Correlation between copy number variations of arm-level result and molecular subtypes
Pan-kidney cohort (KICH+KIRC+KIRP) (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C12806TP
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C12806TP
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 82 arm-level events and 12 molecular subtypes across 882 patients, 697 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

  • 2q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 3p 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'.

  • 3q 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'.

  • 4p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 4q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 6p gain cnv correlated to 'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 6q gain cnv correlated to 'RPPA_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 7p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 9p gain cnv correlated to 'MRNA_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 9q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

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

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

  • 14q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 15q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 16q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17p 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'.

  • 17q 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'.

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

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

  • 19p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 19q gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 20p gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 20q 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'.

  • 21q gain cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 22q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • xp 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'.

  • xq 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'.

  • 1p 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'.

  • 1q 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'.

  • 2p 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'.

  • 2q 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'.

  • 3p 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'.

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

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

  • 4q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 6p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 6q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7p loss cnv correlated to 'RPPA_CHIERARCHICAL'.

  • 7q loss cnv correlated to 'RPPA_CHIERARCHICAL'.

  • 8p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 9p 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'.

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

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

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

  • 11q loss cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 12q loss cnv correlated to 'CN_CNMF'.

  • 13q 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'.

  • 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 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16p loss cnv correlated to 'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17p 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'.

  • 17q 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'.

  • 18p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 18q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

  • 21q 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'.

  • 22q 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'.

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

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 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, 697 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
17p gain 197 (22%) 685 1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.0459
(0.0654) 		0.00125
(0.00224) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
20q gain 237 (27%) 645 0.0202
(0.0308) 		0.0494
(0.0698) 		1e-05
(2.34e-05) 		5e-05
(0.000108) 		0.00929
(0.0147) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		5e-05
(0.000108) 		1e-05
(2.34e-05) 		0.00781
(0.0125) 		0.00302
(0.00507)
3p loss 412 (47%) 470 1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.00088
(0.00163) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
9p loss 192 (22%) 690 0.011
(0.0173) 		0.0211
(0.0321) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		2e-05
(4.48e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		9e-05
(0.000187) 		3e-05
(6.65e-05)
9q loss 195 (22%) 687 0.0221
(0.0334) 		0.0391
(0.0565) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.00011
(0.000227) 		4e-05
(8.73e-05)
14q loss 265 (30%) 617 7e-05
(0.000147) 		8e-05
(0.000167) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
3p gain 102 (12%) 780 0.00112
(0.00203) 		0.00809
(0.0129) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.263
(0.319) 		0.0181
(0.0276) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
3q gain 158 (18%) 724 0.00776
(0.0124) 		0.0322
(0.0473) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.321
(0.378) 		0.00456
(0.00749) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
12p gain 252 (29%) 630 0.0177
(0.0272) 		0.0628
(0.0867) 		1e-05
(2.34e-05) 		2e-05
(4.48e-05) 		0.0295
(0.0438) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		4e-05
(8.73e-05) 		2e-05
(4.48e-05)
12q gain 256 (29%) 626 0.0178
(0.0273) 		0.062
(0.0857) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.0107
(0.0169) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		7e-05
(0.000147) 		1e-05
(2.34e-05)
17q gain 222 (25%) 660 1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.156
(0.202) 		0.00223
(0.00385) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
20p gain 233 (26%) 649 0.0394
(0.0568) 		0.0762
(0.103) 		1e-05
(2.34e-05) 		4e-05
(8.73e-05) 		0.0188
(0.0287) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		8e-05
(0.000167) 		1e-05
(2.34e-05) 		0.00523
(0.00851) 		0.00169
(0.00297)
xp gain 124 (14%) 758 0.0035
(0.00583) 		0.00277
(0.0047) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.203
(0.256) 		0.00297
(0.005) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
xq gain 125 (14%) 757 0.00014
(0.000286) 		4e-05
(8.73e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.37
(0.43) 		0.0143
(0.0222) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
1p loss 145 (16%) 737 0.00125
(0.00224) 		0.0133
(0.0208) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.397
(0.459) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
1q loss 110 (12%) 772 0.00837
(0.0133) 		0.00815
(0.013) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.926
(0.965) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
2p loss 65 (7%) 817 1e-05
(2.34e-05) 		0.00029
(0.000571) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.14
(0.183) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
2q loss 63 (7%) 819 0.00021
(0.000422) 		8e-05
(0.000167) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.322
(0.379) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
6p loss 172 (20%) 710 0.0025
(0.00429) 		0.00356
(0.00592) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.00033
(0.000644) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.0937
(0.125) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
6q loss 206 (23%) 676 0.00311
(0.00521) 		0.00346
(0.00577) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.00123
(0.00222) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.672
(0.727) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
13q loss 137 (16%) 745 0.00296
(0.005) 		0.0113
(0.0178) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.0758
(0.103) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.00067
(0.00126) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
17p loss 110 (12%) 772 0.00089
(0.00165) 		0.00301
(0.00506) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.664
(0.72) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
17q loss 82 (9%) 800 0.00016
(0.000324) 		0.00022
(0.00044) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.423
(0.483) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
21q loss 133 (15%) 749 0.0159
(0.0246) 		0.0236
(0.0355) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.959
(0.995) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		2e-05
(4.48e-05) 		1e-05
(2.34e-05)
22q loss 107 (12%) 775 0.00546
(0.00884) 		0.0366
(0.0531) 		1e-05
(2.34e-05) 		0.00026
(0.000518) 		0.337
(0.395) 		6e-05
(0.000128) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		4e-05
(8.73e-05) 		1e-05
(2.34e-05) 		0.0018
(0.00315) 		2e-05
(4.48e-05)
5p gain 237 (27%) 645 0.539
(0.599) 		0.606
(0.661) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.0339
(0.0495) 		7e-05
(0.000147) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
7p gain 368 (42%) 514 0.0901
(0.121) 		0.109
(0.145) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.0145
(0.0225) 		0.00128
(0.00229) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
7q gain 370 (42%) 512 0.0892
(0.12) 		0.109
(0.144) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.013
(0.0204) 		0.0015
(0.00265) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
8q gain 99 (11%) 783 0.0601
(0.0834) 		0.241
(0.295) 		1e-05
(2.34e-05) 		0.00559
(0.00902) 		0.00212
(0.00367) 		0.00058
(0.0011) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.0207
(0.0315) 		0.012
(0.0188) 		0.00093
(0.00171) 		3e-05
(6.65e-05)
16p gain 281 (32%) 601 0.0598
(0.0832) 		0.0661
(0.0906) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.0051
(0.00831) 		0.00053
(0.00101) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
16q gain 268 (30%) 614 0.0632
(0.0871) 		0.0589
(0.0821) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.00251
(0.0043) 		0.00028
(0.000554) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
19q gain 78 (9%) 804 0.0395
(0.0569) 		0.064
(0.0881) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.0417
(0.0598) 		0.00044
(0.000846) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.25
(0.304) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
4p loss 98 (11%) 784 0.578
(0.632) 		0.486
(0.548) 		1e-05
(2.34e-05) 		2e-05
(4.48e-05) 		0.0258
(0.0387) 		3e-05
(6.65e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.00035
(0.000682) 		0.00014
(0.000286) 		0.00095
(0.00174) 		1e-05
(2.34e-05)
4p gain 46 (5%) 836 0.158
(0.203) 		0.417
(0.478) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.637
(0.693) 		0.0018
(0.00315) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
4q gain 46 (5%) 836 0.295
(0.351) 		0.645
(0.7) 		2e-05
(4.48e-05) 		1e-05
(2.34e-05) 		0.54
(0.599) 		0.00341
(0.0057) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		2e-05
(4.48e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
5q gain 248 (28%) 634 0.166
(0.212) 		0.208
(0.26) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.334
(0.392) 		2e-05
(4.48e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
14q gain 39 (4%) 843 0.745
(0.799) 		0.745
(0.799) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.743
(0.799) 		0.00275
(0.00467) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.00044
(0.000846) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
3q loss 124 (14%) 758 0.0861
(0.116) 		0.059
(0.0822) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.867
(0.916) 		0.00019
(0.000383) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		2e-05
(4.48e-05) 		0.00016
(0.000324)
4q loss 92 (10%) 790 0.491
(0.551) 		0.623
(0.678) 		1e-05
(2.34e-05) 		0.0008
(0.00149) 		0.153
(0.199) 		0.00011
(0.000227) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.00137
(0.00243) 		0.00044
(0.000846) 		0.00059
(0.00112) 		1e-05
(2.34e-05)
5p loss 24 (3%) 858 8e-05
(0.000167) 		1e-05
(2.34e-05) 		0.0365
(0.0529) 		0.0533
(0.0749) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.00196
(0.00342) 		1e-05
(2.34e-05) 		7e-05
(0.000147) 		1e-05
(2.34e-05)
10p loss 131 (15%) 751 0.26
(0.316) 		0.359
(0.419) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.559
(0.617) 		0.0001
(0.000207) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.00029
(0.000571) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
11p loss 43 (5%) 839 0.0349
(0.0509) 		0.0719
(0.0975) 		6e-05
(0.000128) 		0.0288
(0.0428) 		0.62
(0.676) 		0.107
(0.143) 		0.00033
(0.000644) 		2e-05
(4.48e-05) 		0.0466
(0.0662) 		0.00382
(0.00634) 		0.0003
(0.000589) 		4e-05
(8.73e-05)
18p loss 142 (16%) 740 0.228
(0.28) 		0.405
(0.466) 		1e-05
(2.34e-05) 		0.0314
(0.0463) 		0.00038
(0.000738) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.00016
(0.000324) 		0.896
(0.939) 		0.00103
(0.00187) 		1e-05
(2.34e-05)
18q loss 149 (17%) 733 0.164
(0.21) 		0.354
(0.414) 		1e-05
(2.34e-05) 		0.0463
(0.0659) 		0.0006
(0.00113) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.0005
(0.000957) 		0.934
(0.973) 		0.00022
(0.00044) 		1e-05
(2.34e-05)
xp loss 118 (13%) 764 0.0535
(0.075) 		0.0799
(0.107) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.411
(0.472) 		6e-05
(0.000128) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
xq loss 116 (13%) 766 0.0742
(0.101) 		0.113
(0.149) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.43
(0.491) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
1q gain 68 (8%) 814 0.552
(0.611) 		0.694
(0.748) 		1e-05
(2.34e-05) 		0.149
(0.195) 		0.00178
(0.00312) 		0.0359
(0.0523) 		5e-05
(0.000108) 		1e-05
(2.34e-05) 		0.00116
(0.0021) 		0.00248
(0.00427) 		0.166
(0.212) 		0.00792
(0.0127)
2q gain 127 (14%) 755 0.524
(0.586) 		0.33
(0.388) 		1e-05
(2.34e-05) 		0.0163
(0.0251) 		0.522
(0.584) 		0.00607
(0.00978) 		0.00084
(0.00157) 		1e-05
(2.34e-05) 		0.217
(0.269) 		0.00027
(0.000536) 		0.00541
(0.00877) 		0.0228
(0.0344)
8p gain 67 (8%) 815 0.293
(0.349) 		0.472
(0.534) 		1e-05
(2.34e-05) 		0.00099
(0.00181) 		0.308
(0.365) 		0.00272
(0.00465) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.202
(0.255) 		7e-05
(0.000147) 		0.00027
(0.000536) 		2e-05
(4.48e-05)
15q gain 52 (6%) 830 0.869
(0.916) 		0.554
(0.612) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.901
(0.943) 		0.0314
(0.0463) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.161
(0.207) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
18p gain 54 (6%) 828 0.489
(0.55) 		0.75
(0.803) 		0.00212
(0.00367) 		0.00015
(0.000306) 		0.786
(0.837) 		0.348
(0.407) 		0.00013
(0.000267) 		6e-05
(0.000128) 		0.0217
(0.0329) 		1e-05
(2.34e-05) 		0.005
(0.00817) 		0.00038
(0.000738)
18q gain 50 (6%) 832 0.525
(0.586) 		0.775
(0.828) 		0.00253
(0.00433) 		0.00014
(0.000286) 		0.685
(0.741) 		0.29
(0.346) 		2e-05
(4.48e-05) 		1e-05
(2.34e-05) 		0.0361
(0.0525) 		1e-05
(2.34e-05) 		0.00043
(0.000831) 		2e-05
(4.48e-05)
19p gain 75 (9%) 807 0.149
(0.194) 		0.215
(0.266) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.13
(0.171) 		0.00087
(0.00162) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.465
(0.528) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
5q loss 22 (2%) 860 3e-05
(6.65e-05) 		1e-05
(2.34e-05) 		0.101
(0.134) 		0.067
(0.0917) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.00504
(0.00822) 		1e-05
(2.34e-05) 		6e-05
(0.000128) 		1e-05
(2.34e-05)
8p loss 164 (19%) 718 0.287
(0.343) 		0.278
(0.333) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.548
(0.608) 		0.0587
(0.082) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
8q loss 87 (10%) 795 0.835
(0.887) 		0.504
(0.565) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.108
(0.143) 		0.688
(0.743) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.00469
(0.00769) 		1e-05
(2.34e-05) 		0.00017
(0.000343) 		0.00042
(0.000814)
10q loss 156 (18%) 726 0.204
(0.257) 		0.24
(0.294) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.487
(0.548) 		0.00145
(0.00257) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.127
(0.166) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
11q loss 52 (6%) 830 0.156
(0.202) 		0.302
(0.358) 		1e-05
(2.34e-05) 		0.19
(0.24) 		0.577
(0.632) 		0.00222
(0.00384) 		2e-05
(4.48e-05) 		1e-05
(2.34e-05) 		0.0405
(0.0581) 		0.0276
(0.0411) 		0.00013
(0.000267) 		3e-05
(6.65e-05)
15q loss 69 (8%) 813 0.207
(0.26) 		0.266
(0.322) 		1e-05
(2.34e-05) 		0.852
(0.903) 		0.235
(0.288) 		0.00092
(0.0017) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.0291
(0.0432) 		0.00173
(0.00304) 		0.00401
(0.00663) 		0.0009
(0.00166)
19q loss 22 (2%) 860 7e-05
(0.000147) 		0.00105
(0.00191) 		0.847
(0.898) 		0.4
(0.461) 		0.0029
(0.00491) 		0.00029
(0.000571) 		0.00483
(0.00791) 		0.00065
(0.00123) 		0.0259
(0.0387) 		0.00333
(0.00557)
2p gain 119 (13%) 763 0.491
(0.551) 		0.563
(0.62) 		1e-05
(2.34e-05) 		0.0502
(0.0708) 		0.482
(0.544) 		0.0177
(0.0272) 		0.00059
(0.00112) 		4e-05
(8.73e-05) 		0.172
(0.22) 		0.00075
(0.0014) 		0.0175
(0.027) 		0.039
(0.0564)
9p gain 26 (3%) 856 0.0359
(0.0523) 		0.0718
(0.0975) 		0.0779
(0.105) 		2e-05
(4.48e-05) 		0.726
(0.781) 		0.563
(0.62) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.212
(0.263) 		1e-05
(2.34e-05) 		0.0013
(0.00232) 		5e-05
(0.000108)
9q gain 24 (3%) 858 0.00802
(0.0128) 		2e-05
(4.48e-05) 		0.77
(0.824) 		0.283
(0.339) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.272
(0.327) 		1e-05
(2.34e-05) 		0.00071
(0.00133) 		2e-05
(4.48e-05)
11p gain 57 (6%) 825 0.29
(0.346) 		0.811
(0.862) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.556
(0.614) 		0.125
(0.165) 		2e-05
(4.48e-05) 		1e-05
(2.34e-05) 		0.314
(0.371) 		1e-05
(2.34e-05) 		0.0001
(0.000207) 		1e-05
(2.34e-05)
11q gain 55 (6%) 827 0.406
(0.466) 		0.912
(0.953) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.691
(0.745) 		0.552
(0.611) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.215
(0.266) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
22q gain 64 (7%) 818 0.279
(0.335) 		0.463
(0.526) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.893
(0.938) 		0.16
(0.207) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		0.957
(0.995) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05) 		1e-05
(2.34e-05)
16p loss 18 (2%) 864 0.0611
(0.0845) 		7e-05
(0.000147) 		0.224
(0.276) 		0.00992
(0.0156) 		0.00021
(0.000422) 		0.00273
(0.00465) 		0.0279
(0.0415) 		0.21
(0.261) 		0.00101
(0.00184) 		9e-05
(0.000187)
19p loss 27 (3%) 855 1e-05
(2.34e-05) 		0.00121
(0.00218) 		0.532
(0.593) 		0.166
(0.212) 		0.00088
(0.00163) 		0.00047
(0.000902) 		0.0523
(0.0735) 		0.00405
(0.00669) 		0.00385
(0.00638) 		0.00058
(0.0011)
6p gain 21 (2%) 861 0.0683
(0.0932) 		0.534
(0.594) 		0.0332
(0.0486) 		0.0467
(0.0662) 		0.938
(0.976) 		0.00227
(0.00391) 		0.401
(0.462) 		0.0311
(0.046) 		0.0447
(0.0638) 		0.00273
(0.00465)
16q loss 28 (3%) 854 0.001
(0.00183) 		0.0088
(0.0139) 		0.152
(0.198) 		0.211
(0.262) 		0.00439
(0.00722) 		0.0007
(0.00131) 		0.0652
(0.0896) 		0.315
(0.371) 		0.0398
(0.0573) 		0.00527
(0.00856)
20p loss 12 (1%) 870 0.666
(0.721) 		0.00551
(0.0089) 		0.205
(0.258) 		0.199
(0.252) 		0.00202
(0.00352) 		0.024
(0.036) 		0.271
(0.326) 		0.0232
(0.035) 		0.001
(0.00183) 		0.00434
(0.00715)
20q loss 6 (1%) 876 0.456
(0.518) 		0.00754
(0.0121) 		0.25
(0.304) 		0.438
(0.5) 		0.022
(0.0334) 		0.0222
(0.0336) 		0.877
(0.923) 		0.00741
(0.0119) 		0.00845
(0.0134) 		0.00134
(0.00239)
1p gain 30 (3%) 852 0.868
(0.916) 		0.916
(0.955) 		1e-05
(2.34e-05) 		0.0545
(0.0763) 		0.00164
(0.00289) 		0.00126
(0.00226) 		0.00024
(0.000479) 		1e-05
(2.34e-05) 		0.0999
(0.133) 		0.615
(0.671) 		0.157
(0.203) 		0.187
(0.237)
10p gain 30 (3%) 852 0.158
(0.204) 		0.422
(0.482) 		1e-05
(2.34e-05) 		0.016
(0.0248) 		0.123
(0.162) 		0.0328
(0.0482) 		0.00135
(0.0024) 		0.00204
(0.00355) 		0.571
(0.627) 		0.749
(0.803) 		0.299
(0.355) 		0.148
(0.193)
21q gain 73 (8%) 809 0.396
(0.459) 		0.452
(0.514) 		1e-05
(2.34e-05) 		0.406
(0.466) 		0.225
(0.277) 		0.0263
(0.0392) 		0.00031
(0.000608) 		0.00158
(0.00279) 		0.0141
(0.022) 		0.147
(0.193) 		0.966
(1.00) 		0.134
(0.176)
13q gain 53 (6%) 829 0.23
(0.282) 		0.296
(0.351) 		0.058
(0.0811) 		0.0607
(0.0842) 		0.246
(0.301) 		0.31
(0.367) 		0.0162
(0.025) 		0.0488
(0.069) 		0.0111
(0.0174) 		0.00292
(0.00494) 		0.39
(0.453) 		0.165
(0.211)
10q gain 23 (3%) 859 0.0512
(0.072) 		0.116
(0.153) 		0.00054
(0.00103) 		0.164
(0.21) 		0.242
(0.296) 		0.367
(0.427) 		0.047
(0.0665) 		0.0453
(0.0646) 		0.525
(0.586) 		0.247
(0.301) 		0.853
(0.903) 		0.45
(0.513)
6q gain 16 (2%) 866 0.0774
(0.104) 		0.266
(0.322) 		0.0296
(0.0439) 		0.179
(0.228) 		0.875
(0.922) 		0.0338
(0.0495) 		0.805
(0.856) 		0.0806
(0.108) 		0.0691
(0.094) 		0.069
(0.094)
7p loss 4 (0%) 878 0.397
(0.459) 		0.778
(0.83) 		0.571
(0.627) 		0.041
(0.0588) 		0.209
(0.261) 		0.183
(0.232) 		0.222
(0.274) 		0.209
(0.261) 		0.268
(0.324) 		0.066
(0.0906)
7q loss 4 (0%) 878 0.398
(0.46) 		0.78
(0.832) 		0.571
(0.627) 		0.0422
(0.0603) 		0.208
(0.26) 		0.18
(0.229) 		0.221
(0.273) 		0.209
(0.261) 		0.268
(0.324) 		0.0677
(0.0925)
12q loss 4 (0%) 878 0.0221
(0.0334) 		0.472
(0.534) 		0.473
(0.535) 		0.387
(0.45) 		0.895
(0.939) 		0.276
(0.332) 		1
(1.00)
12p loss 7 (1%) 875 0.19
(0.24) 		0.108
(0.144) 		0.343
(0.402) 		0.911
(0.952) 		1
(1.00) 		0.381
(0.443) 		0.892
(0.938) 		0.595
(0.65) 		0.154
(0.2) 		0.269
(0.324)
'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
1P GAIN MUTATED 3 5 22
1P GAIN WILD-TYPE 279 305 268

