Correlation between copy number variations of arm-level result and molecular subtypes
Breast Invasive Carcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C18G8JKN
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 variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C18G8JKN
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 80 arm-level events and 12 molecular subtypes across 1079 patients, 567 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • 1q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • 3p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 3q gain 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'.

  • 4p gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 4q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 5q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 6p gain 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'.

  • 6q gain 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'.

  • 7p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 7q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 8p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 8q gain 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'.

  • 9p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 9q gain cnv correlated to 'CN_CNMF'.

  • 10p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 10q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 11p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 12p gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 12q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 13q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 14q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 15q gain cnv correlated to 'CN_CNMF'.

  • 16p gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 16q gain cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

  • 17p gain cnv correlated to 'CN_CNMF'.

  • 17q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 18p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 18q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 19p gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 19q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 20p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 20q gain 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'.

  • 21q gain 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'.

  • 22q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • xq gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 1p loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 1q loss cnv correlated to 'CN_CNMF'.

  • 2p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 2q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

  • 3q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 4p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 4q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • 6p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 6q loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 7p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 8p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 9p loss 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'.

  • 9q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 10p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 10q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 11p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 11q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 12q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 13q loss 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'.

  • 14q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 15q loss 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'.

  • 16p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 16q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 17q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 18p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 18q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 19p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 19q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 20p loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 20q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 21q loss cnv correlated to 'CN_CNMF'.

  • 22q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • xq loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level 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, 567 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
1p gain 205 (19%) 874 1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00021
(0.0932)
2p gain 123 (11%) 956 1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00014
(0.0655)
10p gain 214 (20%) 865 1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		2e-05
(0.011) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096)
4p loss 353 (33%) 726 1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		2e-05
(0.011) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		5e-05
(0.0246)
5p loss 140 (13%) 939 1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096)
5q loss 228 (21%) 851 1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096)
9q loss 282 (26%) 797 0.0001
(0.0477) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00031
(0.132) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096)
12q loss 131 (12%) 948 1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00018
(0.081) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096)
14q loss 266 (25%) 813 1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		2e-05
(0.011) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096)
2q gain 73 (7%) 1006 1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		2e-05
(0.011) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.0939
(1.00)
6p gain 207 (19%) 872 1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00014
(0.0655) 		0.00129
(0.461) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096)
6q gain 149 (14%) 930 1e-05
(0.0096) 		2e-05
(0.011) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00456
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096)
18p gain 177 (16%) 902 1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00098
(0.369) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		3e-05
(0.0154)
21q gain 195 (18%) 884 1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.0003
(0.128) 		0.00064
(0.252) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096)
16q loss 593 (55%) 486 1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00034
(0.143) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00121
(0.443) 		7e-05
(0.0337)
17q loss 275 (25%) 804 1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		2e-05
(0.011) 		0.00258
(0.838)
19p loss 193 (18%) 886 1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.0275
(1.00) 		0.00014
(0.0655) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096)
3q gain 212 (20%) 867 0.00043
(0.175) 		0.00017
(0.0775) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.0228
(1.00) 		0.0381
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00021
(0.0932)
8q gain 528 (49%) 551 2e-05
(0.011) 		3e-05
(0.0154) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.0736
(1.00) 		0.214
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096)
9p gain 141 (13%) 938 1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00718
(1.00) 		2e-05
(0.011) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00046
(0.187) 		0.115
(1.00)
20q gain 450 (42%) 629 5e-05
(0.0246) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.0697
(1.00) 		0.133
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00017
(0.0775)
22q gain 98 (9%) 981 1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00053
(0.213) 		2e-05
(0.011) 		0.00082
(0.317) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00034
(0.143) 		0.00612
(1.00)
3p loss 186 (17%) 893 1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00174
(0.597) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00681
(1.00)
4q loss 312 (29%) 767 1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00053
(0.213) 		0.00266
(0.857) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.0076
(1.00)
9p loss 312 (29%) 767 2e-05
(0.011) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00248
(0.813) 		0.00837
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00012
(0.0565) 		1e-05
(0.0096)
13q loss 432 (40%) 647 5e-05
(0.0246) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.297
(1.00) 		0.00077
(0.301) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00041
(0.169)
15q loss 319 (30%) 760 5e-05
(0.0246) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00273
(0.876) 		0.00609
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		3e-05
(0.0154)
17p loss 579 (54%) 500 1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		3e-05
(0.0154) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.0751
(1.00) 		0.121
(1.00)
16p gain 463 (43%) 616 0.00011
(0.0522) 		0.00128
(0.458) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.0156
(1.00) 		1e-05
(0.0096) 		2e-05
(0.011) 		2e-05
(0.011) 		2e-05
(0.011) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00345
(1.00)
8p loss 399 (37%) 680 3e-05
(0.0154) 		0.00018
(0.081) 		1e-05
(0.0096) 		2e-05
(0.011) 		0.148
(1.00) 		0.00035
(0.146) 		1e-05
(0.0096) 		1e-05
(0.0096) 		2e-05
(0.011) 		3e-05
(0.0154) 		0.00118
(0.435) 		0.00091
(0.346)
19q loss 161 (15%) 918 0.0052
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.124
(1.00) 		0.00491
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00021
(0.0932) 		1e-05
(0.0096)
20p loss 93 (9%) 986 0.00317
(1.00) 		9e-05
(0.043) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.111
(1.00) 		0.174
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		8e-05
(0.0383)
17q gain 216 (20%) 863 1e-05
(0.0096) 		0.00014
(0.0655) 		1e-05
(0.0096) 		0.00012
(0.0565) 		0.531
(1.00) 		0.00013
(0.061) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.194
(1.00) 		0.00023
(0.101) 		0.00112
(0.416) 		0.00173
(0.595)
18q gain 153 (14%) 926 1e-05
(0.0096) 		5e-05
(0.0246) 		1e-05
(0.0096) 		5e-05
(0.0246) 		0.0761
(1.00) 		0.00178
(0.607) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00103
(0.385) 		0.00182
(0.613)
20p gain 415 (38%) 664 3e-05
(0.0154) 		2e-05
(0.011) 		1e-05
(0.0096) 		0.00376
(1.00) 		0.00506
(1.00) 		0.334
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		2e-05
(0.011) 		0.00502
(1.00)
2p loss 181 (17%) 898 0.0081
(1.00) 		0.0123
(1.00) 		1e-05
(0.0096) 		0.00046
(0.187) 		0.0012
(0.44) 		0.00055
(0.218) 		1e-05
(0.0096) 		1e-05
(0.0096) 		4e-05
(0.02) 		0.00032
(0.135) 		1e-05
(0.0096) 		0.0512
(1.00)
12p loss 151 (14%) 928 0.00178
(0.607) 		0.00155
(0.539) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.0196
(1.00) 		0.00775
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096)
20q loss 55 (5%) 1024 0.0118
(1.00) 		0.00518
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.14
(1.00) 		0.0402
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00021
(0.0932)
5q gain 211 (20%) 868 0.0109
(1.00) 		0.00607
(1.00) 		1e-05
(0.0096) 		0.00051
(0.206) 		0.00152
(0.53) 		0.00015
(0.0691) 		0.00062
(0.244) 		0.0002
(0.0892) 		0.00188
(0.632) 		1e-05
(0.0096) 		0.00041
(0.169) 		0.0464
(1.00)
xq gain 140 (13%) 939 0.00034
(0.143) 		0.0009
(0.343) 		1e-05
(0.0096) 		2e-05
(0.011) 		0.457
(1.00) 		0.177
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00073
(0.286) 		0.0083
(1.00)
10q loss 229 (21%) 850 0.00288
(0.919) 		0.00887
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.0022
(0.724) 		0.0456
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00027
(0.117) 		1e-05
(0.0096) 		0.0001
(0.0477) 		0.0102
(1.00)
11p loss 275 (25%) 804 0.00372
(1.00) 		0.0164
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.0236
(1.00) 		0.00032
(0.135) 		1e-05
(0.0096) 		1e-05
(0.0096) 		3e-05
(0.0154) 		1e-05
(0.0096) 		0.00341
(1.00) 		0.00404
(1.00)
18p loss 320 (30%) 759 0.00029
(0.125) 		0.00042
(0.172) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.205
(1.00) 		0.276
(1.00) 		0.00039
(0.161) 		1e-05
(0.0096) 		0.00516
(1.00) 		2e-05
(0.011) 		0.392
(1.00) 		0.94
(1.00)
18q loss 321 (30%) 758 0.00025
(0.109) 		0.00014
(0.0655) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.0499
(1.00) 		0.11
(1.00) 		2e-05
(0.011) 		1e-05
(0.0096) 		0.00433
(1.00) 		1e-05
(0.0096) 		0.205
(1.00) 		0.612
(1.00)
10q gain 124 (11%) 955 0.0323
(1.00) 		0.00107
(0.399) 		1e-05
(0.0096) 		0.00315
(0.999) 		0.0233
(1.00) 		0.0611
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00014
(0.0655) 		0.00251
(0.821)
11q gain 94 (9%) 985 0.181
(1.00) 		0.0476
(1.00) 		1e-05
(0.0096) 		0.00055
(0.218) 		0.827
(1.00) 		0.76
(1.00) 		2e-05
(0.011) 		0.00017
(0.0775) 		3e-05
(0.0154) 		0.0003
(0.128) 		0.0573
(1.00) 		0.0421
(1.00)
12p gain 227 (21%) 852 0.00087
(0.332) 		4e-05
(0.02) 		1e-05
(0.0096) 		0.00129
(0.461) 		0.102
(1.00) 		0.0184
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00015
(0.0691) 		0.00118
(0.435) 		0.0195
(1.00)
19p gain 189 (18%) 890 0.00025
(0.109) 		0.00559
(1.00) 		1e-05
(0.0096) 		0.0134
(1.00) 		0.00786
(1.00) 		0.0292
(1.00) 		1e-05
(0.0096) 		4e-05
(0.02) 		2e-05
(0.011) 		0.00018
(0.081) 		0.0167
(1.00) 		0.416
(1.00)
1p loss 243 (23%) 836 0.00161
(0.559) 		2e-05
(0.011) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.499
(1.00) 		0.437
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.0179
(1.00) 		1e-05
(0.0096) 		0.0018
(0.61) 		0.698
(1.00)
7p loss 111 (10%) 968 0.0203
(1.00) 		0.001
(0.376) 		1e-05
(0.0096) 		0.00086
(0.329) 		0.143
(1.00) 		0.0334
(1.00) 		1e-05
(0.0096) 		4e-05
(0.02) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.0008
(0.311) 		0.00016
(0.0733)
11q loss 364 (34%) 715 4e-05
(0.02) 		6e-05
(0.029) 		1e-05
(0.0096) 		2e-05
(0.011) 		0.906
(1.00) 		0.00253
(0.825) 		0.00017
(0.0775) 		1e-05
(0.0096) 		0.0497
(1.00) 		0.00672
(1.00) 		0.0117
(1.00) 		0.0289
(1.00)
3p gain 135 (13%) 944 0.0271
(1.00) 		0.0439
(1.00) 		1e-05
(0.0096) 		0.00017
(0.0775) 		0.476
(1.00) 		0.0678
(1.00) 		1e-05
(0.0096) 		3e-05
(0.0154) 		0.0118
(1.00) 		6e-05
(0.029) 		0.0778
(1.00) 		0.207
(1.00)
7q gain 266 (25%) 813 0.00334
(1.00) 		0.027
(1.00) 		1e-05
(0.0096) 		2e-05
(0.011) 		0.0837
(1.00) 		0.295
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00411
(1.00) 		3e-05
(0.0154) 		0.00597
(1.00) 		0.567
(1.00)
13q gain 92 (9%) 987 0.22
(1.00) 		0.282
(1.00) 		1e-05
(0.0096) 		0.0242
(1.00) 		0.0219
(1.00) 		0.138
(1.00) 		4e-05
(0.02) 		1e-05
(0.0096) 		0.00027
(0.117) 		0.00045
(0.183) 		0.0815
(1.00) 		0.0255
(1.00)
19q gain 222 (21%) 857 0.00108
(0.402) 		0.00379
(1.00) 		1e-05
(0.0096) 		0.00203
(0.674) 		0.00451
(1.00) 		0.0512
(1.00) 		2e-05
(0.011) 		2e-05
(0.011) 		1e-05
(0.0096) 		3e-05
(0.0154) 		0.0158
(1.00) 		0.0707
(1.00)
2q loss 210 (19%) 869 0.0877
(1.00) 		0.0282
(1.00) 		1e-05
(0.0096) 		0.0418
(1.00) 		0.00082
(0.317) 		0.00205
(0.679) 		3e-05
(0.0154) 		1e-05
(0.0096) 		0.00061
(0.241) 		0.00167
(0.578) 		0.00027
(0.117) 		0.0747
(1.00)
3q loss 103 (10%) 976 0.00123
(0.448) 		0.00024
(0.105) 		1e-05
(0.0096) 		0.00151
(0.528) 		0.28
(1.00) 		0.0131
(1.00) 		0.0008
(0.311) 		2e-05
(0.011) 		3e-05
(0.0154) 		0.00018
(0.081) 		0.0834
(1.00) 		0.0756
(1.00)
xq loss 185 (17%) 894 0.155
(1.00) 		0.0026
(0.842) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.041
(1.00) 		0.0154
(1.00) 		0.00011
(0.0522) 		1e-05
(0.0096) 		0.00037
(0.154) 		0.00143
(0.503) 		0.00668
(1.00) 		0.00599
(1.00)
4p gain 76 (7%) 1003 0.00053
(0.213) 		0.00127
(0.457) 		1e-05
(0.0096) 		0.0281
(1.00) 		0.74
(1.00) 		0.162
(1.00) 		0.0103
(1.00) 		3e-05
(0.0154) 		0.486
(1.00) 		0.00039
(0.161) 		0.315
(1.00) 		0.0929
(1.00)
4q gain 73 (7%) 1006 2e-05
(0.011) 		0.00021
(0.0932) 		1e-05
(0.0096) 		0.0127
(1.00) 		0.243
(1.00) 		0.0225
(1.00) 		0.015
(1.00) 		1e-05
(0.0096) 		0.49
(1.00) 		0.0119
(1.00) 		0.105
(1.00) 		0.0212
(1.00)
7p gain 309 (29%) 770 0.0069
(1.00) 		0.129
(1.00) 		1e-05
(0.0096) 		3e-05
(0.0154) 		0.657
(1.00) 		0.75
(1.00) 		0.00017
(0.0775) 		4e-05
(0.02) 		0.0759
(1.00) 		0.0193
(1.00) 		0.0752
(1.00) 		0.724
(1.00)
8p gain 289 (27%) 790 0.181
(1.00) 		0.11
(1.00) 		1e-05
(0.0096) 		0.00034
(0.143) 		0.773
(1.00) 		0.0215
(1.00) 		0.00052
(0.209) 		1e-05
(0.0096) 		0.0172
(1.00) 		0.0467
(1.00) 		0.00527
(1.00) 		0.114
(1.00)
11p gain 137 (13%) 942 0.789
(1.00) 		0.0812
(1.00) 		1e-05
(0.0096) 		0.00386
(1.00) 		0.966
(1.00) 		0.728
(1.00) 		0.00053
(0.213) 		0.00085
(0.327) 		6e-05
(0.029) 		0.00143
(0.503) 		0.00357
(1.00) 		0.00029
(0.125)
14q gain 143 (13%) 936 0.00121
(0.443) 		0.0139
(1.00) 		1e-05
(0.0096) 		0.0019
(0.636) 		0.498
(1.00) 		0.234
(1.00) 		5e-05
(0.0246) 		2e-05
(0.011) 		0.292
(1.00) 		1e-05
(0.0096) 		0.00138
(0.487) 		0.321
(1.00)
6q loss 276 (26%) 803 0.00031
(0.132) 		0.0126
(1.00) 		1e-05
(0.0096) 		0.00989
(1.00) 		0.185
(1.00) 		0.0673
(1.00) 		0.00028
(0.121) 		0.00011
(0.0522) 		0.099
(1.00) 		0.00091
(0.346) 		0.00982
(1.00) 		0.363
(1.00)
7q loss 119 (11%) 960 0.0371
(1.00) 		0.00177
(0.605) 		2e-05
(0.011) 		0.0605
(1.00) 		0.686
(1.00) 		0.492
(1.00) 		0.0002
(0.0892) 		0.00197
(0.656) 		1e-05
(0.0096) 		2e-05
(0.011) 		0.0251
(1.00) 		0.00462
(1.00)
10p loss 173 (16%) 906 0.282
(1.00) 		0.232
(1.00) 		1e-05
(0.0096) 		0.00014
(0.0655) 		0.32
(1.00) 		0.479
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.153
(1.00) 		0.00181
(0.612) 		0.201
(1.00) 		0.61
(1.00)
16p loss 173 (16%) 906 0.218
(1.00) 		0.0973
(1.00) 		0.00011
(0.0522) 		0.0148
(1.00) 		0.0256
(1.00) 		0.0762
(1.00) 		0.00126
(0.456) 		0.0003
(0.128) 		5e-05
(0.0246) 		0.00077
(0.301) 		0.00022
(0.0966) 		0.03
(1.00)
1q gain 706 (65%) 373 0.00131
(0.465) 		0.00572
(1.00) 		1e-05
(0.0096) 		0.0703
(1.00) 		0.602
(1.00) 		0.292
(1.00) 		0.966
(1.00) 		2e-05
(0.011) 		0.913
(1.00) 		0.0005
(0.202) 		0.12
(1.00) 		0.214
(1.00)
12q gain 190 (18%) 889 0.00127
(0.457) 		0.00137
(0.485) 		1e-05
(0.0096) 		0.00405
(1.00) 		0.284
(1.00) 		0.11
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.216
(1.00) 		0.0221
(1.00) 		0.00126
(0.456) 		0.708
(1.00)
22q loss 482 (45%) 597 0.0539
(1.00) 		0.00569
(1.00) 		1e-05
(0.0096) 		0.0542
(1.00) 		0.0217
(1.00) 		0.00091
(0.346) 		7e-05
(0.0337) 		1e-05
(0.0096) 		0.0372
(1.00) 		0.00283
(0.906) 		0.00342
(1.00) 		0.149
(1.00)
6p loss 188 (17%) 891 0.0239
(1.00) 		0.161
(1.00) 		1e-05
(0.0096) 		0.173
(1.00) 		0.586
(1.00) 		0.0373
(1.00) 		0.00033
(0.139) 		0.00301
(0.957) 		0.308
(1.00) 		0.0892
(1.00) 		0.00669
(1.00) 		0.528
(1.00)
5p gain 315 (29%) 764 0.021
(1.00) 		0.0411
(1.00) 		1e-05
(0.0096) 		0.00706
(1.00) 		0.97
(1.00) 		0.112
(1.00) 		0.268
(1.00) 		0.0248
(1.00) 		0.182
(1.00) 		0.0755
(1.00) 		0.243
(1.00) 		0.311
(1.00)
9q gain 119 (11%) 960 0.273
(1.00) 		0.00101
(0.379) 		1e-05
(0.0096) 		0.144
(1.00) 		0.876
(1.00) 		0.148
(1.00) 		0.00658
(1.00) 		0.0144
(1.00) 		0.0699
(1.00) 		0.0369
(1.00) 		0.0971
(1.00) 		0.0471
(1.00)
15q gain 87 (8%) 992 0.0416
(1.00) 		0.279
(1.00) 		0.00015
(0.0691) 		0.0354
(1.00) 		0.49
(1.00) 		0.0623
(1.00) 		0.00532
(1.00) 		0.00085
(0.327) 		0.352
(1.00) 		0.00521
(1.00) 		0.504
(1.00) 		0.133
(1.00)
16q gain 141 (13%) 938 0.482
(1.00) 		0.403
(1.00) 		0.00641
(1.00) 		0.02
(1.00) 		0.351
(1.00) 		0.603
(1.00) 		0.0573
(1.00) 		0.00401
(1.00) 		0.00488
(1.00) 		0.00016
(0.0733) 		0.133
(1.00) 		0.248
(1.00)
17p gain 106 (10%) 973 0.03
(1.00) 		0.329
(1.00) 		1e-05
(0.0096) 		0.0303
(1.00) 		0.527
(1.00) 		0.431
(1.00) 		0.0254
(1.00) 		0.00431
(1.00) 		0.816
(1.00) 		0.00495
(1.00) 		0.478
(1.00) 		0.0245
(1.00)
1q loss 51 (5%) 1028 0.0735
(1.00) 		0.0118
(1.00) 		0.0004
(0.165) 		0.211
(1.00) 		0.337
(1.00) 		0.176
(1.00) 		0.0043
(1.00) 		0.00219
(0.723) 		0.0147
(1.00) 		0.00113
(0.418) 		0.0947
(1.00) 		0.477
(1.00)
21q loss 180 (17%) 899 0.0345
(1.00) 		0.151
(1.00) 		1e-05
(0.0096) 		0.0017
(0.586) 		0.806
(1.00) 		0.176
(1.00) 		0.00125
(0.454) 		0.00191
(0.638) 		0.00859
(1.00) 		0.0469
(1.00) 		0.0197
(1.00) 		0.0518
(1.00)
8q loss 93 (9%) 986 0.0514
(1.00) 		0.104
(1.00) 		0.00593
(1.00) 		0.0191
(1.00) 		0.801
(1.00) 		0.337
(1.00) 		0.00265
(0.856) 		0.0945
(1.00) 		0.387
(1.00) 		0.856
(1.00) 		0.22
(1.00) 		0.385
(1.00)
'1p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S1.  Gene #1: '1p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
1P GAIN MUTATED 2 3 16 39 6 19 6 5
1P GAIN WILD-TYPE 19 33 103 57 103 53 14 35

