Correlation between copy number variations of arm-level result and molecular subtypes
Pan-kidney cohort (KICH+KIRC+KIRP) (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1K936X5
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1K936X5
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, 691 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • 1q 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'.

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

  • 10q gain cnv correlated to 'MRNA_CNMF'.

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

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

  • 20p 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'.

  • 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',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

  • 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',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  '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_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • 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 '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 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, 691 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 196 (22%) 686 1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0308
(0.0454) 		0.00071
(0.00132) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
20q gain 237 (27%) 645 0.0356
(0.0519) 		0.0496
(0.0707) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0097
(0.0152) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0001
(0.000208) 		1e-05
(2.35e-05) 		0.00854
(0.0135) 		0.00014
(0.000286)
3p loss 411 (47%) 471 1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0006
(0.00113) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
9p loss 192 (22%) 690 0.017
(0.026) 		0.0211
(0.0318) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		2e-05
(4.44e-05) 		0.0001
(0.000208)
9q loss 195 (22%) 687 0.0383
(0.0556) 		0.0388
(0.0563) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		4e-05
(8.63e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		2e-05
(4.44e-05) 		8e-05
(0.000169)
14q loss 265 (30%) 617 5e-05
(0.000107) 		0.0001
(0.000208) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
3p gain 103 (12%) 779 0.00157
(0.00276) 		0.00749
(0.0119) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.211
(0.266) 		0.00702
(0.0112) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
3q gain 161 (18%) 721 0.0184
(0.0279) 		0.0475
(0.0679) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.34
(0.403) 		0.00289
(0.00489) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
12p gain 252 (29%) 630 0.0313
(0.046) 		0.0644
(0.0893) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0292
(0.0433) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		4e-05
(8.63e-05) 		1e-05
(2.35e-05) 		0.00024
(0.000481) 		1e-05
(2.35e-05)
12q gain 256 (29%) 626 0.0308
(0.0454) 		0.0629
(0.0878) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0117
(0.0181) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		2e-05
(4.44e-05) 		1e-05
(2.35e-05) 		0.0003
(0.000593) 		1e-05
(2.35e-05)
17q gain 222 (25%) 660 1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.152
(0.197) 		0.00338
(0.00562) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
xp gain 129 (15%) 753 0.011
(0.017) 		0.0089
(0.014) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.291
(0.353) 		0.00222
(0.00381) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
xq gain 130 (15%) 752 0.00023
(0.000462) 		0.00056
(0.00106) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.633
(0.689) 		0.00438
(0.00718) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
1p loss 145 (16%) 737 0.00313
(0.00526) 		0.0131
(0.0202) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.357
(0.42) 		3e-05
(6.56e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
1q loss 110 (12%) 772 0.0188
(0.0284) 		0.0137
(0.0211) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.79
(0.84) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
2p loss 65 (7%) 817 1e-05
(2.35e-05) 		0.00041
(0.00079) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.14
(0.182) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
2q loss 63 (7%) 819 0.00018
(0.000364) 		6e-05
(0.000128) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.324
(0.387) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
6p loss 171 (19%) 711 0.00633
(0.0102) 		0.00356
(0.00591) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0008
(0.00147) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.155
(0.201) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
6q loss 206 (23%) 676 0.00822
(0.013) 		0.00358
(0.00593) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00213
(0.00368) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.67
(0.727) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
13q loss 137 (16%) 745 0.00652
(0.0104) 		0.0113
(0.0176) 		2e-05
(4.44e-05) 		1e-05
(2.35e-05) 		0.0759
(0.104) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00164
(0.00288) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
17p loss 111 (13%) 771 0.00206
(0.00356) 		0.00311
(0.00523) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.586
(0.643) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
17q loss 82 (9%) 800 0.00034
(0.000666) 		0.00036
(0.000704) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.623
(0.68) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
21q loss 133 (15%) 749 0.0263
(0.0391) 		0.0241
(0.0361) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.957
(0.992) 		2e-05
(4.44e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		2e-05
(4.44e-05) 		1e-05
(2.35e-05)
22q loss 107 (12%) 775 0.00721
(0.0115) 		0.0375
(0.0545) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.339
(0.402) 		7e-05
(0.000148) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		2e-05
(4.44e-05) 		1e-05
(2.35e-05) 		0.00032
(0.00063) 		3e-05
(6.56e-05)
xp loss 114 (13%) 768 0.0297
(0.0439) 		0.0307
(0.0453) 		2e-05
(4.44e-05) 		1e-05
(2.35e-05) 		0.53
(0.595) 		0.00014
(0.000286) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
1q gain 68 (8%) 814 0.601
(0.658) 		0.695
(0.749) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00307
(0.00518) 		0.0276
(0.041) 		0.00021
(0.000423) 		1e-05
(2.35e-05) 		0.0031
(0.00522) 		1e-05
(2.35e-05) 		0.0342
(0.0502) 		1e-05
(2.35e-05)
5p gain 238 (27%) 644 0.486
(0.549) 		0.603
(0.66) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0344
(0.0503) 		7e-05
(0.000148) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
7p gain 369 (42%) 513 0.118
(0.157) 		0.11
(0.147) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0101
(0.0158) 		0.00194
(0.00337) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
7q gain 371 (42%) 511 0.119
(0.158) 		0.109
(0.146) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0142
(0.0218) 		0.00117
(0.00208) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
8q gain 103 (12%) 779 0.0976
(0.131) 		0.243
(0.3) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00605
(0.00973) 		0.00019
(0.000384) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0255
(0.0381) 		1e-05
(2.35e-05) 		0.0014
(0.00247) 		4e-05
(8.63e-05)
16p gain 281 (32%) 601 0.0826
(0.112) 		0.0681
(0.0941) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00518
(0.00842) 		0.00049
(0.000933) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
16q gain 268 (30%) 614 0.0887
(0.12) 		0.0573
(0.0809) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00285
(0.00484) 		0.00037
(0.000715) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
20p gain 233 (26%) 649 0.0632
(0.0879) 		0.0763
(0.104) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0183
(0.0278) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		9e-05
(0.000189) 		1e-05
(2.35e-05) 		0.00687
(0.011) 		0.00012
(0.000249)
4p loss 98 (11%) 784 0.491
(0.554) 		0.48
(0.543) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0256
(0.0382) 		4e-05
(8.63e-05) 		2e-05
(4.44e-05) 		1e-05
(2.35e-05) 		0.00069
(0.00128) 		1e-05
(2.35e-05) 		0.00102
(0.00183) 		0.00012
(0.000249)
18p loss 141 (16%) 741 0.3
(0.363) 		0.408
(0.474) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0004
(0.000772) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00189
(0.00329) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		8e-05
(0.000169)
18q loss 148 (17%) 734 0.227
(0.282) 		0.353
(0.417) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00072
(0.00133) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00817
(0.0129) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
4p gain 47 (5%) 835 0.196
(0.249) 		0.42
(0.486) 		0.00029
(0.000575) 		1e-05
(2.35e-05) 		0.538
(0.602) 		0.00092
(0.00168) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		2e-05
(4.44e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
4q gain 46 (5%) 836 0.365
(0.428) 		0.649
(0.705) 		0.00043
(0.000823) 		1e-05
(2.35e-05) 		0.54
(0.603) 		0.0033
(0.0055) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		2e-05
(4.44e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
5q gain 253 (29%) 629 0.16
(0.206) 		0.207
(0.262) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.568
(0.63) 		3e-05
(6.56e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
14q gain 39 (4%) 843 0.758
(0.811) 		0.743
(0.797) 		0.00055
(0.00104) 		1e-05
(2.35e-05) 		0.744
(0.797) 		0.00257
(0.00438) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00095
(0.00172) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
3q loss 119 (13%) 763 0.139
(0.182) 		0.139
(0.182) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.888
(0.934) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		5e-05
(0.000107) 		0.00104
(0.00187)
4q loss 92 (10%) 790 0.502
(0.565) 		0.624
(0.68) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.152
(0.197) 		5e-05
(0.000107) 		2e-05
(4.44e-05) 		1e-05
(2.35e-05) 		0.0029
(0.0049) 		1e-05
(2.35e-05) 		0.00321
(0.00538) 		4e-05
(8.63e-05)
5p loss 24 (3%) 858 0.00017
(0.000346) 		1e-05
(2.35e-05) 		0.0433
(0.0623) 		0.0447
(0.0643) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.066
(0.0912) 		1e-05
(2.35e-05) 		0.00063
(0.00118) 		6e-05
(0.000128)
10p loss 133 (15%) 749 0.378
(0.44) 		0.358
(0.421) 		2e-05
(4.44e-05) 		1e-05
(2.35e-05) 		0.57
(0.632) 		6e-05
(0.000128) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00037
(0.000715) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
xq loss 113 (13%) 769 0.0619
(0.0865) 		0.0559
(0.0792) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.697
(0.75) 		3e-05
(6.56e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
1p gain 31 (4%) 851 0.87
(0.919) 		0.915
(0.956) 		2e-05
(4.44e-05) 		1e-05
(2.35e-05) 		0.00031
(0.000611) 		0.00075
(0.00138) 		0.00601
(0.00968) 		1e-05
(2.35e-05) 		0.266
(0.327) 		1e-05
(2.35e-05) 		0.0642
(0.0892) 		0.0102
(0.0158)
2q gain 127 (14%) 755 0.459
(0.525) 		0.327
(0.39) 		1e-05
(2.35e-05) 		0.00029
(0.000575) 		0.523
(0.587) 		0.00599
(0.00966) 		0.00326
(0.00545) 		1e-05
(2.35e-05) 		0.191
(0.243) 		0.00078
(0.00144) 		0.0201
(0.0304) 		0.00206
(0.00356)
8p gain 69 (8%) 813 0.365
(0.428) 		0.471
(0.536) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.222
(0.277) 		0.00037
(0.000715) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.201
(0.255) 		1e-05
(2.35e-05) 		0.00081
(0.00148) 		0.00056
(0.00106)
15q gain 52 (6%) 830 0.873
(0.921) 		0.556
(0.619) 		0.00044
(0.000841) 		1e-05
(2.35e-05) 		0.898
(0.941) 		0.0312
(0.0459) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.232
(0.288) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
19p gain 74 (8%) 808 0.196
(0.249) 		0.217
(0.272) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.177
(0.227) 		0.0022
(0.00378) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.5
(0.564) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
19q gain 78 (9%) 804 0.0653
(0.0903) 		0.0645
(0.0894) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0619
(0.0865) 		0.00037
(0.000715) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.195
(0.248) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
5q loss 23 (3%) 859 2e-05
(4.44e-05) 		1e-05
(2.35e-05) 		0.149
(0.194) 		0.0512
(0.0727) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0261
(0.0389) 		1e-05
(2.35e-05) 		0.00037
(0.000715) 		6e-05
(0.000128)
8p loss 161 (18%) 721 0.133
(0.174) 		0.276
(0.338) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.596
(0.654) 		0.128
(0.17) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
8q loss 83 (9%) 799 0.353
(0.417) 		0.504
(0.567) 		0.00069
(0.00128) 		2e-05
(4.44e-05) 		0.289
(0.353) 		0.876
(0.923) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00984
(0.0154) 		0.00013
(0.000267) 		0.00115
(0.00205) 		0.00092
(0.00168)
10q loss 157 (18%) 725 0.277
(0.339) 		0.238
(0.294) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.428
(0.495) 		0.0009
(0.00165) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.119
(0.158) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
11q loss 52 (6%) 830 0.177
(0.227) 		0.304
(0.366) 		2e-05
(4.44e-05) 		1e-05
(2.35e-05) 		0.577
(0.636) 		0.0024
(0.0041) 		0.00011
(0.000229) 		1e-05
(2.35e-05) 		0.12
(0.158) 		0.00016
(0.000326) 		2e-05
(4.44e-05) 		0.00033
(0.000648)
15q loss 68 (8%) 814 0.25
(0.308) 		0.269
(0.33) 		2e-05
(4.44e-05) 		1e-05
(2.35e-05) 		0.184
(0.235) 		0.00043
(0.000823) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0975
(0.131) 		0.00146
(0.00257) 		0.00391
(0.00643) 		0.0022
(0.00378)
16p loss 18 (2%) 864 0.539
(0.602) 		0.00378
(0.00623) 		0.225
(0.28) 		0.0094
(0.0147) 		0.00027
(0.00054) 		0.00062
(0.00116) 		0.034
(0.0499) 		0.00479
(0.00783) 		0.00014
(0.000286) 		0.00397
(0.00652)
2p gain 120 (14%) 762 0.46
(0.525) 		0.33
(0.392) 		1e-05
(2.35e-05) 		0.00106
(0.0019) 		0.484
(0.547) 		0.0174
(0.0265) 		0.00244
(0.00416) 		2e-05
(4.44e-05) 		0.0894
(0.121) 		0.00188
(0.00329) 		0.0517
(0.0735) 		0.00203
(0.00352)
9q gain 24 (3%) 858 0.0485
(0.0692) 		1e-05
(2.35e-05) 		0.771
(0.823) 		0.284
(0.347) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.318
(0.38) 		1e-05
(2.35e-05) 		0.0005
(0.00095) 		0.00013
(0.000267)
11p gain 58 (7%) 824 0.355
(0.418) 		0.812
(0.86) 		0.00119
(0.00211) 		2e-05
(4.44e-05) 		0.436
(0.501) 		0.0793
(0.108) 		3e-05
(6.56e-05) 		1e-05
(2.35e-05) 		0.21
(0.265) 		1e-05
(2.35e-05) 		0.00013
(0.000267) 		1e-05
(2.35e-05)
11q gain 55 (6%) 827 0.476
(0.539) 		0.914
(0.956) 		0.00238
(0.00407) 		1e-05
(2.35e-05) 		0.69
(0.745) 		0.548
(0.612) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.161
(0.208) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
18p gain 54 (6%) 828 0.574
(0.634) 		0.749
(0.802) 		0.435
(0.501) 		2e-05
(4.44e-05) 		0.788
(0.839) 		0.356
(0.419) 		3e-05
(6.56e-05) 		0.00018
(0.000364) 		0.0232
(0.0349) 		2e-05
(4.44e-05) 		0.00095
(0.00172) 		0.00099
(0.00179)
18q gain 50 (6%) 832 0.64
(0.696) 		0.774
(0.825) 		0.579
(0.638) 		1e-05
(2.35e-05) 		0.687
(0.743) 		0.291
(0.353) 		4e-05
(8.63e-05) 		1e-05
(2.35e-05) 		0.0452
(0.0648) 		1e-05
(2.35e-05) 		0.0003
(0.000593) 		3e-05
(6.56e-05)
22q gain 64 (7%) 818 0.37
(0.432) 		0.467
(0.533) 		0.00029
(0.000575) 		1e-05
(2.35e-05) 		0.894
(0.939) 		0.16
(0.206) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.929
(0.969) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
11p loss 42 (5%) 840 0.059
(0.0829) 		0.0713
(0.0982) 		0.00515
(0.00839) 		9e-05
(0.000189) 		0.572
(0.632) 		0.158
(0.205) 		0.00094
(0.00171) 		2e-05
(4.44e-05) 		0.113
(0.15) 		0.001
(0.0018) 		2e-05
(4.44e-05) 		0.00185
(0.00324)
16q loss 28 (3%) 854 0.0215
(0.0323) 		0.00046
(0.000877) 		0.151
(0.196) 		0.213
(0.267) 		0.00664
(0.0106) 		0.00059
(0.00111) 		0.0789
(0.108) 		0.00114
(0.00203) 		0.00111
(0.00199) 		0.00866
(0.0136)
19q loss 23 (3%) 859 0.00363
(0.006) 		0.00096
(0.00174) 		0.693
(0.748) 		0.309
(0.371) 		0.00215
(0.00371) 		0.00071
(0.00132) 		0.00465
(0.00761) 		0.0403
(0.0583) 		0.00145
(0.00256) 		0.0828
(0.112)
9p gain 26 (3%) 856 0.0579
(0.0816) 		0.0723
(0.0994) 		0.141
(0.183) 		1e-05
(2.35e-05) 		0.725
(0.779) 		0.556
(0.619) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.325
(0.387) 		1e-05
(2.35e-05) 		0.00066
(0.00123) 		0.00037
(0.000715)
19p loss 29 (3%) 853 0.00112
(0.002) 		0.00029
(0.000575) 		0.374
(0.436) 		0.0631
(0.0879) 		0.00059
(0.00111) 		0.00022
(0.000443) 		0.131
(0.172) 		0.0235
(0.0353) 		0.00081
(0.00148) 		0.112
(0.149)
20p loss 12 (1%) 870 0.936
(0.975) 		0.00714
(0.0114) 		0.204
(0.258) 		0.199
(0.252) 		0.00043
(0.000823) 		0.014
(0.0215) 		0.536
(0.601) 		0.00378
(0.00623) 		0.00598
(0.00966) 		0.0138
(0.0213)
20q loss 6 (1%) 876 0.584
(0.643) 		0.00497
(0.00811) 		0.249
(0.307) 		0.437
(0.503) 		0.00272
(0.00462) 		0.0145
(0.0222) 		1
(1.00) 		0.00585
(0.00947) 		0.00866
(0.0136) 		0.00581
(0.00942)
13q gain 52 (6%) 830 0.221
(0.275) 		0.297
(0.36) 		0.00331
(0.00551) 		0.0972
(0.131) 		0.346
(0.41) 		0.302
(0.364) 		0.0345
(0.0504) 		0.0179
(0.0273) 		0.0371
(0.0539) 		0.015
(0.023) 		0.298
(0.361) 		0.211
(0.266)
21q gain 72 (8%) 810 0.444
(0.51) 		0.453
(0.519) 		1e-05
(2.35e-05) 		0.0498
(0.071) 		0.301
(0.363) 		0.0203
(0.0307) 		0.00013
(0.000267) 		0.00132
(0.00234) 		0.0566
(0.08) 		0.132
(0.173) 		0.944
(0.981) 		0.954
(0.99)
6p gain 22 (2%) 860 0.397
(0.462) 		0.129
(0.171) 		0.0462
(0.0662) 		0.0906
(0.122) 		0.943
(0.981) 		0.0109
(0.017) 		0.433
(0.5) 		0.0741
(0.102) 		0.00189
(0.00329) 		0.0253
(0.0378)
10p gain 28 (3%) 854 0.195
(0.248) 		0.421
(0.488) 		0.0183
(0.0278) 		0.183
(0.234) 		0.225
(0.28) 		0.106
(0.143) 		0.00322
(0.00539) 		0.00574
(0.00932) 		0.47
(0.535) 		0.00812
(0.0129) 		0.219
(0.274) 		0.47
(0.535)
10q gain 22 (2%) 860 0.0391
(0.0565) 		0.118
(0.157) 		0.0583
(0.082) 		0.801
(0.85) 		0.317
(0.38) 		0.576
(0.636) 		0.058
(0.0816) 		0.0787
(0.108) 		0.759
(0.811) 		0.0592
(0.0829) 		0.884
(0.931) 		0.802
(0.851)
7p loss 4 (0%) 878 0.683
(0.74) 		0.13
(0.171) 		0.571
(0.632) 		0.041
(0.0592) 		0.214
(0.268) 		0.3
(0.363) 		0.279
(0.341) 		0.174
(0.224) 		0.0839
(0.114) 		0.373
(0.436)
7q loss 4 (0%) 878 0.685
(0.741) 		0.13
(0.171) 		0.571
(0.632) 		0.0418
(0.0602) 		0.217
(0.271) 		0.302
(0.364) 		0.276
(0.339) 		0.175
(0.224) 		0.084
(0.114) 		0.371
(0.434)
6q gain 16 (2%) 866 0.623
(0.68) 		0.401
(0.466) 		0.103
(0.138) 		0.312
(0.374) 		0.863
(0.912) 		0.159
(0.205) 		0.851
(0.9) 		0.309
(0.371) 		0.0725
(0.0997) 		0.45
(0.516)
12p loss 7 (1%) 875 0.895
(0.939) 		0.248
(0.306) 		0.342
(0.404) 		0.913
(0.956) 		0.954
(0.99) 		0.557
(0.619) 		0.797
(0.847) 		0.434
(0.501) 		0.0533
(0.0756) 		0.279
(0.341)
12q loss 4 (0%) 878 1
(1.00) 		0.471
(0.536) 		0.473
(0.537) 		0.333
(0.395) 		0.683
(0.74) 		0.221
(0.275) 		0.713
(0.767)
'1p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
1P GAIN MUTATED 5 1 25
1P GAIN WILD-TYPE 323 199 329

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S2.  Gene #1: '1p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
1P GAIN MUTATED 3 8 0 9 0
1P GAIN WILD-TYPE 99 115 171 61 186

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

'1p gain' versus 'RPPA_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.00061

Table S3.  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 1 12
1P GAIN WILD-TYPE 170 179 186 185

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

'1p gain' versus 'RPPA_CHIERARCHICAL'

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

Table S4.  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 1 8
1P GAIN WILD-TYPE 195 64 108 144 54 70 85

Figure S4.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'1p gain' versus 'MRNASEQ_CNMF'

P value = 0.00601 (Fisher's exact test), Q value = 0.0097

Table S5.  Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
1P GAIN MUTATED 4 15 5 6
1P GAIN WILD-TYPE 118 184 280 267

Figure S5.  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 = 2.4e-05

Table S6.  Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
1P GAIN MUTATED 1 5 1 4 11 5 3 0 0
1P GAIN WILD-TYPE 87 56 147 80 110 33 108 59 169

Figure S6.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S7.  Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
1P GAIN MUTATED 1 28 2 0
1P GAIN WILD-TYPE 75 319 231 208

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

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.016

Table S8.  Gene #1: '1p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
1P GAIN MUTATED 0 7 0 0 3 1 1
1P GAIN WILD-TYPE 91 76 49 20 43 76 45

Figure S8.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S9.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
1Q GAIN MUTATED 7 4 57
1Q GAIN WILD-TYPE 321 196 297

Figure S9.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S10.  Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
1Q GAIN MUTATED 2 15 6 16 3
1Q GAIN WILD-TYPE 100 108 165 54 183

Figure S10.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q gain' versus 'RPPA_CNMF'

P value = 0.00307 (Fisher's exact test), Q value = 0.0052

Table S11.  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 26
1Q GAIN WILD-TYPE 166 173 179 171

Figure S11.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'1q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0276 (Fisher's exact test), Q value = 0.041

Table S12.  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 11 1 10 12 9 3 12
1Q GAIN WILD-TYPE 186 63 106 135 50 68 81

Figure S12.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00042

Table S13.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
1Q GAIN MUTATED 4 30 18 14
1Q GAIN WILD-TYPE 118 169 267 259

Figure S13.  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 = 2.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
1Q GAIN MUTATED 0 8 11 11 20 7 6 3 0
1Q GAIN WILD-TYPE 88 53 137 73 101 31 105 56 169

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

'1q gain' versus 'MIRSEQ_CNMF'

P value = 0.0031 (Fisher's exact test), Q value = 0.0052

Table S15.  Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
1Q GAIN MUTATED 14 17 35
1Q GAIN WILD-TYPE 328 177 293

Figure S15.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S16.  Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
1Q GAIN MUTATED 0 52 13 1
1Q GAIN WILD-TYPE 76 295 220 207

Figure S16.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0342 (Fisher's exact test), Q value = 0.05

Table S17.  Gene #2: '1q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
1Q GAIN MUTATED 5 3 9 7
1Q GAIN WILD-TYPE 151 66 56 115

Figure S17.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S18.  Gene #2: '1q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
1Q GAIN MUTATED 2 17 0 0 3 2 0
1Q GAIN WILD-TYPE 89 66 49 20 43 75 46

Figure S18.  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 = 2.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
2P GAIN MUTATED 37 1 82
2P GAIN WILD-TYPE 291 199 272

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.0019

Table S20.  Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
2P GAIN MUTATED 4 14 23 18 27
2P GAIN WILD-TYPE 98 109 148 52 159

Figure S20.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0174 (Fisher's exact test), Q value = 0.026

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.00244 (Fisher's exact test), Q value = 0.0042

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
2P GAIN MUTATED 6 38 38 37
2P GAIN WILD-TYPE 116 161 247 236

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

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
2P GAIN MUTATED 1 12 18 7 30 4 18 2 27
2P GAIN WILD-TYPE 87 49 130 77 91 34 93 57 142

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

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00188 (Fisher's exact test), Q value = 0.0033

Table S24.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
2P GAIN MUTATED 1 51 37 31
2P GAIN WILD-TYPE 75 296 196 177

Figure S24.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00203 (Fisher's exact test), Q value = 0.0035

Table S25.  Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
2P GAIN MUTATED 15 17 3 0 11 8 1
2P GAIN WILD-TYPE 76 66 46 20 35 69 45

Figure S25.  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 = 2.4e-05

Table S26.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
2Q GAIN MUTATED 41 2 84
2Q GAIN WILD-TYPE 287 198 270

Figure S26.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.00058

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
2Q GAIN MUTATED 4 13 25 19 31
2Q GAIN WILD-TYPE 98 110 146 51 155

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

'2q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00599 (Fisher's exact test), Q value = 0.0097

Table S28.  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 S28.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.00326 (Fisher's exact test), Q value = 0.0054

Table S29.  Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
2Q GAIN MUTATED 6 37 42 42
2Q GAIN WILD-TYPE 116 162 243 231

Figure S29.  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 = 2.4e-05

Table S30.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
2Q GAIN MUTATED 1 12 18 8 29 5 21 2 31
2Q GAIN WILD-TYPE 87 49 130 76 92 33 90 57 138

Figure S30.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.0014

Table S31.  Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
2Q GAIN MUTATED 1 52 39 34
2Q GAIN WILD-TYPE 75 295 194 174

Figure S31.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.03

Table S32.  Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
2Q GAIN MUTATED 24 3 14 20
2Q GAIN WILD-TYPE 132 66 51 102

Figure S32.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00206 (Fisher's exact test), Q value = 0.0036

Table S33.  Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
2Q GAIN MUTATED 16 19 5 0 11 9 1
2Q GAIN WILD-TYPE 75 64 44 20 35 68 45

Figure S33.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p gain' versus 'MRNA_CNMF'

P value = 0.00157 (Fisher's exact test), Q value = 0.0028

Table S34.  Gene #5: '3p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 25 13 17
3P GAIN MUTATED 0 2 2 6
3P GAIN WILD-TYPE 31 23 11 11

Figure S34.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00749 (Fisher's exact test), Q value = 0.012

Table S35.  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 S35.  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 = 2.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
3P GAIN MUTATED 90 1 12
3P GAIN WILD-TYPE 238 199 342

Figure S36.  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 = 2.4e-05

Table S37.  Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
3P GAIN MUTATED 12 12 1 4 59
3P GAIN WILD-TYPE 90 111 170 66 127

Figure S37.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00702 (Fisher's exact test), Q value = 0.011

Table S38.  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 10 20 14 4 12 3
3P GAIN WILD-TYPE 180 54 96 133 55 59 90

Figure S38.  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 = 2.4e-05

Table S39.  Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
3P GAIN MUTATED 15 11 2 75
3P GAIN WILD-TYPE 107 188 283 198

Figure S39.  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 = 2.4e-05

Table S40.  Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
3P GAIN MUTATED 13 8 1 7 6 2 2 0 64
3P GAIN WILD-TYPE 75 53 147 77 115 36 109 59 105

Figure S40.  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 = 2.4e-05

Table S41.  Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
3P GAIN MUTATED 88 9 6
3P GAIN WILD-TYPE 254 185 322

Figure S41.  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 = 2.4e-05

Table S42.  Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
3P GAIN MUTATED 11 22 2 68
3P GAIN WILD-TYPE 65 325 231 140

Figure S42.  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 = 2.4e-05

Table S43.  Gene #5: '3p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
3P GAIN MUTATED 46 8 7 3
3P GAIN WILD-TYPE 110 61 58 119

Figure S43.  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 = 2.4e-05

Table S44.  Gene #5: '3p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
3P GAIN MUTATED 29 8 17 0 2 1 7
3P GAIN WILD-TYPE 62 75 32 20 44 76 39

Figure S44.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q gain' versus 'MRNA_CNMF'

P value = 0.0184 (Fisher's exact test), Q value = 0.028

Table S45.  Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 25 13 17
3Q GAIN MUTATED 1 6 2 6
3Q GAIN WILD-TYPE 30 19 11 11

Figure S45.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0475 (Fisher's exact test), Q value = 0.068

Table S46.  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 6 6 0 2
3Q GAIN WILD-TYPE 19 18 12 13 9

Figure S46.  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 = 2.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
3Q GAIN MUTATED 107 4 50
3Q GAIN WILD-TYPE 221 196 304

Figure S47.  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 = 2.4e-05

Table S48.  Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
3Q GAIN MUTATED 12 23 7 13 75
3Q GAIN WILD-TYPE 90 100 164 57 111

Figure S48.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00289 (Fisher's exact test), Q value = 0.0049

Table S49.  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 12 36 20 10 15 10
3Q GAIN WILD-TYPE 169 52 80 127 49 56 83

Figure S49.  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 = 2.4e-05

Table S50.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
3Q GAIN MUTATED 16 36 13 96
3Q GAIN WILD-TYPE 106 163 272 177

Figure S50.  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 = 2.4e-05

Table S51.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
3Q GAIN MUTATED 13 12 8 13 25 6 5 3 76
3Q GAIN WILD-TYPE 75 49 140 71 96 32 106 56 93

Figure S51.  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 = 2.4e-05

Table S52.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
3Q GAIN MUTATED 106 29 25
3Q GAIN WILD-TYPE 236 165 303

Figure S52.  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 = 2.4e-05

Table S53.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
3Q GAIN MUTATED 11 55 11 83
3Q GAIN WILD-TYPE 65 292 222 125

Figure S53.  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 = 2.4e-05

Table S54.  Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
3Q GAIN MUTATED 59 8 13 9
3Q GAIN WILD-TYPE 97 61 52 113

Figure S54.  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 = 2.4e-05

Table S55.  Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
3Q GAIN MUTATED 39 18 16 0 6 3 7
3Q GAIN WILD-TYPE 52 65 33 20 40 74 39

Figure S55.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.00058

Table S56.  Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
4P GAIN MUTATED 30 3 14
4P GAIN WILD-TYPE 298 197 340

Figure S56.  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 = 2.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
4P GAIN MUTATED 25 4 1 2 5
4P GAIN WILD-TYPE 77 119 170 68 181

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

'4p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00092 (Fisher's exact test), Q value = 0.0017

Table S58.  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 14 1 2 2 2
4P GAIN WILD-TYPE 184 59 102 146 57 69 91

Figure S58.  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 = 2.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
4P GAIN MUTATED 27 8 3 8
4P GAIN WILD-TYPE 95 191 282 265

Figure S59.  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 = 2.4e-05

Table S60.  Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
4P GAIN MUTATED 27 5 0 3 5 1 0 1 4
4P GAIN WILD-TYPE 61 56 148 81 116 37 111 58 165

Figure S60.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S61.  Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
4P GAIN MUTATED 35 5 7
4P GAIN WILD-TYPE 307 189 321

Figure S61.  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 = 2.4e-05

Table S62.  Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
4P GAIN MUTATED 27 11 3 6
4P GAIN WILD-TYPE 49 336 230 202

Figure S62.  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 = 2.4e-05

Table S63.  Gene #7: '4p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
4P GAIN MUTATED 5 21 3 2
4P GAIN WILD-TYPE 151 48 62 120

Figure S63.  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 = 2.4e-05

Table S64.  Gene #7: '4p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
4P GAIN MUTATED 4 2 1 1 2 1 20
4P GAIN WILD-TYPE 87 81 48 19 44 76 26

Figure S64.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.00082

Table S65.  Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
4Q GAIN MUTATED 29 3 14
4Q GAIN WILD-TYPE 299 197 340

Figure S65.  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 = 2.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
4Q GAIN MUTATED 25 3 2 2 5
4Q GAIN WILD-TYPE 77 120 169 68 181

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

'4q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0033 (Fisher's exact test), Q value = 0.0055

Table S67.  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 S67.  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 = 2.4e-05

Table S68.  Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
4Q GAIN MUTATED 27 7 4 7
4Q GAIN WILD-TYPE 95 192 281 266

Figure S68.  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 = 2.4e-05

Table S69.  Gene #8: '4q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
4Q GAIN MUTATED 27 4 0 2 5 1 1 1 4
4Q GAIN WILD-TYPE 61 57 148 82 116 37 110 58 165

Figure S69.  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 = 4.4e-05

Table S70.  Gene #8: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
4Q GAIN MUTATED 34 5 7
4Q GAIN WILD-TYPE 308 189 321

Figure S70.  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 = 2.4e-05

Table S71.  Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
4Q GAIN MUTATED 27 9 4 6
4Q GAIN WILD-TYPE 49 338 229 202

Figure S71.  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 = 2.4e-05

Table S72.  Gene #8: '4q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
4Q GAIN MUTATED 5 21 2 2
4Q GAIN WILD-TYPE 151 48 63 120

Figure S72.  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 = 2.4e-05

Table S73.  Gene #8: '4q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
4Q GAIN MUTATED 4 1 1 1 2 1 20
4Q GAIN WILD-TYPE 87 82 48 19 44 76 26

Figure S73.  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 = 2.4e-05

Table S74.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
5P GAIN MUTATED 40 26 172
5P GAIN WILD-TYPE 288 174 182

Figure S74.  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 = 2.4e-05

Table S75.  Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
5P GAIN MUTATED 13 44 58 26 14
5P GAIN WILD-TYPE 89 79 113 44 172

Figure S75.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p gain' versus 'RPPA_CNMF'

P value = 0.0344 (Fisher's exact test), Q value = 0.05

Table S76.  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 S76.  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 S77.  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 49 6 40 45 29 17 27
5P GAIN WILD-TYPE 148 58 76 102 30 54 66

Figure S77.  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 = 2.4e-05

Table S78.  Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
5P GAIN MUTATED 18 86 101 31
5P GAIN WILD-TYPE 104 113 184 242

Figure S78.  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 = 2.4e-05

Table S79.  Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
5P GAIN MUTATED 11 14 57 16 59 16 31 20 12
5P GAIN WILD-TYPE 77 47 91 68 62 22 80 39 157

Figure S79.  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 = 2.4e-05

Table S80.  Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
5P GAIN MUTATED 42 59 133
5P GAIN WILD-TYPE 300 135 195

Figure S80.  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 = 2.4e-05

Table S81.  Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
5P GAIN MUTATED 9 124 82 19
5P GAIN WILD-TYPE 67 223 151 189

Figure S81.  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 = 2.4e-05

Table S82.  Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
5P GAIN MUTATED 17 9 17 51
5P GAIN WILD-TYPE 139 60 48 71

Figure S82.  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 = 2.4e-05

Table S83.  Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
5P GAIN MUTATED 13 19 2 1 19 34 6
5P GAIN WILD-TYPE 78 64 47 19 27 43 40

Figure S83.  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 = 2.4e-05

Table S84.  Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
5Q GAIN MUTATED 36 42 175
5Q GAIN WILD-TYPE 292 158 179

Figure S84.  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 = 2.4e-05

Table S85.  Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
5Q GAIN MUTATED 12 45 68 28 13
5Q GAIN WILD-TYPE 90 78 103 42 173

Figure S85.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q gain' versus 'RPPA_CHIERARCHICAL'

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

Table S86.  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 56 30 18 30
5Q GAIN WILD-TYPE 147 58 78 91 29 53 63

Figure S86.  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 = 2.4e-05

Table S87.  Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
5Q GAIN MUTATED 16 87 117 31
5Q GAIN WILD-TYPE 106 112 168 242

Figure S87.  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 = 2.4e-05

Table S88.  Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
5Q GAIN MUTATED 11 11 64 16 61 16 37 25 10
5Q GAIN WILD-TYPE 77 50 84 68 60 22 74 34 159

Figure S88.  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 = 2.4e-05

Table S89.  Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
5Q GAIN MUTATED 40 62 145
5Q GAIN WILD-TYPE 302 132 183

Figure S89.  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 = 2.4e-05

Table S90.  Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
5Q GAIN MUTATED 9 125 94 19
5Q GAIN WILD-TYPE 67 222 139 189

Figure S90.  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 = 2.4e-05

Table S91.  Gene #10: '5q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
5Q GAIN MUTATED 17 8 13 52
5Q GAIN WILD-TYPE 139 61 52 70

Figure S91.  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 = 2.4e-05

Table S92.  Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
5Q GAIN MUTATED 13 15 2 0 18 36 6
5Q GAIN WILD-TYPE 78 68 47 20 28 41 40

Figure S92.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p gain' versus 'RPPA_CNMF'

P value = 0.0462 (Fisher's exact test), Q value = 0.066

Table S93.  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 4
6P GAIN WILD-TYPE 175 180 178 193

Figure S93.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.017

Table S94.  Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
6P GAIN MUTATED 1 3 3 8 2 0 2 2 1
6P GAIN WILD-TYPE 87 58 145 76 119 38 109 57 168

Figure S94.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00189 (Fisher's exact test), Q value = 0.0033

Table S95.  Gene #11: '6p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
6P GAIN MUTATED 2 3 7 1
6P GAIN WILD-TYPE 154 66 58 121

Figure S95.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0253 (Fisher's exact test), Q value = 0.038

Table S96.  Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
6P GAIN MUTATED 2 5 0 3 2 1 0
6P GAIN WILD-TYPE 89 78 49 17 44 76 46

Figure S96.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S97.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
7P GAIN MUTATED 202 20 147
7P GAIN WILD-TYPE 126 180 207

Figure S97.  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 = 2.4e-05

Table S98.  Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
7P GAIN MUTATED 29 41 38 31 134
7P GAIN WILD-TYPE 73 82 133 39 52

Figure S98.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.016

Table S99.  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 75 100
7P GAIN WILD-TYPE 120 108 112 97

Figure S99.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00194 (Fisher's exact test), Q value = 0.0034

Table S100.  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 46 29 35 27
7P GAIN WILD-TYPE 104 40 60 101 30 36 66

Figure S100.  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 = 2.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
7P GAIN MUTATED 37 88 71 171
7P GAIN WILD-TYPE 85 111 214 102

Figure S101.  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 = 2.4e-05

Table S102.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
7P GAIN MUTATED 30 19 46 22 54 12 26 16 142
7P GAIN WILD-TYPE 58 42 102 62 67 26 85 43 27

Figure S102.  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 = 2.4e-05

Table S103.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
7P GAIN MUTATED 192 67 107
7P GAIN WILD-TYPE 150 127 221

Figure S103.  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 = 2.4e-05

Table S104.  Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
7P GAIN MUTATED 29 119 68 150
7P GAIN WILD-TYPE 47 228 165 58

Figure S104.  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 = 2.4e-05

Table S105.  Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
7P GAIN MUTATED 109 23 25 40
7P GAIN WILD-TYPE 47 46 40 82

Figure S105.  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 = 2.4e-05

Table S106.  Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
7P GAIN MUTATED 60 36 42 1 13 25 20
7P GAIN WILD-TYPE 31 47 7 19 33 52 26

Figure S106.  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 = 2.4e-05

Table S107.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
7Q GAIN MUTATED 202 19 150
7Q GAIN WILD-TYPE 126 181 204

Figure S107.  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 = 2.4e-05

Table S108.  Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
7Q GAIN MUTATED 29 43 40 32 134
7Q GAIN WILD-TYPE 73 80 131 38 52

Figure S108.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.022

Table S109.  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 73 76 100
7Q GAIN WILD-TYPE 119 108 111 97

Figure S109.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00117 (Fisher's exact test), Q value = 0.0021

Table S110.  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 96 24 56 43 29 34 30
7Q GAIN WILD-TYPE 101 40 60 104 30 37 63

Figure S110.  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 = 2.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
7Q GAIN MUTATED 37 89 72 171
7Q GAIN WILD-TYPE 85 110 213 102

Figure S111.  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 = 2.4e-05

Table S112.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
7Q GAIN MUTATED 30 19 46 22 55 14 26 15 142
7Q GAIN WILD-TYPE 58 42 102 62 66 24 85 44 27

Figure S112.  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 = 2.4e-05

Table S113.  Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
7Q GAIN MUTATED 192 70 106
7Q GAIN WILD-TYPE 150 124 222

Figure S113.  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 = 2.4e-05

Table S114.  Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
7Q GAIN MUTATED 29 123 66 150
7Q GAIN WILD-TYPE 47 224 167 58

Figure S114.  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 = 2.4e-05

Table S115.  Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
7Q GAIN MUTATED 109 23 25 39
7Q GAIN WILD-TYPE 47 46 40 83

Figure S115.  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 = 2.4e-05

Table S116.  Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
7Q GAIN MUTATED 60 36 42 1 13 24 20
7Q GAIN WILD-TYPE 31 47 7 19 33 53 26

Figure S116.  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 = 2.4e-05

Table S117.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
8P GAIN MUTATED 33 0 36
8P GAIN WILD-TYPE 295 200 318

Figure S117.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S118.  Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
8P GAIN MUTATED 17 13 3 16 9
8P GAIN WILD-TYPE 85 110 168 54 177

Figure S118.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.00072

Table S119.  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 17 7 17 5 11 5 2
8P GAIN WILD-TYPE 180 57 99 142 48 66 91

Figure S119.  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 = 2.4e-05

Table S120.  Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
8P GAIN MUTATED 19 28 5 17
8P GAIN WILD-TYPE 103 171 280 256

Figure S120.  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 = 2.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
8P GAIN MUTATED 16 6 4 10 20 2 0 3 8
8P GAIN WILD-TYPE 72 55 144 74 101 36 111 56 161

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

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S122.  Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
8P GAIN MUTATED 16 40 4 9
8P GAIN WILD-TYPE 60 307 229 199

Figure S122.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0015

Table S123.  Gene #15: '8p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
8P GAIN MUTATED 10 14 11 6
8P GAIN WILD-TYPE 146 55 54 116

Figure S123.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0011

Table S124.  Gene #15: '8p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
8P GAIN MUTATED 6 13 2 0 3 4 13
8P GAIN WILD-TYPE 85 70 47 20 43 73 33

Figure S124.  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 = 2.4e-05

Table S125.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
8Q GAIN MUTATED 37 2 64
8Q GAIN WILD-TYPE 291 198 290

Figure S125.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S126.  Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
8Q GAIN MUTATED 20 24 5 21 11
8Q GAIN WILD-TYPE 82 99 166 49 175

Figure S126.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 0.00605 (Fisher's exact test), Q value = 0.0097

Table S127.  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 27 15 17 37
8Q GAIN WILD-TYPE 155 166 170 160

Figure S127.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00038

Table S128.  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 10 16 7 7
8Q GAIN WILD-TYPE 174 57 90 137 43 64 86

Figure S128.  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 = 2.4e-05

Table S129.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
8Q GAIN MUTATED 22 51 8 21
8Q GAIN WILD-TYPE 100 148 277 252

Figure S129.  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 = 2.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
8Q GAIN MUTATED 17 10 7 12 40 4 0 4 8
8Q GAIN WILD-TYPE 71 51 141 72 81 34 111 55 161

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

'8q gain' versus 'MIRSEQ_CNMF'

P value = 0.0255 (Fisher's exact test), Q value = 0.038

Table S131.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
8Q GAIN MUTATED 35 34 33
8Q GAIN WILD-TYPE 307 160 295

Figure S131.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S132.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
8Q GAIN MUTATED 17 67 8 10
8Q GAIN WILD-TYPE 59 280 225 198

Figure S132.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0014 (Fisher's exact test), Q value = 0.0025

Table S133.  Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
8Q GAIN MUTATED 11 16 14 13
8Q GAIN WILD-TYPE 145 53 51 109

Figure S133.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.6e-05

Table S134.  Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
8Q GAIN MUTATED 7 20 2 0 5 6 14
8Q GAIN WILD-TYPE 84 63 47 20 41 71 32

Figure S134.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
9P GAIN MUTATED 12 2 3 2 0
9P GAIN WILD-TYPE 90 121 168 68 186

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 = 2.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
9P GAIN MUTATED 14 2 9 1
9P GAIN WILD-TYPE 108 197 276 272

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 = 2.4e-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 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
9P GAIN MUTATED 12 4 3 1 0 2 4 0 0
9P GAIN WILD-TYPE 76 57 145 83 121 36 107 59 169

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 = 2.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
9P GAIN MUTATED 12 8 6 0
9P GAIN WILD-TYPE 64 339 227 208

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

'9p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0012

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
9P GAIN MUTATED 1 8 4 3
9P GAIN WILD-TYPE 155 61 61 119

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 = 0.00037 (Fisher's exact test), Q value = 0.00072

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
9P GAIN MUTATED 0 3 0 0 2 3 8
9P GAIN WILD-TYPE 91 80 49 20 44 74 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 = 0.0485 (Fisher's exact test), Q value = 0.069

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
9Q GAIN MUTATED 15 3 6
9Q GAIN WILD-TYPE 313 197 348

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

'9q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
9Q GAIN MUTATED 12 4 2 2 0
9Q GAIN WILD-TYPE 90 119 169 68 186

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 = 2.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
9Q GAIN MUTATED 13 4 6 1
9Q GAIN WILD-TYPE 109 195 279 272

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 = 2.4e-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 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
9Q GAIN MUTATED 12 4 1 1 1 2 3 0 0
9Q GAIN WILD-TYPE 76 57 147 83 120 36 108 59 169

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 = 2.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
9Q GAIN MUTATED 12 9 3 0
9Q GAIN WILD-TYPE 64 338 230 208

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

'9q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.00095

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
9Q GAIN MUTATED 1 8 3 2
9Q GAIN WILD-TYPE 155 61 62 120

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 = 0.00013 (Fisher's exact test), Q value = 0.00027

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
9Q GAIN MUTATED 0 2 0 0 2 2 8
9Q GAIN WILD-TYPE 91 81 49 20 44 75 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 = 0.0183 (Fisher's exact test), Q value = 0.028

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
10P GAIN MUTATED 11 1 16
10P GAIN WILD-TYPE 317 199 338

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

'10p gain' versus 'MRNASEQ_CNMF'

P value = 0.00322 (Fisher's exact test), Q value = 0.0054

Table S149.  Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
10P GAIN MUTATED 6 13 3 6
10P GAIN WILD-TYPE 116 186 282 267

Figure S149.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00574 (Fisher's exact test), Q value = 0.0093

Table S150.  Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
10P GAIN MUTATED 4 5 2 2 9 2 0 1 3
10P GAIN WILD-TYPE 84 56 146 82 112 36 111 58 166

Figure S150.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00812 (Fisher's exact test), Q value = 0.013

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
10P GAIN MUTATED 3 19 2 4
10P GAIN WILD-TYPE 73 328 231 204

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

'10q gain' versus 'MRNA_CNMF'

P value = 0.0391 (Fisher's exact test), Q value = 0.057

Table S152.  Gene #20: '10q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 25 13 17
10Q GAIN MUTATED 0 0 1 2
10Q GAIN WILD-TYPE 31 25 12 15

Figure S152.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 0.00119 (Fisher's exact test), Q value = 0.0021

Table S153.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
11P GAIN MUTATED 26 3 29
11P GAIN WILD-TYPE 302 197 325

Figure S153.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S154.  Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
11P GAIN MUTATED 19 6 7 7 4
11P GAIN WILD-TYPE 83 117 164 63 182

Figure S154.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CNMF'

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

Table S155.  Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
11P GAIN MUTATED 22 15 13 8
11P GAIN WILD-TYPE 100 184 272 265

Figure S155.  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 = 2.4e-05

Table S156.  Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
11P GAIN MUTATED 19 6 7 5 11 3 4 2 1
11P GAIN WILD-TYPE 69 55 141 79 110 35 107 57 168

Figure S156.  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 = 2.4e-05

Table S157.  Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
11P GAIN MUTATED 18 24 9 7
11P GAIN WILD-TYPE 58 323 224 201

Figure S157.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00027

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
11P GAIN MUTATED 5 14 4 4
11P GAIN WILD-TYPE 151 55 61 118

Figure S158.  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 = 2.4e-05

Table S159.  Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
11P GAIN MUTATED 3 6 0 0 2 2 14
11P GAIN WILD-TYPE 88 77 49 20 44 75 32

Figure S159.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 0.00238 (Fisher's exact test), Q value = 0.0041

Table S160.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
11Q GAIN MUTATED 24 3 28
11Q GAIN WILD-TYPE 304 197 326

Figure S160.  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 = 2.4e-05

Table S161.  Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
11Q GAIN MUTATED 20 2 7 6 5
11Q GAIN WILD-TYPE 82 121 164 64 181

Figure S161.  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 = 2.4e-05

Table S162.  Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
11Q GAIN MUTATED 22 12 14 7
11Q GAIN WILD-TYPE 100 187 271 266

Figure S162.  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 = 2.4e-05

Table S163.  Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
11Q GAIN MUTATED 20 4 8 5 8 3 4 2 1
11Q GAIN WILD-TYPE 68 57 140 79 113 35 107 57 168

Figure S163.  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 = 2.4e-05

Table S164.  Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
11Q GAIN MUTATED 19 21 10 5
11Q GAIN WILD-TYPE 57 326 223 203

Figure S164.  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 = 2.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
11Q GAIN MUTATED 4 15 3 4
11Q GAIN WILD-TYPE 152 54 62 118

Figure S165.  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 = 2.4e-05

Table S166.  Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
11Q GAIN MUTATED 3 5 0 0 1 2 15
11Q GAIN WILD-TYPE 88 78 49 20 45 75 31

Figure S166.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'MRNA_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.046

Table S167.  Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 25 13 17
12P GAIN MUTATED 3 10 2 6
12P GAIN WILD-TYPE 28 15 11 11

Figure S167.  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 = 2.4e-05

Table S168.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
12P GAIN MUTATED 131 10 111
12P GAIN WILD-TYPE 197 190 243

Figure S168.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S169.  Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
12P GAIN MUTATED 25 41 25 30 80
12P GAIN WILD-TYPE 77 82 146 40 106

Figure S169.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'RPPA_CNMF'

P value = 0.0292 (Fisher's exact test), Q value = 0.043

Table S170.  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 S170.  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 = 2.4e-05

Table S171.  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 S171.  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 = 2.4e-05

Table S172.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
12P GAIN MUTATED 29 75 36 111
12P GAIN WILD-TYPE 93 124 249 162

Figure S172.  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 = 2.4e-05

Table S173.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
12P GAIN MUTATED 24 20 22 19 54 11 10 9 82
12P GAIN WILD-TYPE 64 41 126 65 67 27 101 50 87

Figure S173.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.6e-05

Table S174.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
12P GAIN MUTATED 129 49 72
12P GAIN WILD-TYPE 213 145 256

Figure S174.  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 = 2.4e-05

Table S175.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
12P GAIN MUTATED 22 110 30 88
12P GAIN WILD-TYPE 54 237 203 120

Figure S175.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S176.  Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
12P GAIN MUTATED 67 19 20 23
12P GAIN WILD-TYPE 89 50 45 99

Figure S176.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
12P GAIN MUTATED 44 33 15 0 9 12 16
12P GAIN WILD-TYPE 47 50 34 20 37 65 30

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

'12q gain' versus 'MRNA_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.045

Table S178.  Gene #24: '12q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 25 13 17
12Q GAIN MUTATED 3 10 2 6
12Q GAIN WILD-TYPE 28 15 11 11

Figure S178.  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 = 2.4e-05

Table S179.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
12Q GAIN MUTATED 134 10 112
12Q GAIN WILD-TYPE 194 190 242

Figure S179.  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 = 2.4e-05

Table S180.  Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
12Q GAIN MUTATED 27 42 25 30 80
12Q GAIN WILD-TYPE 75 81 146 40 106

Figure S180.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'RPPA_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.018

Table S181.  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 S181.  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 = 2.4e-05

Table S182.  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 S182.  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 = 2.4e-05

Table S183.  Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
12Q GAIN MUTATED 31 77 36 111
12Q GAIN WILD-TYPE 91 122 249 162

Figure S183.  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 = 2.4e-05

Table S184.  Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
12Q GAIN MUTATED 26 21 22 19 55 11 10 9 82
12Q GAIN WILD-TYPE 62 40 126 65 66 27 101 50 87

Figure S184.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S185.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
12Q GAIN MUTATED 131 50 73
12Q GAIN WILD-TYPE 211 144 255

Figure S185.  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 = 2.4e-05

Table S186.  Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
12Q GAIN MUTATED 24 112 30 88
12Q GAIN WILD-TYPE 52 235 203 120

Figure S186.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.00059

Table S187.  Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
12Q GAIN MUTATED 67 21 21 23
12Q GAIN WILD-TYPE 89 48 44 99

Figure S187.  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 = 2.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
12Q GAIN MUTATED 44 34 15 0 9 12 18
12Q GAIN WILD-TYPE 47 49 34 20 37 65 28

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

'13q gain' versus 'CN_CNMF'

P value = 0.00331 (Fisher's exact test), Q value = 0.0055

Table S189.  Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
13Q GAIN MUTATED 29 4 19
13Q GAIN WILD-TYPE 299 196 335

Figure S189.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 0.0345 (Fisher's exact test), Q value = 0.05

Table S190.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
13Q GAIN MUTATED 6 9 11 26
13Q GAIN WILD-TYPE 116 190 274 247

Figure S190.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0179 (Fisher's exact test), Q value = 0.027

Table S191.  Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
13Q GAIN MUTATED 3 3 11 6 7 0 3 0 19
13Q GAIN WILD-TYPE 85 58 137 78 114 38 108 59 150

Figure S191.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 0.0371 (Fisher's exact test), Q value = 0.054

Table S192.  Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
13Q GAIN MUTATED 29 9 13
13Q GAIN WILD-TYPE 313 185 315

Figure S192.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 0.023

Table S193.  Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
13Q GAIN MUTATED 2 18 9 22
13Q GAIN WILD-TYPE 74 329 224 186

Figure S193.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.001

Table S194.  Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
14Q GAIN MUTATED 25 2 12
14Q GAIN WILD-TYPE 303 198 342

Figure S194.  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 = 2.4e-05

Table S195.  Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
14Q GAIN MUTATED 25 7 0 1 0
14Q GAIN WILD-TYPE 77 116 171 69 186

Figure S195.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00257 (Fisher's exact test), Q value = 0.0044

Table S196.  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 S196.  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 = 2.4e-05

Table S197.  Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
14Q GAIN MUTATED 27 8 3 1
14Q GAIN WILD-TYPE 95 191 282 272

Figure S197.  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 = 2.4e-05

Table S198.  Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
14Q GAIN MUTATED 25 5 2 1 4 0 1 1 0
14Q GAIN WILD-TYPE 63 56 146 83 117 38 110 58 169

Figure S198.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0017

Table S199.  Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
14Q GAIN MUTATED 26 3 9
14Q GAIN WILD-TYPE 316 191 319

Figure S199.  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 = 2.4e-05

Table S200.  Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
14Q GAIN MUTATED 24 12 2 0
14Q GAIN WILD-TYPE 52 335 231 208

Figure S200.  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 = 2.4e-05

Table S201.  Gene #26: '14q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
14Q GAIN MUTATED 0 18 3 0
14Q GAIN WILD-TYPE 156 51 62 122

Figure S201.  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 = 2.4e-05

Table S202.  Gene #26: '14q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
14Q GAIN MUTATED 0 3 0 0 1 0 17
14Q GAIN WILD-TYPE 91 80 49 20 45 77 29

Figure S202.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.00084

Table S203.  Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
15Q GAIN MUTATED 27 2 23
15Q GAIN WILD-TYPE 301 198 331

Figure S203.  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 = 2.4e-05

Table S204.  Gene #27: '15q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
15Q GAIN MUTATED 23 1 7 5 3
15Q GAIN WILD-TYPE 79 122 164 65 183

Figure S204.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0312 (Fisher's exact test), Q value = 0.046

Table S205.  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 S205.  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 = 2.4e-05

Table S206.  Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
15Q GAIN MUTATED 25 10 12 4
15Q GAIN WILD-TYPE 97 189 273 269

Figure S206.  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 = 2.4e-05

Table S207.  Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
15Q GAIN MUTATED 24 2 8 3 4 4 2 3 1
15Q GAIN WILD-TYPE 64 59 140 81 117 34 109 56 168

Figure S207.  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 = 2.4e-05

Table S208.  Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
15Q GAIN MUTATED 24 16 9 2
15Q GAIN WILD-TYPE 52 331 224 206

Figure S208.  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 = 2.4e-05

Table S209.  Gene #27: '15q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
15Q GAIN MUTATED 0 17 1 5
15Q GAIN WILD-TYPE 156 52 64 117

Figure S209.  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 = 2.4e-05

Table S210.  Gene #27: '15q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
15Q GAIN MUTATED 0 1 0 0 0 5 17
15Q GAIN WILD-TYPE 91 82 49 20 46 72 29

Figure S210.  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 = 2.4e-05

Table S211.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
16P GAIN MUTATED 172 11 98
16P GAIN WILD-TYPE 156 189 256

Figure S211.  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 = 2.4e-05

Table S212.  Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
16P GAIN MUTATED 27 28 26 27 119
16P GAIN WILD-TYPE 75 95 145 43 67

Figure S212.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p gain' versus 'RPPA_CNMF'

P value = 0.00518 (Fisher's exact test), Q value = 0.0084

Table S213.  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 S213.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'16p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.00093

Table S214.  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 S214.  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 = 2.4e-05

Table S215.  Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
16P GAIN MUTATED 33 49 45 154
16P GAIN WILD-TYPE 89 150 240 119

Figure S215.  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 = 2.4e-05

Table S216.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
16P GAIN MUTATED 27 11 24 38 35 6 17 11 112
16P GAIN WILD-TYPE 61 50 124 46 86 32 94 48 57

Figure S216.  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 = 2.4e-05

Table S217.  Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
16P GAIN MUTATED 178 35 67
16P GAIN WILD-TYPE 164 159 261

Figure S217.  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 = 2.4e-05

Table S218.  Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
16P GAIN MUTATED 24 89 36 131
16P GAIN WILD-TYPE 52 258 197 77

Figure S218.  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 = 2.4e-05

Table S219.  Gene #28: '16p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
16P GAIN MUTATED 96 20 20 25
16P GAIN WILD-TYPE 60 49 45 97

Figure S219.  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 = 2.4e-05

Table S220.  Gene #28: '16p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
16P GAIN MUTATED 64 29 26 0 9 15 18
16P GAIN WILD-TYPE 27 54 23 20 37 62 28

Figure S220.  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 = 2.4e-05

Table S221.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
16Q GAIN MUTATED 170 11 87
16Q GAIN WILD-TYPE 158 189 267

Figure S221.  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 = 2.4e-05

Table S222.  Gene #29: '16q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
16Q GAIN MUTATED 27 27 23 22 119
16Q GAIN WILD-TYPE 75 96 148 48 67

Figure S222.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q gain' versus 'RPPA_CNMF'

P value = 0.00285 (Fisher's exact test), Q value = 0.0048

Table S223.  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 S223.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'16q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.00072

Table S224.  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 S224.  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 = 2.4e-05

Table S225.  Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
16Q GAIN MUTATED 31 48 41 148
16Q GAIN WILD-TYPE 91 151 244 125

Figure S225.  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 = 2.4e-05

Table S226.  Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
16Q GAIN MUTATED 26 11 19 33 34 6 17 11 111
16Q GAIN WILD-TYPE 62 50 129 51 87 32 94 48 58

Figure S226.  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 = 2.4e-05

Table S227.  Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
16Q GAIN MUTATED 173 34 60
16Q GAIN WILD-TYPE 169 160 268

Figure S227.  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 = 2.4e-05

Table S228.  Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
16Q GAIN MUTATED 24 78 34 131
16Q GAIN WILD-TYPE 52 269 199 77

Figure S228.  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 = 2.4e-05

Table S229.  Gene #29: '16q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
16Q GAIN MUTATED 94 20 17 22
16Q GAIN WILD-TYPE 62 49 48 100

Figure S229.  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 = 2.4e-05

Table S230.  Gene #29: '16q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
16Q GAIN MUTATED 64 25 25 0 8 13 18
16Q GAIN WILD-TYPE 27 58 24 20 38 64 28

Figure S230.  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 = 2.4e-05

Table S231.  Gene #30: '17p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 25 13 17
17P GAIN MUTATED 1 0 2 11
17P GAIN WILD-TYPE 30 25 11 6

Figure S231.  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 = 2.4e-05

Table S232.  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 S232.  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 = 2.4e-05

Table S233.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
17P GAIN MUTATED 172 1 23
17P GAIN WILD-TYPE 156 199 331

Figure S233.  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 = 2.4e-05

Table S234.  Gene #30: '17p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
17P GAIN MUTATED 5 18 7 8 140
17P GAIN WILD-TYPE 97 105 164 62 46

Figure S234.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p gain' versus 'RPPA_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.045

Table S235.  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 25 44 44 35
17P GAIN WILD-TYPE 157 137 143 162

Figure S235.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'17p gain' versus 'RPPA_CHIERARCHICAL'

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

Table S236.  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 9
17P GAIN WILD-TYPE 147 48 95 124 53 48 84

Figure S236.  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 = 2.4e-05

Table S237.  Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
17P GAIN MUTATED 6 12 9 169
17P GAIN WILD-TYPE 116 187 276 104

Figure S237.  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 = 2.4e-05

Table S238.  Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
17P GAIN MUTATED 1 12 6 19 6 3 1 1 147
17P GAIN WILD-TYPE 87 49 142 65 115 35 110 58 22

Figure S238.  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 = 2.4e-05

Table S239.  Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
17P GAIN MUTATED 168 15 12
17P GAIN WILD-TYPE 174 179 316

Figure S239.  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 = 2.4e-05

Table S240.  Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
17P GAIN MUTATED 0 36 7 152
17P GAIN WILD-TYPE 76 311 226 56

Figure S240.  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 = 2.4e-05

Table S241.  Gene #30: '17p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
17P GAIN MUTATED 109 5 14 3
17P GAIN WILD-TYPE 47 64 51 119

Figure S241.  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 = 2.4e-05

Table S242.  Gene #30: '17p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
17P GAIN MUTATED 62 20 44 2 2 1 0
17P GAIN WILD-TYPE 29 63 5 18 44 76 46

Figure S242.  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 = 2.4e-05

Table S243.  Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 25 13 17
17Q GAIN MUTATED 1 1 2 12
17Q GAIN WILD-TYPE 30 24 11 5

Figure S243.  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 = 2.4e-05

Table S244.  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 S244.  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 = 2.4e-05

Table S245.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
17Q GAIN MUTATED 184 3 35
17Q GAIN WILD-TYPE 144 197 319

Figure S245.  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 = 2.4e-05

Table S246.  Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
17Q GAIN MUTATED 7 24 8 16 144
17Q GAIN WILD-TYPE 95 99 163 54 42

Figure S246.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00338 (Fisher's exact test), Q value = 0.0056

Table S247.  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 51 20 24 25 7 26 16
17Q GAIN WILD-TYPE 146 44 92 122 52 45 77

Figure S247.  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 = 2.4e-05

Table S248.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
17Q GAIN MUTATED 8 18 10 186
17Q GAIN WILD-TYPE 114 181 275 87

Figure S248.  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 = 2.4e-05

Table S249.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
17Q GAIN MUTATED 1 16 7 32 10 4 1 2 149
17Q GAIN WILD-TYPE 87 45 141 52 111 34 110 57 20

Figure S249.  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 = 2.4e-05

Table S250.  Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
17Q GAIN MUTATED 180 28 13
17Q GAIN WILD-TYPE 162 166 315

Figure S250.  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 = 2.4e-05

Table S251.  Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
17Q GAIN MUTATED 0 53 8 160
17Q GAIN WILD-TYPE 76 294 225 48

Figure S251.  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 = 2.4e-05

Table S252.  Gene #31: '17q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
17Q GAIN MUTATED 117 5 24 3
17Q GAIN WILD-TYPE 39 64 41 119

Figure S252.  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 = 2.4e-05

Table S253.  Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
17Q GAIN MUTATED 66 32 45 2 3 1 0
17Q GAIN WILD-TYPE 25 51 4 18 43 76 46

Figure S253.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S254.  Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
18P GAIN MUTATED 19 0 11 2 8
18P GAIN WILD-TYPE 83 123 160 68 178

Figure S254.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

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

Table S255.  Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
18P GAIN MUTATED 21 8 14 11
18P GAIN WILD-TYPE 101 191 271 262

Figure S255.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00036

Table S256.  Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
18P GAIN MUTATED 18 4 6 2 3 1 8 4 8
18P GAIN WILD-TYPE 70 57 142 82 118 37 103 55 161

Figure S256.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 0.0232 (Fisher's exact test), Q value = 0.035

Table S257.  Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
18P GAIN MUTATED 30 6 17
18P GAIN WILD-TYPE 312 188 311

Figure S257.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S258.  Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
18P GAIN MUTATED 17 16 12 8
18P GAIN WILD-TYPE 59 331 221 200

Figure S258.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0017

Table S259.  Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
18P GAIN MUTATED 8 15 3 8
18P GAIN WILD-TYPE 148 54 62 114

Figure S259.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S260.  Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
18P GAIN MUTATED 5 4 3 1 1 7 13
18P GAIN WILD-TYPE 86 79 46 19 45 70 33

Figure S260.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S261.  Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
18Q GAIN MUTATED 18 0 11 2 7
18Q GAIN WILD-TYPE 84 123 160 68 179

Figure S261.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.6e-05

Table S262.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
18Q GAIN MUTATED 20 8 14 8
18Q GAIN WILD-TYPE 102 191 271 265

Figure S262.  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 = 2.4e-05

Table S263.  Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
18Q GAIN MUTATED 18 3 5 0 4 1 8 4 7
18Q GAIN WILD-TYPE 70 58 143 84 117 37 103 55 162

Figure S263.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 0.0452 (Fisher's exact test), Q value = 0.065

Table S264.  Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
18Q GAIN MUTATED 26 5 18
18Q GAIN WILD-TYPE 316 189 310

Figure S264.  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 = 2.4e-05

Table S265.  Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
18Q GAIN MUTATED 17 13 12 7
18Q GAIN WILD-TYPE 59 334 221 201

Figure S265.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.00059

Table S266.  Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
18Q GAIN MUTATED 7 14 1 8
18Q GAIN WILD-TYPE 149 55 64 114

Figure S266.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S267.  Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
18Q GAIN MUTATED 5 1 2 1 1 7 13
18Q GAIN WILD-TYPE 86 82 47 19 45 70 33

Figure S267.  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 = 2.4e-05

Table S268.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
19P GAIN MUTATED 25 3 46
19P GAIN WILD-TYPE 303 197 308

Figure S268.  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 = 2.4e-05

Table S269.  Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
19P GAIN MUTATED 24 8 11 13 2
19P GAIN WILD-TYPE 78 115 160 57 184

Figure S269.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0022 (Fisher's exact test), Q value = 0.0038

Table S270.  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 13 3 7
19P GAIN WILD-TYPE 179 62 99 138 46 68 86

Figure S270.  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 = 2.4e-05

Table S271.  Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
19P GAIN MUTATED 27 28 17 2
19P GAIN WILD-TYPE 95 171 268 271

Figure S271.  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 = 2.4e-05

Table S272.  Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
19P GAIN MUTATED 25 6 10 1 21 3 5 3 0
19P GAIN WILD-TYPE 63 55 138 83 100 35 106 56 169

Figure S272.  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 = 2.4e-05

Table S273.  Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
19P GAIN MUTATED 23 34 15 1
19P GAIN WILD-TYPE 53 313 218 207

Figure S273.  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 = 2.4e-05

Table S274.  Gene #34: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
19P GAIN MUTATED 1 16 2 11
19P GAIN WILD-TYPE 155 53 63 111

Figure S274.  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 = 2.4e-05

Table S275.  Gene #34: '19p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
19P GAIN MUTATED 1 3 0 0 3 7 16
19P GAIN WILD-TYPE 90 80 49 20 43 70 30

Figure S275.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S276.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
19Q GAIN MUTATED 24 3 51
19Q GAIN WILD-TYPE 304 197 303

Figure S276.  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 = 2.4e-05

Table S277.  Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
19Q GAIN MUTATED 23 7 11 16 2
19Q GAIN WILD-TYPE 79 116 160 54 184

Figure S277.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.00072

Table S278.  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 S278.  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 = 2.4e-05

Table S279.  Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
19Q GAIN MUTATED 26 31 18 2
19Q GAIN WILD-TYPE 96 168 267 271

Figure S279.  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 = 2.4e-05

Table S280.  Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
19Q GAIN MUTATED 24 5 11 1 25 3 5 3 0
19Q GAIN WILD-TYPE 64 56 137 83 96 35 106 56 169

Figure S280.  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 = 2.4e-05

Table S281.  Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
19Q GAIN MUTATED 22 37 16 1
19Q GAIN WILD-TYPE 54 310 217 207

Figure S281.  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 = 2.4e-05

Table S282.  Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
19Q GAIN MUTATED 1 15 2 12
19Q GAIN WILD-TYPE 155 54 63 110

Figure S282.  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 = 2.4e-05

Table S283.  Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
19Q GAIN MUTATED 1 3 0 0 3 8 15
19Q GAIN WILD-TYPE 90 80 49 20 43 69 31

Figure S283.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S284.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
20P GAIN MUTATED 119 7 107
20P GAIN WILD-TYPE 209 193 247

Figure S284.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S285.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
20P GAIN MUTATED 26 38 15 28 71
20P GAIN WILD-TYPE 76 85 156 42 115

Figure S285.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 0.0183 (Fisher's exact test), Q value = 0.028

Table S286.  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 S286.  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 = 2.4e-05

Table S287.  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 S287.  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 = 2.4e-05

Table S288.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
20P GAIN MUTATED 31 83 26 93
20P GAIN WILD-TYPE 91 116 259 180

Figure S288.  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 = 2.4e-05

Table S289.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
20P GAIN MUTATED 26 18 19 14 62 4 8 7 75
20P GAIN WILD-TYPE 62 43 129 70 59 34 103 52 94

Figure S289.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00019

Table S290.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
20P GAIN MUTATED 118 50 64
20P GAIN WILD-TYPE 224 144 264