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

'1p gain' versus 'RPPA_CNMF'

P value = 0.00164 (Fisher's exact test), Q value = 0.0029

Table S2.  Gene #1: '1p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 182 181 187 197
1P GAIN MUTATED 12 2 2 12
1P GAIN WILD-TYPE 170 179 185 185

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

'1p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00126 (Fisher's exact test), Q value = 0.0023

Table S3.  Gene #1: '1p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
1P GAIN MUTATED 2 0 8 3 5 2 8
1P GAIN WILD-TYPE 195 64 108 144 54 69 85

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

'1p gain' versus 'MRNASEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00048

Table S4.  Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
1P GAIN MUTATED 3 17 5 4
1P GAIN WILD-TYPE 116 178 292 264

Figure S4.  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 = 2.3e-05

Table S5.  Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
1P GAIN MUTATED 1 8 1 16 3 0
1P GAIN WILD-TYPE 87 137 206 143 108 169

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

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S6.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
1Q GAIN MUTATED 6 16 46
1Q GAIN WILD-TYPE 276 294 244

Figure S6.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'RPPA_CNMF'

P value = 0.00178 (Fisher's exact test), Q value = 0.0031

Table S7.  Gene #2: '1q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 182 181 187 197
1Q GAIN MUTATED 16 8 8 27
1Q GAIN WILD-TYPE 166 173 179 170

Figure S7.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'1q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0359 (Fisher's exact test), Q value = 0.052

Table S8.  Gene #2: '1q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
1Q GAIN MUTATED 12 1 10 12 9 3 12
1Q GAIN WILD-TYPE 185 63 106 135 50 68 81

Figure S8.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00011

Table S9.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
1Q GAIN MUTATED 3 31 20 12
1Q GAIN WILD-TYPE 116 164 277 256

Figure S9.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S10.  Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
1Q GAIN MUTATED 0 18 15 27 6 0
1Q GAIN WILD-TYPE 88 127 192 132 105 169

Figure S10.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 0.00116 (Fisher's exact test), Q value = 0.0021

Table S11.  Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
1Q GAIN MUTATED 12 17 37
1Q GAIN WILD-TYPE 315 176 307

Figure S11.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00248 (Fisher's exact test), Q value = 0.0043

Table S12.  Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
1Q GAIN MUTATED 0 20 46
1Q GAIN WILD-TYPE 77 285 436

Figure S12.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00792 (Fisher's exact test), Q value = 0.013

Table S13.  Gene #2: '1q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
1Q GAIN MUTATED 0 4 12 8 0
1Q GAIN WILD-TYPE 47 94 85 116 46

Figure S13.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S14.  Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
2P GAIN MUTATED 32 6 81
2P GAIN WILD-TYPE 250 304 209

Figure S14.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

'2p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0177 (Fisher's exact test), Q value = 0.027

Table S15.  Gene #3: '2p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
2P GAIN MUTATED 18 3 17 23 14 11 16
2P GAIN WILD-TYPE 179 61 99 124 45 60 77

Figure S15.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.0011

Table S16.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
2P GAIN MUTATED 5 39 37 37
2P GAIN WILD-TYPE 114 156 260 231

Figure S16.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.7e-05

Table S17.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
2P GAIN MUTATED 1 19 20 34 17 27
2P GAIN WILD-TYPE 87 126 187 125 94 142

Figure S17.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00075 (Fisher's exact test), Q value = 0.0014

Table S18.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
2P GAIN MUTATED 1 46 72
2P GAIN WILD-TYPE 76 259 410

Figure S18.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.027

Table S19.  Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
2P GAIN MUTATED 20 3 14 18
2P GAIN WILD-TYPE 133 68 49 107

Figure S19.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.039 (Fisher's exact test), Q value = 0.056

Table S20.  Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
2P GAIN MUTATED 4 14 19 17 1
2P GAIN WILD-TYPE 43 84 78 107 45

Figure S20.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S21.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
2Q GAIN MUTATED 35 11 81
2Q GAIN WILD-TYPE 247 299 209

Figure S21.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.025

Table S22.  Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
2Q GAIN MUTATED 9 44 39
2Q GAIN WILD-TYPE 119 259 182

Figure S22.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00607 (Fisher's exact test), Q value = 0.0098

Table S23.  Gene #4: '2q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
2Q GAIN MUTATED 18 3 17 26 14 12 18
2Q GAIN WILD-TYPE 179 61 99 121 45 59 75

Figure S23.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.0016

Table S24.  Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
2Q GAIN MUTATED 5 38 42 42
2Q GAIN WILD-TYPE 114 157 255 226

Figure S24.  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 = 2.3e-05

Table S25.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
2Q GAIN MUTATED 1 20 20 34 21 31
2Q GAIN WILD-TYPE 87 125 187 125 90 138

Figure S25.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.00054

Table S26.  Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
2Q GAIN MUTATED 1 51 74
2Q GAIN WILD-TYPE 76 254 408

Figure S26.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00541 (Fisher's exact test), Q value = 0.0088

Table S27.  Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
2Q GAIN MUTATED 23 3 16 19
2Q GAIN WILD-TYPE 130 68 47 106

Figure S27.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0228 (Fisher's exact test), Q value = 0.034

Table S28.  Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
2Q GAIN MUTATED 5 16 21 18 1
2Q GAIN WILD-TYPE 42 82 76 106 45

Figure S28.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p gain' versus 'MRNA_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.002

Table S29.  Gene #5: '3p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 24 12 17
3P GAIN MUTATED 0 2 2 6
3P GAIN WILD-TYPE 33 22 10 11

Figure S29.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00809 (Fisher's exact test), Q value = 0.013

Table S30.  Gene #5: '3p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 20 24 18 13 11
3P GAIN MUTATED 0 2 6 0 2
3P GAIN WILD-TYPE 20 22 12 13 9

Figure S30.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S31.  Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
3P GAIN MUTATED 85 3 14
3P GAIN WILD-TYPE 197 307 276

Figure S31.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

'3p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S32.  Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
3P GAIN MUTATED 16 7 65
3P GAIN WILD-TYPE 112 296 156

Figure S32.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0181 (Fisher's exact test), Q value = 0.028

Table S33.  Gene #5: '3p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
3P GAIN MUTATED 17 9 19 14 5 12 3
3P GAIN WILD-TYPE 180 55 97 133 54 59 90

Figure S33.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S34.  Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
3P GAIN MUTATED 14 12 2 74
3P GAIN WILD-TYPE 105 183 295 194

Figure S34.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S35.  Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
3P GAIN MUTATED 12 15 0 9 2 64
3P GAIN WILD-TYPE 76 130 207 150 109 105

Figure S35.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S36.  Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
3P GAIN MUTATED 87 10 5
3P GAIN WILD-TYPE 240 183 339

Figure S36.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S37.  Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
3P GAIN MUTATED 11 80 11
3P GAIN WILD-TYPE 66 225 471

Figure S37.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S38.  Gene #5: '3p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
3P GAIN MUTATED 47 7 6 3
3P GAIN WILD-TYPE 106 64 57 122

Figure S38.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S39.  Gene #5: '3p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
3P GAIN MUTATED 15 31 9 2 6
3P GAIN WILD-TYPE 32 67 88 122 40

Figure S39.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q gain' versus 'MRNA_CNMF'

P value = 0.00776 (Fisher's exact test), Q value = 0.012

Table S40.  Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 24 12 17
3Q GAIN MUTATED 1 7 2 6
3Q GAIN WILD-TYPE 32 17 10 11

Figure S40.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0322 (Fisher's exact test), Q value = 0.047

Table S41.  Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 20 24 18 13 11
3Q GAIN MUTATED 1 7 6 0 2
3Q GAIN WILD-TYPE 19 17 12 13 9

Figure S41.  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 = 2.3e-05

Table S42.  Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
3Q GAIN MUTATED 101 7 50
3Q GAIN WILD-TYPE 181 303 240

Figure S42.  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 = 2.3e-05

Table S43.  Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
3Q GAIN MUTATED 17 28 85
3Q GAIN WILD-TYPE 111 275 136

Figure S43.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00456 (Fisher's exact test), Q value = 0.0075

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
3Q GAIN MUTATED 28 11 34 19 11 15 9
3Q GAIN WILD-TYPE 169 53 82 128 48 56 84

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

'3q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S45.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
3Q GAIN MUTATED 15 34 14 95
3Q GAIN WILD-TYPE 104 161 283 173

Figure S45.  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 = 2.3e-05

Table S46.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
3Q GAIN MUTATED 12 25 10 31 4 76
3Q GAIN WILD-TYPE 76 120 197 128 107 93

Figure S46.  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 = 2.3e-05

Table S47.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
3Q GAIN MUTATED 104 29 24
3Q GAIN WILD-TYPE 223 164 320

Figure S47.  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 = 2.3e-05

Table S48.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
3Q GAIN MUTATED 11 102 44
3Q GAIN WILD-TYPE 66 203 438

Figure S48.  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 = 2.3e-05

Table S49.  Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
3Q GAIN MUTATED 59 7 13 8
3Q GAIN WILD-TYPE 94 64 50 117

Figure S49.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S50.  Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
3Q GAIN MUTATED 14 42 21 4 6
3Q GAIN WILD-TYPE 33 56 76 120 40

Figure S50.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S51.  Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
4P GAIN MUTATED 22 2 22
4P GAIN WILD-TYPE 260 308 268

Figure S51.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S52.  Gene #7: '4p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
4P GAIN MUTATED 27 3 6
4P GAIN WILD-TYPE 101 300 215

Figure S52.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0018 (Fisher's exact test), Q value = 0.0031

Table S53.  Gene #7: '4p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
4P GAIN MUTATED 13 5 13 1 2 2 2
4P GAIN WILD-TYPE 184 59 103 146 57 69 91

Figure S53.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
4P GAIN MUTATED 26 8 3 8
4P GAIN WILD-TYPE 93 187 294 260

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

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S55.  Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
4P GAIN MUTATED 26 8 1 6 0 4
4P GAIN WILD-TYPE 62 137 206 153 111 165

Figure S55.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S56.  Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
4P GAIN MUTATED 33 6 7
4P GAIN WILD-TYPE 294 187 337

Figure S56.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
4P GAIN MUTATED 26 12 8
4P GAIN WILD-TYPE 51 293 474

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

'4p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S58.  Gene #7: '4p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
4P GAIN MUTATED 5 20 3 2
4P GAIN WILD-TYPE 148 51 60 123

Figure S58.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S59.  Gene #7: '4p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
4P GAIN MUTATED 1 4 4 2 19
4P GAIN WILD-TYPE 46 94 93 122 27

Figure S59.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
4Q GAIN MUTATED 22 2 22
4Q GAIN WILD-TYPE 260 308 268

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

'4q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
4Q GAIN MUTATED 27 4 6
4Q GAIN WILD-TYPE 101 299 215

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

'4q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00341 (Fisher's exact test), Q value = 0.0057

Table S62.  Gene #8: '4q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
4Q GAIN MUTATED 13 5 13 1 2 2 3
4Q GAIN WILD-TYPE 184 59 103 146 57 69 90

Figure S62.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S63.  Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
4Q GAIN MUTATED 27 7 4 7
4Q GAIN WILD-TYPE 92 188 293 261

Figure S63.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S64.  Gene #8: '4q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
4Q GAIN MUTATED 27 6 1 6 1 4
4Q GAIN WILD-TYPE 61 139 206 153 110 165

Figure S64.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S65.  Gene #8: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
4Q GAIN MUTATED 33 6 7
4Q GAIN WILD-TYPE 294 187 337

Figure S65.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S66.  Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
4Q GAIN MUTATED 27 10 9
4Q GAIN WILD-TYPE 50 295 473

Figure S66.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S67.  Gene #8: '4q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
4Q GAIN MUTATED 5 21 2 2
4Q GAIN WILD-TYPE 148 50 61 123

Figure S67.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S68.  Gene #8: '4q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
4Q GAIN MUTATED 1 4 3 2 20
4Q GAIN WILD-TYPE 46 94 94 122 26

Figure S68.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S69.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
5P GAIN MUTATED 37 46 154
5P GAIN WILD-TYPE 245 264 136

Figure S69.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S70.  Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
5P GAIN MUTATED 21 111 21
5P GAIN WILD-TYPE 107 192 200

Figure S70.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p gain' versus 'RPPA_CNMF'

P value = 0.0339 (Fisher's exact test), Q value = 0.05

Table S71.  Gene #9: '5p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 182 181 187 197
5P GAIN MUTATED 49 41 52 71
5P GAIN WILD-TYPE 133 140 135 126

Figure S71.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'5p gain' versus 'RPPA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00015

Table S72.  Gene #9: '5p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
5P GAIN MUTATED 50 6 40 44 29 17 27
5P GAIN WILD-TYPE 147 58 76 103 30 54 66

Figure S72.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S73.  Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
5P GAIN MUTATED 17 85 104 29
5P GAIN WILD-TYPE 102 110 193 239

Figure S73.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S74.  Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
5P GAIN MUTATED 11 29 77 75 31 12
5P GAIN WILD-TYPE 77 116 130 84 80 157

Figure S74.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S75.  Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
5P GAIN MUTATED 37 57 139
5P GAIN WILD-TYPE 290 136 205

Figure S75.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S76.  Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
5P GAIN MUTATED 10 42 181
5P GAIN WILD-TYPE 67 263 301

Figure S76.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S77.  Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
5P GAIN MUTATED 17 9 17 52
5P GAIN WILD-TYPE 136 62 46 73

Figure S77.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S78.  Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
5P GAIN MUTATED 3 13 19 54 6
5P GAIN WILD-TYPE 44 85 78 70 40