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

'1p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S2.  Gene #1: '1p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
1P GAIN MUTATED 13 16 27 35 5
1P GAIN WILD-TYPE 88 136 87 53 53

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

'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
1P GAIN MUTATED 36 48 8 103 10
1P GAIN WILD-TYPE 224 364 85 162 39

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S4.  Gene #1: '1p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
1P GAIN MUTATED 52 21 28 10 30
1P GAIN WILD-TYPE 80 176 149 78 98

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

'1p gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S5.  Gene #1: '1p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
1P GAIN MUTATED 51 17 13
1P GAIN WILD-TYPE 98 115 104

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

'1p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S6.  Gene #1: '1p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
1P GAIN MUTATED 4 12 30 25 10
1P GAIN WILD-TYPE 60 94 60 82 21

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

'1p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S7.  Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
1P GAIN MUTATED 62 115 27
1P GAIN WILD-TYPE 481 183 205

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

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S8.  Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
1P GAIN MUTATED 26 33 38 11 77 19
1P GAIN WILD-TYPE 193 131 268 130 106 41

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

'1p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S9.  Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
1P GAIN MUTATED 109 36 57
1P GAIN WILD-TYPE 222 217 419

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

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S10.  Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
1P GAIN MUTATED 42 48 36 12 7 57
1P GAIN WILD-TYPE 189 112 286 115 79 77

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

'1p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S11.  Gene #1: '1p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
1P GAIN MUTATED 25 60 10 17 17
1P GAIN WILD-TYPE 155 79 89 94 116

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

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.093

Table S12.  Gene #1: '1p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
1P GAIN MUTATED 80 37 12
1P GAIN WILD-TYPE 225 210 98

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

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S13.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
1Q GAIN MUTATED 172 242 89 172 31
1Q GAIN WILD-TYPE 88 170 4 93 18

Figure S13.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S14.  Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
1Q GAIN MUTATED 114 123 203 104 122 36
1Q GAIN WILD-TYPE 105 41 103 37 61 24

Figure S14.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.2

Table S15.  Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
1Q GAIN MUTATED 141 102 215 101 44 91
1Q GAIN WILD-TYPE 90 58 107 26 42 43

Figure S15.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
2P GAIN MUTATED 1 1 6 31 1 20 1 0
2P GAIN WILD-TYPE 20 35 113 65 108 52 19 40

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

'2p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
2P GAIN MUTATED 5 1 27 27 1
2P GAIN WILD-TYPE 96 151 87 61 57

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

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
2P GAIN MUTATED 24 14 7 72 6
2P GAIN WILD-TYPE 236 398 86 193 43

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
2P GAIN MUTATED 38 2 19 6 13
2P GAIN WILD-TYPE 94 195 158 82 115

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

'2p gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
2P GAIN MUTATED 40 2 9
2P GAIN WILD-TYPE 109 130 108

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

'2p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
2P GAIN MUTATED 1 5 32 8 5
2P GAIN WILD-TYPE 63 101 58 99 26

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
2P GAIN MUTATED 29 93 1
2P GAIN WILD-TYPE 514 205 231

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

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
2P GAIN MUTATED 8 27 6 2 57 23
2P GAIN WILD-TYPE 211 137 300 139 126 37

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

'2p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
2P GAIN MUTATED 88 9 20
2P GAIN WILD-TYPE 243 244 456

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

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
2P GAIN MUTATED 27 40 6 3 1 40
2P GAIN WILD-TYPE 204 120 316 124 85 94

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

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
2P GAIN MUTATED 11 47 4 6 10
2P GAIN WILD-TYPE 169 92 95 105 123

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

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.066

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
2P GAIN MUTATED 53 20 5
2P GAIN WILD-TYPE 252 227 105

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

'2q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S28.  Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
2Q GAIN MUTATED 1 1 5 18 1 13 0 0
2Q GAIN WILD-TYPE 20 35 114 78 108 59 20 40

Figure S28.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S29.  Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
2Q GAIN MUTATED 4 1 17 16 1
2Q GAIN WILD-TYPE 97 151 97 72 57

Figure S29.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S30.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
2Q GAIN MUTATED 13 10 6 43 1
2Q GAIN WILD-TYPE 247 402 87 222 48

Figure S30.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S31.  Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
2Q GAIN MUTATED 22 1 12 3 4
2Q GAIN WILD-TYPE 110 196 165 85 124

Figure S31.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S32.  Gene #4: '2q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
2Q GAIN MUTATED 26 2 4
2Q GAIN WILD-TYPE 123 130 113

Figure S32.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'2q gain' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S33.  Gene #4: '2q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
2Q GAIN MUTATED 1 3 19 5 4
2Q GAIN WILD-TYPE 63 103 71 102 27

Figure S33.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S34.  Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
2Q GAIN MUTATED 17 55 1
2Q GAIN WILD-TYPE 526 243 231

Figure S34.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S35.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
2Q GAIN MUTATED 4 20 2 2 33 12
2Q GAIN WILD-TYPE 215 144 304 139 150 48

Figure S35.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S36.  Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
2Q GAIN MUTATED 48 7 13
2Q GAIN WILD-TYPE 283 246 463

Figure S36.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S37.  Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
2Q GAIN MUTATED 17 27 4 3 0 17
2Q GAIN WILD-TYPE 214 133 318 124 86 117

Figure S37.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S38.  Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
2Q GAIN MUTATED 6 29 2 6 6
2Q GAIN WILD-TYPE 174 110 97 105 127

Figure S38.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S39.  Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
3P GAIN MUTATED 46 13 20 46 10
3P GAIN WILD-TYPE 214 399 73 219 39

Figure S39.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.078

Table S40.  Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
3P GAIN MUTATED 30 15 20 6 7
3P GAIN WILD-TYPE 102 182 157 82 121

