Correlation between copy number variation genes (focal events) and molecular subtypes
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C14T6H2Z
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C14T6H2Z
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 99 focal events and 12 molecular subtypes across 524 patients, 742 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1p35.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_1p34.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_1p22.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_1q21.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_1q22 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_1q44 cnv correlated to 'CN_CNMF'.

  • amp_2p24.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_2q13 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_3p14.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_3q26.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_3q26.2 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_4p16.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  '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_5q35.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_6p24.2 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_6q25.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_7q22.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

  • amp_9p24.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_9q34.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_10q22.2 cnv correlated to 'CN_CNMF'.

  • amp_11p11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_11q13.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

  • amp_12p12.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_12q13.11 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_12q13.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_14q24.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_15q26.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_16p11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_17q11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_17q25.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_18p11.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_19p13.2 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_19p13.12 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_20p13 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_20q11.21 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_20q13.12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_20q13.33 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_22q12.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_xp11.23 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • amp_xq28 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_1p36.21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_1p36.11 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_2p25.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • del_2q37.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_3p14.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3q13.31 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • del_4p15.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_4q22.1 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_4q34.3 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_6q26 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_7q11.22 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_7q31.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • del_8p21.2 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_9q21.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • del_11q14.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • del_12q24.33 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_13q11 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_14q13.1 cnv correlated to 'CN_CNMF',  'METHLYATION_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',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_15q23 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_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',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_16q21 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • del_17p11.2 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_17p11.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_17q11.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • del_18q21.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • del_19p12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_19q13.43 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_20p12.1 cnv correlated to 'CN_CNMF'.

  • del_22q11.1 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_22q13.31 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_xp21.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 99 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, 742 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 Chi-square test Fisher's exact test Chi-square 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 2 167 (32%) 357 5.45e-05
(0.0282) 		6.42e-05
(0.0328) 		1.92e-68
(2.24e-65) 		7.17e-19
(7.2e-16) 		0.000353
(0.158) 		0.0154
(1.00) 		2.82e-34
(3.17e-31) 		3.25e-33
(3.64e-30) 		1.32e-27
(1.45e-24) 		1.28e-12
(1.09e-09) 		1.31e-07
(8.71e-05) 		5.21e-11
(4.12e-08)
del 19p13 3 147 (28%) 377 8.71e-07
(0.000541) 		3.64e-08
(2.49e-05) 		1.36e-78
(1.59e-75) 		2.37e-33
(2.65e-30) 		4.33e-05
(0.0226) 		0.0423
(1.00) 		8.04e-46
(9.23e-43) 		4.6e-40
(5.24e-37) 		1.45e-34
(1.63e-31) 		6.43e-20
(6.55e-17) 		1.12e-10
(8.74e-08) 		3.13e-18
(3.1e-15)
amp 3q26 2 156 (30%) 368 0.000341
(0.154) 		0.000312
(0.142) 		2.67e-67
(3.12e-64) 		4.05e-20
(4.14e-17) 		0.0015
(0.6) 		0.0249
(1.00) 		1.47e-32
(1.64e-29) 		3.03e-33
(3.39e-30) 		4.96e-25
(5.37e-22) 		1.12e-15
(1.04e-12) 		1.94e-08
(1.35e-05) 		1.19e-13
(1.05e-10)
amp 6p24 2 111 (21%) 413 0.00295
(1.00) 		0.000312
(0.142) 		1.23e-41
(1.41e-38) 		1.62e-13
(1.43e-10) 		0.000109
(0.0542) 		0.0408
(1.00) 		2.9e-21
(3.02e-18) 		5.89e-20
(6e-17) 		4.85e-15
(4.46e-12) 		1.11e-10
(8.66e-08) 		2.05e-05
(0.0113) 		3.43e-09
(2.5e-06)
amp 17q25 1 100 (19%) 424 3.19e-05
(0.017) 		2.42e-06
(0.00145) 		1.45e-42
(1.66e-39) 		1.4e-13
(1.24e-10) 		0.00741
(1.00) 		0.386
(1.00) 		2.58e-21
(2.69e-18) 		1.12e-20
(1.16e-17) 		9.22e-18
(9.05e-15) 		2.69e-12
(2.26e-09) 		2.66e-05
(0.0144) 		3.03e-10
(2.31e-07)
amp 19p13 2 88 (17%) 436 2.35e-05
(0.0129) 		1.13e-06
(0.000696) 		1.49e-47
(1.71e-44) 		6.88e-11
(5.42e-08) 		0.15
(1.00) 		0.0408
(1.00) 		1.61e-22
(1.71e-19) 		2.95e-21
(3.07e-18) 		1.74e-17
(1.69e-14) 		1.62e-08
(1.14e-05) 		0.000193
(0.0918) 		2.12e-07
(0.000138)
del 7p22 3 70 (13%) 454 0.000567
(0.245) 		4.17e-05
(0.022) 		2.67e-30
(2.96e-27) 		1.73e-10
(1.34e-07) 		0.0312
(1.00) 		0.0935
(1.00) 		1.15e-18
(1.15e-15) 		1.71e-16
(1.63e-13) 		3.26e-13
(2.84e-10) 		1.92e-09
(1.41e-06) 		2.46e-05
(0.0134) 		1.46e-08
(1.03e-05)
del 9q21 2 123 (23%) 401 2.35e-05
(0.0129) 		1.13e-06
(0.000696) 		1.34e-51
(1.55e-48) 		1.77e-12
(1.5e-09) 		0.000759
(0.32) 		0.205
(1.00) 		1.05e-21
(1.11e-18) 		1.67e-18
(1.66e-15) 		3.03e-16
(2.87e-13) 		3.59e-11
(2.86e-08) 		0.000403
(0.179) 		1.09e-07
(7.24e-05)
del 9q34 2 128 (24%) 396 2.35e-05
(0.0129) 		1.13e-06
(0.000696) 		5.97e-55
(6.92e-52) 		1.99e-14
(1.81e-11) 		0.000953
(0.394) 		0.0423
(1.00) 		3.29e-22
(3.47e-19) 		7.71e-19
(7.72e-16) 		1.85e-17
(1.8e-14) 		2.94e-10
(2.24e-07) 		5.67e-05
(0.0292) 		2.62e-07
(0.000169)
del 17p11 2 116 (22%) 408 0.000111
(0.0549) 		7.26e-06
(0.00418) 		3.66e-55
(4.25e-52) 		7.1e-14
(6.36e-11) 		0.0247
(1.00) 		0.378
(1.00) 		6.63e-26
(7.2e-23) 		8.16e-22
(8.58e-19) 		5.37e-16
(5.06e-13) 		1.31e-11
(1.06e-08) 		0.000131
(0.0639) 		7.28e-07
(0.000457)
del 22q13 31 132 (25%) 392 3.62e-06
(0.00215) 		2.4e-07
(0.000155) 		7.72e-59
(8.99e-56) 		2.49e-14
(2.25e-11) 		0.0018
(0.708) 		0.153
(1.00) 		4.62e-25
(5e-22) 		7.93e-22
(8.35e-19) 		1.29e-17
(1.26e-14) 		3.77e-12
(3.14e-09) 		0.000127
(0.0622) 		1.95e-07
(0.000126)
amp 8q24 21 202 (39%) 322 0.0121
(1.00) 		0.0416
(1.00) 		1.12e-37
(1.28e-34) 		4.42e-07
(0.000282) 		8.75e-05
(0.0441) 		0.504
(1.00) 		1.55e-16
(1.49e-13) 		4.06e-15
(3.76e-12) 		4.75e-12
(3.93e-09) 		2.16e-09
(1.58e-06) 		5.52e-05
(0.0285) 		6.05e-06
(0.00352)
amp 8q24 21 208 (40%) 316 0.00295
(1.00) 		0.00421
(1.00) 		1.31e-37
(1.48e-34) 		6.09e-06
(0.00354) 		7.26e-07
(0.000456) 		0.141
(1.00) 		7.29e-16
(6.83e-13) 		3.41e-15
(3.16e-12) 		3.57e-13
(3.11e-10) 		9.75e-09
(6.98e-06) 		6.03e-05
(0.0309) 		2.53e-05
(0.0138)
amp 19p13 12 91 (17%) 433 0.00381
(1.00) 		0.000454
(0.199) 		7.59e-47
(8.72e-44) 		2e-11
(1.6e-08) 		0.0261
(1.00) 		0.157
(1.00) 		3.4e-23
(3.62e-20) 		1.23e-21
(1.29e-18) 		3.15e-16
(2.99e-13) 		2.2e-09
(1.62e-06) 		1.16e-05
(0.00654) 		1.01e-07
(6.71e-05)
amp 19q12 115 (22%) 409 0.00518
(1.00) 		0.000168
(0.0803) 		1.84e-58
(2.14e-55) 		6.92e-18
(6.81e-15) 		0.00374
(1.00) 		0.142
(1.00) 		2.63e-35
(2.97e-32) 		2.32e-32
(2.59e-29) 		2.22e-24
(2.4e-21) 		8.83e-15
(8.09e-12) 		2.24e-07
(0.000144) 		1.64e-12
(1.39e-09)
amp 20q11 21 142 (27%) 382 0.00253
(0.932) 		0.000168
(0.0803) 		3.76e-53
(4.35e-50) 		1.27e-13
(1.12e-10) 		0.000964
(0.397) 		0.153
(1.00) 		1.71e-24
(1.84e-21) 		1.18e-20
(1.22e-17) 		5.18e-18
(5.11e-15) 		1.68e-10
(1.3e-07) 		9.32e-06
(0.00531) 		3.23e-07
(0.000207)
del 4q22 1 102 (19%) 422 0.00381
(1.00) 		0.000454
(0.199) 		1.97e-44
(2.26e-41) 		5.5e-18
(5.42e-15) 		0.0252
(1.00) 		0.102
(1.00) 		9.3e-25
(1e-21) 		1.16e-21
(1.22e-18) 		1.55e-20
(1.6e-17) 		1.17e-17
(1.15e-14) 		1.45e-08
(1.03e-05) 		6.67e-13
(5.73e-10)
del 4q34 3 125 (24%) 399 0.00381
(1.00) 		0.000454
(0.199) 		7.01e-54
(8.12e-51) 		1.69e-16
(1.62e-13) 		0.0599
(1.00) 		0.521
(1.00) 		1.8e-30
(1.99e-27) 		1.43e-27
(1.56e-24) 		2.43e-20
(2.49e-17) 		1.61e-18
(1.6e-15) 		3.19e-09
(2.33e-06) 		1.31e-14
(1.19e-11)
del 8p23 2 113 (22%) 411 0.00202
(0.769) 		0.000218
(0.102) 		1.17e-47
(1.34e-44) 		2.16e-21
(2.26e-18) 		0.0469
(1.00) 		0.378
(1.00) 		6.61e-32
(7.36e-29) 		7.89e-27
(8.62e-24) 		1.37e-26
(1.49e-23) 		9.57e-18
(9.39e-15) 		4.14e-12
(3.44e-09) 		3.47e-16
(3.28e-13)
del 8p21 2 111 (21%) 413 0.00202
(0.769) 		0.000218
(0.102) 		1.54e-53
(1.79e-50) 		3.02e-26
(3.28e-23) 		0.017
(1.00) 		0.168
(1.00) 		3.83e-37
(4.34e-34) 		2.89e-31
(3.22e-28) 		7.59e-31
(8.43e-28) 		1.25e-20
(1.29e-17) 		8.64e-16
(8.07e-13) 		1.35e-19
(1.37e-16)
del 15q23 110 (21%) 414 0.00202
(0.769) 		0.000218
(0.102) 		7e-43
(8.01e-40) 		1.13e-16
(1.08e-13) 		0.104
(1.00) 		0.812
(1.00) 		1.23e-22
(1.31e-19) 		1.71e-20
(1.75e-17) 		8.2e-15
(7.52e-12) 		2.22e-13
(1.94e-10) 		3.68e-08
(2.51e-05) 		4.14e-10
(3.14e-07)
del 16q21 150 (29%) 374 0.000771
(0.325) 		9.8e-05
(0.049) 		4.14e-59
(4.82e-56) 		9.18e-18
(9.02e-15) 		0.0797
(1.00) 		1
(1.00) 		2.81e-26
(3.06e-23) 		5.85e-23
(6.22e-20) 		3.88e-18
(3.84e-15) 		1.12e-11
(9.11e-09) 		1.41e-07
(9.32e-05) 		2.5e-10
(1.92e-07)
del 16q23 1 161 (31%) 363 0.00295
(1.00) 		0.000312
(0.142) 		1.86e-60
(2.18e-57) 		8.53e-17
(8.22e-14) 		0.0275
(1.00) 		0.369
(1.00) 		9.28e-29
(1.02e-25) 		5.77e-25
(6.23e-22) 		6.23e-21
(6.46e-18) 		1.78e-13
(1.57e-10) 		6e-08
(4.04e-05) 		1.15e-11
(9.34e-09)
del 17p11 2 122 (23%) 402 0.000771
(0.325) 		9.8e-05
(0.049) 		1.88e-55
(2.18e-52) 		2.7e-14
(2.45e-11) 		0.00346
(1.00) 		0.665
(1.00) 		1.26e-27
(1.38e-24) 		2.76e-23
(2.94e-20) 		2.66e-16
(2.53e-13) 		3.62e-13
(3.15e-10) 		0.0003
(0.137) 		6.2e-07
(0.000392)
del 19q13 43 64 (12%) 460 0.000771
(0.325) 		9.8e-05
(0.049) 		1.61e-23
(1.71e-20) 		2.41e-10
(1.85e-07) 		0.0782
(1.00) 		0.56
(1.00) 		1.25e-14
(1.14e-11) 		7.08e-13
(6.07e-10) 		3.07e-14
(2.77e-11) 		7.24e-10
(5.43e-07) 		1.8e-05
(0.01) 		1.07e-07
(7.14e-05)
del xp21 1 84 (16%) 440 0.000567
(0.245) 		4.17e-05
(0.022) 		9.13e-35
(1.03e-31) 		1.82e-08
(1.27e-05) 		0.00401
(1.00) 		0.346
(1.00) 		4.87e-18
(4.81e-15) 		9.25e-17
(8.91e-14) 		1.67e-11
(1.34e-08) 		1.72e-09
(1.26e-06) 		0.00108
(0.439) 		7.76e-06
(0.00446)
amp 1p34 2 71 (14%) 453 0.0129
(1.00) 		0.00193
(0.751) 		2.24e-34
(2.52e-31) 		1.03e-09
(7.71e-07) 		0.0209
(1.00) 		0.393
(1.00) 		1.32e-17
(1.28e-14) 		6.21e-16
(5.82e-13) 		3.47e-15
(3.21e-12) 		2.05e-10
(1.58e-07) 		1.3e-05
(0.00735) 		3.72e-08
(2.54e-05)
amp 2q13 114 (22%) 410 0.159
(1.00) 		0.0362
(1.00) 		1.86e-37
(2.11e-34) 		8.14e-14
(7.28e-11) 		0.0025
(0.923) 		0.153
(1.00) 		1.08e-19
(1.1e-16) 		2.8e-19
(2.83e-16) 		6.59e-19
(6.62e-16) 		3.41e-12
(2.85e-09) 		6.41e-08
(4.31e-05) 		2.51e-12
(2.11e-09)
amp 5p15 33 83 (16%) 441 0.231
(1.00) 		0.0213
(1.00) 		5.19e-35
(5.86e-32) 		9.49e-12
(7.74e-09) 		0.221
(1.00) 		0.612
(1.00) 		5.33e-20
(5.44e-17) 		2.3e-16
(2.19e-13) 		4.8e-15
(4.42e-12) 		3.65e-10
(2.77e-07) 		8.65e-07
(0.000538) 		9.94e-09
(7.1e-06)
amp 12p12 1 87 (17%) 437 0.327
(1.00) 		0.683
(1.00) 		6.67e-17
(6.45e-14) 		9.3e-09
(6.68e-06) 		0.48
(1.00) 		0.665
(1.00) 		6.46e-09
(4.67e-06) 		5.8e-08
(3.92e-05) 		7.46e-08
(5.01e-05) 		0.000391
(0.175) 		0.000159
(0.0762) 		4.49e-06
(0.00264)
amp 12q13 11 85 (16%) 439 0.377
(1.00) 		0.59
(1.00) 		1.57e-19
(1.59e-16) 		1.12e-09
(8.29e-07) 		0.491
(1.00) 		0.244
(1.00) 		8.03e-11
(6.29e-08) 		7.84e-10
(5.87e-07) 		1.68e-08
(1.18e-05) 		9.33e-05
(0.0468) 		2.53e-05
(0.0138) 		3.66e-06
(0.00217)
amp 12q13 2 98 (19%) 426 0.181
(1.00) 		0.259
(1.00) 		2.69e-22
(2.84e-19) 		1.82e-08
(1.27e-05) 		0.298
(1.00) 		0.274
(1.00) 		2.75e-12
(2.3e-09) 		3.86e-11
(3.07e-08) 		1.1e-09
(8.17e-07) 		1.88e-05
(0.0104) 		1.42e-05
(0.00799) 		7.91e-06
(0.00454)
amp 13q34 56 (11%) 468 0.689
(1.00) 		0.272
(1.00) 		4.69e-23
(4.99e-20) 		1.87e-08
(1.3e-05) 		0.231
(1.00) 		0.0831
(1.00) 		4.29e-13
(3.71e-10) 		9.13e-14
(8.12e-11) 		4.77e-13
(4.12e-10) 		1.83e-07
(0.000119) 		2.78e-05
(0.0151) 		8.18e-08
(5.48e-05)
amp 17q11 2 67 (13%) 457 0.151
(1.00) 		0.0272
(1.00) 		2.02e-28
(2.22e-25) 		1.11e-13
(9.83e-11) 		0.0201
(1.00) 		0.0052
(1.00) 		8.42e-16
(7.88e-13) 		1.55e-17
(1.51e-14) 		1.98e-14
(1.8e-11) 		8.34e-12
(6.81e-09) 		6.35e-06
(0.00368) 		8.53e-10
(6.38e-07)
amp 17q12 71 (14%) 453 0.108
(1.00) 		0.0272
(1.00) 		9.06e-27
(9.9e-24) 		1.69e-14
(1.54e-11) 		0.0111
(1.00) 		0.438
(1.00) 		3.01e-20
(3.08e-17) 		2.8e-19
(2.83e-16) 		5.42e-16
(5.1e-13) 		1.58e-11
(1.28e-08) 		4.79e-06
(0.00281) 		2.35e-12
(1.98e-09)
amp 18p11 31 91 (17%) 433 0.154
(1.00) 		0.0276
(1.00) 		1.45e-37
(1.65e-34) 		1.87e-12
(1.58e-09) 		0.0101
(1.00) 		0.0197
(1.00) 		9.26e-22
(9.72e-19) 		2.67e-20
(2.74e-17) 		9.58e-18
(9.39e-15) 		1.54e-11
(1.24e-08) 		1.34e-06
(0.000813) 		2.12e-12
(1.79e-09)
amp 18q11 2 67 (13%) 457 0.108
(1.00) 		0.0272
(1.00) 		2.59e-28
(2.84e-25) 		8.89e-11
(6.96e-08) 		0.156
(1.00) 		0.0444
(1.00) 		2.54e-17
(2.47e-14) 		1.55e-16
(1.49e-13) 		8.24e-15
(7.55e-12) 		4.4e-12
(3.64e-09) 		1.01e-08
(7.21e-06) 		2.53e-13
(2.21e-10)
amp 20p13 113 (22%) 411 0.151
(1.00) 		0.0272
(1.00) 		1.16e-35
(1.31e-32) 		8.23e-12
(6.74e-09) 		0.117
(1.00) 		0.512
(1.00) 		3.71e-15
(3.43e-12) 		4.14e-12
(3.44e-09) 		1.22e-12
(1.04e-09) 		5.31e-09
(3.84e-06) 		3.02e-05
(0.0162) 		9.2e-09
(6.61e-06)
amp 20q13 12 145 (28%) 379 0.0129
(1.00) 		0.00193
(0.751) 		9.63e-52
(1.11e-48) 		1.87e-14
(1.7e-11) 		0.00478
(1.00) 		0.105
(1.00) 		9.34e-23
(9.9e-20) 		5.56e-19
(5.6e-16) 		5.12e-18
(5.06e-15) 		1.83e-11
(1.47e-08) 		3.11e-05
(0.0166) 		8.18e-07
(0.00051)
amp 20q13 33 142 (27%) 382 0.0243
(1.00) 		0.00409
(1.00) 		2.91e-48
(3.35e-45) 		6.14e-12
(5.06e-09) 		0.0674
(1.00) 		0.686
(1.00) 		5.12e-19
(5.17e-16) 		8.47e-16
(7.92e-13) 		1.06e-15
(9.84e-13) 		4.17e-09
(3.03e-06) 		0.00029
(0.133) 		1.56e-06
(0.000945)
amp 22q12 2 59 (11%) 465 0.379
(1.00) 		0.0902
(1.00) 		3.71e-20
(3.8e-17) 		2.3e-16
(2.19e-13) 		0.181
(1.00) 		0.0546
(1.00) 		1.03e-20
(1.07e-17) 		7.98e-19
(7.99e-16) 		1.06e-20
(1.1e-17) 		2.62e-12
(2.2e-09) 		2.66e-10
(2.04e-07) 		4.84e-13
(4.18e-10)
del 1p36 21 70 (13%) 454 0.0243
(1.00) 		0.00409
(1.00) 		4.91e-25
(5.31e-22) 		2.13e-07
(0.000138) 		0.00518
(1.00) 		0.267
(1.00) 		3.62e-14
(3.27e-11) 		2.08e-12
(1.75e-09) 		3.83e-09
(2.79e-06) 		1.68e-08
(1.18e-05) 		0.000232
(0.107) 		4.12e-05
(0.0218)
del 1p36 11 82 (16%) 442 0.0515
(1.00) 		0.00755
(1.00) 		1.39e-33
(1.56e-30) 		4.08e-12
(3.39e-09) 		0.0339
(1.00) 		0.393
(1.00) 		9.34e-19
(9.34e-16) 		1.73e-16
(1.65e-13) 		2.12e-12
(1.79e-09) 		1.49e-12
(1.26e-09) 		1.82e-05
(0.0101) 		9.33e-08
(6.24e-05)
del 3p14 2 75 (14%) 449 0.0515
(1.00) 		0.00755
(1.00) 		1.28e-32
(1.43e-29) 		4.22e-10
(3.19e-07) 		0.000952
(0.394) 		0.0197
(1.00) 		8.2e-22
(8.62e-19) 		2.41e-18
(2.4e-15) 		1.69e-13
(1.49e-10) 		1.13e-08
(8.01e-06) 		1.09e-05
(0.0062) 		1.84e-07
(0.00012)
del 4p16 3 91 (17%) 433 0.0129
(1.00) 		0.00193
(0.751) 		3.28e-31
(3.65e-28) 		7.98e-13
(6.84e-10) 		0.0096
(1.00) 		0.244
(1.00) 		3.32e-17
(3.22e-14) 		1.14e-14
(1.05e-11) 		3.53e-12
(2.95e-09) 		7.17e-11
(5.63e-08) 		6.84e-05
(0.0347) 		1.8e-07
(0.000118)
del 4p15 31 95 (18%) 429 0.0129
(1.00) 		0.00193
(0.751) 		5.83e-35
(6.57e-32) 		1.64e-15
(1.52e-12) 		0.0203
(1.00) 		0.346
(1.00) 		1.07e-19
(1.09e-16) 		5.26e-17
(5.1e-14) 		9.9e-16
(9.24e-13) 		8.69e-14
(7.75e-11) 		9.34e-07
(0.000578) 		1.22e-09
(9.07e-07)
del 5q11 2 106 (20%) 418 0.0129
(1.00) 		0.00193
(0.751) 		3.45e-48
(3.98e-45) 		2e-16
(1.91e-13) 		0.000858
(0.357) 		0.01
(1.00) 		5.02e-24
(5.38e-21) 		1.78e-21
(1.87e-18) 		1.63e-18
(1.63e-15) 		2.23e-13
(1.95e-10) 		6.67e-07
(0.000419) 		1.48e-09
(1.09e-06)
del 6q26 45 (9%) 479 0.379
(1.00) 		0.0902
(1.00) 		3.83e-14
(3.45e-11) 		3.54e-08
(2.42e-05) 		0.675
(1.00) 		0.301
(1.00) 		3.01e-11
(2.4e-08) 		5.1e-10
(3.84e-07) 		3.36e-08
(2.3e-05) 		2.68e-08
(1.85e-05) 		0.000338
(0.152) 		4.36e-05
(0.0228)
del 7q31 1 53 (10%) 471 0.137
(1.00) 		0.0194
(1.00) 		1.69e-28
(1.86e-25) 		6.9e-11
(5.42e-08) 		0.0899
(1.00) 		0.0192
(1.00) 		1.2e-18
(1.2e-15) 		1.52e-15
(1.41e-12) 		1.5e-11
(1.21e-08) 		4.27e-08
(2.9e-05) 		0.000196
(0.0931) 		5.51e-08
(3.73e-05)
del 7q36 1 62 (12%) 462 0.333
(1.00) 		0.0623
(1.00) 		4.26e-31
(4.73e-28) 		4.87e-12
(4.02e-09) 		0.0198
(1.00) 		0.00216
(0.809) 		1.78e-22
(1.89e-19) 		6.33e-19
(6.37e-16) 		3.41e-16
(3.22e-13) 		1.05e-10
(8.24e-08) 		2.78e-05
(0.0151) 		1.74e-10
(1.35e-07)
del 10q23 31 73 (14%) 451 0.137
(1.00) 		0.0194
(1.00) 		2.24e-29
(2.48e-26) 		8.46e-09
(6.1e-06) 		0.116
(1.00) 		0.796
(1.00) 		5.31e-13
(4.58e-10) 		2.64e-11
(2.1e-08) 		1.69e-11
(1.36e-08) 		2.58e-06
(0.00154) 		0.000311
(0.141) 		1.58e-06
(0.000957)
del 11p15 5 99 (19%) 425 0.379
(1.00) 		0.0902
(1.00) 		9.7e-42
(1.11e-38) 		5.89e-16
(5.53e-13) 		0.248
(1.00) 		0.309
(1.00) 		1.42e-20
(1.46e-17) 		2.34e-17
(2.27e-14) 		4.98e-14
(4.48e-11) 		2.7e-08
(1.86e-05) 		1.89e-06
(0.00114) 		2.03e-08
(1.41e-05)
del 11q14 1 66 (13%) 458 2.18e-23
(2.33e-20) 		4.74e-10
(3.58e-07) 		0.477
(1.00) 		0.243
(1.00) 		6.65e-14
(5.97e-11) 		4.84e-12
(4e-09) 		3.19e-10
(2.43e-07) 		1.09e-08
(7.77e-06) 		0.000218
(0.102) 		1.6e-08
(1.13e-05)
del 11q25 89 (17%) 435 5.29e-30
(5.86e-27) 		1.12e-14
(1.03e-11) 		0.134
(1.00) 		0.804
(1.00) 		4.53e-15
(4.18e-12) 		6.32e-14
(5.68e-11) 		3.91e-10
(2.96e-07) 		6.37e-10
(4.78e-07) 		2.14e-05
(0.0118) 		4.42e-08
(3e-05)
del 12q23 1 53 (10%) 471 4.87e-24
(5.23e-21) 		7.56e-12
(6.2e-09) 		0.0349
(1.00) 		0.00949
(1.00) 		3.93e-13
(3.41e-10) 		5.26e-11
(4.15e-08) 		7.66e-12
(6.27e-09) 		2.35e-09
(1.72e-06) 		1.5e-05
(0.0084) 		3.45e-08
(2.37e-05)
del 12q24 33 64 (12%) 460 2.24e-29
(2.48e-26) 		5.33e-11
(4.21e-08) 		0.0569
(1.00) 		0.301
(1.00) 		7.62e-19
(7.65e-16) 		8.48e-17
(8.19e-14) 		3.26e-13
(2.85e-10) 		2.46e-08
(1.7e-05) 		1.47e-07
(9.64e-05) 		9.59e-08
(6.41e-05)
del 14q13 1 69 (13%) 455 0.00809
(1.00) 		0.00105
(0.428) 		2.82e-26
(3.06e-23) 		1.21e-11
(9.8e-09) 		0.0681
(1.00) 		0.106
(1.00) 		1.82e-13
(1.6e-10) 		4.92e-13
(4.24e-10) 		1.07e-10
(8.38e-08) 		2.74e-12
(2.29e-09) 		1.76e-05
(0.0098) 		2.18e-06
(0.00131)
del 15q15 1 135 (26%) 389 0.0129
(1.00) 		0.00193
(0.751) 		5.6e-57
(6.51e-54) 		6.42e-18
(6.32e-15) 		0.00247
(0.913) 		0.205
(1.00) 		2.31e-29
(2.56e-26) 		2.37e-25
(2.57e-22) 		2.08e-21
(2.17e-18) 		4.45e-17
(4.31e-14) 		1.44e-07
(9.47e-05) 		6.62e-11
(5.22e-08)
del 16p13 3 88 (17%) 436 0.0129
(1.00) 		0.00193
(0.751) 		2.85e-39
(3.25e-36) 		2.42e-15
(2.24e-12) 		0.0547
(1.00) 		0.176
(1.00) 		6.07e-23
(6.45e-20) 		3.61e-19
(3.65e-16) 		4.82e-16
(4.54e-13) 		8.92e-14
(7.95e-11) 		1.06e-05
(0.00602) 		2.1e-10
(1.61e-07)
del 17p13 3 115 (22%) 409 0.000771
(0.325) 		9.8e-05
(0.049) 		6.45e-51
(7.44e-48) 		8.78e-12
(7.17e-09) 		0.000824
(0.344) 		0.665
(1.00) 		4.99e-22
(5.26e-19) 		2.63e-18
(2.61e-15) 		2.16e-14
(1.96e-11) 		3.44e-10
(2.62e-07) 		0.0019
(0.742) 		5.1e-06
(0.00298)
del 17q11 2 101 (19%) 423 0.000567
(0.245) 		4.17e-05
(0.022) 		1.7e-43
(1.94e-40) 		1.43e-07
(9.47e-05) 		0.013
(1.00) 		0.647
(1.00) 		2.97e-16
(2.82e-13) 		2.78e-14
(2.51e-11) 		4.58e-11
(3.63e-08) 		7.84e-07
(0.000489) 		0.003
(1.00) 		0.00132
(0.529)
del 17q21 31 100 (19%) 424 0.000567
(0.245) 		4.17e-05
(0.022) 		3.41e-45
(3.91e-42) 		2.12e-08
(1.47e-05) 		0.0261
(1.00) 		0.346
(1.00) 		3.04e-16
(2.88e-13) 		4.23e-15
(3.9e-12) 		1.05e-08
(7.47e-06) 		1.21e-06
(0.000738) 		0.00409
(1.00) 		0.00426
(1.00)
del 18q21 2 90 (17%) 434 0.617
(1.00) 		0.173
(1.00) 		7.46e-33
(8.34e-30) 		1.34e-10
(1.04e-07) 		0.0705
(1.00) 		0.142
(1.00) 		5.49e-16
(5.16e-13) 		8.26e-14
(7.37e-11) 		3.77e-13
(3.27e-10) 		3.74e-10
(2.84e-07) 		0.000199
(0.094) 		6.51e-05
(0.0332)
amp 1p35 2 55 (10%) 469 0.0515
(1.00) 		0.00755
(1.00) 		1.4e-22
(1.48e-19) 		4.01e-07
(0.000256) 		0.000446
(0.196) 		0.196
(1.00) 		6.35e-13
(5.46e-10) 		4.2e-12
(3.48e-09) 		2.91e-08
(2e-05) 		1.2e-06
(0.000733) 		0.00233
(0.865) 		0.00158
(0.629)
amp 1q22 247 (47%) 277 0.0238
(1.00) 		0.0448
(1.00) 		1.06e-16
(1.01e-13) 		0.000294
(0.135) 		0.195
(1.00) 		0.233
(1.00) 		7.72e-07
(0.000482) 		6.41e-06
(0.00371) 		1.27e-05
(0.00718) 		0.000394
(0.176) 		0.122
(1.00) 		7.43e-05
(0.0376)
amp 2p24 3 117 (22%) 407 0.682
(1.00) 		0.434
(1.00) 		1.42e-28
(1.57e-25) 		4.14e-08
(2.82e-05) 		0.0386
(1.00) 		0.695
(1.00) 		1.23e-09
(9.13e-07) 		1.04e-09
(7.74e-07) 		6.48e-07
(0.000408) 		7.2e-05
(0.0365) 		0.000596
(0.254) 		2.09e-05
(0.0115)
amp 3p25 1 77 (15%) 447 0.188
(1.00) 		0.247
(1.00) 		5.06e-29
(5.57e-26) 		3.72e-06
(0.0022) 		0.0611
(1.00) 		0.309
(1.00) 		3.88e-13
(3.36e-10) 		2.02e-13
(1.77e-10) 		1.75e-08
(1.22e-05) 		0.000156
(0.0748) 		0.0028
(1.00) 		6.6e-05
(0.0336)
amp 4p16 3 52 (10%) 472 0.0515
(1.00) 		0.00755
(1.00) 		2.26e-24
(2.43e-21) 		0.000356
(0.159) 		0.113
(1.00) 		0.0106
(1.00) 		7.78e-15
(7.15e-12) 		3.62e-12
(3.02e-09) 		2.25e-10
(1.73e-07) 		1.71e-06
(0.00104) 		0.00351
(1.00) 		2.81e-05
(0.0151)
amp 5q35 3 54 (10%) 470 0.137
(1.00) 		0.0194
(1.00) 		5.78e-20
(5.89e-17) 		5.67e-05
(0.0292) 		0.104
(1.00) 		0.507
(1.00) 		2.39e-11
(1.91e-08) 		5.68e-10
(4.27e-07) 		8.11e-08
(5.44e-05) 		0.000409
(0.181) 		0.00797
(1.00) 		9.08e-05
(0.0457)
amp 6q25 1 84 (16%) 440 0.284
(1.00) 		0.312
(1.00) 		1.65e-25
(1.79e-22) 		8.62e-09
(6.21e-06) 		0.0973
(1.00) 		0.0197
(1.00) 		1.69e-08
(1.19e-05) 		1.59e-07
(0.000104) 		4.36e-06
(0.00258) 		1.33e-05
(0.00749) 		0.00183
(0.716) 		0.000467
(0.203)
amp 9p24 2 63 (12%) 461 0.129
(1.00) 		0.0606
(1.00) 		2.78e-24
(2.99e-21) 		3.74e-09
(2.72e-06) 		0.00104
(0.427) 		0.00216
(0.809) 		1.16e-13
(1.03e-10) 		7.3e-12
(6e-09) 		1.42e-12
(1.21e-09) 		2.05e-07
(0.000133) 		0.000738
(0.312) 		0.000109
(0.0542)
amp 11p11 2 49 (9%) 475 0.00202
(0.769) 		0.00755
(1.00) 		8.07e-17
(7.8e-14) 		2.84e-05
(0.0152) 		0.0161
(1.00) 		1
(1.00) 		4.66e-08
(3.15e-05) 		7.42e-07
(0.000464) 		2.59e-08
(1.79e-05) 		8.07e-05
(0.0407) 		0.034
(1.00) 		0.000157
(0.0752)
amp 14q24 3 62 (12%) 462 0.0605
(1.00) 		0.0951
(1.00) 		3.66e-19
(3.7e-16) 		3.14e-05
(0.0168) 		0.129
(1.00) 		0.267
(1.00) 		7.41e-14
(6.63e-11) 		1.16e-13
(1.03e-10) 		1.61e-07
(0.000105) 		3.52e-05
(0.0187) 		0.0802
(1.00) 		0.000289
(0.133)
amp 16p11 2 63 (12%) 461 0.00809
(1.00) 		0.00105
(0.428) 		5.11e-24
(5.47e-21) 		8.14e-06
(0.00466) 		0.0667
(1.00) 		0.142
(1.00) 		1.03e-12
(8.79e-10) 		7.3e-12
(6e-09) 		3.43e-11
(2.73e-08) 		0.00015
(0.0725) 		0.0016
(0.633) 		4.23e-05
(0.0222)
del 7q11 22 41 (8%) 483 3.11e-21
(3.23e-18) 		5.42e-06
(0.00316) 		0.0668
(1.00) 		0.00669
(1.00) 		1.4e-12
(1.19e-09) 		2.86e-10
(2.19e-07) 		1.44e-07
(9.49e-05) 		1.42e-05
(0.00799) 		0.00201
(0.767) 		5.09e-05
(0.0264)
del 9p23 75 (14%) 449 0.379
(1.00) 		0.0902
(1.00) 		1.53e-26
(1.67e-23) 		4.73e-07
(3e-04) 		0.0369
(1.00) 		0.295
(1.00) 		4.44e-11
(3.52e-08) 		1.32e-09
(9.78e-07) 		1.65e-07
(0.000108) 		4.41e-05
(0.023) 		0.0172
(1.00) 		0.000286
(0.132)
del 13q11 96 (18%) 428 0.333
(1.00) 		0.158
(1.00) 		7.73e-35
(8.71e-32) 		1.36e-09
(1.01e-06) 		0.162
(1.00) 		0.126
(1.00) 		1.82e-13
(1.6e-10) 		6.84e-12
(5.63e-09) 		9.99e-10
(7.47e-07) 		4.32e-09
(3.13e-06) 		0.0117
(1.00) 		4.71e-05
(0.0245)
del 18q23 96 (18%) 428 0.617
(1.00) 		0.173
(1.00) 		4.21e-35
(4.76e-32) 		1.28e-11
(1.04e-08) 		0.0427
(1.00) 		0.0354
(1.00) 		2.95e-18
(2.93e-15) 		3.61e-16
(3.41e-13) 		1.54e-12
(1.31e-09) 		1.27e-10
(9.86e-08) 		0.000589
(0.252) 		4.15e-06
(0.00246)
del 22q11 1 84 (16%) 440 0.00202
(0.769) 		0.000218
(0.102) 		2.43e-29
(2.68e-26) 		3.77e-05
(0.02) 		0.451
(1.00) 		0.796
(1.00) 		1.23e-10
(9.55e-08) 		4.31e-09
(3.13e-06) 		2.5e-06
(0.0015) 		1.1e-06
(0.000679) 		0.184
(1.00) 		0.0711
(1.00)
amp 1p22 3 92 (18%) 432 0.0196
(1.00) 		0.0165
(1.00) 		2.31e-11
(1.85e-08) 		0.00876
(1.00) 		0.866
(1.00) 		0.674
(1.00) 		3.41e-06
(0.00203) 		2.97e-06
(0.00177) 		4.79e-07
(0.000304) 		0.000465
(0.202) 		0.00118
(0.478) 		0.000128
(0.0628)
amp 1q21 3 233 (44%) 291 0.0157
(1.00) 		0.0274
(1.00) 		1.15e-13
(1.02e-10) 		0.00265
(0.969) 		0.396
(1.00) 		0.229
(1.00) 		2.56e-06
(0.00153) 		1.11e-05
(0.00628) 		5.86e-06
(0.00342) 		0.000222
(0.103) 		0.0563
(1.00) 		0.000133
(0.0646)
amp 9q34 3 37 (7%) 487 0.243
(1.00) 		0.158
(1.00) 		4.25e-14
(3.82e-11) 		0.000123
(0.0603) 		0.336
(1.00) 		0.507
(1.00) 		2.89e-08
(1.99e-05) 		3.71e-07
(0.000237) 		0.000136
(0.0656) 		0.000139
(0.0671) 		0.0125
(1.00) 		0.0364
(1.00)
del 2q22 1 46 (9%) 478 0.0391
(1.00) 		0.00466
(1.00) 		4.78e-20
(4.88e-17) 		2.29e-05
(0.0126) 		0.0823
(1.00) 		0.155
(1.00) 		1.22e-11
(9.88e-09) 		1.45e-09
(1.07e-06) 		3.29e-07
(0.000211) 		6.68e-06
(0.00385) 		0.00919
(1.00) 		0.00306
(1.00)
del 13q14 2 103 (20%) 421 0.617
(1.00) 		0.301
(1.00) 		6.13e-37
(6.94e-34) 		1.37e-08
(9.76e-06) 		0.0746
(1.00) 		0.102
(1.00) 		4.9e-13
(4.23e-10) 		2.06e-11
(1.65e-08) 		4.92e-07
(0.000311) 		9.73e-09
(6.97e-06) 		0.0448
(1.00) 		0.00158
(0.63)
del 19p12 56 (11%) 468 1.66e-19
(1.69e-16) 		1.46e-07
(9.6e-05) 		0.21
(1.00) 		0.507
(1.00) 		2.14e-08
(1.48e-05) 		3.48e-07
(0.000223) 		1.07e-06
(0.000662) 		6.33e-07
(0.000399) 		0.00253
(0.932) 		0.000721
(0.306)
amp 3p14 1 61 (12%) 463 0.536
(1.00) 		1
(1.00) 		1.53e-23
(1.64e-20) 		0.00064
(0.273) 		0.0546
(1.00) 		0.243
(1.00) 		1.69e-08
(1.18e-05) 		1.38e-08
(9.77e-06) 		2.81e-05
(0.0151) 		0.000445
(0.196) 		0.0533
(1.00) 		0.00523
(1.00)
amp 8p11 21 156 (30%) 368 0.0106
(1.00) 		0.015
(1.00) 		9.36e-24
(1e-20) 		0.0107
(1.00) 		0.00111
(0.45) 		0.719
(1.00) 		1.53e-06
(0.000931) 		9.02e-07
(0.000559) 		0.000134
(0.0651) 		0.00044
(0.194) 		0.0103
(1.00) 		0.0208
(1.00)
amp 11q13 2 71 (14%) 453 0.00202
(0.769) 		0.00755
(1.00) 		1.59e-20
(1.63e-17) 		0.000196
(0.0929) 		0.0868
(1.00) 		0.476
(1.00) 		3.88e-07
(0.000248) 		4.41e-06
(0.0026) 		0.000125
(0.0613) 		0.00159
(0.633) 		0.0806
(1.00) 		0.0777
(1.00)
amp 11q14 1 56 (11%) 468 0.379
(1.00) 		0.667
(1.00) 		1.01e-16
(9.68e-14) 		0.000693
(0.295) 		0.504
(1.00) 		0.419
(1.00) 		4.71e-06
(0.00276) 		3.88e-05
(0.0206) 		0.000198
(0.0938) 		8.47e-06
(0.00484) 		0.073
(1.00) 		0.0582
(1.00)
amp 15q26 3 37 (7%) 487 5.09e-10
(3.84e-07) 		0.0131
(1.00) 		0.218
(1.00) 		0.155
(1.00) 		1.15e-06
(0.000702) 		1.36e-06
(0.000828) 		5.22e-05
(0.027) 		0.000206
(0.0969) 		0.0102
(1.00) 		0.00508
(1.00)
del 2q37 3 51 (10%) 473 1.1e-17
(1.08e-14) 		6.38e-05
(0.0326) 		0.276
(1.00) 		0.507
(1.00) 		1.06e-07
(7.09e-05) 		1.75e-06
(0.00105) 		0.000134
(0.0651) 		0.00111
(0.45) 		0.043
(1.00) 		0.0103
(1.00)
del 3q13 31 31 (6%) 493 0.379
(1.00) 		0.0902
(1.00) 		8.48e-13
(7.26e-10) 		0.00358
(1.00) 		0.0559
(1.00) 		1
(1.00) 		1.28e-06
(0.000781) 		8.67e-06
(0.00495) 		6.39e-06
(0.0037) 		0.00021
(0.0986) 		0.193
(1.00) 		0.0135
(1.00)
amp xp11 23 87 (17%) 437 0.355
(1.00) 		0.683
(1.00) 		4.92e-24
(5.28e-21) 		0.00353
(1.00) 		0.783
(1.00) 		0.399
(1.00) 		0.00023
(0.107) 		0.000116
(0.057) 		2.06e-05
(0.0114) 		0.0155
(1.00) 		0.0183
(1.00) 		0.00505
(1.00)
del 2p25 3 25 (5%) 499 7.51e-09
(5.43e-06) 		0.000502
(0.217) 		0.268
(1.00) 		0.652
(1.00) 		9.58e-05
(0.048) 		0.000398
(0.177) 		0.0016
(0.633) 		0.0133
(1.00) 		0.376
(1.00) 		0.0644
(1.00)
amp 7q22 1 90 (17%) 434 0.678
(1.00) 		0.744
(1.00) 		4.35e-21
(4.52e-18) 		0.00616
(1.00) 		0.5
(1.00) 		0.827
(1.00) 		1.75e-05
(0.00978) 		0.000307
(0.14) 		0.00103
(0.424) 		0.00226
(0.845) 		0.0261
(1.00) 		0.0738
(1.00)
amp xq28 89 (17%) 435 0.0872
(1.00) 		0.0426
(1.00) 		2.71e-21
(2.83e-18) 		0.0718
(1.00) 		0.228
(1.00) 		0.831
(1.00) 		0.00135
(0.543) 		0.00042
(0.186) 		0.00183
(0.716) 		0.115
(1.00) 		0.146
(1.00) 		0.237
(1.00)
amp 1q44 213 (41%) 311 0.0329
(1.00) 		0.102
(1.00) 		4.63e-07
(0.000294) 		0.0735
(1.00) 		0.678
(1.00) 		0.0359
(1.00) 		0.00328
(1.00) 		0.00292
(1.00) 		0.00169
(0.666) 		0.238
(1.00) 		0.71
(1.00) 		0.117
(1.00)
amp 10q22 2 140 (27%) 384 0.0318
(1.00) 		0.0668
(1.00) 		1.97e-10
(1.52e-07) 		0.395
(1.00) 		0.273
(1.00) 		0.414
(1.00) 		0.0285
(1.00) 		0.183
(1.00) 		0.596
(1.00) 		0.582
(1.00) 		0.119
(1.00) 		0.0426
(1.00)
del 20p12 1 34 (6%) 490 1
(1.00) 		0.491
(1.00) 		2.49e-05
(0.0136) 		0.125
(1.00) 		0.0877
(1.00) 		0.507
(1.00) 		0.000887
(0.368) 		0.0013
(0.525) 		0.00278
(1.00) 		0.00229
(0.852) 		0.347
(1.00) 		0.347
(1.00)
'amp_1p35.2' versus 'CN_CNMF'