Figure S78.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S79.  Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
5Q GAIN MUTATED 34 60 154
5Q GAIN WILD-TYPE 248 250 136

Figure S79.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S80.  Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
5Q GAIN MUTATED 19 122 20
5Q GAIN WILD-TYPE 109 181 201

Figure S80.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q gain' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S81.  Gene #10: '5q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
5Q GAIN MUTATED 50 6 38 52 30 17 30
5Q GAIN WILD-TYPE 147 58 78 95 29 54 63

Figure S81.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S82.  Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
5Q GAIN MUTATED 16 83 118 29
5Q GAIN WILD-TYPE 103 112 179 239

Figure S82.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S83.  Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
5Q GAIN MUTATED 11 27 86 76 36 10
5Q GAIN WILD-TYPE 77 118 121 83 75 159

Figure S83.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S84.  Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
5Q GAIN MUTATED 36 57 149
5Q GAIN WILD-TYPE 291 136 195

Figure S84.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S85.  Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
5Q GAIN MUTATED 10 39 193
5Q GAIN WILD-TYPE 67 266 289

Figure S85.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S86.  Gene #10: '5q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
5Q GAIN MUTATED 17 8 14 52
5Q GAIN WILD-TYPE 136 63 49 73

Figure S86.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S87.  Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
5Q GAIN MUTATED 3 13 15 54 6
5Q GAIN WILD-TYPE 44 85 82 70 40

Figure S87.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p gain' versus 'RPPA_CNMF'

P value = 0.0332 (Fisher's exact test), Q value = 0.049

Table S88.  Gene #11: '6p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 182 181 187 197
6P GAIN MUTATED 7 1 9 3
6P GAIN WILD-TYPE 175 180 178 194

Figure S88.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'6p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0467 (Fisher's exact test), Q value = 0.066

Table S89.  Gene #11: '6p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
6P GAIN MUTATED 3 4 6 1 0 2 4
6P GAIN WILD-TYPE 194 60 110 146 59 69 89

Figure S89.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00227 (Fisher's exact test), Q value = 0.0039

Table S90.  Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
6P GAIN MUTATED 1 11 5 1 2 1
6P GAIN WILD-TYPE 87 134 202 158 109 168

Figure S90.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0311 (Fisher's exact test), Q value = 0.046

Table S91.  Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
6P GAIN MUTATED 0 13 8
6P GAIN WILD-TYPE 77 292 474

Figure S91.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0447 (Fisher's exact test), Q value = 0.064

Table S92.  Gene #11: '6p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
6P GAIN MUTATED 2 3 5 2
6P GAIN WILD-TYPE 151 68 58 123

Figure S92.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00273 (Fisher's exact test), Q value = 0.0046

Table S93.  Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
6P GAIN MUTATED 1 1 9 1 0
6P GAIN WILD-TYPE 46 97 88 123 46

Figure S93.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'RPPA_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 0.044

Table S94.  Gene #12: '6q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 182 181 187 197
6Q GAIN MUTATED 6 1 7 1
6Q GAIN WILD-TYPE 176 180 180 196

Figure S94.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0338 (Fisher's exact test), Q value = 0.05

Table S95.  Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
6Q GAIN MUTATED 1 8 4 1 1 1
6Q GAIN WILD-TYPE 87 137 203 158 110 168

Figure S95.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S96.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
7P GAIN MUTATED 190 41 137
7P GAIN WILD-TYPE 92 269 153

Figure S96.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S97.  Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
7P GAIN MUTATED 40 80 153
7P GAIN WILD-TYPE 88 223 68

Figure S97.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.023

Table S98.  Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 182 181 187 197
7P GAIN MUTATED 62 73 75 99
7P GAIN WILD-TYPE 120 108 112 98

Figure S98.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00128 (Fisher's exact test), Q value = 0.0023

Table S99.  Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
7P GAIN MUTATED 93 24 56 45 29 35 27
7P GAIN WILD-TYPE 104 40 60 102 30 36 66

Figure S99.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S100.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
7P GAIN MUTATED 36 87 72 171
7P GAIN WILD-TYPE 83 108 225 97

Figure S100.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S101.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
7P GAIN MUTATED 30 41 61 66 26 142
7P GAIN WILD-TYPE 58 104 146 93 85 27

Figure S101.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S102.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
7P GAIN MUTATED 186 70 109
7P GAIN WILD-TYPE 141 123 235

Figure S102.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S103.  Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
7P GAIN MUTATED 29 189 147
7P GAIN WILD-TYPE 48 116 335

Figure S103.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S104.  Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
7P GAIN MUTATED 108 24 26 38
7P GAIN WILD-TYPE 45 47 37 87

Figure S104.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S105.  Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
7P GAIN MUTATED 38 66 35 37 20
7P GAIN WILD-TYPE 9 32 62 87 26

Figure S105.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S106.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
7Q GAIN MUTATED 190 40 140
7Q GAIN WILD-TYPE 92 270 150

Figure S106.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S107.  Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
7Q GAIN MUTATED 40 84 153
7Q GAIN WILD-TYPE 88 219 68

Figure S107.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.02

Table S108.  Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 182 181 187 197
7Q GAIN MUTATED 63 72 76 100
7Q GAIN WILD-TYPE 119 109 111 97

Figure S108.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0015 (Fisher's exact test), Q value = 0.0027

Table S109.  Gene #14: '7q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
7Q GAIN MUTATED 95 24 56 43 29 34 30
7Q GAIN WILD-TYPE 102 40 60 104 30 37 63

Figure S109.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S110.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
7Q GAIN MUTATED 36 88 73 171
7Q GAIN WILD-TYPE 83 107 224 97

Figure S110.  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 = 2.3e-05

Table S111.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
7Q GAIN MUTATED 30 41 60 69 26 142
7Q GAIN WILD-TYPE 58 104 147 90 85 27

Figure S111.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S112.  Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
7Q GAIN MUTATED 186 73 108
7Q GAIN WILD-TYPE 141 120 236

Figure S112.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S113.  Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
7Q GAIN MUTATED 29 189 149
7Q GAIN WILD-TYPE 48 116 333

Figure S113.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S114.  Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
7Q GAIN MUTATED 108 24 26 37
7Q GAIN WILD-TYPE 45 47 37 88

Figure S114.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S115.  Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
7Q GAIN MUTATED 38 66 35 36 20
7Q GAIN WILD-TYPE 9 32 62 88 26

Figure S115.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S116.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
8P GAIN MUTATED 26 3 38
8P GAIN WILD-TYPE 256 307 252

Figure S116.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.00099 (Fisher's exact test), Q value = 0.0018

Table S117.  Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
8P GAIN MUTATED 23 20 15
8P GAIN WILD-TYPE 105 283 206

Figure S117.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00272 (Fisher's exact test), Q value = 0.0046

Table S118.  Gene #15: '8p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
8P GAIN MUTATED 18 7 16 5 9 5 2
8P GAIN WILD-TYPE 179 57 100 142 50 66 91

Figure S118.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S119.  Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
8P GAIN MUTATED 20 24 6 17
8P GAIN WILD-TYPE 99 171 291 251

Figure S119.  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 = 2.3e-05

Table S120.  Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
8P GAIN MUTATED 17 16 7 19 0 8
8P GAIN WILD-TYPE 71 129 200 140 111 161

Figure S120.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00015

Table S121.  Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
8P GAIN MUTATED 17 23 27
8P GAIN WILD-TYPE 60 282 455

Figure S121.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.00054

Table S122.  Gene #15: '8p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
8P GAIN MUTATED 10 15 10 5
8P GAIN WILD-TYPE 143 56 53 120

Figure S122.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S123.  Gene #15: '8p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
8P GAIN MUTATED 2 7 14 3 14
8P GAIN WILD-TYPE 45 91 83 121 32

Figure S123.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S124.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
8Q GAIN MUTATED 30 4 65
8Q GAIN WILD-TYPE 252 306 225

Figure S124.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.00559 (Fisher's exact test), Q value = 0.009

Table S125.  Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
8Q GAIN MUTATED 25 35 17
8Q GAIN WILD-TYPE 103 268 204

Figure S125.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 0.00212 (Fisher's exact test), Q value = 0.0037

Table S126.  Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 182 181 187 197
8Q GAIN MUTATED 25 15 15 38
8Q GAIN WILD-TYPE 157 166 172 159

Figure S126.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.0011

Table S127.  Gene #16: '8q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
8Q GAIN MUTATED 23 7 26 9 14 7 7
8Q GAIN WILD-TYPE 174 57 90 138 45 64 86

Figure S127.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S128.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
8Q GAIN MUTATED 22 48 8 20
8Q GAIN WILD-TYPE 97 147 289 248

Figure S128.  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 = 2.3e-05

Table S129.  Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
8Q GAIN MUTATED 17 21 10 42 0 8
8Q GAIN WILD-TYPE 71 124 197 117 111 161

Figure S129.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.032

Table S130.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
8Q GAIN MUTATED 33 33 32
8Q GAIN WILD-TYPE 294 160 312

Figure S130.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.019

Table S131.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
8Q GAIN MUTATED 17 29 52
8Q GAIN WILD-TYPE 60 276 430

Figure S131.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.0017

Table S132.  Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
8Q GAIN MUTATED 11 16 14 11
8Q GAIN WILD-TYPE 142 55 49 114

Figure S132.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.6e-05

Table S133.  Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
8Q GAIN MUTATED 1 9 20 8 14
8Q GAIN WILD-TYPE 46 89 77 116 32

Figure S133.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'MRNA_CNMF'

P value = 0.0359 (Fisher's exact test), Q value = 0.052

Table S134.  Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 24 12 17
9P GAIN MUTATED 0 1 2 0
9P GAIN WILD-TYPE 33 23 10 17

Figure S134.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S135.  Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
9P GAIN MUTATED 13 5 1
9P GAIN WILD-TYPE 115 298 220

Figure S135.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S136.  Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
9P GAIN MUTATED 14 2 9 1
9P GAIN WILD-TYPE 105 193 288 267

Figure S136.  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 = 2.3e-05

Table S137.  Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
9P GAIN MUTATED 12 4 3 3 4 0
9P GAIN WILD-TYPE 76 141 204 156 107 169

Figure S137.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S138.  Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
9P GAIN MUTATED 12 4 10
9P GAIN WILD-TYPE 65 301 472

Figure S138.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0013 (Fisher's exact test), Q value = 0.0023

Table S139.  Gene #17: '9p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
9P GAIN MUTATED 1 8 3 3
9P GAIN WILD-TYPE 152 63 60 122

Figure S139.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00011

Table S140.  Gene #17: '9p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
9P GAIN MUTATED 0 0 4 3 8
9P GAIN WILD-TYPE 47 98 93 121 38

Figure S140.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 0.00802 (Fisher's exact test), Q value = 0.013

Table S141.  Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
9Q GAIN MUTATED 12 2 10
9Q GAIN WILD-TYPE 270 308 280

Figure S141.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S142.  Gene #18: '9q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
9Q GAIN MUTATED 14 5 1
9Q GAIN WILD-TYPE 114 298 220

Figure S142.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S143.  Gene #18: '9q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
9Q GAIN MUTATED 13 4 6 1
9Q GAIN WILD-TYPE 106 191 291 267

Figure S143.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S144.  Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
9Q GAIN MUTATED 12 5 1 3 3 0
9Q GAIN WILD-TYPE 76 140 206 156 108 169

Figure S144.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S145.  Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
9Q GAIN MUTATED 12 5 7
9Q GAIN WILD-TYPE 65 300 475

Figure S145.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0013

Table S146.  Gene #18: '9q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
9Q GAIN MUTATED 1 8 3 2
9Q GAIN WILD-TYPE 152 63 60 123

Figure S146.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S147.  Gene #18: '9q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
9Q GAIN MUTATED 0 0 4 2 8
9Q GAIN WILD-TYPE 47 98 93 122 38

Figure S147.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S148.  Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
10P GAIN MUTATED 8 1 21
10P GAIN WILD-TYPE 274 309 269

Figure S148.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.025

Table S149.  Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
10P GAIN MUTATED 9 9 3
10P GAIN WILD-TYPE 119 294 218

Figure S149.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0328 (Fisher's exact test), Q value = 0.048

Table S150.  Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
10P GAIN MUTATED 3 2 10 4 4 1 2
10P GAIN WILD-TYPE 194 62 106 143 55 70 91

Figure S150.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.0024

Table S151.  Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
10P GAIN MUTATED 6 14 3 7
10P GAIN WILD-TYPE 113 181 294 261

Figure S151.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00204 (Fisher's exact test), Q value = 0.0035

Table S152.  Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
10P GAIN MUTATED 4 8 3 12 0 3
10P GAIN WILD-TYPE 84 137 204 147 111 166

Figure S152.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.001

Table S153.  Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
10Q GAIN MUTATED 7 1 15
10Q GAIN WILD-TYPE 275 309 275

Figure S153.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 0.047 (Fisher's exact test), Q value = 0.066

Table S154.  Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
10Q GAIN MUTATED 3 10 3 7
10Q GAIN WILD-TYPE 116 185 294 261

Figure S154.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0453 (Fisher's exact test), Q value = 0.065

Table S155.  Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
10Q GAIN MUTATED 2 7 3 8 0 3
10Q GAIN WILD-TYPE 86 138 204 151 111 166

Figure S155.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S156.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
11P GAIN MUTATED 17 1 39
11P GAIN WILD-TYPE 265 309 251

Figure S156.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S157.  Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
11P GAIN MUTATED 23 15 4
11P GAIN WILD-TYPE 105 288 217

Figure S157.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S158.  Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
11P GAIN MUTATED 22 15 13 7
11P GAIN WILD-TYPE 97 180 284 261

Figure S158.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S159.  Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
11P GAIN MUTATED 19 10 9 14 4 1
11P GAIN WILD-TYPE 69 135 198 145 107 168

Figure S159.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S160.  Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
11P GAIN MUTATED 18 12 27
11P GAIN WILD-TYPE 59 293 455

Figure S160.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00021

Table S161.  Gene #21: '11p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
11P GAIN MUTATED 4 14 4 4
11P GAIN WILD-TYPE 149 57 59 121

Figure S161.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S162.  Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
11P GAIN MUTATED 0 3 6 3 14
11P GAIN WILD-TYPE 47 95 91 121 32

Figure S162.  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 = 2.3e-05

Table S163.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
11Q GAIN MUTATED 16 1 38
11Q GAIN WILD-TYPE 266 309 252

Figure S163.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S164.  Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
11Q GAIN MUTATED 23 13 4
11Q GAIN WILD-TYPE 105 290 217

Figure S164.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S165.  Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
11Q GAIN MUTATED 22 12 14 7
11Q GAIN WILD-TYPE 97 183 283 261

Figure S165.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S166.  Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
11Q GAIN MUTATED 20 9 10 11 4 1
11Q GAIN WILD-TYPE 68 136 197 148 107 168

Figure S166.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S167.  Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
11Q GAIN MUTATED 19 11 25
11Q GAIN WILD-TYPE 58 294 457

Figure S167.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S168.  Gene #22: '11q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
11Q GAIN MUTATED 4 15 3 4
11Q GAIN WILD-TYPE 149 56 60 121

Figure S168.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S169.  Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
11Q GAIN MUTATED 0 3 5 3 15
11Q GAIN WILD-TYPE 47 95 92 121 31

Figure S169.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'MRNA_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.027

Table S170.  Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 24 12 17
12P GAIN MUTATED 3 10 2 6
12P GAIN WILD-TYPE 30 14 10 11

Figure S170.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S171.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
12P GAIN MUTATED 115 32 105
12P GAIN WILD-TYPE 167 278 185

Figure S171.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S172.  Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
12P GAIN MUTATED 34 72 95
12P GAIN WILD-TYPE 94 231 126

Figure S172.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'RPPA_CNMF'

P value = 0.0295 (Fisher's exact test), Q value = 0.044

Table S173.  Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 182 181 187 197
12P GAIN MUTATED 53 38 49 68
12P GAIN WILD-TYPE 129 143 138 129

Figure S173.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'12p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S174.  Gene #23: '12p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
12P GAIN MUTATED 48 15 45 24 29 24 23
12P GAIN WILD-TYPE 149 49 71 123 30 47 70

Figure S174.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S175.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
12P GAIN MUTATED 29 75 37 110
12P GAIN WILD-TYPE 90 120 260 158

Figure S175.  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 = 2.3e-05

Table S176.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
12P GAIN MUTATED 24 39 31 65 10 82
12P GAIN WILD-TYPE 64 106 176 94 101 87

Figure S176.  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 = 2.3e-05

Table S177.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
12P GAIN MUTATED 126 52 72
12P GAIN WILD-TYPE 201 141 272

Figure S177.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S178.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
12P GAIN MUTATED 23 123 104
12P GAIN WILD-TYPE 54 182 378

Figure S178.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.7e-05

Table S179.  Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
12P GAIN MUTATED 67 19 21 22
12P GAIN WILD-TYPE 86 52 42 103

Figure S179.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S180.  Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
12P GAIN MUTATED 14 48 31 20 16
12P GAIN WILD-TYPE 33 50 66 104 30

Figure S180.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'MRNA_CNMF'

P value = 0.0178 (Fisher's exact test), Q value = 0.027

Table S181.  Gene #24: '12q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 24 12 17
12Q GAIN MUTATED 3 10 2 6
12Q GAIN WILD-TYPE 30 14 10 11

Figure S181.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S182.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
12Q GAIN MUTATED 118 32 106
12Q GAIN WILD-TYPE 164 278 184

Figure S182.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S183.  Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
12Q GAIN MUTATED 37 72 95
12Q GAIN WILD-TYPE 91 231 126

Figure S183.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'RPPA_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.017