Figure S40.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S41.  Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
3P GAIN MUTATED 78 49 7
3P GAIN WILD-TYPE 465 249 225

Figure S41.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S42.  Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
3P GAIN MUTATED 36 25 18 12 38 5
3P GAIN WILD-TYPE 183 139 288 129 145 55

Figure S42.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.029

Table S43.  Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
3P GAIN MUTATED 28 24 18 21 11 29
3P GAIN WILD-TYPE 203 136 304 106 75 105

Figure S43.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MRNA_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.18

Table S44.  Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
3Q GAIN MUTATED 2 7 29 32 16 17 7 1
3Q GAIN WILD-TYPE 19 29 90 64 93 55 13 39

Figure S44.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.078

Table S45.  Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
3Q GAIN MUTATED 21 16 33 29 12
3Q GAIN WILD-TYPE 80 136 81 59 46

Figure S45.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S46.  Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
3Q GAIN MUTATED 59 23 25 94 11
3Q GAIN WILD-TYPE 201 389 68 171 38

Figure S46.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S47.  Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
3Q GAIN MUTATED 52 19 34 10 11
3Q GAIN WILD-TYPE 80 178 143 78 117

Figure S47.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S48.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
3Q GAIN MUTATED 102 98 11
3Q GAIN WILD-TYPE 441 200 221

Figure S48.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S49.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
3Q GAIN MUTATED 44 38 28 13 75 13
3Q GAIN WILD-TYPE 175 126 278 128 108 47

Figure S49.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S50.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
3Q GAIN MUTATED 107 31 70
3Q GAIN WILD-TYPE 224 222 406

Figure S50.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S51.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
3Q GAIN MUTATED 39 44 34 22 12 57
3Q GAIN WILD-TYPE 192 116 288 105 74 77

Figure S51.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S52.  Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
3Q GAIN MUTATED 31 55 11 10 17
3Q GAIN WILD-TYPE 149 84 88 101 116

Figure S52.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.093

Table S53.  Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
3Q GAIN MUTATED 78 33 13
3Q GAIN WILD-TYPE 227 214 97

Figure S53.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'MRNA_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.21

Table S54.  Gene #7: '4p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
4P GAIN MUTATED 1 2 22 3 3 4 0 2
4P GAIN WILD-TYPE 20 34 97 93 106 68 20 38

Figure S54.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S55.  Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
4P GAIN MUTATED 45 7 3 17 4
4P GAIN WILD-TYPE 215 405 90 248 45

Figure S55.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S56.  Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
4P GAIN MUTATED 31 17 15 3 7 3
4P GAIN WILD-TYPE 188 147 291 138 176 57

Figure S56.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.16

Table S57.  Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
4P GAIN MUTATED 25 18 14 3 10 5
4P GAIN WILD-TYPE 206 142 308 124 76 129

Figure S57.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S58.  Gene #8: '4q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
4Q GAIN MUTATED 1 2 23 2 3 2 0 2
4Q GAIN WILD-TYPE 20 34 96 94 106 70 20 38

Figure S58.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.093

Table S59.  Gene #8: '4q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
4Q GAIN MUTATED 18 8 6 2 1
4Q GAIN WILD-TYPE 83 144 108 86 57

Figure S59.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S60.  Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
4Q GAIN MUTATED 44 7 2 14 6
4Q GAIN WILD-TYPE 216 405 91 251 43

Figure S60.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S61.  Gene #8: '4q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
4Q GAIN MUTATED 33 13 13 2 9 3
4Q GAIN WILD-TYPE 186 151 293 139 174 57

Figure S61.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S62.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
5P GAIN MUTATED 114 58 49 80 14
5P GAIN WILD-TYPE 146 354 44 185 35

Figure S62.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S63.  Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
5Q GAIN MUTATED 84 48 47 21 11
5Q GAIN WILD-TYPE 176 364 46 244 38

Figure S63.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.21

Table S64.  Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
5Q GAIN MUTATED 16 50 44 17 13
5Q GAIN WILD-TYPE 116 147 133 71 115

Figure S64.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.069

Table S65.  Gene #10: '5q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
5Q GAIN MUTATED 22 23 5 24 7
5Q GAIN WILD-TYPE 42 83 85 83 24

Figure S65.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.24

Table S66.  Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
5Q GAIN MUTATED 125 37 48
5Q GAIN WILD-TYPE 418 261 184

Figure S66.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.089

Table S67.  Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
5Q GAIN MUTATED 56 40 57 33 17 7
5Q GAIN WILD-TYPE 163 124 249 108 166 53

Figure S67.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S68.  Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
5Q GAIN MUTATED 49 27 62 41 20 9
5Q GAIN WILD-TYPE 182 133 260 86 66 125

Figure S68.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.17

Table S69.  Gene #10: '5q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
5Q GAIN MUTATED 51 15 22 26 18
5Q GAIN WILD-TYPE 129 124 77 85 115

Figure S69.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S70.  Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
6P GAIN MUTATED 2 2 18 36 13 19 7 2
6P GAIN WILD-TYPE 19 34 101 60 96 53 13 38

Figure S70.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S71.  Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
6P GAIN MUTATED 15 13 34 31 6
6P GAIN WILD-TYPE 86 139 80 57 52

Figure S71.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S72.  Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
6P GAIN MUTATED 43 20 20 114 10
6P GAIN WILD-TYPE 217 392 73 151 39

Figure S72.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S73.  Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
6P GAIN MUTATED 58 19 42 5 13
6P GAIN WILD-TYPE 74 178 135 83 115

Figure S73.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p gain' versus 'RPPA_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.066

Table S74.  Gene #11: '6p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
6P GAIN MUTATED 46 18 14
6P GAIN WILD-TYPE 103 114 103

Figure S74.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S75.  Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
6P GAIN MUTATED 85 108 13
6P GAIN WILD-TYPE 458 190 219

Figure S75.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S76.  Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
6P GAIN MUTATED 29 50 26 10 79 12
6P GAIN WILD-TYPE 190 114 280 131 104 48

Figure S76.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S77.  Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
6P GAIN MUTATED 116 24 59
6P GAIN WILD-TYPE 215 229 417

Figure S77.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S78.  Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
6P GAIN MUTATED 46 46 23 16 10 58
6P GAIN WILD-TYPE 185 114 299 111 76 76

Figure S78.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S79.  Gene #11: '6p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
6P GAIN MUTATED 22 61 13 8 17
6P GAIN WILD-TYPE 158 78 86 103 116

Figure S79.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S80.  Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
6P GAIN MUTATED 82 32 7
6P GAIN WILD-TYPE 223 215 103

Figure S80.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S81.  Gene #12: '6q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
6Q GAIN MUTATED 1 0 9 29 11 13 7 2
6Q GAIN WILD-TYPE 20 36 110 67 98 59 13 38

Figure S81.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6q gain' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S82.  Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
6Q GAIN MUTATED 9 11 24 24 4
6Q GAIN WILD-TYPE 92 141 90 64 54

Figure S82.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S83.  Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
6Q GAIN MUTATED 19 15 16 92 7
6Q GAIN WILD-TYPE 241 397 77 173 42

Figure S83.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S84.  Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
6Q GAIN MUTATED 43 9 29 3 11
6Q GAIN WILD-TYPE 89 188 148 85 117

Figure S84.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S85.  Gene #12: '6q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
6Q GAIN MUTATED 39 9 10
6Q GAIN WILD-TYPE 110 123 107

Figure S85.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S86.  Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
6Q GAIN MUTATED 54 83 11
6Q GAIN WILD-TYPE 489 215 221

Figure S86.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S87.  Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
6Q GAIN MUTATED 18 36 22 6 58 8
6Q GAIN WILD-TYPE 201 128 284 135 125 52

Figure S87.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S88.  Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
6Q GAIN MUTATED 92 17 34
6Q GAIN WILD-TYPE 239 236 442

Figure S88.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S89.  Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
6Q GAIN MUTATED 31 41 16 8 7 40
6Q GAIN WILD-TYPE 200 119 306 119 79 94

Figure S89.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S90.  Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
6Q GAIN MUTATED 17 48 11 6 12
6Q GAIN WILD-TYPE 163 91 88 105 121

Figure S90.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S91.  Gene #12: '6q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
6Q GAIN MUTATED 65 22 7
6Q GAIN WILD-TYPE 240 225 103

Figure S91.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S92.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
7P GAIN MUTATED 76 73 50 95 15
7P GAIN WILD-TYPE 184 339 43 170 34

Figure S92.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S93.  Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
7P GAIN MUTATED 52 51 60 23 17
7P GAIN WILD-TYPE 80 146 117 65 111

Figure S93.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.078

Table S94.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
7P GAIN MUTATED 156 107 45
7P GAIN WILD-TYPE 387 191 187

Figure S94.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S95.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
7P GAIN MUTATED 62 64 59 35 61 27
7P GAIN WILD-TYPE 157 100 247 106 122 33

Figure S95.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S96.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
7Q GAIN MUTATED 63 58 45 88 12
7Q GAIN WILD-TYPE 197 354 48 177 37

Figure S96.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S97.  Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
7Q GAIN MUTATED 50 45 45 17 14
7Q GAIN WILD-TYPE 82 152 132 71 114

Figure S97.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S98.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
7Q GAIN MUTATED 123 103 39
7Q GAIN WILD-TYPE 420 195 193

Figure S98.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S99.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
7Q GAIN MUTATED 49 48 46 31 70 21
7Q GAIN WILD-TYPE 170 116 260 110 113 39

Figure S99.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S100.  Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
7Q GAIN MUTATED 45 43 68 37 12 54
7Q GAIN WILD-TYPE 186 117 254 90 74 80

Figure S100.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S101.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
8P GAIN MUTATED 69 81 37 77 25
8P GAIN WILD-TYPE 191 331 56 188 24

Figure S101.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.14

Table S102.  Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
8P GAIN MUTATED 53 47 49 24 20
8P GAIN WILD-TYPE 79 150 128 64 108

Figure S102.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.21

Table S103.  Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
8P GAIN MUTATED 156 92 40
8P GAIN WILD-TYPE 387 206 192

Figure S103.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S104.  Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
8P GAIN MUTATED 84 41 60 25 66 12
8P GAIN WILD-TYPE 135 123 246 116 117 48

Figure S104.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S105.  Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
8Q GAIN MUTATED 14 12 74 62 43 35 15 14
8Q GAIN WILD-TYPE 7 24 45 34 66 37 5 26

Figure S105.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8q gain' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S106.  Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
8Q GAIN MUTATED 65 68 64 56 16
8Q GAIN WILD-TYPE 36 84 50 32 42

Figure S106.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S107.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
8Q GAIN MUTATED 152 122 40 170 44
8Q GAIN WILD-TYPE 108 290 53 95 5

Figure S107.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S108.  Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
8Q GAIN MUTATED 91 75 91 31 54
8Q GAIN WILD-TYPE 41 122 86 57 74

Figure S108.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S109.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
8Q GAIN MUTATED 274 178 73
8Q GAIN WILD-TYPE 269 120 159

Figure S109.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S110.  Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
8Q GAIN MUTATED 142 93 112 27 121 30
8Q GAIN WILD-TYPE 77 71 194 114 62 30

Figure S110.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S111.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
8Q GAIN MUTATED 213 89 216
8Q GAIN WILD-TYPE 118 164 260

Figure S111.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S112.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
8Q GAIN MUTATED 128 91 102 63 42 92
8Q GAIN WILD-TYPE 103 69 220 64 44 42

Figure S112.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S113.  Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
8Q GAIN MUTATED 94 99 35 35 51
8Q GAIN WILD-TYPE 86 40 64 76 82

Figure S113.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S114.  Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
8Q GAIN MUTATED 180 92 42
8Q GAIN WILD-TYPE 125 155 68

Figure S114.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S115.  Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
9P GAIN MUTATED 1 2 3 34 14 9 0 5
9P GAIN WILD-TYPE 20 34 116 62 95 63 20 35

Figure S115.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S116.  Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
9P GAIN MUTATED 0 15 13 31 9
9P GAIN WILD-TYPE 101 137 101 57 49

Figure S116.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S117.  Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
9P GAIN MUTATED 13 25 29 66 8
9P GAIN WILD-TYPE 247 387 64 199 41

Figure S117.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S118.  Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
9P GAIN MUTATED 36 22 15 6 11
9P GAIN WILD-TYPE 96 175 162 82 117

Figure S118.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p gain' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S119.  Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
9P GAIN MUTATED 9 9 26 4 6
9P GAIN WILD-TYPE 55 97 64 103 25

Figure S119.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S120.  Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
9P GAIN MUTATED 48 75 18
9P GAIN WILD-TYPE 495 223 214

Figure S120.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S121.  Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
9P GAIN MUTATED 19 22 22 14 58 6
9P GAIN WILD-TYPE 200 142 284 127 125 54

Figure S121.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S122.  Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
9P GAIN MUTATED 72 22 43
9P GAIN WILD-TYPE 259 231 433

Figure S122.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S123.  Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
9P GAIN MUTATED 25 21 26 17 5 43
9P GAIN WILD-TYPE 206 139 296 110 81 91

Figure S123.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.19

Table S124.  Gene #17: '9p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
9P GAIN MUTATED 24 34 9 13 9
9P GAIN WILD-TYPE 156 105 90 98 124

Figure S124.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S125.  Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
9Q GAIN MUTATED 18 24 29 42 6
9Q GAIN WILD-TYPE 242 388 64 223 43

Figure S125.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S126.  Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
10P GAIN MUTATED 2 4 17 42 11 27 6 4
10P GAIN WILD-TYPE 19 32 102 54 98 45 14 36

Figure S126.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S127.  Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
10P GAIN MUTATED 10 18 41 39 5
10P GAIN WILD-TYPE 91 134 73 49 53

Figure S127.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S128.  Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
10P GAIN MUTATED 47 28 15 116 8
10P GAIN WILD-TYPE 213 384 78 149 41