P value = 1.4e-22 (Chi-square test), Q value = 1.5e-19

Table S1.  Gene #1: 'amp_1p35.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 1(1P35.2) MUTATED 0 7 48 0 0
AMP PEAK 1(1P35.2) WILD-TYPE 305 41 106 12 5

Figure S1.  Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1p35.2' versus 'METHLYATION_CNMF'

P value = 4.01e-07 (Fisher's exact test), Q value = 0.00026

Table S2.  Gene #1: 'amp_1p35.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 1(1P35.2) MUTATED 33 5 6
AMP PEAK 1(1P35.2) WILD-TYPE 119 89 158

Figure S2.  Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1p35.2' versus 'RPPA_CNMF'

P value = 0.000446 (Chi-square test), Q value = 0.2

Table S3.  Gene #1: 'amp_1p35.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
AMP PEAK 1(1P35.2) MUTATED 2 10 2 0 0 3
AMP PEAK 1(1P35.2) WILD-TYPE 39 27 37 12 41 21

Figure S3.  Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_1p35.2' versus 'MRNASEQ_CNMF'

P value = 6.35e-13 (Fisher's exact test), Q value = 5.5e-10

Table S4.  Gene #1: 'amp_1p35.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 1(1P35.2) MUTATED 48 1 5
AMP PEAK 1(1P35.2) WILD-TYPE 176 149 140

Figure S4.  Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1p35.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.2e-12 (Fisher's exact test), Q value = 3.5e-09

Table S5.  Gene #1: 'amp_1p35.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 1(1P35.2) MUTATED 6 0 48
AMP PEAK 1(1P35.2) WILD-TYPE 141 132 192

Figure S5.  Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1p35.2' versus 'MIRSEQ_CNMF'

P value = 2.91e-08 (Fisher's exact test), Q value = 2e-05

Table S6.  Gene #1: 'amp_1p35.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 1(1P35.2) MUTATED 41 5 6
AMP PEAK 1(1P35.2) WILD-TYPE 164 154 135

Figure S6.  Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1p35.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.2e-06 (Fisher's exact test), Q value = 0.00073

Table S7.  Gene #1: 'amp_1p35.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 1(1P35.2) MUTATED 2 6 44
AMP PEAK 1(1P35.2) WILD-TYPE 6 210 237

Figure S7.  Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1p34.2' versus 'CN_CNMF'

P value = 2.24e-34 (Chi-square test), Q value = 2.5e-31

Table S8.  Gene #2: 'amp_1p34.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 2(1P34.2) MUTATED 0 5 66 0 0
AMP PEAK 2(1P34.2) WILD-TYPE 305 43 88 12 5

Figure S8.  Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1p34.2' versus 'METHLYATION_CNMF'

P value = 1.03e-09 (Fisher's exact test), Q value = 7.7e-07

Table S9.  Gene #2: 'amp_1p34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 2(1P34.2) MUTATED 42 14 5
AMP PEAK 2(1P34.2) WILD-TYPE 110 80 159

Figure S9.  Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1p34.2' versus 'MRNASEQ_CNMF'

P value = 1.32e-17 (Fisher's exact test), Q value = 1.3e-14

Table S10.  Gene #2: 'amp_1p34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 2(1P34.2) MUTATED 63 2 5
AMP PEAK 2(1P34.2) WILD-TYPE 161 148 140

Figure S10.  Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1p34.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.21e-16 (Fisher's exact test), Q value = 5.8e-13

Table S11.  Gene #2: 'amp_1p34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 2(1P34.2) MUTATED 6 1 63
AMP PEAK 2(1P34.2) WILD-TYPE 141 131 177

Figure S11.  Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1p34.2' versus 'MIRSEQ_CNMF'

P value = 3.47e-15 (Fisher's exact test), Q value = 3.2e-12

Table S12.  Gene #2: 'amp_1p34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 2(1P34.2) MUTATED 58 4 6
AMP PEAK 2(1P34.2) WILD-TYPE 147 155 135

Figure S12.  Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1p34.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.05e-10 (Fisher's exact test), Q value = 1.6e-07

Table S13.  Gene #2: 'amp_1p34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 2(1P34.2) MUTATED 2 6 60
AMP PEAK 2(1P34.2) WILD-TYPE 6 210 221

Figure S13.  Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1p34.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.3e-05 (Fisher's exact test), Q value = 0.0073

Table S14.  Gene #2: 'amp_1p34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
AMP PEAK 2(1P34.2) MUTATED 42 6 9
AMP PEAK 2(1P34.2) WILD-TYPE 133 111 81

Figure S14.  Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1p34.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.72e-08 (Fisher's exact test), Q value = 2.5e-05

Table S15.  Gene #2: 'amp_1p34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 2(1P34.2) MUTATED 2 49 6
AMP PEAK 2(1P34.2) WILD-TYPE 28 149 148

Figure S15.  Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1p22.3' versus 'CN_CNMF'

P value = 2.31e-11 (Chi-square test), Q value = 1.8e-08

Table S16.  Gene #3: 'amp_1p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 3(1P22.3) MUTATED 31 7 48 1 5
AMP PEAK 3(1P22.3) WILD-TYPE 274 41 106 11 0

Figure S16.  Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1p22.3' versus 'MRNASEQ_CNMF'

P value = 3.41e-06 (Fisher's exact test), Q value = 0.002

Table S17.  Gene #3: 'amp_1p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 3(1P22.3) MUTATED 55 27 8
AMP PEAK 3(1P22.3) WILD-TYPE 169 123 137

Figure S17.  Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1p22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.97e-06 (Fisher's exact test), Q value = 0.0018

Table S18.  Gene #3: 'amp_1p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 3(1P22.3) MUTATED 8 24 58
AMP PEAK 3(1P22.3) WILD-TYPE 139 108 182

Figure S18.  Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1p22.3' versus 'MIRSEQ_CNMF'

P value = 4.79e-07 (Fisher's exact test), Q value = 3e-04

Table S19.  Gene #3: 'amp_1p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 3(1P22.3) MUTATED 47 8 33
AMP PEAK 3(1P22.3) WILD-TYPE 158 151 108

Figure S19.  Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1p22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000465 (Fisher's exact test), Q value = 0.2

Table S20.  Gene #3: 'amp_1p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 3(1P22.3) MUTATED 1 22 65
AMP PEAK 3(1P22.3) WILD-TYPE 7 194 216

Figure S20.  Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000128 (Fisher's exact test), Q value = 0.063

Table S21.  Gene #3: 'amp_1p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 3(1P22.3) MUTATED 5 50 13
AMP PEAK 3(1P22.3) WILD-TYPE 25 148 141

Figure S21.  Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q21.3' versus 'CN_CNMF'

P value = 1.15e-13 (Chi-square test), Q value = 1e-10

Table S22.  Gene #4: 'amp_1q21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 4(1Q21.3) MUTATED 91 29 99 9 5
AMP PEAK 4(1Q21.3) WILD-TYPE 214 19 55 3 0

Figure S22.  Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 2.56e-06 (Fisher's exact test), Q value = 0.0015

Table S23.  Gene #4: 'amp_1q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 4(1Q21.3) MUTATED 123 67 41
AMP PEAK 4(1Q21.3) WILD-TYPE 101 83 104

Figure S23.  Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0063

Table S24.  Gene #4: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 4(1Q21.3) MUTATED 42 62 127
AMP PEAK 4(1Q21.3) WILD-TYPE 105 70 113

Figure S24.  Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 5.86e-06 (Fisher's exact test), Q value = 0.0034

Table S25.  Gene #4: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 4(1Q21.3) MUTATED 108 46 72
AMP PEAK 4(1Q21.3) WILD-TYPE 97 113 69

Figure S25.  Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000222 (Fisher's exact test), Q value = 0.1

Table S26.  Gene #4: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 4(1Q21.3) MUTATED 6 76 144
AMP PEAK 4(1Q21.3) WILD-TYPE 2 140 137

Figure S26.  Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000133 (Fisher's exact test), Q value = 0.065

Table S27.  Gene #4: 'amp_1q21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 4(1Q21.3) MUTATED 11 109 51
AMP PEAK 4(1Q21.3) WILD-TYPE 19 89 103

Figure S27.  Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q22' versus 'CN_CNMF'

P value = 1.06e-16 (Chi-square test), Q value = 1e-13

Table S28.  Gene #5: 'amp_1q22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 5(1Q22) MUTATED 94 30 109 9 5
AMP PEAK 5(1Q22) WILD-TYPE 211 18 45 3 0

Figure S28.  Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q22' versus 'METHLYATION_CNMF'

P value = 0.000294 (Fisher's exact test), Q value = 0.13

Table S29.  Gene #5: 'amp_1q22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 5(1Q22) MUTATED 89 39 60
AMP PEAK 5(1Q22) WILD-TYPE 63 55 104

Figure S29.  Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q22' versus 'MRNASEQ_CNMF'

P value = 7.72e-07 (Fisher's exact test), Q value = 0.00048

Table S30.  Gene #5: 'amp_1q22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 5(1Q22) MUTATED 132 68 45
AMP PEAK 5(1Q22) WILD-TYPE 92 82 100

Figure S30.  Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.41e-06 (Fisher's exact test), Q value = 0.0037

Table S31.  Gene #5: 'amp_1q22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 5(1Q22) MUTATED 46 63 136
AMP PEAK 5(1Q22) WILD-TYPE 101 69 104

Figure S31.  Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q22' versus 'MIRSEQ_CNMF'

P value = 1.27e-05 (Fisher's exact test), Q value = 0.0072

Table S32.  Gene #5: 'amp_1q22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 5(1Q22) MUTATED 115 51 73
AMP PEAK 5(1Q22) WILD-TYPE 90 108 68

Figure S32.  Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000394 (Fisher's exact test), Q value = 0.18

Table S33.  Gene #5: 'amp_1q22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 5(1Q22) MUTATED 6 82 151
AMP PEAK 5(1Q22) WILD-TYPE 2 134 130

Figure S33.  Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.43e-05 (Fisher's exact test), Q value = 0.038

Table S34.  Gene #5: 'amp_1q22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 5(1Q22) MUTATED 11 116 56
AMP PEAK 5(1Q22) WILD-TYPE 19 82 98

Figure S34.  Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q44' versus 'CN_CNMF'

P value = 4.63e-07 (Chi-square test), Q value = 0.00029

Table S35.  Gene #6: 'amp_1q44' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 6(1Q44) MUTATED 95 27 77 9 5
AMP PEAK 6(1Q44) WILD-TYPE 210 21 77 3 0

Figure S35.  Get High-res Image Gene #6: 'amp_1q44' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2p24.3' versus 'CN_CNMF'

P value = 1.42e-28 (Chi-square test), Q value = 1.6e-25

Table S36.  Gene #7: 'amp_2p24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 7(2P24.3) MUTATED 15 29 68 3 2
AMP PEAK 7(2P24.3) WILD-TYPE 290 19 86 9 3

Figure S36.  Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2p24.3' versus 'METHLYATION_CNMF'

P value = 4.14e-08 (Fisher's exact test), Q value = 2.8e-05

Table S37.  Gene #7: 'amp_2p24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 7(2P24.3) MUTATED 58 15 19
AMP PEAK 7(2P24.3) WILD-TYPE 94 79 145

Figure S37.  Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2p24.3' versus 'MRNASEQ_CNMF'

P value = 1.23e-09 (Fisher's exact test), Q value = 9.1e-07

Table S38.  Gene #7: 'amp_2p24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 7(2P24.3) MUTATED 80 21 15
AMP PEAK 7(2P24.3) WILD-TYPE 144 129 130

Figure S38.  Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2p24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.04e-09 (Fisher's exact test), Q value = 7.7e-07

Table S39.  Gene #7: 'amp_2p24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 7(2P24.3) MUTATED 17 15 84
AMP PEAK 7(2P24.3) WILD-TYPE 130 117 156

Figure S39.  Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_2p24.3' versus 'MIRSEQ_CNMF'

P value = 6.48e-07 (Fisher's exact test), Q value = 0.00041

Table S40.  Gene #7: 'amp_2p24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 7(2P24.3) MUTATED 70 20 22
AMP PEAK 7(2P24.3) WILD-TYPE 135 139 119

Figure S40.  Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_2p24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.2e-05 (Fisher's exact test), Q value = 0.036

Table S41.  Gene #7: 'amp_2p24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 7(2P24.3) MUTATED 1 29 82
AMP PEAK 7(2P24.3) WILD-TYPE 7 187 199

Figure S41.  Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_2p24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.09e-05 (Fisher's exact test), Q value = 0.012

Table S42.  Gene #7: 'amp_2p24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 7(2P24.3) MUTATED 5 63 18
AMP PEAK 7(2P24.3) WILD-TYPE 25 135 136

Figure S42.  Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_2q13' versus 'CN_CNMF'

P value = 1.86e-37 (Chi-square test), Q value = 2.1e-34

Table S43.  Gene #8: 'amp_2q13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 8(2Q13) MUTATED 7 23 82 1 1
AMP PEAK 8(2Q13) WILD-TYPE 298 25 72 11 4

Figure S43.  Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2q13' versus 'METHLYATION_CNMF'

P value = 8.14e-14 (Fisher's exact test), Q value = 7.3e-11

Table S44.  Gene #8: 'amp_2q13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 8(2Q13) MUTATED 63 18 10
AMP PEAK 8(2Q13) WILD-TYPE 89 76 154

Figure S44.  Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2q13' versus 'MRNASEQ_CNMF'

P value = 1.08e-19 (Fisher's exact test), Q value = 1.1e-16

Table S45.  Gene #8: 'amp_2q13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 8(2Q13) MUTATED 91 13 8
AMP PEAK 8(2Q13) WILD-TYPE 133 137 137

Figure S45.  Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2q13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.8e-19 (Fisher's exact test), Q value = 2.8e-16

Table S46.  Gene #8: 'amp_2q13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 8(2Q13) MUTATED 9 9 94
AMP PEAK 8(2Q13) WILD-TYPE 138 123 146

Figure S46.  Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_2q13' versus 'MIRSEQ_CNMF'

P value = 6.59e-19 (Fisher's exact test), Q value = 6.6e-16

Table S47.  Gene #8: 'amp_2q13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 8(2Q13) MUTATED 86 10 14
AMP PEAK 8(2Q13) WILD-TYPE 119 149 127

Figure S47.  Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_2q13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.41e-12 (Fisher's exact test), Q value = 2.8e-09

Table S48.  Gene #8: 'amp_2q13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 8(2Q13) MUTATED 0 17 93
AMP PEAK 8(2Q13) WILD-TYPE 8 199 188

Figure S48.  Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_2q13' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.41e-08 (Fisher's exact test), Q value = 4.3e-05

Table S49.  Gene #8: 'amp_2q13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
AMP PEAK 8(2Q13) MUTATED 57 7 23
AMP PEAK 8(2Q13) WILD-TYPE 118 110 67

Figure S49.  Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_2q13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.51e-12 (Fisher's exact test), Q value = 2.1e-09

Table S50.  Gene #8: 'amp_2q13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 8(2Q13) MUTATED 2 74 11
AMP PEAK 8(2Q13) WILD-TYPE 28 124 143

Figure S50.  Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3p25.1' versus 'CN_CNMF'

P value = 5.06e-29 (Chi-square test), Q value = 5.6e-26

Table S51.  Gene #9: 'amp_3p25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 9(3P25.1) MUTATED 4 6 56 9 2
AMP PEAK 9(3P25.1) WILD-TYPE 301 42 98 3 3

Figure S51.  Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3p25.1' versus 'METHLYATION_CNMF'

P value = 3.72e-06 (Fisher's exact test), Q value = 0.0022

Table S52.  Gene #9: 'amp_3p25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 9(3P25.1) MUTATED 38 16 9
AMP PEAK 9(3P25.1) WILD-TYPE 114 78 155

Figure S52.  Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3p25.1' versus 'MRNASEQ_CNMF'

P value = 3.88e-13 (Fisher's exact test), Q value = 3.4e-10

Table S53.  Gene #9: 'amp_3p25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 9(3P25.1) MUTATED 62 4 10
AMP PEAK 9(3P25.1) WILD-TYPE 162 146 135

Figure S53.  Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3p25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.02e-13 (Fisher's exact test), Q value = 1.8e-10

Table S54.  Gene #9: 'amp_3p25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 9(3P25.1) MUTATED 10 2 64
AMP PEAK 9(3P25.1) WILD-TYPE 137 130 176

Figure S54.  Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3p25.1' versus 'MIRSEQ_CNMF'

P value = 1.75e-08 (Fisher's exact test), Q value = 1.2e-05

Table S55.  Gene #9: 'amp_3p25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 9(3P25.1) MUTATED 52 11 8
AMP PEAK 9(3P25.1) WILD-TYPE 153 148 133

Figure S55.  Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3p25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000156 (Fisher's exact test), Q value = 0.075

Table S56.  Gene #9: 'amp_3p25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 9(3P25.1) MUTATED 1 15 55
AMP PEAK 9(3P25.1) WILD-TYPE 7 201 226

Figure S56.  Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3p25.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.6e-05 (Fisher's exact test), Q value = 0.034

Table S57.  Gene #9: 'amp_3p25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 9(3P25.1) MUTATED 3 45 10
AMP PEAK 9(3P25.1) WILD-TYPE 27 153 144

Figure S57.  Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3p14.1' versus 'CN_CNMF'

P value = 1.53e-23 (Chi-square test), Q value = 1.6e-20

Table S58.  Gene #10: 'amp_3p14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 10(3P14.1) MUTATED 4 6 40 9 2
AMP PEAK 10(3P14.1) WILD-TYPE 301 42 114 3 3

Figure S58.  Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3p14.1' versus 'MRNASEQ_CNMF'

P value = 1.69e-08 (Fisher's exact test), Q value = 1.2e-05

Table S59.  Gene #10: 'amp_3p14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 10(3P14.1) MUTATED 46 3 11
AMP PEAK 10(3P14.1) WILD-TYPE 178 147 134

Figure S59.  Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3p14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.38e-08 (Fisher's exact test), Q value = 9.8e-06

Table S60.  Gene #10: 'amp_3p14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 10(3P14.1) MUTATED 10 2 48
AMP PEAK 10(3P14.1) WILD-TYPE 137 130 192

Figure S60.  Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3p14.1' versus 'MIRSEQ_CNMF'

P value = 2.81e-05 (Fisher's exact test), Q value = 0.015

Table S61.  Gene #10: 'amp_3p14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 10(3P14.1) MUTATED 40 10 8
AMP PEAK 10(3P14.1) WILD-TYPE 165 149 133

Figure S61.  Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3p14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000445 (Fisher's exact test), Q value = 0.2

Table S62.  Gene #10: 'amp_3p14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 10(3P14.1) MUTATED 2 12 44
AMP PEAK 10(3P14.1) WILD-TYPE 6 204 237

Figure S62.  Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MRNA_CNMF'

P value = 5.45e-05 (Fisher's exact test), Q value = 0.028

Table S63.  Gene #11: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
AMP PEAK 11(3Q26.2) MUTATED 1 11 1 0
AMP PEAK 11(3Q26.2) WILD-TYPE 13 6 11 10

Figure S63.  Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.2' versus 'MRNA_CHIERARCHICAL'

P value = 6.42e-05 (Fisher's exact test), Q value = 0.033

Table S64.  Gene #11: 'amp_3q26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
AMP PEAK 11(3Q26.2) MUTATED 2 1 10
AMP PEAK 11(3Q26.2) WILD-TYPE 17 18 5

Figure S64.  Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_3q26.2' versus 'CN_CNMF'

P value = 1.92e-68 (Chi-square test), Q value = 2.2e-65

Table S65.  Gene #11: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 11(3Q26.2) MUTATED 12 12 128 11 4
AMP PEAK 11(3Q26.2) WILD-TYPE 293 36 26 1 1

Figure S65.  Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 7.17e-19 (Fisher's exact test), Q value = 7.2e-16

Table S66.  Gene #11: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 11(3Q26.2) MUTATED 93 27 22
AMP PEAK 11(3Q26.2) WILD-TYPE 59 67 142

Figure S66.  Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'RPPA_CNMF'

P value = 0.000353 (Chi-square test), Q value = 0.16

Table S67.  Gene #11: 'amp_3q26.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
AMP PEAK 11(3Q26.2) MUTATED 11 15 4 1 1 6
AMP PEAK 11(3Q26.2) WILD-TYPE 30 22 35 11 40 18

Figure S67.  Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CNMF'

P value = 2.82e-34 (Fisher's exact test), Q value = 3.2e-31

Table S68.  Gene #11: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 11(3Q26.2) MUTATED 134 9 22
AMP PEAK 11(3Q26.2) WILD-TYPE 90 141 123

Figure S68.  Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.25e-33 (Fisher's exact test), Q value = 3.6e-30

Table S69.  Gene #11: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 11(3Q26.2) MUTATED 23 5 137
AMP PEAK 11(3Q26.2) WILD-TYPE 124 127 103

Figure S69.  Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_CNMF'

P value = 1.32e-27 (Fisher's exact test), Q value = 1.4e-24

Table S70.  Gene #11: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 11(3Q26.2) MUTATED 121 23 15
AMP PEAK 11(3Q26.2) WILD-TYPE 84 136 126

Figure S70.  Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.28e-12 (Fisher's exact test), Q value = 1.1e-09

Table S71.  Gene #11: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 11(3Q26.2) MUTATED 5 32 122
AMP PEAK 11(3Q26.2) WILD-TYPE 3 184 159

Figure S71.  Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.31e-07 (Fisher's exact test), Q value = 8.7e-05

Table S72.  Gene #11: 'amp_3q26.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
AMP PEAK 11(3Q26.2) MUTATED 86 21 28
AMP PEAK 11(3Q26.2) WILD-TYPE 89 96 62

Figure S72.  Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.21e-11 (Fisher's exact test), Q value = 4.1e-08

Table S73.  Gene #11: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 11(3Q26.2) MUTATED 8 101 26
AMP PEAK 11(3Q26.2) WILD-TYPE 22 97 128

Figure S73.  Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.2' versus 'MRNA_CNMF'

P value = 0.000341 (Fisher's exact test), Q value = 0.15

Table S74.  Gene #12: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
AMP PEAK 12(3Q26.2) MUTATED 1 10 1 0
AMP PEAK 12(3Q26.2) WILD-TYPE 13 7 11 10

Figure S74.  Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.000312 (Fisher's exact test), Q value = 0.14

Table S75.  Gene #12: 'amp_3q26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
AMP PEAK 12(3Q26.2) MUTATED 2 1 9
AMP PEAK 12(3Q26.2) WILD-TYPE 17 18 6

Figure S75.  Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_3q26.2' versus 'CN_CNMF'

P value = 2.67e-67 (Chi-square test), Q value = 3.1e-64

Table S76.  Gene #12: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 12(3Q26.2) MUTATED 8 11 122 11 4
AMP PEAK 12(3Q26.2) WILD-TYPE 297 37 32 1 1

Figure S76.  Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 4.05e-20 (Fisher's exact test), Q value = 4.1e-17

Table S77.  Gene #12: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 12(3Q26.2) MUTATED 91 23 19
AMP PEAK 12(3Q26.2) WILD-TYPE 61 71 145

Figure S77.  Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CNMF'

P value = 1.47e-32 (Fisher's exact test), Q value = 1.6e-29

Table S78.  Gene #12: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 12(3Q26.2) MUTATED 127 9 18
AMP PEAK 12(3Q26.2) WILD-TYPE 97 141 127

Figure S78.  Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.03e-33 (Fisher's exact test), Q value = 3.4e-30

Table S79.  Gene #12: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 12(3Q26.2) MUTATED 19 4 131
AMP PEAK 12(3Q26.2) WILD-TYPE 128 128 109

Figure S79.  Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_CNMF'

P value = 4.96e-25 (Fisher's exact test), Q value = 5.4e-22

Table S80.  Gene #12: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 12(3Q26.2) MUTATED 113 19 16
AMP PEAK 12(3Q26.2) WILD-TYPE 92 140 125

Figure S80.  Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.12e-15 (Fisher's exact test), Q value = 1e-12

Table S81.  Gene #12: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 12(3Q26.2) MUTATED 5 24 119
AMP PEAK 12(3Q26.2) WILD-TYPE 3 192 162

Figure S81.  Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.94e-08 (Fisher's exact test), Q value = 1.3e-05

Table S82.  Gene #12: 'amp_3q26.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
AMP PEAK 12(3Q26.2) MUTATED 82 17 26
AMP PEAK 12(3Q26.2) WILD-TYPE 93 100 64

Figure S82.  Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.19e-13 (Fisher's exact test), Q value = 1.1e-10

Table S83.  Gene #12: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 12(3Q26.2) MUTATED 6 99 20
AMP PEAK 12(3Q26.2) WILD-TYPE 24 99 134

Figure S83.  Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4p16.3' versus 'CN_CNMF'

P value = 2.26e-24 (Chi-square test), Q value = 2.4e-21

Table S84.  Gene #13: 'amp_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 13(4P16.3) MUTATED 2 1 49 0 0
AMP PEAK 13(4P16.3) WILD-TYPE 303 47 105 12 5

Figure S84.  Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_4p16.3' versus 'METHLYATION_CNMF'

P value = 0.000356 (Fisher's exact test), Q value = 0.16

Table S85.  Gene #13: 'amp_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 13(4P16.3) MUTATED 25 12 6
AMP PEAK 13(4P16.3) WILD-TYPE 127 82 158

Figure S85.  Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_4p16.3' versus 'MRNASEQ_CNMF'

P value = 7.78e-15 (Fisher's exact test), Q value = 7.2e-12

Table S86.  Gene #13: 'amp_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 13(4P16.3) MUTATED 48 1 2
AMP PEAK 13(4P16.3) WILD-TYPE 176 149 143

Figure S86.  Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.62e-12 (Fisher's exact test), Q value = 3e-09

Table S87.  Gene #13: 'amp_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 13(4P16.3) MUTATED 3 1 47
AMP PEAK 13(4P16.3) WILD-TYPE 144 131 193

Figure S87.  Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_4p16.3' versus 'MIRSEQ_CNMF'

P value = 2.25e-10 (Fisher's exact test), Q value = 1.7e-07

Table S88.  Gene #13: 'amp_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 13(4P16.3) MUTATED 41 4 3
AMP PEAK 13(4P16.3) WILD-TYPE 164 155 138

Figure S88.  Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.71e-06 (Fisher's exact test), Q value = 0.001

Table S89.  Gene #13: 'amp_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 13(4P16.3) MUTATED 1 5 42
AMP PEAK 13(4P16.3) WILD-TYPE 7 211 239

Figure S89.  Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.81e-05 (Fisher's exact test), Q value = 0.015

Table S90.  Gene #13: 'amp_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 13(4P16.3) MUTATED 0 34 6
AMP PEAK 13(4P16.3) WILD-TYPE 30 164 148

Figure S90.  Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 5.19e-35 (Chi-square test), Q value = 5.9e-32

Table S91.  Gene #14: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 14(5P15.33) MUTATED 4 5 73 0 1
AMP PEAK 14(5P15.33) WILD-TYPE 301 43 81 12 4

Figure S91.  Get High-res Image Gene #14: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 9.49e-12 (Fisher's exact test), Q value = 7.7e-09

Table S92.  Gene #14: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 14(5P15.33) MUTATED 51 12 7
AMP PEAK 14(5P15.33) WILD-TYPE 101 82 157

Figure S92.  Get High-res Image Gene #14: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 5.33e-20 (Fisher's exact test), Q value = 5.4e-17

Table S93.  Gene #14: 'amp_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 14(5P15.33) MUTATED 73 6 3
AMP PEAK 14(5P15.33) WILD-TYPE 151 144 142

Figure S93.  Get High-res Image Gene #14: 'amp_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.3e-16 (Fisher's exact test), Q value = 2.2e-13

Table S94.  Gene #14: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 14(5P15.33) MUTATED 5 5 72
AMP PEAK 14(5P15.33) WILD-TYPE 142 127 168

Figure S94.  Get High-res Image Gene #14: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 4.8e-15 (Fisher's exact test), Q value = 4.4e-12

Table S95.  Gene #14: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 14(5P15.33) MUTATED 65 5 11
AMP PEAK 14(5P15.33) WILD-TYPE 140 154 130

Figure S95.  Get High-res Image Gene #14: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.65e-10 (Fisher's exact test), Q value = 2.8e-07

Table S96.  Gene #14: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 14(5P15.33) MUTATED 3 10 68
AMP PEAK 14(5P15.33) WILD-TYPE 5 206 213

Figure S96.  Get High-res Image Gene #14: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.65e-07 (Fisher's exact test), Q value = 0.00054

Table S97.  Gene #14: 'amp_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
AMP PEAK 14(5P15.33) MUTATED 49 6 13
AMP PEAK 14(5P15.33) WILD-TYPE 126 111 77

Figure S97.  Get High-res Image Gene #14: 'amp_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.94e-09 (Fisher's exact test), Q value = 7.1e-06

Table S98.  Gene #14: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 14(5P15.33) MUTATED 6 55 7
AMP PEAK 14(5P15.33) WILD-TYPE 24 143 147

Figure S98.  Get High-res Image Gene #14: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5q35.3' versus 'CN_CNMF'

P value = 5.78e-20 (Chi-square test), Q value = 5.9e-17

Table S99.  Gene #15: 'amp_5q35.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 15(5Q35.3) MUTATED 2 5 46 0 1
AMP PEAK 15(5Q35.3) WILD-TYPE 303 43 108 12 4

Figure S99.  Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5q35.3' versus 'METHLYATION_CNMF'

P value = 5.67e-05 (Fisher's exact test), Q value = 0.029

Table S100.  Gene #15: 'amp_5q35.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 15(5Q35.3) MUTATED 28 13 6
AMP PEAK 15(5Q35.3) WILD-TYPE 124 81 158

Figure S100.  Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_5q35.3' versus 'MRNASEQ_CNMF'

P value = 2.39e-11 (Fisher's exact test), Q value = 1.9e-08

Table S101.  Gene #15: 'amp_5q35.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 15(5Q35.3) MUTATED 47 4 3
AMP PEAK 15(5Q35.3) WILD-TYPE 177 146 142

Figure S101.  Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5q35.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.68e-10 (Fisher's exact test), Q value = 4.3e-07

Table S102.  Gene #15: 'amp_5q35.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 15(5Q35.3) MUTATED 3 4 47
AMP PEAK 15(5Q35.3) WILD-TYPE 144 128 193

Figure S102.  Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5q35.3' versus 'MIRSEQ_CNMF'

P value = 8.11e-08 (Fisher's exact test), Q value = 5.4e-05

Table S103.  Gene #15: 'amp_5q35.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 15(5Q35.3) MUTATED 39 4 7
AMP PEAK 15(5Q35.3) WILD-TYPE 166 155 134

Figure S103.  Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_5q35.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000409 (Fisher's exact test), Q value = 0.18

Table S104.  Gene #15: 'amp_5q35.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 15(5Q35.3) MUTATED 1 9 40
AMP PEAK 15(5Q35.3) WILD-TYPE 7 207 241

Figure S104.  Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5q35.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.08e-05 (Fisher's exact test), Q value = 0.046

Table S105.  Gene #15: 'amp_5q35.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 15(5Q35.3) MUTATED 4 33 5
AMP PEAK 15(5Q35.3) WILD-TYPE 26 165 149

Figure S105.  Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6p24.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.000312 (Fisher's exact test), Q value = 0.14

Table S106.  Gene #16: 'amp_6p24.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
AMP PEAK 16(6P24.2) MUTATED 1 2 9
AMP PEAK 16(6P24.2) WILD-TYPE 18 17 6

Figure S106.  Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_6p24.2' versus 'CN_CNMF'

P value = 1.23e-41 (Chi-square test), Q value = 1.4e-38

Table S107.  Gene #16: 'amp_6p24.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 16(6P24.2) MUTATED 9 5 89 7 1
AMP PEAK 16(6P24.2) WILD-TYPE 296 43 65 5 4

Figure S107.  Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p24.2' versus 'METHLYATION_CNMF'

P value = 1.62e-13 (Fisher's exact test), Q value = 1.4e-10

Table S108.  Gene #16: 'amp_6p24.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 16(6P24.2) MUTATED 64 19 11
AMP PEAK 16(6P24.2) WILD-TYPE 88 75 153

Figure S108.  Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6p24.2' versus 'RPPA_CNMF'

P value = 0.000109 (Chi-square test), Q value = 0.054

Table S109.  Gene #16: 'amp_6p24.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
AMP PEAK 16(6P24.2) MUTATED 5 13 2 1 0 3
AMP PEAK 16(6P24.2) WILD-TYPE 36 24 37 11 41 21

Figure S109.  Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_6p24.2' versus 'MRNASEQ_CNMF'

P value = 2.9e-21 (Fisher's exact test), Q value = 3e-18

Table S110.  Gene #16: 'amp_6p24.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 16(6P24.2) MUTATED 91 5 15
AMP PEAK 16(6P24.2) WILD-TYPE 133 145 130

Figure S110.  Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6p24.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.89e-20 (Fisher's exact test), Q value = 6e-17

Table S111.  Gene #16: 'amp_6p24.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 16(6P24.2) MUTATED 14 4 93
AMP PEAK 16(6P24.2) WILD-TYPE 133 128 147

Figure S111.  Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6p24.2' versus 'MIRSEQ_CNMF'

P value = 4.85e-15 (Fisher's exact test), Q value = 4.5e-12

Table S112.  Gene #16: 'amp_6p24.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 16(6P24.2) MUTATED 80 12 15
AMP PEAK 16(6P24.2) WILD-TYPE 125 147 126

Figure S112.  Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_6p24.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.11e-10 (Fisher's exact test), Q value = 8.7e-08

Table S113.  Gene #16: 'amp_6p24.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 16(6P24.2) MUTATED 3 17 87
AMP PEAK 16(6P24.2) WILD-TYPE 5 199 194

Figure S113.  Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6p24.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.05e-05 (Fisher's exact test), Q value = 0.011

Table S114.  Gene #16: 'amp_6p24.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
AMP PEAK 16(6P24.2) MUTATED 58 12 21
AMP PEAK 16(6P24.2) WILD-TYPE 117 105 69

Figure S114.  Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_6p24.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.43e-09 (Fisher's exact test), Q value = 2.5e-06

Table S115.  Gene #16: 'amp_6p24.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 16(6P24.2) MUTATED 5 72 14
AMP PEAK 16(6P24.2) WILD-TYPE 25 126 140

Figure S115.  Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q25.1' versus 'CN_CNMF'

P value = 1.65e-25 (Chi-square test), Q value = 1.8e-22

Table S116.  Gene #17: 'amp_6q25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 17(6Q25.1) MUTATED 7 8 61 7 1
AMP PEAK 17(6Q25.1) WILD-TYPE 298 40 93 5 4

Figure S116.  Get High-res Image Gene #17: 'amp_6q25.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6q25.1' versus 'METHLYATION_CNMF'

P value = 8.62e-09 (Fisher's exact test), Q value = 6.2e-06

Table S117.  Gene #17: 'amp_6q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 17(6Q25.1) MUTATED 51 11 13
AMP PEAK 17(6Q25.1) WILD-TYPE 101 83 151

Figure S117.  Get High-res Image Gene #17: 'amp_6q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6q25.1' versus 'MRNASEQ_CNMF'

P value = 1.69e-08 (Fisher's exact test), Q value = 1.2e-05

Table S118.  Gene #17: 'amp_6q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 17(6Q25.1) MUTATED 59 7 17
AMP PEAK 17(6Q25.1) WILD-TYPE 165 143 128

Figure S118.  Get High-res Image Gene #17: 'amp_6q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6q25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.59e-07 (Fisher's exact test), Q value = 1e-04

Table S119.  Gene #17: 'amp_6q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 17(6Q25.1) MUTATED 17 6 60
AMP PEAK 17(6Q25.1) WILD-TYPE 130 126 180

Figure S119.  Get High-res Image Gene #17: 'amp_6q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6q25.1' versus 'MIRSEQ_CNMF'

P value = 4.36e-06 (Fisher's exact test), Q value = 0.0026

Table S120.  Gene #17: 'amp_6q25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 17(6Q25.1) MUTATED 54 13 16
AMP PEAK 17(6Q25.1) WILD-TYPE 151 146 125

Figure S120.  Get High-res Image Gene #17: 'amp_6q25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_6q25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.33e-05 (Fisher's exact test), Q value = 0.0075

Table S121.  Gene #17: 'amp_6q25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 17(6Q25.1) MUTATED 2 17 64
AMP PEAK 17(6Q25.1) WILD-TYPE 6 199 217

Figure S121.  Get High-res Image Gene #17: 'amp_6q25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6q25.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000467 (Fisher's exact test), Q value = 0.2

Table S122.  Gene #17: 'amp_6q25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 17(6Q25.1) MUTATED 7 50 15
AMP PEAK 17(6Q25.1) WILD-TYPE 23 148 139

Figure S122.  Get High-res Image Gene #17: 'amp_6q25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q22.1' versus 'CN_CNMF'

P value = 4.35e-21 (Chi-square test), Q value = 4.5e-18

Table S123.  Gene #18: 'amp_7q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 18(7Q22.1) MUTATED 13 26 45 4 2
AMP PEAK 18(7Q22.1) WILD-TYPE 292 22 109 8 3

Figure S123.  Get High-res Image Gene #18: 'amp_7q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q22.1' versus 'MRNASEQ_CNMF'

P value = 1.75e-05 (Fisher's exact test), Q value = 0.0098

Table S124.  Gene #18: 'amp_7q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 18(7Q22.1) MUTATED 58 16 14
AMP PEAK 18(7Q22.1) WILD-TYPE 166 134 131

Figure S124.  Get High-res Image Gene #18: 'amp_7q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000307 (Fisher's exact test), Q value = 0.14

Table S125.  Gene #18: 'amp_7q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 18(7Q22.1) MUTATED 16 14 58
AMP PEAK 18(7Q22.1) WILD-TYPE 131 118 182

Figure S125.  Get High-res Image Gene #18: 'amp_7q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'CN_CNMF'

P value = 9.36e-24 (Chi-square test), Q value = 1e-20

Table S126.  Gene #19: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 19(8P11.21) MUTATED 39 25 78 12 2
AMP PEAK 19(8P11.21) WILD-TYPE 266 23 76 0 3

Figure S126.  Get High-res Image Gene #19: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CNMF'

P value = 1.53e-06 (Fisher's exact test), Q value = 0.00093

Table S127.  Gene #19: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 19(8P11.21) MUTATED 94 29 33
AMP PEAK 19(8P11.21) WILD-TYPE 130 121 112

Figure S127.  Get High-res Image Gene #19: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.02e-07 (Fisher's exact test), Q value = 0.00056

Table S128.  Gene #19: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 19(8P11.21) MUTATED 34 23 99
AMP PEAK 19(8P11.21) WILD-TYPE 113 109 141

Figure S128.  Get High-res Image Gene #19: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_CNMF'

P value = 0.000134 (Fisher's exact test), Q value = 0.065

Table S129.  Gene #19: 'amp_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 19(8P11.21) MUTATED 82 33 35
AMP PEAK 19(8P11.21) WILD-TYPE 123 126 106

Figure S129.  Get High-res Image Gene #19: 'amp_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.19

Table S130.  Gene #19: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 19(8P11.21) MUTATED 3 45 102
AMP PEAK 19(8P11.21) WILD-TYPE 5 171 179

Figure S130.  Get High-res Image Gene #19: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1.12e-37 (Chi-square test), Q value = 1.3e-34

Table S131.  Gene #20: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 20(8Q24.21) MUTATED 46 27 114 12 3
AMP PEAK 20(8Q24.21) WILD-TYPE 259 21 40 0 2

Figure S131.  Get High-res Image Gene #20: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 4.42e-07 (Fisher's exact test), Q value = 0.00028

Table S132.  Gene #20: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 20(8Q24.21) MUTATED 89 38 47
AMP PEAK 20(8Q24.21) WILD-TYPE 63 56 117

Figure S132.  Get High-res Image Gene #20: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'RPPA_CNMF'

P value = 8.75e-05 (Chi-square test), Q value = 0.044

Table S133.  Gene #20: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
AMP PEAK 20(8Q24.21) MUTATED 12 14 8 2 2 14
AMP PEAK 20(8Q24.21) WILD-TYPE 29 23 31 10 39 10

Figure S133.  Get High-res Image Gene #20: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1.55e-16 (Fisher's exact test), Q value = 1.5e-13

Table S134.  Gene #20: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 20(8Q24.21) MUTATED 133 30 38
AMP PEAK 20(8Q24.21) WILD-TYPE 91 120 107

Figure S134.  Get High-res Image Gene #20: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.06e-15 (Fisher's exact test), Q value = 3.8e-12

Table S135.  Gene #20: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 20(8Q24.21) MUTATED 39 25 137
AMP PEAK 20(8Q24.21) WILD-TYPE 108 107 103

Figure S135.  Get High-res Image Gene #20: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 4.75e-12 (Fisher's exact test), Q value = 3.9e-09

Table S136.  Gene #20: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 20(8Q24.21) MUTATED 117 38 38
AMP PEAK 20(8Q24.21) WILD-TYPE 88 121 103

Figure S136.  Get High-res Image Gene #20: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.16e-09 (Fisher's exact test), Q value = 1.6e-06

Table S137.  Gene #20: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 20(8Q24.21) MUTATED 5 50 138
AMP PEAK 20(8Q24.21) WILD-TYPE 3 166 143

Figure S137.  Get High-res Image Gene #20: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.52e-05 (Fisher's exact test), Q value = 0.028

Table S138.  Gene #20: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
AMP PEAK 20(8Q24.21) MUTATED 93 32 36
AMP PEAK 20(8Q24.21) WILD-TYPE 82 85 54

Figure S138.  Get High-res Image Gene #20: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.05e-06 (Fisher's exact test), Q value = 0.0035

Table S139.  Gene #20: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 20(8Q24.21) MUTATED 16 103 42
AMP PEAK 20(8Q24.21) WILD-TYPE 14 95 112

Figure S139.  Get High-res Image Gene #20: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1.31e-37 (Chi-square test), Q value = 1.5e-34

Table S140.  Gene #21: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 21(8Q24.21) MUTATED 49 28 116 12 3
AMP PEAK 21(8Q24.21) WILD-TYPE 256 20 38 0 2

Figure S140.  Get High-res Image Gene #21: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 6.09e-06 (Fisher's exact test), Q value = 0.0035

Table S141.  Gene #21: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 21(8Q24.21) MUTATED 89 37 52
AMP PEAK 21(8Q24.21) WILD-TYPE 63 57 112

Figure S141.  Get High-res Image Gene #21: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'RPPA_CNMF'

P value = 7.26e-07 (Chi-square test), Q value = 0.00046

Table S142.  Gene #21: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
AMP PEAK 21(8Q24.21) MUTATED 12 17 7 2 2 16
AMP PEAK 21(8Q24.21) WILD-TYPE 29 20 32 10 39 8

Figure S142.  Get High-res Image Gene #21: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 7.29e-16 (Fisher's exact test), Q value = 6.8e-13

Table S143.  Gene #21: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 21(8Q24.21) MUTATED 135 33 39
AMP PEAK 21(8Q24.21) WILD-TYPE 89 117 106

Figure S143.  Get High-res Image Gene #21: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.41e-15 (Fisher's exact test), Q value = 3.2e-12

Table S144.  Gene #21: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 21(8Q24.21) MUTATED 41 26 140
AMP PEAK 21(8Q24.21) WILD-TYPE 106 106 100

Figure S144.  Get High-res Image Gene #21: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 3.57e-13 (Fisher's exact test), Q value = 3.1e-10

Table S145.  Gene #21: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 21(8Q24.21) MUTATED 122 40 38
AMP PEAK 21(8Q24.21) WILD-TYPE 83 119 103

Figure S145.  Get High-res Image Gene #21: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.75e-09 (Fisher's exact test), Q value = 7e-06

Table S146.  Gene #21: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 21(8Q24.21) MUTATED 5 54 141
AMP PEAK 21(8Q24.21) WILD-TYPE 3 162 140

Figure S146.  Get High-res Image Gene #21: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.03e-05 (Fisher's exact test), Q value = 0.031

Table S147.  Gene #21: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
AMP PEAK 21(8Q24.21) MUTATED 97 35 36
AMP PEAK 21(8Q24.21) WILD-TYPE 78 82 54

Figure S147.  Get High-res Image Gene #21: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.53e-05 (Fisher's exact test), Q value = 0.014

Table S148.  Gene #21: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 21(8Q24.21) MUTATED 16 106 46
AMP PEAK 21(8Q24.21) WILD-TYPE 14 92 108

Figure S148.  Get High-res Image Gene #21: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9p24.2' versus 'CN_CNMF'

P value = 2.78e-24 (Chi-square test), Q value = 3e-21

Table S149.  Gene #22: 'amp_9p24.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 22(9P24.2) MUTATED 5 3 55 0 0
AMP PEAK 22(9P24.2) WILD-TYPE 300 45 99 12 5

Figure S149.  Get High-res Image Gene #22: 'amp_9p24.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_9p24.2' versus 'METHLYATION_CNMF'

P value = 3.74e-09 (Fisher's exact test), Q value = 2.7e-06

Table S150.  Gene #22: 'amp_9p24.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 22(9P24.2) MUTATED 39 8 5
AMP PEAK 22(9P24.2) WILD-TYPE 113 86 159

Figure S150.  Get High-res Image Gene #22: 'amp_9p24.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_9p24.2' versus 'MRNASEQ_CNMF'

P value = 1.16e-13 (Fisher's exact test), Q value = 1e-10

Table S151.  Gene #22: 'amp_9p24.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 22(9P24.2) MUTATED 55 3 5
AMP PEAK 22(9P24.2) WILD-TYPE 169 147 140

Figure S151.  Get High-res Image Gene #22: 'amp_9p24.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_9p24.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.3e-12 (Fisher's exact test), Q value = 6e-09

Table S152.  Gene #22: 'amp_9p24.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 22(9P24.2) MUTATED 4 4 55
AMP PEAK 22(9P24.2) WILD-TYPE 143 128 185

Figure S152.  Get High-res Image Gene #22: 'amp_9p24.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_9p24.2' versus 'MIRSEQ_CNMF'

P value = 1.42e-12 (Fisher's exact test), Q value = 1.2e-09

Table S153.  Gene #22: 'amp_9p24.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 22(9P24.2) MUTATED 50 2 9
AMP PEAK 22(9P24.2) WILD-TYPE 155 157 132

Figure S153.  Get High-res Image Gene #22: 'amp_9p24.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_9p24.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.05e-07 (Fisher's exact test), Q value = 0.00013

Table S154.  Gene #22: 'amp_9p24.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 22(9P24.2) MUTATED 3 8 50
AMP PEAK 22(9P24.2) WILD-TYPE 5 208 231

Figure S154.  Get High-res Image Gene #22: 'amp_9p24.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_9p24.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000109 (Fisher's exact test), Q value = 0.054

Table S155.  Gene #22: 'amp_9p24.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 22(9P24.2) MUTATED 2 39 8
AMP PEAK 22(9P24.2) WILD-TYPE 28 159 146

Figure S155.  Get High-res Image Gene #22: 'amp_9p24.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9q34.3' versus 'CN_CNMF'

P value = 4.25e-14 (Chi-square test), Q value = 3.8e-11

Table S156.  Gene #23: 'amp_9q34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 23(9Q34.3) MUTATED 3 1 33 0 0
AMP PEAK 23(9Q34.3) WILD-TYPE 302 47 121 12 5

Figure S156.  Get High-res Image Gene #23: 'amp_9q34.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_9q34.3' versus 'METHLYATION_CNMF'

P value = 0.000123 (Fisher's exact test), Q value = 0.06

Table S157.  Gene #23: 'amp_9q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 23(9Q34.3) MUTATED 19 7 2
AMP PEAK 23(9Q34.3) WILD-TYPE 133 87 162

Figure S157.  Get High-res Image Gene #23: 'amp_9q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_9q34.3' versus 'MRNASEQ_CNMF'

P value = 2.89e-08 (Fisher's exact test), Q value = 2e-05

Table S158.  Gene #23: 'amp_9q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 23(9Q34.3) MUTATED 32 3 1
AMP PEAK 23(9Q34.3) WILD-TYPE 192 147 144

Figure S158.  Get High-res Image Gene #23: 'amp_9q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_9q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.71e-07 (Fisher's exact test), Q value = 0.00024

Table S159.  Gene #23: 'amp_9q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 23(9Q34.3) MUTATED 2 2 32
AMP PEAK 23(9Q34.3) WILD-TYPE 145 130 208

Figure S159.  Get High-res Image Gene #23: 'amp_9q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_9q34.3' versus 'MIRSEQ_CNMF'

P value = 0.000136 (Fisher's exact test), Q value = 0.066

Table S160.  Gene #23: 'amp_9q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 23(9Q34.3) MUTATED 24 3 4
AMP PEAK 23(9Q34.3) WILD-TYPE 181 156 137

Figure S160.  Get High-res Image Gene #23: 'amp_9q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_9q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000139 (Fisher's exact test), Q value = 0.067

Table S161.  Gene #23: 'amp_9q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 23(9Q34.3) MUTATED 1 3 27
AMP PEAK 23(9Q34.3) WILD-TYPE 7 213 254

Figure S161.  Get High-res Image Gene #23: 'amp_9q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_10q22.2' versus 'CN_CNMF'

P value = 1.97e-10 (Chi-square test), Q value = 1.5e-07

Table S162.  Gene #24: 'amp_10q22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 24(10Q22.2) MUTATED 47 25 60 6 2
AMP PEAK 24(10Q22.2) WILD-TYPE 258 23 94 6 3

Figure S162.  Get High-res Image Gene #24: 'amp_10q22.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11p11.2' versus 'CN_CNMF'

P value = 8.07e-17 (Chi-square test), Q value = 7.8e-14

Table S163.  Gene #25: 'amp_11p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 25(11P11.2) MUTATED 1 7 40 1 0
AMP PEAK 25(11P11.2) WILD-TYPE 304 41 114 11 5

Figure S163.  Get High-res Image Gene #25: 'amp_11p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11p11.2' versus 'METHLYATION_CNMF'

P value = 2.84e-05 (Fisher's exact test), Q value = 0.015

Table S164.  Gene #25: 'amp_11p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 25(11P11.2) MUTATED 25 12 4
AMP PEAK 25(11P11.2) WILD-TYPE 127 82 160

Figure S164.  Get High-res Image Gene #25: 'amp_11p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11p11.2' versus 'MRNASEQ_CNMF'

P value = 4.66e-08 (Fisher's exact test), Q value = 3.2e-05

Table S165.  Gene #25: 'amp_11p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 25(11P11.2) MUTATED 40 3 6
AMP PEAK 25(11P11.2) WILD-TYPE 184 147 139

Figure S165.  Get High-res Image Gene #25: 'amp_11p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.42e-07 (Fisher's exact test), Q value = 0.00046

Table S166.  Gene #25: 'amp_11p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 25(11P11.2) MUTATED 6 3 40
AMP PEAK 25(11P11.2) WILD-TYPE 141 129 200

Figure S166.  Get High-res Image Gene #25: 'amp_11p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11p11.2' versus 'MIRSEQ_CNMF'

P value = 2.59e-08 (Fisher's exact test), Q value = 1.8e-05

Table S167.  Gene #25: 'amp_11p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 25(11P11.2) MUTATED 38 6 3
AMP PEAK 25(11P11.2) WILD-TYPE 167 153 138

Figure S167.  Get High-res Image Gene #25: 'amp_11p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.07e-05 (Fisher's exact test), Q value = 0.041

Table S168.  Gene #25: 'amp_11p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 25(11P11.2) MUTATED 1 7 39
AMP PEAK 25(11P11.2) WILD-TYPE 7 209 242

Figure S168.  Get High-res Image Gene #25: 'amp_11p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000157 (Fisher's exact test), Q value = 0.075

Table S169.  Gene #25: 'amp_11p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 25(11P11.2) MUTATED 1 31 5
AMP PEAK 25(11P11.2) WILD-TYPE 29 167 149

Figure S169.  Get High-res Image Gene #25: 'amp_11p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q13.2' versus 'CN_CNMF'

P value = 1.59e-20 (Chi-square test), Q value = 1.6e-17

Table S170.  Gene #26: 'amp_11q13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 26(11Q13.2) MUTATED 6 10 54 1 0
AMP PEAK 26(11Q13.2) WILD-TYPE 299 38 100 11 5

Figure S170.  Get High-res Image Gene #26: 'amp_11q13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q13.2' versus 'METHLYATION_CNMF'

P value = 0.000196 (Fisher's exact test), Q value = 0.093

Table S171.  Gene #26: 'amp_11q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 26(11Q13.2) MUTATED 36 12 12
AMP PEAK 26(11Q13.2) WILD-TYPE 116 82 152

Figure S171.  Get High-res Image Gene #26: 'amp_11q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q13.2' versus 'MRNASEQ_CNMF'

P value = 3.88e-07 (Fisher's exact test), Q value = 0.00025

Table S172.  Gene #26: 'amp_11q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 26(11Q13.2) MUTATED 50 6 14
AMP PEAK 26(11Q13.2) WILD-TYPE 174 144 131

Figure S172.  Get High-res Image Gene #26: 'amp_11q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.41e-06 (Fisher's exact test), Q value = 0.0026

Table S173.  Gene #26: 'amp_11q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 26(11Q13.2) MUTATED 15 5 50
AMP PEAK 26(11Q13.2) WILD-TYPE 132 127 190

Figure S173.  Get High-res Image Gene #26: 'amp_11q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.2' versus 'MIRSEQ_CNMF'

P value = 0.000125 (Fisher's exact test), Q value = 0.061

Table S174.  Gene #26: 'amp_11q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 26(11Q13.2) MUTATED 43 15 9
AMP PEAK 26(11Q13.2) WILD-TYPE 162 144 132

Figure S174.  Get High-res Image Gene #26: 'amp_11q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q14.1' versus 'CN_CNMF'

P value = 1.01e-16 (Chi-square test), Q value = 9.7e-14

Table S175.  Gene #27: 'amp_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 27(11Q14.1) MUTATED 4 7 44 1 0
AMP PEAK 27(11Q14.1) WILD-TYPE 301 41 110 11 5

Figure S175.  Get High-res Image Gene #27: 'amp_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q14.1' versus 'MRNASEQ_CNMF'

P value = 4.71e-06 (Fisher's exact test), Q value = 0.0028

Table S176.  Gene #27: 'amp_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 27(11Q14.1) MUTATED 41 6 8
AMP PEAK 27(11Q14.1) WILD-TYPE 183 144 137

Figure S176.  Get High-res Image Gene #27: 'amp_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.88e-05 (Fisher's exact test), Q value = 0.021

Table S177.  Gene #27: 'amp_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 27(11Q14.1) MUTATED 9 5 41
AMP PEAK 27(11Q14.1) WILD-TYPE 138 127 199

Figure S177.  Get High-res Image Gene #27: 'amp_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q14.1' versus 'MIRSEQ_CNMF'

P value = 0.000198 (Fisher's exact test), Q value = 0.094

Table S178.  Gene #27: 'amp_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 27(11Q14.1) MUTATED 37 12 7
AMP PEAK 27(11Q14.1) WILD-TYPE 168 147 134

Figure S178.  Get High-res Image Gene #27: 'amp_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.47e-06 (Fisher's exact test), Q value = 0.0048

Table S179.  Gene #27: 'amp_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 27(11Q14.1) MUTATED 5 12 39
AMP PEAK 27(11Q14.1) WILD-TYPE 3 204 242

Figure S179.  Get High-res Image Gene #27: 'amp_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'CN_CNMF'

P value = 6.67e-17 (Chi-square test), Q value = 6.4e-14

Table S180.  Gene #28: 'amp_12p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 28(12P12.1) MUTATED 14 14 54 2 3
AMP PEAK 28(12P12.1) WILD-TYPE 291 34 100 10 2

Figure S180.  Get High-res Image Gene #28: 'amp_12p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p12.1' versus 'METHLYATION_CNMF'

P value = 9.3e-09 (Fisher's exact test), Q value = 6.7e-06

Table S181.  Gene #28: 'amp_12p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 28(12P12.1) MUTATED 48 13 10
AMP PEAK 28(12P12.1) WILD-TYPE 104 81 154

Figure S181.  Get High-res Image Gene #28: 'amp_12p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CNMF'

P value = 6.46e-09 (Fisher's exact test), Q value = 4.7e-06

Table S182.  Gene #28: 'amp_12p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 28(12P12.1) MUTATED 63 12 11
AMP PEAK 28(12P12.1) WILD-TYPE 161 138 134

Figure S182.  Get High-res Image Gene #28: 'amp_12p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.8e-08 (Fisher's exact test), Q value = 3.9e-05

Table S183.  Gene #28: 'amp_12p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 28(12P12.1) MUTATED 13 9 64
AMP PEAK 28(12P12.1) WILD-TYPE 134 123 176

Figure S183.  Get High-res Image Gene #28: 'amp_12p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_CNMF'

P value = 7.46e-08 (Fisher's exact test), Q value = 5e-05

Table S184.  Gene #28: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 28(12P12.1) MUTATED 59 14 13
AMP PEAK 28(12P12.1) WILD-TYPE 146 145 128

Figure S184.  Get High-res Image Gene #28: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000391 (Fisher's exact test), Q value = 0.17

Table S185.  Gene #28: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 28(12P12.1) MUTATED 0 22 64
AMP PEAK 28(12P12.1) WILD-TYPE 8 194 217

Figure S185.  Get High-res Image Gene #28: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000159 (Fisher's exact test), Q value = 0.076

Table S186.  Gene #28: 'amp_12p12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
AMP PEAK 28(12P12.1) MUTATED 44 8 15
AMP PEAK 28(12P12.1) WILD-TYPE 131 109 75

Figure S186.  Get High-res Image Gene #28: 'amp_12p12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.49e-06 (Fisher's exact test), Q value = 0.0026

Table S187.  Gene #28: 'amp_12p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 28(12P12.1) MUTATED 7 50 10
AMP PEAK 28(12P12.1) WILD-TYPE 23 148 144

Figure S187.  Get High-res Image Gene #28: 'amp_12p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q13.11' versus 'CN_CNMF'

P value = 1.57e-19 (Chi-square test), Q value = 1.6e-16

Table S188.  Gene #29: 'amp_12q13.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 29(12Q13.11) MUTATED 11 15 55 1 3
AMP PEAK 29(12Q13.11) WILD-TYPE 294 33 99 11 2

Figure S188.  Get High-res Image Gene #29: 'amp_12q13.11' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q13.11' versus 'METHLYATION_CNMF'

P value = 1.12e-09 (Fisher's exact test), Q value = 8.3e-07

Table S189.  Gene #29: 'amp_12q13.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 29(12Q13.11) MUTATED 46 16 7
AMP PEAK 29(12Q13.11) WILD-TYPE 106 78 157

Figure S189.  Get High-res Image Gene #29: 'amp_12q13.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q13.11' versus 'MRNASEQ_CNMF'

P value = 8.03e-11 (Fisher's exact test), Q value = 6.3e-08

Table S190.  Gene #29: 'amp_12q13.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 29(12Q13.11) MUTATED 64 9 10
AMP PEAK 29(12Q13.11) WILD-TYPE 160 141 135

Figure S190.  Get High-res Image Gene #29: 'amp_12q13.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q13.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.84e-10 (Fisher's exact test), Q value = 5.9e-07

Table S191.  Gene #29: 'amp_12q13.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 29(12Q13.11) MUTATED 11 7 65
AMP PEAK 29(12Q13.11) WILD-TYPE 136 125 175

Figure S191.  Get High-res Image Gene #29: 'amp_12q13.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q13.11' versus 'MIRSEQ_CNMF'

P value = 1.68e-08 (Fisher's exact test), Q value = 1.2e-05

Table S192.  Gene #29: 'amp_12q13.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 29(12Q13.11) MUTATED 59 13 12
AMP PEAK 29(12Q13.11) WILD-TYPE 146 146 129

Figure S192.  Get High-res Image Gene #29: 'amp_12q13.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q13.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.33e-05 (Fisher's exact test), Q value = 0.047

Table S193.  Gene #29: 'amp_12q13.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 29(12Q13.11) MUTATED 1 19 64
AMP PEAK 29(12Q13.11) WILD-TYPE 7 197 217

Figure S193.  Get High-res Image Gene #29: 'amp_12q13.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q13.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.53e-05 (Fisher's exact test), Q value = 0.014

Table S194.  Gene #29: 'amp_12q13.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
AMP PEAK 29(12Q13.11) MUTATED 43 6 15
AMP PEAK 29(12Q13.11) WILD-TYPE 132 111 75

Figure S194.  Get High-res Image Gene #29: 'amp_12q13.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12q13.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.66e-06 (Fisher's exact test), Q value = 0.0022

Table S195.  Gene #29: 'amp_12q13.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 29(12Q13.11) MUTATED 7 48 9
AMP PEAK 29(12Q13.11) WILD-TYPE 23 150 145

Figure S195.  Get High-res Image Gene #29: 'amp_12q13.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q13.2' versus 'CN_CNMF'

P value = 2.69e-22 (Chi-square test), Q value = 2.8e-19

Table S196.  Gene #30: 'amp_12q13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 30(12Q13.2) MUTATED 14 15 65 1 3
AMP PEAK 30(12Q13.2) WILD-TYPE 291 33 89 11 2

Figure S196.  Get High-res Image Gene #30: 'amp_12q13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q13.2' versus 'METHLYATION_CNMF'

P value = 1.82e-08 (Fisher's exact test), Q value = 1.3e-05

Table S197.  Gene #30: 'amp_12q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 30(12Q13.2) MUTATED 52 15 13
AMP PEAK 30(12Q13.2) WILD-TYPE 100 79 151

Figure S197.  Get High-res Image Gene #30: 'amp_12q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q13.2' versus 'MRNASEQ_CNMF'

P value = 2.75e-12 (Fisher's exact test), Q value = 2.3e-09

Table S198.  Gene #30: 'amp_12q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 30(12Q13.2) MUTATED 73 9 14
AMP PEAK 30(12Q13.2) WILD-TYPE 151 141 131

Figure S198.  Get High-res Image Gene #30: 'amp_12q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.86e-11 (Fisher's exact test), Q value = 3.1e-08

Table S199.  Gene #30: 'amp_12q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 30(12Q13.2) MUTATED 15 7 74
AMP PEAK 30(12Q13.2) WILD-TYPE 132 125 166

Figure S199.  Get High-res Image Gene #30: 'amp_12q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q13.2' versus 'MIRSEQ_CNMF'

P value = 1.1e-09 (Fisher's exact test), Q value = 8.2e-07

Table S200.  Gene #30: 'amp_12q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 30(12Q13.2) MUTATED 66 16 12
AMP PEAK 30(12Q13.2) WILD-TYPE 139 143 129

Figure S200.  Get High-res Image Gene #30: 'amp_12q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.88e-05 (Fisher's exact test), Q value = 0.01

Table S201.  Gene #30: 'amp_12q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 30(12Q13.2) MUTATED 2 21 71
AMP PEAK 30(12Q13.2) WILD-TYPE 6 195 210

Figure S201.  Get High-res Image Gene #30: 'amp_12q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.42e-05 (Fisher's exact test), Q value = 0.008

Table S202.  Gene #30: 'amp_12q13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
AMP PEAK 30(12Q13.2) MUTATED 52 10 13
AMP PEAK 30(12Q13.2) WILD-TYPE 123 107 77

Figure S202.  Get High-res Image Gene #30: 'amp_12q13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.91e-06 (Fisher's exact test), Q value = 0.0045

Table S203.  Gene #30: 'amp_12q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 30(12Q13.2) MUTATED 6 56 13
AMP PEAK 30(12Q13.2) WILD-TYPE 24 142 141

Figure S203.  Get High-res Image Gene #30: 'amp_12q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q34' versus 'CN_CNMF'

P value = 4.69e-23 (Chi-square test), Q value = 5e-20

Table S204.  Gene #31: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 31(13Q34) MUTATED 4 0 50 1 1
AMP PEAK 31(13Q34) WILD-TYPE 301 48 104 11 4

Figure S204.  Get High-res Image Gene #31: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q34' versus 'METHLYATION_CNMF'

P value = 1.87e-08 (Fisher's exact test), Q value = 1.3e-05

Table S205.  Gene #31: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 31(13Q34) MUTATED 36 11 4
AMP PEAK 31(13Q34) WILD-TYPE 116 83 160

Figure S205.  Get High-res Image Gene #31: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q34' versus 'MRNASEQ_CNMF'

P value = 4.29e-13 (Fisher's exact test), Q value = 3.7e-10

Table S206.  Gene #31: 'amp_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 31(13Q34) MUTATED 50 3 3
AMP PEAK 31(13Q34) WILD-TYPE 174 147 142

Figure S206.  Get High-res Image Gene #31: 'amp_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.13e-14 (Fisher's exact test), Q value = 8.1e-11

Table S207.  Gene #31: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 31(13Q34) MUTATED 2 2 52
AMP PEAK 31(13Q34) WILD-TYPE 145 130 188

Figure S207.  Get High-res Image Gene #31: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q34' versus 'MIRSEQ_CNMF'

P value = 4.77e-13 (Fisher's exact test), Q value = 4.1e-10

Table S208.  Gene #31: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 31(13Q34) MUTATED 48 4 3
AMP PEAK 31(13Q34) WILD-TYPE 157 155 138

Figure S208.  Get High-res Image Gene #31: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.83e-07 (Fisher's exact test), Q value = 0.00012

Table S209.  Gene #31: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 31(13Q34) MUTATED 0 6 49
AMP PEAK 31(13Q34) WILD-TYPE 8 210 232

Figure S209.  Get High-res Image Gene #31: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_13q34' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.78e-05 (Fisher's exact test), Q value = 0.015

Table S210.  Gene #31: 'amp_13q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
AMP PEAK 31(13Q34) MUTATED 34 3 12
AMP PEAK 31(13Q34) WILD-TYPE 141 114 78

Figure S210.  Get High-res Image Gene #31: 'amp_13q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_13q34' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.18e-08 (Fisher's exact test), Q value = 5.5e-05

Table S211.  Gene #31: 'amp_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 31(13Q34) MUTATED 2 43 4
AMP PEAK 31(13Q34) WILD-TYPE 28 155 150

Figure S211.  Get High-res Image Gene #31: 'amp_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_14q24.3' versus 'CN_CNMF'

P value = 3.66e-19 (Chi-square test), Q value = 3.7e-16

Table S212.  Gene #32: 'amp_14q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 32(14Q24.3) MUTATED 4 7 49 2 0
AMP PEAK 32(14Q24.3) WILD-TYPE 301 41 105 10 5

Figure S212.  Get High-res Image Gene #32: 'amp_14q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_14q24.3' versus 'METHLYATION_CNMF'

P value = 3.14e-05 (Fisher's exact test), Q value = 0.017

Table S213.  Gene #32: 'amp_14q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 32(14Q24.3) MUTATED 33 11 8
AMP PEAK 32(14Q24.3) WILD-TYPE 119 83 156

Figure S213.  Get High-res Image Gene #32: 'amp_14q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_14q24.3' versus 'MRNASEQ_CNMF'

P value = 7.41e-14 (Fisher's exact test), Q value = 6.6e-11

Table S214.  Gene #32: 'amp_14q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 32(14Q24.3) MUTATED 53 1 7
AMP PEAK 32(14Q24.3) WILD-TYPE 171 149 138

Figure S214.  Get High-res Image Gene #32: 'amp_14q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_14q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.16e-13 (Fisher's exact test), Q value = 1e-10

Table S215.  Gene #32: 'amp_14q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 32(14Q24.3) MUTATED 7 0 54
AMP PEAK 32(14Q24.3) WILD-TYPE 140 132 186

Figure S215.  Get High-res Image Gene #32: 'amp_14q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_14q24.3' versus 'MIRSEQ_CNMF'

P value = 1.61e-07 (Fisher's exact test), Q value = 0.00011

Table S216.  Gene #32: 'amp_14q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 32(14Q24.3) MUTATED 44 9 6
AMP PEAK 32(14Q24.3) WILD-TYPE 161 150 135

Figure S216.  Get High-res Image Gene #32: 'amp_14q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_14q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.52e-05 (Fisher's exact test), Q value = 0.019

Table S217.  Gene #32: 'amp_14q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 32(14Q24.3) MUTATED 1 10 48
AMP PEAK 32(14Q24.3) WILD-TYPE 7 206 233

Figure S217.  Get High-res Image Gene #32: 'amp_14q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_14q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000289 (Fisher's exact test), Q value = 0.13

Table S218.  Gene #32: 'amp_14q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 32(14Q24.3) MUTATED 1 39 10
AMP PEAK 32(14Q24.3) WILD-TYPE 29 159 144

Figure S218.  Get High-res Image Gene #32: 'amp_14q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_15q26.3' versus 'CN_CNMF'

P value = 5.09e-10 (Chi-square test), Q value = 3.8e-07

Table S219.  Gene #33: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 33(15Q26.3) MUTATED 4 4 29 0 0
AMP PEAK 33(15Q26.3) WILD-TYPE 301 44 125 12 5

Figure S219.  Get High-res Image Gene #33: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CNMF'

P value = 1.15e-06 (Fisher's exact test), Q value = 7e-04

Table S220.  Gene #33: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 33(15Q26.3) MUTATED 31 4 2
AMP PEAK 33(15Q26.3) WILD-TYPE 193 146 143

Figure S220.  Get High-res Image Gene #33: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.36e-06 (Fisher's exact test), Q value = 0.00083

Table S221.  Gene #33: 'amp_15q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 33(15Q26.3) MUTATED 2 3 32
AMP PEAK 33(15Q26.3) WILD-TYPE 145 129 208

Figure S221.  Get High-res Image Gene #33: 'amp_15q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'MIRSEQ_CNMF'

P value = 5.22e-05 (Fisher's exact test), Q value = 0.027

Table S222.  Gene #33: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 33(15Q26.3) MUTATED 26 2 8
AMP PEAK 33(15Q26.3) WILD-TYPE 179 157 133

Figure S222.  Get High-res Image Gene #33: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_15q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000206 (Fisher's exact test), Q value = 0.097

Table S223.  Gene #33: 'amp_15q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 33(15Q26.3) MUTATED 2 5 29
AMP PEAK 33(15Q26.3) WILD-TYPE 6 211 252

Figure S223.  Get High-res Image Gene #33: 'amp_15q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'CN_CNMF'

P value = 5.11e-24 (Chi-square test), Q value = 5.5e-21

Table S224.  Gene #34: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 34(16P11.2) MUTATED 2 6 54 1 0
AMP PEAK 34(16P11.2) WILD-TYPE 303 42 100 11 5

Figure S224.  Get High-res Image Gene #34: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_16p11.2' versus 'METHLYATION_CNMF'

P value = 8.14e-06 (Fisher's exact test), Q value = 0.0047

Table S225.  Gene #34: 'amp_16p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 34(16P11.2) MUTATED 35 11 8
AMP PEAK 34(16P11.2) WILD-TYPE 117 83 156

Figure S225.  Get High-res Image Gene #34: 'amp_16p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_16p11.2' versus 'MRNASEQ_CNMF'

P value = 1.03e-12 (Fisher's exact test), Q value = 8.8e-10

Table S226.  Gene #34: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 34(16P11.2) MUTATED 54 6 3
AMP PEAK 34(16P11.2) WILD-TYPE 170 144 142

Figure S226.  Get High-res Image Gene #34: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_16p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.3e-12 (Fisher's exact test), Q value = 6e-09

Table S227.  Gene #34: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 34(16P11.2) MUTATED 4 4 55
AMP PEAK 34(16P11.2) WILD-TYPE 143 128 185

Figure S227.  Get High-res Image Gene #34: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'MIRSEQ_CNMF'

P value = 3.43e-11 (Fisher's exact test), Q value = 2.7e-08

Table S228.  Gene #34: 'amp_16p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 34(16P11.2) MUTATED 48 5 5
AMP PEAK 34(16P11.2) WILD-TYPE 157 154 136

Figure S228.  Get High-res Image Gene #34: 'amp_16p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_16p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.072

Table S229.  Gene #34: 'amp_16p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 34(16P11.2) MUTATED 2 11 45
AMP PEAK 34(16P11.2) WILD-TYPE 6 205 236

Figure S229.  Get High-res Image Gene #34: 'amp_16p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.23e-05 (Fisher's exact test), Q value = 0.022

Table S230.  Gene #34: 'amp_16p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 34(16P11.2) MUTATED 2 39 7
AMP PEAK 34(16P11.2) WILD-TYPE 28 159 147

Figure S230.  Get High-res Image Gene #34: 'amp_16p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q11.2' versus 'CN_CNMF'

P value = 2.02e-28 (Chi-square test), Q value = 2.2e-25

Table S231.  Gene #35: 'amp_17q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 35(17Q11.2) MUTATED 4 1 60 1 1
AMP PEAK 35(17Q11.2) WILD-TYPE 301 47 94 11 4

Figure S231.  Get High-res Image Gene #35: 'amp_17q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q11.2' versus 'METHLYATION_CNMF'

P value = 1.11e-13 (Fisher's exact test), Q value = 9.8e-11

Table S232.  Gene #35: 'amp_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 35(17Q11.2) MUTATED 47 9 3
AMP PEAK 35(17Q11.2) WILD-TYPE 105 85 161

Figure S232.  Get High-res Image Gene #35: 'amp_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q11.2' versus 'MRNASEQ_CNMF'

P value = 8.42e-16 (Fisher's exact test), Q value = 7.9e-13

Table S233.  Gene #35: 'amp_17q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 35(17Q11.2) MUTATED 59 3 4
AMP PEAK 35(17Q11.2) WILD-TYPE 165 147 141

Figure S233.  Get High-res Image Gene #35: 'amp_17q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.55e-17 (Fisher's exact test), Q value = 1.5e-14

Table S234.  Gene #35: 'amp_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 35(17Q11.2) MUTATED 3 1 62
AMP PEAK 35(17Q11.2) WILD-TYPE 144 131 178

Figure S234.  Get High-res Image Gene #35: 'amp_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q11.2' versus 'MIRSEQ_CNMF'

P value = 1.98e-14 (Fisher's exact test), Q value = 1.8e-11

Table S235.  Gene #35: 'amp_17q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 35(17Q11.2) MUTATED 54 2 8
AMP PEAK 35(17Q11.2) WILD-TYPE 151 157 133

Figure S235.  Get High-res Image Gene #35: 'amp_17q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.34e-12 (Fisher's exact test), Q value = 6.8e-09

Table S236.  Gene #35: 'amp_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 35(17Q11.2) MUTATED 0 4 60
AMP PEAK 35(17Q11.2) WILD-TYPE 8 212 221

Figure S236.  Get High-res Image Gene #35: 'amp_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.35e-06 (Fisher's exact test), Q value = 0.0037

Table S237.  Gene #35: 'amp_17q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
AMP PEAK 35(17Q11.2) MUTATED 40 4 12
AMP PEAK 35(17Q11.2) WILD-TYPE 135 113 78

Figure S237.  Get High-res Image Gene #35: 'amp_17q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.53e-10 (Fisher's exact test), Q value = 6.4e-07

Table S238.  Gene #35: 'amp_17q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 35(17Q11.2) MUTATED 2 50 4
AMP PEAK 35(17Q11.2) WILD-TYPE 28 148 150

Figure S238.  Get High-res Image Gene #35: 'amp_17q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 9.06e-27 (Chi-square test), Q value = 9.9e-24

Table S239.  Gene #36: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 36(17Q12) MUTATED 6 2 61 1 1
AMP PEAK 36(17Q12) WILD-TYPE 299 46 93 11 4

Figure S239.  Get High-res Image Gene #36: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 1.69e-14 (Fisher's exact test), Q value = 1.5e-11

Table S240.  Gene #36: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 36(17Q12) MUTATED 47 10 2
AMP PEAK 36(17Q12) WILD-TYPE 105 84 162

Figure S240.  Get High-res Image Gene #36: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 3.01e-20 (Fisher's exact test), Q value = 3.1e-17

Table S241.  Gene #36: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 36(17Q12) MUTATED 66 2 3
AMP PEAK 36(17Q12) WILD-TYPE 158 148 142

Figure S241.  Get High-res Image Gene #36: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.8e-19 (Fisher's exact test), Q value = 2.8e-16

Table S242.  Gene #36: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 36(17Q12) MUTATED 2 2 67
AMP PEAK 36(17Q12) WILD-TYPE 145 130 173

Figure S242.  Get High-res Image Gene #36: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 5.42e-16 (Fisher's exact test), Q value = 5.1e-13

Table S243.  Gene #36: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 36(17Q12) MUTATED 58 3 6
AMP PEAK 36(17Q12) WILD-TYPE 147 156 135

Figure S243.  Get High-res Image Gene #36: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.58e-11 (Fisher's exact test), Q value = 1.3e-08

Table S244.  Gene #36: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 36(17Q12) MUTATED 0 5 62
AMP PEAK 36(17Q12) WILD-TYPE 8 211 219

Figure S244.  Get High-res Image Gene #36: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.79e-06 (Fisher's exact test), Q value = 0.0028

Table S245.  Gene #36: 'amp_17q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
AMP PEAK 36(17Q12) MUTATED 37 3 15
AMP PEAK 36(17Q12) WILD-TYPE 138 114 75

Figure S245.  Get High-res Image Gene #36: 'amp_17q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.35e-12 (Fisher's exact test), Q value = 2e-09

Table S246.  Gene #36: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 36(17Q12) MUTATED 0 52 3
AMP PEAK 36(17Q12) WILD-TYPE 30 146 151

Figure S246.  Get High-res Image Gene #36: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q25.1' versus 'MRNA_CNMF'

P value = 3.19e-05 (Fisher's exact test), Q value = 0.017

Table S247.  Gene #37: 'amp_17q25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
AMP PEAK 37(17Q25.1) MUTATED 0 10 1 0
AMP PEAK 37(17Q25.1) WILD-TYPE 14 7 11 10

Figure S247.  Get High-res Image Gene #37: 'amp_17q25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q25.1' versus 'MRNA_CHIERARCHICAL'

P value = 2.42e-06 (Fisher's exact test), Q value = 0.0014

Table S248.  Gene #37: 'amp_17q25.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
AMP PEAK 37(17Q25.1) MUTATED 1 0 10
AMP PEAK 37(17Q25.1) WILD-TYPE 18 19 5

Figure S248.  Get High-res Image Gene #37: 'amp_17q25.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q25.1' versus 'CN_CNMF'

P value = 1.45e-42 (Chi-square test), Q value = 1.7e-39

Table S249.  Gene #37: 'amp_17q25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 37(17Q25.1) MUTATED 5 6 87 1 1
AMP PEAK 37(17Q25.1) WILD-TYPE 300 42 67 11 4

Figure S249.  Get High-res Image Gene #37: 'amp_17q25.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q25.1' versus 'METHLYATION_CNMF'

P value = 1.4e-13 (Fisher's exact test), Q value = 1.2e-10

Table S250.  Gene #37: 'amp_17q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 37(17Q25.1) MUTATED 55 19 6
AMP PEAK 37(17Q25.1) WILD-TYPE 97 75 158

Figure S250.  Get High-res Image Gene #37: 'amp_17q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q25.1' versus 'MRNASEQ_CNMF'

P value = 2.58e-21 (Fisher's exact test), Q value = 2.7e-18

Table S251.  Gene #37: 'amp_17q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 37(17Q25.1) MUTATED 85 6 8
AMP PEAK 37(17Q25.1) WILD-TYPE 139 144 137

Figure S251.  Get High-res Image Gene #37: 'amp_17q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.12e-20 (Fisher's exact test), Q value = 1.2e-17

Table S252.  Gene #37: 'amp_17q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 37(17Q25.1) MUTATED 8 4 87
AMP PEAK 37(17Q25.1) WILD-TYPE 139 128 153

Figure S252.  Get High-res Image Gene #37: 'amp_17q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q25.1' versus 'MIRSEQ_CNMF'

P value = 9.22e-18 (Fisher's exact test), Q value = 9.1e-15

Table S253.  Gene #37: 'amp_17q25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 37(17Q25.1) MUTATED 76 8 10
AMP PEAK 37(17Q25.1) WILD-TYPE 129 151 131

Figure S253.  Get High-res Image Gene #37: 'amp_17q25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.69e-12 (Fisher's exact test), Q value = 2.3e-09

Table S254.  Gene #37: 'amp_17q25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 37(17Q25.1) MUTATED 2 11 81
AMP PEAK 37(17Q25.1) WILD-TYPE 6 205 200

Figure S254.  Get High-res Image Gene #37: 'amp_17q25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q25.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.66e-05 (Fisher's exact test), Q value = 0.014

Table S255.  Gene #37: 'amp_17q25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
AMP PEAK 37(17Q25.1) MUTATED 48 8 18
AMP PEAK 37(17Q25.1) WILD-TYPE 127 109 72

Figure S255.  Get High-res Image Gene #37: 'amp_17q25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q25.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.03e-10 (Fisher's exact test), Q value = 2.3e-07

Table S256.  Gene #37: 'amp_17q25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 37(17Q25.1) MUTATED 1 63 10
AMP PEAK 37(17Q25.1) WILD-TYPE 29 135 144

Figure S256.  Get High-res Image Gene #37: 'amp_17q25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18p11.31' versus 'CN_CNMF'

P value = 1.45e-37 (Chi-square test), Q value = 1.6e-34

Table S257.  Gene #38: 'amp_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 38(18P11.31) MUTATED 5 6 79 1 0
AMP PEAK 38(18P11.31) WILD-TYPE 300 42 75 11 5

Figure S257.  Get High-res Image Gene #38: 'amp_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

'amp_18p11.31' versus 'METHLYATION_CNMF'

P value = 1.87e-12 (Fisher's exact test), Q value = 1.6e-09

Table S258.  Gene #38: 'amp_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 38(18P11.31) MUTATED 54 19 7
AMP PEAK 38(18P11.31) WILD-TYPE 98 75 157

Figure S258.  Get High-res Image Gene #38: 'amp_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_18p11.31' versus 'MRNASEQ_CNMF'

P value = 9.26e-22 (Fisher's exact test), Q value = 9.7e-19

Table S259.  Gene #38: 'amp_18p11.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 38(18P11.31) MUTATED 80 3 8
AMP PEAK 38(18P11.31) WILD-TYPE 144 147 137

Figure S259.  Get High-res Image Gene #38: 'amp_18p11.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_18p11.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.67e-20 (Fisher's exact test), Q value = 2.7e-17

Table S260.  Gene #38: 'amp_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 38(18P11.31) MUTATED 8 2 81
AMP PEAK 38(18P11.31) WILD-TYPE 139 130 159

Figure S260.  Get High-res Image Gene #38: 'amp_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_18p11.31' versus 'MIRSEQ_CNMF'

P value = 9.58e-18 (Fisher's exact test), Q value = 9.4e-15

Table S261.  Gene #38: 'amp_18p11.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 38(18P11.31) MUTATED 72 7 8
AMP PEAK 38(18P11.31) WILD-TYPE 133 152 133

Figure S261.  Get High-res Image Gene #38: 'amp_18p11.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_18p11.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.54e-11 (Fisher's exact test), Q value = 1.2e-08

Table S262.  Gene #38: 'amp_18p11.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 38(18P11.31) MUTATED 1 10 76
AMP PEAK 38(18P11.31) WILD-TYPE 7 206 205

Figure S262.  Get High-res Image Gene #38: 'amp_18p11.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_18p11.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.34e-06 (Fisher's exact test), Q value = 0.00081

Table S263.  Gene #38: 'amp_18p11.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
AMP PEAK 38(18P11.31) MUTATED 48 6 21
AMP PEAK 38(18P11.31) WILD-TYPE 127 111 69

Figure S263.  Get High-res Image Gene #38: 'amp_18p11.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_18p11.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.12e-12 (Fisher's exact test), Q value = 1.8e-09

Table S264.  Gene #38: 'amp_18p11.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 38(18P11.31) MUTATED 2 66 7
AMP PEAK 38(18P11.31) WILD-TYPE 28 132 147

Figure S264.  Get High-res Image Gene #38: 'amp_18p11.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18q11.2' versus 'CN_CNMF'

P value = 2.59e-28 (Chi-square test), Q value = 2.8e-25

Table S265.  Gene #39: 'amp_18q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 39(18Q11.2) MUTATED 3 3 60 1 0
AMP PEAK 39(18Q11.2) WILD-TYPE 302 45 94 11 5

Figure S265.  Get High-res Image Gene #39: 'amp_18q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 8.89e-11 (Fisher's exact test), Q value = 7e-08

Table S266.  Gene #39: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 39(18Q11.2) MUTATED 40 16 3
AMP PEAK 39(18Q11.2) WILD-TYPE 112 78 161

Figure S266.  Get High-res Image Gene #39: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CNMF'

P value = 2.54e-17 (Fisher's exact test), Q value = 2.5e-14

Table S267.  Gene #39: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 39(18Q11.2) MUTATED 61 3 3
AMP PEAK 39(18Q11.2) WILD-TYPE 163 147 142

Figure S267.  Get High-res Image Gene #39: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.55e-16 (Fisher's exact test), Q value = 1.5e-13

Table S268.  Gene #39: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 39(18Q11.2) MUTATED 3 2 62
AMP PEAK 39(18Q11.2) WILD-TYPE 144 130 178

Figure S268.  Get High-res Image Gene #39: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_CNMF'

P value = 8.24e-15 (Fisher's exact test), Q value = 7.6e-12

Table S269.  Gene #39: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 39(18Q11.2) MUTATED 55 2 8
AMP PEAK 39(18Q11.2) WILD-TYPE 150 157 133

Figure S269.  Get High-res Image Gene #39: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.4e-12 (Fisher's exact test), Q value = 3.6e-09

Table S270.  Gene #39: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 39(18Q11.2) MUTATED 0 4 61
AMP PEAK 39(18Q11.2) WILD-TYPE 8 212 220

Figure S270.  Get High-res Image Gene #39: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.01e-08 (Fisher's exact test), Q value = 7.2e-06

Table S271.  Gene #39: 'amp_18q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
AMP PEAK 39(18Q11.2) MUTATED 41 1 13
AMP PEAK 39(18Q11.2) WILD-TYPE 134 116 77

Figure S271.  Get High-res Image Gene #39: 'amp_18q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.53e-13 (Fisher's exact test), Q value = 2.2e-10

Table S272.  Gene #39: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 39(18Q11.2) MUTATED 2 52 1
AMP PEAK 39(18Q11.2) WILD-TYPE 28 146 153

Figure S272.  Get High-res Image Gene #39: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.2' versus 'MRNA_CNMF'

P value = 2.35e-05 (Fisher's exact test), Q value = 0.013

Table S273.  Gene #40: 'amp_19p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
AMP PEAK 40(19P13.2) MUTATED 0 9 0 0
AMP PEAK 40(19P13.2) WILD-TYPE 14 8 12 10

Figure S273.  Get High-res Image Gene #40: 'amp_19p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19p13.2' versus 'MRNA_CHIERARCHICAL'

P value = 1.13e-06 (Fisher's exact test), Q value = 7e-04

Table S274.  Gene #40: 'amp_19p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
AMP PEAK 40(19P13.2) MUTATED 0 0 9
AMP PEAK 40(19P13.2) WILD-TYPE 19 19 6

Figure S274.  Get High-res Image Gene #40: 'amp_19p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

P value = 1.49e-47 (Chi-square test), Q value = 1.7e-44

Table S275.  Gene #40: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 40(19P13.2) MUTATED 0 2 84 2 0
AMP PEAK 40(19P13.2) WILD-TYPE 305 46 70 10 5

Figure S275.  Get High-res Image Gene #40: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.2' versus 'METHLYATION_CNMF'

P value = 6.88e-11 (Fisher's exact test), Q value = 5.4e-08

Table S276.  Gene #40: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 40(19P13.2) MUTATED 49 21 7
AMP PEAK 40(19P13.2) WILD-TYPE 103 73 157

Figure S276.  Get High-res Image Gene #40: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CNMF'

P value = 1.61e-22 (Fisher's exact test), Q value = 1.7e-19

Table S277.  Gene #40: 'amp_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 40(19P13.2) MUTATED 78 2 7
AMP PEAK 40(19P13.2) WILD-TYPE 146 148 138

Figure S277.  Get High-res Image Gene #40: 'amp_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.95e-21 (Fisher's exact test), Q value = 3.1e-18

Table S278.  Gene #40: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 40(19P13.2) MUTATED 7 1 79
AMP PEAK 40(19P13.2) WILD-TYPE 140 131 161

Figure S278.  Get High-res Image Gene #40: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'MIRSEQ_CNMF'

P value = 1.74e-17 (Fisher's exact test), Q value = 1.7e-14

Table S279.  Gene #40: 'amp_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 40(19P13.2) MUTATED 70 8 6
AMP PEAK 40(19P13.2) WILD-TYPE 135 151 135

Figure S279.  Get High-res Image Gene #40: 'amp_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.62e-08 (Fisher's exact test), Q value = 1.1e-05

Table S280.  Gene #40: 'amp_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 40(19P13.2) MUTATED 3 13 68
AMP PEAK 40(19P13.2) WILD-TYPE 5 203 213

Figure S280.  Get High-res Image Gene #40: 'amp_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000193 (Fisher's exact test), Q value = 0.092

Table S281.  Gene #40: 'amp_19p13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
AMP PEAK 40(19P13.2) MUTATED 46 9 17
AMP PEAK 40(19P13.2) WILD-TYPE 129 108 73

Figure S281.  Get High-res Image Gene #40: 'amp_19p13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.12e-07 (Fisher's exact test), Q value = 0.00014

Table S282.  Gene #40: 'amp_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 40(19P13.2) MUTATED 2 58 12
AMP PEAK 40(19P13.2) WILD-TYPE 28 140 142

Figure S282.  Get High-res Image Gene #40: 'amp_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.12' versus 'MRNA_CHIERARCHICAL'

P value = 0.000454 (Fisher's exact test), Q value = 0.2

Table S283.  Gene #41: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
AMP PEAK 41(19P13.12) MUTATED 1 0 7
AMP PEAK 41(19P13.12) WILD-TYPE 18 19 8

Figure S283.  Get High-res Image Gene #41: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19p13.12' versus 'CN_CNMF'

P value = 7.59e-47 (Chi-square test), Q value = 8.7e-44

Table S284.  Gene #41: 'amp_19p13.12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 41(19P13.12) MUTATED 0 3 85 2 1
AMP PEAK 41(19P13.12) WILD-TYPE 305 45 69 10 4

Figure S284.  Get High-res Image Gene #41: 'amp_19p13.12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.12' versus 'METHLYATION_CNMF'

P value = 2e-11 (Fisher's exact test), Q value = 1.6e-08

Table S285.  Gene #41: 'amp_19p13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 41(19P13.12) MUTATED 51 19 7
AMP PEAK 41(19P13.12) WILD-TYPE 101 75 157

Figure S285.  Get High-res Image Gene #41: 'amp_19p13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.12' versus 'MRNASEQ_CNMF'

P value = 3.4e-23 (Fisher's exact test), Q value = 3.6e-20

Table S286.  Gene #41: 'amp_19p13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 41(19P13.12) MUTATED 81 4 5
AMP PEAK 41(19P13.12) WILD-TYPE 143 146 140

Figure S286.  Get High-res Image Gene #41: 'amp_19p13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19p13.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.23e-21 (Fisher's exact test), Q value = 1.3e-18

Table S287.  Gene #41: 'amp_19p13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 41(19P13.12) MUTATED 5 3 82
AMP PEAK 41(19P13.12) WILD-TYPE 142 129 158

Figure S287.  Get High-res Image Gene #41: 'amp_19p13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.12' versus 'MIRSEQ_CNMF'

P value = 3.15e-16 (Fisher's exact test), Q value = 3e-13

Table S288.  Gene #41: 'amp_19p13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 41(19P13.12) MUTATED 71 8 9
AMP PEAK 41(19P13.12) WILD-TYPE 134 151 132

Figure S288.  Get High-res Image Gene #41: 'amp_19p13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19p13.12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.2e-09 (Fisher's exact test), Q value = 1.6e-06

Table S289.  Gene #41: 'amp_19p13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 41(19P13.12) MUTATED 3 13 72
AMP PEAK 41(19P13.12) WILD-TYPE 5 203 209

Figure S289.  Get High-res Image Gene #41: 'amp_19p13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19p13.12' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.16e-05 (Fisher's exact test), Q value = 0.0065

Table S290.  Gene #41: 'amp_19p13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
AMP PEAK 41(19P13.12) MUTATED 47 7 19
AMP PEAK 41(19P13.12) WILD-TYPE 128 110 71

Figure S290.  Get High-res Image Gene #41: 'amp_19p13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19p13.12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.01e-07 (Fisher's exact test), Q value = 6.7e-05

Table S291.  Gene #41: 'amp_19p13.12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 41(19P13.12) MUTATED 3 59 11
AMP PEAK 41(19P13.12) WILD-TYPE 27 139 143

Figure S291.  Get High-res Image Gene #41: 'amp_19p13.12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.000168 (Fisher's exact test), Q value = 0.08

Table S292.  Gene #42: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
AMP PEAK 42(19Q12) MUTATED 2 0 8
AMP PEAK 42(19Q12) WILD-TYPE 17 19 7

Figure S292.  Get High-res Image Gene #42: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1.84e-58 (Chi-square test), Q value = 2.1e-55

Table S293.  Gene #42: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 42(19Q12) MUTATED 3 5 105 2 0
AMP PEAK 42(19Q12) WILD-TYPE 302 43 49 10 5

Figure S293.  Get High-res Image Gene #42: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 6.92e-18 (Fisher's exact test), Q value = 6.8e-15

Table S294.  Gene #42: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 42(19Q12) MUTATED 70 23 8
AMP PEAK 42(19Q12) WILD-TYPE 82 71 156

Figure S294.  Get High-res Image Gene #42: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 2.63e-35 (Fisher's exact test), Q value = 3e-32

Table S295.  Gene #42: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 42(19Q12) MUTATED 106 2 7
AMP PEAK 42(19Q12) WILD-TYPE 118 148 138

Figure S295.  Get High-res Image Gene #42: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.32e-32 (Fisher's exact test), Q value = 2.6e-29

Table S296.  Gene #42: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 42(19Q12) MUTATED 6 2 107
AMP PEAK 42(19Q12) WILD-TYPE 141 130 133

Figure S296.  Get High-res Image Gene #42: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 2.22e-24 (Fisher's exact test), Q value = 2.4e-21

Table S297.  Gene #42: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 42(19Q12) MUTATED 90 8 9
AMP PEAK 42(19Q12) WILD-TYPE 115 151 132

Figure S297.  Get High-res Image Gene #42: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.83e-15 (Fisher's exact test), Q value = 8.1e-12

Table S298.  Gene #42: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 42(19Q12) MUTATED 3 12 92
AMP PEAK 42(19Q12) WILD-TYPE 5 204 189

Figure S298.  Get High-res Image Gene #42: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.24e-07 (Fisher's exact test), Q value = 0.00014

Table S299.  Gene #42: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
AMP PEAK 42(19Q12) MUTATED 60 9 24
AMP PEAK 42(19Q12) WILD-TYPE 115 108 66

Figure S299.  Get High-res Image Gene #42: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.64e-12 (Fisher's exact test), Q value = 1.4e-09

Table S300.  Gene #42: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 42(19Q12) MUTATED 3 78 12
AMP PEAK 42(19Q12) WILD-TYPE 27 120 142

Figure S300.  Get High-res Image Gene #42: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20p13' versus 'CN_CNMF'

P value = 1.16e-35 (Chi-square test), Q value = 1.3e-32

Table S301.  Gene #43: 'amp_20p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 43(20P13) MUTATED 8 20 82 1 2
AMP PEAK 43(20P13) WILD-TYPE 297 28 72 11 3

Figure S301.  Get High-res Image Gene #43: 'amp_20p13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p13' versus 'METHLYATION_CNMF'

P value = 8.23e-12 (Fisher's exact test), Q value = 6.7e-09

Table S302.  Gene #43: 'amp_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 43(20P13) MUTATED 67 20 16
AMP PEAK 43(20P13) WILD-TYPE 85 74 148

Figure S302.  Get High-res Image Gene #43: 'amp_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20p13' versus 'MRNASEQ_CNMF'

P value = 3.71e-15 (Fisher's exact test), Q value = 3.4e-12

Table S303.  Gene #43: 'amp_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 43(20P13) MUTATED 86 12 14
AMP PEAK 43(20P13) WILD-TYPE 138 138 131

Figure S303.  Get High-res Image Gene #43: 'amp_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.14e-12 (Fisher's exact test), Q value = 3.4e-09

Table S304.  Gene #43: 'amp_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 43(20P13) MUTATED 17 10 85
AMP PEAK 43(20P13) WILD-TYPE 130 122 155

Figure S304.  Get High-res Image Gene #43: 'amp_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20p13' versus 'MIRSEQ_CNMF'

P value = 1.22e-12 (Fisher's exact test), Q value = 1e-09

Table S305.  Gene #43: 'amp_20p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 43(20P13) MUTATED 79 15 17
AMP PEAK 43(20P13) WILD-TYPE 126 144 124

Figure S305.  Get High-res Image Gene #43: 'amp_20p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.31e-09 (Fisher's exact test), Q value = 3.8e-06

Table S306.  Gene #43: 'amp_20p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 43(20P13) MUTATED 1 21 89
AMP PEAK 43(20P13) WILD-TYPE 7 195 192