Table S184.  Gene #24: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 182 181 187 197
12Q GAIN MUTATED 54 38 49 71
12Q GAIN WILD-TYPE 128 143 138 126

Figure S184.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'12q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S185.  Gene #24: '12q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
12Q GAIN MUTATED 48 15 47 24 31 24 23
12Q GAIN WILD-TYPE 149 49 69 123 28 47 70

Figure S185.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S186.  Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
12Q GAIN MUTATED 31 77 37 110
12Q GAIN WILD-TYPE 88 118 260 158

Figure S186.  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 = 2.3e-05

Table S187.  Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
12Q GAIN MUTATED 26 40 31 66 10 82
12Q GAIN WILD-TYPE 62 105 176 93 101 87

Figure S187.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S188.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
12Q GAIN MUTATED 128 53 73
12Q GAIN WILD-TYPE 199 140 271

Figure S188.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S189.  Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
12Q GAIN MUTATED 25 123 106
12Q GAIN WILD-TYPE 52 182 376

Figure S189.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00015

Table S190.  Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
12Q GAIN MUTATED 67 21 22 22
12Q GAIN WILD-TYPE 86 50 41 103

Figure S190.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S191.  Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
12Q GAIN MUTATED 14 48 31 21 18
12Q GAIN WILD-TYPE 33 50 66 103 28

Figure S191.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.025

Table S192.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
13Q GAIN MUTATED 4 9 13 27
13Q GAIN WILD-TYPE 115 186 284 241

Figure S192.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0488 (Fisher's exact test), Q value = 0.069

Table S193.  Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
13Q GAIN MUTATED 3 10 11 7 3 19
13Q GAIN WILD-TYPE 85 135 196 152 108 150

Figure S193.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.017

Table S194.  Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
13Q GAIN MUTATED 30 9 13
13Q GAIN WILD-TYPE 297 184 331

Figure S194.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00292 (Fisher's exact test), Q value = 0.0049

Table S195.  Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
13Q GAIN MUTATED 2 30 20
13Q GAIN WILD-TYPE 75 275 462

Figure S195.  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 = 2.3e-05

Table S196.  Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
14Q GAIN MUTATED 20 1 18
14Q GAIN WILD-TYPE 262 309 272

Figure S196.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S197.  Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
14Q GAIN MUTATED 28 5 0
14Q GAIN WILD-TYPE 100 298 221

Figure S197.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00275 (Fisher's exact test), Q value = 0.0047

Table S198.  Gene #26: '14q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
14Q GAIN MUTATED 10 5 12 2 5 1 1
14Q GAIN WILD-TYPE 187 59 104 145 54 70 92

Figure S198.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S199.  Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
14Q GAIN MUTATED 27 8 3 1
14Q GAIN WILD-TYPE 92 187 294 267

Figure S199.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S200.  Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
14Q GAIN MUTATED 25 6 3 4 1 0
14Q GAIN WILD-TYPE 63 139 204 155 110 169

Figure S200.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.00085

Table S201.  Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
14Q GAIN MUTATED 26 3 9
14Q GAIN WILD-TYPE 301 190 335

Figure S201.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S202.  Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
14Q GAIN MUTATED 25 4 9
14Q GAIN WILD-TYPE 52 301 473

Figure S202.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S203.  Gene #26: '14q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
14Q GAIN MUTATED 0 18 3 0
14Q GAIN WILD-TYPE 153 53 60 125

Figure S203.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S204.  Gene #26: '14q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
14Q GAIN MUTATED 0 0 4 0 17
14Q GAIN WILD-TYPE 47 98 93 124 29

Figure S204.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S205.  Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
15Q GAIN MUTATED 21 1 30
15Q GAIN WILD-TYPE 261 309 260

Figure S205.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

'15q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S206.  Gene #27: '15q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
15Q GAIN MUTATED 25 11 3
15Q GAIN WILD-TYPE 103 292 218

Figure S206.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0314 (Fisher's exact test), Q value = 0.046

Table S207.  Gene #27: '15q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
15Q GAIN MUTATED 12 4 12 9 8 1 2
15Q GAIN WILD-TYPE 185 60 104 138 51 70 91

Figure S207.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S208.  Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
15Q GAIN MUTATED 25 10 12 4
15Q GAIN WILD-TYPE 94 185 285 264

Figure S208.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S209.  Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
15Q GAIN MUTATED 24 5 11 8 2 1
15Q GAIN WILD-TYPE 64 140 196 151 109 168

Figure S209.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S210.  Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
15Q GAIN MUTATED 24 5 22
15Q GAIN WILD-TYPE 53 300 460

Figure S210.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S211.  Gene #27: '15q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
15Q GAIN MUTATED 0 17 1 5
15Q GAIN WILD-TYPE 153 54 62 120

Figure S211.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S212.  Gene #27: '15q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
15Q GAIN MUTATED 0 0 1 5 17
15Q GAIN WILD-TYPE 47 98 96 119 29

Figure S212.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S213.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
16P GAIN MUTATED 156 24 101
16P GAIN WILD-TYPE 126 286 189

Figure S213.  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 = 2.3e-05

Table S214.  Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
16P GAIN MUTATED 34 57 136
16P GAIN WILD-TYPE 94 246 85

Figure S214.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p gain' versus 'RPPA_CNMF'

P value = 0.0051 (Fisher's exact test), Q value = 0.0083

Table S215.  Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 182 181 187 197
16P GAIN MUTATED 42 53 75 60
16P GAIN WILD-TYPE 140 128 112 137

Figure S215.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'16p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.001

Table S216.  Gene #28: '16p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
16P GAIN MUTATED 60 33 32 36 22 28 19
16P GAIN WILD-TYPE 137 31 84 111 37 43 74

Figure S216.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S217.  Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
16P GAIN MUTATED 32 49 46 154
16P GAIN WILD-TYPE 87 146 251 114

Figure S217.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S218.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
16P GAIN MUTATED 27 49 35 41 17 112
16P GAIN WILD-TYPE 61 96 172 118 94 57

Figure S218.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S219.  Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
16P GAIN MUTATED 173 37 70
16P GAIN WILD-TYPE 154 156 274

Figure S219.  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 = 2.3e-05

Table S220.  Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
16P GAIN MUTATED 25 159 96
16P GAIN WILD-TYPE 52 146 386

Figure S220.  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 = 2.3e-05

Table S221.  Gene #28: '16p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
16P GAIN MUTATED 95 21 19 26
16P GAIN WILD-TYPE 58 50 44 99

Figure S221.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S222.  Gene #28: '16p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
16P GAIN MUTATED 24 67 29 23 18
16P GAIN WILD-TYPE 23 31 68 101 28

Figure S222.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S223.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
16Q GAIN MUTATED 155 22 91
16Q GAIN WILD-TYPE 127 288 199

Figure S223.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S224.  Gene #29: '16q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
16Q GAIN MUTATED 34 52 132
16Q GAIN WILD-TYPE 94 251 89

Figure S224.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q gain' versus 'RPPA_CNMF'

P value = 0.00251 (Fisher's exact test), Q value = 0.0043

Table S225.  Gene #29: '16q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 182 181 187 197
16Q GAIN MUTATED 39 50 73 58
16Q GAIN WILD-TYPE 143 131 114 139

Figure S225.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'16q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.00055

Table S226.  Gene #29: '16q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
16Q GAIN MUTATED 57 32 31 33 22 27 18
16Q GAIN WILD-TYPE 140 32 85 114 37 44 75

Figure S226.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S227.  Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
16Q GAIN MUTATED 31 48 41 148
16Q GAIN WILD-TYPE 88 147 256 120

Figure S227.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S228.  Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
16Q GAIN MUTATED 26 44 30 40 17 111
16Q GAIN WILD-TYPE 62 101 177 119 94 58

Figure S228.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S229.  Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
16Q GAIN MUTATED 168 36 63
16Q GAIN WILD-TYPE 159 157 281

Figure S229.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S230.  Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
16Q GAIN MUTATED 25 154 88
16Q GAIN WILD-TYPE 52 151 394

Figure S230.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S231.  Gene #29: '16q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
16Q GAIN MUTATED 93 21 17 22
16Q GAIN WILD-TYPE 60 50 46 103

Figure S231.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S232.  Gene #29: '16q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
16Q GAIN MUTATED 23 67 25 20 18
16Q GAIN WILD-TYPE 24 31 72 104 28

Figure S232.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S233.  Gene #30: '17p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 24 12 17
17P GAIN MUTATED 1 0 2 11
17P GAIN WILD-TYPE 32 24 10 6

Figure S233.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S234.  Gene #30: '17p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 20 24 18 13 11
17P GAIN MUTATED 1 0 12 0 1
17P GAIN WILD-TYPE 19 24 6 13 10

Figure S234.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S235.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
17P GAIN MUTATED 164 7 26
17P GAIN WILD-TYPE 118 303 264

Figure S235.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S236.  Gene #30: '17p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
17P GAIN MUTATED 15 12 152
17P GAIN WILD-TYPE 113 291 69

Figure S236.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p gain' versus 'RPPA_CNMF'

P value = 0.0459 (Fisher's exact test), Q value = 0.065

Table S237.  Gene #30: '17p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 182 181 187 197
17P GAIN MUTATED 26 44 44 35
17P GAIN WILD-TYPE 156 137 143 162

Figure S237.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'17p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00125 (Fisher's exact test), Q value = 0.0022

Table S238.  Gene #30: '17p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
17P GAIN MUTATED 50 16 21 23 6 23 10
17P GAIN WILD-TYPE 147 48 95 124 53 48 83

Figure S238.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S239.  Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
17P GAIN MUTATED 5 14 9 169
17P GAIN WILD-TYPE 114 181 288 99

Figure S239.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S240.  Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
17P GAIN MUTATED 1 32 7 9 1 147
17P GAIN WILD-TYPE 87 113 200 150 110 22

Figure S240.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S241.  Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
17P GAIN MUTATED 165 19 12
17P GAIN WILD-TYPE 162 174 332

Figure S241.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S242.  Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
17P GAIN MUTATED 0 180 16
17P GAIN WILD-TYPE 77 125 466

Figure S242.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S243.  Gene #30: '17p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
17P GAIN MUTATED 110 5 14 3
17P GAIN WILD-TYPE 43 66 49 122

Figure S243.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S244.  Gene #30: '17p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
17P GAIN MUTATED 40 69 22 1 0
17P GAIN WILD-TYPE 7 29 75 123 46

Figure S244.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S245.  Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 24 12 17
17Q GAIN MUTATED 1 1 2 12
17Q GAIN WILD-TYPE 32 23 10 5

Figure S245.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S246.  Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 20 24 18 13 11
17Q GAIN MUTATED 1 1 13 0 1
17Q GAIN WILD-TYPE 19 23 5 13 10

Figure S246.  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 = 2.3e-05

Table S247.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
17Q GAIN MUTATED 170 13 39
17Q GAIN WILD-TYPE 112 297 251

Figure S247.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S248.  Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
17Q GAIN MUTATED 17 18 165
17Q GAIN WILD-TYPE 111 285 56

Figure S248.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00223 (Fisher's exact test), Q value = 0.0038

Table S249.  Gene #31: '17q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
17Q GAIN MUTATED 52 20 23 25 7 26 16
17Q GAIN WILD-TYPE 145 44 93 122 52 45 77

Figure S249.  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 = 2.3e-05

Table S250.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
17Q GAIN MUTATED 7 18 10 187
17Q GAIN WILD-TYPE 112 177 287 81

Figure S250.  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 = 2.3e-05

Table S251.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
17Q GAIN MUTATED 1 49 9 13 1 149
17Q GAIN WILD-TYPE 87 96 198 146 110 20

Figure S251.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S252.  Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
17Q GAIN MUTATED 178 30 13
17Q GAIN WILD-TYPE 149 163 331

Figure S252.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S253.  Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
17Q GAIN MUTATED 0 200 21
17Q GAIN WILD-TYPE 77 105 461

Figure S253.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S254.  Gene #31: '17q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
17Q GAIN MUTATED 118 5 23 3
17Q GAIN WILD-TYPE 35 66 40 122

Figure S254.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S255.  Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
17Q GAIN MUTATED 42 72 34 1 0
17Q GAIN WILD-TYPE 5 26 63 123 46

Figure S255.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 0.00212 (Fisher's exact test), Q value = 0.0037

Table S256.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
18P GAIN MUTATED 17 9 28
18P GAIN WILD-TYPE 265 301 262

Figure S256.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00031

Table S257.  Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
18P GAIN MUTATED 19 12 9
18P GAIN WILD-TYPE 109 291 212

Figure S257.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00027

Table S258.  Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
18P GAIN MUTATED 20 9 14 11
18P GAIN WILD-TYPE 99 186 283 257

Figure S258.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00013

Table S259.  Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
18P GAIN MUTATED 18 6 10 4 8 8
18P GAIN WILD-TYPE 70 139 197 155 103 161

Figure S259.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.033

Table S260.  Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
18P GAIN MUTATED 29 6 18
18P GAIN WILD-TYPE 298 187 326

Figure S260.  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 = 2.3e-05

Table S261.  Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
18P GAIN MUTATED 17 14 22
18P GAIN WILD-TYPE 60 291 460

Figure S261.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.005 (Fisher's exact test), Q value = 0.0082

Table S262.  Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
18P GAIN MUTATED 8 14 3 9
18P GAIN WILD-TYPE 145 57 60 116

Figure S262.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.00074

Table S263.  Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
18P GAIN MUTATED 3 5 5 8 13
18P GAIN WILD-TYPE 44 93 92 116 33

Figure S263.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 0.00253 (Fisher's exact test), Q value = 0.0043

Table S264.  Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
18Q GAIN MUTATED 16 8 26
18Q GAIN WILD-TYPE 266 302 264

Figure S264.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00029

Table S265.  Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
18Q GAIN MUTATED 18 13 7
18Q GAIN WILD-TYPE 110 290 214

Figure S265.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S266.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
18Q GAIN MUTATED 20 8 14 8
18Q GAIN WILD-TYPE 99 187 283 260

Figure S266.  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 = 2.3e-05

Table S267.  Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
18Q GAIN MUTATED 18 3 9 5 8 7
18Q GAIN WILD-TYPE 70 142 198 154 103 162

Figure S267.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 0.0361 (Fisher's exact test), Q value = 0.052

Table S268.  Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
18Q GAIN MUTATED 26 5 18
18Q GAIN WILD-TYPE 301 188 326

Figure S268.  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 = 2.3e-05

Table S269.  Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
18Q GAIN MUTATED 17 10 22
18Q GAIN WILD-TYPE 60 295 460

Figure S269.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.00083

Table S270.  Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
18Q GAIN MUTATED 7 14 1 8
18Q GAIN WILD-TYPE 146 57 62 117

Figure S270.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S271.  Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
18Q GAIN MUTATED 2 5 2 8 13
18Q GAIN WILD-TYPE 45 93 95 116 33

Figure S271.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S272.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
19P GAIN MUTATED 17 1 57
19P GAIN WILD-TYPE 265 309 233

Figure S272.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S273.  Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
19P GAIN MUTATED 26 29 3
19P GAIN WILD-TYPE 102 274 218

Figure S273.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00087 (Fisher's exact test), Q value = 0.0016

Table S274.  Gene #34: '19p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
19P GAIN MUTATED 18 2 17 9 14 3 7
19P GAIN WILD-TYPE 179 62 99 138 45 68 86

Figure S274.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S275.  Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
19P GAIN MUTATED 26 30 17 2
19P GAIN WILD-TYPE 93 165 280 266

Figure S275.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S276.  Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
19P GAIN MUTATED 24 8 13 25 5 0
19P GAIN WILD-TYPE 64 137 194 134 106 169

Figure S276.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S277.  Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
19P GAIN MUTATED 23 9 42
19P GAIN WILD-TYPE 54 296 440

Figure S277.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S278.  Gene #34: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
19P GAIN MUTATED 1 15 2 12
19P GAIN WILD-TYPE 152 56 61 113

Figure S278.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S279.  Gene #34: '19p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
19P GAIN MUTATED 0 1 3 11 15
19P GAIN WILD-TYPE 47 97 94 113 31

Figure S279.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q gain' versus 'MRNA_CNMF'

P value = 0.0395 (Fisher's exact test), Q value = 0.057

Table S280.  Gene #35: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 24 12 17
19Q GAIN MUTATED 1 3 3 0
19Q GAIN WILD-TYPE 32 21 9 17

Figure S280.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S281.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
19Q GAIN MUTATED 16 1 61
19Q GAIN WILD-TYPE 266 309 229

Figure S281.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S282.  Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
19Q GAIN MUTATED 24 31 3
19Q GAIN WILD-TYPE 104 272 218

Figure S282.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'RPPA_CNMF'

P value = 0.0417 (Fisher's exact test), Q value = 0.06

Table S283.  Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 182 181 187 197
19Q GAIN MUTATED 18 12 14 29
19Q GAIN WILD-TYPE 164 169 173 168

Figure S283.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'19q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.00085

Table S284.  Gene #35: '19q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
19Q GAIN MUTATED 19 2 19 9 14 3 7
19Q GAIN WILD-TYPE 178 62 97 138 45 68 86

Figure S284.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S285.  Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
19Q GAIN MUTATED 25 32 18 2
19Q GAIN WILD-TYPE 94 163 279 266

Figure S285.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S286.  Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
19Q GAIN MUTATED 23 7 14 28 5 0
19Q GAIN WILD-TYPE 65 138 193 131 106 169

Figure S286.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S287.  Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
19Q GAIN MUTATED 22 9 45
19Q GAIN WILD-TYPE 55 296 437

Figure S287.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S288.  Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
19Q GAIN MUTATED 1 14 2 12
19Q GAIN WILD-TYPE 152 57 61 113

Figure S288.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S289.  Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
19Q GAIN MUTATED 0 1 3 11 14
19Q GAIN WILD-TYPE 47 97 94 113 32

Figure S289.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'MRNA_CNMF'

P value = 0.0394 (Fisher's exact test), Q value = 0.057

Table S290.  Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 24 12 17
20P GAIN MUTATED 3 7 4 7
20P GAIN WILD-TYPE 30 17 8 10

Figure S290.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S291.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
20P GAIN MUTATED 111 13 109
20P GAIN WILD-TYPE 171 297 181

Figure S291.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.7e-05

Table S292.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
20P GAIN MUTATED 35 60 83
20P GAIN WILD-TYPE 93 243 138

Figure S292.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.029

Table S293.  Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 182 181 187 197
20P GAIN MUTATED 45 41 39 67
20P GAIN WILD-TYPE 137 140 148 130

Figure S293.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S294.  Gene #36: '20p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
20P GAIN MUTATED 52 9 47 23 27 16 18
20P GAIN WILD-TYPE 145 55 69 124 32 55 75

Figure S294.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S295.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
20P GAIN MUTATED 31 82 27 93
20P GAIN WILD-TYPE 88 113 270 175

Figure S295.  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 = 2.3e-05

Table S296.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
20P GAIN MUTATED 26 32 26 66 8 75
20P GAIN WILD-TYPE 62 113 181 93 103 94

Figure S296.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00017

Table S297.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
20P GAIN MUTATED 115 49 68
20P GAIN WILD-TYPE 212 144 276

Figure S297.  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 = 2.3e-05

Table S298.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
20P GAIN MUTATED 25 111 96
20P GAIN WILD-TYPE 52 194 386

Figure S298.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00523 (Fisher's exact test), Q value = 0.0085

Table S299.  Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
20P GAIN MUTATED 56 19 22 23
20P GAIN WILD-TYPE 97 52 41 102

Figure S299.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00169 (Fisher's exact test), Q value = 0.003

Table S300.  Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
20P GAIN MUTATED 16 38 30 20 16
20P GAIN WILD-TYPE 31 60 67 104 30

Figure S300.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 0.0202 (Fisher's exact test), Q value = 0.031

Table S301.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 24 12 17
20Q GAIN MUTATED 3 8 5 7
20Q GAIN WILD-TYPE 30 16 7 10

Figure S301.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0494 (Fisher's exact test), Q value = 0.07

Table S302.  Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 20 24 18 13 11
20Q GAIN MUTATED 2 8 8 1 4
20Q GAIN WILD-TYPE 18 16 10 12 7

Figure S302.  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 = 2.3e-05

Table S303.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
20Q GAIN MUTATED 110 15 112
20Q GAIN WILD-TYPE 172 295 178

Figure S303.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00011

Table S304.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
20Q GAIN MUTATED 35 61 83
20Q GAIN WILD-TYPE 93 242 138

Figure S304.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.00929 (Fisher's exact test), Q value = 0.015

Table S305.  Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 182 181 187 197
20Q GAIN MUTATED 46 40 40 69
20Q GAIN WILD-TYPE 136 141 147 128

Figure S305.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S306.  Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
20Q GAIN MUTATED 52 10 47 22 29 16 19
20Q GAIN WILD-TYPE 145 54 69 125 30 55 74

Figure S306.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S307.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
20Q GAIN MUTATED 32 85 27 93
20Q GAIN WILD-TYPE 87 110 270 175

Figure S307.  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 = 2.3e-05

Table S308.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
20Q GAIN MUTATED 26 34 26 69 8 74
20Q GAIN WILD-TYPE 62 111 181 90 103 95

Figure S308.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00011

Table S309.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
20Q GAIN MUTATED 116 51 69
20Q GAIN WILD-TYPE 211 142 275

Figure S309.  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 = 2.3e-05

Table S310.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
20Q GAIN MUTATED 25 113 98
20Q GAIN WILD-TYPE 52 192 384

Figure S310.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00781 (Fisher's exact test), Q value = 0.012

Table S311.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
20Q GAIN MUTATED 56 20 23 24
20Q GAIN WILD-TYPE 97 51 40 101

Figure S311.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00302 (Fisher's exact test), Q value = 0.0051

Table S312.  Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
20Q GAIN MUTATED 16 38 32 21 16
20Q GAIN WILD-TYPE 31 60 65 103 30

Figure S312.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S313.  Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
21Q GAIN MUTATED 19 4 50
21Q GAIN WILD-TYPE 263 306 240

Figure S313.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0263 (Fisher's exact test), Q value = 0.039

Table S314.  Gene #38: '21q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
21Q GAIN MUTATED 13 2 10 13 13 6 7
21Q GAIN WILD-TYPE 184 62 106 134 46 65 86

Figure S314.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.00061

Table S315.  Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
21Q GAIN MUTATED 8 32 16 17
21Q GAIN WILD-TYPE 111 163 281 251

Figure S315.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00158 (Fisher's exact test), Q value = 0.0028

Table S316.  Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
21Q GAIN MUTATED 5 7 14 28 6 13
21Q GAIN WILD-TYPE 83 138 193 131 105 156

Figure S316.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.022

Table S317.  Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
21Q GAIN MUTATED 21 11 41
21Q GAIN WILD-TYPE 306 182 303

Figure S317.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S318.  Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
22Q GAIN MUTATED 19 4 41
22Q GAIN WILD-TYPE 263 306 249

Figure S318.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S319.  Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
22Q GAIN MUTATED 23 20 4
22Q GAIN WILD-TYPE 105 283 217

Figure S319.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S320.  Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
22Q GAIN MUTATED 24 20 16 4
22Q GAIN WILD-TYPE 95 175 281 264

Figure S320.  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 = 2.3e-05

Table S321.  Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
22Q GAIN MUTATED 23 4 11 19 4 3
22Q GAIN WILD-TYPE 65 141 196 140 107 166

Figure S321.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S322.  Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
22Q GAIN MUTATED 23 7 33
22Q GAIN WILD-TYPE 54 298 449

Figure S322.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S323.  Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
22Q GAIN MUTATED 3 16 3 3
22Q GAIN WILD-TYPE 150 55 60 122

Figure S323.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S324.  Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
22Q GAIN MUTATED 0 3 3 3 16
22Q GAIN WILD-TYPE 47 95 94 121 30

Figure S324.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp gain' versus 'MRNA_CNMF'

P value = 0.0035 (Fisher's exact test), Q value = 0.0058

Table S325.  Gene #40: 'xp gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 24 12 17
XP GAIN MUTATED 2 1 1 7
XP GAIN WILD-TYPE 31 23 11 10

Figure S325.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00277 (Fisher's exact test), Q value = 0.0047

Table S326.  Gene #40: 'xp gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 20 24 18 13 11
XP GAIN MUTATED 0 1 7 2 1
XP GAIN WILD-TYPE 20 23 11 11 10

Figure S326.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xp gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S327.  Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
XP GAIN MUTATED 93 4 27
XP GAIN WILD-TYPE 189 306 263

Figure S327.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S328.  Gene #40: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
XP GAIN MUTATED 14 10 77
XP GAIN WILD-TYPE 114 293 144

Figure S328.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00297 (Fisher's exact test), Q value = 0.005

Table S329.  Gene #40: 'xp gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
XP GAIN MUTATED 30 10 20 11 5 15 4
XP GAIN WILD-TYPE 167 54 96 136 54 56 89

Figure S329.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S330.  Gene #40: 'xp gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
XP GAIN MUTATED 11 19 8 86
XP GAIN WILD-TYPE 108 176 289 182

Figure S330.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xp gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S331.  Gene #40: 'xp gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
XP GAIN MUTATED 8 15 4 16 4 77
XP GAIN WILD-TYPE 80 130 203 143 107 92

Figure S331.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S332.  Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
XP GAIN MUTATED 92 12 20
XP GAIN WILD-TYPE 235 181 324

Figure S332.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xp gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S333.  Gene #40: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
XP GAIN MUTATED 7 92 25
XP GAIN WILD-TYPE 70 213 457

Figure S333.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S334.  Gene #40: 'xp gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
XP GAIN MUTATED 55 9 3 6
XP GAIN WILD-TYPE 98 62 60 119

Figure S334.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S335.  Gene #40: 'xp gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
XP GAIN MUTATED 14 39 9 5 6
XP GAIN WILD-TYPE 33 59 88 119 40

Figure S335.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'MRNA_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00029

Table S336.  Gene #41: 'xq gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 24 12 17
XQ GAIN MUTATED 2 0 1 8
XQ GAIN WILD-TYPE 31 24 11 9

Figure S336.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'xq gain' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.7e-05

Table S337.  Gene #41: 'xq gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 20 24 18 13 11
XQ GAIN MUTATED 0 0 8 2 1
XQ GAIN WILD-TYPE 20 24 10 11 10

Figure S337.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S338.  Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
XQ GAIN MUTATED 92 7 26
XQ GAIN WILD-TYPE 190 303 264

Figure S338.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S339.  Gene #41: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
XQ GAIN MUTATED 13 13 77
XQ GAIN WILD-TYPE 115 290 144

Figure S339.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.022

Table S340.  Gene #41: 'xq gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
XQ GAIN MUTATED 30 10 18 13 4 15 5
XQ GAIN WILD-TYPE 167 54 98 134 55 56 88

Figure S340.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S341.  Gene #41: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
XQ GAIN MUTATED 11 18 10 86
XQ GAIN WILD-TYPE 108 177 287 182

Figure S341.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S342.  Gene #41: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
XQ GAIN MUTATED 8 14 5 16 5 77
XQ GAIN WILD-TYPE 80 131 202 143 106 92

Figure S342.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S343.  Gene #41: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
XQ GAIN MUTATED 93 13 19
XQ GAIN WILD-TYPE 234 180 325

Figure S343.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S344.  Gene #41: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
XQ GAIN MUTATED 7 91 27
XQ GAIN WILD-TYPE 70 214 455

Figure S344.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S345.  Gene #41: 'xq gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
XQ GAIN MUTATED 55 9 3 7
XQ GAIN WILD-TYPE 98 62 60 118

Figure S345.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S346.  Gene #41: 'xq gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
XQ GAIN MUTATED 14 39 9 6 6
XQ GAIN WILD-TYPE 33 59 88 118 40

Figure S346.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'MRNA_CNMF'

P value = 0.00125 (Fisher's exact test), Q value = 0.0022

Table S347.  Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 24 12 17
1P LOSS MUTATED 2 3 7 2
1P LOSS WILD-TYPE 31 21 5 15

Figure S347.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0133 (Fisher's exact test), Q value = 0.021

Table S348.  Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 20 24 18 13 11
1P LOSS MUTATED 1 3 3 1 6
1P LOSS WILD-TYPE 19 21 15 12 5

Figure S348.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S349.  Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
1P LOSS MUTATED 79 7 59
1P LOSS WILD-TYPE 203 303 231

Figure S349.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S350.  Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
1P LOSS MUTATED 67 28 20
1P LOSS WILD-TYPE 61 275 201

Figure S350.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S351.  Gene #42: '1p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
1P LOSS MUTATED 34 18 36 15 10 5 9
1P LOSS WILD-TYPE 163 46 80 132 49 66 84

Figure S351.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S352.  Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
1P LOSS MUTATED 70 20 25 30
1P LOSS WILD-TYPE 49 175 272 238

Figure S352.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S353.  Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
1P LOSS MUTATED 69 29 20 13 6 8
1P LOSS WILD-TYPE 19 116 187 146 105 161

Figure S353.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S354.  Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
1P LOSS MUTATED 89 22 34
1P LOSS WILD-TYPE 238 171 310

Figure S354.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S355.  Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
1P LOSS MUTATED 68 37 40
1P LOSS WILD-TYPE 9 268 442

Figure S355.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S356.  Gene #42: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
1P LOSS MUTATED 12 41 9 10
1P LOSS WILD-TYPE 141 30 54 115

Figure S356.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S357.  Gene #42: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
1P LOSS MUTATED 1 10 15 7 39
1P LOSS WILD-TYPE 46 88 82 117 7

Figure S357.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'MRNA_CNMF'

P value = 0.00837 (Fisher's exact test), Q value = 0.013

Table S358.  Gene #43: '1q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 24 12 17
1Q LOSS MUTATED 2 1 5 1
1Q LOSS WILD-TYPE 31 23 7 16

Figure S358.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00815 (Fisher's exact test), Q value = 0.013

Table S359.  Gene #43: '1q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 20 24 18 13 11
1Q LOSS MUTATED 1 1 1 1 5
1Q LOSS WILD-TYPE 19 23 17 12 6

Figure S359.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S360.  Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
1Q LOSS MUTATED 75 1 34
1Q LOSS WILD-TYPE 207 309 256

Figure S360.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S361.  Gene #43: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
1Q LOSS MUTATED 62 15 15
1Q LOSS WILD-TYPE 66 288 206

Figure S361.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S362.  Gene #43: '1q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
1Q LOSS MUTATED 26 13 34 9 8 3 4
1Q LOSS WILD-TYPE 171 51 82 138 51 68 89

Figure S362.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S363.  Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
1Q LOSS MUTATED 65 15 12 18
1Q LOSS WILD-TYPE 54 180 285 250

Figure S363.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S364.  Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
1Q LOSS MUTATED 65 16 8 9 4 8
1Q LOSS WILD-TYPE 23 129 199 150 107 161

Figure S364.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S365.  Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
1Q LOSS MUTATED 76 15 19
1Q LOSS WILD-TYPE 251 178 325

Figure S365.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S366.  Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
1Q LOSS MUTATED 65 23 22
1Q LOSS WILD-TYPE 12 282 460

Figure S366.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S367.  Gene #43: '1q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
1Q LOSS MUTATED 8 38 7 5
1Q LOSS WILD-TYPE 145 33 56 120

Figure S367.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S368.  Gene #43: '1q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
1Q LOSS MUTATED 1 7 8 4 38
1Q LOSS WILD-TYPE 46 91 89 120 8

Figure S368.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S369.  Gene #44: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 24 12 17
2P LOSS MUTATED 0 1 6 0
2P LOSS WILD-TYPE 33 23 6 17

Figure S369.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.00057

Table S370.  Gene #44: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 20 24 18 13 11
2P LOSS MUTATED 0 1 1 0 5
2P LOSS WILD-TYPE 20 23 17 13 6

Figure S370.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S371.  Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
2P LOSS MUTATED 53 0 12
2P LOSS WILD-TYPE 229 310 278

Figure S371.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S372.  Gene #44: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
2P LOSS MUTATED 52 3 2
2P LOSS WILD-TYPE 76 300 219

Figure S372.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S373.  Gene #44: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
2P LOSS MUTATED 15 13 21 3 3 1 1
2P LOSS WILD-TYPE 182 51 95 144 56 70 92

Figure S373.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S374.  Gene #44: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
2P LOSS MUTATED 60 2 0 3
2P LOSS WILD-TYPE 59 193 297 265

Figure S374.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S375.  Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
2P LOSS MUTATED 58 5 0 2 0 0
2P LOSS WILD-TYPE 30 140 207 157 111 169

Figure S375.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S376.  Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
2P LOSS MUTATED 59 3 3
2P LOSS WILD-TYPE 268 190 341

Figure S376.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S377.  Gene #44: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
2P LOSS MUTATED 58 5 2
2P LOSS WILD-TYPE 19 300 480

Figure S377.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S378.  Gene #44: '2p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
2P LOSS MUTATED 1 36 0 1
2P LOSS WILD-TYPE 152 35 63 124

Figure S378.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S379.  Gene #44: '2p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
2P LOSS MUTATED 0 1 1 1 35
2P LOSS WILD-TYPE 47 97 96 123 11

Figure S379.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'MRNA_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00042

Table S380.  Gene #45: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 24 12 17
2Q LOSS MUTATED 0 1 5 0
2Q LOSS WILD-TYPE 33 23 7 17

Figure S380.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q loss' versus 'MRNA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00017

Table S381.  Gene #45: '2q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 20 24 18 13 11
2Q LOSS MUTATED 0 1 0 0 5
2Q LOSS WILD-TYPE 20 23 18 13 6

Figure S381.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S382.  Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
2Q LOSS MUTATED 52 0 11
2Q LOSS WILD-TYPE 230 310 279

Figure S382.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S383.  Gene #45: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
2Q LOSS MUTATED 53 2 1
2Q LOSS WILD-TYPE 75 301 220

Figure S383.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S384.  Gene #45: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
2Q LOSS MUTATED 15 12 21 3 3 1 1
2Q LOSS WILD-TYPE 182 52 95 144 56 70 92

Figure S384.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S385.  Gene #45: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
2Q LOSS MUTATED 59 3 0 1
2Q LOSS WILD-TYPE 60 192 297 267

Figure S385.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S386.  Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
2Q LOSS MUTATED 58 3 0 2 0 0
2Q LOSS WILD-TYPE 30 142 207 157 111 169

Figure S386.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S387.  Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
2Q LOSS MUTATED 57 2 4
2Q LOSS WILD-TYPE 270 191 340

Figure S387.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S388.  Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
2Q LOSS MUTATED 58 2 3
2Q LOSS WILD-TYPE 19 303 479

Figure S388.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S389.  Gene #45: '2q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
2Q LOSS MUTATED 1 36 0 1
2Q LOSS WILD-TYPE 152 35 63 124

Figure S389.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S390.  Gene #45: '2q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
2Q LOSS MUTATED 0 1 1 1 35
2Q LOSS WILD-TYPE 47 97 96 123 11

Figure S390.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S391.  Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 24 12 17
3P LOSS MUTATED 22 20 3 0
3P LOSS WILD-TYPE 11 4 9 17