Figure S128.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S129.  Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
10P GAIN MUTATED 59 13 34 5 22
10P GAIN WILD-TYPE 73 184 143 83 106

Figure S129.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p gain' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S130.  Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
10P GAIN MUTATED 53 17 20
10P GAIN WILD-TYPE 96 115 97

Figure S130.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S131.  Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
10P GAIN MUTATED 7 18 40 19 6
10P GAIN WILD-TYPE 57 88 50 88 25

Figure S131.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S132.  Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
10P GAIN MUTATED 79 118 17
10P GAIN WILD-TYPE 464 180 215

Figure S132.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S133.  Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
10P GAIN MUTATED 33 42 33 4 81 21
10P GAIN WILD-TYPE 186 122 273 137 102 39

Figure S133.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S134.  Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
10P GAIN MUTATED 122 26 62
10P GAIN WILD-TYPE 209 227 414

Figure S134.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S135.  Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
10P GAIN MUTATED 50 54 24 18 7 57
10P GAIN WILD-TYPE 181 106 298 109 79 77

Figure S135.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S136.  Gene #19: '10p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
10P GAIN MUTATED 29 62 11 10 16
10P GAIN WILD-TYPE 151 77 88 101 117

Figure S136.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S137.  Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
10P GAIN MUTATED 89 26 13
10P GAIN WILD-TYPE 216 221 97

Figure S137.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S138.  Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
10Q GAIN MUTATED 29 21 13 56 5
10Q GAIN WILD-TYPE 231 391 80 209 44

Figure S138.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S139.  Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
10Q GAIN MUTATED 57 57 10
10Q GAIN WILD-TYPE 486 241 222

Figure S139.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S140.  Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
10Q GAIN MUTATED 24 28 23 3 32 14
10Q GAIN WILD-TYPE 195 136 283 138 151 46

Figure S140.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S141.  Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
10Q GAIN MUTATED 65 16 41
10Q GAIN WILD-TYPE 266 237 435

Figure S141.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S142.  Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
10Q GAIN MUTATED 31 30 17 15 4 25
10Q GAIN WILD-TYPE 200 130 305 112 82 109

Figure S142.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.066

Table S143.  Gene #20: '10q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
10Q GAIN MUTATED 21 30 5 7 9
10Q GAIN WILD-TYPE 159 109 94 104 124

Figure S143.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S144.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
11P GAIN MUTATED 46 18 14 53 6
11P GAIN WILD-TYPE 214 394 79 212 43

Figure S144.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'MRNASEQ_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.21

Table S145.  Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
11P GAIN MUTATED 67 54 16
11P GAIN WILD-TYPE 476 244 216

Figure S145.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p gain' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.029

Table S146.  Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
11P GAIN MUTATED 58 14 63
11P GAIN WILD-TYPE 273 239 413

Figure S146.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.12

Table S147.  Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
11P GAIN MUTATED 53 15 15
11P GAIN WILD-TYPE 252 232 95

Figure S147.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S148.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
11Q GAIN MUTATED 20 11 11 46 6
11Q GAIN WILD-TYPE 240 401 82 219 43

Figure S148.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.22

Table S149.  Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
11Q GAIN MUTATED 25 16 10 5 6
11Q GAIN WILD-TYPE 107 181 167 83 122

Figure S149.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S150.  Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
11Q GAIN MUTATED 38 47 9
11Q GAIN WILD-TYPE 505 251 223

Figure S150.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.078

Table S151.  Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
11Q GAIN MUTATED 13 19 17 7 27 11
11Q GAIN WILD-TYPE 206 145 289 134 156 49

Figure S151.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S152.  Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
11Q GAIN MUTATED 48 10 33
11Q GAIN WILD-TYPE 283 243 443

Figure S152.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.13

Table S153.  Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
11Q GAIN MUTATED 14 25 17 8 7 20
11Q GAIN WILD-TYPE 217 135 305 119 79 114

Figure S153.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S154.  Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
12P GAIN MUTATED 27 16 33 29 9
12P GAIN WILD-TYPE 74 136 81 59 49

Figure S154.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S155.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
12P GAIN MUTATED 87 21 24 84 11
12P GAIN WILD-TYPE 173 391 69 181 38

Figure S155.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S156.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
12P GAIN MUTATED 124 83 20
12P GAIN WILD-TYPE 419 215 212

Figure S156.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S157.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
12P GAIN MUTATED 56 51 38 12 57 13
12P GAIN WILD-TYPE 163 113 268 129 126 47

Figure S157.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S158.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
12P GAIN MUTATED 101 35 84
12P GAIN WILD-TYPE 230 218 392

Figure S158.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.069

Table S159.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
12P GAIN MUTATED 56 37 45 26 12 44
12P GAIN WILD-TYPE 175 123 277 101 74 90

Figure S159.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S160.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
12Q GAIN MUTATED 93 20 25 42 10
12Q GAIN WILD-TYPE 167 392 68 223 39

Figure S160.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S161.  Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
12Q GAIN MUTATED 127 44 18
12Q GAIN WILD-TYPE 416 254 214

Figure S161.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S162.  Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
12Q GAIN MUTATED 56 50 35 17 22 9
12Q GAIN WILD-TYPE 163 114 271 124 161 51

Figure S162.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S163.  Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
13Q GAIN MUTATED 23 14 9 41 5
13Q GAIN WILD-TYPE 237 398 84 224 44

Figure S163.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S164.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
13Q GAIN MUTATED 47 39 6
13Q GAIN WILD-TYPE 496 259 226

Figure S164.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S165.  Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
13Q GAIN MUTATED 21 17 9 11 23 11
13Q GAIN WILD-TYPE 198 147 297 130 160 49

Figure S165.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.12

Table S166.  Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
13Q GAIN MUTATED 46 15 29
13Q GAIN WILD-TYPE 285 238 447

Figure S166.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.18

Table S167.  Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
13Q GAIN MUTATED 19 27 13 11 6 14
13Q GAIN WILD-TYPE 212 133 309 116 80 120

Figure S167.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S168.  Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
14Q GAIN MUTATED 58 29 19 30 7
14Q GAIN WILD-TYPE 202 383 74 235 42

Figure S168.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.025

Table S169.  Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
14Q GAIN MUTATED 95 32 15
14Q GAIN WILD-TYPE 448 266 217

Figure S169.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S170.  Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
14Q GAIN MUTATED 40 34 26 17 12 13
14Q GAIN WILD-TYPE 179 130 280 124 171 47

Figure S170.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S171.  Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
14Q GAIN MUTATED 45 33 27 27 6 4
14Q GAIN WILD-TYPE 186 127 295 100 80 130

Figure S171.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.069

Table S172.  Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
15Q GAIN MUTATED 30 19 4 33 1
15Q GAIN WILD-TYPE 230 393 89 232 48

Figure S172.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'MRNA_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.052

Table S173.  Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
16P GAIN MUTATED 11 14 52 33 73 36 12 14
16P GAIN WILD-TYPE 10 22 67 63 36 36 8 26

Figure S173.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S174.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
16P GAIN MUTATED 124 156 64 98 21
16P GAIN WILD-TYPE 136 256 29 167 28

Figure S174.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S175.  Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
16P GAIN MUTATED 44 100 86 31 31
16P GAIN WILD-TYPE 88 97 91 57 97

Figure S175.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S176.  Gene #28: '16p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
16P GAIN MUTATED 48 54 31 45 11
16P GAIN WILD-TYPE 16 52 59 62 20

Figure S176.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S177.  Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
16P GAIN MUTATED 270 96 95
16P GAIN WILD-TYPE 273 202 137

Figure S177.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S178.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
16P GAIN MUTATED 111 81 126 70 47 26
16P GAIN WILD-TYPE 108 83 180 71 136 34

Figure S178.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S179.  Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
16P GAIN MUTATED 115 96 241
16P GAIN WILD-TYPE 216 157 235

Figure S179.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S180.  Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
16P GAIN MUTATED 97 76 127 78 44 30
16P GAIN WILD-TYPE 134 84 195 49 42 104

Figure S180.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S181.  Gene #28: '16p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
16P GAIN MUTATED 96 35 47 45 50
16P GAIN WILD-TYPE 84 104 52 66 83

Figure S181.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.073

Table S182.  Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
16Q GAIN MUTATED 26 41 33 11 12 15
16Q GAIN WILD-TYPE 205 119 289 116 74 119

Figure S182.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S183.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
17P GAIN MUTATED 49 19 10 21 7
17P GAIN WILD-TYPE 211 393 83 244 42

Figure S183.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S184.  Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
17Q GAIN MUTATED 3 8 46 8 10 11 5 4
17Q GAIN WILD-TYPE 18 28 73 88 99 61 15 36

Figure S184.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.066

Table S185.  Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
17Q GAIN MUTATED 34 23 24 7 7
17Q GAIN WILD-TYPE 67 129 90 81 51

Figure S185.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S186.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
17Q GAIN MUTATED 115 35 14 37 15
17Q GAIN WILD-TYPE 145 377 79 228 34

Figure S186.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.057

Table S187.  Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
17Q GAIN MUTATED 17 41 60 15 21
17Q GAIN WILD-TYPE 115 156 117 73 107

Figure S187.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.061

Table S188.  Gene #31: '17q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
17Q GAIN MUTATED 6 21 8 36 4
17Q GAIN WILD-TYPE 58 85 82 71 27

Figure S188.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S189.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
17Q GAIN MUTATED 145 41 29
17Q GAIN WILD-TYPE 398 257 203

Figure S189.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S190.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
17Q GAIN MUTATED 88 40 42 18 19 8
17Q GAIN WILD-TYPE 131 124 264 123 164 52

Figure S190.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.1

Table S191.  Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
17Q GAIN MUTATED 64 31 56 22 25 13
17Q GAIN WILD-TYPE 167 129 266 105 61 121

Figure S191.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S192.  Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
18P GAIN MUTATED 1 1 19 35 16 10 4 1
18P GAIN WILD-TYPE 20 35 100 61 93 62 16 39

Figure S192.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S193.  Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
18P GAIN MUTATED 20 13 17 32 5
18P GAIN WILD-TYPE 81 139 97 56 53

Figure S193.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S194.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
18P GAIN MUTATED 41 23 19 82 12
18P GAIN WILD-TYPE 219 389 74 183 37

Figure S194.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S195.  Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
18P GAIN MUTATED 52 22 15 6 13
18P GAIN WILD-TYPE 80 175 162 82 115

Figure S195.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S196.  Gene #32: '18p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
18P GAIN MUTATED 13 9 34 10 4
18P GAIN WILD-TYPE 51 97 56 97 27

Figure S196.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S197.  Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
18P GAIN MUTATED 84 86 7
18P GAIN WILD-TYPE 459 212 225

Figure S197.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S198.  Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
18P GAIN MUTATED 43 21 13 16 70 14
18P GAIN WILD-TYPE 176 143 293 125 113 46

Figure S198.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S199.  Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
18P GAIN MUTATED 97 22 51
18P GAIN WILD-TYPE 234 231 425

Figure S199.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S200.  Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
18P GAIN MUTATED 24 37 23 19 13 54
18P GAIN WILD-TYPE 207 123 299 108 73 80

Figure S200.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S201.  Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
18P GAIN MUTATED 26 51 10 11 11
18P GAIN WILD-TYPE 154 88 89 100 122

Figure S201.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S202.  Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
18P GAIN MUTATED 72 21 16
18P GAIN WILD-TYPE 233 226 94

Figure S202.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S203.  Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
18Q GAIN MUTATED 2 1 21 30 17 5 4 1
18Q GAIN WILD-TYPE 19 35 98 66 92 67 16 39

Figure S203.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q gain' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.025

Table S204.  Gene #33: '18q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
18Q GAIN MUTATED 22 13 14 27 5
18Q GAIN WILD-TYPE 79 139 100 61 53

Figure S204.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S205.  Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
18Q GAIN MUTATED 37 17 20 67 12
18Q GAIN WILD-TYPE 223 395 73 198 37

Figure S205.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.025

Table S206.  Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
18Q GAIN MUTATED 34 24 15 6 11
18Q GAIN WILD-TYPE 98 173 162 82 117

Figure S206.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S207.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
18Q GAIN MUTATED 83 62 8
18Q GAIN WILD-TYPE 460 236 224

Figure S207.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S208.  Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
18Q GAIN MUTATED 46 17 16 15 53 6
18Q GAIN WILD-TYPE 173 147 290 126 130 54

Figure S208.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S209.  Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
18Q GAIN MUTATED 76 19 52
18Q GAIN WILD-TYPE 255 234 424

Figure S209.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S210.  Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
18Q GAIN MUTATED 27 24 23 20 13 40
18Q GAIN WILD-TYPE 204 136 299 107 73 94

Figure S210.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MRNA_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.11

Table S211.  Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
19P GAIN MUTATED 6 3 15 29 15 11 9 4
19P GAIN WILD-TYPE 15 33 104 67 94 61 11 36

Figure S211.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S212.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
19P GAIN MUTATED 38 36 29 78 8
19P GAIN WILD-TYPE 222 376 64 187 41

Figure S212.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S213.  Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
19P GAIN MUTATED 77 81 30
19P GAIN WILD-TYPE 466 217 202

Figure S213.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S214.  Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
19P GAIN MUTATED 31 27 44 15 55 16
19P GAIN WILD-TYPE 188 137 262 126 128 44

Figure S214.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S215.  Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
19P GAIN MUTATED 86 40 60
19P GAIN WILD-TYPE 245 213 416

Figure S215.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.081

Table S216.  Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
19P GAIN MUTATED 38 40 41 18 10 39
19P GAIN WILD-TYPE 193 120 281 109 76 95

Figure S216.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S217.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
19Q GAIN MUTATED 48 40 31 90 13
19Q GAIN WILD-TYPE 212 372 62 175 36

Figure S217.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S218.  Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
19Q GAIN MUTATED 94 91 36
19Q GAIN WILD-TYPE 449 207 196