Figure S306.  Get High-res Image Gene #43: 'amp_20p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.02e-05 (Fisher's exact test), Q value = 0.016

Table S307.  Gene #43: 'amp_20p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
AMP PEAK 43(20P13) MUTATED 61 14 20
AMP PEAK 43(20P13) WILD-TYPE 114 103 70

Figure S307.  Get High-res Image Gene #43: 'amp_20p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.2e-09 (Fisher's exact test), Q value = 6.6e-06

Table S308.  Gene #43: 'amp_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 43(20P13) MUTATED 5 74 16
AMP PEAK 43(20P13) WILD-TYPE 25 124 138

Figure S308.  Get High-res Image Gene #43: 'amp_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.000168 (Fisher's exact test), Q value = 0.08

Table S309.  Gene #44: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
AMP PEAK 44(20Q11.21) MUTATED 2 0 8
AMP PEAK 44(20Q11.21) WILD-TYPE 17 19 7

Figure S309.  Get High-res Image Gene #44: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q11.21' versus 'CN_CNMF'

P value = 3.76e-53 (Chi-square test), Q value = 4.4e-50

Table S310.  Gene #44: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 44(20Q11.21) MUTATED 7 26 106 1 2
AMP PEAK 44(20Q11.21) WILD-TYPE 298 22 48 11 3

Figure S310.  Get High-res Image Gene #44: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q11.21' versus 'METHLYATION_CNMF'

P value = 1.27e-13 (Fisher's exact test), Q value = 1.1e-10

Table S311.  Gene #44: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 44(20Q11.21) MUTATED 79 24 21
AMP PEAK 44(20Q11.21) WILD-TYPE 73 70 143

Figure S311.  Get High-res Image Gene #44: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CNMF'

P value = 1.71e-24 (Fisher's exact test), Q value = 1.8e-21

Table S312.  Gene #44: 'amp_20q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 44(20Q11.21) MUTATED 112 10 19
AMP PEAK 44(20Q11.21) WILD-TYPE 112 140 126

Figure S312.  Get High-res Image Gene #44: 'amp_20q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.18e-20 (Fisher's exact test), Q value = 1.2e-17

Table S313.  Gene #44: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 44(20Q11.21) MUTATED 20 9 112
AMP PEAK 44(20Q11.21) WILD-TYPE 127 123 128

Figure S313.  Get High-res Image Gene #44: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_CNMF'

P value = 5.18e-18 (Fisher's exact test), Q value = 5.1e-15

Table S314.  Gene #44: 'amp_20q11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 44(20Q11.21) MUTATED 99 19 18
AMP PEAK 44(20Q11.21) WILD-TYPE 106 140 123

Figure S314.  Get High-res Image Gene #44: 'amp_20q11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.68e-10 (Fisher's exact test), Q value = 1.3e-07

Table S315.  Gene #44: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 44(20Q11.21) MUTATED 4 27 105
AMP PEAK 44(20Q11.21) WILD-TYPE 4 189 176

Figure S315.  Get High-res Image Gene #44: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.32e-06 (Fisher's exact test), Q value = 0.0053

Table S316.  Gene #44: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
AMP PEAK 44(20Q11.21) MUTATED 74 20 22
AMP PEAK 44(20Q11.21) WILD-TYPE 101 97 68

Figure S316.  Get High-res Image Gene #44: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.23e-07 (Fisher's exact test), Q value = 0.00021

Table S317.  Gene #44: 'amp_20q11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 44(20Q11.21) MUTATED 9 83 24
AMP PEAK 44(20Q11.21) WILD-TYPE 21 115 130

Figure S317.  Get High-res Image Gene #44: 'amp_20q11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.12' versus 'CN_CNMF'

P value = 9.63e-52 (Chi-square test), Q value = 1.1e-48

Table S318.  Gene #45: 'amp_20q13.12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 45(20Q13.12) MUTATED 9 28 105 1 2
AMP PEAK 45(20Q13.12) WILD-TYPE 296 20 49 11 3

Figure S318.  Get High-res Image Gene #45: 'amp_20q13.12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.12' versus 'METHLYATION_CNMF'

P value = 1.87e-14 (Fisher's exact test), Q value = 1.7e-11

Table S319.  Gene #45: 'amp_20q13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 45(20Q13.12) MUTATED 84 23 24
AMP PEAK 45(20Q13.12) WILD-TYPE 68 71 140

Figure S319.  Get High-res Image Gene #45: 'amp_20q13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.12' versus 'MRNASEQ_CNMF'

P value = 9.34e-23 (Fisher's exact test), Q value = 9.9e-20

Table S320.  Gene #45: 'amp_20q13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 45(20Q13.12) MUTATED 112 12 20
AMP PEAK 45(20Q13.12) WILD-TYPE 112 138 125

Figure S320.  Get High-res Image Gene #45: 'amp_20q13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q13.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.56e-19 (Fisher's exact test), Q value = 5.6e-16

Table S321.  Gene #45: 'amp_20q13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 45(20Q13.12) MUTATED 21 11 112
AMP PEAK 45(20Q13.12) WILD-TYPE 126 121 128

Figure S321.  Get High-res Image Gene #45: 'amp_20q13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.12' versus 'MIRSEQ_CNMF'

P value = 5.12e-18 (Fisher's exact test), Q value = 5.1e-15

Table S322.  Gene #45: 'amp_20q13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 45(20Q13.12) MUTATED 102 22 18
AMP PEAK 45(20Q13.12) WILD-TYPE 103 137 123

Figure S322.  Get High-res Image Gene #45: 'amp_20q13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q13.12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.83e-11 (Fisher's exact test), Q value = 1.5e-08

Table S323.  Gene #45: 'amp_20q13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 45(20Q13.12) MUTATED 5 28 109
AMP PEAK 45(20Q13.12) WILD-TYPE 3 188 172

Figure S323.  Get High-res Image Gene #45: 'amp_20q13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.12' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.11e-05 (Fisher's exact test), Q value = 0.017

Table S324.  Gene #45: 'amp_20q13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
AMP PEAK 45(20Q13.12) MUTATED 76 22 25
AMP PEAK 45(20Q13.12) WILD-TYPE 99 95 65

Figure S324.  Get High-res Image Gene #45: 'amp_20q13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.18e-07 (Fisher's exact test), Q value = 0.00051

Table S325.  Gene #45: 'amp_20q13.12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 45(20Q13.12) MUTATED 10 86 27
AMP PEAK 45(20Q13.12) WILD-TYPE 20 112 127

Figure S325.  Get High-res Image Gene #45: 'amp_20q13.12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.33' versus 'CN_CNMF'

P value = 2.91e-48 (Chi-square test), Q value = 3.4e-45

Table S326.  Gene #46: 'amp_20q13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 46(20Q13.33) MUTATED 10 30 99 1 2
AMP PEAK 46(20Q13.33) WILD-TYPE 295 18 55 11 3

Figure S326.  Get High-res Image Gene #46: 'amp_20q13.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.33' versus 'METHLYATION_CNMF'

P value = 6.14e-12 (Fisher's exact test), Q value = 5.1e-09

Table S327.  Gene #46: 'amp_20q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 46(20Q13.33) MUTATED 78 24 24
AMP PEAK 46(20Q13.33) WILD-TYPE 74 70 140

Figure S327.  Get High-res Image Gene #46: 'amp_20q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CNMF'

P value = 5.12e-19 (Fisher's exact test), Q value = 5.2e-16

Table S328.  Gene #46: 'amp_20q13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 46(20Q13.33) MUTATED 107 15 20
AMP PEAK 46(20Q13.33) WILD-TYPE 117 135 125

Figure S328.  Get High-res Image Gene #46: 'amp_20q13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.47e-16 (Fisher's exact test), Q value = 7.9e-13

Table S329.  Gene #46: 'amp_20q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 46(20Q13.33) MUTATED 22 13 107
AMP PEAK 46(20Q13.33) WILD-TYPE 125 119 133

Figure S329.  Get High-res Image Gene #46: 'amp_20q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_CNMF'

P value = 1.06e-15 (Fisher's exact test), Q value = 9.8e-13

Table S330.  Gene #46: 'amp_20q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 46(20Q13.33) MUTATED 97 23 18
AMP PEAK 46(20Q13.33) WILD-TYPE 108 136 123

Figure S330.  Get High-res Image Gene #46: 'amp_20q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.17e-09 (Fisher's exact test), Q value = 3e-06

Table S331.  Gene #46: 'amp_20q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 46(20Q13.33) MUTATED 4 30 104
AMP PEAK 46(20Q13.33) WILD-TYPE 4 186 177

Figure S331.  Get High-res Image Gene #46: 'amp_20q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.13

Table S332.  Gene #46: 'amp_20q13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
AMP PEAK 46(20Q13.33) MUTATED 71 22 25
AMP PEAK 46(20Q13.33) WILD-TYPE 104 95 65

Figure S332.  Get High-res Image Gene #46: 'amp_20q13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.56e-06 (Fisher's exact test), Q value = 0.00095

Table S333.  Gene #46: 'amp_20q13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 46(20Q13.33) MUTATED 9 83 26
AMP PEAK 46(20Q13.33) WILD-TYPE 21 115 128

Figure S333.  Get High-res Image Gene #46: 'amp_20q13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_22q12.2' versus 'CN_CNMF'

P value = 3.71e-20 (Chi-square test), Q value = 3.8e-17

Table S334.  Gene #47: 'amp_22q12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 47(22Q12.2) MUTATED 4 5 49 0 1
AMP PEAK 47(22Q12.2) WILD-TYPE 301 43 105 12 4

Figure S334.  Get High-res Image Gene #47: 'amp_22q12.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_22q12.2' versus 'METHLYATION_CNMF'

P value = 2.3e-16 (Fisher's exact test), Q value = 2.2e-13

Table S335.  Gene #47: 'amp_22q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
AMP PEAK 47(22Q12.2) MUTATED 45 9 0
AMP PEAK 47(22Q12.2) WILD-TYPE 107 85 164

Figure S335.  Get High-res Image Gene #47: 'amp_22q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_22q12.2' versus 'MRNASEQ_CNMF'

P value = 1.03e-20 (Fisher's exact test), Q value = 1.1e-17

Table S336.  Gene #47: 'amp_22q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 47(22Q12.2) MUTATED 57 1 0
AMP PEAK 47(22Q12.2) WILD-TYPE 167 149 145

Figure S336.  Get High-res Image Gene #47: 'amp_22q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_22q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.98e-19 (Fisher's exact test), Q value = 8e-16

Table S337.  Gene #47: 'amp_22q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 47(22Q12.2) MUTATED 0 1 57
AMP PEAK 47(22Q12.2) WILD-TYPE 147 131 183

Figure S337.  Get High-res Image Gene #47: 'amp_22q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_22q12.2' versus 'MIRSEQ_CNMF'

P value = 1.06e-20 (Fisher's exact test), Q value = 1.1e-17

Table S338.  Gene #47: 'amp_22q12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 47(22Q12.2) MUTATED 55 0 2
AMP PEAK 47(22Q12.2) WILD-TYPE 150 159 139

Figure S338.  Get High-res Image Gene #47: 'amp_22q12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_22q12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.62e-12 (Fisher's exact test), Q value = 2.2e-09

Table S339.  Gene #47: 'amp_22q12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
AMP PEAK 47(22Q12.2) MUTATED 0 2 55
AMP PEAK 47(22Q12.2) WILD-TYPE 8 214 226

Figure S339.  Get High-res Image Gene #47: 'amp_22q12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_22q12.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.66e-10 (Fisher's exact test), Q value = 2e-07

Table S340.  Gene #47: 'amp_22q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
AMP PEAK 47(22Q12.2) MUTATED 44 1 7
AMP PEAK 47(22Q12.2) WILD-TYPE 131 116 83

Figure S340.  Get High-res Image Gene #47: 'amp_22q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_22q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.84e-13 (Fisher's exact test), Q value = 4.2e-10

Table S341.  Gene #47: 'amp_22q12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
AMP PEAK 47(22Q12.2) MUTATED 1 50 1
AMP PEAK 47(22Q12.2) WILD-TYPE 29 148 153

Figure S341.  Get High-res Image Gene #47: 'amp_22q12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xp11.23' versus 'CN_CNMF'

P value = 4.92e-24 (Chi-square test), Q value = 5.3e-21

Table S342.  Gene #48: 'amp_xp11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 48(XP11.23) MUTATED 11 20 44 10 2
AMP PEAK 48(XP11.23) WILD-TYPE 294 28 110 2 3

Figure S342.  Get High-res Image Gene #48: 'amp_xp11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xp11.23' versus 'MRNASEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.11

Table S343.  Gene #48: 'amp_xp11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
AMP PEAK 48(XP11.23) MUTATED 54 15 16
AMP PEAK 48(XP11.23) WILD-TYPE 170 135 129

Figure S343.  Get High-res Image Gene #48: 'amp_xp11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xp11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000116 (Fisher's exact test), Q value = 0.057

Table S344.  Gene #48: 'amp_xp11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 48(XP11.23) MUTATED 17 11 57
AMP PEAK 48(XP11.23) WILD-TYPE 130 121 183

Figure S344.  Get High-res Image Gene #48: 'amp_xp11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.23' versus 'MIRSEQ_CNMF'

P value = 2.06e-05 (Fisher's exact test), Q value = 0.011

Table S345.  Gene #48: 'amp_xp11.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
AMP PEAK 48(XP11.23) MUTATED 54 16 15
AMP PEAK 48(XP11.23) WILD-TYPE 151 143 126

Figure S345.  Get High-res Image Gene #48: 'amp_xp11.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_xq28' versus 'CN_CNMF'

P value = 2.71e-21 (Chi-square test), Q value = 2.8e-18

Table S346.  Gene #49: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
AMP PEAK 49(XQ28) MUTATED 13 20 45 9 2
AMP PEAK 49(XQ28) WILD-TYPE 292 28 109 3 3

Figure S346.  Get High-res Image Gene #49: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xq28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.19

Table S347.  Gene #49: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
AMP PEAK 49(XQ28) MUTATED 17 13 57
AMP PEAK 49(XQ28) WILD-TYPE 130 119 183

Figure S347.  Get High-res Image Gene #49: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.21' versus 'CN_CNMF'

P value = 4.91e-25 (Chi-square test), Q value = 5.3e-22

Table S348.  Gene #50: 'del_1p36.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 1(1P36.21) MUTATED 3 8 57 0 2
DEL PEAK 1(1P36.21) WILD-TYPE 302 40 97 12 3

Figure S348.  Get High-res Image Gene #50: 'del_1p36.21' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.21' versus 'METHLYATION_CNMF'

P value = 2.13e-07 (Fisher's exact test), Q value = 0.00014

Table S349.  Gene #50: 'del_1p36.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 1(1P36.21) MUTATED 36 17 6
DEL PEAK 1(1P36.21) WILD-TYPE 116 77 158

Figure S349.  Get High-res Image Gene #50: 'del_1p36.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.21' versus 'MRNASEQ_CNMF'

P value = 3.62e-14 (Fisher's exact test), Q value = 3.3e-11

Table S350.  Gene #50: 'del_1p36.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 1(1P36.21) MUTATED 60 6 4
DEL PEAK 1(1P36.21) WILD-TYPE 164 144 141

Figure S350.  Get High-res Image Gene #50: 'del_1p36.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.08e-12 (Fisher's exact test), Q value = 1.8e-09

Table S351.  Gene #50: 'del_1p36.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 1(1P36.21) MUTATED 4 6 60
DEL PEAK 1(1P36.21) WILD-TYPE 143 126 180

Figure S351.  Get High-res Image Gene #50: 'del_1p36.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.21' versus 'MIRSEQ_CNMF'

P value = 3.83e-09 (Fisher's exact test), Q value = 2.8e-06

Table S352.  Gene #50: 'del_1p36.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 1(1P36.21) MUTATED 49 7 8
DEL PEAK 1(1P36.21) WILD-TYPE 156 152 133

Figure S352.  Get High-res Image Gene #50: 'del_1p36.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.68e-08 (Fisher's exact test), Q value = 1.2e-05

Table S353.  Gene #50: 'del_1p36.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 1(1P36.21) MUTATED 2 7 55
DEL PEAK 1(1P36.21) WILD-TYPE 6 209 226

Figure S353.  Get High-res Image Gene #50: 'del_1p36.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000232 (Fisher's exact test), Q value = 0.11

Table S354.  Gene #50: 'del_1p36.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 1(1P36.21) MUTATED 28 6 22
DEL PEAK 1(1P36.21) WILD-TYPE 147 111 68

Figure S354.  Get High-res Image Gene #50: 'del_1p36.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.12e-05 (Fisher's exact test), Q value = 0.022

Table S355.  Gene #50: 'del_1p36.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 1(1P36.21) MUTATED 3 44 9
DEL PEAK 1(1P36.21) WILD-TYPE 27 154 145

Figure S355.  Get High-res Image Gene #50: 'del_1p36.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.11' versus 'CN_CNMF'

P value = 1.39e-33 (Chi-square test), Q value = 1.6e-30

Table S356.  Gene #51: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 2(1P36.11) MUTATED 2 8 70 0 2
DEL PEAK 2(1P36.11) WILD-TYPE 303 40 84 12 3

Figure S356.  Get High-res Image Gene #51: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 4.08e-12 (Fisher's exact test), Q value = 3.4e-09

Table S357.  Gene #51: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 2(1P36.11) MUTATED 51 16 6
DEL PEAK 2(1P36.11) WILD-TYPE 101 78 158

Figure S357.  Get High-res Image Gene #51: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 9.34e-19 (Fisher's exact test), Q value = 9.3e-16

Table S358.  Gene #51: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 2(1P36.11) MUTATED 72 6 4
DEL PEAK 2(1P36.11) WILD-TYPE 152 144 141

Figure S358.  Get High-res Image Gene #51: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.73e-16 (Fisher's exact test), Q value = 1.7e-13

Table S359.  Gene #51: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 2(1P36.11) MUTATED 4 6 72
DEL PEAK 2(1P36.11) WILD-TYPE 143 126 168

Figure S359.  Get High-res Image Gene #51: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CNMF'

P value = 2.12e-12 (Fisher's exact test), Q value = 1.8e-09

Table S360.  Gene #51: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 2(1P36.11) MUTATED 61 8 9
DEL PEAK 2(1P36.11) WILD-TYPE 144 151 132

Figure S360.  Get High-res Image Gene #51: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.49e-12 (Fisher's exact test), Q value = 1.3e-09

Table S361.  Gene #51: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 2(1P36.11) MUTATED 4 7 67
DEL PEAK 2(1P36.11) WILD-TYPE 4 209 214

Figure S361.  Get High-res Image Gene #51: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.82e-05 (Fisher's exact test), Q value = 0.01

Table S362.  Gene #51: 'del_1p36.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 2(1P36.11) MUTATED 46 7 19
DEL PEAK 2(1P36.11) WILD-TYPE 129 110 71

Figure S362.  Get High-res Image Gene #51: 'del_1p36.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.33e-08 (Fisher's exact test), Q value = 6.2e-05

Table S363.  Gene #51: 'del_1p36.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 2(1P36.11) MUTATED 4 58 10
DEL PEAK 2(1P36.11) WILD-TYPE 26 140 144

Figure S363.  Get High-res Image Gene #51: 'del_1p36.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2p25.3' versus 'CN_CNMF'

P value = 7.51e-09 (Chi-square test), Q value = 5.4e-06

Table S364.  Gene #52: 'del_2p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 3(2P25.3) MUTATED 2 1 22 0 0
DEL PEAK 3(2P25.3) WILD-TYPE 303 47 132 12 5

Figure S364.  Get High-res Image Gene #52: 'del_2p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_2p25.3' versus 'METHLYATION_CNMF'

P value = 0.000502 (Fisher's exact test), Q value = 0.22

Table S365.  Gene #52: 'del_2p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 3(2P25.3) MUTATED 17 5 2
DEL PEAK 3(2P25.3) WILD-TYPE 135 89 162

Figure S365.  Get High-res Image Gene #52: 'del_2p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2p25.3' versus 'MRNASEQ_CNMF'

P value = 9.58e-05 (Fisher's exact test), Q value = 0.048

Table S366.  Gene #52: 'del_2p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 3(2P25.3) MUTATED 21 1 3
DEL PEAK 3(2P25.3) WILD-TYPE 203 149 142

Figure S366.  Get High-res Image Gene #52: 'del_2p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000398 (Fisher's exact test), Q value = 0.18

Table S367.  Gene #52: 'del_2p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 3(2P25.3) MUTATED 3 1 21
DEL PEAK 3(2P25.3) WILD-TYPE 144 131 219

Figure S367.  Get High-res Image Gene #52: 'del_2p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'CN_CNMF'

P value = 4.78e-20 (Chi-square test), Q value = 4.9e-17

Table S368.  Gene #53: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 4(2Q22.1) MUTATED 0 4 42 0 0
DEL PEAK 4(2Q22.1) WILD-TYPE 305 44 112 12 5

Figure S368.  Get High-res Image Gene #53: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 2.29e-05 (Fisher's exact test), Q value = 0.013

Table S369.  Gene #53: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 4(2Q22.1) MUTATED 26 10 4
DEL PEAK 4(2Q22.1) WILD-TYPE 126 84 160

Figure S369.  Get High-res Image Gene #53: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 1.22e-11 (Fisher's exact test), Q value = 9.9e-09

Table S370.  Gene #53: 'del_2q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 4(2Q22.1) MUTATED 41 0 5
DEL PEAK 4(2Q22.1) WILD-TYPE 183 150 140

Figure S370.  Get High-res Image Gene #53: 'del_2q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.45e-09 (Fisher's exact test), Q value = 1.1e-06

Table S371.  Gene #53: 'del_2q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 4(2Q22.1) MUTATED 6 0 40
DEL PEAK 4(2Q22.1) WILD-TYPE 141 132 200

Figure S371.  Get High-res Image Gene #53: 'del_2q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_CNMF'

P value = 3.29e-07 (Fisher's exact test), Q value = 0.00021

Table S372.  Gene #53: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 4(2Q22.1) MUTATED 35 4 5
DEL PEAK 4(2Q22.1) WILD-TYPE 170 155 136

Figure S372.  Get High-res Image Gene #53: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.68e-06 (Fisher's exact test), Q value = 0.0039

Table S373.  Gene #53: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 4(2Q22.1) MUTATED 2 5 37
DEL PEAK 4(2Q22.1) WILD-TYPE 6 211 244

Figure S373.  Get High-res Image Gene #53: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 1.1e-17 (Chi-square test), Q value = 1.1e-14

Table S374.  Gene #54: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 5(2Q37.3) MUTATED 2 7 42 0 0
DEL PEAK 5(2Q37.3) WILD-TYPE 303 41 112 12 5

Figure S374.  Get High-res Image Gene #54: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 6.38e-05 (Fisher's exact test), Q value = 0.033

Table S375.  Gene #54: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 5(2Q37.3) MUTATED 31 8 8
DEL PEAK 5(2Q37.3) WILD-TYPE 121 86 156

Figure S375.  Get High-res Image Gene #54: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 1.06e-07 (Fisher's exact test), Q value = 7.1e-05

Table S376.  Gene #54: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 5(2Q37.3) MUTATED 40 3 7
DEL PEAK 5(2Q37.3) WILD-TYPE 184 147 138

Figure S376.  Get High-res Image Gene #54: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.75e-06 (Fisher's exact test), Q value = 0.0011

Table S377.  Gene #54: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 5(2Q37.3) MUTATED 7 3 40
DEL PEAK 5(2Q37.3) WILD-TYPE 140 129 200

Figure S377.  Get High-res Image Gene #54: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 0.000134 (Fisher's exact test), Q value = 0.065

Table S378.  Gene #54: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 5(2Q37.3) MUTATED 34 8 7
DEL PEAK 5(2Q37.3) WILD-TYPE 171 151 134

Figure S378.  Get High-res Image Gene #54: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p14.2' versus 'CN_CNMF'

P value = 1.28e-32 (Chi-square test), Q value = 1.4e-29

Table S379.  Gene #55: 'del_3p14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 6(3P14.2) MUTATED 0 8 66 0 1
DEL PEAK 6(3P14.2) WILD-TYPE 305 40 88 12 4

Figure S379.  Get High-res Image Gene #55: 'del_3p14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p14.2' versus 'METHLYATION_CNMF'

P value = 4.22e-10 (Fisher's exact test), Q value = 3.2e-07

Table S380.  Gene #55: 'del_3p14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 6(3P14.2) MUTATED 43 16 5
DEL PEAK 6(3P14.2) WILD-TYPE 109 78 159

Figure S380.  Get High-res Image Gene #55: 'del_3p14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p14.2' versus 'MRNASEQ_CNMF'

P value = 8.2e-22 (Fisher's exact test), Q value = 8.6e-19

Table S381.  Gene #55: 'del_3p14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 6(3P14.2) MUTATED 69 1 4
DEL PEAK 6(3P14.2) WILD-TYPE 155 149 141

Figure S381.  Get High-res Image Gene #55: 'del_3p14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.41e-18 (Fisher's exact test), Q value = 2.4e-15

Table S382.  Gene #55: 'del_3p14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 6(3P14.2) MUTATED 5 1 68
DEL PEAK 6(3P14.2) WILD-TYPE 142 131 172

Figure S382.  Get High-res Image Gene #55: 'del_3p14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_CNMF'

P value = 1.69e-13 (Fisher's exact test), Q value = 1.5e-10

Table S383.  Gene #55: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 6(3P14.2) MUTATED 58 4 10
DEL PEAK 6(3P14.2) WILD-TYPE 147 155 131

Figure S383.  Get High-res Image Gene #55: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.13e-08 (Fisher's exact test), Q value = 8e-06

Table S384.  Gene #55: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 6(3P14.2) MUTATED 1 9 62
DEL PEAK 6(3P14.2) WILD-TYPE 7 207 219

Figure S384.  Get High-res Image Gene #55: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.09e-05 (Fisher's exact test), Q value = 0.0062

Table S385.  Gene #55: 'del_3p14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 6(3P14.2) MUTATED 42 5 14
DEL PEAK 6(3P14.2) WILD-TYPE 133 112 76

Figure S385.  Get High-res Image Gene #55: 'del_3p14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.84e-07 (Fisher's exact test), Q value = 0.00012

Table S386.  Gene #55: 'del_3p14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 6(3P14.2) MUTATED 4 50 7
DEL PEAK 6(3P14.2) WILD-TYPE 26 148 147

Figure S386.  Get High-res Image Gene #55: 'del_3p14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q13.31' versus 'CN_CNMF'

P value = 8.48e-13 (Chi-square test), Q value = 7.3e-10

Table S387.  Gene #56: 'del_3q13.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 7(3Q13.31) MUTATED 1 1 28 0 1
DEL PEAK 7(3Q13.31) WILD-TYPE 304 47 126 12 4

Figure S387.  Get High-res Image Gene #56: 'del_3q13.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q13.31' versus 'MRNASEQ_CNMF'

P value = 1.28e-06 (Fisher's exact test), Q value = 0.00078

Table S388.  Gene #56: 'del_3q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 7(3Q13.31) MUTATED 27 1 3
DEL PEAK 7(3Q13.31) WILD-TYPE 197 149 142

Figure S388.  Get High-res Image Gene #56: 'del_3q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.67e-06 (Fisher's exact test), Q value = 0.005

Table S389.  Gene #56: 'del_3q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 7(3Q13.31) MUTATED 3 1 27
DEL PEAK 7(3Q13.31) WILD-TYPE 144 131 213

Figure S389.  Get High-res Image Gene #56: 'del_3q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3q13.31' versus 'MIRSEQ_CNMF'

P value = 6.39e-06 (Fisher's exact test), Q value = 0.0037

Table S390.  Gene #56: 'del_3q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 7(3Q13.31) MUTATED 25 2 3
DEL PEAK 7(3Q13.31) WILD-TYPE 180 157 138

Figure S390.  Get High-res Image Gene #56: 'del_3q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.099

Table S391.  Gene #56: 'del_3q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 7(3Q13.31) MUTATED 1 3 26
DEL PEAK 7(3Q13.31) WILD-TYPE 7 213 255

Figure S391.  Get High-res Image Gene #56: 'del_3q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'CN_CNMF'

P value = 3.28e-31 (Chi-square test), Q value = 3.6e-28

Table S392.  Gene #57: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 8(4P16.3) MUTATED 4 13 71 1 2
DEL PEAK 8(4P16.3) WILD-TYPE 301 35 83 11 3

Figure S392.  Get High-res Image Gene #57: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

P value = 7.98e-13 (Fisher's exact test), Q value = 6.8e-10

Table S393.  Gene #57: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 8(4P16.3) MUTATED 55 17 7
DEL PEAK 8(4P16.3) WILD-TYPE 97 77 157

Figure S393.  Get High-res Image Gene #57: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p16.3' versus 'MRNASEQ_CNMF'

P value = 3.32e-17 (Fisher's exact test), Q value = 3.2e-14

Table S394.  Gene #57: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 8(4P16.3) MUTATED 76 6 9
DEL PEAK 8(4P16.3) WILD-TYPE 148 144 136

Figure S394.  Get High-res Image Gene #57: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.14e-14 (Fisher's exact test), Q value = 1e-11

Table S395.  Gene #57: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 8(4P16.3) MUTATED 8 7 76
DEL PEAK 8(4P16.3) WILD-TYPE 139 125 164

Figure S395.  Get High-res Image Gene #57: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_CNMF'

P value = 3.53e-12 (Fisher's exact test), Q value = 2.9e-09

Table S396.  Gene #57: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 8(4P16.3) MUTATED 65 9 12
DEL PEAK 8(4P16.3) WILD-TYPE 140 150 129

Figure S396.  Get High-res Image Gene #57: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.17e-11 (Fisher's exact test), Q value = 5.6e-08

Table S397.  Gene #57: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 8(4P16.3) MUTATED 4 11 71
DEL PEAK 8(4P16.3) WILD-TYPE 4 205 210

Figure S397.  Get High-res Image Gene #57: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.84e-05 (Fisher's exact test), Q value = 0.035

Table S398.  Gene #57: 'del_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 8(4P16.3) MUTATED 48 9 20
DEL PEAK 8(4P16.3) WILD-TYPE 127 108 70

Figure S398.  Get High-res Image Gene #57: 'del_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.8e-07 (Fisher's exact test), Q value = 0.00012

Table S399.  Gene #57: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 8(4P16.3) MUTATED 7 59 11
DEL PEAK 8(4P16.3) WILD-TYPE 23 139 143

Figure S399.  Get High-res Image Gene #57: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p15.31' versus 'CN_CNMF'

P value = 5.83e-35 (Chi-square test), Q value = 6.6e-32

Table S400.  Gene #58: 'del_4p15.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 9(4P15.31) MUTATED 3 13 76 1 2
DEL PEAK 9(4P15.31) WILD-TYPE 302 35 78 11 3

Figure S400.  Get High-res Image Gene #58: 'del_4p15.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p15.31' versus 'METHLYATION_CNMF'

P value = 1.64e-15 (Fisher's exact test), Q value = 1.5e-12

Table S401.  Gene #58: 'del_4p15.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 9(4P15.31) MUTATED 60 18 6
DEL PEAK 9(4P15.31) WILD-TYPE 92 76 158

Figure S401.  Get High-res Image Gene #58: 'del_4p15.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p15.31' versus 'MRNASEQ_CNMF'

P value = 1.07e-19 (Fisher's exact test), Q value = 1.1e-16

Table S402.  Gene #58: 'del_4p15.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 9(4P15.31) MUTATED 81 6 8
DEL PEAK 9(4P15.31) WILD-TYPE 143 144 137

Figure S402.  Get High-res Image Gene #58: 'del_4p15.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p15.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.26e-17 (Fisher's exact test), Q value = 5.1e-14

Table S403.  Gene #58: 'del_4p15.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 9(4P15.31) MUTATED 8 6 81
DEL PEAK 9(4P15.31) WILD-TYPE 139 126 159

Figure S403.  Get High-res Image Gene #58: 'del_4p15.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p15.31' versus 'MIRSEQ_CNMF'

P value = 9.9e-16 (Fisher's exact test), Q value = 9.2e-13

Table S404.  Gene #58: 'del_4p15.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 9(4P15.31) MUTATED 72 8 11
DEL PEAK 9(4P15.31) WILD-TYPE 133 151 130

Figure S404.  Get High-res Image Gene #58: 'del_4p15.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4p15.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.69e-14 (Fisher's exact test), Q value = 7.8e-11

Table S405.  Gene #58: 'del_4p15.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 9(4P15.31) MUTATED 4 9 78
DEL PEAK 9(4P15.31) WILD-TYPE 4 207 203

Figure S405.  Get High-res Image Gene #58: 'del_4p15.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4p15.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.34e-07 (Fisher's exact test), Q value = 0.00058

Table S406.  Gene #58: 'del_4p15.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 9(4P15.31) MUTATED 55 8 19
DEL PEAK 9(4P15.31) WILD-TYPE 120 109 71

Figure S406.  Get High-res Image Gene #58: 'del_4p15.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4p15.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.22e-09 (Fisher's exact test), Q value = 9.1e-07

Table S407.  Gene #58: 'del_4p15.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 9(4P15.31) MUTATED 6 66 10
DEL PEAK 9(4P15.31) WILD-TYPE 24 132 144

Figure S407.  Get High-res Image Gene #58: 'del_4p15.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.000454 (Fisher's exact test), Q value = 0.2

Table S408.  Gene #59: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 10(4Q22.1) MUTATED 1 0 7
DEL PEAK 10(4Q22.1) WILD-TYPE 18 19 8

Figure S408.  Get High-res Image Gene #59: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 1.97e-44 (Chi-square test), Q value = 2.3e-41

Table S409.  Gene #59: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 10(4Q22.1) MUTATED 2 9 88 1 2
DEL PEAK 10(4Q22.1) WILD-TYPE 303 39 66 11 3

Figure S409.  Get High-res Image Gene #59: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 5.5e-18 (Fisher's exact test), Q value = 5.4e-15

Table S410.  Gene #59: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 10(4Q22.1) MUTATED 64 19 5
DEL PEAK 10(4Q22.1) WILD-TYPE 88 75 159

Figure S410.  Get High-res Image Gene #59: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 9.3e-25 (Fisher's exact test), Q value = 1e-21

Table S411.  Gene #59: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 10(4Q22.1) MUTATED 90 6 6
DEL PEAK 10(4Q22.1) WILD-TYPE 134 144 139

Figure S411.  Get High-res Image Gene #59: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.16e-21 (Fisher's exact test), Q value = 1.2e-18

Table S412.  Gene #59: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 10(4Q22.1) MUTATED 7 5 90
DEL PEAK 10(4Q22.1) WILD-TYPE 140 127 150

Figure S412.  Get High-res Image Gene #59: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_CNMF'

P value = 1.55e-20 (Fisher's exact test), Q value = 1.6e-17

Table S413.  Gene #59: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 10(4Q22.1) MUTATED 81 7 10
DEL PEAK 10(4Q22.1) WILD-TYPE 124 152 131

Figure S413.  Get High-res Image Gene #59: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.17e-17 (Fisher's exact test), Q value = 1.1e-14

Table S414.  Gene #59: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 10(4Q22.1) MUTATED 4 7 87
DEL PEAK 10(4Q22.1) WILD-TYPE 4 209 194

Figure S414.  Get High-res Image Gene #59: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.45e-08 (Fisher's exact test), Q value = 1e-05

Table S415.  Gene #59: 'del_4q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 10(4Q22.1) MUTATED 56 6 25
DEL PEAK 10(4Q22.1) WILD-TYPE 119 111 65

Figure S415.  Get High-res Image Gene #59: 'del_4q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.67e-13 (Fisher's exact test), Q value = 5.7e-10

Table S416.  Gene #59: 'del_4q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 10(4Q22.1) MUTATED 6 73 8
DEL PEAK 10(4Q22.1) WILD-TYPE 24 125 146

Figure S416.  Get High-res Image Gene #59: 'del_4q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.000454 (Fisher's exact test), Q value = 0.2

Table S417.  Gene #60: 'del_4q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 11(4Q34.3) MUTATED 1 0 7
DEL PEAK 11(4Q34.3) WILD-TYPE 18 19 8

Figure S417.  Get High-res Image Gene #60: 'del_4q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 7.01e-54 (Chi-square test), Q value = 8.1e-51

Table S418.  Gene #60: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 11(4Q34.3) MUTATED 6 10 106 1 2
DEL PEAK 11(4Q34.3) WILD-TYPE 299 38 48 11 3

Figure S418.  Get High-res Image Gene #60: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 1.69e-16 (Fisher's exact test), Q value = 1.6e-13

Table S419.  Gene #60: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 11(4Q34.3) MUTATED 72 26 11
DEL PEAK 11(4Q34.3) WILD-TYPE 80 68 153

Figure S419.  Get High-res Image Gene #60: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 1.8e-30 (Fisher's exact test), Q value = 2e-27

Table S420.  Gene #60: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 11(4Q34.3) MUTATED 109 9 7
DEL PEAK 11(4Q34.3) WILD-TYPE 115 141 138

Figure S420.  Get High-res Image Gene #60: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.43e-27 (Fisher's exact test), Q value = 1.6e-24

Table S421.  Gene #60: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 11(4Q34.3) MUTATED 8 7 110
DEL PEAK 11(4Q34.3) WILD-TYPE 139 125 130

Figure S421.  Get High-res Image Gene #60: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CNMF'

P value = 2.43e-20 (Fisher's exact test), Q value = 2.5e-17

Table S422.  Gene #60: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 11(4Q34.3) MUTATED 91 8 20
DEL PEAK 11(4Q34.3) WILD-TYPE 114 151 121

Figure S422.  Get High-res Image Gene #60: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.61e-18 (Fisher's exact test), Q value = 1.6e-15

Table S423.  Gene #60: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 11(4Q34.3) MUTATED 5 12 102
DEL PEAK 11(4Q34.3) WILD-TYPE 3 204 179

Figure S423.  Get High-res Image Gene #60: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.19e-09 (Fisher's exact test), Q value = 2.3e-06

Table S424.  Gene #60: 'del_4q34.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 11(4Q34.3) MUTATED 67 9 29
DEL PEAK 11(4Q34.3) WILD-TYPE 108 108 61

Figure S424.  Get High-res Image Gene #60: 'del_4q34.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.31e-14 (Fisher's exact test), Q value = 1.2e-11

Table S425.  Gene #60: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 11(4Q34.3) MUTATED 8 86 11
DEL PEAK 11(4Q34.3) WILD-TYPE 22 112 143

Figure S425.  Get High-res Image Gene #60: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q11.2' versus 'CN_CNMF'

P value = 3.45e-48 (Chi-square test), Q value = 4e-45

Table S426.  Gene #61: 'del_5q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 12(5Q11.2) MUTATED 0 12 92 1 1
DEL PEAK 12(5Q11.2) WILD-TYPE 305 36 62 11 4

Figure S426.  Get High-res Image Gene #61: 'del_5q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q11.2' versus 'METHLYATION_CNMF'

P value = 2e-16 (Fisher's exact test), Q value = 1.9e-13

Table S427.  Gene #61: 'del_5q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 12(5Q11.2) MUTATED 66 18 8
DEL PEAK 12(5Q11.2) WILD-TYPE 86 76 156

Figure S427.  Get High-res Image Gene #61: 'del_5q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q11.2' versus 'MRNASEQ_CNMF'

P value = 5.02e-24 (Fisher's exact test), Q value = 5.4e-21

Table S428.  Gene #61: 'del_5q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 12(5Q11.2) MUTATED 91 5 9
DEL PEAK 12(5Q11.2) WILD-TYPE 133 145 136

Figure S428.  Get High-res Image Gene #61: 'del_5q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.78e-21 (Fisher's exact test), Q value = 1.9e-18

Table S429.  Gene #61: 'del_5q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 12(5Q11.2) MUTATED 11 3 91
DEL PEAK 12(5Q11.2) WILD-TYPE 136 129 149

Figure S429.  Get High-res Image Gene #61: 'del_5q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_CNMF'

P value = 1.63e-18 (Fisher's exact test), Q value = 1.6e-15

Table S430.  Gene #61: 'del_5q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 12(5Q11.2) MUTATED 83 10 12
DEL PEAK 12(5Q11.2) WILD-TYPE 122 149 129

Figure S430.  Get High-res Image Gene #61: 'del_5q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.23e-13 (Fisher's exact test), Q value = 1.9e-10

Table S431.  Gene #61: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 12(5Q11.2) MUTATED 3 13 89
DEL PEAK 12(5Q11.2) WILD-TYPE 5 203 192

Figure S431.  Get High-res Image Gene #61: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.67e-07 (Fisher's exact test), Q value = 0.00042

Table S432.  Gene #61: 'del_5q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 12(5Q11.2) MUTATED 62 11 18
DEL PEAK 12(5Q11.2) WILD-TYPE 113 106 72

Figure S432.  Get High-res Image Gene #61: 'del_5q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.48e-09 (Fisher's exact test), Q value = 1.1e-06

Table S433.  Gene #61: 'del_5q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 12(5Q11.2) MUTATED 6 72 13
DEL PEAK 12(5Q11.2) WILD-TYPE 24 126 141

Figure S433.  Get High-res Image Gene #61: 'del_5q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

P value = 3.83e-14 (Chi-square test), Q value = 3.4e-11

Table S434.  Gene #62: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 13(6Q26) MUTATED 4 4 37 0 0
DEL PEAK 13(6Q26) WILD-TYPE 301 44 117 12 5

Figure S434.  Get High-res Image Gene #62: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 3.54e-08 (Fisher's exact test), Q value = 2.4e-05

Table S435.  Gene #62: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 13(6Q26) MUTATED 27 11 1
DEL PEAK 13(6Q26) WILD-TYPE 125 83 163

Figure S435.  Get High-res Image Gene #62: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 3.01e-11 (Fisher's exact test), Q value = 2.4e-08

Table S436.  Gene #62: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 13(6Q26) MUTATED 41 2 2
DEL PEAK 13(6Q26) WILD-TYPE 183 148 143

Figure S436.  Get High-res Image Gene #62: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.1e-10 (Fisher's exact test), Q value = 3.8e-07

Table S437.  Gene #62: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 13(6Q26) MUTATED 2 2 41
DEL PEAK 13(6Q26) WILD-TYPE 145 130 199

Figure S437.  Get High-res Image Gene #62: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 3.36e-08 (Fisher's exact test), Q value = 2.3e-05

Table S438.  Gene #62: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 13(6Q26) MUTATED 35 2 6
DEL PEAK 13(6Q26) WILD-TYPE 170 157 135

Figure S438.  Get High-res Image Gene #62: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.68e-08 (Fisher's exact test), Q value = 1.9e-05

Table S439.  Gene #62: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 13(6Q26) MUTATED 1 2 40
DEL PEAK 13(6Q26) WILD-TYPE 7 214 241

Figure S439.  Get High-res Image Gene #62: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000338 (Fisher's exact test), Q value = 0.15

Table S440.  Gene #62: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 13(6Q26) MUTATED 23 2 13
DEL PEAK 13(6Q26) WILD-TYPE 152 115 77

Figure S440.  Get High-res Image Gene #62: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.36e-05 (Fisher's exact test), Q value = 0.023

Table S441.  Gene #62: 'del_6q26' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 13(6Q26) MUTATED 2 32 4
DEL PEAK 13(6Q26) WILD-TYPE 28 166 150

Figure S441.  Get High-res Image Gene #62: 'del_6q26' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7p22.3' versus 'MRNA_CNMF'

P value = 0.000567 (Fisher's exact test), Q value = 0.24

Table S442.  Gene #63: 'del_7p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 14(7P22.3) MUTATED 0 7 0 0
DEL PEAK 14(7P22.3) WILD-TYPE 14 10 12 10

Figure S442.  Get High-res Image Gene #63: 'del_7p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_7p22.3' versus 'MRNA_CHIERARCHICAL'

P value = 4.17e-05 (Fisher's exact test), Q value = 0.022

Table S443.  Gene #63: 'del_7p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 14(7P22.3) MUTATED 0 0 7
DEL PEAK 14(7P22.3) WILD-TYPE 19 19 8

Figure S443.  Get High-res Image Gene #63: 'del_7p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_7p22.3' versus 'CN_CNMF'

P value = 2.67e-30 (Chi-square test), Q value = 3e-27

Table S444.  Gene #63: 'del_7p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 14(7P22.3) MUTATED 4 2 63 0 1
DEL PEAK 14(7P22.3) WILD-TYPE 301 46 91 12 4

Figure S444.  Get High-res Image Gene #63: 'del_7p22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_7p22.3' versus 'METHLYATION_CNMF'

P value = 1.73e-10 (Fisher's exact test), Q value = 1.3e-07

Table S445.  Gene #63: 'del_7p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 14(7P22.3) MUTATED 42 15 4
DEL PEAK 14(7P22.3) WILD-TYPE 110 79 160

Figure S445.  Get High-res Image Gene #63: 'del_7p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_7p22.3' versus 'MRNASEQ_CNMF'

P value = 1.15e-18 (Fisher's exact test), Q value = 1.1e-15

Table S446.  Gene #63: 'del_7p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 14(7P22.3) MUTATED 64 2 4
DEL PEAK 14(7P22.3) WILD-TYPE 160 148 141

Figure S446.  Get High-res Image Gene #63: 'del_7p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7p22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.71e-16 (Fisher's exact test), Q value = 1.6e-13

Table S447.  Gene #63: 'del_7p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 14(7P22.3) MUTATED 4 2 64
DEL PEAK 14(7P22.3) WILD-TYPE 143 130 176

Figure S447.  Get High-res Image Gene #63: 'del_7p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7p22.3' versus 'MIRSEQ_CNMF'

P value = 3.26e-13 (Fisher's exact test), Q value = 2.8e-10

Table S448.  Gene #63: 'del_7p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 14(7P22.3) MUTATED 56 5 7
DEL PEAK 14(7P22.3) WILD-TYPE 149 154 134

Figure S448.  Get High-res Image Gene #63: 'del_7p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_7p22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.92e-09 (Fisher's exact test), Q value = 1.4e-06

Table S449.  Gene #63: 'del_7p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 14(7P22.3) MUTATED 1 7 60
DEL PEAK 14(7P22.3) WILD-TYPE 7 209 221

Figure S449.  Get High-res Image Gene #63: 'del_7p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7p22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.46e-05 (Fisher's exact test), Q value = 0.013

Table S450.  Gene #63: 'del_7p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 14(7P22.3) MUTATED 36 4 17
DEL PEAK 14(7P22.3) WILD-TYPE 139 113 73

Figure S450.  Get High-res Image Gene #63: 'del_7p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.46e-08 (Fisher's exact test), Q value = 1e-05

Table S451.  Gene #63: 'del_7p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 14(7P22.3) MUTATED 3 49 5
DEL PEAK 14(7P22.3) WILD-TYPE 27 149 149

Figure S451.  Get High-res Image Gene #63: 'del_7p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q11.22' versus 'CN_CNMF'

P value = 3.11e-21 (Chi-square test), Q value = 3.2e-18

Table S452.  Gene #64: 'del_7q11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 15(7Q11.22) MUTATED 0 0 40 0 1
DEL PEAK 15(7Q11.22) WILD-TYPE 305 48 114 12 4

Figure S452.  Get High-res Image Gene #64: 'del_7q11.22' versus Molecular Subtype #3: 'CN_CNMF'

'del_7q11.22' versus 'METHLYATION_CNMF'

P value = 5.42e-06 (Fisher's exact test), Q value = 0.0032

Table S453.  Gene #64: 'del_7q11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 15(7Q11.22) MUTATED 26 9 3
DEL PEAK 15(7Q11.22) WILD-TYPE 126 85 161

Figure S453.  Get High-res Image Gene #64: 'del_7q11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_7q11.22' versus 'MRNASEQ_CNMF'

P value = 1.4e-12 (Fisher's exact test), Q value = 1.2e-09

Table S454.  Gene #64: 'del_7q11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 15(7Q11.22) MUTATED 39 0 2
DEL PEAK 15(7Q11.22) WILD-TYPE 185 150 143

Figure S454.  Get High-res Image Gene #64: 'del_7q11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7q11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.86e-10 (Fisher's exact test), Q value = 2.2e-07

Table S455.  Gene #64: 'del_7q11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 15(7Q11.22) MUTATED 3 0 38
DEL PEAK 15(7Q11.22) WILD-TYPE 144 132 202

Figure S455.  Get High-res Image Gene #64: 'del_7q11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7q11.22' versus 'MIRSEQ_CNMF'

P value = 1.44e-07 (Fisher's exact test), Q value = 9.5e-05

Table S456.  Gene #64: 'del_7q11.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 15(7Q11.22) MUTATED 33 3 4
DEL PEAK 15(7Q11.22) WILD-TYPE 172 156 137

Figure S456.  Get High-res Image Gene #64: 'del_7q11.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_7q11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.42e-05 (Fisher's exact test), Q value = 0.008

Table S457.  Gene #64: 'del_7q11.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 15(7Q11.22) MUTATED 1 4 35
DEL PEAK 15(7Q11.22) WILD-TYPE 7 212 246

Figure S457.  Get High-res Image Gene #64: 'del_7q11.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7q11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.09e-05 (Fisher's exact test), Q value = 0.026

Table S458.  Gene #64: 'del_7q11.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 15(7Q11.22) MUTATED 1 31 4
DEL PEAK 15(7Q11.22) WILD-TYPE 29 167 150

Figure S458.  Get High-res Image Gene #64: 'del_7q11.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q31.1' versus 'CN_CNMF'

P value = 1.69e-28 (Chi-square test), Q value = 1.9e-25

Table S459.  Gene #65: 'del_7q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 16(7Q31.1) MUTATED 0 0 52 0 1
DEL PEAK 16(7Q31.1) WILD-TYPE 305 48 102 12 4

Figure S459.  Get High-res Image Gene #65: 'del_7q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_7q31.1' versus 'METHLYATION_CNMF'

P value = 6.9e-11 (Fisher's exact test), Q value = 5.4e-08

Table S460.  Gene #65: 'del_7q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 16(7Q31.1) MUTATED 35 12 1
DEL PEAK 16(7Q31.1) WILD-TYPE 117 82 163

Figure S460.  Get High-res Image Gene #65: 'del_7q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_7q31.1' versus 'MRNASEQ_CNMF'

P value = 1.2e-18 (Fisher's exact test), Q value = 1.2e-15

Table S461.  Gene #65: 'del_7q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 16(7Q31.1) MUTATED 52 0 1
DEL PEAK 16(7Q31.1) WILD-TYPE 172 150 144

Figure S461.  Get High-res Image Gene #65: 'del_7q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.52e-15 (Fisher's exact test), Q value = 1.4e-12

Table S462.  Gene #65: 'del_7q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 16(7Q31.1) MUTATED 2 0 51
DEL PEAK 16(7Q31.1) WILD-TYPE 145 132 189

Figure S462.  Get High-res Image Gene #65: 'del_7q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7q31.1' versus 'MIRSEQ_CNMF'

P value = 1.5e-11 (Fisher's exact test), Q value = 1.2e-08

Table S463.  Gene #65: 'del_7q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 16(7Q31.1) MUTATED 44 3 4
DEL PEAK 16(7Q31.1) WILD-TYPE 161 156 137

Figure S463.  Get High-res Image Gene #65: 'del_7q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_7q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.27e-08 (Fisher's exact test), Q value = 2.9e-05

Table S464.  Gene #65: 'del_7q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 16(7Q31.1) MUTATED 1 4 46
DEL PEAK 16(7Q31.1) WILD-TYPE 7 212 235

Figure S464.  Get High-res Image Gene #65: 'del_7q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7q31.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000196 (Fisher's exact test), Q value = 0.093

Table S465.  Gene #65: 'del_7q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 16(7Q31.1) MUTATED 30 3 11
DEL PEAK 16(7Q31.1) WILD-TYPE 145 114 79

Figure S465.  Get High-res Image Gene #65: 'del_7q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.51e-08 (Fisher's exact test), Q value = 3.7e-05

Table S466.  Gene #65: 'del_7q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 16(7Q31.1) MUTATED 0 40 4
DEL PEAK 16(7Q31.1) WILD-TYPE 30 158 150

Figure S466.  Get High-res Image Gene #65: 'del_7q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q36.1' versus 'CN_CNMF'

P value = 4.26e-31 (Chi-square test), Q value = 4.7e-28

Table S467.  Gene #66: 'del_7q36.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 17(7Q36.1) MUTATED 1 1 59 0 1
DEL PEAK 17(7Q36.1) WILD-TYPE 304 47 95 12 4

Figure S467.  Get High-res Image Gene #66: 'del_7q36.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_7q36.1' versus 'METHLYATION_CNMF'

P value = 4.87e-12 (Fisher's exact test), Q value = 4e-09

Table S468.  Gene #66: 'del_7q36.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 17(7Q36.1) MUTATED 38 14 1
DEL PEAK 17(7Q36.1) WILD-TYPE 114 80 163

Figure S468.  Get High-res Image Gene #66: 'del_7q36.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_7q36.1' versus 'MRNASEQ_CNMF'

P value = 1.78e-22 (Fisher's exact test), Q value = 1.9e-19

Table S469.  Gene #66: 'del_7q36.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 17(7Q36.1) MUTATED 61 0 1
DEL PEAK 17(7Q36.1) WILD-TYPE 163 150 144

Figure S469.  Get High-res Image Gene #66: 'del_7q36.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7q36.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.33e-19 (Fisher's exact test), Q value = 6.4e-16

Table S470.  Gene #66: 'del_7q36.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 17(7Q36.1) MUTATED 2 0 60
DEL PEAK 17(7Q36.1) WILD-TYPE 145 132 180

Figure S470.  Get High-res Image Gene #66: 'del_7q36.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7q36.1' versus 'MIRSEQ_CNMF'

P value = 3.41e-16 (Fisher's exact test), Q value = 3.2e-13

Table S471.  Gene #66: 'del_7q36.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 17(7Q36.1) MUTATED 54 3 3
DEL PEAK 17(7Q36.1) WILD-TYPE 151 156 138

Figure S471.  Get High-res Image Gene #66: 'del_7q36.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_7q36.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.05e-10 (Fisher's exact test), Q value = 8.2e-08

Table S472.  Gene #66: 'del_7q36.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 17(7Q36.1) MUTATED 0 4 56
DEL PEAK 17(7Q36.1) WILD-TYPE 8 212 225

Figure S472.  Get High-res Image Gene #66: 'del_7q36.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7q36.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.78e-05 (Fisher's exact test), Q value = 0.015

Table S473.  Gene #66: 'del_7q36.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 17(7Q36.1) MUTATED 34 3 12
DEL PEAK 17(7Q36.1) WILD-TYPE 141 114 78

Figure S473.  Get High-res Image Gene #66: 'del_7q36.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7q36.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.74e-10 (Fisher's exact test), Q value = 1.3e-07

Table S474.  Gene #66: 'del_7q36.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 17(7Q36.1) MUTATED 0 46 3
DEL PEAK 17(7Q36.1) WILD-TYPE 30 152 151

Figure S474.  Get High-res Image Gene #66: 'del_7q36.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.000218 (Fisher's exact test), Q value = 0.1

Table S475.  Gene #67: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 18(8P23.2) MUTATED 0 0 6
DEL PEAK 18(8P23.2) WILD-TYPE 19 19 9

Figure S475.  Get High-res Image Gene #67: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 1.17e-47 (Chi-square test), Q value = 1.3e-44

Table S476.  Gene #67: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 18(8P23.2) MUTATED 8 7 97 0 1
DEL PEAK 18(8P23.2) WILD-TYPE 297 41 57 12 4

Figure S476.  Get High-res Image Gene #67: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 2.16e-21 (Fisher's exact test), Q value = 2.3e-18

Table S477.  Gene #67: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 18(8P23.2) MUTATED 72 22 5
DEL PEAK 18(8P23.2) WILD-TYPE 80 72 159

Figure S477.  Get High-res Image Gene #67: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 6.61e-32 (Fisher's exact test), Q value = 7.4e-29

Table S478.  Gene #67: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 18(8P23.2) MUTATED 102 6 4
DEL PEAK 18(8P23.2) WILD-TYPE 122 144 141

Figure S478.  Get High-res Image Gene #67: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.89e-27 (Fisher's exact test), Q value = 8.6e-24

Table S479.  Gene #67: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 18(8P23.2) MUTATED 6 5 101
DEL PEAK 18(8P23.2) WILD-TYPE 141 127 139

Figure S479.  Get High-res Image Gene #67: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 1.37e-26 (Fisher's exact test), Q value = 1.5e-23

Table S480.  Gene #67: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 18(8P23.2) MUTATED 92 8 7
DEL PEAK 18(8P23.2) WILD-TYPE 113 151 134

Figure S480.  Get High-res Image Gene #67: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.57e-18 (Fisher's exact test), Q value = 9.4e-15

Table S481.  Gene #67: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 18(8P23.2) MUTATED 3 9 95
DEL PEAK 18(8P23.2) WILD-TYPE 5 207 186

Figure S481.  Get High-res Image Gene #67: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.14e-12 (Fisher's exact test), Q value = 3.4e-09

Table S482.  Gene #67: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 18(8P23.2) MUTATED 65 4 22
DEL PEAK 18(8P23.2) WILD-TYPE 110 113 68

Figure S482.  Get High-res Image Gene #67: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.47e-16 (Fisher's exact test), Q value = 3.3e-13

Table S483.  Gene #67: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 18(8P23.2) MUTATED 4 80 7
DEL PEAK 18(8P23.2) WILD-TYPE 26 118 147

Figure S483.  Get High-res Image Gene #67: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p21.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.000218 (Fisher's exact test), Q value = 0.1

Table S484.  Gene #68: 'del_8p21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 19(8P21.2) MUTATED 0 0 6
DEL PEAK 19(8P21.2) WILD-TYPE 19 19 9

Figure S484.  Get High-res Image Gene #68: 'del_8p21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p21.2' versus 'CN_CNMF'

P value = 1.54e-53 (Chi-square test), Q value = 1.8e-50

Table S485.  Gene #68: 'del_8p21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 19(8P21.2) MUTATED 5 5 100 0 1
DEL PEAK 19(8P21.2) WILD-TYPE 300 43 54 12 4

Figure S485.  Get High-res Image Gene #68: 'del_8p21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p21.2' versus 'METHLYATION_CNMF'

P value = 3.02e-26 (Fisher's exact test), Q value = 3.3e-23

Table S486.  Gene #68: 'del_8p21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 19(8P21.2) MUTATED 75 20 2
DEL PEAK 19(8P21.2) WILD-TYPE 77 74 162

Figure S486.  Get High-res Image Gene #68: 'del_8p21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p21.2' versus 'MRNASEQ_CNMF'

P value = 3.83e-37 (Fisher's exact test), Q value = 4.3e-34

Table S487.  Gene #68: 'del_8p21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 19(8P21.2) MUTATED 104 5 1
DEL PEAK 19(8P21.2) WILD-TYPE 120 145 144

Figure S487.  Get High-res Image Gene #68: 'del_8p21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.89e-31 (Fisher's exact test), Q value = 3.2e-28

Table S488.  Gene #68: 'del_8p21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 19(8P21.2) MUTATED 3 4 103
DEL PEAK 19(8P21.2) WILD-TYPE 144 128 137

Figure S488.  Get High-res Image Gene #68: 'del_8p21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p21.2' versus 'MIRSEQ_CNMF'

P value = 7.59e-31 (Fisher's exact test), Q value = 8.4e-28

Table S489.  Gene #68: 'del_8p21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 19(8P21.2) MUTATED 94 4 7
DEL PEAK 19(8P21.2) WILD-TYPE 111 155 134

Figure S489.  Get High-res Image Gene #68: 'del_8p21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.25e-20 (Fisher's exact test), Q value = 1.3e-17

Table S490.  Gene #68: 'del_8p21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 19(8P21.2) MUTATED 2 6 97
DEL PEAK 19(8P21.2) WILD-TYPE 6 210 184

Figure S490.  Get High-res Image Gene #68: 'del_8p21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.64e-16 (Fisher's exact test), Q value = 8.1e-13

Table S491.  Gene #68: 'del_8p21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 19(8P21.2) MUTATED 66 1 23
DEL PEAK 19(8P21.2) WILD-TYPE 109 116 67

Figure S491.  Get High-res Image Gene #68: 'del_8p21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.35e-19 (Fisher's exact test), Q value = 1.4e-16

Table S492.  Gene #68: 'del_8p21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 19(8P21.2) MUTATED 4 82 4
DEL PEAK 19(8P21.2) WILD-TYPE 26 116 150

Figure S492.  Get High-res Image Gene #68: 'del_8p21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1.53e-26 (Chi-square test), Q value = 1.7e-23

Table S493.  Gene #69: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 20(9P23) MUTATED 2 13 59 0 1
DEL PEAK 20(9P23) WILD-TYPE 303 35 95 12 4

Figure S493.  Get High-res Image Gene #69: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 4.73e-07 (Fisher's exact test), Q value = 3e-04

Table S494.  Gene #69: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 20(9P23) MUTATED 37 21 8
DEL PEAK 20(9P23) WILD-TYPE 115 73 156

Figure S494.  Get High-res Image Gene #69: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 4.44e-11 (Fisher's exact test), Q value = 3.5e-08

Table S495.  Gene #69: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 20(9P23) MUTATED 59 5 11
DEL PEAK 20(9P23) WILD-TYPE 165 145 134

Figure S495.  Get High-res Image Gene #69: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.32e-09 (Fisher's exact test), Q value = 9.8e-07

Table S496.  Gene #69: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 20(9P23) MUTATED 12 4 59
DEL PEAK 20(9P23) WILD-TYPE 135 128 181

Figure S496.  Get High-res Image Gene #69: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 1.65e-07 (Fisher's exact test), Q value = 0.00011

Table S497.  Gene #69: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 20(9P23) MUTATED 50 14 7
DEL PEAK 20(9P23) WILD-TYPE 155 145 134

Figure S497.  Get High-res Image Gene #69: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.41e-05 (Fisher's exact test), Q value = 0.023

Table S498.  Gene #69: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 20(9P23) MUTATED 1 14 56
DEL PEAK 20(9P23) WILD-TYPE 7 202 225

Figure S498.  Get High-res Image Gene #69: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000286 (Fisher's exact test), Q value = 0.13

Table S499.  Gene #69: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 20(9P23) MUTATED 4 46 12
DEL PEAK 20(9P23) WILD-TYPE 26 152 142

Figure S499.  Get High-res Image Gene #69: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q21.2' versus 'MRNA_CNMF'

P value = 2.35e-05 (Fisher's exact test), Q value = 0.013

Table S500.  Gene #70: 'del_9q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 21(9Q21.2) MUTATED 0 9 0 0
DEL PEAK 21(9Q21.2) WILD-TYPE 14 8 12 10

Figure S500.  Get High-res Image Gene #70: 'del_9q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9q21.2' versus 'MRNA_CHIERARCHICAL'

P value = 1.13e-06 (Fisher's exact test), Q value = 7e-04

Table S501.  Gene #70: 'del_9q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 21(9Q21.2) MUTATED 0 0 9
DEL PEAK 21(9Q21.2) WILD-TYPE 19 19 6

Figure S501.  Get High-res Image Gene #70: 'del_9q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9q21.2' versus 'CN_CNMF'

P value = 1.34e-51 (Chi-square test), Q value = 1.5e-48

Table S502.  Gene #70: 'del_9q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 21(9Q21.2) MUTATED 3 19 100 0 1
DEL PEAK 21(9Q21.2) WILD-TYPE 302 29 54 12 4

Figure S502.  Get High-res Image Gene #70: 'del_9q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q21.2' versus 'METHLYATION_CNMF'

P value = 1.77e-12 (Fisher's exact test), Q value = 1.5e-09

Table S503.  Gene #70: 'del_9q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 21(9Q21.2) MUTATED 68 24 15
DEL PEAK 21(9Q21.2) WILD-TYPE 84 70 149

Figure S503.  Get High-res Image Gene #70: 'del_9q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q21.2' versus 'MRNASEQ_CNMF'

P value = 1.05e-21 (Fisher's exact test), Q value = 1.1e-18

Table S504.  Gene #70: 'del_9q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 21(9Q21.2) MUTATED 99 8 16
DEL PEAK 21(9Q21.2) WILD-TYPE 125 142 129

Figure S504.  Get High-res Image Gene #70: 'del_9q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.67e-18 (Fisher's exact test), Q value = 1.7e-15

Table S505.  Gene #70: 'del_9q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 21(9Q21.2) MUTATED 17 7 99
DEL PEAK 21(9Q21.2) WILD-TYPE 130 125 141

Figure S505.  Get High-res Image Gene #70: 'del_9q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.2' versus 'MIRSEQ_CNMF'

P value = 3.03e-16 (Fisher's exact test), Q value = 2.9e-13

Table S506.  Gene #70: 'del_9q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 21(9Q21.2) MUTATED 88 18 13
DEL PEAK 21(9Q21.2) WILD-TYPE 117 141 128

Figure S506.  Get High-res Image Gene #70: 'del_9q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.59e-11 (Fisher's exact test), Q value = 2.9e-08

Table S507.  Gene #70: 'del_9q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 21(9Q21.2) MUTATED 5 21 93
DEL PEAK 21(9Q21.2) WILD-TYPE 3 195 188

Figure S507.  Get High-res Image Gene #70: 'del_9q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000403 (Fisher's exact test), Q value = 0.18

Table S508.  Gene #70: 'del_9q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 21(9Q21.2) MUTATED 61 17 26
DEL PEAK 21(9Q21.2) WILD-TYPE 114 100 64

Figure S508.  Get High-res Image Gene #70: 'del_9q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.09e-07 (Fisher's exact test), Q value = 7.2e-05

Table S509.  Gene #70: 'del_9q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 21(9Q21.2) MUTATED 5 78 21
DEL PEAK 21(9Q21.2) WILD-TYPE 25 120 133

Figure S509.  Get High-res Image Gene #70: 'del_9q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q34.2' versus 'MRNA_CNMF'

P value = 2.35e-05 (Fisher's exact test), Q value = 0.013

Table S510.  Gene #71: 'del_9q34.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 22(9Q34.2) MUTATED 0 9 0 0
DEL PEAK 22(9Q34.2) WILD-TYPE 14 8 12 10

Figure S510.  Get High-res Image Gene #71: 'del_9q34.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9q34.2' versus 'MRNA_CHIERARCHICAL'

P value = 1.13e-06 (Fisher's exact test), Q value = 7e-04

Table S511.  Gene #71: 'del_9q34.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 22(9Q34.2) MUTATED 0 0 9
DEL PEAK 22(9Q34.2) WILD-TYPE 19 19 6

Figure S511.  Get High-res Image Gene #71: 'del_9q34.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9q34.2' versus 'CN_CNMF'

P value = 5.97e-55 (Chi-square test), Q value = 6.9e-52

Table S512.  Gene #71: 'del_9q34.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 22(9Q34.2) MUTATED 4 19 105 0 0
DEL PEAK 22(9Q34.2) WILD-TYPE 301 29 49 12 5

Figure S512.  Get High-res Image Gene #71: 'del_9q34.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q34.2' versus 'METHLYATION_CNMF'

P value = 1.99e-14 (Fisher's exact test), Q value = 1.8e-11

Table S513.  Gene #71: 'del_9q34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 22(9Q34.2) MUTATED 70 27 13
DEL PEAK 22(9Q34.2) WILD-TYPE 82 67 151

Figure S513.  Get High-res Image Gene #71: 'del_9q34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q34.2' versus 'MRNASEQ_CNMF'

P value = 3.29e-22 (Fisher's exact test), Q value = 3.5e-19

Table S514.  Gene #71: 'del_9q34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 22(9Q34.2) MUTATED 102 9 16
DEL PEAK 22(9Q34.2) WILD-TYPE 122 141 129

Figure S514.  Get High-res Image Gene #71: 'del_9q34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9q34.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.71e-19 (Fisher's exact test), Q value = 7.7e-16

Table S515.  Gene #71: 'del_9q34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 22(9Q34.2) MUTATED 17 8 102
DEL PEAK 22(9Q34.2) WILD-TYPE 130 124 138

Figure S515.  Get High-res Image Gene #71: 'del_9q34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q34.2' versus 'MIRSEQ_CNMF'

P value = 1.85e-17 (Fisher's exact test), Q value = 1.8e-14

Table S516.  Gene #71: 'del_9q34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 22(9Q34.2) MUTATED 92 19 13
DEL PEAK 22(9Q34.2) WILD-TYPE 113 140 128

Figure S516.  Get High-res Image Gene #71: 'del_9q34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9q34.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.94e-10 (Fisher's exact test), Q value = 2.2e-07

Table S517.  Gene #71: 'del_9q34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 22(9Q34.2) MUTATED 5 24 95
DEL PEAK 22(9Q34.2) WILD-TYPE 3 192 186

Figure S517.  Get High-res Image Gene #71: 'del_9q34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q34.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.67e-05 (Fisher's exact test), Q value = 0.029

Table S518.  Gene #71: 'del_9q34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 22(9Q34.2) MUTATED 66 17 24
DEL PEAK 22(9Q34.2) WILD-TYPE 109 100 66

Figure S518.  Get High-res Image Gene #71: 'del_9q34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9q34.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.62e-07 (Fisher's exact test), Q value = 0.00017

Table S519.  Gene #71: 'del_9q34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 22(9Q34.2) MUTATED 8 78 21
DEL PEAK 22(9Q34.2) WILD-TYPE 22 120 133

Figure S519.  Get High-res Image Gene #71: 'del_9q34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 2.24e-29 (Chi-square test), Q value = 2.5e-26

Table S520.  Gene #72: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 23(10Q23.31) MUTATED 5 4 64 0 0
DEL PEAK 23(10Q23.31) WILD-TYPE 300 44 90 12 5

Figure S520.  Get High-res Image Gene #72: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 8.46e-09 (Fisher's exact test), Q value = 6.1e-06

Table S521.  Gene #72: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 23(10Q23.31) MUTATED 41 17 6
DEL PEAK 23(10Q23.31) WILD-TYPE 111 77 158

Figure S521.  Get High-res Image Gene #72: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 5.31e-13 (Fisher's exact test), Q value = 4.6e-10

Table S522.  Gene #72: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 23(10Q23.31) MUTATED 60 5 7
DEL PEAK 23(10Q23.31) WILD-TYPE 164 145 138

Figure S522.  Get High-res Image Gene #72: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.64e-11 (Fisher's exact test), Q value = 2.1e-08

Table S523.  Gene #72: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 23(10Q23.31) MUTATED 8 4 60
DEL PEAK 23(10Q23.31) WILD-TYPE 139 128 180

Figure S523.  Get High-res Image Gene #72: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 1.69e-11 (Fisher's exact test), Q value = 1.4e-08

Table S524.  Gene #72: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 23(10Q23.31) MUTATED 56 8 7
DEL PEAK 23(10Q23.31) WILD-TYPE 149 151 134

Figure S524.  Get High-res Image Gene #72: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.58e-06 (Fisher's exact test), Q value = 0.0015

Table S525.  Gene #72: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 23(10Q23.31) MUTATED 2 12 57
DEL PEAK 23(10Q23.31) WILD-TYPE 6 204 224

Figure S525.  Get High-res Image Gene #72: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000311 (Fisher's exact test), Q value = 0.14

Table S526.  Gene #72: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 23(10Q23.31) MUTATED 40 7 15
DEL PEAK 23(10Q23.31) WILD-TYPE 135 110 75

Figure S526.  Get High-res Image Gene #72: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.58e-06 (Fisher's exact test), Q value = 0.00096

Table S527.  Gene #72: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 23(10Q23.31) MUTATED 6 48 8
DEL PEAK 23(10Q23.31) WILD-TYPE 24 150 146