Figure S391.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S392.  Gene #46: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 20 24 18 13 11
3P LOSS MUTATED 15 20 1 7 2
3P LOSS WILD-TYPE 5 4 17 6 9

Figure S392.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S393.  Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
3P LOSS MUTATED 1 165 246
3P LOSS WILD-TYPE 281 145 44

Figure S393.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S394.  Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
3P LOSS MUTATED 16 236 11
3P LOSS WILD-TYPE 112 67 210

Figure S394.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CNMF'

P value = 0.00088 (Fisher's exact test), Q value = 0.0016

Table S395.  Gene #46: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 182 181 187 197
3P LOSS MUTATED 88 93 71 115
3P LOSS WILD-TYPE 94 88 116 82

Figure S395.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S396.  Gene #46: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
3P LOSS MUTATED 105 2 44 87 38 38 53
3P LOSS WILD-TYPE 92 62 72 60 21 33 40

Figure S396.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S397.  Gene #46: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
3P LOSS MUTATED 19 136 237 18
3P LOSS WILD-TYPE 100 59 60 250

Figure S397.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S398.  Gene #46: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
3P LOSS MUTATED 11 23 169 121 84 2
3P LOSS WILD-TYPE 77 122 38 38 27 167

Figure S398.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S399.  Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
3P LOSS MUTATED 24 100 274
3P LOSS WILD-TYPE 303 93 70

Figure S399.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S400.  Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
3P LOSS MUTATED 10 24 364
3P LOSS WILD-TYPE 67 281 118

Figure S400.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S401.  Gene #46: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
3P LOSS MUTATED 7 7 15 94
3P LOSS WILD-TYPE 146 64 48 31

Figure S401.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S402.  Gene #46: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
3P LOSS MUTATED 0 5 21 91 6
3P LOSS WILD-TYPE 47 93 76 33 40

Figure S402.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S403.  Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
3Q LOSS MUTATED 1 34 89
3Q LOSS WILD-TYPE 281 276 201

Figure S403.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S404.  Gene #47: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
3Q LOSS MUTATED 11 62 4
3Q LOSS WILD-TYPE 117 241 217

Figure S404.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00038

Table S405.  Gene #47: '3q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
3Q LOSS MUTATED 30 1 12 23 18 10 19
3Q LOSS WILD-TYPE 167 63 104 124 41 61 74

Figure S405.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S406.  Gene #47: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
3Q LOSS MUTATED 13 48 58 5
3Q LOSS WILD-TYPE 106 147 239 263

Figure S406.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S407.  Gene #47: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
3Q LOSS MUTATED 9 9 58 33 14 1
3Q LOSS WILD-TYPE 79 136 149 126 97 168

Figure S407.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S408.  Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
3Q LOSS MUTATED 13 25 82
3Q LOSS WILD-TYPE 314 168 262

Figure S408.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S409.  Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
3Q LOSS MUTATED 9 9 102
3Q LOSS WILD-TYPE 68 296 380

Figure S409.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S410.  Gene #47: '3q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
3Q LOSS MUTATED 2 5 5 22
3Q LOSS WILD-TYPE 151 66 58 103

Figure S410.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00032

Table S411.  Gene #47: '3q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
3Q LOSS MUTATED 0 2 6 21 5
3Q LOSS WILD-TYPE 47 96 91 103 41

Figure S411.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S412.  Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
4P LOSS MUTATED 16 10 72
4P LOSS WILD-TYPE 266 300 218

Figure S412.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S413.  Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
4P LOSS MUTATED 15 51 9
4P LOSS WILD-TYPE 113 252 212

Figure S413.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CNMF'

P value = 0.0258 (Fisher's exact test), Q value = 0.039

Table S414.  Gene #48: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 182 181 187 197
4P LOSS MUTATED 30 20 13 28
4P LOSS WILD-TYPE 152 161 174 169

Figure S414.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p loss' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.6e-05

Table S415.  Gene #48: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
4P LOSS MUTATED 19 1 22 9 13 8 19
4P LOSS WILD-TYPE 178 63 94 138 46 63 74

Figure S415.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S416.  Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
4P LOSS MUTATED 4 40 35 18
4P LOSS WILD-TYPE 115 155 262 250

Figure S416.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S417.  Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
4P LOSS MUTATED 0 29 23 31 13 1
4P LOSS WILD-TYPE 88 116 184 128 98 168

Figure S417.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.00068

Table S418.  Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
4P LOSS MUTATED 20 33 43
4P LOSS WILD-TYPE 307 160 301

Figure S418.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00029

Table S419.  Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
4P LOSS MUTATED 0 30 66
4P LOSS WILD-TYPE 77 275 416

Figure S419.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0017

Table S420.  Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
4P LOSS MUTATED 6 4 13 15
4P LOSS WILD-TYPE 147 67 50 110

Figure S420.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S421.  Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
4P LOSS MUTATED 0 4 21 13 0
4P LOSS WILD-TYPE 47 94 76 111 46

Figure S421.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S422.  Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
4Q LOSS MUTATED 16 6 70
4Q LOSS WILD-TYPE 266 304 220

Figure S422.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0015

Table S423.  Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
4Q LOSS MUTATED 15 45 11
4Q LOSS WILD-TYPE 113 258 210

Figure S423.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00023

Table S424.  Gene #49: '4q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
4Q LOSS MUTATED 18 1 23 8 13 8 14
4Q LOSS WILD-TYPE 179 63 93 139 46 63 79

Figure S424.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S425.  Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
4Q LOSS MUTATED 4 40 29 19
4Q LOSS WILD-TYPE 115 155 268 249

Figure S425.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S426.  Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
4Q LOSS MUTATED 0 30 20 31 10 1
4Q LOSS WILD-TYPE 88 115 187 128 101 168

Figure S426.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 0.00137 (Fisher's exact test), Q value = 0.0024

Table S427.  Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
4Q LOSS MUTATED 21 32 38
4Q LOSS WILD-TYPE 306 161 306

Figure S427.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.00085

Table S428.  Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
4Q LOSS MUTATED 0 31 60
4Q LOSS WILD-TYPE 77 274 422

Figure S428.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.0011

Table S429.  Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
4Q LOSS MUTATED 7 3 14 13
4Q LOSS WILD-TYPE 146 68 49 112

Figure S429.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S430.  Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
4Q LOSS MUTATED 0 4 21 12 0
4Q LOSS WILD-TYPE 47 94 76 112 46

Figure S430.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00017

Table S431.  Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
5P LOSS MUTATED 17 1 6
5P LOSS WILD-TYPE 265 309 284

Figure S431.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S432.  Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
5P LOSS MUTATED 19 2 2
5P LOSS WILD-TYPE 109 301 219

Figure S432.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'RPPA_CNMF'

P value = 0.0365 (Fisher's exact test), Q value = 0.053

Table S433.  Gene #50: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 182 181 187 197
5P LOSS MUTATED 11 4 2 4
5P LOSS WILD-TYPE 171 177 185 193

Figure S433.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S434.  Gene #50: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
5P LOSS MUTATED 13 9 0 2
5P LOSS WILD-TYPE 106 186 297 266

Figure S434.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S435.  Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
5P LOSS MUTATED 11 9 0 3 0 1
5P LOSS WILD-TYPE 77 136 207 156 111 168

Figure S435.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 0.00196 (Fisher's exact test), Q value = 0.0034

Table S436.  Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
5P LOSS MUTATED 14 8 2
5P LOSS WILD-TYPE 313 185 342

Figure S436.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S437.  Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
5P LOSS MUTATED 11 9 4
5P LOSS WILD-TYPE 66 296 478

Figure S437.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00015

Table S438.  Gene #50: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
5P LOSS MUTATED 2 9 5 1
5P LOSS WILD-TYPE 151 62 58 124

Figure S438.  Get High-res Image Gene #50: '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 = 2.3e-05

Table S439.  Gene #50: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
5P LOSS MUTATED 0 1 8 0 8
5P LOSS WILD-TYPE 47 97 89 124 38

Figure S439.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 6.6e-05

Table S440.  Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
5Q LOSS MUTATED 16 0 6
5Q LOSS WILD-TYPE 266 310 284

Figure S440.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S441.  Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
5Q LOSS MUTATED 19 1 2
5Q LOSS WILD-TYPE 109 302 219

Figure S441.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S442.  Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
5Q LOSS MUTATED 13 8 0 1
5Q LOSS WILD-TYPE 106 187 297 267

Figure S442.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S443.  Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
5Q LOSS MUTATED 11 8 0 2 0 1
5Q LOSS WILD-TYPE 77 137 207 157 111 168

Figure S443.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 0.00504 (Fisher's exact test), Q value = 0.0082

Table S444.  Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
5Q LOSS MUTATED 13 7 2
5Q LOSS WILD-TYPE 314 186 342

Figure S444.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S445.  Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
5Q LOSS MUTATED 11 9 2
5Q LOSS WILD-TYPE 66 296 480

Figure S445.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00013

Table S446.  Gene #51: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
5Q LOSS MUTATED 2 9 5 1
5Q LOSS WILD-TYPE 151 62 58 124

Figure S446.  Get High-res Image Gene #51: '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 = 2.3e-05

Table S447.  Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
5Q LOSS MUTATED 0 1 8 0 8
5Q LOSS WILD-TYPE 47 97 89 124 38

Figure S447.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'MRNA_CNMF'

P value = 0.0025 (Fisher's exact test), Q value = 0.0043

Table S448.  Gene #52: '6p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 24 12 17
6P LOSS MUTATED 4 10 6 1
6P LOSS WILD-TYPE 29 14 6 16

Figure S448.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00356 (Fisher's exact test), Q value = 0.0059

Table S449.  Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 20 24 18 13 11
6P LOSS MUTATED 3 10 1 1 6
6P LOSS WILD-TYPE 17 14 17 12 5

Figure S449.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S450.  Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
6P LOSS MUTATED 65 2 105
6P LOSS WILD-TYPE 217 308 185

Figure S450.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S451.  Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
6P LOSS MUTATED 63 47 12
6P LOSS WILD-TYPE 65 256 209

Figure S451.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p loss' versus 'RPPA_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.00064

Table S452.  Gene #52: '6p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 182 181 187 197
6P LOSS MUTATED 31 33 29 62
6P LOSS WILD-TYPE 151 148 158 135

Figure S452.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'6p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S453.  Gene #52: '6p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
6P LOSS MUTATED 44 12 45 17 23 4 10
6P LOSS WILD-TYPE 153 52 71 130 36 67 83

Figure S453.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S454.  Gene #52: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
6P LOSS MUTATED 65 63 27 15
6P LOSS WILD-TYPE 54 132 270 253

Figure S454.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S455.  Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
6P LOSS MUTATED 61 20 24 51 8 6
6P LOSS WILD-TYPE 27 125 183 108 103 163

Figure S455.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S456.  Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
6P LOSS MUTATED 61 28 79
6P LOSS WILD-TYPE 16 277 403

Figure S456.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S457.  Gene #52: '6p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
6P LOSS MUTATED 8 38 12 14
6P LOSS WILD-TYPE 145 33 51 111

Figure S457.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S458.  Gene #52: '6p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
6P LOSS MUTATED 1 7 14 13 37
6P LOSS WILD-TYPE 46 91 83 111 9

Figure S458.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'MRNA_CNMF'

P value = 0.00311 (Fisher's exact test), Q value = 0.0052

Table S459.  Gene #53: '6q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 24 12 17
6Q LOSS MUTATED 7 11 7 1
6Q LOSS WILD-TYPE 26 13 5 16

Figure S459.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'6q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00346 (Fisher's exact test), Q value = 0.0058

Table S460.  Gene #53: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 20 24 18 13 11
6Q LOSS MUTATED 4 11 1 3 7
6Q LOSS WILD-TYPE 16 13 17 10 4

Figure S460.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S461.  Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
6Q LOSS MUTATED 66 2 138
6Q LOSS WILD-TYPE 216 308 152

Figure S461.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S462.  Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
6Q LOSS MUTATED 65 63 16
6Q LOSS WILD-TYPE 63 240 205

Figure S462.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'RPPA_CNMF'

P value = 0.00123 (Fisher's exact test), Q value = 0.0022

Table S463.  Gene #53: '6q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 182 181 187 197
6Q LOSS MUTATED 36 45 36 69
6Q LOSS WILD-TYPE 146 136 151 128

Figure S463.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'6q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S464.  Gene #53: '6q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
6Q LOSS MUTATED 55 13 48 29 24 5 12
6Q LOSS WILD-TYPE 142 51 68 118 35 66 81

Figure S464.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S465.  Gene #53: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
6Q LOSS MUTATED 66 65 51 22
6Q LOSS WILD-TYPE 53 130 246 246

Figure S465.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S466.  Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
6Q LOSS MUTATED 61 28 35 53 22 5
6Q LOSS WILD-TYPE 27 117 172 106 89 164

Figure S466.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S467.  Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
6Q LOSS MUTATED 61 34 107
6Q LOSS WILD-TYPE 16 271 375

Figure S467.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S468.  Gene #53: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
6Q LOSS MUTATED 10 39 13 22
6Q LOSS WILD-TYPE 143 32 50 103

Figure S468.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S469.  Gene #53: '6q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
6Q LOSS MUTATED 2 7 18 20 37
6Q LOSS WILD-TYPE 45 91 79 104 9

Figure S469.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.041 (Fisher's exact test), Q value = 0.059

Table S470.  Gene #54: '7p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
7P LOSS MUTATED 0 0 3 0 0 0 0
7P LOSS WILD-TYPE 197 64 113 147 59 71 93

Figure S470.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0422 (Fisher's exact test), Q value = 0.06

Table S471.  Gene #55: '7q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
7Q LOSS MUTATED 0 0 3 0 0 0 0
7Q LOSS WILD-TYPE 197 64 113 147 59 71 93

Figure S471.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S472.  Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
8P LOSS MUTATED 25 39 100
8P LOSS WILD-TYPE 257 271 190

Figure S472.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S473.  Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
8P LOSS MUTATED 18 73 8
8P LOSS WILD-TYPE 110 230 213

Figure S473.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S474.  Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
8P LOSS MUTATED 19 61 71 12
8P LOSS WILD-TYPE 100 134 226 256

Figure S474.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S475.  Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
8P LOSS MUTATED 16 14 56 51 23 3
8P LOSS WILD-TYPE 72 131 151 108 88 166

Figure S475.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S476.  Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
8P LOSS MUTATED 28 43 90
8P LOSS WILD-TYPE 299 150 254

Figure S476.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S477.  Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
8P LOSS MUTATED 15 18 128
8P LOSS WILD-TYPE 62 287 354

Figure S477.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S478.  Gene #56: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
8P LOSS MUTATED 5 9 5 33
8P LOSS WILD-TYPE 148 62 58 92

Figure S478.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S479.  Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
8P LOSS MUTATED 1 4 8 33 6
8P LOSS WILD-TYPE 46 94 89 91 40

Figure S479.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S480.  Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
8Q LOSS MUTATED 17 20 50
8Q LOSS WILD-TYPE 265 290 240

Figure S480.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S481.  Gene #57: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
8Q LOSS MUTATED 15 37 4
8Q LOSS WILD-TYPE 113 266 217

Figure S481.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S482.  Gene #57: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
8Q LOSS MUTATED 16 21 44 6
8Q LOSS WILD-TYPE 103 174 253 262

Figure S482.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S483.  Gene #57: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
8Q LOSS MUTATED 14 8 37 16 11 1
8Q LOSS WILD-TYPE 74 137 170 143 100 168

Figure S483.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_CNMF'

P value = 0.00469 (Fisher's exact test), Q value = 0.0077

Table S484.  Gene #57: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
8Q LOSS MUTATED 19 23 44
8Q LOSS WILD-TYPE 308 170 300

Figure S484.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S485.  Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
8Q LOSS MUTATED 13 10 63
8Q LOSS WILD-TYPE 64 295 419

Figure S485.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00034

Table S486.  Gene #57: '8q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
8Q LOSS MUTATED 2 7 3 17
8Q LOSS WILD-TYPE 151 64 60 108

Figure S486.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.00081

Table S487.  Gene #57: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
8Q LOSS MUTATED 0 2 4 17 6
8Q LOSS WILD-TYPE 47 96 93 107 40

Figure S487.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'MRNA_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.017

Table S488.  Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 24 12 17
9P LOSS MUTATED 5 12 1 3
9P LOSS WILD-TYPE 28 12 11 14

Figure S488.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0211 (Fisher's exact test), Q value = 0.032

Table S489.  Gene #58: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 20 24 18 13 11
9P LOSS MUTATED 4 12 3 1 1
9P LOSS WILD-TYPE 16 12 15 12 10

Figure S489.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S490.  Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
9P LOSS MUTATED 21 33 138
9P LOSS WILD-TYPE 261 277 152

Figure S490.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S491.  Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
9P LOSS MUTATED 24 90 19
9P LOSS WILD-TYPE 104 213 202

Figure S491.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S492.  Gene #58: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 182 181 187 197
9P LOSS MUTATED 48 34 24 67
9P LOSS WILD-TYPE 134 147 163 130

Figure S492.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S493.  Gene #58: '9p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
9P LOSS MUTATED 40 6 41 22 28 11 25
9P LOSS WILD-TYPE 157 58 75 125 31 60 68

Figure S493.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S494.  Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
9P LOSS MUTATED 18 103 42 28
9P LOSS WILD-TYPE 101 92 255 240

Figure S494.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S495.  Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
9P LOSS MUTATED 11 38 44 85 10 3
9P LOSS WILD-TYPE 77 107 163 74 101 166

Figure S495.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S496.  Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
9P LOSS MUTATED 35 65 87
9P LOSS WILD-TYPE 292 128 257