Figure S290.  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 = 2.4e-05

Table S291.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
20P GAIN MUTATED 24 99 28 81
20P GAIN WILD-TYPE 52 248 205 127

Figure S291.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00687 (Fisher's exact test), Q value = 0.011

Table S292.  Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
20P GAIN MUTATED 57 20 21 22
20P GAIN WILD-TYPE 99 49 44 100

Figure S292.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00025

Table S293.  Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
20P GAIN MUTATED 38 28 14 1 14 9 16
20P GAIN WILD-TYPE 53 55 35 19 32 68 30

Figure S293.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 0.0356 (Fisher's exact test), Q value = 0.052

Table S294.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 25 13 17
20Q GAIN MUTATED 3 8 5 7
20Q GAIN WILD-TYPE 28 17 8 10

Figure S294.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0496 (Fisher's exact test), Q value = 0.071

Table S295.  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 S295.  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 = 2.4e-05

Table S296.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
20Q GAIN MUTATED 119 8 110
20Q GAIN WILD-TYPE 209 192 244

Figure S296.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S297.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
20Q GAIN MUTATED 27 37 15 29 71
20Q GAIN WILD-TYPE 75 86 156 41 115

Figure S297.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.0097 (Fisher's exact test), Q value = 0.015

Table S298.  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 S298.  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 = 2.4e-05

Table S299.  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 S299.  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 = 2.4e-05

Table S300.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
20Q GAIN MUTATED 32 86 26 93
20Q GAIN WILD-TYPE 90 113 259 180

Figure S300.  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 = 2.4e-05

Table S301.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
20Q GAIN MUTATED 26 19 19 15 65 4 8 7 74
20Q GAIN WILD-TYPE 62 42 129 69 56 34 103 52 95

Figure S301.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

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

Table S302.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
20Q GAIN MUTATED 120 51 65
20Q GAIN WILD-TYPE 222 143 263

Figure S302.  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 = 2.4e-05

Table S303.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
20Q GAIN MUTATED 24 103 28 81
20Q GAIN WILD-TYPE 52 244 205 127

Figure S303.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00854 (Fisher's exact test), Q value = 0.013

Table S304.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
20Q GAIN MUTATED 57 20 23 23
20Q GAIN WILD-TYPE 99 49 42 99

Figure S304.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00029

Table S305.  Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
20Q GAIN MUTATED 38 30 14 1 14 10 16
20Q GAIN WILD-TYPE 53 53 35 19 32 67 30

Figure S305.  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 = 2.4e-05

Table S306.  Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
21Q GAIN MUTATED 21 1 50
21Q GAIN WILD-TYPE 307 199 304

Figure S306.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.0498 (Fisher's exact test), Q value = 0.071

Table S307.  Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
21Q GAIN MUTATED 5 11 10 12 13
21Q GAIN WILD-TYPE 97 112 161 58 173

Figure S307.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0203 (Fisher's exact test), Q value = 0.031

Table S308.  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 12 2 10 13 13 6 7
21Q GAIN WILD-TYPE 185 62 106 134 46 65 86

Figure S308.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00027

Table S309.  Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
21Q GAIN MUTATED 8 33 14 17
21Q GAIN WILD-TYPE 114 166 271 256

Figure S309.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00132 (Fisher's exact test), Q value = 0.0023

Table S310.  Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
21Q GAIN MUTATED 5 5 8 2 24 4 6 5 13
21Q GAIN WILD-TYPE 83 56 140 82 97 34 105 54 156

Figure S310.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.00058

Table S311.  Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
22Q GAIN MUTATED 28 3 33
22Q GAIN WILD-TYPE 300 197 321

Figure S311.  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 = 2.4e-05

Table S312.  Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
22Q GAIN MUTATED 21 6 10 7 3
22Q GAIN WILD-TYPE 81 117 161 63 183

Figure S312.  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 = 2.4e-05

Table S313.  Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
22Q GAIN MUTATED 24 20 16 4
22Q GAIN WILD-TYPE 98 179 269 269

Figure S313.  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 = 2.4e-05

Table S314.  Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
22Q GAIN MUTATED 23 3 10 1 16 3 4 1 3
22Q GAIN WILD-TYPE 65 58 138 83 105 35 107 58 166

Figure S314.  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 = 2.4e-05

Table S315.  Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
22Q GAIN MUTATED 22 22 16 3
22Q GAIN WILD-TYPE 54 325 217 205

Figure S315.  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 = 2.4e-05

Table S316.  Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
22Q GAIN MUTATED 3 16 3 3
22Q GAIN WILD-TYPE 153 53 62 119

Figure S316.  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 = 2.4e-05

Table S317.  Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
22Q GAIN MUTATED 2 1 1 0 3 2 16
22Q GAIN WILD-TYPE 89 82 48 20 43 75 30

Figure S317.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp gain' versus 'MRNA_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.017

Table S318.  Gene #40: 'xp gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 25 13 17
XP GAIN MUTATED 2 2 1 7
XP GAIN WILD-TYPE 29 23 12 10

Figure S318.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0089 (Fisher's exact test), Q value = 0.014

Table S319.  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 2 7 2 1
XP GAIN WILD-TYPE 20 22 11 11 10

Figure S319.  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 = 2.4e-05

Table S320.  Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
XP GAIN MUTATED 98 5 26
XP GAIN WILD-TYPE 230 195 328

Figure S320.  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 = 2.4e-05

Table S321.  Gene #40: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
XP GAIN MUTATED 11 10 4 6 74
XP GAIN WILD-TYPE 91 113 167 64 112

Figure S321.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00222 (Fisher's exact test), Q value = 0.0038

Table S322.  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 32 10 21 11 5 16 5
XP GAIN WILD-TYPE 165 54 95 136 54 55 88

Figure S322.  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 = 2.4e-05

Table S323.  Gene #40: 'xp gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
XP GAIN MUTATED 13 20 9 87
XP GAIN WILD-TYPE 109 179 276 186

Figure S323.  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 = 2.4e-05

Table S324.  Gene #40: 'xp gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
XP GAIN MUTATED 9 5 4 10 17 2 4 0 78
XP GAIN WILD-TYPE 79 56 144 74 104 36 107 59 91

Figure S324.  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 = 2.4e-05

Table S325.  Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
XP GAIN MUTATED 97 13 19
XP GAIN WILD-TYPE 245 181 309

Figure S325.  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 = 2.4e-05

Table S326.  Gene #40: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
XP GAIN MUTATED 8 31 9 81
XP GAIN WILD-TYPE 68 316 224 127

Figure S326.  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 = 2.4e-05

Table S327.  Gene #40: 'xp gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
XP GAIN MUTATED 56 9 3 7
XP GAIN WILD-TYPE 100 60 62 115

Figure S327.  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 = 2.4e-05

Table S328.  Gene #40: 'xp gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
XP GAIN MUTATED 35 11 17 1 3 2 6
XP GAIN WILD-TYPE 56 72 32 19 43 75 40

Figure S328.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'MRNA_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00046

Table S329.  Gene #41: 'xq gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 25 13 17
XQ GAIN MUTATED 3 0 1 8
XQ GAIN WILD-TYPE 28 25 12 9

Figure S329.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'xq gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0011

Table S330.  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 1 0 8 2 1
XQ GAIN WILD-TYPE 19 24 10 11 10

Figure S330.  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 = 2.4e-05

Table S331.  Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
XQ GAIN MUTATED 97 7 26
XQ GAIN WILD-TYPE 231 193 328

Figure S331.  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 = 2.4e-05

Table S332.  Gene #41: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
XQ GAIN MUTATED 11 11 5 6 74
XQ GAIN WILD-TYPE 91 112 166 64 112

Figure S332.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00438 (Fisher's exact test), Q value = 0.0072

Table S333.  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 33 10 19 13 4 16 5
XQ GAIN WILD-TYPE 164 54 97 134 55 55 88

Figure S333.  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 = 2.4e-05

Table S334.  Gene #41: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
XQ GAIN MUTATED 13 17 12 88
XQ GAIN WILD-TYPE 109 182 273 185

Figure S334.  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 = 2.4e-05

Table S335.  Gene #41: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
XQ GAIN MUTATED 9 5 5 10 14 3 5 1 78
XQ GAIN WILD-TYPE 79 56 143 74 107 35 106 58 91

Figure S335.  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 = 2.4e-05

Table S336.  Gene #41: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
XQ GAIN MUTATED 99 12 19
XQ GAIN WILD-TYPE 243 182 309

Figure S336.  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 = 2.4e-05

Table S337.  Gene #41: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
XQ GAIN MUTATED 8 28 11 83
XQ GAIN WILD-TYPE 68 319 222 125

Figure S337.  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 = 2.4e-05

Table S338.  Gene #41: 'xq gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
XQ GAIN MUTATED 57 9 3 7
XQ GAIN WILD-TYPE 99 60 62 115

Figure S338.  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 = 2.4e-05

Table S339.  Gene #41: 'xq gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
XQ GAIN MUTATED 35 13 17 1 2 2 6
XQ GAIN WILD-TYPE 56 70 32 19 44 75 40

Figure S339.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'MRNA_CNMF'

P value = 0.00313 (Fisher's exact test), Q value = 0.0053

Table S340.  Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 25 13 17
1P LOSS MUTATED 2 3 7 2
1P LOSS WILD-TYPE 29 22 6 15

Figure S340.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 0.02

Table S341.  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 S341.  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 = 2.4e-05

Table S342.  Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
1P LOSS MUTATED 87 13 45
1P LOSS WILD-TYPE 241 187 309

Figure S342.  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 = 2.4e-05

Table S343.  Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
1P LOSS MUTATED 61 12 14 14 14
1P LOSS WILD-TYPE 41 111 157 56 172

Figure S343.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'RPPA_CHIERARCHICAL'

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

Table S344.  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 6 10
1P LOSS WILD-TYPE 163 46 80 132 49 65 83

Figure S344.  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 = 2.4e-05

Table S345.  Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
1P LOSS MUTATED 70 20 24 31
1P LOSS WILD-TYPE 52 179 261 242

Figure S345.  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 = 2.4e-05

Table S346.  Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
1P LOSS MUTATED 69 14 14 15 11 2 6 6 8
1P LOSS WILD-TYPE 19 47 134 69 110 36 105 53 161

Figure S346.  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 = 2.4e-05

Table S347.  Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
1P LOSS MUTATED 92 20 33
1P LOSS WILD-TYPE 250 174 295

Figure S347.  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 = 2.4e-05

Table S348.  Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
1P LOSS MUTATED 67 37 20 21
1P LOSS WILD-TYPE 9 310 213 187

Figure S348.  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 = 2.4e-05

Table S349.  Gene #42: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
1P LOSS MUTATED 14 42 8 8
1P LOSS WILD-TYPE 142 27 57 114

Figure S349.  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 = 2.4e-05

Table S350.  Gene #42: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
1P LOSS MUTATED 11 9 1 2 5 5 39
1P LOSS WILD-TYPE 80 74 48 18 41 72 7

Figure S350.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'MRNA_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.028

Table S351.  Gene #43: '1q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 25 13 17
1Q LOSS MUTATED 2 1 5 2
1Q LOSS WILD-TYPE 29 24 8 15

Figure S351.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 0.021

Table S352.  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 2 1 5
1Q LOSS WILD-TYPE 19 23 16 12 6

Figure S352.  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 = 2.4e-05

Table S353.  Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
1Q LOSS MUTATED 80 7 23
1Q LOSS WILD-TYPE 248 193 331

Figure S353.  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 = 2.4e-05

Table S354.  Gene #43: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
1Q LOSS MUTATED 56 9 10 5 11
1Q LOSS WILD-TYPE 46 114 161 65 175

Figure S354.  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 = 2.4e-05

Table S355.  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 28 13 33 10 7 3 4
1Q LOSS WILD-TYPE 169 51 83 137 52 68 89

Figure S355.  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 = 2.4e-05

Table S356.  Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
1Q LOSS MUTATED 65 13 14 18
1Q LOSS WILD-TYPE 57 186 271 255

Figure S356.  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 = 2.4e-05

Table S357.  Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
1Q LOSS MUTATED 65 10 6 5 6 2 5 3 8
1Q LOSS WILD-TYPE 23 51 142 79 115 36 106 56 161

Figure S357.  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 = 2.4e-05

Table S358.  Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
1Q LOSS MUTATED 77 14 19
1Q LOSS WILD-TYPE 265 180 309

Figure S358.  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 = 2.4e-05

Table S359.  Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
1Q LOSS MUTATED 64 17 12 17
1Q LOSS WILD-TYPE 12 330 221 191

Figure S359.  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 = 2.4e-05

Table S360.  Gene #43: '1q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
1Q LOSS MUTATED 9 38 5 7
1Q LOSS WILD-TYPE 147 31 60 115

Figure S360.  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 = 2.4e-05

Table S361.  Gene #43: '1q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
1Q LOSS MUTATED 7 4 1 0 5 4 38
1Q LOSS WILD-TYPE 84 79 48 20 41 73 8

Figure S361.  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 = 2.4e-05

Table S362.  Gene #44: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 25 13 17
2P LOSS MUTATED 0 1 6 0
2P LOSS WILD-TYPE 31 24 7 17

Figure S362.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.00079

Table S363.  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 S363.  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 = 2.4e-05

Table S364.  Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
2P LOSS MUTATED 57 4 4
2P LOSS WILD-TYPE 271 196 350

Figure S364.  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 = 2.4e-05

Table S365.  Gene #44: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
2P LOSS MUTATED 52 1 0 4 0
2P LOSS WILD-TYPE 50 122 171 66 186

Figure S365.  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 = 2.4e-05

Table S366.  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 S366.  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 = 2.4e-05

Table S367.  Gene #44: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
2P LOSS MUTATED 60 2 0 3
2P LOSS WILD-TYPE 62 197 285 270

Figure S367.  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 = 2.4e-05

Table S368.  Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
2P LOSS MUTATED 58 1 0 4 2 0 0 0 0
2P LOSS WILD-TYPE 30 60 148 80 119 38 111 59 169

Figure S368.  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 = 2.4e-05

Table S369.  Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
2P LOSS MUTATED 60 2 3
2P LOSS WILD-TYPE 282 192 325

Figure S369.  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 = 2.4e-05

Table S370.  Gene #44: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
2P LOSS MUTATED 57 6 0 2
2P LOSS WILD-TYPE 19 341 233 206

Figure S370.  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 = 2.4e-05

Table S371.  Gene #44: '2p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
2P LOSS MUTATED 1 36 0 1
2P LOSS WILD-TYPE 155 33 65 121

Figure S371.  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 = 2.4e-05

Table S372.  Gene #44: '2p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
2P LOSS MUTATED 1 1 0 0 0 1 35
2P LOSS WILD-TYPE 90 82 49 20 46 76 11

Figure S372.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'MRNA_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00036

Table S373.  Gene #45: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 25 13 17
2Q LOSS MUTATED 0 1 5 0
2Q LOSS WILD-TYPE 31 24 8 17

Figure S373.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q loss' versus 'MRNA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00013

Table S374.  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 S374.  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 = 2.4e-05

Table S375.  Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
2Q LOSS MUTATED 55 4 4
2Q LOSS WILD-TYPE 273 196 350

Figure S375.  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 = 2.4e-05

Table S376.  Gene #45: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
2Q LOSS MUTATED 52 2 0 2 0
2Q LOSS WILD-TYPE 50 121 171 68 186

Figure S376.  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 = 2.4e-05

Table S377.  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 S377.  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 = 2.4e-05

Table S378.  Gene #45: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
2Q LOSS MUTATED 59 3 0 1
2Q LOSS WILD-TYPE 63 196 285 272

Figure S378.  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 = 2.4e-05

Table S379.  Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
2Q LOSS MUTATED 58 2 0 1 2 0 0 0 0
2Q LOSS WILD-TYPE 30 59 148 83 119 38 111 59 169

Figure S379.  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 = 2.4e-05

Table S380.  Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
2Q LOSS MUTATED 58 1 4
2Q LOSS WILD-TYPE 284 193 324

Figure S380.  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 = 2.4e-05

Table S381.  Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
2Q LOSS MUTATED 57 5 0 1
2Q LOSS WILD-TYPE 19 342 233 207

Figure S381.  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 = 2.4e-05

Table S382.  Gene #45: '2q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
2Q LOSS MUTATED 1 36 0 1
2Q LOSS WILD-TYPE 155 33 65 121

Figure S382.  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 = 2.4e-05

Table S383.  Gene #45: '2q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
2Q LOSS MUTATED 1 1 0 0 0 1 35
2Q LOSS WILD-TYPE 90 82 49 20 46 76 11

Figure S383.  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 = 2.4e-05

Table S384.  Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 25 13 17
3P LOSS MUTATED 20 21 4 0
3P LOSS WILD-TYPE 11 4 9 17

Figure S384.  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 = 2.4e-05

Table S385.  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 S385.  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 = 2.4e-05

Table S386.  Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
3P LOSS MUTATED 7 107 297
3P LOSS WILD-TYPE 321 93 57

Figure S386.  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 = 2.4e-05

Table S387.  Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
3P LOSS MUTATED 13 64 138 43 5
3P LOSS WILD-TYPE 89 59 33 27 181

Figure S387.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0011

Table S388.  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 70 115
3P LOSS WILD-TYPE 94 88 117 82

Figure S388.  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 = 2.4e-05

Table S389.  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 1 43 87 39 38 53
3P LOSS WILD-TYPE 92 63 73 60 20 33 40

Figure S389.  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 = 2.4e-05

Table S390.  Gene #46: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
3P LOSS MUTATED 20 140 228 21
3P LOSS WILD-TYPE 102 59 57 252

Figure S390.  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 = 2.4e-05

Table S391.  Gene #46: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
3P LOSS MUTATED 10 10 121 13 94 28 84 47 2
3P LOSS WILD-TYPE 78 51 27 71 27 10 27 12 167