Figure S527.  Get High-res Image Gene #72: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 9.7e-42 (Chi-square test), Q value = 1.1e-38

Table S528.  Gene #73: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 24(11P15.5) MUTATED 1 13 83 0 2
DEL PEAK 24(11P15.5) WILD-TYPE 304 35 71 12 3

Figure S528.  Get High-res Image Gene #73: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 5.89e-16 (Fisher's exact test), Q value = 5.5e-13

Table S529.  Gene #73: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 24(11P15.5) MUTATED 61 23 6
DEL PEAK 24(11P15.5) WILD-TYPE 91 71 158

Figure S529.  Get High-res Image Gene #73: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 1.42e-20 (Fisher's exact test), Q value = 1.5e-17

Table S530.  Gene #73: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 24(11P15.5) MUTATED 83 4 11
DEL PEAK 24(11P15.5) WILD-TYPE 141 146 134

Figure S530.  Get High-res Image Gene #73: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.34e-17 (Fisher's exact test), Q value = 2.3e-14

Table S531.  Gene #73: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 24(11P15.5) MUTATED 13 3 82
DEL PEAK 24(11P15.5) WILD-TYPE 134 129 158

Figure S531.  Get High-res Image Gene #73: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 4.98e-14 (Fisher's exact test), Q value = 4.5e-11

Table S532.  Gene #73: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 24(11P15.5) MUTATED 73 13 10
DEL PEAK 24(11P15.5) WILD-TYPE 132 146 131

Figure S532.  Get High-res Image Gene #73: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.7e-08 (Fisher's exact test), Q value = 1.9e-05

Table S533.  Gene #73: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 24(11P15.5) MUTATED 3 17 76
DEL PEAK 24(11P15.5) WILD-TYPE 5 199 205

Figure S533.  Get High-res Image Gene #73: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.89e-06 (Fisher's exact test), Q value = 0.0011

Table S534.  Gene #73: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 24(11P15.5) MUTATED 61 12 16
DEL PEAK 24(11P15.5) WILD-TYPE 114 105 74

Figure S534.  Get High-res Image Gene #73: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.03e-08 (Fisher's exact test), Q value = 1.4e-05

Table S535.  Gene #73: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 24(11P15.5) MUTATED 4 70 15
DEL PEAK 24(11P15.5) WILD-TYPE 26 128 139

Figure S535.  Get High-res Image Gene #73: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q14.1' versus 'CN_CNMF'

P value = 2.18e-23 (Chi-square test), Q value = 2.3e-20

Table S536.  Gene #74: 'del_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 25(11Q14.1) MUTATED 1 12 51 0 2
DEL PEAK 25(11Q14.1) WILD-TYPE 304 36 103 12 3

Figure S536.  Get High-res Image Gene #74: 'del_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q14.1' versus 'METHLYATION_CNMF'

P value = 4.74e-10 (Fisher's exact test), Q value = 3.6e-07

Table S537.  Gene #74: 'del_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 25(11Q14.1) MUTATED 43 14 5
DEL PEAK 25(11Q14.1) WILD-TYPE 109 80 159

Figure S537.  Get High-res Image Gene #74: 'del_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q14.1' versus 'MRNASEQ_CNMF'

P value = 6.65e-14 (Fisher's exact test), Q value = 6e-11

Table S538.  Gene #74: 'del_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 25(11Q14.1) MUTATED 56 2 7
DEL PEAK 25(11Q14.1) WILD-TYPE 168 148 138

Figure S538.  Get High-res Image Gene #74: 'del_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.84e-12 (Fisher's exact test), Q value = 4e-09

Table S539.  Gene #74: 'del_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 25(11Q14.1) MUTATED 7 2 56
DEL PEAK 25(11Q14.1) WILD-TYPE 140 130 184

Figure S539.  Get High-res Image Gene #74: 'del_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q14.1' versus 'MIRSEQ_CNMF'

P value = 3.19e-10 (Fisher's exact test), Q value = 2.4e-07

Table S540.  Gene #74: 'del_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 25(11Q14.1) MUTATED 51 8 6
DEL PEAK 25(11Q14.1) WILD-TYPE 154 151 135

Figure S540.  Get High-res Image Gene #74: 'del_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.09e-08 (Fisher's exact test), Q value = 7.8e-06

Table S541.  Gene #74: 'del_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 25(11Q14.1) MUTATED 1 7 57
DEL PEAK 25(11Q14.1) WILD-TYPE 7 209 224

Figure S541.  Get High-res Image Gene #74: 'del_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000218 (Fisher's exact test), Q value = 0.1

Table S542.  Gene #74: 'del_11q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 25(11Q14.1) MUTATED 42 8 11
DEL PEAK 25(11Q14.1) WILD-TYPE 133 109 79

Figure S542.  Get High-res Image Gene #74: 'del_11q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.6e-08 (Fisher's exact test), Q value = 1.1e-05

Table S543.  Gene #74: 'del_11q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 25(11Q14.1) MUTATED 0 52 9
DEL PEAK 25(11Q14.1) WILD-TYPE 30 146 145

Figure S543.  Get High-res Image Gene #74: 'del_11q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q25' versus 'CN_CNMF'

P value = 5.29e-30 (Chi-square test), Q value = 5.9e-27

Table S544.  Gene #75: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 26(11Q25) MUTATED 4 16 67 0 2
DEL PEAK 26(11Q25) WILD-TYPE 301 32 87 12 3

Figure S544.  Get High-res Image Gene #75: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q25' versus 'METHLYATION_CNMF'

P value = 1.12e-14 (Fisher's exact test), Q value = 1e-11

Table S545.  Gene #75: 'del_11q25' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 26(11Q25) MUTATED 59 14 7
DEL PEAK 26(11Q25) WILD-TYPE 93 80 157

Figure S545.  Get High-res Image Gene #75: 'del_11q25' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q25' versus 'MRNASEQ_CNMF'

P value = 4.53e-15 (Fisher's exact test), Q value = 4.2e-12

Table S546.  Gene #75: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 26(11Q25) MUTATED 72 7 9
DEL PEAK 26(11Q25) WILD-TYPE 152 143 136

Figure S546.  Get High-res Image Gene #75: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q25' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.32e-14 (Fisher's exact test), Q value = 5.7e-11

Table S547.  Gene #75: 'del_11q25' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 26(11Q25) MUTATED 10 5 73
DEL PEAK 26(11Q25) WILD-TYPE 137 127 167

Figure S547.  Get High-res Image Gene #75: 'del_11q25' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q25' versus 'MIRSEQ_CNMF'

P value = 3.91e-10 (Fisher's exact test), Q value = 3e-07

Table S548.  Gene #75: 'del_11q25' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 26(11Q25) MUTATED 63 12 12
DEL PEAK 26(11Q25) WILD-TYPE 142 147 129

Figure S548.  Get High-res Image Gene #75: 'del_11q25' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11q25' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.37e-10 (Fisher's exact test), Q value = 4.8e-07

Table S549.  Gene #75: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 26(11Q25) MUTATED 3 12 72
DEL PEAK 26(11Q25) WILD-TYPE 5 204 209

Figure S549.  Get High-res Image Gene #75: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11q25' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.14e-05 (Fisher's exact test), Q value = 0.012

Table S550.  Gene #75: 'del_11q25' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 26(11Q25) MUTATED 53 10 17
DEL PEAK 26(11Q25) WILD-TYPE 122 107 73

Figure S550.  Get High-res Image Gene #75: 'del_11q25' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11q25' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.42e-08 (Fisher's exact test), Q value = 3e-05

Table S551.  Gene #75: 'del_11q25' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 26(11Q25) MUTATED 3 64 13
DEL PEAK 26(11Q25) WILD-TYPE 27 134 141

Figure S551.  Get High-res Image Gene #75: 'del_11q25' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q23.1' versus 'CN_CNMF'

P value = 4.87e-24 (Chi-square test), Q value = 5.2e-21

Table S552.  Gene #76: 'del_12q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 27(12Q23.1) MUTATED 0 3 49 1 0
DEL PEAK 27(12Q23.1) WILD-TYPE 305 45 105 11 5

Figure S552.  Get High-res Image Gene #76: 'del_12q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q23.1' versus 'METHLYATION_CNMF'

P value = 7.56e-12 (Fisher's exact test), Q value = 6.2e-09

Table S553.  Gene #76: 'del_12q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 27(12Q23.1) MUTATED 34 11 0
DEL PEAK 27(12Q23.1) WILD-TYPE 118 83 164

Figure S553.  Get High-res Image Gene #76: 'del_12q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12q23.1' versus 'MRNASEQ_CNMF'

P value = 3.93e-13 (Fisher's exact test), Q value = 3.4e-10

Table S554.  Gene #76: 'del_12q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 27(12Q23.1) MUTATED 48 2 3
DEL PEAK 27(12Q23.1) WILD-TYPE 176 148 142

Figure S554.  Get High-res Image Gene #76: 'del_12q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.26e-11 (Fisher's exact test), Q value = 4.2e-08

Table S555.  Gene #76: 'del_12q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 27(12Q23.1) MUTATED 5 1 47
DEL PEAK 27(12Q23.1) WILD-TYPE 142 131 193

Figure S555.  Get High-res Image Gene #76: 'del_12q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q23.1' versus 'MIRSEQ_CNMF'

P value = 7.66e-12 (Fisher's exact test), Q value = 6.3e-09

Table S556.  Gene #76: 'del_12q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 27(12Q23.1) MUTATED 44 2 5
DEL PEAK 27(12Q23.1) WILD-TYPE 161 157 136

Figure S556.  Get High-res Image Gene #76: 'del_12q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_12q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.35e-09 (Fisher's exact test), Q value = 1.7e-06

Table S557.  Gene #76: 'del_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 27(12Q23.1) MUTATED 0 3 48
DEL PEAK 27(12Q23.1) WILD-TYPE 8 213 233

Figure S557.  Get High-res Image Gene #76: 'del_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.5e-05 (Fisher's exact test), Q value = 0.0084

Table S558.  Gene #76: 'del_12q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 27(12Q23.1) MUTATED 32 2 11
DEL PEAK 27(12Q23.1) WILD-TYPE 143 115 79

Figure S558.  Get High-res Image Gene #76: 'del_12q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_12q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.45e-08 (Fisher's exact test), Q value = 2.4e-05

Table S559.  Gene #76: 'del_12q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 27(12Q23.1) MUTATED 5 38 2
DEL PEAK 27(12Q23.1) WILD-TYPE 25 160 152

Figure S559.  Get High-res Image Gene #76: 'del_12q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q24.33' versus 'CN_CNMF'

P value = 2.24e-29 (Chi-square test), Q value = 2.5e-26

Table S560.  Gene #77: 'del_12q24.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 28(12Q24.33) MUTATED 1 3 59 1 0
DEL PEAK 28(12Q24.33) WILD-TYPE 304 45 95 11 5

Figure S560.  Get High-res Image Gene #77: 'del_12q24.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q24.33' versus 'METHLYATION_CNMF'

P value = 5.33e-11 (Fisher's exact test), Q value = 4.2e-08

Table S561.  Gene #77: 'del_12q24.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 28(12Q24.33) MUTATED 41 14 3
DEL PEAK 28(12Q24.33) WILD-TYPE 111 80 161

Figure S561.  Get High-res Image Gene #77: 'del_12q24.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12q24.33' versus 'MRNASEQ_CNMF'

P value = 7.62e-19 (Fisher's exact test), Q value = 7.6e-16

Table S562.  Gene #77: 'del_12q24.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 28(12Q24.33) MUTATED 60 1 3
DEL PEAK 28(12Q24.33) WILD-TYPE 164 149 142

Figure S562.  Get High-res Image Gene #77: 'del_12q24.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q24.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.48e-17 (Fisher's exact test), Q value = 8.2e-14

Table S563.  Gene #77: 'del_12q24.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 28(12Q24.33) MUTATED 3 1 60
DEL PEAK 28(12Q24.33) WILD-TYPE 144 131 180

Figure S563.  Get High-res Image Gene #77: 'del_12q24.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q24.33' versus 'MIRSEQ_CNMF'

P value = 3.26e-13 (Fisher's exact test), Q value = 2.8e-10

Table S564.  Gene #77: 'del_12q24.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 28(12Q24.33) MUTATED 51 3 6
DEL PEAK 28(12Q24.33) WILD-TYPE 154 156 135

Figure S564.  Get High-res Image Gene #77: 'del_12q24.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_12q24.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.46e-08 (Fisher's exact test), Q value = 1.7e-05

Table S565.  Gene #77: 'del_12q24.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 28(12Q24.33) MUTATED 1 6 53
DEL PEAK 28(12Q24.33) WILD-TYPE 7 210 228

Figure S565.  Get High-res Image Gene #77: 'del_12q24.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q24.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.47e-07 (Fisher's exact test), Q value = 9.6e-05

Table S566.  Gene #77: 'del_12q24.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 28(12Q24.33) MUTATED 43 3 10
DEL PEAK 28(12Q24.33) WILD-TYPE 132 114 80

Figure S566.  Get High-res Image Gene #77: 'del_12q24.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_12q24.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.59e-08 (Fisher's exact test), Q value = 6.4e-05

Table S567.  Gene #77: 'del_12q24.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 28(12Q24.33) MUTATED 5 46 5
DEL PEAK 28(12Q24.33) WILD-TYPE 25 152 149

Figure S567.  Get High-res Image Gene #77: 'del_12q24.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q11' versus 'CN_CNMF'

P value = 7.73e-35 (Chi-square test), Q value = 8.7e-32

Table S568.  Gene #78: 'del_13q11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 29(13Q11) MUTATED 2 19 73 1 1
DEL PEAK 29(13Q11) WILD-TYPE 303 29 81 11 4

Figure S568.  Get High-res Image Gene #78: 'del_13q11' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q11' versus 'METHLYATION_CNMF'

P value = 1.36e-09 (Fisher's exact test), Q value = 1e-06

Table S569.  Gene #78: 'del_13q11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 29(13Q11) MUTATED 51 21 10
DEL PEAK 29(13Q11) WILD-TYPE 101 73 154

Figure S569.  Get High-res Image Gene #78: 'del_13q11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q11' versus 'MRNASEQ_CNMF'

P value = 1.82e-13 (Fisher's exact test), Q value = 1.6e-10

Table S570.  Gene #78: 'del_13q11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 29(13Q11) MUTATED 74 7 15
DEL PEAK 29(13Q11) WILD-TYPE 150 143 130

Figure S570.  Get High-res Image Gene #78: 'del_13q11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.84e-12 (Fisher's exact test), Q value = 5.6e-09

Table S571.  Gene #78: 'del_13q11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 29(13Q11) MUTATED 17 5 74
DEL PEAK 29(13Q11) WILD-TYPE 130 127 166

Figure S571.  Get High-res Image Gene #78: 'del_13q11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q11' versus 'MIRSEQ_CNMF'

P value = 9.99e-10 (Fisher's exact test), Q value = 7.5e-07

Table S572.  Gene #78: 'del_13q11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 29(13Q11) MUTATED 65 13 14
DEL PEAK 29(13Q11) WILD-TYPE 140 146 127

Figure S572.  Get High-res Image Gene #78: 'del_13q11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.32e-09 (Fisher's exact test), Q value = 3.1e-06

Table S573.  Gene #78: 'del_13q11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 29(13Q11) MUTATED 5 16 71
DEL PEAK 29(13Q11) WILD-TYPE 3 200 210

Figure S573.  Get High-res Image Gene #78: 'del_13q11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.71e-05 (Fisher's exact test), Q value = 0.024

Table S574.  Gene #78: 'del_13q11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 29(13Q11) MUTATED 3 59 18
DEL PEAK 29(13Q11) WILD-TYPE 27 139 136

Figure S574.  Get High-res Image Gene #78: 'del_13q11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 6.13e-37 (Chi-square test), Q value = 6.9e-34

Table S575.  Gene #79: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 30(13Q14.2) MUTATED 3 21 77 1 1
DEL PEAK 30(13Q14.2) WILD-TYPE 302 27 77 11 4

Figure S575.  Get High-res Image Gene #79: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 1.37e-08 (Fisher's exact test), Q value = 9.8e-06

Table S576.  Gene #79: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 30(13Q14.2) MUTATED 52 25 13
DEL PEAK 30(13Q14.2) WILD-TYPE 100 69 151

Figure S576.  Get High-res Image Gene #79: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 4.9e-13 (Fisher's exact test), Q value = 4.2e-10

Table S577.  Gene #79: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 30(13Q14.2) MUTATED 77 8 18
DEL PEAK 30(13Q14.2) WILD-TYPE 147 142 127

Figure S577.  Get High-res Image Gene #79: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.06e-11 (Fisher's exact test), Q value = 1.6e-08

Table S578.  Gene #79: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 30(13Q14.2) MUTATED 20 6 77
DEL PEAK 30(13Q14.2) WILD-TYPE 127 126 163

Figure S578.  Get High-res Image Gene #79: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 4.92e-07 (Fisher's exact test), Q value = 0.00031

Table S579.  Gene #79: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 30(13Q14.2) MUTATED 64 17 18
DEL PEAK 30(13Q14.2) WILD-TYPE 141 142 123

Figure S579.  Get High-res Image Gene #79: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.73e-09 (Fisher's exact test), Q value = 7e-06

Table S580.  Gene #79: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 30(13Q14.2) MUTATED 6 20 73
DEL PEAK 30(13Q14.2) WILD-TYPE 2 196 208

Figure S580.  Get High-res Image Gene #79: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q13.1' versus 'CN_CNMF'

P value = 2.82e-26 (Chi-square test), Q value = 3.1e-23

Table S581.  Gene #80: 'del_14q13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 31(14Q13.1) MUTATED 2 6 58 1 2
DEL PEAK 31(14Q13.1) WILD-TYPE 303 42 96 11 3

Figure S581.  Get High-res Image Gene #80: 'del_14q13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q13.1' versus 'METHLYATION_CNMF'

P value = 1.21e-11 (Fisher's exact test), Q value = 9.8e-09

Table S582.  Gene #80: 'del_14q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 31(14Q13.1) MUTATED 46 9 5
DEL PEAK 31(14Q13.1) WILD-TYPE 106 85 159

Figure S582.  Get High-res Image Gene #80: 'del_14q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q13.1' versus 'MRNASEQ_CNMF'

P value = 1.82e-13 (Fisher's exact test), Q value = 1.6e-10

Table S583.  Gene #80: 'del_14q13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 31(14Q13.1) MUTATED 58 4 6
DEL PEAK 31(14Q13.1) WILD-TYPE 166 146 139

Figure S583.  Get High-res Image Gene #80: 'del_14q13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.92e-13 (Fisher's exact test), Q value = 4.2e-10

Table S584.  Gene #80: 'del_14q13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 31(14Q13.1) MUTATED 7 2 59
DEL PEAK 31(14Q13.1) WILD-TYPE 140 130 181

Figure S584.  Get High-res Image Gene #80: 'del_14q13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q13.1' versus 'MIRSEQ_CNMF'

P value = 1.07e-10 (Fisher's exact test), Q value = 8.4e-08

Table S585.  Gene #80: 'del_14q13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 31(14Q13.1) MUTATED 51 4 11
DEL PEAK 31(14Q13.1) WILD-TYPE 154 155 130

Figure S585.  Get High-res Image Gene #80: 'del_14q13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_14q13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.74e-12 (Fisher's exact test), Q value = 2.3e-09

Table S586.  Gene #80: 'del_14q13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 31(14Q13.1) MUTATED 3 4 59
DEL PEAK 31(14Q13.1) WILD-TYPE 5 212 222

Figure S586.  Get High-res Image Gene #80: 'del_14q13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.76e-05 (Fisher's exact test), Q value = 0.0098

Table S587.  Gene #80: 'del_14q13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 31(14Q13.1) MUTATED 41 5 14
DEL PEAK 31(14Q13.1) WILD-TYPE 134 112 76

Figure S587.  Get High-res Image Gene #80: 'del_14q13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_14q13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.18e-06 (Fisher's exact test), Q value = 0.0013

Table S588.  Gene #80: 'del_14q13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 31(14Q13.1) MUTATED 4 48 8
DEL PEAK 31(14Q13.1) WILD-TYPE 26 150 146

Figure S588.  Get High-res Image Gene #80: 'del_14q13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q15.1' versus 'CN_CNMF'

P value = 5.6e-57 (Chi-square test), Q value = 6.5e-54

Table S589.  Gene #81: 'del_15q15.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 32(15Q15.1) MUTATED 5 18 110 0 2
DEL PEAK 32(15Q15.1) WILD-TYPE 300 30 44 12 3

Figure S589.  Get High-res Image Gene #81: 'del_15q15.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q15.1' versus 'METHLYATION_CNMF'

P value = 6.42e-18 (Fisher's exact test), Q value = 6.3e-15

Table S590.  Gene #81: 'del_15q15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 32(15Q15.1) MUTATED 77 30 12
DEL PEAK 32(15Q15.1) WILD-TYPE 75 64 152

Figure S590.  Get High-res Image Gene #81: 'del_15q15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q15.1' versus 'MRNASEQ_CNMF'

P value = 2.31e-29 (Fisher's exact test), Q value = 2.6e-26

Table S591.  Gene #81: 'del_15q15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 32(15Q15.1) MUTATED 114 10 11
DEL PEAK 32(15Q15.1) WILD-TYPE 110 140 134

Figure S591.  Get High-res Image Gene #81: 'del_15q15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.37e-25 (Fisher's exact test), Q value = 2.6e-22

Table S592.  Gene #81: 'del_15q15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 32(15Q15.1) MUTATED 13 8 114
DEL PEAK 32(15Q15.1) WILD-TYPE 134 124 126

Figure S592.  Get High-res Image Gene #81: 'del_15q15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_CNMF'

P value = 2.08e-21 (Fisher's exact test), Q value = 2.2e-18

Table S593.  Gene #81: 'del_15q15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 32(15Q15.1) MUTATED 99 13 17
DEL PEAK 32(15Q15.1) WILD-TYPE 106 146 124

Figure S593.  Get High-res Image Gene #81: 'del_15q15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.45e-17 (Fisher's exact test), Q value = 4.3e-14

Table S594.  Gene #81: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 32(15Q15.1) MUTATED 6 17 106
DEL PEAK 32(15Q15.1) WILD-TYPE 2 199 175

Figure S594.  Get High-res Image Gene #81: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.44e-07 (Fisher's exact test), Q value = 9.5e-05

Table S595.  Gene #81: 'del_15q15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 32(15Q15.1) MUTATED 70 13 29
DEL PEAK 32(15Q15.1) WILD-TYPE 105 104 61

Figure S595.  Get High-res Image Gene #81: 'del_15q15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.62e-11 (Fisher's exact test), Q value = 5.2e-08

Table S596.  Gene #81: 'del_15q15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 32(15Q15.1) MUTATED 7 87 18
DEL PEAK 32(15Q15.1) WILD-TYPE 23 111 136

Figure S596.  Get High-res Image Gene #81: 'del_15q15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q23' versus 'MRNA_CHIERARCHICAL'

P value = 0.000218 (Fisher's exact test), Q value = 0.1

Table S597.  Gene #82: 'del_15q23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 33(15Q23) MUTATED 0 0 6
DEL PEAK 33(15Q23) WILD-TYPE 19 19 9

Figure S597.  Get High-res Image Gene #82: 'del_15q23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q23' versus 'CN_CNMF'

P value = 7e-43 (Chi-square test), Q value = 8e-40

Table S598.  Gene #82: 'del_15q23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 33(15Q23) MUTATED 4 15 88 0 3
DEL PEAK 33(15Q23) WILD-TYPE 301 33 66 12 2

Figure S598.  Get High-res Image Gene #82: 'del_15q23' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q23' versus 'METHLYATION_CNMF'

P value = 1.13e-16 (Fisher's exact test), Q value = 1.1e-13

Table S599.  Gene #82: 'del_15q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 33(15Q23) MUTATED 67 21 8
DEL PEAK 33(15Q23) WILD-TYPE 85 73 156

Figure S599.  Get High-res Image Gene #82: 'del_15q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q23' versus 'MRNASEQ_CNMF'

P value = 1.23e-22 (Fisher's exact test), Q value = 1.3e-19

Table S600.  Gene #82: 'del_15q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 33(15Q23) MUTATED 93 9 8
DEL PEAK 33(15Q23) WILD-TYPE 131 141 137

Figure S600.  Get High-res Image Gene #82: 'del_15q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.71e-20 (Fisher's exact test), Q value = 1.8e-17

Table S601.  Gene #82: 'del_15q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 33(15Q23) MUTATED 9 7 94
DEL PEAK 33(15Q23) WILD-TYPE 138 125 146

Figure S601.  Get High-res Image Gene #82: 'del_15q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q23' versus 'MIRSEQ_CNMF'

P value = 8.2e-15 (Fisher's exact test), Q value = 7.5e-12

Table S602.  Gene #82: 'del_15q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 33(15Q23) MUTATED 78 11 15
DEL PEAK 33(15Q23) WILD-TYPE 127 148 126

Figure S602.  Get High-res Image Gene #82: 'del_15q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.22e-13 (Fisher's exact test), Q value = 1.9e-10

Table S603.  Gene #82: 'del_15q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 33(15Q23) MUTATED 4 13 87
DEL PEAK 33(15Q23) WILD-TYPE 4 203 194

Figure S603.  Get High-res Image Gene #82: 'del_15q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_15q23' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.68e-08 (Fisher's exact test), Q value = 2.5e-05

Table S604.  Gene #82: 'del_15q23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 33(15Q23) MUTATED 63 9 18
DEL PEAK 33(15Q23) WILD-TYPE 112 108 72

Figure S604.  Get High-res Image Gene #82: 'del_15q23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.14e-10 (Fisher's exact test), Q value = 3.1e-07

Table S605.  Gene #82: 'del_15q23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 33(15Q23) MUTATED 6 72 12
DEL PEAK 33(15Q23) WILD-TYPE 24 126 142

Figure S605.  Get High-res Image Gene #82: 'del_15q23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16p13.3' versus 'CN_CNMF'

P value = 2.85e-39 (Chi-square test), Q value = 3.2e-36

Table S606.  Gene #83: 'del_16p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 34(16P13.3) MUTATED 2 8 78 0 0
DEL PEAK 34(16P13.3) WILD-TYPE 303 40 76 12 5

Figure S606.  Get High-res Image Gene #83: 'del_16p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_16p13.3' versus 'METHLYATION_CNMF'

P value = 2.42e-15 (Fisher's exact test), Q value = 2.2e-12

Table S607.  Gene #83: 'del_16p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 34(16P13.3) MUTATED 55 20 4
DEL PEAK 34(16P13.3) WILD-TYPE 97 74 160

Figure S607.  Get High-res Image Gene #83: 'del_16p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16p13.3' versus 'MRNASEQ_CNMF'

P value = 6.07e-23 (Fisher's exact test), Q value = 6.4e-20

Table S608.  Gene #83: 'del_16p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 34(16P13.3) MUTATED 79 2 7
DEL PEAK 34(16P13.3) WILD-TYPE 145 148 138

Figure S608.  Get High-res Image Gene #83: 'del_16p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.61e-19 (Fisher's exact test), Q value = 3.6e-16

Table S609.  Gene #83: 'del_16p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 34(16P13.3) MUTATED 8 2 78
DEL PEAK 34(16P13.3) WILD-TYPE 139 130 162

Figure S609.  Get High-res Image Gene #83: 'del_16p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_CNMF'

P value = 4.82e-16 (Fisher's exact test), Q value = 4.5e-13

Table S610.  Gene #83: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 34(16P13.3) MUTATED 69 7 9
DEL PEAK 34(16P13.3) WILD-TYPE 136 152 132

Figure S610.  Get High-res Image Gene #83: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.92e-14 (Fisher's exact test), Q value = 8e-11

Table S611.  Gene #83: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 34(16P13.3) MUTATED 2 7 76
DEL PEAK 34(16P13.3) WILD-TYPE 6 209 205

Figure S611.  Get High-res Image Gene #83: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.06e-05 (Fisher's exact test), Q value = 0.006

Table S612.  Gene #83: 'del_16p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 34(16P13.3) MUTATED 50 8 19
DEL PEAK 34(16P13.3) WILD-TYPE 125 109 71

Figure S612.  Get High-res Image Gene #83: 'del_16p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.1e-10 (Fisher's exact test), Q value = 1.6e-07

Table S613.  Gene #83: 'del_16p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 34(16P13.3) MUTATED 3 65 9
DEL PEAK 34(16P13.3) WILD-TYPE 27 133 145

Figure S613.  Get High-res Image Gene #83: 'del_16p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q21' versus 'MRNA_CHIERARCHICAL'

P value = 9.8e-05 (Fisher's exact test), Q value = 0.049

Table S614.  Gene #84: 'del_16q21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 35(16Q21) MUTATED 0 1 8
DEL PEAK 35(16Q21) WILD-TYPE 19 18 7

Figure S614.  Get High-res Image Gene #84: 'del_16q21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_16q21' versus 'CN_CNMF'

P value = 4.14e-59 (Chi-square test), Q value = 4.8e-56

Table S615.  Gene #84: 'del_16q21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 35(16Q21) MUTATED 15 14 121 0 0
DEL PEAK 35(16Q21) WILD-TYPE 290 34 33 12 5

Figure S615.  Get High-res Image Gene #84: 'del_16q21' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q21' versus 'METHLYATION_CNMF'

P value = 9.18e-18 (Fisher's exact test), Q value = 9e-15

Table S616.  Gene #84: 'del_16q21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 35(16Q21) MUTATED 83 32 16
DEL PEAK 35(16Q21) WILD-TYPE 69 62 148

Figure S616.  Get High-res Image Gene #84: 'del_16q21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q21' versus 'MRNASEQ_CNMF'

P value = 2.81e-26 (Fisher's exact test), Q value = 3.1e-23

Table S617.  Gene #84: 'del_16q21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 35(16Q21) MUTATED 119 15 15
DEL PEAK 35(16Q21) WILD-TYPE 105 135 130

Figure S617.  Get High-res Image Gene #84: 'del_16q21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16q21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.85e-23 (Fisher's exact test), Q value = 6.2e-20

Table S618.  Gene #84: 'del_16q21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 35(16Q21) MUTATED 16 13 120
DEL PEAK 35(16Q21) WILD-TYPE 131 119 120

Figure S618.  Get High-res Image Gene #84: 'del_16q21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16q21' versus 'MIRSEQ_CNMF'

P value = 3.88e-18 (Fisher's exact test), Q value = 3.8e-15

Table S619.  Gene #84: 'del_16q21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 35(16Q21) MUTATED 102 17 24
DEL PEAK 35(16Q21) WILD-TYPE 103 142 117

Figure S619.  Get High-res Image Gene #84: 'del_16q21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16q21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.12e-11 (Fisher's exact test), Q value = 9.1e-09

Table S620.  Gene #84: 'del_16q21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 35(16Q21) MUTATED 5 28 110
DEL PEAK 35(16Q21) WILD-TYPE 3 188 171

Figure S620.  Get High-res Image Gene #84: 'del_16q21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16q21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.41e-07 (Fisher's exact test), Q value = 9.3e-05

Table S621.  Gene #84: 'del_16q21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 35(16Q21) MUTATED 79 17 30
DEL PEAK 35(16Q21) WILD-TYPE 96 100 60

Figure S621.  Get High-res Image Gene #84: 'del_16q21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16q21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.5e-10 (Fisher's exact test), Q value = 1.9e-07

Table S622.  Gene #84: 'del_16q21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 35(16Q21) MUTATED 9 94 23
DEL PEAK 35(16Q21) WILD-TYPE 21 104 131

Figure S622.  Get High-res Image Gene #84: 'del_16q21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.000312 (Fisher's exact test), Q value = 0.14

Table S623.  Gene #85: 'del_16q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 36(16Q23.1) MUTATED 1 2 9
DEL PEAK 36(16Q23.1) WILD-TYPE 18 17 6

Figure S623.  Get High-res Image Gene #85: 'del_16q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 1.86e-60 (Chi-square test), Q value = 2.2e-57

Table S624.  Gene #85: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 36(16Q23.1) MUTATED 20 14 127 0 0
DEL PEAK 36(16Q23.1) WILD-TYPE 285 34 27 12 5

Figure S624.  Get High-res Image Gene #85: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 8.53e-17 (Fisher's exact test), Q value = 8.2e-14

Table S625.  Gene #85: 'del_16q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 36(16Q23.1) MUTATED 85 33 19
DEL PEAK 36(16Q23.1) WILD-TYPE 67 61 145

Figure S625.  Get High-res Image Gene #85: 'del_16q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 9.28e-29 (Fisher's exact test), Q value = 1e-25

Table S626.  Gene #85: 'del_16q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 36(16Q23.1) MUTATED 128 17 16
DEL PEAK 36(16Q23.1) WILD-TYPE 96 133 129

Figure S626.  Get High-res Image Gene #85: 'del_16q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.77e-25 (Fisher's exact test), Q value = 6.2e-22

Table S627.  Gene #85: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 36(16Q23.1) MUTATED 17 15 129
DEL PEAK 36(16Q23.1) WILD-TYPE 130 117 111

Figure S627.  Get High-res Image Gene #85: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 6.23e-21 (Fisher's exact test), Q value = 6.5e-18

Table S628.  Gene #85: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 36(16Q23.1) MUTATED 110 18 24
DEL PEAK 36(16Q23.1) WILD-TYPE 95 141 117

Figure S628.  Get High-res Image Gene #85: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.78e-13 (Fisher's exact test), Q value = 1.6e-10

Table S629.  Gene #85: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 36(16Q23.1) MUTATED 4 28 120
DEL PEAK 36(16Q23.1) WILD-TYPE 4 188 161

Figure S629.  Get High-res Image Gene #85: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-08 (Fisher's exact test), Q value = 4e-05

Table S630.  Gene #85: 'del_16q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 36(16Q23.1) MUTATED 80 17 34
DEL PEAK 36(16Q23.1) WILD-TYPE 95 100 56

Figure S630.  Get High-res Image Gene #85: 'del_16q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.15e-11 (Fisher's exact test), Q value = 9.3e-09

Table S631.  Gene #85: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 36(16Q23.1) MUTATED 9 99 23
DEL PEAK 36(16Q23.1) WILD-TYPE 21 99 131

Figure S631.  Get High-res Image Gene #85: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p13.3' versus 'MRNA_CHIERARCHICAL'

P value = 9.8e-05 (Fisher's exact test), Q value = 0.049

Table S632.  Gene #86: 'del_17p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 37(17P13.3) MUTATED 1 0 8
DEL PEAK 37(17P13.3) WILD-TYPE 18 19 7

Figure S632.  Get High-res Image Gene #86: 'del_17p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p13.3' versus 'CN_CNMF'

P value = 6.45e-51 (Chi-square test), Q value = 7.4e-48

Table S633.  Gene #86: 'del_17p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 37(17P13.3) MUTATED 3 14 98 0 0
DEL PEAK 37(17P13.3) WILD-TYPE 302 34 56 12 5

Figure S633.  Get High-res Image Gene #86: 'del_17p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p13.3' versus 'METHLYATION_CNMF'

P value = 8.78e-12 (Fisher's exact test), Q value = 7.2e-09

Table S634.  Gene #86: 'del_17p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 37(17P13.3) MUTATED 61 24 12
DEL PEAK 37(17P13.3) WILD-TYPE 91 70 152

Figure S634.  Get High-res Image Gene #86: 'del_17p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p13.3' versus 'MRNASEQ_CNMF'

P value = 4.99e-22 (Fisher's exact test), Q value = 5.3e-19

Table S635.  Gene #86: 'del_17p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 37(17P13.3) MUTATED 94 6 14
DEL PEAK 37(17P13.3) WILD-TYPE 130 144 131

Figure S635.  Get High-res Image Gene #86: 'del_17p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.63e-18 (Fisher's exact test), Q value = 2.6e-15

Table S636.  Gene #86: 'del_17p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 37(17P13.3) MUTATED 16 5 93
DEL PEAK 37(17P13.3) WILD-TYPE 131 127 147