Figure S218.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S219.  Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
19Q GAIN MUTATED 42 34 49 15 62 19
19Q GAIN WILD-TYPE 177 130 257 126 121 41

Figure S219.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S220.  Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
19Q GAIN MUTATED 102 43 75
19Q GAIN WILD-TYPE 229 210 401

Figure S220.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S221.  Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
19Q GAIN MUTATED 49 52 49 19 11 40
19Q GAIN WILD-TYPE 182 108 273 108 75 94

Figure S221.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S222.  Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
20P GAIN MUTATED 8 13 49 42 34 42 15 7
20P GAIN WILD-TYPE 13 23 70 54 75 30 5 33

Figure S222.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S223.  Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
20P GAIN MUTATED 42 45 68 38 17
20P GAIN WILD-TYPE 59 107 46 50 41

Figure S223.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S224.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
20P GAIN MUTATED 146 59 56 132 22
20P GAIN WILD-TYPE 114 353 37 133 27

Figure S224.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S225.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
20P GAIN MUTATED 229 131 53
20P GAIN WILD-TYPE 314 167 179

Figure S225.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S226.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
20P GAIN MUTATED 103 91 86 33 77 23
20P GAIN WILD-TYPE 116 73 220 108 106 37

Figure S226.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S227.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
20P GAIN MUTATED 160 65 184
20P GAIN WILD-TYPE 171 188 292

Figure S227.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S228.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
20P GAIN MUTATED 102 81 83 61 27 55
20P GAIN WILD-TYPE 129 79 239 66 59 79

Figure S228.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S229.  Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
20P GAIN MUTATED 90 68 32 37 35
20P GAIN WILD-TYPE 90 71 67 74 98

Figure S229.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.025

Table S230.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
20Q GAIN MUTATED 7 13 61 40 35 42 15 10
20Q GAIN WILD-TYPE 14 23 58 56 74 30 5 30

Figure S230.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S231.  Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
20Q GAIN MUTATED 52 49 71 34 17
20Q GAIN WILD-TYPE 49 103 43 54 41

Figure S231.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S232.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
20Q GAIN MUTATED 170 62 55 139 24
20Q GAIN WILD-TYPE 90 350 38 126 25

Figure S232.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S233.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
20Q GAIN MUTATED 62 71 98 25 40
20Q GAIN WILD-TYPE 70 126 79 63 88

Figure S233.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S234.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
20Q GAIN MUTATED 257 136 55
20Q GAIN WILD-TYPE 286 162 177

Figure S234.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S235.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
20Q GAIN MUTATED 123 96 91 34 78 26
20Q GAIN WILD-TYPE 96 68 215 107 105 34

Figure S235.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S236.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
20Q GAIN MUTATED 171 69 205
20Q GAIN WILD-TYPE 160 184 271

Figure S236.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S237.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
20Q GAIN MUTATED 127 82 88 59 31 58
20Q GAIN WILD-TYPE 104 78 234 68 55 76

Figure S237.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S238.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
20Q GAIN MUTATED 103 72 37 40 39
20Q GAIN WILD-TYPE 77 67 62 71 94

Figure S238.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.078

Table S239.  Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
20Q GAIN MUTATED 158 84 49
20Q GAIN WILD-TYPE 147 163 61

Figure S239.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S240.  Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
21Q GAIN MUTATED 2 2 16 31 11 31 8 3
21Q GAIN WILD-TYPE 19 34 103 65 98 41 12 37

Figure S240.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S241.  Gene #38: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
21Q GAIN MUTATED 12 15 44 27 6
21Q GAIN WILD-TYPE 89 137 70 61 52

Figure S241.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S242.  Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
21Q GAIN MUTATED 39 30 22 92 12
21Q GAIN WILD-TYPE 221 382 71 173 37

Figure S242.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S243.  Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
21Q GAIN MUTATED 47 16 33 10 15
21Q GAIN WILD-TYPE 85 181 144 78 113

Figure S243.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q gain' versus 'RPPA_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.13

Table S244.  Gene #38: '21q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
21Q GAIN MUTATED 47 16 22
21Q GAIN WILD-TYPE 102 116 95

Figure S244.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S245.  Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
21Q GAIN MUTATED 77 104 14
21Q GAIN WILD-TYPE 466 194 218

Figure S245.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S246.  Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
21Q GAIN MUTATED 36 43 21 10 61 24
21Q GAIN WILD-TYPE 183 121 285 131 122 36

Figure S246.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S247.  Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
21Q GAIN MUTATED 101 28 61
21Q GAIN WILD-TYPE 230 225 415

Figure S247.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S248.  Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
21Q GAIN MUTATED 40 51 29 18 8 44
21Q GAIN WILD-TYPE 191 109 293 109 78 90

Figure S248.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S249.  Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
21Q GAIN MUTATED 29 51 6 12 19
21Q GAIN WILD-TYPE 151 88 93 99 114

Figure S249.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S250.  Gene #38: '21q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
21Q GAIN MUTATED 78 30 9
21Q GAIN WILD-TYPE 227 217 101

Figure S250.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S251.  Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
22Q GAIN MUTATED 3 0 12 18 2 15 2 0
22Q GAIN WILD-TYPE 18 36 107 78 107 57 18 40

Figure S251.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S252.  Gene #39: '22q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
22Q GAIN MUTATED 9 3 24 15 1
22Q GAIN WILD-TYPE 92 149 90 73 57

Figure S252.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S253.  Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
22Q GAIN MUTATED 25 9 3 55 6
22Q GAIN WILD-TYPE 235 403 90 210 43

Figure S253.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.21

Table S254.  Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
22Q GAIN MUTATED 22 8 19 3 9
22Q GAIN WILD-TYPE 110 189 158 85 119

Figure S254.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S255.  Gene #39: '22q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
22Q GAIN MUTATED 31 5 8
22Q GAIN WILD-TYPE 118 127 109

Figure S255.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S256.  Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
22Q GAIN MUTATED 36 60 1
22Q GAIN WILD-TYPE 507 238 231

Figure S256.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S257.  Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
22Q GAIN MUTATED 19 24 7 2 33 12
22Q GAIN WILD-TYPE 200 140 299 139 150 48

Figure S257.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S258.  Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
22Q GAIN MUTATED 55 7 33
22Q GAIN WILD-TYPE 276 246 443

Figure S258.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S259.  Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
22Q GAIN MUTATED 26 28 10 3 6 22
22Q GAIN WILD-TYPE 205 132 312 124 80 112

Figure S259.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.14

Table S260.  Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
22Q GAIN MUTATED 13 25 6 4 6
22Q GAIN WILD-TYPE 167 114 93 107 127

Figure S260.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'MRNA_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.14

Table S261.  Gene #40: 'xq gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
XQ GAIN MUTATED 2 1 17 25 13 19 4 1
XQ GAIN WILD-TYPE 19 35 102 71 96 53 16 39

Figure S261.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S262.  Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
XQ GAIN MUTATED 37 15 22 57 9
XQ GAIN WILD-TYPE 223 397 71 208 40

Figure S262.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S263.  Gene #40: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
XQ GAIN MUTATED 27 19 22 4 3
XQ GAIN WILD-TYPE 105 178 155 84 125

Figure S263.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S264.  Gene #40: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
XQ GAIN MUTATED 72 58 9
XQ GAIN WILD-TYPE 471 240 223

Figure S264.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S265.  Gene #40: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
XQ GAIN MUTATED 31 27 14 15 44 8
XQ GAIN WILD-TYPE 188 137 292 126 139 52

Figure S265.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S266.  Gene #40: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
XQ GAIN MUTATED 73 9 51
XQ GAIN WILD-TYPE 258 244 425

Figure S266.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S267.  Gene #40: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
XQ GAIN MUTATED 31 25 13 17 14 33
XQ GAIN WILD-TYPE 200 135 309 110 72 101

Figure S267.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S268.  Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
1P LOSS MUTATED 33 23 42 10 14
1P LOSS WILD-TYPE 68 129 72 78 44

Figure S268.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S269.  Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
1P LOSS MUTATED 96 37 47 49 14
1P LOSS WILD-TYPE 164 375 46 216 35

Figure S269.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S270.  Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
1P LOSS MUTATED 21 40 63 12 17
1P LOSS WILD-TYPE 111 157 114 76 111

Figure S270.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S271.  Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
1P LOSS MUTATED 166 47 28
1P LOSS WILD-TYPE 377 251 204

Figure S271.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S272.  Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
1P LOSS MUTATED 67 67 51 25 22 9
1P LOSS WILD-TYPE 152 97 255 116 161 51

Figure S272.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S273.  Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
1P LOSS MUTATED 65 34 51 48 24 16
1P LOSS WILD-TYPE 166 126 271 79 62 118

Figure S273.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.16

Table S274.  Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
1Q LOSS MUTATED 19 6 4 18 4
1Q LOSS WILD-TYPE 241 406 89 247 45

Figure S274.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S275.  Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
2P LOSS MUTATED 76 30 26 36 13
2P LOSS WILD-TYPE 184 382 67 229 36

Figure S275.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.19

Table S276.  Gene #43: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
2P LOSS MUTATED 14 43 37 9 10
2P LOSS WILD-TYPE 118 154 140 79 118

Figure S276.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.22

Table S277.  Gene #43: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
2P LOSS MUTATED 18 11 8 29 6
2P LOSS WILD-TYPE 46 95 82 78 25

Figure S277.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S278.  Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
2P LOSS MUTATED 130 27 22
2P LOSS WILD-TYPE 413 271 210

Figure S278.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S279.  Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
2P LOSS MUTATED 63 42 36 20 16 2
2P LOSS WILD-TYPE 156 122 270 121 167 58

Figure S279.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S280.  Gene #43: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
2P LOSS MUTATED 46 26 105
2P LOSS WILD-TYPE 285 227 371

Figure S280.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.14

Table S281.  Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
2P LOSS MUTATED 51 20 42 30 21 13
2P LOSS WILD-TYPE 180 140 280 97 65 121

Figure S281.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S282.  Gene #43: '2p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
2P LOSS MUTATED 49 10 10 16 15
2P LOSS WILD-TYPE 131 129 89 95 118

Figure S282.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S283.  Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
2Q LOSS MUTATED 82 33 28 51 16
2Q LOSS WILD-TYPE 178 379 65 214 33

Figure S283.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S284.  Gene #44: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
2Q LOSS MUTATED 132 52 24
2Q LOSS WILD-TYPE 411 246 208

Figure S284.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S285.  Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
2Q LOSS MUTATED 64 46 41 20 33 4
2Q LOSS WILD-TYPE 155 118 265 121 150 56

Figure S285.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.24

Table S286.  Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
2Q LOSS MUTATED 69 29 108
2Q LOSS WILD-TYPE 262 224 368

Figure S286.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.12

Table S287.  Gene #44: '2q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
2Q LOSS MUTATED 53 22 11 18 16
2Q LOSS WILD-TYPE 127 117 88 93 117

Figure S287.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S288.  Gene #45: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
3P LOSS MUTATED 0 7 19 29 4 17 6 4
3P LOSS WILD-TYPE 21 29 100 67 105 55 14 36

Figure S288.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S289.  Gene #45: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
3P LOSS MUTATED 15 18 27 26 0
3P LOSS WILD-TYPE 86 134 87 62 58

Figure S289.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S290.  Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
3P LOSS MUTATED 54 28 13 86 5
3P LOSS WILD-TYPE 206 384 80 179 44

Figure S290.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S291.  Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
3P LOSS MUTATED 38 15 45 9 17
3P LOSS WILD-TYPE 94 182 132 79 111

Figure S291.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S292.  Gene #45: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
3P LOSS MUTATED 2 14 31 19 7
3P LOSS WILD-TYPE 62 92 59 88 24

Figure S292.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S293.  Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
3P LOSS MUTATED 76 89 20
3P LOSS WILD-TYPE 467 209 212

Figure S293.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S294.  Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
3P LOSS MUTATED 33 43 35 4 55 15
3P LOSS WILD-TYPE 186 121 271 137 128 45

Figure S294.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S295.  Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
3P LOSS MUTATED 99 29 52
3P LOSS WILD-TYPE 232 224 424

Figure S295.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S296.  Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
3P LOSS MUTATED 50 41 35 9 6 39
3P LOSS WILD-TYPE 181 119 287 118 80 95

Figure S296.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S297.  Gene #45: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
3P LOSS MUTATED 27 48 9 9 24
3P LOSS WILD-TYPE 153 91 90 102 109

Figure S297.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.1

Table S298.  Gene #46: '3q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
3Q LOSS MUTATED 10 7 19 12 0
3Q LOSS WILD-TYPE 91 145 95 76 58

Figure S298.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S299.  Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
3Q LOSS MUTATED 33 13 9 44 4
3Q LOSS WILD-TYPE 227 399 84 221 45

Figure S299.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S300.  Gene #46: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
3Q LOSS MUTATED 22 28 16 4 24 9
3Q LOSS WILD-TYPE 197 136 290 137 159 51

Figure S300.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S301.  Gene #46: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
3Q LOSS MUTATED 52 16 31
3Q LOSS WILD-TYPE 279 237 445

Figure S301.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.081

Table S302.  Gene #46: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
3Q LOSS MUTATED 34 21 17 5 5 17
3Q LOSS WILD-TYPE 197 139 305 122 81 117

Figure S302.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S303.  Gene #47: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
4P LOSS MUTATED 4 7 25 60 22 41 8 7
4P LOSS WILD-TYPE 17 29 94 36 87 31 12 33

Figure S303.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S304.  Gene #47: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
4P LOSS MUTATED 24 28 57 54 11
4P LOSS WILD-TYPE 77 124 57 34 47

Figure S304.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S305.  Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
4P LOSS MUTATED 77 53 45 164 14
4P LOSS WILD-TYPE 183 359 48 101 35

Figure S305.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S306.  Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
4P LOSS MUTATED 90 38 53 15 28
4P LOSS WILD-TYPE 42 159 124 73 100