Figure S391.  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 = 2.4e-05

Table S392.  Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
3P LOSS MUTATED 28 109 260
3P LOSS WILD-TYPE 314 85 68

Figure S392.  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 = 2.4e-05

Table S393.  Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
3P LOSS MUTATED 9 194 186 8
3P LOSS WILD-TYPE 67 153 47 200

Figure S393.  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 = 2.4e-05

Table S394.  Gene #46: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
3P LOSS MUTATED 8 8 14 92
3P LOSS WILD-TYPE 148 61 51 30

Figure S394.  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 = 2.4e-05

Table S395.  Gene #46: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
3P LOSS MUTATED 5 22 0 2 25 63 5
3P LOSS WILD-TYPE 86 61 49 18 21 14 41

Figure S395.  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 = 2.4e-05

Table S396.  Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
3Q LOSS MUTATED 6 22 91
3Q LOSS WILD-TYPE 322 178 263

Figure S396.  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 = 2.4e-05

Table S397.  Gene #47: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
3Q LOSS MUTATED 9 14 36 15 2
3Q LOSS WILD-TYPE 93 109 135 55 184

Figure S397.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S398.  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 29 0 10 21 19 10 18
3Q LOSS WILD-TYPE 168 64 106 126 40 61 75

Figure S398.  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 = 2.4e-05

Table S399.  Gene #47: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
3Q LOSS MUTATED 13 46 54 6
3Q LOSS WILD-TYPE 109 153 231 267

Figure S399.  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 = 2.4e-05

Table S400.  Gene #47: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
3Q LOSS MUTATED 8 6 35 3 28 5 12 21 1
3Q LOSS WILD-TYPE 80 55 113 81 93 33 99 38 168

Figure S400.  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 = 2.4e-05

Table S401.  Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
3Q LOSS MUTATED 14 26 76
3Q LOSS WILD-TYPE 328 168 252

Figure S401.  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 = 2.4e-05

Table S402.  Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
3Q LOSS MUTATED 8 65 40 3
3Q LOSS WILD-TYPE 68 282 193 205

Figure S402.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S403.  Gene #47: '3q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
3Q LOSS MUTATED 2 5 5 20
3Q LOSS WILD-TYPE 154 64 60 102

Figure S403.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00104 (Fisher's exact test), Q value = 0.0019

Table S404.  Gene #47: '3q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
3Q LOSS MUTATED 2 8 0 0 4 14 4
3Q LOSS WILD-TYPE 89 75 49 20 42 63 42

Figure S404.  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 = 2.4e-05

Table S405.  Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
4P LOSS MUTATED 20 9 69
4P LOSS WILD-TYPE 308 191 285

Figure S405.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S406.  Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
4P LOSS MUTATED 5 19 21 26 4
4P LOSS WILD-TYPE 97 104 150 44 182

Figure S406.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CNMF'

P value = 0.0256 (Fisher's exact test), Q value = 0.038

Table S407.  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 S407.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p loss' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.6e-05

Table S408.  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 S408.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S409.  Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
4P LOSS MUTATED 4 40 34 19
4P LOSS WILD-TYPE 118 159 251 254

Figure S409.  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 = 2.4e-05

Table S410.  Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
4P LOSS MUTATED 0 17 18 12 27 4 13 5 1
4P LOSS WILD-TYPE 88 44 130 72 94 34 98 54 168

Figure S410.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0013

Table S411.  Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
4P LOSS MUTATED 22 32 42
4P LOSS WILD-TYPE 320 162 286

Figure S411.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S412.  Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
4P LOSS MUTATED 0 60 26 10
4P LOSS WILD-TYPE 76 287 207 198

Figure S412.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.0018

Table S413.  Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
4P LOSS MUTATED 6 4 13 15
4P LOSS WILD-TYPE 150 65 52 107

Figure S413.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00025

Table S414.  Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
4P LOSS MUTATED 4 16 0 2 7 9 0
4P LOSS WILD-TYPE 87 67 49 18 39 68 46

Figure S414.  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 = 2.4e-05

Table S415.  Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
4Q LOSS MUTATED 20 3 69
4Q LOSS WILD-TYPE 308 197 285

Figure S415.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S416.  Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
4Q LOSS MUTATED 4 17 19 26 5
4Q LOSS WILD-TYPE 98 106 152 44 181

Figure S416.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'RPPA_CHIERARCHICAL'

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

Table S417.  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 S417.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S418.  Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
4Q LOSS MUTATED 4 40 28 20
4Q LOSS WILD-TYPE 118 159 257 253

Figure S418.  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 = 2.4e-05

Table S419.  Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
4Q LOSS MUTATED 0 17 16 13 27 4 10 4 1
4Q LOSS WILD-TYPE 88 44 132 71 94 34 101 55 168

Figure S419.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 0.0029 (Fisher's exact test), Q value = 0.0049

Table S420.  Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
4Q LOSS MUTATED 23 31 37
4Q LOSS WILD-TYPE 319 163 291

Figure S420.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S421.  Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
4Q LOSS MUTATED 0 60 21 10
4Q LOSS WILD-TYPE 76 287 212 198

Figure S421.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00321 (Fisher's exact test), Q value = 0.0054

Table S422.  Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
4Q LOSS MUTATED 7 4 13 13
4Q LOSS WILD-TYPE 149 65 52 109

Figure S422.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.6e-05

Table S423.  Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
4Q LOSS MUTATED 4 17 0 2 7 7 0
4Q LOSS WILD-TYPE 87 66 49 18 39 70 46

Figure S423.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00035

Table S424.  Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
5P LOSS MUTATED 19 1 4
5P LOSS WILD-TYPE 309 199 350

Figure S424.  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 = 2.4e-05

Table S425.  Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
5P LOSS MUTATED 13 5 0 3 1
5P LOSS WILD-TYPE 89 118 171 67 185

Figure S425.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'RPPA_CNMF'

P value = 0.0433 (Fisher's exact test), Q value = 0.062

Table S426.  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 5
5P LOSS WILD-TYPE 171 177 185 192

Figure S426.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5p loss' versus 'RPPA_CHIERARCHICAL'

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

Table S427.  Gene #50: '5p 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
5P LOSS MUTATED 5 3 5 0 3 1 5
5P LOSS WILD-TYPE 192 61 111 147 56 70 88

Figure S427.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S428.  Gene #50: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
5P LOSS MUTATED 12 10 0 2
5P LOSS WILD-TYPE 110 189 285 271

Figure S428.  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 = 2.4e-05

Table S429.  Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
5P LOSS MUTATED 11 7 0 1 4 0 0 0 1
5P LOSS WILD-TYPE 77 54 148 83 117 38 111 59 168

Figure S429.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S430.  Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
5P LOSS MUTATED 11 12 0 1
5P LOSS WILD-TYPE 65 335 233 207

Figure S430.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.0012

Table S431.  Gene #50: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
5P LOSS MUTATED 2 8 5 2
5P LOSS WILD-TYPE 154 61 60 120

Figure S431.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00013

Table S432.  Gene #50: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
5P LOSS MUTATED 1 7 0 0 1 0 8
5P LOSS WILD-TYPE 90 76 49 20 45 77 38

Figure S432.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S433.  Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
5Q LOSS MUTATED 19 0 4
5Q LOSS WILD-TYPE 309 200 350

Figure S433.  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 = 2.4e-05

Table S434.  Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
5Q LOSS MUTATED 13 6 0 2 1
5Q LOSS WILD-TYPE 89 117 171 68 185

Figure S434.  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 = 2.4e-05

Table S435.  Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
5Q LOSS MUTATED 13 9 0 1
5Q LOSS WILD-TYPE 109 190 285 272

Figure S435.  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 = 2.4e-05

Table S436.  Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
5Q LOSS MUTATED 11 8 0 0 3 0 0 0 1
5Q LOSS WILD-TYPE 77 53 148 84 118 38 111 59 168

Figure S436.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 0.0261 (Fisher's exact test), Q value = 0.039

Table S437.  Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
5Q LOSS MUTATED 14 6 3
5Q LOSS WILD-TYPE 328 188 325

Figure S437.  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 = 2.4e-05

Table S438.  Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
5Q LOSS MUTATED 11 11 0 1
5Q LOSS WILD-TYPE 65 336 233 207

Figure S438.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.00072

Table S439.  Gene #51: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
5Q LOSS MUTATED 2 8 6 2
5Q LOSS WILD-TYPE 154 61 59 120

Figure S439.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00013

Table S440.  Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
5Q LOSS MUTATED 1 8 0 0 1 0 8
5Q LOSS WILD-TYPE 90 75 49 20 45 77 38

Figure S440.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'MRNA_CNMF'

P value = 0.00633 (Fisher's exact test), Q value = 0.01

Table S441.  Gene #52: '6p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 25 13 17
6P LOSS MUTATED 4 10 6 1
6P LOSS WILD-TYPE 27 15 7 16

Figure S441.  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 S442.  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 S442.  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 = 2.4e-05

Table S443.  Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
6P LOSS MUTATED 75 8 88
6P LOSS WILD-TYPE 253 192 266

Figure S443.  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 = 2.4e-05

Table S444.  Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
6P LOSS MUTATED 58 22 14 19 9
6P LOSS WILD-TYPE 44 101 157 51 177

Figure S444.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p loss' versus 'RPPA_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0015

Table S445.  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 61
6P LOSS WILD-TYPE 151 148 158 136

Figure S445.  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 = 2.4e-05

Table S446.  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 22 4 10
6P LOSS WILD-TYPE 153 52 71 130 37 67 83

Figure S446.  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 = 2.4e-05

Table S447.  Gene #52: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
6P LOSS MUTATED 65 62 26 16
6P LOSS WILD-TYPE 57 137 259 257

Figure S447.  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 = 2.4e-05

Table S448.  Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
6P LOSS MUTATED 61 16 13 4 44 6 8 11 6
6P LOSS WILD-TYPE 27 45 135 80 77 32 103 48 163

Figure S448.  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 = 2.4e-05

Table S449.  Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
6P LOSS MUTATED 60 73 19 15
6P LOSS WILD-TYPE 16 274 214 193

Figure S449.  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 = 2.4e-05

Table S450.  Gene #52: '6p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
6P LOSS MUTATED 9 39 10 13
6P LOSS WILD-TYPE 147 30 55 109

Figure S450.  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 = 2.4e-05

Table S451.  Gene #52: '6p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
6P LOSS MUTATED 7 10 1 0 11 5 37
6P LOSS WILD-TYPE 84 73 48 20 35 72 9

Figure S451.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'MRNA_CNMF'

P value = 0.00822 (Fisher's exact test), Q value = 0.013

Table S452.  Gene #53: '6q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 25 13 17
6Q LOSS MUTATED 7 11 7 1
6Q LOSS WILD-TYPE 24 14 6 16

Figure S452.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'6q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00358 (Fisher's exact test), Q value = 0.0059

Table S453.  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 S453.  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 = 2.4e-05

Table S454.  Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
6Q LOSS MUTATED 78 8 120
6Q LOSS WILD-TYPE 250 192 234

Figure S454.  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 = 2.4e-05

Table S455.  Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
6Q LOSS MUTATED 58 28 24 24 11
6Q LOSS WILD-TYPE 44 95 147 46 175

Figure S455.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'RPPA_CNMF'

P value = 0.00213 (Fisher's exact test), Q value = 0.0037

Table S456.  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 37 45 36 68
6Q LOSS WILD-TYPE 145 136 151 129

Figure S456.  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 = 2.4e-05

Table S457.  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 23 5 13
6Q LOSS WILD-TYPE 142 51 68 118 36 66 80

Figure S457.  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 = 2.4e-05

Table S458.  Gene #53: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
6Q LOSS MUTATED 66 65 49 24
6Q LOSS WILD-TYPE 56 134 236 249

Figure S458.  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 = 2.4e-05

Table S459.  Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
6Q LOSS MUTATED 61 18 22 11 44 8 22 13 5
6Q LOSS WILD-TYPE 27 43 126 73 77 30 89 46 164

Figure S459.  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 = 2.4e-05

Table S460.  Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
6Q LOSS MUTATED 60 83 40 19
6Q LOSS WILD-TYPE 16 264 193 189

Figure S460.  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 = 2.4e-05

Table S461.  Gene #53: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
6Q LOSS MUTATED 10 39 14 21
6Q LOSS WILD-TYPE 146 30 51 101

Figure S461.  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 = 2.4e-05

Table S462.  Gene #53: '6q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
6Q LOSS MUTATED 7 14 2 0 13 11 37
6Q LOSS WILD-TYPE 84 69 47 20 33 66 9

Figure S462.  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 S463.  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 S463.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0418 (Fisher's exact test), Q value = 0.06

Table S464.  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 S464.  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 = 2.4e-05

Table S465.  Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
8P LOSS MUTATED 28 28 105
8P LOSS WILD-TYPE 300 172 249

Figure S465.  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 = 2.4e-05

Table S466.  Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
8P LOSS MUTATED 14 23 37 17 7
8P LOSS WILD-TYPE 88 100 134 53 179

Figure S466.  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 = 2.4e-05

Table S467.  Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
8P LOSS MUTATED 20 60 67 13
8P LOSS WILD-TYPE 102 139 218 260

Figure S467.  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 = 2.4e-05

Table S468.  Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
8P LOSS MUTATED 16 10 38 4 44 4 23 18 3
8P LOSS WILD-TYPE 72 51 110 80 77 34 88 41 166

Figure S468.  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 = 2.4e-05

Table S469.  Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
8P LOSS MUTATED 30 42 86
8P LOSS WILD-TYPE 312 152 242

Figure S469.  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 = 2.4e-05

Table S470.  Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
8P LOSS MUTATED 14 87 51 6
8P LOSS WILD-TYPE 62 260 182 202

Figure S470.  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 = 2.4e-05

Table S471.  Gene #56: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
8P LOSS MUTATED 4 9 6 31
8P LOSS WILD-TYPE 152 60 59 91

Figure S471.  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 = 2.4e-05

Table S472.  Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
8P LOSS MUTATED 3 8 1 2 15 15 6
8P LOSS WILD-TYPE 88 75 48 18 31 62 40

Figure S472.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0013

Table S473.  Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
8Q LOSS MUTATED 21 12 50
8Q LOSS WILD-TYPE 307 188 304

Figure S473.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S474.  Gene #57: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
8Q LOSS MUTATED 12 4 25 7 4
8Q LOSS WILD-TYPE 90 119 146 63 182

Figure S474.  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 = 2.4e-05

Table S475.  Gene #57: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
8Q LOSS MUTATED 17 21 39 6
8Q LOSS WILD-TYPE 105 178 246 267

Figure S475.  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 = 2.4e-05

Table S476.  Gene #57: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
8Q LOSS MUTATED 14 6 26 1 13 1 11 10 1
8Q LOSS WILD-TYPE 74 55 122 83 108 37 100 49 168

Figure S476.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_CNMF'

P value = 0.00984 (Fisher's exact test), Q value = 0.015

Table S477.  Gene #57: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
8Q LOSS MUTATED 20 23 39
8Q LOSS WILD-TYPE 322 171 289

Figure S477.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00027

Table S478.  Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
8Q LOSS MUTATED 12 38 27 5
8Q LOSS WILD-TYPE 64 309 206 203

Figure S478.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00115 (Fisher's exact test), Q value = 0.002

Table S479.  Gene #57: '8q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
8Q LOSS MUTATED 2 7 4 14
8Q LOSS WILD-TYPE 154 62 61 108

Figure S479.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00092 (Fisher's exact test), Q value = 0.0017

Table S480.  Gene #57: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
8Q LOSS MUTATED 2 3 0 1 9 6 6
8Q LOSS WILD-TYPE 89 80 49 19 37 71 40

Figure S480.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'MRNA_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.026

Table S481.  Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 25 13 17
9P LOSS MUTATED 5 12 1 3
9P LOSS WILD-TYPE 26 13 12 14

Figure S481.  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 S482.  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 S482.  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 = 2.4e-05

Table S483.  Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
9P LOSS MUTATED 31 14 147
9P LOSS WILD-TYPE 297 186 207

Figure S483.  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 = 2.4e-05

Table S484.  Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
9P LOSS MUTATED 16 45 24 41 7
9P LOSS WILD-TYPE 86 78 147 29 179

Figure S484.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S485.  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 S485.  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 = 2.4e-05

Table S486.  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 40 22 29 11 25
9P LOSS WILD-TYPE 157 58 76 125 30 60 68

Figure S486.  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 = 2.4e-05

Table S487.  Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
9P LOSS MUTATED 18 105 37 31
9P LOSS WILD-TYPE 104 94 248 242

Figure S487.  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 = 2.4e-05

Table S488.  Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
9P LOSS MUTATED 11 22 24 15 74 12 10 20 3
9P LOSS WILD-TYPE 77 39 124 69 47 26 101 39 166

Figure S488.  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 = 2.4e-05

Table S489.  Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
9P LOSS MUTATED 38 63 86
9P LOSS WILD-TYPE 304 131 242

Figure S489.  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 = 2.4e-05

Table S490.  Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
9P LOSS MUTATED 10 130 32 15
9P LOSS WILD-TYPE 66 217 201 193

Figure S490.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S491.  Gene #58: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
9P LOSS MUTATED 10 10 21 26
9P LOSS WILD-TYPE 146 59 44 96

Figure S491.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S492.  Gene #58: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
9P LOSS MUTATED 7 24 2 4 14 10 6
9P LOSS WILD-TYPE 84 59 47 16 32 67 40

Figure S492.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'MRNA_CNMF'

P value = 0.0383 (Fisher's exact test), Q value = 0.056

Table S493.  Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 25 13 17
9Q LOSS MUTATED 5 12 2 3
9Q LOSS WILD-TYPE 26 13 11 14