Figure S636.  Get High-res Image Gene #86: 'del_17p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.3' versus 'MIRSEQ_CNMF'

P value = 2.16e-14 (Fisher's exact test), Q value = 2e-11

Table S637.  Gene #86: 'del_17p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 37(17P13.3) MUTATED 81 15 14
DEL PEAK 37(17P13.3) WILD-TYPE 124 144 127

Figure S637.  Get High-res Image Gene #86: 'del_17p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.44e-10 (Fisher's exact test), Q value = 2.6e-07

Table S638.  Gene #86: 'del_17p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 37(17P13.3) MUTATED 4 19 87
DEL PEAK 37(17P13.3) WILD-TYPE 4 197 194

Figure S638.  Get High-res Image Gene #86: 'del_17p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.1e-06 (Fisher's exact test), Q value = 0.003

Table S639.  Gene #86: 'del_17p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 37(17P13.3) MUTATED 4 68 20
DEL PEAK 37(17P13.3) WILD-TYPE 26 130 134

Figure S639.  Get High-res Image Gene #86: 'del_17p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 9.8e-05 (Fisher's exact test), Q value = 0.049

Table S640.  Gene #87: 'del_17p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 38(17P11.2) MUTATED 1 0 8
DEL PEAK 38(17P11.2) WILD-TYPE 18 19 7

Figure S640.  Get High-res Image Gene #87: 'del_17p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p11.2' versus 'CN_CNMF'

P value = 1.88e-55 (Chi-square test), Q value = 2.2e-52

Table S641.  Gene #87: 'del_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 38(17P11.2) MUTATED 4 13 105 0 0
DEL PEAK 38(17P11.2) WILD-TYPE 301 35 49 12 5

Figure S641.  Get High-res Image Gene #87: 'del_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p11.2' versus 'METHLYATION_CNMF'

P value = 2.7e-14 (Fisher's exact test), Q value = 2.4e-11

Table S642.  Gene #87: 'del_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 38(17P11.2) MUTATED 68 26 12
DEL PEAK 38(17P11.2) WILD-TYPE 84 68 152

Figure S642.  Get High-res Image Gene #87: 'del_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p11.2' versus 'MRNASEQ_CNMF'

P value = 1.26e-27 (Fisher's exact test), Q value = 1.4e-24

Table S643.  Gene #87: 'del_17p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 38(17P11.2) MUTATED 104 5 13
DEL PEAK 38(17P11.2) WILD-TYPE 120 145 132

Figure S643.  Get High-res Image Gene #87: 'del_17p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.76e-23 (Fisher's exact test), Q value = 2.9e-20

Table S644.  Gene #87: 'del_17p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 38(17P11.2) MUTATED 15 4 103
DEL PEAK 38(17P11.2) WILD-TYPE 132 128 137

Figure S644.  Get High-res Image Gene #87: 'del_17p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p11.2' versus 'MIRSEQ_CNMF'

P value = 2.66e-16 (Fisher's exact test), Q value = 2.5e-13

Table S645.  Gene #87: 'del_17p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 38(17P11.2) MUTATED 86 16 13
DEL PEAK 38(17P11.2) WILD-TYPE 119 143 128

Figure S645.  Get High-res Image Gene #87: 'del_17p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.62e-13 (Fisher's exact test), Q value = 3.2e-10

Table S646.  Gene #87: 'del_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 38(17P11.2) MUTATED 5 17 93
DEL PEAK 38(17P11.2) WILD-TYPE 3 199 188

Figure S646.  Get High-res Image Gene #87: 'del_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.14

Table S647.  Gene #87: 'del_17p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 38(17P11.2) MUTATED 60 16 24
DEL PEAK 38(17P11.2) WILD-TYPE 115 101 66

Figure S647.  Get High-res Image Gene #87: 'del_17p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.2e-07 (Fisher's exact test), Q value = 0.00039

Table S648.  Gene #87: 'del_17p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 38(17P11.2) MUTATED 6 74 20
DEL PEAK 38(17P11.2) WILD-TYPE 24 124 134

Figure S648.  Get High-res Image Gene #87: 'del_17p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p11.2' versus 'MRNA_CNMF'

P value = 0.000111 (Fisher's exact test), Q value = 0.055

Table S649.  Gene #88: 'del_17p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 39(17P11.2) MUTATED 0 8 0 0
DEL PEAK 39(17P11.2) WILD-TYPE 14 9 12 10

Figure S649.  Get High-res Image Gene #88: 'del_17p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 7.26e-06 (Fisher's exact test), Q value = 0.0042

Table S650.  Gene #88: 'del_17p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 39(17P11.2) MUTATED 0 0 8
DEL PEAK 39(17P11.2) WILD-TYPE 19 19 7

Figure S650.  Get High-res Image Gene #88: 'del_17p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p11.2' versus 'CN_CNMF'

P value = 3.66e-55 (Chi-square test), Q value = 4.2e-52

Table S651.  Gene #88: 'del_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 39(17P11.2) MUTATED 2 12 102 0 0
DEL PEAK 39(17P11.2) WILD-TYPE 303 36 52 12 5

Figure S651.  Get High-res Image Gene #88: 'del_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p11.2' versus 'METHLYATION_CNMF'

P value = 7.1e-14 (Fisher's exact test), Q value = 6.4e-11

Table S652.  Gene #88: 'del_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 39(17P11.2) MUTATED 65 26 11
DEL PEAK 39(17P11.2) WILD-TYPE 87 68 153

Figure S652.  Get High-res Image Gene #88: 'del_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p11.2' versus 'MRNASEQ_CNMF'

P value = 6.63e-26 (Fisher's exact test), Q value = 7.2e-23

Table S653.  Gene #88: 'del_17p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 39(17P11.2) MUTATED 99 5 12
DEL PEAK 39(17P11.2) WILD-TYPE 125 145 133

Figure S653.  Get High-res Image Gene #88: 'del_17p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.16e-22 (Fisher's exact test), Q value = 8.6e-19

Table S654.  Gene #88: 'del_17p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 39(17P11.2) MUTATED 14 4 98
DEL PEAK 39(17P11.2) WILD-TYPE 133 128 142

Figure S654.  Get High-res Image Gene #88: 'del_17p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p11.2' versus 'MIRSEQ_CNMF'

P value = 5.37e-16 (Fisher's exact test), Q value = 5.1e-13

Table S655.  Gene #88: 'del_17p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 39(17P11.2) MUTATED 83 15 12
DEL PEAK 39(17P11.2) WILD-TYPE 122 144 129

Figure S655.  Get High-res Image Gene #88: 'del_17p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.31e-11 (Fisher's exact test), Q value = 1.1e-08

Table S656.  Gene #88: 'del_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 39(17P11.2) MUTATED 4 17 89
DEL PEAK 39(17P11.2) WILD-TYPE 4 199 192

Figure S656.  Get High-res Image Gene #88: 'del_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000131 (Fisher's exact test), Q value = 0.064

Table S657.  Gene #88: 'del_17p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 39(17P11.2) MUTATED 60 15 22
DEL PEAK 39(17P11.2) WILD-TYPE 115 102 68

Figure S657.  Get High-res Image Gene #88: 'del_17p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.28e-07 (Fisher's exact test), Q value = 0.00046

Table S658.  Gene #88: 'del_17p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 39(17P11.2) MUTATED 6 72 19
DEL PEAK 39(17P11.2) WILD-TYPE 24 126 135

Figure S658.  Get High-res Image Gene #88: 'del_17p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q11.2' versus 'MRNA_CNMF'

P value = 0.000567 (Fisher's exact test), Q value = 0.24

Table S659.  Gene #89: 'del_17q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 40(17Q11.2) MUTATED 0 7 0 0
DEL PEAK 40(17Q11.2) WILD-TYPE 14 10 12 10

Figure S659.  Get High-res Image Gene #89: 'del_17q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 4.17e-05 (Fisher's exact test), Q value = 0.022

Table S660.  Gene #89: 'del_17q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 40(17Q11.2) MUTATED 0 0 7
DEL PEAK 40(17Q11.2) WILD-TYPE 19 19 8

Figure S660.  Get High-res Image Gene #89: 'del_17q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17q11.2' versus 'CN_CNMF'

P value = 1.7e-43 (Chi-square test), Q value = 1.9e-40

Table S661.  Gene #89: 'del_17q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 40(17Q11.2) MUTATED 2 13 86 0 0
DEL PEAK 40(17Q11.2) WILD-TYPE 303 35 68 12 5

Figure S661.  Get High-res Image Gene #89: 'del_17q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_17q11.2' versus 'METHLYATION_CNMF'

P value = 1.43e-07 (Fisher's exact test), Q value = 9.5e-05

Table S662.  Gene #89: 'del_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 40(17Q11.2) MUTATED 51 21 14
DEL PEAK 40(17Q11.2) WILD-TYPE 101 73 150

Figure S662.  Get High-res Image Gene #89: 'del_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17q11.2' versus 'MRNASEQ_CNMF'

P value = 2.97e-16 (Fisher's exact test), Q value = 2.8e-13

Table S663.  Gene #89: 'del_17q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 40(17Q11.2) MUTATED 80 7 13
DEL PEAK 40(17Q11.2) WILD-TYPE 144 143 132

Figure S663.  Get High-res Image Gene #89: 'del_17q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.78e-14 (Fisher's exact test), Q value = 2.5e-11

Table S664.  Gene #89: 'del_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 40(17Q11.2) MUTATED 15 5 80
DEL PEAK 40(17Q11.2) WILD-TYPE 132 127 160

Figure S664.  Get High-res Image Gene #89: 'del_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17q11.2' versus 'MIRSEQ_CNMF'

P value = 4.58e-11 (Fisher's exact test), Q value = 3.6e-08

Table S665.  Gene #89: 'del_17q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 40(17Q11.2) MUTATED 69 16 11
DEL PEAK 40(17Q11.2) WILD-TYPE 136 143 130

Figure S665.  Get High-res Image Gene #89: 'del_17q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.84e-07 (Fisher's exact test), Q value = 0.00049

Table S666.  Gene #89: 'del_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 40(17Q11.2) MUTATED 4 20 72
DEL PEAK 40(17Q11.2) WILD-TYPE 4 196 209

Figure S666.  Get High-res Image Gene #89: 'del_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17q21.31' versus 'MRNA_CNMF'

P value = 0.000567 (Fisher's exact test), Q value = 0.24

Table S667.  Gene #90: 'del_17q21.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 41(17Q21.31) MUTATED 0 7 0 0
DEL PEAK 41(17Q21.31) WILD-TYPE 14 10 12 10

Figure S667.  Get High-res Image Gene #90: 'del_17q21.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17q21.31' versus 'MRNA_CHIERARCHICAL'

P value = 4.17e-05 (Fisher's exact test), Q value = 0.022

Table S668.  Gene #90: 'del_17q21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 41(17Q21.31) MUTATED 0 0 7
DEL PEAK 41(17Q21.31) WILD-TYPE 19 19 8

Figure S668.  Get High-res Image Gene #90: 'del_17q21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17q21.31' versus 'CN_CNMF'

P value = 3.41e-45 (Chi-square test), Q value = 3.9e-42

Table S669.  Gene #90: 'del_17q21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 41(17Q21.31) MUTATED 1 12 87 0 0
DEL PEAK 41(17Q21.31) WILD-TYPE 304 36 67 12 5

Figure S669.  Get High-res Image Gene #90: 'del_17q21.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_17q21.31' versus 'METHLYATION_CNMF'

P value = 2.12e-08 (Fisher's exact test), Q value = 1.5e-05

Table S670.  Gene #90: 'del_17q21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 41(17Q21.31) MUTATED 52 23 13
DEL PEAK 41(17Q21.31) WILD-TYPE 100 71 151

Figure S670.  Get High-res Image Gene #90: 'del_17q21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17q21.31' versus 'MRNASEQ_CNMF'

P value = 3.04e-16 (Fisher's exact test), Q value = 2.9e-13

Table S671.  Gene #90: 'del_17q21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 41(17Q21.31) MUTATED 79 6 14
DEL PEAK 41(17Q21.31) WILD-TYPE 145 144 131

Figure S671.  Get High-res Image Gene #90: 'del_17q21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17q21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.23e-15 (Fisher's exact test), Q value = 3.9e-12

Table S672.  Gene #90: 'del_17q21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 41(17Q21.31) MUTATED 15 4 80
DEL PEAK 41(17Q21.31) WILD-TYPE 132 128 160

Figure S672.  Get High-res Image Gene #90: 'del_17q21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17q21.31' versus 'MIRSEQ_CNMF'

P value = 1.05e-08 (Fisher's exact test), Q value = 7.5e-06

Table S673.  Gene #90: 'del_17q21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 41(17Q21.31) MUTATED 65 17 13
DEL PEAK 41(17Q21.31) WILD-TYPE 140 142 128

Figure S673.  Get High-res Image Gene #90: 'del_17q21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17q21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.21e-06 (Fisher's exact test), Q value = 0.00074

Table S674.  Gene #90: 'del_17q21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 41(17Q21.31) MUTATED 4 20 71
DEL PEAK 41(17Q21.31) WILD-TYPE 4 196 210

Figure S674.  Get High-res Image Gene #90: 'del_17q21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'CN_CNMF'

P value = 7.46e-33 (Chi-square test), Q value = 8.3e-30

Table S675.  Gene #91: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 42(18Q21.2) MUTATED 2 17 69 0 2
DEL PEAK 42(18Q21.2) WILD-TYPE 303 31 85 12 3

Figure S675.  Get High-res Image Gene #91: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 1.34e-10 (Fisher's exact test), Q value = 1e-07

Table S676.  Gene #91: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 42(18Q21.2) MUTATED 54 16 10
DEL PEAK 42(18Q21.2) WILD-TYPE 98 78 154

Figure S676.  Get High-res Image Gene #91: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 5.49e-16 (Fisher's exact test), Q value = 5.2e-13

Table S677.  Gene #91: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 42(18Q21.2) MUTATED 74 6 10
DEL PEAK 42(18Q21.2) WILD-TYPE 150 144 135

Figure S677.  Get High-res Image Gene #91: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.26e-14 (Fisher's exact test), Q value = 7.4e-11

Table S678.  Gene #91: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 42(18Q21.2) MUTATED 11 5 74
DEL PEAK 42(18Q21.2) WILD-TYPE 136 127 166

Figure S678.  Get High-res Image Gene #91: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CNMF'

P value = 3.77e-13 (Fisher's exact test), Q value = 3.3e-10

Table S679.  Gene #91: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 42(18Q21.2) MUTATED 67 11 9
DEL PEAK 42(18Q21.2) WILD-TYPE 138 148 132

Figure S679.  Get High-res Image Gene #91: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.74e-10 (Fisher's exact test), Q value = 2.8e-07

Table S680.  Gene #91: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 42(18Q21.2) MUTATED 5 13 69
DEL PEAK 42(18Q21.2) WILD-TYPE 3 203 212

Figure S680.  Get High-res Image Gene #91: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000199 (Fisher's exact test), Q value = 0.094

Table S681.  Gene #91: 'del_18q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 42(18Q21.2) MUTATED 50 11 16
DEL PEAK 42(18Q21.2) WILD-TYPE 125 106 74

Figure S681.  Get High-res Image Gene #91: 'del_18q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.51e-05 (Fisher's exact test), Q value = 0.033

Table S682.  Gene #91: 'del_18q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 42(18Q21.2) MUTATED 7 55 15
DEL PEAK 42(18Q21.2) WILD-TYPE 23 143 139

Figure S682.  Get High-res Image Gene #91: 'del_18q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q23' versus 'CN_CNMF'

P value = 4.21e-35 (Chi-square test), Q value = 4.8e-32

Table S683.  Gene #92: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 43(18Q23) MUTATED 2 18 74 1 1
DEL PEAK 43(18Q23) WILD-TYPE 303 30 80 11 4

Figure S683.  Get High-res Image Gene #92: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q23' versus 'METHLYATION_CNMF'

P value = 1.28e-11 (Fisher's exact test), Q value = 1e-08

Table S684.  Gene #92: 'del_18q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 43(18Q23) MUTATED 57 17 10
DEL PEAK 43(18Q23) WILD-TYPE 95 77 154

Figure S684.  Get High-res Image Gene #92: 'del_18q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q23' versus 'MRNASEQ_CNMF'

P value = 2.95e-18 (Fisher's exact test), Q value = 2.9e-15

Table S685.  Gene #92: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 43(18Q23) MUTATED 80 6 10
DEL PEAK 43(18Q23) WILD-TYPE 144 144 135

Figure S685.  Get High-res Image Gene #92: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.61e-16 (Fisher's exact test), Q value = 3.4e-13

Table S686.  Gene #92: 'del_18q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 43(18Q23) MUTATED 12 4 80
DEL PEAK 43(18Q23) WILD-TYPE 135 128 160

Figure S686.  Get High-res Image Gene #92: 'del_18q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_CNMF'

P value = 1.54e-12 (Fisher's exact test), Q value = 1.3e-09

Table S687.  Gene #92: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 43(18Q23) MUTATED 69 12 11
DEL PEAK 43(18Q23) WILD-TYPE 136 147 130

Figure S687.  Get High-res Image Gene #92: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18q23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.27e-10 (Fisher's exact test), Q value = 9.9e-08

Table S688.  Gene #92: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 43(18Q23) MUTATED 4 13 75
DEL PEAK 43(18Q23) WILD-TYPE 4 203 206

Figure S688.  Get High-res Image Gene #92: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.15e-06 (Fisher's exact test), Q value = 0.0025

Table S689.  Gene #92: 'del_18q23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 43(18Q23) MUTATED 5 61 15
DEL PEAK 43(18Q23) WILD-TYPE 25 137 139

Figure S689.  Get High-res Image Gene #92: 'del_18q23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'MRNA_CNMF'

P value = 8.71e-07 (Fisher's exact test), Q value = 0.00054

Table S690.  Gene #93: 'del_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 44(19P13.3) MUTATED 0 11 0 0
DEL PEAK 44(19P13.3) WILD-TYPE 14 6 12 10

Figure S690.  Get High-res Image Gene #93: 'del_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19p13.3' versus 'MRNA_CHIERARCHICAL'

P value = 3.64e-08 (Fisher's exact test), Q value = 2.5e-05

Table S691.  Gene #93: 'del_19p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 44(19P13.3) MUTATED 0 0 11
DEL PEAK 44(19P13.3) WILD-TYPE 19 19 4

Figure S691.  Get High-res Image Gene #93: 'del_19p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 1.36e-78 (Chi-square test), Q value = 1.6e-75

Table S692.  Gene #93: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 44(19P13.3) MUTATED 1 14 131 0 1
DEL PEAK 44(19P13.3) WILD-TYPE 304 34 23 12 4

Figure S692.  Get High-res Image Gene #93: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 2.37e-33 (Fisher's exact test), Q value = 2.7e-30

Table S693.  Gene #93: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 44(19P13.3) MUTATED 96 28 5
DEL PEAK 44(19P13.3) WILD-TYPE 56 66 159

Figure S693.  Get High-res Image Gene #93: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p13.3' versus 'RPPA_CNMF'

P value = 4.33e-05 (Chi-square test), Q value = 0.023

Table S694.  Gene #93: 'del_19p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
DEL PEAK 44(19P13.3) MUTATED 7 14 2 0 1 7
DEL PEAK 44(19P13.3) WILD-TYPE 34 23 37 12 40 17

Figure S694.  Get High-res Image Gene #93: 'del_19p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 8.04e-46 (Fisher's exact test), Q value = 9.2e-43

Table S695.  Gene #93: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 44(19P13.3) MUTATED 133 4 9
DEL PEAK 44(19P13.3) WILD-TYPE 91 146 136

Figure S695.  Get High-res Image Gene #93: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.6e-40 (Fisher's exact test), Q value = 5.2e-37

Table S696.  Gene #93: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 44(19P13.3) MUTATED 9 4 133
DEL PEAK 44(19P13.3) WILD-TYPE 138 128 107

Figure S696.  Get High-res Image Gene #93: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 1.45e-34 (Fisher's exact test), Q value = 1.6e-31

Table S697.  Gene #93: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 44(19P13.3) MUTATED 117 11 11
DEL PEAK 44(19P13.3) WILD-TYPE 88 148 130

Figure S697.  Get High-res Image Gene #93: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.43e-20 (Fisher's exact test), Q value = 6.5e-17

Table S698.  Gene #93: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 44(19P13.3) MUTATED 4 16 119
DEL PEAK 44(19P13.3) WILD-TYPE 4 200 162

Figure S698.  Get High-res Image Gene #93: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.12e-10 (Fisher's exact test), Q value = 8.7e-08

Table S699.  Gene #93: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 44(19P13.3) MUTATED 81 12 30
DEL PEAK 44(19P13.3) WILD-TYPE 94 105 60

Figure S699.  Get High-res Image Gene #93: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.13e-18 (Fisher's exact test), Q value = 3.1e-15

Table S700.  Gene #93: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 44(19P13.3) MUTATED 5 103 15
DEL PEAK 44(19P13.3) WILD-TYPE 25 95 139

Figure S700.  Get High-res Image Gene #93: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p12' versus 'CN_CNMF'

P value = 1.66e-19 (Chi-square test), Q value = 1.7e-16

Table S701.  Gene #94: 'del_19p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 45(19P12) MUTATED 1 13 42 0 0
DEL PEAK 45(19P12) WILD-TYPE 304 35 112 12 5

Figure S701.  Get High-res Image Gene #94: 'del_19p12' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p12' versus 'METHLYATION_CNMF'

P value = 1.46e-07 (Fisher's exact test), Q value = 9.6e-05

Table S702.  Gene #94: 'del_19p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 45(19P12) MUTATED 33 13 4
DEL PEAK 45(19P12) WILD-TYPE 119 81 160

Figure S702.  Get High-res Image Gene #94: 'del_19p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p12' versus 'MRNASEQ_CNMF'

P value = 2.14e-08 (Fisher's exact test), Q value = 1.5e-05

Table S703.  Gene #94: 'del_19p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 45(19P12) MUTATED 45 5 6
DEL PEAK 45(19P12) WILD-TYPE 179 145 139

Figure S703.  Get High-res Image Gene #94: 'del_19p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.48e-07 (Fisher's exact test), Q value = 0.00022

Table S704.  Gene #94: 'del_19p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 45(19P12) MUTATED 6 5 45
DEL PEAK 45(19P12) WILD-TYPE 141 127 195

Figure S704.  Get High-res Image Gene #94: 'del_19p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p12' versus 'MIRSEQ_CNMF'

P value = 1.07e-06 (Fisher's exact test), Q value = 0.00066

Table S705.  Gene #94: 'del_19p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 45(19P12) MUTATED 39 5 9
DEL PEAK 45(19P12) WILD-TYPE 166 154 132

Figure S705.  Get High-res Image Gene #94: 'del_19p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.33e-07 (Fisher's exact test), Q value = 4e-04

Table S706.  Gene #94: 'del_19p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 45(19P12) MUTATED 2 6 45
DEL PEAK 45(19P12) WILD-TYPE 6 210 236

Figure S706.  Get High-res Image Gene #94: 'del_19p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.43' versus 'MRNA_CHIERARCHICAL'

P value = 9.8e-05 (Fisher's exact test), Q value = 0.049

Table S707.  Gene #95: 'del_19q13.43' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 46(19Q13.43) MUTATED 1 0 8
DEL PEAK 46(19Q13.43) WILD-TYPE 18 19 7

Figure S707.  Get High-res Image Gene #95: 'del_19q13.43' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19q13.43' versus 'CN_CNMF'

P value = 1.61e-23 (Chi-square test), Q value = 1.7e-20

Table S708.  Gene #95: 'del_19q13.43' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 46(19Q13.43) MUTATED 2 9 53 0 0
DEL PEAK 46(19Q13.43) WILD-TYPE 303 39 101 12 5

Figure S708.  Get High-res Image Gene #95: 'del_19q13.43' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.43' versus 'METHLYATION_CNMF'

P value = 2.41e-10 (Fisher's exact test), Q value = 1.9e-07

Table S709.  Gene #95: 'del_19q13.43' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 46(19Q13.43) MUTATED 36 15 2
DEL PEAK 46(19Q13.43) WILD-TYPE 116 79 162

Figure S709.  Get High-res Image Gene #95: 'del_19q13.43' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.43' versus 'MRNASEQ_CNMF'

P value = 1.25e-14 (Fisher's exact test), Q value = 1.1e-11

Table S710.  Gene #95: 'del_19q13.43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 46(19Q13.43) MUTATED 56 4 3
DEL PEAK 46(19Q13.43) WILD-TYPE 168 146 142

Figure S710.  Get High-res Image Gene #95: 'del_19q13.43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19q13.43' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.08e-13 (Fisher's exact test), Q value = 6.1e-10

Table S711.  Gene #95: 'del_19q13.43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 46(19Q13.43) MUTATED 4 3 56
DEL PEAK 46(19Q13.43) WILD-TYPE 143 129 184

Figure S711.  Get High-res Image Gene #95: 'del_19q13.43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.43' versus 'MIRSEQ_CNMF'

P value = 3.07e-14 (Fisher's exact test), Q value = 2.8e-11

Table S712.  Gene #95: 'del_19q13.43' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 46(19Q13.43) MUTATED 51 4 3
DEL PEAK 46(19Q13.43) WILD-TYPE 154 155 138

Figure S712.  Get High-res Image Gene #95: 'del_19q13.43' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19q13.43' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.24e-10 (Fisher's exact test), Q value = 5.4e-07

Table S713.  Gene #95: 'del_19q13.43' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 46(19Q13.43) MUTATED 1 4 53
DEL PEAK 46(19Q13.43) WILD-TYPE 7 212 228

Figure S713.  Get High-res Image Gene #95: 'del_19q13.43' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.43' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.8e-05 (Fisher's exact test), Q value = 0.01

Table S714.  Gene #95: 'del_19q13.43' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 46(19Q13.43) MUTATED 34 3 15
DEL PEAK 46(19Q13.43) WILD-TYPE 141 114 75

Figure S714.  Get High-res Image Gene #95: 'del_19q13.43' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19q13.43' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.07e-07 (Fisher's exact test), Q value = 7.1e-05

Table S715.  Gene #95: 'del_19q13.43' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 46(19Q13.43) MUTATED 6 42 4
DEL PEAK 46(19Q13.43) WILD-TYPE 24 156 150

Figure S715.  Get High-res Image Gene #95: 'del_19q13.43' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p12.1' versus 'CN_CNMF'

P value = 2.49e-05 (Chi-square test), Q value = 0.014

Table S716.  Gene #96: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 47(20P12.1) MUTATED 6 6 21 1 0
DEL PEAK 47(20P12.1) WILD-TYPE 299 42 133 11 5

Figure S716.  Get High-res Image Gene #96: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q11.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.000218 (Fisher's exact test), Q value = 0.1

Table S717.  Gene #97: 'del_22q11.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 48(22Q11.1) MUTATED 0 0 6
DEL PEAK 48(22Q11.1) WILD-TYPE 19 19 9

Figure S717.  Get High-res Image Gene #97: 'del_22q11.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_22q11.1' versus 'CN_CNMF'

P value = 2.43e-29 (Chi-square test), Q value = 2.7e-26

Table S718.  Gene #97: 'del_22q11.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 48(22Q11.1) MUTATED 3 15 65 0 1
DEL PEAK 48(22Q11.1) WILD-TYPE 302 33 89 12 4

Figure S718.  Get High-res Image Gene #97: 'del_22q11.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q11.1' versus 'METHLYATION_CNMF'

P value = 3.77e-05 (Fisher's exact test), Q value = 0.02

Table S719.  Gene #97: 'del_22q11.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 48(22Q11.1) MUTATED 42 18 14
DEL PEAK 48(22Q11.1) WILD-TYPE 110 76 150

Figure S719.  Get High-res Image Gene #97: 'del_22q11.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q11.1' versus 'MRNASEQ_CNMF'

P value = 1.23e-10 (Fisher's exact test), Q value = 9.6e-08

Table S720.  Gene #97: 'del_22q11.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 48(22Q11.1) MUTATED 63 6 15
DEL PEAK 48(22Q11.1) WILD-TYPE 161 144 130

Figure S720.  Get High-res Image Gene #97: 'del_22q11.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q11.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.31e-09 (Fisher's exact test), Q value = 3.1e-06

Table S721.  Gene #97: 'del_22q11.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 48(22Q11.1) MUTATED 16 5 63
DEL PEAK 48(22Q11.1) WILD-TYPE 131 127 177

Figure S721.  Get High-res Image Gene #97: 'del_22q11.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q11.1' versus 'MIRSEQ_CNMF'

P value = 2.5e-06 (Fisher's exact test), Q value = 0.0015

Table S722.  Gene #97: 'del_22q11.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 48(22Q11.1) MUTATED 54 17 11
DEL PEAK 48(22Q11.1) WILD-TYPE 151 142 130

Figure S722.  Get High-res Image Gene #97: 'del_22q11.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_22q11.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.1e-06 (Fisher's exact test), Q value = 0.00068

Table S723.  Gene #97: 'del_22q11.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 48(22Q11.1) MUTATED 6 19 57
DEL PEAK 48(22Q11.1) WILD-TYPE 2 197 224

Figure S723.  Get High-res Image Gene #97: 'del_22q11.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MRNA_CNMF'

P value = 3.62e-06 (Fisher's exact test), Q value = 0.0022

Table S724.  Gene #98: 'del_22q13.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 49(22Q13.31) MUTATED 0 10 0 0
DEL PEAK 49(22Q13.31) WILD-TYPE 14 7 12 10

Figure S724.  Get High-res Image Gene #98: 'del_22q13.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_22q13.31' versus 'MRNA_CHIERARCHICAL'

P value = 2.4e-07 (Fisher's exact test), Q value = 0.00016

Table S725.  Gene #98: 'del_22q13.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 49(22Q13.31) MUTATED 0 0 10
DEL PEAK 49(22Q13.31) WILD-TYPE 19 19 5

Figure S725.  Get High-res Image Gene #98: 'del_22q13.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_22q13.31' versus 'CN_CNMF'

P value = 7.72e-59 (Chi-square test), Q value = 9e-56

Table S726.  Gene #98: 'del_22q13.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 49(22Q13.31) MUTATED 4 15 111 0 2
DEL PEAK 49(22Q13.31) WILD-TYPE 301 33 43 12 3

Figure S726.  Get High-res Image Gene #98: 'del_22q13.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.31' versus 'METHLYATION_CNMF'

P value = 2.49e-14 (Fisher's exact test), Q value = 2.3e-11

Table S727.  Gene #98: 'del_22q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 49(22Q13.31) MUTATED 73 27 15
DEL PEAK 49(22Q13.31) WILD-TYPE 79 67 149

Figure S727.  Get High-res Image Gene #98: 'del_22q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q13.31' versus 'MRNASEQ_CNMF'

P value = 4.62e-25 (Fisher's exact test), Q value = 5e-22

Table S728.  Gene #98: 'del_22q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 49(22Q13.31) MUTATED 107 8 16
DEL PEAK 49(22Q13.31) WILD-TYPE 117 142 129

Figure S728.  Get High-res Image Gene #98: 'del_22q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.93e-22 (Fisher's exact test), Q value = 8.4e-19

Table S729.  Gene #98: 'del_22q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 49(22Q13.31) MUTATED 18 6 107
DEL PEAK 49(22Q13.31) WILD-TYPE 129 126 133

Figure S729.  Get High-res Image Gene #98: 'del_22q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_CNMF'

P value = 1.29e-17 (Fisher's exact test), Q value = 1.3e-14

Table S730.  Gene #98: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 49(22Q13.31) MUTATED 92 20 12
DEL PEAK 49(22Q13.31) WILD-TYPE 113 139 129

Figure S730.  Get High-res Image Gene #98: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_22q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.77e-12 (Fisher's exact test), Q value = 3.1e-09

Table S731.  Gene #98: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 49(22Q13.31) MUTATED 6 22 96
DEL PEAK 49(22Q13.31) WILD-TYPE 2 194 185

Figure S731.  Get High-res Image Gene #98: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000127 (Fisher's exact test), Q value = 0.062

Table S732.  Gene #98: 'del_22q13.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 117 90
DEL PEAK 49(22Q13.31) MUTATED 66 18 24
DEL PEAK 49(22Q13.31) WILD-TYPE 109 99 66

Figure S732.  Get High-res Image Gene #98: 'del_22q13.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_22q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.95e-07 (Fisher's exact test), Q value = 0.00013

Table S733.  Gene #98: 'del_22q13.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 49(22Q13.31) MUTATED 5 80 23
DEL PEAK 49(22Q13.31) WILD-TYPE 25 118 131

Figure S733.  Get High-res Image Gene #98: 'del_22q13.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp21.1' versus 'MRNA_CNMF'

P value = 0.000567 (Fisher's exact test), Q value = 0.24

Table S734.  Gene #99: 'del_xp21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 50(XP21.1) MUTATED 0 7 0 0
DEL PEAK 50(XP21.1) WILD-TYPE 14 10 12 10

Figure S734.  Get High-res Image Gene #99: 'del_xp21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_xp21.1' versus 'MRNA_CHIERARCHICAL'

P value = 4.17e-05 (Fisher's exact test), Q value = 0.022

Table S735.  Gene #99: 'del_xp21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 50(XP21.1) MUTATED 0 0 7
DEL PEAK 50(XP21.1) WILD-TYPE 19 19 8

Figure S735.  Get High-res Image Gene #99: 'del_xp21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_xp21.1' versus 'CN_CNMF'

P value = 9.13e-35 (Chi-square test), Q value = 1e-31

Table S736.  Gene #99: 'del_xp21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
DEL PEAK 50(XP21.1) MUTATED 2 10 72 0 0
DEL PEAK 50(XP21.1) WILD-TYPE 303 38 82 12 5

Figure S736.  Get High-res Image Gene #99: 'del_xp21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 1.82e-08 (Fisher's exact test), Q value = 1.3e-05

Table S737.  Gene #99: 'del_xp21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 94 164
DEL PEAK 50(XP21.1) MUTATED 46 16 9
DEL PEAK 50(XP21.1) WILD-TYPE 106 78 155

Figure S737.  Get High-res Image Gene #99: 'del_xp21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xp21.1' versus 'MRNASEQ_CNMF'

P value = 4.87e-18 (Fisher's exact test), Q value = 4.8e-15

Table S738.  Gene #99: 'del_xp21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
DEL PEAK 50(XP21.1) MUTATED 72 5 6
DEL PEAK 50(XP21.1) WILD-TYPE 152 145 139

Figure S738.  Get High-res Image Gene #99: 'del_xp21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_xp21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.25e-17 (Fisher's exact test), Q value = 8.9e-14

Table S739.  Gene #99: 'del_xp21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 132 240
DEL PEAK 50(XP21.1) MUTATED 6 4 73
DEL PEAK 50(XP21.1) WILD-TYPE 141 128 167

Figure S739.  Get High-res Image Gene #99: 'del_xp21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_CNMF'

P value = 1.67e-11 (Fisher's exact test), Q value = 1.3e-08

Table S740.  Gene #99: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 205 159 141
DEL PEAK 50(XP21.1) MUTATED 61 9 10
DEL PEAK 50(XP21.1) WILD-TYPE 144 150 131

Figure S740.  Get High-res Image Gene #99: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_xp21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.72e-09 (Fisher's exact test), Q value = 1.3e-06

Table S741.  Gene #99: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 216 281
DEL PEAK 50(XP21.1) MUTATED 5 12 63
DEL PEAK 50(XP21.1) WILD-TYPE 3 204 218

Figure S741.  Get High-res Image Gene #99: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.76e-06 (Fisher's exact test), Q value = 0.0045

Table S742.  Gene #99: 'del_xp21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 198 154
DEL PEAK 50(XP21.1) MUTATED 5 54 12
DEL PEAK 50(XP21.1) WILD-TYPE 25 144 142

Figure S742.  Get High-res Image Gene #99: 'del_xp21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Molecular subtype file = UCEC-TP.transferedmergedcluster.txt

  • Number of patients = 524

  • Number of significantly focal cnvs = 99

  • 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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