Figure S306.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S307.  Gene #47: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
4P LOSS MUTATED 77 39 25
4P LOSS WILD-TYPE 72 93 92

Figure S307.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S308.  Gene #47: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
4P LOSS MUTATED 18 28 53 29 13
4P LOSS WILD-TYPE 46 78 37 78 18

Figure S308.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S309.  Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
4P LOSS MUTATED 141 180 30
4P LOSS WILD-TYPE 402 118 202

Figure S309.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S310.  Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
4P LOSS MUTATED 52 70 53 24 120 32
4P LOSS WILD-TYPE 167 94 253 117 63 28

Figure S310.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S311.  Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
4P LOSS MUTATED 178 47 117
4P LOSS WILD-TYPE 153 206 359

Figure S311.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S312.  Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
4P LOSS MUTATED 69 74 52 40 18 89
4P LOSS WILD-TYPE 162 86 270 87 68 45

Figure S312.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S313.  Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
4P LOSS MUTATED 49 93 19 27 25
4P LOSS WILD-TYPE 131 46 80 84 108

Figure S313.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.025

Table S314.  Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
4P LOSS MUTATED 124 56 33
4P LOSS WILD-TYPE 181 191 77

Figure S314.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S315.  Gene #48: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
4Q LOSS MUTATED 4 7 24 46 21 36 7 7
4Q LOSS WILD-TYPE 17 29 95 50 88 36 13 33

Figure S315.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S316.  Gene #48: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
4Q LOSS MUTATED 24 26 50 41 11
4Q LOSS WILD-TYPE 77 126 64 47 47

Figure S316.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S317.  Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
4Q LOSS MUTATED 69 50 45 136 12
4Q LOSS WILD-TYPE 191 362 48 129 37

Figure S317.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S318.  Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
4Q LOSS MUTATED 72 40 46 15 28
4Q LOSS WILD-TYPE 60 157 131 73 100

Figure S318.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'RPPA_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.21

Table S319.  Gene #48: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
4Q LOSS MUTATED 64 35 25
4Q LOSS WILD-TYPE 85 97 92

Figure S319.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S320.  Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
4Q LOSS MUTATED 137 147 26
4Q LOSS WILD-TYPE 406 151 206

Figure S320.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S321.  Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
4Q LOSS MUTATED 47 67 51 24 94 27
4Q LOSS WILD-TYPE 172 97 255 117 89 33

Figure S321.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S322.  Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
4Q LOSS MUTATED 142 45 114
4Q LOSS WILD-TYPE 189 208 362

Figure S322.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S323.  Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
4Q LOSS MUTATED 63 63 50 39 18 68
4Q LOSS WILD-TYPE 168 97 272 88 68 66

Figure S323.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S324.  Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
4Q LOSS MUTATED 46 69 19 27 21
4Q LOSS WILD-TYPE 134 70 80 84 112

Figure S324.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S325.  Gene #49: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
5P LOSS MUTATED 1 1 8 40 5 11 1 2
5P LOSS WILD-TYPE 20 35 111 56 104 61 19 38

Figure S325.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S326.  Gene #49: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
5P LOSS MUTATED 9 5 17 37 1
5P LOSS WILD-TYPE 92 147 97 51 57

Figure S326.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S327.  Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
5P LOSS MUTATED 18 13 4 97 8
5P LOSS WILD-TYPE 242 399 89 168 41

Figure S327.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S328.  Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
5P LOSS MUTATED 51 8 13 4 17
5P LOSS WILD-TYPE 81 189 164 84 111

Figure S328.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S329.  Gene #49: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
5P LOSS MUTATED 43 9 9
5P LOSS WILD-TYPE 106 123 108

Figure S329.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S330.  Gene #49: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
5P LOSS MUTATED 1 7 38 12 3
5P LOSS WILD-TYPE 63 99 52 95 28

Figure S330.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S331.  Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
5P LOSS MUTATED 40 94 5
5P LOSS WILD-TYPE 503 204 227

Figure S331.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S332.  Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
5P LOSS MUTATED 15 25 12 1 78 8
5P LOSS WILD-TYPE 204 139 294 140 105 52

Figure S332.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S333.  Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
5P LOSS MUTATED 97 15 25
5P LOSS WILD-TYPE 234 238 451

Figure S333.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S334.  Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
5P LOSS MUTATED 28 30 10 3 5 61
5P LOSS WILD-TYPE 203 130 312 124 81 73

Figure S334.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S335.  Gene #49: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
5P LOSS MUTATED 12 56 5 4 9
5P LOSS WILD-TYPE 168 83 94 107 124

Figure S335.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S336.  Gene #49: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
5P LOSS MUTATED 70 12 4
5P LOSS WILD-TYPE 235 235 106

Figure S336.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S337.  Gene #50: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
5Q LOSS MUTATED 2 3 14 60 4 21 5 3
5Q LOSS WILD-TYPE 19 33 105 36 105 51 15 37

Figure S337.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S338.  Gene #50: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
5Q LOSS MUTATED 14 10 32 55 1
5Q LOSS WILD-TYPE 87 142 82 33 57

Figure S338.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S339.  Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
5Q LOSS MUTATED 29 19 5 164 11
5Q LOSS WILD-TYPE 231 393 88 101 38

Figure S339.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S340.  Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
5Q LOSS MUTATED 86 8 21 7 29
5Q LOSS WILD-TYPE 46 189 156 81 99

Figure S340.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S341.  Gene #50: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
5Q LOSS MUTATED 68 10 18
5Q LOSS WILD-TYPE 81 122 99

Figure S341.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S342.  Gene #50: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
5Q LOSS MUTATED 3 14 55 18 6
5Q LOSS WILD-TYPE 61 92 35 89 25

Figure S342.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S343.  Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
5Q LOSS MUTATED 61 156 10
5Q LOSS WILD-TYPE 482 142 222

Figure S343.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S344.  Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
5Q LOSS MUTATED 24 38 24 2 119 20
5Q LOSS WILD-TYPE 195 126 282 139 64 40

Figure S344.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S345.  Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
5Q LOSS MUTATED 162 23 38
5Q LOSS WILD-TYPE 169 230 438

Figure S345.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S346.  Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
5Q LOSS MUTATED 44 58 15 6 6 94
5Q LOSS WILD-TYPE 187 102 307 121 80 40

Figure S346.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S347.  Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
5Q LOSS MUTATED 16 88 13 9 14
5Q LOSS WILD-TYPE 164 51 86 102 119

Figure S347.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S348.  Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
5Q LOSS MUTATED 107 25 8
5Q LOSS WILD-TYPE 198 222 102

Figure S348.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S349.  Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
6P LOSS MUTATED 82 45 17 32 12
6P LOSS WILD-TYPE 178 367 76 233 37

Figure S349.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.14

Table S350.  Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
6P LOSS MUTATED 119 36 31
6P LOSS WILD-TYPE 424 262 201

Figure S350.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNA_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.13

Table S351.  Gene #52: '6q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
6Q LOSS MUTATED 6 13 44 13 23 14 1 14
6Q LOSS WILD-TYPE 15 23 75 83 86 58 19 26

Figure S351.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S352.  Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
6Q LOSS MUTATED 117 77 23 41 18
6Q LOSS WILD-TYPE 143 335 70 224 31

Figure S352.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.12

Table S353.  Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
6Q LOSS MUTATED 164 52 58
6Q LOSS WILD-TYPE 379 246 174

Figure S353.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.052

Table S354.  Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
6Q LOSS MUTATED 78 43 79 32 26 16
6Q LOSS WILD-TYPE 141 121 227 109 157 44

Figure S354.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S355.  Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
7P LOSS MUTATED 40 10 6 52 3
7P LOSS WILD-TYPE 220 402 87 213 46

Figure S355.  Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S356.  Gene #53: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
7P LOSS MUTATED 55 49 6
7P LOSS WILD-TYPE 488 249 226

Figure S356.  Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S357.  Gene #53: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
7P LOSS MUTATED 27 25 15 7 31 5
7P LOSS WILD-TYPE 192 139 291 134 152 55

Figure S357.  Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S358.  Gene #53: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
7P LOSS MUTATED 61 6 42
7P LOSS WILD-TYPE 270 247 434

Figure S358.  Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S359.  Gene #53: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
7P LOSS MUTATED 32 22 8 12 9 26
7P LOSS WILD-TYPE 199 138 314 115 77 108

Figure S359.  Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.073

Table S360.  Gene #53: '7p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
7P LOSS MUTATED 44 13 5
7P LOSS WILD-TYPE 261 234 105

Figure S360.  Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S361.  Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
7Q LOSS MUTATED 44 21 10 41 3
7Q LOSS WILD-TYPE 216 391 83 224 46

Figure S361.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.089

Table S362.  Gene #54: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
7Q LOSS MUTATED 74 34 10
7Q LOSS WILD-TYPE 469 264 222

Figure S362.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S363.  Gene #54: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
7Q LOSS MUTATED 54 8 55
7Q LOSS WILD-TYPE 277 245 421

Figure S363.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S364.  Gene #54: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
7Q LOSS MUTATED 37 26 13 17 11 13
7Q LOSS WILD-TYPE 194 134 309 110 75 121

Figure S364.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S365.  Gene #55: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
8P LOSS MUTATED 5 10 56 45 22 37 11 17
8P LOSS WILD-TYPE 16 26 63 51 87 35 9 23

Figure S365.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.081

Table S366.  Gene #55: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
8P LOSS MUTATED 48 45 58 39 13
8P LOSS WILD-TYPE 53 107 56 49 45

Figure S366.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S367.  Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
8P LOSS MUTATED 124 94 19 140 22
8P LOSS WILD-TYPE 136 318 74 125 27

Figure S367.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S368.  Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
8P LOSS MUTATED 58 54 80 15 49
8P LOSS WILD-TYPE 74 143 97 73 79

Figure S368.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.15

Table S369.  Gene #55: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
8P LOSS MUTATED 11 50 40 50 15
8P LOSS WILD-TYPE 53 56 50 57 16

Figure S369.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S370.  Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
8P LOSS MUTATED 200 137 58
8P LOSS WILD-TYPE 343 161 174

Figure S370.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S371.  Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
8P LOSS MUTATED 92 85 92 18 74 34
8P LOSS WILD-TYPE 127 79 214 123 109 26

Figure S371.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S372.  Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
8P LOSS MUTATED 154 75 164
8P LOSS WILD-TYPE 177 178 312

Figure S372.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S373.  Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
8P LOSS MUTATED 98 80 88 38 30 59
8P LOSS WILD-TYPE 133 80 234 89 56 75

Figure S373.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S374.  Gene #57: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
9P LOSS MUTATED 7 10 53 30 18 33 10 6
9P LOSS WILD-TYPE 14 26 66 66 91 39 10 34

Figure S374.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S375.  Gene #57: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
9P LOSS MUTATED 43 31 59 25 9
9P LOSS WILD-TYPE 58 121 55 63 49

Figure S375.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S376.  Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
9P LOSS MUTATED 143 40 15 101 13
9P LOSS WILD-TYPE 117 372 78 164 36

Figure S376.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S377.  Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
9P LOSS MUTATED 49 41 76 13 24
9P LOSS WILD-TYPE 83 156 101 75 104

Figure S377.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S378.  Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
9P LOSS MUTATED 182 99 30
9P LOSS WILD-TYPE 361 199 202

Figure S378.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S379.  Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
9P LOSS MUTATED 94 77 53 13 50 24
9P LOSS WILD-TYPE 125 87 253 128 133 36

Figure S379.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S380.  Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
9P LOSS MUTATED 130 39 137
9P LOSS WILD-TYPE 201 214 339

Figure S380.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S381.  Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
9P LOSS MUTATED 98 70 46 35 21 36
9P LOSS WILD-TYPE 133 90 276 92 65 98

Figure S381.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.057

Table S382.  Gene #57: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
9P LOSS MUTATED 65 52 21 19 28
9P LOSS WILD-TYPE 115 87 78 92 105

Figure S382.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S383.  Gene #57: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
9P LOSS MUTATED 119 48 18
9P LOSS WILD-TYPE 186 199 92

Figure S383.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'MRNA_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.048

Table S384.  Gene #58: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
9Q LOSS MUTATED 7 5 41 41 19 23 8 5
9Q LOSS WILD-TYPE 14 31 78 55 90 49 12 35

Figure S384.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S385.  Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
9Q LOSS MUTATED 36 23 47 35 8
9Q LOSS WILD-TYPE 65 129 67 53 50

Figure S385.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S386.  Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
9Q LOSS MUTATED 112 36 14 106 14
9Q LOSS WILD-TYPE 148 376 79 159 35

Figure S386.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S387.  Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
9Q LOSS MUTATED 59 40 57 10 22
9Q LOSS WILD-TYPE 73 157 120 78 106

Figure S387.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S388.  Gene #58: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
9Q LOSS MUTATED 66 28 23
9Q LOSS WILD-TYPE 83 104 94

Figure S388.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.13

Table S389.  Gene #58: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
9Q LOSS MUTATED 11 21 40 33 12
9Q LOSS WILD-TYPE 53 85 50 74 19

Figure S389.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S390.  Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
9Q LOSS MUTATED 151 109 21
9Q LOSS WILD-TYPE 392 189 211

Figure S390.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S391.  Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
9Q LOSS MUTATED 77 61 43 13 68 19
9Q LOSS WILD-TYPE 142 103 263 128 115 41

Figure S391.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S392.  Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
9Q LOSS MUTATED 132 32 109
9Q LOSS WILD-TYPE 199 221 367

Figure S392.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S393.  Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
9Q LOSS MUTATED 78 64 31 28 19 53
9Q LOSS WILD-TYPE 153 96 291 99 67 81

Figure S393.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S394.  Gene #58: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
9Q LOSS MUTATED 51 57 19 15 24
9Q LOSS WILD-TYPE 129 82 80 96 109

Figure S394.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S395.  Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
9Q LOSS MUTATED 111 41 14
9Q LOSS WILD-TYPE 194 206 96