Figure S493.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0388 (Fisher's exact test), Q value = 0.056

Table S494.  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 S494.  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 = 2.4e-05

Table S495.  Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
9Q LOSS MUTATED 33 14 148
9Q LOSS WILD-TYPE 295 186 206

Figure S495.  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 = 2.4e-05

Table S496.  Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
9Q LOSS MUTATED 19 44 23 41 6
9Q LOSS WILD-TYPE 83 79 148 29 180

Figure S496.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.6e-05

Table S497.  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 S497.  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 = 2.4e-05

Table S498.  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 S498.  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 = 2.4e-05

Table S499.  Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
9Q LOSS MUTATED 22 106 38 28
9Q LOSS WILD-TYPE 100 93 247 245

Figure S499.  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 = 2.4e-05

Table S500.  Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
9Q LOSS MUTATED 13 22 25 15 75 12 9 20 3
9Q LOSS WILD-TYPE 75 39 123 69 46 26 102 39 166

Figure S500.  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 = 2.4e-05

Table S501.  Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
9Q LOSS MUTATED 41 63 85
9Q LOSS WILD-TYPE 301 131 243

Figure S501.  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 = 2.4e-05

Table S502.  Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
9Q LOSS MUTATED 12 132 31 14
9Q LOSS WILD-TYPE 64 215 202 194

Figure S502.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S503.  Gene #59: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
9Q LOSS MUTATED 11 12 21 27
9Q LOSS WILD-TYPE 145 57 44 95

Figure S503.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00017

Table S504.  Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
9Q LOSS MUTATED 7 23 2 4 16 11 8
9Q LOSS WILD-TYPE 84 60 47 16 30 66 38

Figure S504.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S505.  Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
10P LOSS MUTATED 62 8 63
10P LOSS WILD-TYPE 266 192 291

Figure S505.  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 = 2.4e-05

Table S506.  Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
10P LOSS MUTATED 54 14 16 16 4
10P LOSS WILD-TYPE 48 109 155 54 182

Figure S506.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'RPPA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00013

Table S507.  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 37 16 10 3 12
10P LOSS WILD-TYPE 166 55 79 131 49 68 81

Figure S507.  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 = 2.4e-05

Table S508.  Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
10P LOSS MUTATED 60 30 29 14
10P LOSS WILD-TYPE 62 169 256 259

Figure S508.  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 = 2.4e-05

Table S509.  Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
10P LOSS MUTATED 58 8 17 12 21 2 9 5 1
10P LOSS WILD-TYPE 30 53 131 72 100 36 102 54 168

Figure S509.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.00072

Table S510.  Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
10P LOSS MUTATED 71 28 32
10P LOSS WILD-TYPE 271 166 296

Figure S510.  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 = 2.4e-05

Table S511.  Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
10P LOSS MUTATED 57 49 18 7
10P LOSS WILD-TYPE 19 298 215 201

Figure S511.  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 = 2.4e-05

Table S512.  Gene #60: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
10P LOSS MUTATED 3 37 10 10
10P LOSS WILD-TYPE 153 32 55 112

Figure S512.  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 = 2.4e-05

Table S513.  Gene #60: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
10P LOSS MUTATED 1 9 1 2 6 7 34
10P LOSS WILD-TYPE 90 74 48 18 40 70 12

Figure S513.  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 = 2.4e-05

Table S514.  Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
10Q LOSS MUTATED 63 13 81
10Q LOSS WILD-TYPE 265 187 273

Figure S514.  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 = 2.4e-05

Table S515.  Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
10Q LOSS MUTATED 56 17 23 22 4
10Q LOSS WILD-TYPE 46 106 148 48 182

Figure S515.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CHIERARCHICAL'

P value = 9e-04 (Fisher's exact test), Q value = 0.0016

Table S516.  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 40 25 12 6 15
10Q LOSS WILD-TYPE 162 54 76 122 47 65 78

Figure S516.  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 = 2.4e-05

Table S517.  Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
10Q LOSS MUTATED 63 40 39 15
10Q LOSS WILD-TYPE 59 159 246 258

Figure S517.  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 = 2.4e-05

Table S518.  Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
10Q LOSS MUTATED 59 9 24 14 27 3 14 6 1
10Q LOSS WILD-TYPE 29 52 124 70 94 35 97 53 168

Figure S518.  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 = 2.4e-05

Table S519.  Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
10Q LOSS MUTATED 58 64 27 6
10Q LOSS WILD-TYPE 18 283 206 202

Figure S519.  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 = 2.4e-05

Table S520.  Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
10Q LOSS MUTATED 3 39 12 15
10Q LOSS WILD-TYPE 153 30 53 107

Figure S520.  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 = 2.4e-05

Table S521.  Gene #61: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
10Q LOSS MUTATED 1 12 1 2 9 9 35
10Q LOSS WILD-TYPE 90 71 48 18 37 68 11

Figure S521.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 0.00515 (Fisher's exact test), Q value = 0.0084

Table S522.  Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
11P LOSS MUTATED 17 2 23
11P LOSS WILD-TYPE 311 198 331

Figure S522.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00019

Table S523.  Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
11P LOSS MUTATED 9 8 4 11 3
11P LOSS WILD-TYPE 93 115 167 59 183

Figure S523.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.00094 (Fisher's exact test), Q value = 0.0017

Table S524.  Gene #62: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
11P LOSS MUTATED 12 13 4 13
11P LOSS WILD-TYPE 110 186 281 260

Figure S524.  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 = 4.4e-05

Table S525.  Gene #62: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
11P LOSS MUTATED 8 12 3 5 8 1 1 1 3
11P LOSS WILD-TYPE 80 49 145 79 113 37 110 58 166

Figure S525.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.001 (Fisher's exact test), Q value = 0.0018

Table S526.  Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
11P LOSS MUTATED 7 25 3 7
11P LOSS WILD-TYPE 69 322 230 201

Figure S526.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S527.  Gene #62: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
11P LOSS MUTATED 4 9 11 1
11P LOSS WILD-TYPE 152 60 54 121

Figure S527.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00185 (Fisher's exact test), Q value = 0.0032

Table S528.  Gene #62: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
11P LOSS MUTATED 3 11 1 1 3 0 6
11P LOSS WILD-TYPE 88 72 48 19 43 77 40

Figure S528.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S529.  Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
11Q LOSS MUTATED 18 1 33
11Q LOSS WILD-TYPE 310 199 321

Figure S529.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S530.  Gene #63: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
11Q LOSS MUTATED 9 13 4 14 4
11Q LOSS WILD-TYPE 93 110 167 56 182

Figure S530.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0024 (Fisher's exact test), Q value = 0.0041

Table S531.  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 S531.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00023

Table S532.  Gene #63: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
11Q LOSS MUTATED 11 18 4 19
11Q LOSS WILD-TYPE 111 181 281 254

Figure S532.  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 = 2.4e-05

Table S533.  Gene #63: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
11Q LOSS MUTATED 7 12 3 11 13 1 1 1 3
11Q LOSS WILD-TYPE 81 49 145 73 108 37 110 58 166

Figure S533.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00033

Table S534.  Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
11Q LOSS MUTATED 7 32 3 10
11Q LOSS WILD-TYPE 69 315 230 198

Figure S534.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S535.  Gene #63: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
11Q LOSS MUTATED 8 8 13 1
11Q LOSS WILD-TYPE 148 61 52 121

Figure S535.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.00065

Table S536.  Gene #63: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
11Q LOSS MUTATED 6 14 1 0 3 0 6
11Q LOSS WILD-TYPE 85 69 48 20 43 77 40

Figure S536.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'MRNA_CNMF'

P value = 0.00652 (Fisher's exact test), Q value = 0.01

Table S537.  Gene #66: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 25 13 17
13Q LOSS MUTATED 0 6 3 1
13Q LOSS WILD-TYPE 31 19 10 16

Figure S537.  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 S538.  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 S538.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S539.  Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
13Q LOSS MUTATED 68 11 58
13Q LOSS WILD-TYPE 260 189 296

Figure S539.  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 = 2.4e-05

Table S540.  Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
13Q LOSS MUTATED 50 28 8 19 6
13Q LOSS WILD-TYPE 52 95 163 51 180

Figure S540.  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 = 2.4e-05

Table S541.  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 S541.  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 = 2.4e-05

Table S542.  Gene #66: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
13Q LOSS MUTATED 55 53 15 14
13Q LOSS WILD-TYPE 67 146 270 259

Figure S542.  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 = 2.4e-05

Table S543.  Gene #66: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
13Q LOSS MUTATED 51 21 6 6 36 6 6 3 2
13Q LOSS WILD-TYPE 37 40 142 78 85 32 105 56 167

Figure S543.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

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

Table S544.  Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
13Q LOSS MUTATED 66 36 33
13Q LOSS WILD-TYPE 276 158 295

Figure S544.  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 = 2.4e-05

Table S545.  Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
13Q LOSS MUTATED 49 65 11 10
13Q LOSS WILD-TYPE 27 282 222 198

Figure S545.  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 = 2.4e-05

Table S546.  Gene #66: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
13Q LOSS MUTATED 7 32 18 9
13Q LOSS WILD-TYPE 149 37 47 113

Figure S546.  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 = 2.4e-05

Table S547.  Gene #66: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
13Q LOSS MUTATED 4 16 1 1 9 4 31
13Q LOSS WILD-TYPE 87 67 48 19 37 73 15

Figure S547.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

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

Table S548.  Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 25 13 17
14Q LOSS MUTATED 8 20 2 4
14Q LOSS WILD-TYPE 23 5 11 13

Figure S548.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

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

Table S549.  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 S549.  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 = 2.4e-05

Table S550.  Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
14Q LOSS MUTATED 42 30 193
14Q LOSS WILD-TYPE 286 170 161

Figure S550.  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 = 2.4e-05

Table S551.  Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
14Q LOSS MUTATED 4 55 52 41 16
14Q LOSS WILD-TYPE 98 68 119 29 170

Figure S551.  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 = 2.4e-05

Table S552.  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 S552.  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 = 2.4e-05

Table S553.  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 S553.  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 = 2.4e-05

Table S554.  Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
14Q LOSS MUTATED 11 116 90 45
14Q LOSS WILD-TYPE 111 83 195 228

Figure S554.  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 = 2.4e-05

Table S555.  Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
14Q LOSS MUTATED 4 22 49 17 73 33 27 26 11
14Q LOSS WILD-TYPE 84 39 99 67 48 5 84 33 158

Figure S555.  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 = 2.4e-05

Table S556.  Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
14Q LOSS MUTATED 44 75 140
14Q LOSS WILD-TYPE 298 119 188

Figure S556.  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 = 2.4e-05

Table S557.  Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
14Q LOSS MUTATED 3 158 77 21
14Q LOSS WILD-TYPE 73 189 156 187

Figure S557.  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 = 2.4e-05

Table S558.  Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
14Q LOSS MUTATED 17 4 21 45
14Q LOSS WILD-TYPE 139 65 44 77

Figure S558.  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 = 2.4e-05

Table S559.  Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
14Q LOSS MUTATED 9 30 4 3 14 26 1
14Q LOSS WILD-TYPE 82 53 45 17 32 51 45

Figure S559.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S560.  Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
15Q LOSS MUTATED 25 3 40
15Q LOSS WILD-TYPE 303 197 314

Figure S560.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S561.  Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
15Q LOSS MUTATED 4 22 5 13 9
15Q LOSS WILD-TYPE 98 101 166 57 177

Figure S561.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.00082

Table S562.  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 11 3 18 6 12 4 8
15Q LOSS WILD-TYPE 186 61 98 141 47 67 85

Figure S562.  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 = 2.4e-05

Table S563.  Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
15Q LOSS MUTATED 4 33 8 23
15Q LOSS WILD-TYPE 118 166 277 250

Figure S563.  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 = 2.4e-05

Table S564.  Gene #68: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
15Q LOSS MUTATED 1 17 6 9 22 2 3 1 7
15Q LOSS WILD-TYPE 87 44 142 75 99 36 108 58 162

Figure S564.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00146 (Fisher's exact test), Q value = 0.0026

Table S565.  Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
15Q LOSS MUTATED 1 39 10 18
15Q LOSS WILD-TYPE 75 308 223 190

Figure S565.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00391 (Fisher's exact test), Q value = 0.0064

Table S566.  Gene #68: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
15Q LOSS MUTATED 13 2 13 7
15Q LOSS WILD-TYPE 143 67 52 115

Figure S566.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0022 (Fisher's exact test), Q value = 0.0038

Table S567.  Gene #68: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
15Q LOSS MUTATED 9 15 2 0 6 3 0
15Q LOSS WILD-TYPE 82 68 47 20 40 74 46

Figure S567.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.00378 (Fisher's exact test), Q value = 0.0062

Table S568.  Gene #69: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
16P LOSS MUTATED 5 6 2 1 0
16P LOSS WILD-TYPE 97 117 169 69 186

Figure S568.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0094 (Fisher's exact test), Q value = 0.015

Table S569.  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 S569.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16p loss' versus 'MRNASEQ_CNMF'

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

Table S570.  Gene #69: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
16P LOSS MUTATED 6 9 2 1
16P LOSS WILD-TYPE 116 190 283 272

Figure S570.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0012

Table S571.  Gene #69: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
16P LOSS MUTATED 3 6 1 1 5 1 1 0 0
16P LOSS WILD-TYPE 85 55 147 83 116 37 110 59 169

Figure S571.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.05

Table S572.  Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
16P LOSS MUTATED 5 9 4
16P LOSS WILD-TYPE 337 185 324

Figure S572.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00479 (Fisher's exact test), Q value = 0.0078

Table S573.  Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
16P LOSS MUTATED 3 13 1 1
16P LOSS WILD-TYPE 73 334 232 207

Figure S573.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00029

Table S574.  Gene #69: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
16P LOSS MUTATED 0 5 5 1
16P LOSS WILD-TYPE 156 64 60 121

Figure S574.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00397 (Fisher's exact test), Q value = 0.0065

Table S575.  Gene #69: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
16P LOSS MUTATED 0 4 0 0 4 0 3
16P LOSS WILD-TYPE 91 79 49 20 42 77 43

Figure S575.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.032

Table S576.  Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
16Q LOSS MUTATED 8 2 18
16Q LOSS WILD-TYPE 320 198 336

Figure S576.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.00088

Table S577.  Gene #70: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
16Q LOSS MUTATED 6 7 3 5 0
16Q LOSS WILD-TYPE 96 116 168 65 186

Figure S577.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 0.00664 (Fisher's exact test), Q value = 0.011

Table S578.  Gene #70: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
16Q LOSS MUTATED 7 12 5 4
16Q LOSS WILD-TYPE 115 187 280 269

Figure S578.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S579.  Gene #70: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
16Q LOSS MUTATED 4 6 3 3 9 1 2 0 0
16Q LOSS WILD-TYPE 84 55 145 81 112 37 109 59 169

Figure S579.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00114 (Fisher's exact test), Q value = 0.002

Table S580.  Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
16Q LOSS MUTATED 4 19 2 2
16Q LOSS WILD-TYPE 72 328 231 206

Figure S580.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.002

Table S581.  Gene #70: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
16Q LOSS MUTATED 1 6 7 5
16Q LOSS WILD-TYPE 155 63 58 117

Figure S581.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00866 (Fisher's exact test), Q value = 0.014

Table S582.  Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
16Q LOSS MUTATED 1 6 0 0 6 2 4
16Q LOSS WILD-TYPE 90 77 49 20 40 75 42

Figure S582.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 0.00206 (Fisher's exact test), Q value = 0.0036

Table S583.  Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 25 13 17
17P LOSS MUTATED 0 5 5 2
17P LOSS WILD-TYPE 31 20 8 15

Figure S583.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00311 (Fisher's exact test), Q value = 0.0052

Table S584.  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 S584.  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 = 2.4e-05

Table S585.  Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
17P LOSS MUTATED 63 5 43
17P LOSS WILD-TYPE 265 195 311

Figure S585.  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 = 2.4e-05

Table S586.  Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
17P LOSS MUTATED 59 8 2 13 2
17P LOSS WILD-TYPE 43 115 169 57 184

Figure S586.  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 = 2.4e-05

Table S587.  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 9
17P LOSS WILD-TYPE 176 52 81 139 51 67 84

Figure S587.  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 = 2.4e-05

Table S588.  Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
17P LOSS MUTATED 67 28 6 10
17P LOSS WILD-TYPE 55 171 279 263

Figure S588.  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 = 2.4e-05

Table S589.  Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
17P LOSS MUTATED 61 8 3 9 24 2 3 1 0
17P LOSS WILD-TYPE 27 53 145 75 97 36 108 58 169

Figure S589.  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 = 2.4e-05

Table S590.  Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
17P LOSS MUTATED 69 21 21
17P LOSS WILD-TYPE 273 173 307

Figure S590.  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 = 2.4e-05

Table S591.  Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
17P LOSS MUTATED 60 42 6 3
17P LOSS WILD-TYPE 16 305 227 205

Figure S591.  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 = 2.4e-05

Table S592.  Gene #71: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
17P LOSS MUTATED 3 37 12 6
17P LOSS WILD-TYPE 153 32 53 116

Figure S592.  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 = 2.4e-05

Table S593.  Gene #71: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
17P LOSS MUTATED 1 12 0 0 7 2 36
17P LOSS WILD-TYPE 90 71 49 20 39 75 10

Figure S593.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'MRNA_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.00067

Table S594.  Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 25 13 17
17Q LOSS MUTATED 0 4 5 0
17Q LOSS WILD-TYPE 31 21 8 17

Figure S594.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 7e-04

Table S595.  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 S595.  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 = 2.4e-05

Table S596.  Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
17Q LOSS MUTATED 55 5 22
17Q LOSS WILD-TYPE 273 195 332