Figure S496.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S497.  Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
9P LOSS MUTATED 10 42 135
9P LOSS WILD-TYPE 67 263 347

Figure S497.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00019

Table S498.  Gene #58: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
9P LOSS MUTATED 11 12 19 26
9P LOSS WILD-TYPE 142 59 44 99

Figure S498.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.6e-05

Table S499.  Gene #58: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
9P LOSS MUTATED 2 7 30 23 6
9P LOSS WILD-TYPE 45 91 67 101 40

Figure S499.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'MRNA_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.033

Table S500.  Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 24 12 17
9Q LOSS MUTATED 5 12 2 3
9Q LOSS WILD-TYPE 28 12 10 14

Figure S500.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0391 (Fisher's exact test), Q value = 0.057

Table S501.  Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 20 24 18 13 11
9Q LOSS MUTATED 4 12 3 1 2
9Q LOSS WILD-TYPE 16 12 15 12 9

Figure S501.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S502.  Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
9Q LOSS MUTATED 21 34 140
9Q LOSS WILD-TYPE 261 276 150

Figure S502.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S503.  Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
9Q LOSS MUTATED 27 89 17
9Q LOSS WILD-TYPE 101 214 204

Figure S503.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S504.  Gene #59: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 182 181 187 197
9Q LOSS MUTATED 49 35 25 67
9Q LOSS WILD-TYPE 133 146 162 130

Figure S504.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S505.  Gene #59: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
9Q LOSS MUTATED 43 7 41 19 30 12 24
9Q LOSS WILD-TYPE 154 57 75 128 29 59 69

Figure S505.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S506.  Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
9Q LOSS MUTATED 22 104 42 26
9Q LOSS WILD-TYPE 97 91 255 242

Figure S506.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S507.  Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
9Q LOSS MUTATED 13 37 45 87 9 3
9Q LOSS WILD-TYPE 75 108 162 72 102 166

Figure S507.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S508.  Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
9Q LOSS MUTATED 38 65 86
9Q LOSS WILD-TYPE 289 128 258

Figure S508.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S509.  Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
9Q LOSS MUTATED 12 42 135
9Q LOSS WILD-TYPE 65 263 347

Figure S509.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00023

Table S510.  Gene #59: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
9Q LOSS MUTATED 11 14 19 27
9Q LOSS WILD-TYPE 142 57 44 98

Figure S510.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.7e-05

Table S511.  Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
9Q LOSS MUTATED 2 7 30 24 8
9Q LOSS WILD-TYPE 45 91 67 100 38

Figure S511.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S512.  Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
10P LOSS MUTATED 58 9 64
10P LOSS WILD-TYPE 224 301 226

Figure S512.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S513.  Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
10P LOSS MUTATED 59 33 11
10P LOSS WILD-TYPE 69 270 210

Figure S513.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00021

Table S514.  Gene #60: '10p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
10P LOSS MUTATED 31 9 36 16 9 3 12
10P LOSS WILD-TYPE 166 55 80 131 50 68 81

Figure S514.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S515.  Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
10P LOSS MUTATED 60 29 29 13
10P LOSS WILD-TYPE 59 166 268 255

Figure S515.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S516.  Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
10P LOSS MUTATED 58 19 22 22 9 1
10P LOSS WILD-TYPE 30 126 185 137 102 168

Figure S516.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.00057

Table S517.  Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
10P LOSS MUTATED 67 30 32
10P LOSS WILD-TYPE 260 163 312

Figure S517.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S518.  Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
10P LOSS MUTATED 58 20 51
10P LOSS WILD-TYPE 19 285 431

Figure S518.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S519.  Gene #60: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
10P LOSS MUTATED 3 36 9 11
10P LOSS WILD-TYPE 150 35 54 114

Figure S519.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S520.  Gene #60: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
10P LOSS MUTATED 1 1 14 9 34
10P LOSS WILD-TYPE 46 97 83 115 12

Figure S520.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S521.  Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
10Q LOSS MUTATED 57 15 84
10Q LOSS WILD-TYPE 225 295 206

Figure S521.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S522.  Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
10Q LOSS MUTATED 62 47 12
10Q LOSS WILD-TYPE 66 256 209

Figure S522.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00145 (Fisher's exact test), Q value = 0.0026

Table S523.  Gene #61: '10q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
10Q LOSS MUTATED 35 10 39 25 12 6 15
10Q LOSS WILD-TYPE 162 54 77 122 47 65 78

Figure S523.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S524.  Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
10Q LOSS MUTATED 63 39 40 14
10Q LOSS WILD-TYPE 56 156 257 254

Figure S524.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S525.  Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
10Q LOSS MUTATED 59 22 30 30 14 1
10Q LOSS WILD-TYPE 29 123 177 129 97 168

Figure S525.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S526.  Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
10Q LOSS MUTATED 59 21 74
10Q LOSS WILD-TYPE 18 284 408

Figure S526.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S527.  Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
10Q LOSS MUTATED 3 38 11 16
10Q LOSS WILD-TYPE 150 33 52 109

Figure S527.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S528.  Gene #61: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
10Q LOSS MUTATED 1 1 17 14 35
10Q LOSS WILD-TYPE 46 97 80 110 11

Figure S528.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'MRNA_CNMF'

P value = 0.0349 (Fisher's exact test), Q value = 0.051

Table S529.  Gene #62: '11p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 24 12 17
11P LOSS MUTATED 0 1 2 0
11P LOSS WILD-TYPE 33 23 10 17

Figure S529.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00013

Table S530.  Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
11P LOSS MUTATED 14 4 25
11P LOSS WILD-TYPE 268 306 265

Figure S530.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.0288 (Fisher's exact test), Q value = 0.043

Table S531.  Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
11P LOSS MUTATED 13 11 12
11P LOSS WILD-TYPE 115 292 209

Figure S531.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.00064

Table S532.  Gene #62: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
11P LOSS MUTATED 12 14 4 13
11P LOSS WILD-TYPE 107 181 293 255

Figure S532.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S533.  Gene #62: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
11P LOSS MUTATED 8 18 4 9 1 3
11P LOSS WILD-TYPE 80 127 203 150 110 166

Figure S533.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 0.0466 (Fisher's exact test), Q value = 0.066

Table S534.  Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
11P LOSS MUTATED 19 14 10
11P LOSS WILD-TYPE 308 179 334

Figure S534.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00382 (Fisher's exact test), Q value = 0.0063

Table S535.  Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
11P LOSS MUTATED 7 22 14
11P LOSS WILD-TYPE 70 283 468

Figure S535.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.00059

Table S536.  Gene #62: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
11P LOSS MUTATED 6 8 10 2
11P LOSS WILD-TYPE 147 63 53 123

Figure S536.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.7e-05

Table S537.  Gene #62: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
11P LOSS MUTATED 1 3 15 1 6
11P LOSS WILD-TYPE 46 95 82 123 40

Figure S537.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S538.  Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
11Q LOSS MUTATED 15 3 34
11Q LOSS WILD-TYPE 267 307 256

Figure S538.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00222 (Fisher's exact test), Q value = 0.0038

Table S539.  Gene #63: '11q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
11Q LOSS MUTATED 6 4 13 4 9 3 8
11Q LOSS WILD-TYPE 191 60 103 143 50 68 85

Figure S539.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S540.  Gene #63: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
11Q LOSS MUTATED 11 19 4 18
11Q LOSS WILD-TYPE 108 176 293 250

Figure S540.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S541.  Gene #63: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
11Q LOSS MUTATED 7 23 4 14 1 3
11Q LOSS WILD-TYPE 81 122 203 145 110 166

Figure S541.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.0405 (Fisher's exact test), Q value = 0.058

Table S542.  Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
11Q LOSS MUTATED 22 17 13
11Q LOSS WILD-TYPE 305 176 331

Figure S542.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0276 (Fisher's exact test), Q value = 0.041

Table S543.  Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
11Q LOSS MUTATED 7 25 20
11Q LOSS WILD-TYPE 70 280 462

Figure S543.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00027

Table S544.  Gene #63: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
11Q LOSS MUTATED 9 7 12 2
11Q LOSS WILD-TYPE 144 64 51 123

Figure S544.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.6e-05

Table S545.  Gene #63: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
11Q LOSS MUTATED 1 6 16 1 6
11Q LOSS WILD-TYPE 46 92 81 123 40

Figure S545.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.033

Table S546.  Gene #65: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
12Q LOSS MUTATED 0 0 4
12Q LOSS WILD-TYPE 282 310 286

Figure S546.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'MRNA_CNMF'

P value = 0.00296 (Fisher's exact test), Q value = 0.005

Table S547.  Gene #66: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 24 12 17
13Q LOSS MUTATED 0 6 3 1
13Q LOSS WILD-TYPE 33 18 9 16

Figure S547.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.018

Table S548.  Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 20 24 18 13 11
13Q LOSS MUTATED 0 6 1 0 3
13Q LOSS WILD-TYPE 20 18 17 13 8

Figure S548.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S549.  Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
13Q LOSS MUTATED 61 8 68
13Q LOSS WILD-TYPE 221 302 222

Figure S549.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S550.  Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
13Q LOSS MUTATED 62 39 10
13Q LOSS WILD-TYPE 66 264 211

Figure S550.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S551.  Gene #66: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
13Q LOSS MUTATED 26 10 39 8 16 7 18
13Q LOSS WILD-TYPE 171 54 77 139 43 64 75

Figure S551.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S552.  Gene #66: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
13Q LOSS MUTATED 55 53 15 14
13Q LOSS WILD-TYPE 64 142 282 254

Figure S552.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S553.  Gene #66: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
13Q LOSS MUTATED 51 27 9 42 6 2
13Q LOSS WILD-TYPE 37 118 198 117 105 167

Figure S553.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0013

Table S554.  Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
13Q LOSS MUTATED 64 37 34
13Q LOSS WILD-TYPE 263 156 310

Figure S554.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S555.  Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
13Q LOSS MUTATED 50 32 53
13Q LOSS WILD-TYPE 27 273 429

Figure S555.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S556.  Gene #66: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
13Q LOSS MUTATED 7 33 17 9
13Q LOSS WILD-TYPE 146 38 46 116

Figure S556.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S557.  Gene #66: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
13Q LOSS MUTATED 1 4 21 9 31
13Q LOSS WILD-TYPE 46 94 76 115 15

Figure S557.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00015

Table S558.  Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 24 12 17
14Q LOSS MUTATED 9 19 2 4
14Q LOSS WILD-TYPE 24 5 10 13

Figure S558.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00017

Table S559.  Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 20 24 18 13 11
14Q LOSS MUTATED 4 19 4 5 2
14Q LOSS WILD-TYPE 16 5 14 8 9

Figure S559.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S560.  Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
14Q LOSS MUTATED 33 76 156
14Q LOSS WILD-TYPE 249 234 134

Figure S560.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S561.  Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
14Q LOSS MUTATED 14 127 27
14Q LOSS WILD-TYPE 114 176 194

Figure S561.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S562.  Gene #67: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 182 181 187 197
14Q LOSS MUTATED 59 55 32 87
14Q LOSS WILD-TYPE 123 126 155 110

Figure S562.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S563.  Gene #67: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
14Q LOSS MUTATED 62 2 45 40 31 17 36
14Q LOSS WILD-TYPE 135 62 71 107 28 54 57

Figure S563.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S564.  Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
14Q LOSS MUTATED 10 115 96 41
14Q LOSS WILD-TYPE 109 80 201 227

Figure S564.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S565.  Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
14Q LOSS MUTATED 4 39 75 106 27 11
14Q LOSS WILD-TYPE 84 106 132 53 84 158

Figure S565.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S566.  Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
14Q LOSS MUTATED 39 75 145
14Q LOSS WILD-TYPE 288 118 199

Figure S566.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S567.  Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
14Q LOSS MUTATED 3 52 204
14Q LOSS WILD-TYPE 74 253 278

Figure S567.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S568.  Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
14Q LOSS MUTATED 15 4 21 47
14Q LOSS WILD-TYPE 138 67 42 78

Figure S568.  Get High-res Image Gene #67: '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 = 2.3e-05

Table S569.  Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
14Q LOSS MUTATED 4 9 30 43 1
14Q LOSS WILD-TYPE 43 89 67 81 45

Figure S569.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S570.  Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
15Q LOSS MUTATED 19 5 45
15Q LOSS WILD-TYPE 263 305 245

Figure S570.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00092 (Fisher's exact test), Q value = 0.0017

Table S571.  Gene #68: '15q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
15Q LOSS MUTATED 12 3 18 6 12 4 8
15Q LOSS WILD-TYPE 185 61 98 141 47 67 85

Figure S571.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S572.  Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
15Q LOSS MUTATED 4 33 9 23
15Q LOSS WILD-TYPE 115 162 288 245

Figure S572.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S573.  Gene #68: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
15Q LOSS MUTATED 1 27 7 24 3 7
15Q LOSS WILD-TYPE 87 118 200 135 108 162

Figure S573.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.0291 (Fisher's exact test), Q value = 0.043

Table S574.  Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
15Q LOSS MUTATED 25 24 20
15Q LOSS WILD-TYPE 302 169 324

Figure S574.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00173 (Fisher's exact test), Q value = 0.003

Table S575.  Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
15Q LOSS MUTATED 1 36 32
15Q LOSS WILD-TYPE 76 269 450

Figure S575.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00401 (Fisher's exact test), Q value = 0.0066

Table S576.  Gene #68: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
15Q LOSS MUTATED 13 2 13 8
15Q LOSS WILD-TYPE 140 69 50 117

Figure S576.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-04 (Fisher's exact test), Q value = 0.0017

Table S577.  Gene #68: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
15Q LOSS MUTATED 3 9 18 6 0
15Q LOSS WILD-TYPE 44 89 79 118 46

Figure S577.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00015

Table S578.  Gene #69: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
16P LOSS MUTATED 9 5 0
16P LOSS WILD-TYPE 119 298 221

Figure S578.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00992 (Fisher's exact test), Q value = 0.016

Table S579.  Gene #69: '16p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
16P LOSS MUTATED 1 0 7 4 3 0 1
16P LOSS WILD-TYPE 196 64 109 143 56 71 92

Figure S579.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00042

Table S580.  Gene #69: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
16P LOSS MUTATED 6 9 2 1
16P LOSS WILD-TYPE 113 186 295 267

Figure S580.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00273 (Fisher's exact test), Q value = 0.0046

Table S581.  Gene #69: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
16P LOSS MUTATED 3 7 1 6 1 0
16P LOSS WILD-TYPE 85 138 206 153 110 169

Figure S581.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 0.0279 (Fisher's exact test), Q value = 0.042

Table S582.  Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
16P LOSS MUTATED 5 9 4
16P LOSS WILD-TYPE 322 184 340

Figure S582.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00101 (Fisher's exact test), Q value = 0.0018

Table S583.  Gene #69: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
16P LOSS MUTATED 0 4 5 2
16P LOSS WILD-TYPE 153 67 58 123

Figure S583.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00019

Table S584.  Gene #69: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
16P LOSS MUTATED 0 0 8 0 3
16P LOSS WILD-TYPE 47 98 89 124 43

Figure S584.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 0.001 (Fisher's exact test), Q value = 0.0018

Table S585.  Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
16Q LOSS MUTATED 7 3 18
16Q LOSS WILD-TYPE 275 307 272

Figure S585.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 0.0088 (Fisher's exact test), Q value = 0.014

Table S586.  Gene #70: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
16Q LOSS MUTATED 9 10 2
16Q LOSS WILD-TYPE 119 293 219

Figure S586.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 0.00439 (Fisher's exact test), Q value = 0.0072

Table S587.  Gene #70: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
16Q LOSS MUTATED 7 12 5 4
16Q LOSS WILD-TYPE 112 183 292 264

Figure S587.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.0013

Table S588.  Gene #70: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
16Q LOSS MUTATED 4 9 3 10 2 0
16Q LOSS WILD-TYPE 84 136 204 149 109 169

Figure S588.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0398 (Fisher's exact test), Q value = 0.057

Table S589.  Gene #70: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
16Q LOSS MUTATED 2 5 5 7
16Q LOSS WILD-TYPE 151 66 58 118

Figure S589.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00527 (Fisher's exact test), Q value = 0.0086

Table S590.  Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
16Q LOSS MUTATED 0 1 10 4 4
16Q LOSS WILD-TYPE 47 97 87 120 42

Figure S590.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.0016

Table S591.  Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 24 12 17
17P LOSS MUTATED 0 5 5 2
17P LOSS WILD-TYPE 33 19 7 15

Figure S591.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00301 (Fisher's exact test), Q value = 0.0051

Table S592.  Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 20 24 18 13 11
17P LOSS MUTATED 0 5 2 0 5
17P LOSS WILD-TYPE 20 19 16 13 6

Figure S592.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S593.  Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
17P LOSS MUTATED 56 6 48
17P LOSS WILD-TYPE 226 304 242

Figure S593.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S594.  Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
17P LOSS MUTATED 61 18 4
17P LOSS WILD-TYPE 67 285 217

Figure S594.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S595.  Gene #71: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
17P LOSS MUTATED 21 12 35 8 8 4 8
17P LOSS WILD-TYPE 176 52 81 139 51 67 85

Figure S595.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S596.  Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
17P LOSS MUTATED 67 27 6 10
17P LOSS WILD-TYPE 52 168 291 258

Figure S596.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S597.  Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
17P LOSS MUTATED 61 16 4 26 3 0
17P LOSS WILD-TYPE 27 129 203 133 108 169

Figure S597.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S598.  Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
17P LOSS MUTATED 66 22 22
17P LOSS WILD-TYPE 261 171 322

Figure S598.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S599.  Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
17P LOSS MUTATED 61 16 33
17P LOSS WILD-TYPE 16 289 449