Figure S395.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S396.  Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
10P LOSS MUTATED 59 29 19 55 11
10P LOSS WILD-TYPE 201 383 74 210 38

Figure S396.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.066

Table S397.  Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
10P LOSS MUTATED 35 31 35 12 8
10P LOSS WILD-TYPE 97 166 142 76 120

Figure S397.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S398.  Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
10P LOSS MUTATED 95 62 15
10P LOSS WILD-TYPE 448 236 217

Figure S398.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S399.  Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
10P LOSS MUTATED 45 41 29 14 32 11
10P LOSS WILD-TYPE 174 123 277 127 151 49

Figure S399.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S400.  Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
10Q LOSS MUTATED 70 33 19 92 15
10Q LOSS WILD-TYPE 190 379 74 173 34

Figure S400.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S401.  Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
10Q LOSS MUTATED 55 34 53 11 12
10Q LOSS WILD-TYPE 77 163 124 77 116

Figure S401.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S402.  Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
10Q LOSS MUTATED 114 96 18
10Q LOSS WILD-TYPE 429 202 214

Figure S402.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S403.  Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
10Q LOSS MUTATED 55 54 31 14 60 14
10Q LOSS WILD-TYPE 164 110 275 127 123 46

Figure S403.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.12

Table S404.  Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
10Q LOSS MUTATED 94 38 92
10Q LOSS WILD-TYPE 237 215 384

Figure S404.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S405.  Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
10Q LOSS MUTATED 60 53 38 18 13 42
10Q LOSS WILD-TYPE 171 107 284 109 73 92

Figure S405.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.048

Table S406.  Gene #60: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
10Q LOSS MUTATED 47 45 17 10 28
10Q LOSS WILD-TYPE 133 94 82 101 105

Figure S406.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S407.  Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
11P LOSS MUTATED 98 41 23 103 10
11P LOSS WILD-TYPE 162 371 70 162 39

Figure S407.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S408.  Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
11P LOSS MUTATED 47 35 64 13 20
11P LOSS WILD-TYPE 85 162 113 75 108

Figure S408.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.14

Table S409.  Gene #61: '11p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
11P LOSS MUTATED 8 22 33 34 15
11P LOSS WILD-TYPE 56 84 57 73 16

Figure S409.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S410.  Gene #61: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
11P LOSS MUTATED 149 99 27
11P LOSS WILD-TYPE 394 199 205

Figure S410.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S411.  Gene #61: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
11P LOSS MUTATED 71 61 52 15 57 19
11P LOSS WILD-TYPE 148 103 254 126 126 41

Figure S411.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S412.  Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
11P LOSS MUTATED 113 46 108
11P LOSS WILD-TYPE 218 207 368

Figure S412.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S413.  Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
11P LOSS MUTATED 81 52 49 26 17 42
11P LOSS WILD-TYPE 150 108 273 101 69 92

Figure S413.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S414.  Gene #62: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
11Q LOSS MUTATED 5 16 65 26 25 27 6 15
11Q LOSS WILD-TYPE 16 20 54 70 84 45 14 25

Figure S414.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q loss' versus 'MRNA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.029

Table S415.  Gene #62: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
11Q LOSS MUTATED 58 49 41 24 13
11Q LOSS WILD-TYPE 43 103 73 64 45

Figure S415.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S416.  Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
11Q LOSS MUTATED 151 75 29 96 13
11Q LOSS WILD-TYPE 109 337 64 169 36

Figure S416.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S417.  Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
11Q LOSS MUTATED 44 67 83 21 27
11Q LOSS WILD-TYPE 88 130 94 67 101

Figure S417.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.078

Table S418.  Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
11Q LOSS MUTATED 215 90 58
11Q LOSS WILD-TYPE 328 208 174

Figure S418.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S419.  Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
11Q LOSS MUTATED 113 64 94 22 53 17
11Q LOSS WILD-TYPE 106 100 212 119 130 43

Figure S419.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S420.  Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
12P LOSS MUTATED 36 31 11 71 2
12P LOSS WILD-TYPE 224 381 82 194 47

Figure S420.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S421.  Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
12P LOSS MUTATED 41 16 21 12 11
12P LOSS WILD-TYPE 91 181 156 76 117

Figure S421.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S422.  Gene #63: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
12P LOSS MUTATED 51 79 20
12P LOSS WILD-TYPE 492 219 212

Figure S422.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S423.  Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
12P LOSS MUTATED 24 25 26 10 50 15
12P LOSS WILD-TYPE 195 139 280 131 133 45

Figure S423.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S424.  Gene #63: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
12P LOSS MUTATED 77 24 48
12P LOSS WILD-TYPE 254 229 428

Figure S424.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S425.  Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
12P LOSS MUTATED 33 33 26 10 10 37
12P LOSS WILD-TYPE 198 127 296 117 76 97

Figure S425.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S426.  Gene #63: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
12P LOSS MUTATED 22 45 9 11 9
12P LOSS WILD-TYPE 158 94 90 100 124

Figure S426.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S427.  Gene #63: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
12P LOSS MUTATED 69 16 11
12P LOSS WILD-TYPE 236 231 99

Figure S427.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S428.  Gene #64: '12q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
12Q LOSS MUTATED 2 3 7 33 5 5 2 3
12Q LOSS WILD-TYPE 19 33 112 63 104 67 18 37

Figure S428.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'12q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S429.  Gene #64: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
12Q LOSS MUTATED 5 8 15 28 4
12Q LOSS WILD-TYPE 96 144 99 60 54

Figure S429.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S430.  Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
12Q LOSS MUTATED 19 20 9 80 3
12Q LOSS WILD-TYPE 241 392 84 185 46

Figure S430.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S431.  Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
12Q LOSS MUTATED 51 9 17 6 8
12Q LOSS WILD-TYPE 81 188 160 82 120

Figure S431.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q loss' versus 'RPPA_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.081

Table S432.  Gene #64: '12q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
12Q LOSS MUTATED 32 9 8
12Q LOSS WILD-TYPE 117 123 109

Figure S432.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'12q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S433.  Gene #64: '12q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
12Q LOSS MUTATED 8 5 28 4 4
12Q LOSS WILD-TYPE 56 101 62 103 27

Figure S433.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S434.  Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
12Q LOSS MUTATED 33 84 13
12Q LOSS WILD-TYPE 510 214 219

Figure S434.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S435.  Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
12Q LOSS MUTATED 13 16 19 6 63 13
12Q LOSS WILD-TYPE 206 148 287 135 120 47

Figure S435.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S436.  Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
12Q LOSS MUTATED 80 18 30
12Q LOSS WILD-TYPE 251 235 446

Figure S436.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S437.  Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
12Q LOSS MUTATED 21 30 16 8 6 47
12Q LOSS WILD-TYPE 210 130 306 119 80 87

Figure S437.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S438.  Gene #64: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
12Q LOSS MUTATED 15 53 6 10 11
12Q LOSS WILD-TYPE 165 86 93 101 122

Figure S438.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S439.  Gene #64: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
12Q LOSS MUTATED 72 16 7
12Q LOSS WILD-TYPE 233 231 103

Figure S439.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'MRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.025

Table S440.  Gene #65: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
13Q LOSS MUTATED 7 14 62 51 30 38 9 8
13Q LOSS WILD-TYPE 14 22 57 45 79 34 11 32

Figure S440.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S441.  Gene #65: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
13Q LOSS MUTATED 58 40 62 47 12
13Q LOSS WILD-TYPE 43 112 52 41 46

Figure S441.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S442.  Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
13Q LOSS MUTATED 141 80 47 137 27
13Q LOSS WILD-TYPE 119 332 46 128 22

Figure S442.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S443.  Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
13Q LOSS MUTATED 76 70 87 18 39
13Q LOSS WILD-TYPE 56 127 90 70 89

Figure S443.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S444.  Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
13Q LOSS MUTATED 219 155 57
13Q LOSS WILD-TYPE 324 143 175

Figure S444.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S445.  Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
13Q LOSS MUTATED 99 84 97 30 98 23
13Q LOSS WILD-TYPE 120 80 209 111 85 37

Figure S445.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S446.  Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
13Q LOSS MUTATED 169 73 183
13Q LOSS WILD-TYPE 162 180 293

Figure S446.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S447.  Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
13Q LOSS MUTATED 112 71 96 42 32 72
13Q LOSS WILD-TYPE 119 89 226 85 54 62

Figure S447.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S448.  Gene #65: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
13Q LOSS MUTATED 78 74 29 24 44
13Q LOSS WILD-TYPE 102 65 70 87 89

Figure S448.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.17

Table S449.  Gene #65: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
13Q LOSS MUTATED 139 78 32
13Q LOSS WILD-TYPE 166 169 78

Figure S449.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S450.  Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
14Q LOSS MUTATED 3 1 30 50 7 14 9 5
14Q LOSS WILD-TYPE 18 35 89 46 102 58 11 35

Figure S450.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S451.  Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
14Q LOSS MUTATED 24 17 29 47 2
14Q LOSS WILD-TYPE 77 135 85 41 56

Figure S451.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S452.  Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
14Q LOSS MUTATED 63 34 19 139 11
14Q LOSS WILD-TYPE 197 378 74 126 38

Figure S452.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S453.  Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
14Q LOSS MUTATED 78 24 40 11 28
14Q LOSS WILD-TYPE 54 173 137 77 100

Figure S453.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S454.  Gene #66: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
14Q LOSS MUTATED 54 16 25
14Q LOSS WILD-TYPE 95 116 92

Figure S454.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S455.  Gene #66: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
14Q LOSS MUTATED 4 20 44 22 5
14Q LOSS WILD-TYPE 60 86 46 85 26

Figure S455.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S456.  Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
14Q LOSS MUTATED 99 143 23
14Q LOSS WILD-TYPE 444 155 209

Figure S456.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S457.  Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
14Q LOSS MUTATED 39 55 38 12 109 12
14Q LOSS WILD-TYPE 180 109 268 129 74 48

Figure S457.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S458.  Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
14Q LOSS MUTATED 147 39 73
14Q LOSS WILD-TYPE 184 214 403

Figure S458.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S459.  Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
14Q LOSS MUTATED 54 56 38 16 9 86
14Q LOSS WILD-TYPE 177 104 284 111 77 48

Figure S459.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S460.  Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
14Q LOSS MUTATED 35 78 19 17 24
14Q LOSS WILD-TYPE 145 61 80 94 109

Figure S460.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S461.  Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
14Q LOSS MUTATED 113 44 16
14Q LOSS WILD-TYPE 192 203 94

Figure S461.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'MRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.025

Table S462.  Gene #67: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
15Q LOSS MUTATED 4 9 32 45 22 33 8 6
15Q LOSS WILD-TYPE 17 27 87 51 87 39 12 34

Figure S462.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S463.  Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
15Q LOSS MUTATED 27 29 48 43 12
15Q LOSS WILD-TYPE 74 123 66 45 46

Figure S463.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S464.  Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
15Q LOSS MUTATED 85 40 43 136 15
15Q LOSS WILD-TYPE 175 372 50 129 34

Figure S464.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S465.  Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
15Q LOSS MUTATED 74 39 59 15 28
15Q LOSS WILD-TYPE 58 158 118 73 100

Figure S465.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S466.  Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
15Q LOSS MUTATED 157 135 25
15Q LOSS WILD-TYPE 386 163 207

Figure S466.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S467.  Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
15Q LOSS MUTATED 64 67 52 24 94 16
15Q LOSS WILD-TYPE 155 97 254 117 89 44

Figure S467.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S468.  Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
15Q LOSS MUTATED 149 40 121
15Q LOSS WILD-TYPE 182 213 355

Figure S468.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S469.  Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
15Q LOSS MUTATED 72 65 44 42 16 71
15Q LOSS WILD-TYPE 159 95 278 85 70 63

Figure S469.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S470.  Gene #67: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
15Q LOSS MUTATED 55 71 23 21 21
15Q LOSS WILD-TYPE 125 68 76 90 112

Figure S470.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S471.  Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
15Q LOSS MUTATED 114 47 30
15Q LOSS WILD-TYPE 191 200 80

Figure S471.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.052

Table S472.  Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
16P LOSS MUTATED 37 49 11 66 10
16P LOSS WILD-TYPE 223 363 82 199 39

Figure S472.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.13

Table S473.  Gene #68: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
16P LOSS MUTATED 35 23 45 12 50 7
16P LOSS WILD-TYPE 184 141 261 129 133 53

Figure S473.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.025

Table S474.  Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
16P LOSS MUTATED 78 34 59
16P LOSS WILD-TYPE 253 219 417

Figure S474.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.097

Table S475.  Gene #68: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
16P LOSS MUTATED 22 42 12 13 21
16P LOSS WILD-TYPE 158 97 87 98 112

Figure S475.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S476.  Gene #69: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
16Q LOSS MUTATED 12 21 63 28 81 38 11 30
16Q LOSS WILD-TYPE 9 15 56 68 28 34 9 10

Figure S476.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S477.  Gene #69: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
16Q LOSS MUTATED 58 102 58 24 42
16Q LOSS WILD-TYPE 43 50 56 64 16

Figure S477.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S478.  Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
16Q LOSS MUTATED 135 245 70 112 31
16Q LOSS WILD-TYPE 125 167 23 153 18

Figure S478.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S479.  Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
16Q LOSS MUTATED 52 131 103 57 57
16Q LOSS WILD-TYPE 80 66 74 31 71

Figure S479.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'RPPA_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.14

Table S480.  Gene #69: '16q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
16Q LOSS MUTATED 60 84 66
16Q LOSS WILD-TYPE 89 48 51

Figure S480.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'16q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S481.  Gene #69: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
16Q LOSS MUTATED 47 60 28 64 11
16Q LOSS WILD-TYPE 17 46 62 43 20

Figure S481.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S482.  Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
16Q LOSS MUTATED 330 108 151
16Q LOSS WILD-TYPE 213 190 81

Figure S482.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S483.  Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
16Q LOSS MUTATED 124 86 205 93 64 17
16Q LOSS WILD-TYPE 95 78 101 48 119 43

Figure S483.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S484.  Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
16Q LOSS MUTATED 130 152 301
16Q LOSS WILD-TYPE 201 101 175

Figure S484.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S485.  Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
16Q LOSS MUTATED 116 56 206 100 50 55
16Q LOSS WILD-TYPE 115 104 116 27 36 79

Figure S485.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.034

Table S486.  Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
16Q LOSS MUTATED 139 153 70
16Q LOSS WILD-TYPE 166 94 40

Figure S486.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S487.  Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
17P LOSS MUTATED 13 23 66 61 30 57 12 21
17P LOSS WILD-TYPE 8 13 53 35 79 15 8 19

Figure S487.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S488.  Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
17P LOSS MUTATED 57 76 85 54 11
17P LOSS WILD-TYPE 44 76 29 34 47

Figure S488.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S489.  Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
17P LOSS MUTATED 172 142 41 198 26
17P LOSS WILD-TYPE 88 270 52 67 23

Figure S489.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S490.  Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
17P LOSS MUTATED 82 90 112 37 52
17P LOSS WILD-TYPE 50 107 65 51 76

Figure S490.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S491.  Gene #70: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
17P LOSS MUTATED 109 55 56
17P LOSS WILD-TYPE 40 77 61

Figure S491.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'17p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S492.  Gene #70: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
17P LOSS MUTATED 21 47 61 68 23
17P LOSS WILD-TYPE 43 59 29 39 8

Figure S492.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S493.  Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
17P LOSS MUTATED 279 198 99
17P LOSS WILD-TYPE 264 100 133

Figure S493.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S494.  Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
17P LOSS MUTATED 119 123 156 26 109 43
17P LOSS WILD-TYPE 100 41 150 115 74 17

Figure S494.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S495.  Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
17P LOSS MUTATED 219 110 240
17P LOSS WILD-TYPE 112 143 236

Figure S495.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S496.  Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
17P LOSS MUTATED 139 95 149 67 29 90
17P LOSS WILD-TYPE 92 65 173 60 57 44

Figure S496.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S497.  Gene #71: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
17Q LOSS MUTATED 4 4 23 50 12 35 4 12
17Q LOSS WILD-TYPE 17 32 96 46 97 37 16 28

Figure S497.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S498.  Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
17Q LOSS MUTATED 21 26 48 44 5
17Q LOSS WILD-TYPE 80 126 66 44 53

Figure S498.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S499.  Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
17Q LOSS MUTATED 57 55 24 132 7
17Q LOSS WILD-TYPE 203 357 69 133 42

Figure S499.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S500.  Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
17Q LOSS MUTATED 64 26 32 11 30
17Q LOSS WILD-TYPE 68 171 145 77 98

Figure S500.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S501.  Gene #71: '17q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 149 132 117
17Q LOSS MUTATED 72 16 30
17Q LOSS WILD-TYPE 77 116 87

Figure S501.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'17q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S502.  Gene #71: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
17Q LOSS MUTATED 8 23 50 22 15
17Q LOSS WILD-TYPE 56 83 40 85 16

Figure S502.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S503.  Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
17Q LOSS MUTATED 101 136 36
17Q LOSS WILD-TYPE 442 162 196

Figure S503.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S504.  Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
17Q LOSS MUTATED 33 59 61 5 83 32
17Q LOSS WILD-TYPE 186 105 245 136 100 28

Figure S504.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S505.  Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
17Q LOSS MUTATED 135 47 88
17Q LOSS WILD-TYPE 196 206 388

Figure S505.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S506.  Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
17Q LOSS MUTATED 62 61 47 27 5 68
17Q LOSS WILD-TYPE 169 99 275 100 81 66

Figure S506.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S507.  Gene #71: '17q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
17Q LOSS MUTATED 37 58 16 23 32
17Q LOSS WILD-TYPE 143 81 83 88 101

Figure S507.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MRNA_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.12

Table S508.  Gene #72: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
18P LOSS MUTATED 6 11 35 27 19 38 9 13
18P LOSS WILD-TYPE 15 25 84 69 90 34 11 27

Figure S508.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.17

Table S509.  Gene #72: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
18P LOSS MUTATED 28 39 55 24 12
18P LOSS WILD-TYPE 73 113 59 64 46

Figure S509.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S510.  Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
18P LOSS MUTATED 108 66 34 100 12
18P LOSS WILD-TYPE 152 346 59 165 37

Figure S510.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S511.  Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
18P LOSS MUTATED 36 39 88 16 31
18P LOSS WILD-TYPE 96 158 89 72 97

Figure S511.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.16

Table S512.  Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
18P LOSS MUTATED 164 107 47
18P LOSS WILD-TYPE 379 191 185

Figure S512.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S513.  Gene #72: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
18P LOSS MUTATED 59 88 79 19 50 23
18P LOSS WILD-TYPE 160 76 227 122 133 37

Figure S513.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S514.  Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
18P LOSS MUTATED 99 57 76 33 18 34
18P LOSS WILD-TYPE 132 103 246 94 68 100

Figure S514.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MRNA_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.11

Table S515.  Gene #73: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
18Q LOSS MUTATED 5 11 34 26 19 38 7 9
18Q LOSS WILD-TYPE 16 25 85 70 90 34 13 31

Figure S515.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.066

Table S516.  Gene #73: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
18Q LOSS MUTATED 27 34 53 24 11
18Q LOSS WILD-TYPE 74 118 61 64 47

Figure S516.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S517.  Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
18Q LOSS MUTATED 106 65 35 104 11
18Q LOSS WILD-TYPE 154 347 58 161 38

Figure S517.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S518.  Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
18Q LOSS MUTATED 45 42 86 15 28
18Q LOSS WILD-TYPE 87 155 91 73 100

Figure S518.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S519.  Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
18Q LOSS MUTATED 164 110 44
18Q LOSS WILD-TYPE 379 188 188

Figure S519.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S520.  Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
18Q LOSS MUTATED 51 89 78 19 56 25
18Q LOSS WILD-TYPE 168 75 228 122 127 35

Figure S520.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S521.  Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
18Q LOSS MUTATED 90 67 73 31 16 39
18Q LOSS WILD-TYPE 141 93 249 96 70 95

Figure S521.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S522.  Gene #74: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
19P LOSS MUTATED 2 6 30 20 8 25 1 2
19P LOSS WILD-TYPE 19 30 89 76 101 47 19 38

Figure S522.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S523.  Gene #74: '19p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
19P LOSS MUTATED 29 13 32 18 2
19P LOSS WILD-TYPE 72 139 82 70 56

Figure S523.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S524.  Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
19P LOSS MUTATED 89 19 9 68 8
19P LOSS WILD-TYPE 171 393 84 197 41

Figure S524.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S525.  Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
19P LOSS MUTATED 36 21 47 5 15
19P LOSS WILD-TYPE 96 176 130 83 113

Figure S525.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.066

Table S526.  Gene #74: '19p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 64 106 90 107 31
19P LOSS MUTATED 3 13 21 27 11
19P LOSS WILD-TYPE 61 93 69 80 20

Figure S526.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S527.  Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
19P LOSS MUTATED 105 75 12
19P LOSS WILD-TYPE 438 223 220

Figure S527.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S528.  Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
19P LOSS MUTATED 50 57 23 8 44 10
19P LOSS WILD-TYPE 169 107 283 133 139 50

Figure S528.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S529.  Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
19P LOSS MUTATED 97 19 72
19P LOSS WILD-TYPE 234 234 404

Figure S529.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S530.  Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
19P LOSS MUTATED 59 40 19 19 18 33
19P LOSS WILD-TYPE 172 120 303 108 68 101

Figure S530.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S531.  Gene #74: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
19P LOSS MUTATED 37 41 13 6 20
19P LOSS WILD-TYPE 143 98 86 105 113

Figure S531.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S532.  Gene #74: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
19P LOSS MUTATED 77 34 6
19P LOSS WILD-TYPE 228 213 104

Figure S532.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S533.  Gene #75: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
19Q LOSS MUTATED 23 10 29 11 2
19Q LOSS WILD-TYPE 78 142 85 77 56

Figure S533.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S534.  Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
19Q LOSS MUTATED 80 16 6 51 8
19Q LOSS WILD-TYPE 180 396 87 214 41

Figure S534.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S535.  Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
19Q LOSS MUTATED 27 17 43 2 15
19Q LOSS WILD-TYPE 105 180 134 86 113

Figure S535.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S536.  Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
19Q LOSS MUTATED 90 61 9
19Q LOSS WILD-TYPE 453 237 223

Figure S536.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S537.  Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
19Q LOSS MUTATED 46 43 19 8 34 10
19Q LOSS WILD-TYPE 173 121 287 133 149 50

Figure S537.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S538.  Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
19Q LOSS MUTATED 76 19 62
19Q LOSS WILD-TYPE 255 234 414

Figure S538.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S539.  Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
19Q LOSS MUTATED 49 26 16 17 20 29
19Q LOSS WILD-TYPE 182 134 306 110 66 105

Figure S539.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.093

Table S540.  Gene #75: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
19Q LOSS MUTATED 30 34 10 6 16
19Q LOSS WILD-TYPE 150 105 89 105 117

Figure S540.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S541.  Gene #75: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
19Q LOSS MUTATED 65 27 4
19Q LOSS WILD-TYPE 240 220 106

Figure S541.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'MRNA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.043

Table S542.  Gene #76: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
20P LOSS MUTATED 9 4 12 14 0
20P LOSS WILD-TYPE 92 148 102 74 58

Figure S542.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S543.  Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
20P LOSS MUTATED 25 10 5 49 4
20P LOSS WILD-TYPE 235 402 88 216 45

Figure S543.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S544.  Gene #76: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
20P LOSS MUTATED 33 6 17 5 4
20P LOSS WILD-TYPE 99 191 160 83 124

Figure S544.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S545.  Gene #76: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
20P LOSS MUTATED 37 53 3
20P LOSS WILD-TYPE 506 245 229

Figure S545.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S546.  Gene #76: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
20P LOSS MUTATED 17 22 6 3 41 4
20P LOSS WILD-TYPE 202 142 300 138 142 56

Figure S546.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S547.  Gene #76: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
20P LOSS MUTATED 51 13 23
20P LOSS WILD-TYPE 280 240 453

Figure S547.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S548.  Gene #76: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
20P LOSS MUTATED 22 11 10 6 6 32
20P LOSS WILD-TYPE 209 149 312 121 80 102

Figure S548.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S549.  Gene #76: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
20P LOSS MUTATED 8 28 6 4 5
20P LOSS WILD-TYPE 172 111 93 107 128

Figure S549.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.038

Table S550.  Gene #76: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
20P LOSS MUTATED 37 13 1
20P LOSS WILD-TYPE 268 234 109

Figure S550.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S551.  Gene #77: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
20Q LOSS MUTATED 10 5 5 32 3
20Q LOSS WILD-TYPE 250 407 88 233 46

Figure S551.  Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

'20q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S552.  Gene #77: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
20Q LOSS MUTATED 24 5 4 3 2
20Q LOSS WILD-TYPE 108 192 173 85 126

Figure S552.  Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S553.  Gene #77: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
20Q LOSS MUTATED 16 36 3
20Q LOSS WILD-TYPE 527 262 229

Figure S553.  Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S554.  Gene #77: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
20Q LOSS MUTATED 8 9 4 1 31 2
20Q LOSS WILD-TYPE 211 155 302 140 152 58

Figure S554.  Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S555.  Gene #77: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
20Q LOSS MUTATED 32 11 9
20Q LOSS WILD-TYPE 299 242 467

Figure S555.  Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S556.  Gene #77: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 231 160 322 127 86 134
20Q LOSS MUTATED 7 9 8 3 2 23
20Q LOSS WILD-TYPE 224 151 314 124 84 111

Figure S556.  Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S557.  Gene #77: '20q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
20Q LOSS MUTATED 2 22 2 2 3
20Q LOSS WILD-TYPE 178 117 97 109 130

Figure S557.  Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.093

Table S558.  Gene #77: '20q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
20Q LOSS MUTATED 25 6 0
20Q LOSS WILD-TYPE 280 241 110

Figure S558.  Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S559.  Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
21Q LOSS MUTATED 74 24 17 55 10
21Q LOSS WILD-TYPE 186 388 76 210 39

Figure S559.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S560.  Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
22Q LOSS MUTATED 148 134 59 117 24
22Q LOSS WILD-TYPE 112 278 34 148 25

Figure S560.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.034

Table S561.  Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
22Q LOSS MUTATED 279 109 91
22Q LOSS WILD-TYPE 264 189 141

Figure S561.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S562.  Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
22Q LOSS MUTATED 119 92 131 52 70 15
22Q LOSS WILD-TYPE 100 72 175 89 113 45

Figure S562.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S563.  Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 260 412 93 265 49
XQ LOSS MUTATED 67 28 14 70 6
XQ LOSS WILD-TYPE 193 384 79 195 43

Figure S563.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S564.  Gene #80: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 132 197 177 88 128
XQ LOSS MUTATED 31 29 45 6 9
XQ LOSS WILD-TYPE 101 168 132 82 119

Figure S564.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.052

Table S565.  Gene #80: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 543 298 232
XQ LOSS MUTATED 101 63 20
XQ LOSS WILD-TYPE 442 235 212

Figure S565.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S566.  Gene #80: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 219 164 306 141 183 60
XQ LOSS MUTATED 49 42 33 15 39 6
XQ LOSS WILD-TYPE 170 122 273 126 144 54

Figure S566.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.15

Table S567.  Gene #80: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 331 253 476
XQ LOSS MUTATED 76 27 79
XQ LOSS WILD-TYPE 255 226 397

Figure S567.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Molecular subtypes file = BRCA-TP.transferedmergedcluster.txt

  • Number of patients = 1079

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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