Figure S596.  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 = 2.4e-05

Table S597.  Gene #72: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
17Q LOSS MUTATED 55 3 1 4 1
17Q LOSS WILD-TYPE 47 120 170 66 185

Figure S597.  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 = 2.4e-05

Table S598.  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 19 11 29 6 3 1 4
17Q LOSS WILD-TYPE 178 53 87 141 56 70 89

Figure S598.  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 = 2.4e-05

Table S599.  Gene #72: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
17Q LOSS MUTATED 62 15 4 1
17Q LOSS WILD-TYPE 60 184 281 272

Figure S599.  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 = 2.4e-05

Table S600.  Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
17Q LOSS MUTATED 61 2 1 1 13 1 2 1 0
17Q LOSS WILD-TYPE 27 59 147 83 108 37 109 58 169

Figure S600.  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 = 2.4e-05

Table S601.  Gene #72: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
17Q LOSS MUTATED 62 6 14
17Q LOSS WILD-TYPE 280 188 314

Figure S601.  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 = 2.4e-05

Table S602.  Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
17Q LOSS MUTATED 60 17 4 1
17Q LOSS WILD-TYPE 16 330 229 207

Figure S602.  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 = 2.4e-05

Table S603.  Gene #72: '17q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
17Q LOSS MUTATED 1 36 2 3
17Q LOSS WILD-TYPE 155 33 63 119

Figure S603.  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 = 2.4e-05

Table S604.  Gene #72: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
17Q LOSS MUTATED 0 2 0 0 3 1 36
17Q LOSS WILD-TYPE 91 81 49 20 43 76 10

Figure S604.  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 = 2.4e-05

Table S605.  Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
18P LOSS MUTATED 42 7 92
18P LOSS WILD-TYPE 286 193 262

Figure S605.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S606.  Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
18P LOSS MUTATED 11 39 12 24 17
18P LOSS WILD-TYPE 91 84 159 46 169

Figure S606.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'RPPA_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.00077

Table S607.  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 35 15 26 46
18P LOSS WILD-TYPE 147 166 161 151

Figure S607.  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 = 2.4e-05

Table S608.  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 19 8 34 13 23 8 17
18P LOSS WILD-TYPE 178 56 82 134 36 63 76

Figure S608.  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 = 2.4e-05

Table S609.  Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
18P LOSS MUTATED 11 76 16 37
18P LOSS WILD-TYPE 111 123 269 236

Figure S609.  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 = 2.4e-05

Table S610.  Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
18P LOSS MUTATED 10 17 6 21 50 10 6 10 10
18P LOSS WILD-TYPE 78 44 142 63 71 28 105 49 159

Figure S610.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 0.00189 (Fisher's exact test), Q value = 0.0033

Table S611.  Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
18P LOSS MUTATED 44 48 49
18P LOSS WILD-TYPE 298 146 279

Figure S611.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S612.  Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
18P LOSS MUTATED 9 98 14 20
18P LOSS WILD-TYPE 67 249 219 188

Figure S612.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S613.  Gene #73: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
18P LOSS MUTATED 17 10 25 11
18P LOSS WILD-TYPE 139 59 40 111

Figure S613.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00017

Table S614.  Gene #73: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
18P LOSS MUTATED 12 25 2 2 11 4 7
18P LOSS WILD-TYPE 79 58 47 18 35 73 39

Figure S614.  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 = 2.4e-05

Table S615.  Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
18Q LOSS MUTATED 44 10 94
18Q LOSS WILD-TYPE 284 190 260

Figure S615.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S616.  Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
18Q LOSS MUTATED 13 40 13 26 16
18Q LOSS WILD-TYPE 89 83 158 44 170

Figure S616.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.0013

Table S617.  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 38 17 27 47
18Q LOSS WILD-TYPE 144 164 160 150

Figure S617.  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 = 2.4e-05

Table S618.  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 18 8 35 16 24 8 20
18Q LOSS WILD-TYPE 179 56 81 131 35 63 73

Figure S618.  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 = 2.4e-05

Table S619.  Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
18Q LOSS MUTATED 14 77 16 40
18Q LOSS WILD-TYPE 108 122 269 233

Figure S619.  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 = 2.4e-05

Table S620.  Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
18Q LOSS MUTATED 11 19 7 25 49 10 6 11 9
18Q LOSS WILD-TYPE 77 42 141 59 72 28 105 48 160

Figure S620.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 0.00817 (Fisher's exact test), Q value = 0.013

Table S621.  Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
18Q LOSS MUTATED 50 48 50
18Q LOSS WILD-TYPE 292 146 278

Figure S621.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S622.  Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
18Q LOSS MUTATED 10 102 16 20
18Q LOSS WILD-TYPE 66 245 217 188

Figure S622.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S623.  Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
18Q LOSS MUTATED 17 12 28 11
18Q LOSS WILD-TYPE 139 57 37 111

Figure S623.  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 = 2.4e-05

Table S624.  Gene #74: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
18Q LOSS MUTATED 12 29 2 2 11 4 8
18Q LOSS WILD-TYPE 79 54 47 18 35 73 38

Figure S624.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

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

Table S625.  Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
19P LOSS MUTATED 11 0 18
19P LOSS WILD-TYPE 317 200 336

Figure S625.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.00058

Table S626.  Gene #75: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
19P LOSS MUTATED 1 5 1 9 8
19P LOSS WILD-TYPE 101 118 170 61 178

Figure S626.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

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

Table S627.  Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
19P LOSS MUTATED 1 10 2 16
19P LOSS WILD-TYPE 121 189 283 257

Figure S627.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.00044

Table S628.  Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
19P LOSS MUTATED 1 7 1 7 7 0 1 0 5
19P LOSS WILD-TYPE 87 54 147 77 114 38 110 59 164

Figure S628.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0235 (Fisher's exact test), Q value = 0.035

Table S629.  Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
19P LOSS MUTATED 1 17 2 9
19P LOSS WILD-TYPE 75 330 231 199

Figure S629.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0015

Table S630.  Gene #75: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
19P LOSS MUTATED 8 1 9 1
19P LOSS WILD-TYPE 148 68 56 121

Figure S630.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 0.00363 (Fisher's exact test), Q value = 0.006

Table S631.  Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
19Q LOSS MUTATED 8 0 15
19Q LOSS WILD-TYPE 320 200 339

Figure S631.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.0017

Table S632.  Gene #76: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
19Q LOSS MUTATED 2 3 0 7 7
19Q LOSS WILD-TYPE 100 120 171 63 179

Figure S632.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 0.00215 (Fisher's exact test), Q value = 0.0037

Table S633.  Gene #76: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
19Q LOSS MUTATED 2 6 1 14
19Q LOSS WILD-TYPE 120 193 284 259

Figure S633.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S634.  Gene #76: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
19Q LOSS MUTATED 2 7 0 5 3 0 1 0 5
19Q LOSS WILD-TYPE 86 54 148 79 118 38 110 59 164

Figure S634.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 0.00465 (Fisher's exact test), Q value = 0.0076

Table S635.  Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
19Q LOSS MUTATED 15 6 2
19Q LOSS WILD-TYPE 327 188 326

Figure S635.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0403 (Fisher's exact test), Q value = 0.058

Table S636.  Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
19Q LOSS MUTATED 2 12 1 8
19Q LOSS WILD-TYPE 74 335 232 200

Figure S636.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00145 (Fisher's exact test), Q value = 0.0026

Table S637.  Gene #76: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
19Q LOSS MUTATED 9 2 7 0
19Q LOSS WILD-TYPE 147 67 58 122

Figure S637.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 0.00714 (Fisher's exact test), Q value = 0.011

Table S638.  Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
20P LOSS MUTATED 5 1 1 1 0
20P LOSS WILD-TYPE 97 122 170 69 186

Figure S638.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.00082

Table S639.  Gene #77: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
20P LOSS MUTATED 4 7 1 0
20P LOSS WILD-TYPE 118 192 284 273

Figure S639.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.022

Table S640.  Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
20P LOSS MUTATED 4 1 1 0 3 1 0 2 0
20P LOSS WILD-TYPE 84 60 147 84 118 37 111 57 169

Figure S640.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00378 (Fisher's exact test), Q value = 0.0062

Table S641.  Gene #77: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
20P LOSS MUTATED 4 7 1 0
20P LOSS WILD-TYPE 72 340 232 208

Figure S641.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00598 (Fisher's exact test), Q value = 0.0097

Table S642.  Gene #77: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
20P LOSS MUTATED 0 4 1 1
20P LOSS WILD-TYPE 156 65 64 121

Figure S642.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0138 (Fisher's exact test), Q value = 0.021

Table S643.  Gene #77: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
20P LOSS MUTATED 0 1 0 0 0 1 4
20P LOSS WILD-TYPE 91 82 49 20 46 76 42

Figure S643.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q loss' versus 'METHLYATION_CNMF'

P value = 0.00497 (Fisher's exact test), Q value = 0.0081

Table S644.  Gene #78: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
20Q LOSS MUTATED 3 0 0 0 0
20Q LOSS WILD-TYPE 99 123 171 70 186

Figure S644.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q loss' versus 'MRNASEQ_CNMF'

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

Table S645.  Gene #78: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
20Q LOSS MUTATED 3 3 0 0
20Q LOSS WILD-TYPE 119 196 285 273

Figure S645.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0145 (Fisher's exact test), Q value = 0.022

Table S646.  Gene #78: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
20Q LOSS MUTATED 3 0 0 0 1 1 0 1 0
20Q LOSS WILD-TYPE 85 61 148 84 120 37 111 58 169

Figure S646.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00585 (Fisher's exact test), Q value = 0.0095

Table S647.  Gene #78: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
20Q LOSS MUTATED 3 3 0 0
20Q LOSS WILD-TYPE 73 344 233 208

Figure S647.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00866 (Fisher's exact test), Q value = 0.014

Table S648.  Gene #78: '20q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
20Q LOSS MUTATED 0 3 0 0
20Q LOSS WILD-TYPE 156 66 65 122

Figure S648.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00581 (Fisher's exact test), Q value = 0.0094

Table S649.  Gene #78: '20q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
20Q LOSS MUTATED 0 0 0 0 0 0 3
20Q LOSS WILD-TYPE 91 83 49 20 46 77 43

Figure S649.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'MRNA_CNMF'

P value = 0.0263 (Fisher's exact test), Q value = 0.039

Table S650.  Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 25 13 17
21Q LOSS MUTATED 1 2 4 4
21Q LOSS WILD-TYPE 30 23 9 13

Figure S650.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0241 (Fisher's exact test), Q value = 0.036

Table S651.  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 S651.  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 = 2.4e-05

Table S652.  Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
21Q LOSS MUTATED 83 9 41
21Q LOSS WILD-TYPE 245 191 313

Figure S652.  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 = 2.4e-05

Table S653.  Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
21Q LOSS MUTATED 40 19 12 17 21
21Q LOSS WILD-TYPE 62 104 159 53 165

Figure S653.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S654.  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 S654.  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 = 2.4e-05

Table S655.  Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
21Q LOSS MUTATED 50 24 17 40
21Q LOSS WILD-TYPE 72 175 268 233

Figure S655.  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 = 2.4e-05

Table S656.  Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
21Q LOSS MUTATED 46 16 9 11 13 2 7 5 22
21Q LOSS WILD-TYPE 42 45 139 73 108 36 104 54 147

Figure S656.  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 = 2.4e-05

Table S657.  Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
21Q LOSS MUTATED 79 29 24
21Q LOSS WILD-TYPE 263 165 304

Figure S657.  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 = 2.4e-05

Table S658.  Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
21Q LOSS MUTATED 45 44 12 31
21Q LOSS WILD-TYPE 31 303 221 177

Figure S658.  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 = 4.4e-05

Table S659.  Gene #79: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
21Q LOSS MUTATED 24 27 14 11
21Q LOSS WILD-TYPE 132 42 51 111

Figure S659.  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 = 2.4e-05

Table S660.  Gene #79: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
21Q LOSS MUTATED 16 18 3 0 6 7 26
21Q LOSS WILD-TYPE 75 65 46 20 40 70 20

Figure S660.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'MRNA_CNMF'

P value = 0.00721 (Fisher's exact test), Q value = 0.011

Table S661.  Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 25 13 17
22Q LOSS MUTATED 0 4 1 5
22Q LOSS WILD-TYPE 31 21 12 12

Figure S661.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0375 (Fisher's exact test), Q value = 0.054

Table S662.  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 S662.  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 = 2.4e-05

Table S663.  Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
22Q LOSS MUTATED 50 4 53
22Q LOSS WILD-TYPE 278 196 301

Figure S663.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S664.  Gene #80: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
22Q LOSS MUTATED 16 18 4 27 24
22Q LOSS WILD-TYPE 86 105 167 43 162

Figure S664.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

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

Table S665.  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 S665.  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 = 2.4e-05

Table S666.  Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
22Q LOSS MUTATED 15 31 7 54
22Q LOSS WILD-TYPE 107 168 278 219

Figure S666.  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 = 2.4e-05

Table S667.  Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
22Q LOSS MUTATED 10 18 8 33 19 3 1 3 12
22Q LOSS WILD-TYPE 78 43 140 51 102 35 110 56 157

Figure S667.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S668.  Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
22Q LOSS MUTATED 64 19 24
22Q LOSS WILD-TYPE 278 175 304

Figure S668.  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 = 2.4e-05

Table S669.  Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
22Q LOSS MUTATED 9 58 8 32
22Q LOSS WILD-TYPE 67 289 225 176

Figure S669.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.00063

Table S670.  Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
22Q LOSS MUTATED 29 12 16 6
22Q LOSS WILD-TYPE 127 57 49 116

Figure S670.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S671.  Gene #80: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
22Q LOSS MUTATED 19 23 2 5 3 3 8
22Q LOSS WILD-TYPE 72 60 47 15 43 74 38

Figure S671.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'MRNA_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.044

Table S672.  Gene #81: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 25 13 17
XP LOSS MUTATED 3 1 5 3
XP LOSS WILD-TYPE 28 24 8 14

Figure S672.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0307 (Fisher's exact test), Q value = 0.045

Table S673.  Gene #81: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 20 24 18 13 11
XP LOSS MUTATED 2 1 3 1 5
XP LOSS WILD-TYPE 18 23 15 12 6

Figure S673.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.4e-05

Table S674.  Gene #81: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
XP LOSS MUTATED 62 10 42
XP LOSS WILD-TYPE 266 190 312

Figure S674.  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 = 2.4e-05

Table S675.  Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
XP LOSS MUTATED 48 8 11 18 8
XP LOSS WILD-TYPE 54 115 160 52 178

Figure S675.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00029

Table S676.  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 29 9 28 10 3 3 14
XP LOSS WILD-TYPE 168 55 88 137 56 68 79

Figure S676.  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 = 2.4e-05

Table S677.  Gene #81: 'xp loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
XP LOSS MUTATED 54 15 19 26
XP LOSS WILD-TYPE 68 184 266 247

Figure S677.  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 = 2.4e-05

Table S678.  Gene #81: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
XP LOSS MUTATED 49 15 6 15 7 4 7 7 4
XP LOSS WILD-TYPE 39 46 142 69 114 34 104 52 165

Figure S678.  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 = 2.4e-05

Table S679.  Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
XP LOSS MUTATED 74 15 24
XP LOSS WILD-TYPE 268 179 304

Figure S679.  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 = 2.4e-05

Table S680.  Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
XP LOSS MUTATED 47 40 13 13
XP LOSS WILD-TYPE 29 307 220 195

Figure S680.  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 = 2.4e-05

Table S681.  Gene #81: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
XP LOSS MUTATED 8 34 13 6
XP LOSS WILD-TYPE 148 35 52 116

Figure S681.  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 = 2.4e-05

Table S682.  Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
XP LOSS MUTATED 5 18 1 3 3 2 29
XP LOSS WILD-TYPE 86 65 48 17 43 75 17

Figure S682.  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 = 2.4e-05

Table S683.  Gene #82: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 328 200 354
XQ LOSS MUTATED 63 8 42
XQ LOSS WILD-TYPE 265 192 312

Figure S683.  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 = 2.4e-05

Table S684.  Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 102 123 171 70 186
XQ LOSS MUTATED 47 8 10 18 8
XQ LOSS WILD-TYPE 55 115 161 52 178

Figure S684.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CHIERARCHICAL'

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

Table S685.  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 28 9 31 8 4 3 13
XQ LOSS WILD-TYPE 169 55 85 139 55 68 80

Figure S685.  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 = 2.4e-05

Table S686.  Gene #82: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 199 285 273
XQ LOSS MUTATED 53 19 16 25
XQ LOSS WILD-TYPE 69 180 269 248

Figure S686.  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 = 2.4e-05

Table S687.  Gene #82: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 88 61 148 84 121 38 111 59 169
XQ LOSS MUTATED 48 16 5 15 10 3 6 6 4
XQ LOSS WILD-TYPE 40 45 143 69 111 35 105 53 165

Figure S687.  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 = 2.4e-05

Table S688.  Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 342 194 328
XQ LOSS MUTATED 71 17 24
XQ LOSS WILD-TYPE 271 177 304

Figure S688.  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 = 2.4e-05

Table S689.  Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 347 233 208
XQ LOSS MUTATED 46 44 11 11
XQ LOSS WILD-TYPE 30 303 222 197

Figure S689.  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 = 2.4e-05

Table S690.  Gene #82: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 69 65 122
XQ LOSS MUTATED 7 33 14 6
XQ LOSS WILD-TYPE 149 36 51 116

Figure S690.  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 = 2.4e-05

Table S691.  Gene #82: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 91 83 49 20 46 77 46
XQ LOSS MUTATED 5 16 1 3 5 2 28
XQ LOSS WILD-TYPE 86 67 48 17 41 75 18

Figure S691.  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/22533780/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIPAN-TP/22570984/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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