Figure S599.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S600.  Gene #71: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
17P LOSS MUTATED 3 37 11 6
17P LOSS WILD-TYPE 150 34 52 119

Figure S600.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S601.  Gene #71: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
17P LOSS MUTATED 0 1 14 6 36
17P LOSS WILD-TYPE 47 97 83 118 10

Figure S601.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'MRNA_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00032

Table S602.  Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 24 12 17
17Q LOSS MUTATED 0 4 5 0
17Q LOSS WILD-TYPE 33 20 7 17

Figure S602.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.00044

Table S603.  Gene #72: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 20 24 18 13 11
17Q LOSS MUTATED 0 4 0 0 5
17Q LOSS WILD-TYPE 20 20 18 13 6

Figure S603.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S604.  Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
17Q LOSS MUTATED 53 1 28
17Q LOSS WILD-TYPE 229 309 262

Figure S604.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S605.  Gene #72: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
17Q LOSS MUTATED 56 7 0
17Q LOSS WILD-TYPE 72 296 221

Figure S605.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S606.  Gene #72: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
17Q LOSS MUTATED 18 11 30 6 3 1 4
17Q LOSS WILD-TYPE 179 53 86 141 56 70 89

Figure S606.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S607.  Gene #72: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
17Q LOSS MUTATED 62 16 4 0
17Q LOSS WILD-TYPE 57 179 293 268

Figure S607.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S608.  Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
17Q LOSS MUTATED 61 2 2 15 2 0
17Q LOSS WILD-TYPE 27 143 205 144 109 169

Figure S608.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S609.  Gene #72: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
17Q LOSS MUTATED 58 10 14
17Q LOSS WILD-TYPE 269 183 330

Figure S609.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S610.  Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
17Q LOSS MUTATED 61 3 18
17Q LOSS WILD-TYPE 16 302 464

Figure S610.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S611.  Gene #72: '17q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
17Q LOSS MUTATED 0 36 3 3
17Q LOSS WILD-TYPE 153 35 60 122

Figure S611.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S612.  Gene #72: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
17Q LOSS MUTATED 0 0 3 3 36
17Q LOSS WILD-TYPE 47 98 94 121 10

Figure S612.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S613.  Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
18P LOSS MUTATED 35 24 83
18P LOSS WILD-TYPE 247 286 207

Figure S613.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 0.0314 (Fisher's exact test), Q value = 0.046

Table S614.  Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
18P LOSS MUTATED 22 58 24
18P LOSS WILD-TYPE 106 245 197

Figure S614.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'RPPA_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.00074

Table S615.  Gene #73: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 182 181 187 197
18P LOSS MUTATED 36 15 26 46
18P LOSS WILD-TYPE 146 166 161 151

Figure S615.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S616.  Gene #73: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
18P LOSS MUTATED 20 8 33 13 24 8 17
18P LOSS WILD-TYPE 177 56 83 134 35 63 76

Figure S616.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S617.  Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
18P LOSS MUTATED 13 74 17 37
18P LOSS WILD-TYPE 106 121 280 231

Figure S617.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S618.  Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
18P LOSS MUTATED 11 38 16 60 6 10
18P LOSS WILD-TYPE 77 107 191 99 105 159

Figure S618.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00032

Table S619.  Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
18P LOSS MUTATED 41 51 50
18P LOSS WILD-TYPE 286 142 294

Figure S619.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.0019

Table S620.  Gene #73: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
18P LOSS MUTATED 18 13 20 12
18P LOSS WILD-TYPE 135 58 43 113

Figure S620.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S621.  Gene #73: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
18P LOSS MUTATED 1 14 30 11 7
18P LOSS WILD-TYPE 46 84 67 113 39

Figure S621.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S622.  Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
18Q LOSS MUTATED 36 25 88
18Q LOSS WILD-TYPE 246 285 202

Figure S622.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 0.0463 (Fisher's exact test), Q value = 0.066

Table S623.  Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
18Q LOSS MUTATED 24 59 26
18Q LOSS WILD-TYPE 104 244 195

Figure S623.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0011

Table S624.  Gene #74: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 182 181 187 197
18Q LOSS MUTATED 39 17 27 47
18Q LOSS WILD-TYPE 143 164 160 150

Figure S624.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S625.  Gene #74: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
18Q LOSS MUTATED 19 8 35 16 24 8 20
18Q LOSS WILD-TYPE 178 56 81 131 35 63 73

Figure S625.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S626.  Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
18Q LOSS MUTATED 15 76 17 40
18Q LOSS WILD-TYPE 104 119 280 228

Figure S626.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S627.  Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
18Q LOSS MUTATED 12 44 18 59 6 9
18Q LOSS WILD-TYPE 76 101 189 100 105 160

Figure S627.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.00096

Table S628.  Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
18Q LOSS MUTATED 45 52 52
18Q LOSS WILD-TYPE 282 141 292

Figure S628.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00044

Table S629.  Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
18Q LOSS MUTATED 19 14 22 13
18Q LOSS WILD-TYPE 134 57 41 112

Figure S629.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S630.  Gene #74: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
18Q LOSS MUTATED 1 14 34 11 8
18Q LOSS WILD-TYPE 46 84 63 113 38

Figure S630.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S631.  Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
19P LOSS MUTATED 10 0 17
19P LOSS WILD-TYPE 272 310 273

Figure S631.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 0.00121 (Fisher's exact test), Q value = 0.0022

Table S632.  Gene #75: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
19P LOSS MUTATED 3 4 16
19P LOSS WILD-TYPE 125 299 205

Figure S632.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 0.00088 (Fisher's exact test), Q value = 0.0016

Table S633.  Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
19P LOSS MUTATED 1 9 2 15
19P LOSS WILD-TYPE 118 186 295 253

Figure S633.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 9e-04

Table S634.  Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
19P LOSS MUTATED 1 13 1 6 1 5
19P LOSS WILD-TYPE 87 132 206 153 110 164

Figure S634.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00405 (Fisher's exact test), Q value = 0.0067

Table S635.  Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
19P LOSS MUTATED 1 18 8
19P LOSS WILD-TYPE 76 287 474

Figure S635.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00385 (Fisher's exact test), Q value = 0.0064

Table S636.  Gene #75: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
19P LOSS MUTATED 9 1 7 1
19P LOSS WILD-TYPE 144 70 56 124

Figure S636.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.0011

Table S637.  Gene #75: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
19P LOSS MUTATED 1 5 11 0 1
19P LOSS WILD-TYPE 46 93 86 124 45

Figure S637.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00015

Table S638.  Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
19Q LOSS MUTATED 8 0 14
19Q LOSS WILD-TYPE 274 310 276

Figure S638.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.0019

Table S639.  Gene #76: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
19Q LOSS MUTATED 4 2 13
19Q LOSS WILD-TYPE 124 301 208

Figure S639.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 0.0029 (Fisher's exact test), Q value = 0.0049

Table S640.  Gene #76: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
19Q LOSS MUTATED 2 6 1 13
19Q LOSS WILD-TYPE 117 189 296 255

Figure S640.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.00057

Table S641.  Gene #76: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
19Q LOSS MUTATED 2 11 0 3 1 5
19Q LOSS WILD-TYPE 86 134 207 156 110 164

Figure S641.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 0.00483 (Fisher's exact test), Q value = 0.0079

Table S642.  Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
19Q LOSS MUTATED 13 7 2
19Q LOSS WILD-TYPE 314 186 342

Figure S642.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00065 (Fisher's exact test), Q value = 0.0012

Table S643.  Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
19Q LOSS MUTATED 2 16 4
19Q LOSS WILD-TYPE 75 289 478

Figure S643.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0259 (Fisher's exact test), Q value = 0.039

Table S644.  Gene #76: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
19Q LOSS MUTATED 10 2 5 1
19Q LOSS WILD-TYPE 143 69 58 124

Figure S644.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00333 (Fisher's exact test), Q value = 0.0056

Table S645.  Gene #76: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
19Q LOSS MUTATED 1 6 9 0 2
19Q LOSS WILD-TYPE 46 92 88 124 44

Figure S645.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'METHLYATION_CNMF'

P value = 0.00551 (Fisher's exact test), Q value = 0.0089

Table S646.  Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
20P LOSS MUTATED 5 3 0
20P LOSS WILD-TYPE 123 300 221

Figure S646.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 0.00202 (Fisher's exact test), Q value = 0.0035

Table S647.  Gene #77: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
20P LOSS MUTATED 4 6 2 0
20P LOSS WILD-TYPE 115 189 295 268

Figure S647.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.024 (Fisher's exact test), Q value = 0.036

Table S648.  Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
20P LOSS MUTATED 4 1 3 4 0 0
20P LOSS WILD-TYPE 84 144 204 155 111 169

Figure S648.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0232 (Fisher's exact test), Q value = 0.035

Table S649.  Gene #77: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
20P LOSS MUTATED 4 2 6
20P LOSS WILD-TYPE 73 303 476

Figure S649.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.001 (Fisher's exact test), Q value = 0.0018

Table S650.  Gene #77: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
20P LOSS MUTATED 0 5 0 1
20P LOSS WILD-TYPE 153 66 63 124

Figure S650.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00434 (Fisher's exact test), Q value = 0.0072

Table S651.  Gene #77: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
20P LOSS MUTATED 0 0 1 1 4
20P LOSS WILD-TYPE 47 98 96 123 42

Figure S651.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q loss' versus 'METHLYATION_CNMF'

P value = 0.00754 (Fisher's exact test), Q value = 0.012

Table S652.  Gene #78: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
20Q LOSS MUTATED 3 0 0
20Q LOSS WILD-TYPE 125 303 221

Figure S652.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q loss' versus 'MRNASEQ_CNMF'

P value = 0.022 (Fisher's exact test), Q value = 0.033

Table S653.  Gene #78: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
20Q LOSS MUTATED 3 2 1 0
20Q LOSS WILD-TYPE 116 193 296 268

Figure S653.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0222 (Fisher's exact test), Q value = 0.034

Table S654.  Gene #78: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
20Q LOSS MUTATED 3 0 1 2 0 0
20Q LOSS WILD-TYPE 85 145 206 157 111 169

Figure S654.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00741 (Fisher's exact test), Q value = 0.012

Table S655.  Gene #78: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
20Q LOSS MUTATED 3 0 3
20Q LOSS WILD-TYPE 74 305 479

Figure S655.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00845 (Fisher's exact test), Q value = 0.013

Table S656.  Gene #78: '20q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
20Q LOSS MUTATED 0 3 0 0
20Q LOSS WILD-TYPE 153 68 63 125

Figure S656.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00134 (Fisher's exact test), Q value = 0.0024

Table S657.  Gene #78: '20q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
20Q LOSS MUTATED 0 0 0 0 3
20Q LOSS WILD-TYPE 47 98 97 124 43

Figure S657.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'MRNA_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.025

Table S658.  Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 24 12 17
21Q LOSS MUTATED 1 2 4 4
21Q LOSS WILD-TYPE 32 22 8 13

Figure S658.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0236 (Fisher's exact test), Q value = 0.036

Table S659.  Gene #79: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 20 24 18 13 11
21Q LOSS MUTATED 0 2 4 1 4
21Q LOSS WILD-TYPE 20 22 14 12 7

Figure S659.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S660.  Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
21Q LOSS MUTATED 73 11 49
21Q LOSS WILD-TYPE 209 299 241

Figure S660.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S661.  Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
21Q LOSS MUTATED 46 31 32
21Q LOSS WILD-TYPE 82 272 189

Figure S661.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S662.  Gene #79: '21q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
21Q LOSS MUTATED 23 13 36 12 14 7 9
21Q LOSS WILD-TYPE 174 51 80 135 45 64 84

Figure S662.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S663.  Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
21Q LOSS MUTATED 49 25 18 39
21Q LOSS WILD-TYPE 70 170 279 229

Figure S663.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S664.  Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
21Q LOSS MUTATED 46 27 14 15 7 22
21Q LOSS WILD-TYPE 42 118 193 144 104 147

Figure S664.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S665.  Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
21Q LOSS MUTATED 78 30 24
21Q LOSS WILD-TYPE 249 163 320

Figure S665.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S666.  Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
21Q LOSS MUTATED 46 48 38
21Q LOSS WILD-TYPE 31 257 444

Figure S666.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S667.  Gene #79: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
21Q LOSS MUTATED 24 27 14 11
21Q LOSS WILD-TYPE 129 44 49 114

Figure S667.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S668.  Gene #79: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
21Q LOSS MUTATED 2 18 18 12 26
21Q LOSS WILD-TYPE 45 80 79 112 20

Figure S668.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'MRNA_CNMF'

P value = 0.00546 (Fisher's exact test), Q value = 0.0088

Table S669.  Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 24 12 17
22Q LOSS MUTATED 0 4 1 5
22Q LOSS WILD-TYPE 33 20 11 12

Figure S669.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0366 (Fisher's exact test), Q value = 0.053

Table S670.  Gene #80: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 20 24 18 13 11
22Q LOSS MUTATED 0 4 5 0 1
22Q LOSS WILD-TYPE 20 20 13 13 10

Figure S670.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S671.  Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
22Q LOSS MUTATED 41 17 49
22Q LOSS WILD-TYPE 241 293 241

Figure S671.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.00052

Table S672.  Gene #80: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
22Q LOSS MUTATED 23 24 42
22Q LOSS WILD-TYPE 105 279 179

Figure S672.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00013

Table S673.  Gene #80: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
22Q LOSS MUTATED 16 14 17 8 15 5 17
22Q LOSS WILD-TYPE 181 50 99 139 44 66 76

Figure S673.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S674.  Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
22Q LOSS MUTATED 14 30 9 54
22Q LOSS WILD-TYPE 105 165 288 214

Figure S674.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S675.  Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
22Q LOSS MUTATED 10 51 11 22 1 12
22Q LOSS WILD-TYPE 78 94 196 137 110 157

Figure S675.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.7e-05

Table S676.  Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
22Q LOSS MUTATED 60 23 24
22Q LOSS WILD-TYPE 267 170 320

Figure S676.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S677.  Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
22Q LOSS MUTATED 9 64 34
22Q LOSS WILD-TYPE 68 241 448

Figure S677.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0018 (Fisher's exact test), Q value = 0.0031

Table S678.  Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
22Q LOSS MUTATED 29 14 13 7
22Q LOSS WILD-TYPE 124 57 50 118

Figure S678.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S679.  Gene #80: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
22Q LOSS MUTATED 3 21 26 5 8
22Q LOSS WILD-TYPE 44 77 71 119 38

Figure S679.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S680.  Gene #81: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
XP LOSS MUTATED 63 7 48
XP LOSS WILD-TYPE 219 303 242

Figure S680.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S681.  Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
XP LOSS MUTATED 53 28 15
XP LOSS WILD-TYPE 75 275 206

Figure S681.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp loss' versus 'RPPA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00013

Table S682.  Gene #81: 'xp loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
XP LOSS MUTATED 30 9 29 10 3 4 15
XP LOSS WILD-TYPE 167 55 87 137 56 67 78

Figure S682.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S683.  Gene #81: 'xp loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
XP LOSS MUTATED 54 18 20 26
XP LOSS WILD-TYPE 65 177 277 242

Figure S683.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S684.  Gene #81: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
XP LOSS MUTATED 49 30 13 14 7 5
XP LOSS WILD-TYPE 39 115 194 145 104 164

Figure S684.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S685.  Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
XP LOSS MUTATED 72 19 26
XP LOSS WILD-TYPE 255 174 318

Figure S685.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S686.  Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
XP LOSS MUTATED 48 33 36
XP LOSS WILD-TYPE 29 272 446

Figure S686.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S687.  Gene #81: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
XP LOSS MUTATED 10 34 10 9
XP LOSS WILD-TYPE 143 37 53 116

Figure S687.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S688.  Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
XP LOSS MUTATED 2 5 21 6 29
XP LOSS WILD-TYPE 45 93 76 118 17

Figure S688.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S689.  Gene #82: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 282 310 290
XQ LOSS MUTATED 62 4 50
XQ LOSS WILD-TYPE 220 306 240

Figure S689.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S690.  Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 303 221
XQ LOSS MUTATED 53 25 15
XQ LOSS WILD-TYPE 75 278 206

Figure S690.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S691.  Gene #82: 'xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 197 64 116 147 59 71 93
XQ LOSS MUTATED 30 9 31 8 4 4 13
XQ LOSS WILD-TYPE 167 55 85 139 55 67 80

Figure S691.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S692.  Gene #82: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 119 195 297 268
XQ LOSS MUTATED 52 20 18 26
XQ LOSS WILD-TYPE 67 175 279 242

Figure S692.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S693.  Gene #82: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 145 207 159 111 169
XQ LOSS MUTATED 47 32 12 14 6 5
XQ LOSS WILD-TYPE 41 113 195 145 105 164

Figure S693.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S694.  Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 327 193 344
XQ LOSS MUTATED 69 19 27
XQ LOSS WILD-TYPE 258 174 317

Figure S694.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S695.  Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 305 482
XQ LOSS MUTATED 46 35 34
XQ LOSS WILD-TYPE 31 270 448

Figure S695.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S696.  Gene #82: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 71 63 125
XQ LOSS MUTATED 10 33 11 8
XQ LOSS WILD-TYPE 143 38 52 117

Figure S696.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S697.  Gene #82: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 98 97 124 46
XQ LOSS MUTATED 2 5 22 5 28
XQ LOSS WILD-TYPE 45 93 75 119 18

Figure S697.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIPAN-TP/19782227/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIPAN-TP/20125873/KIPAN-TP.transferedmergedcluster.txt

  • Number of patients = 882

  • Number of significantly arm-level cnvs = 82

  • 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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