TYPE 146 117 72

Figure S595.  Get High-res Image Gene #73: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_21q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S596.  Gene #73: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 44(21Q11.2) MUTATED 17 17 52 30 52 7
DEL PEAK 44(21Q11.2) WILD-TYPE 54 22 93 100 44 22

Figure S596.  Get High-res Image Gene #73: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S597.  Gene #73: 'del_21q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
DEL PEAK 44(21Q11.2) MUTATED 5 45 41 9 19 28
DEL PEAK 44(21Q11.2) WILD-TYPE 54 45 54 34 51 49

Figure S597.  Get High-res Image Gene #73: 'del_21q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_21q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S598.  Gene #73: 'del_21q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
DEL PEAK 44(21Q11.2) MUTATED 16 108 23
DEL PEAK 44(21Q11.2) WILD-TYPE 88 130 69

Figure S598.  Get High-res Image Gene #73: 'del_21q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S599.  Gene #74: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 45(22Q13.32) MUTATED 89 82 28 51
DEL PEAK 45(22Q13.32) WILD-TYPE 83 56 104 23

Figure S599.  Get High-res Image Gene #74: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S600.  Gene #74: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 45(22Q13.32) MUTATED 94 95 31
DEL PEAK 45(22Q13.32) WILD-TYPE 62 75 98

Figure S600.  Get High-res Image Gene #74: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q13.32' versus 'RPPA_CNMF'

P value = 0.00824 (Fisher's exact test), Q value = 0.015

Table S601.  Gene #74: 'del_22q13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 45(22Q13.32) MUTATED 45 7 24 48 53
DEL PEAK 45(22Q13.32) WILD-TYPE 46 15 42 27 56

Figure S601.  Get High-res Image Gene #74: 'del_22q13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_22q13.32' versus 'RPPA_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.00096

Table S602.  Gene #74: 'del_22q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
DEL PEAK 45(22Q13.32) MUTATED 64 81 32
DEL PEAK 45(22Q13.32) WILD-TYPE 103 52 31

Figure S602.  Get High-res Image Gene #74: 'del_22q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S603.  Gene #74: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 45(22Q13.32) MUTATED 77 34 43 79 14
DEL PEAK 45(22Q13.32) WILD-TYPE 53 85 47 36 44

Figure S603.  Get High-res Image Gene #74: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S604.  Gene #74: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 45(22Q13.32) MUTATED 26 66 53 15 41 28 18
DEL PEAK 45(22Q13.32) WILD-TYPE 52 44 44 33 12 21 59

Figure S604.  Get High-res Image Gene #74: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S605.  Gene #74: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
DEL PEAK 45(22Q13.32) MUTATED 65 135 46
DEL PEAK 45(22Q13.32) WILD-TYPE 121 86 57

Figure S605.  Get High-res Image Gene #74: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_22q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S606.  Gene #74: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
DEL PEAK 45(22Q13.32) MUTATED 23 25 90 41 58 9
DEL PEAK 45(22Q13.32) WILD-TYPE 48 14 55 89 38 20

Figure S606.  Get High-res Image Gene #74: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.00084

Table S607.  Gene #74: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
DEL PEAK 45(22Q13.32) MUTATED 18 60 50 20 29 33
DEL PEAK 45(22Q13.32) WILD-TYPE 41 30 45 23 41 44

Figure S607.  Get High-res Image Gene #74: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_22q13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00015

Table S608.  Gene #74: 'del_22q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
DEL PEAK 45(22Q13.32) MUTATED 33 136 41
DEL PEAK 45(22Q13.32) WILD-TYPE 71 102 51

Figure S608.  Get High-res Image Gene #74: 'del_22q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp22.2' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.7e-05

Table S609.  Gene #75: 'del_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
DEL PEAK 46(XP22.2) MUTATED 68 37 18 22
DEL PEAK 46(XP22.2) WILD-TYPE 104 101 114 52

Figure S609.  Get High-res Image Gene #75: 'del_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_xp22.2' versus 'METHLYATION_CNMF'

P value = 0.0176 (Fisher's exact test), Q value = 0.03

Table S610.  Gene #75: 'del_xp22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
DEL PEAK 46(XP22.2) MUTATED 43 58 25
DEL PEAK 46(XP22.2) WILD-TYPE 113 112 104

Figure S610.  Get High-res Image Gene #75: 'del_xp22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xp22.2' versus 'RPPA_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.035

Table S611.  Gene #75: 'del_xp22.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
DEL PEAK 46(XP22.2) MUTATED 34 5 10 25 27
DEL PEAK 46(XP22.2) WILD-TYPE 57 17 56 50 82

Figure S611.  Get High-res Image Gene #75: 'del_xp22.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_xp22.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7e-05

Table S612.  Gene #75: 'del_xp22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
DEL PEAK 46(XP22.2) MUTATED 58 31 19 27 9
DEL PEAK 46(XP22.2) WILD-TYPE 72 88 71 88 49

Figure S612.  Get High-res Image Gene #75: 'del_xp22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_xp22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00026

Table S613.  Gene #75: 'del_xp22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
DEL PEAK 46(XP22.2) MUTATED 23 49 33 9 8 8 14
DEL PEAK 46(XP22.2) WILD-TYPE 55 61 64 39 45 41 63

Figure S613.  Get High-res Image Gene #75: 'del_xp22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = all_lesions.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUAD-TP/22531212/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LUAD-TP/22552673/LUAD-TP.transferedmergedcluster.txt

  • Number of patients = 516

  • Number of significantly focal cnvs = 75

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
Copyright © 2016 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle