Correlation between copy number variations of arm-level result and molecular subtypes
Glioma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1H41QTX
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/C1H41QTX
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 14 molecular subtypes across 1090 patients, 593 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p 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'.

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

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

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

  • 3p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 3q gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

  • 5p 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'.

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

  • 6p gain cnv correlated to 'MRNA_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 6q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 8p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • 10q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

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

  • 16p gain cnv correlated to 'MRNA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF', and 'MRNASEQ_CNMF'.

  • 17q gain cnv correlated to 'MRNA_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

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

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

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

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

  • 20q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_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 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 22q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • xp gain cnv correlated to 'METHLYATION_CNMF'.

  • xq gain cnv correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 1p 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'.

  • 1q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.

  • 2p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'METHLYATION_CNMF',  'RPPA_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 2q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 3p loss cnv correlated to 'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 3q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 5p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 6p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 6q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7p loss cnv correlated to 'MRNA_CNMF'.

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

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

  • 9p loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 9q loss cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 10q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 12p loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 12q loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 13q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 15q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 17p loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17q loss cnv correlated to 'MRNA_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 18p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'METHLYATION_CNMF'.

  • 18q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • 19p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'CN_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 19q 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'.

  • 20p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF', and 'CN_CNMF'.

  • 20q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 21q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 22q 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'.

  • xp loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • xq loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  '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 14 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 593 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		MIR
CNMF 		MIR
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 Fisher's exact test Fisher's exact test
7p gain 594 (54%) 496 1e-05
(7e-05) 		1e-05
(7e-05) 		0.0005
(0.00208) 		1e-05
(7e-05) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.00049
(0.00205) 		0.00018
(0.000865) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.00145
(0.00532) 		1e-05
(7e-05) 		1e-05
(7e-05) 		1e-05
(7e-05)
20q gain 263 (24%) 827 1e-05
(7e-05) 		1e-05
(7e-05) 		0.00211
(0.00727) 		3e-05
(0.000178) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.00246
(0.00828) 		1e-05
(7e-05) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.032
(0.0683) 		1e-05
(7e-05) 		0.00017
(0.000834) 		1e-05
(7e-05)
10p loss 563 (52%) 527 1e-05
(7e-05) 		1e-05
(7e-05) 		0.0145
(0.0369) 		0.00011
(0.000559) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.00217
(0.00746) 		7e-05
(0.000376) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.00019
(0.000905) 		1e-05
(7e-05) 		1e-05
(7e-05) 		1e-05
(7e-05)
10q loss 591 (54%) 499 1e-05
(7e-05) 		1e-05
(7e-05) 		0.00465
(0.0141) 		0.00011
(0.000559) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.00023
(0.00106) 		0.00013
(0.000655) 		1e-05
(7e-05) 		1e-05
(7e-05) 		2e-05
(0.000128) 		1e-05
(7e-05) 		1e-05
(7e-05) 		1e-05
(7e-05)
7q gain 631 (58%) 459 1e-05
(7e-05) 		1e-05
(7e-05) 		0.00358
(0.0114) 		0.0001
(0.000515) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.0639
(0.119) 		0.0138
(0.0355) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.00755
(0.0216) 		1e-05
(7e-05) 		2e-05
(0.000128) 		1e-05
(7e-05)
19p gain 324 (30%) 766 1e-05
(7e-05) 		4e-05
(0.00023) 		0.11
(0.18) 		0.00046
(0.00195) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.0359
(0.0741) 		0.00144
(0.0053) 		4e-05
(0.00023) 		1e-05
(7e-05) 		0.0124
(0.0326) 		0.0312
(0.067) 		0.00049
(0.00205) 		2e-05
(0.000128)
20p gain 266 (24%) 824 1e-05
(7e-05) 		1e-05
(7e-05) 		0.00359
(0.0114) 		1e-05
(7e-05) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.00975
(0.0265) 		4e-05
(0.00023) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.135
(0.21) 		1e-05
(7e-05) 		0.00026
(0.00118) 		1e-05
(7e-05)
19q gain 223 (20%) 867 1e-05
(7e-05) 		1e-05
(7e-05) 		0.184
(0.27) 		0.00456
(0.0139) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.0779
(0.139) 		0.0039
(0.0122) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.00116
(0.00444) 		1e-05
(7e-05) 		3e-05
(0.000178) 		1e-05
(7e-05)
4q loss 149 (14%) 941 0.00092
(0.00359) 		0.00062
(0.0025) 		0.0174
(0.0427) 		0.104
(0.173) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.00341
(0.0109) 		0.99
(1.00) 		0.00401
(0.0125) 		0.00018
(0.000865) 		0.00031
(0.00138) 		0.0115
(0.0304) 		0.00703
(0.0203) 		1e-05
(7e-05)
19q loss 244 (22%) 846 0.00233
(0.00794) 		0.0107
(0.0288) 		0.208
(0.299) 		0.0788
(0.14) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.00292
(0.00958) 		0.0002
(0.000941) 		1e-05
(7e-05) 		1e-05
(7e-05) 		1e-05
(7e-05) 		1e-05
(7e-05) 		1e-05
(7e-05) 		1e-05
(7e-05)
4p loss 127 (12%) 963 0.0569
(0.108) 		0.00164
(0.00592) 		0.0325
(0.069) 		0.176
(0.26) 		0.00869
(0.0242) 		1e-05
(7e-05) 		0.00654
(0.0192) 		0.909
(0.932) 		0.0356
(0.0736) 		0.00335
(0.0107) 		8e-05
(0.000421) 		0.00149
(0.00543) 		0.0004
(0.00173) 		1e-05
(7e-05)
5q loss 80 (7%) 1010 1e-05
(7e-05) 		2e-05
(0.000128) 		0.00057
(0.00232) 		0.118
(0.189) 		2e-05
(0.000128) 		3e-05
(0.000178) 		0.0316
(0.0678) 		0.0548
(0.104) 		0.0412
(0.0832) 		0.00319
(0.0104) 		0.00019
(0.000905) 		0.17
(0.253) 		0.0168
(0.0415) 		5e-05
(0.000279)
11p loss 162 (15%) 928 1e-05
(7e-05) 		1e-05
(7e-05) 		0.9
(0.926) 		0.0179
(0.0434) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.076
(0.136) 		0.431
(0.532) 		1e-05
(7e-05) 		1e-05
(7e-05) 		3e-05
(0.000178) 		5e-05
(0.000279) 		0.00066
(0.00265) 		1e-05
(7e-05)
xp loss 212 (19%) 878 0.011
(0.0293) 		0.00821
(0.023) 		0.0453
(0.0899) 		0.102
(0.17) 		0.215
(0.307) 		0.0078
(0.0222) 		0.00252
(0.00843) 		0.0138
(0.0355) 		0.0243
(0.0555) 		0.0193
(0.0461) 		0.0218
(0.051) 		0.279
(0.378) 		0.00122
(0.00464) 		0.0003
(0.00135)
10p gain 70 (6%) 1020 0.00137
(0.00512) 		0.0001
(0.000515) 		0.16
(0.241) 		0.0596
(0.113) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.0003
(0.00135) 		0.137
(0.213) 		0.00046
(0.00195) 		1e-05
(7e-05) 		0.0277
(0.0613) 		0.293
(0.39) 		0.0186
(0.0448) 		1e-05
(7e-05)
18q gain 75 (7%) 1015 1e-05
(7e-05) 		0.00021
(0.000976) 		0.308
(0.405) 		0.391
(0.494) 		2e-05
(0.000128) 		0.0015
(0.00545) 		0.0405
(0.0822) 		0.137
(0.212) 		1e-05
(7e-05) 		2e-05
(0.000128) 		0.375
(0.478) 		0.00959
(0.0262) 		0.0348
(0.0727) 		0.00036
(0.00157)
1p loss 200 (18%) 890 0.755
(0.813) 		0.828
(0.868) 		0.76
(0.817) 		0.173
(0.257) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.00205
(0.00713) 		1e-05
(7e-05) 		1e-05
(7e-05) 		1e-05
(7e-05) 		1e-05
(7e-05) 		1e-05
(7e-05) 		1e-05
(7e-05) 		1e-05
(7e-05)
14q loss 227 (21%) 863 1e-05
(7e-05) 		0.00015
(0.000749) 		0.6
(0.681) 		0.538
(0.624) 		1e-05
(7e-05) 		0.00181
(0.00645) 		0.238
(0.334) 		0.245
(0.34) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.00845
(0.0236) 		0.0012
(0.00458) 		0.0169
(0.0417) 		0.00229
(0.00785)
1p gain 95 (9%) 995 0.545
(0.629) 		0.129
(0.203) 		0.428
(0.531) 		0.25
(0.346) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.0897
(0.155) 		0.00582
(0.0173) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.0066
(0.0192) 		1e-05
(7e-05) 		0.00292
(0.00958) 		0.0011
(0.00424)
5p gain 60 (6%) 1030 0.124
(0.197) 		0.157
(0.237) 		0.218
(0.31) 		0.344
(0.444) 		1e-05
(7e-05) 		0.00975
(0.0265) 		0.123
(0.196) 		0.00796
(0.0225) 		2e-05
(0.000128) 		4e-05
(0.00023) 		0.0259
(0.0585) 		0.0269
(0.06) 		1e-05
(7e-05) 		0.0009
(0.00353)
8p gain 101 (9%) 989 2e-05
(0.000128) 		0.00059
(0.00239) 		0.0379
(0.0772) 		0.56
(0.642) 		0.00896
(0.0247) 		6e-05
(0.000328) 		0.00888
(0.0246) 		0.0785
(0.139) 		0.309
(0.406) 		0.00178
(0.00637) 		0.271
(0.37) 		0.326
(0.426) 		0.049
(0.0952) 		0.00286
(0.00946)
8q gain 117 (11%) 973 2e-05
(0.000128) 		2e-05
(0.000128) 		0.04
(0.0813) 		0.452
(0.548) 		0.00245
(0.00827) 		1e-05
(7e-05) 		0.0202
(0.048) 		0.155
(0.235) 		0.12
(0.192) 		0.00045
(0.00193) 		0.108
(0.177) 		0.134
(0.209) 		0.0434
(0.087) 		0.00024
(0.0011)
12q gain 65 (6%) 1025 0.591
(0.673) 		0.955
(0.971) 		0.401
(0.503) 		0.0104
(0.028) 		3e-05
(0.000178) 		0.0199
(0.0475) 		0.00262
(0.00872) 		0.43
(0.532) 		0.00302
(0.00988) 		0.00072
(0.00286) 		0.0367
(0.0755) 		0.00923
(0.0254) 		0.0632
(0.118) 		0.0203
(0.048)
11q loss 112 (10%) 978 3e-05
(0.000178) 		0.0002
(0.000941) 		0.826
(0.868) 		0.0904
(0.156) 		1e-05
(7e-05) 		9e-05
(0.000468) 		0.186
(0.272) 		0.541
(0.626) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.104
(0.173) 		0.00018
(0.000865) 		0.00493
(0.0149) 		0.00376
(0.0118)
22q loss 240 (22%) 850 0.614
(0.692) 		0.794
(0.842) 		0.544
(0.629) 		0.925
(0.947) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.00784
(0.0222) 		0.0322
(0.0686) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.514
(0.605) 		0.00032
(0.00142) 		0.00171
(0.00615) 		3e-05
(0.000178)
5q gain 50 (5%) 1040 0.13
(0.203) 		0.233
(0.327) 		0.162
(0.243) 		0.0536
(0.103) 		1e-05
(7e-05) 		0.00088
(0.00347) 		0.403
(0.505) 		0.013
(0.034) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.0803
(0.141) 		0.00558
(0.0167) 		9e-05
(0.000468) 		0.00061
(0.00247)
12p gain 93 (9%) 997 0.786
(0.838) 		0.793
(0.842) 		0.683
(0.75) 		0.166
(0.248) 		0.0219
(0.0512) 		0.00423
(0.013) 		0.0307
(0.0664) 		0.381
(0.484) 		0.0212
(0.0498) 		0.0234
(0.054) 		0.0394
(0.0803) 		0.015
(0.038) 		0.0848
(0.148) 		0.0227
(0.0527)
6q loss 189 (17%) 901 0.929
(0.95) 		0.644
(0.719) 		0.33
(0.429) 		0.843
(0.879) 		7e-05
(0.000376) 		0.00105
(0.00407) 		0.104
(0.173) 		0.00195
(0.00685) 		5e-05
(0.000279) 		3e-05
(0.000178) 		0.00107
(0.00414) 		0.168
(0.251) 		0.029
(0.0634) 		0.00233
(0.00794)
8q loss 52 (5%) 1038 0.45
(0.547) 		0.21
(0.301) 		0.034
(0.0714) 		0.749
(0.809) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.165
(0.246) 		0.611
(0.69) 		3e-05
(0.000178) 		1e-05
(7e-05) 		0.287
(0.386) 		0.00071
(0.00283) 		0.0489
(0.0952) 		1e-05
(7e-05)
13q loss 298 (27%) 792 2e-05
(0.000128) 		0.00159
(0.00576) 		0.606
(0.686) 		0.591
(0.673) 		0.00329
(0.0106) 		0.0156
(0.0391) 		0.0633
(0.118) 		0.825
(0.868) 		0.00031
(0.00138) 		0.00048
(0.00203) 		0.0644
(0.119) 		0.00933
(0.0256) 		0.438
(0.538) 		0.0349
(0.0729)
15q loss 154 (14%) 936 8e-05
(0.000421) 		1e-05
(7e-05) 		0.00144
(0.0053) 		0.00192
(0.00678) 		0.0857
(0.149) 		0.00021
(0.000976) 		0.0336
(0.0709) 		0.289
(0.387) 		0.0293
(0.0642) 		0.513
(0.605) 		0.0834
(0.146) 		0.485
(0.578) 		0.0683
(0.125) 		0.00041
(0.00176)
16q loss 104 (10%) 986 0.0342
(0.0718) 		0.301
(0.396) 		0.282
(0.381) 		0.815
(0.859) 		1e-05
(7e-05) 		2e-05
(0.000128) 		0.0175
(0.0427) 		0.00016
(0.000795) 		2e-05
(0.000128) 		1e-05
(7e-05) 		0.7
(0.766) 		0.00328
(0.0106) 		0.282
(0.381) 		0.129
(0.203)
17q loss 51 (5%) 1039 0.00874
(0.0242) 		0.061
(0.115) 		0.154
(0.233) 		0.0433
(0.0869) 		1e-05
(7e-05) 		0.00288
(0.0095) 		0.05
(0.0968) 		0.0141
(0.0362) 		0.00126
(0.00476) 		0.0002
(0.000941) 		0.079
(0.14) 		0.0933
(0.16) 		0.423
(0.527) 		0.127
(0.201)
xq loss 174 (16%) 916 0.035
(0.073) 		0.0251
(0.0569) 		0.151
(0.231) 		0.12
(0.192) 		0.686
(0.752) 		0.00024
(0.0011) 		0.00051
(0.0021) 		0.107
(0.176) 		0.00191
(0.00677) 		0.132
(0.207) 		4e-05
(0.00023) 		0.259
(0.357) 		0.00035
(0.00154) 		0.0009
(0.00353)
1q gain 112 (10%) 978 0.0945
(0.161) 		0.0897
(0.155) 		0.106
(0.174) 		0.624
(0.701) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.125
(0.197) 		0.105
(0.174) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.0189
(0.0452) 		0.0304
(0.0658) 		0.0113
(0.0299) 		0.272
(0.371)
2q gain 48 (4%) 1042 0.795
(0.842) 		0.91
(0.932) 		0.118
(0.19) 		0.203
(0.292) 		0.00098
(0.00381) 		0.0353
(0.0733) 		0.387
(0.49) 		0.343
(0.444) 		0.00683
(0.0198) 		0.00052
(0.00213) 		0.523
(0.613) 		0.0175
(0.0427) 		0.0119
(0.0315) 		0.0271
(0.0602)
3p gain 68 (6%) 1022 0.00174
(0.00624) 		0.0283
(0.0623) 		0.378
(0.48) 		0.0257
(0.0581) 		1e-05
(7e-05) 		0.0163
(0.0405) 		0.114
(0.185) 		0.49
(0.581) 		0.00038
(0.00165) 		0.00029
(0.00132) 		0.0798
(0.141) 		0.447
(0.544) 		0.28
(0.378) 		0.504
(0.596)
4q gain 43 (4%) 1047 0.226
(0.319) 		0.195
(0.282) 		0.159
(0.24) 		0.658
(0.731) 		0.00033
(0.00146) 		0.0114
(0.0303) 		0.258
(0.357) 		0.187
(0.273) 		3e-05
(0.000178) 		6e-05
(0.000328) 		0.335
(0.434) 		0.0204
(0.0482) 		0.0263
(0.0591) 		0.0149
(0.0378)
9p gain 64 (6%) 1026 0.0112
(0.0298) 		0.0304
(0.0658) 		0.844
(0.879) 		0.431
(0.532) 		8e-05
(0.000421) 		0.0181
(0.0436) 		0.662
(0.735) 		0.273
(0.371) 		3e-05
(0.000178) 		0.00046
(0.00195) 		0.731
(0.794) 		0.0277
(0.0612) 		0.973
(0.988) 		0.244
(0.339)
11q gain 74 (7%) 1016 0.147
(0.226) 		0.0643
(0.119) 		0.529
(0.617) 		0.243
(0.339) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.202
(0.291) 		0.0491
(0.0952) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.433
(0.533) 		0.0378
(0.0772) 		0.421
(0.526) 		0.0265
(0.0594)
18p gain 78 (7%) 1012 1e-05
(7e-05) 		0.00051
(0.0021) 		0.436
(0.537) 		0.365
(0.467) 		1e-05
(7e-05) 		0.0183
(0.0441) 		0.287
(0.386) 		0.106
(0.174) 		9e-05
(0.000468) 		0.00025
(0.00114) 		0.771
(0.826) 		0.0768
(0.137) 		0.187
(0.273) 		0.00592
(0.0176)
21q gain 88 (8%) 1002 0.00276
(0.00916) 		0.00764
(0.0218) 		0.0173
(0.0425) 		0.00411
(0.0128) 		1e-05
(7e-05) 		0.0734
(0.133) 		0.061
(0.115) 		0.124
(0.197) 		0.00015
(0.000749) 		1e-05
(7e-05) 		0.437
(0.538) 		0.0988
(0.166) 		0.787
(0.838) 		0.315
(0.413)
5p loss 80 (7%) 1010 1e-05
(7e-05) 		1e-05
(7e-05) 		0.00207
(0.00718) 		0.0734
(0.133) 		1e-05
(7e-05) 		5e-05
(0.000279) 		0.0752
(0.135) 		0.446
(0.543) 		0.114
(0.185) 		0.0249
(0.0565) 		0.114
(0.185) 		0.288
(0.386) 		0.179
(0.263) 		8e-05
(0.000421)
8p loss 75 (7%) 1015 0.285
(0.384) 		0.444
(0.542) 		0.221
(0.314) 		0.778
(0.833) 		6e-05
(0.000328) 		1e-05
(7e-05) 		0.323
(0.422) 		0.293
(0.39) 		1e-05
(7e-05) 		4e-05
(0.00023) 		0.299
(0.395) 		0.00143
(0.0053) 		0.00735
(0.021) 		1e-05
(7e-05)
17p loss 78 (7%) 1012 0.103
(0.171) 		0.0269
(0.06) 		0.323
(0.422) 		0.483
(0.578) 		1e-05
(7e-05) 		0.00021
(0.000976) 		0.474
(0.57) 		0.194
(0.281) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.0968
(0.164) 		0.00202
(0.00705) 		0.439
(0.538) 		0.0454
(0.0899)
4p gain 48 (4%) 1042 0.189
(0.275) 		0.753
(0.812) 		0.256
(0.353) 		0.488
(0.579) 		0.00511
(0.0154) 		0.0466
(0.0914) 		0.487
(0.579) 		0.0408
(0.0827) 		0.00307
(0.01) 		0.00084
(0.00333) 		0.478
(0.572) 		0.0767
(0.137) 		0.0243
(0.0555) 		0.259
(0.357)
6p gain 35 (3%) 1055 0.0351
(0.073) 		0.0977
(0.165) 		0.855
(0.888) 		0.283
(0.381) 		0.176
(0.26) 		0.0108
(0.0289) 		0.00656
(0.0192) 		0.557
(0.641) 		0.298
(0.394) 		0.278
(0.377) 		0.0129
(0.0338) 		0.024
(0.0553) 		0.0623
(0.117) 		0.0312
(0.067)
11p gain 49 (4%) 1041 0.93
(0.95) 		0.879
(0.907) 		0.691
(0.757) 		0.944
(0.962) 		0.0225
(0.0523) 		0.00017
(0.000834) 		0.466
(0.562) 		0.515
(0.606) 		0.0798
(0.141) 		0.00989
(0.0268) 		0.045
(0.0895) 		0.012
(0.0317) 		0.083
(0.146) 		0.00424
(0.013)
15q gain 37 (3%) 1053 0.083
(0.146) 		0.0976
(0.165) 		0.77
(0.826) 		0.0779
(0.139) 		0.0228
(0.0529) 		0.0136
(0.0353) 		0.0172
(0.0423) 		0.00322
(0.0104) 		0.0299
(0.0651) 		0.00421
(0.013) 		0.217
(0.309) 		0.439
(0.538) 		0.0534
(0.102) 		0.234
(0.328)
17p gain 73 (7%) 1017 0.00017
(0.000834) 		0.0141
(0.0362) 		0.0426
(0.0857) 		0.0153
(0.0387) 		0.0249
(0.0565) 		0.249
(0.345) 		0.0525
(0.101) 		0.276
(0.375) 		0.0273
(0.0605) 		0.203
(0.292) 		0.097
(0.164) 		0.721
(0.786) 		0.562
(0.645) 		0.189
(0.275)
17q gain 87 (8%) 1003 0.00137
(0.00512) 		0.0626
(0.117) 		0.0546
(0.104) 		0.0241
(0.0553) 		0.00683
(0.0198) 		0.115
(0.185) 		0.147
(0.225) 		0.521
(0.611) 		0.00131
(0.00493) 		0.0167
(0.0413) 		0.027
(0.0601) 		0.472
(0.568) 		0.27
(0.37) 		0.057
(0.108)
22q gain 57 (5%) 1033 2e-05
(0.000128) 		0.00545
(0.0164) 		0.479
(0.573) 		0.229
(0.322) 		0.873
(0.901) 		3e-05
(0.000178) 		0.584
(0.668) 		0.328
(0.427) 		0.464
(0.561) 		0.0362
(0.0747) 		0.0671
(0.123) 		0.631
(0.708) 		0.00249
(0.00836) 		0.00491
(0.0149)
2q loss 52 (5%) 1038 0.00198
(0.00693) 		0.0131
(0.0342) 		0.343
(0.444) 		0.666
(0.737) 		0.185
(0.271) 		0.00789
(0.0223) 		0.00208
(0.00719) 		0.266
(0.366) 		0.133
(0.209) 		0.0568
(0.108) 		0.0355
(0.0736) 		0.673
(0.74) 		0.164
(0.246) 		0.00443
(0.0135)
3p loss 70 (6%) 1020 0.892
(0.918) 		0.788
(0.838) 		0.664
(0.736) 		0.15
(0.228) 		0.177
(0.26) 		0.296
(0.394) 		0.00262
(0.00872) 		0.0336
(0.0709) 		0.0301
(0.0654) 		0.0422
(0.0851) 		0.0014
(0.0052) 		0.00056
(0.00229) 		0.0723
(0.131) 		0.129
(0.203)
6p loss 117 (11%) 973 0.624
(0.701) 		0.426
(0.529) 		0.591
(0.673) 		0.648
(0.722) 		2e-05
(0.000128) 		0.00189
(0.00672) 		0.376
(0.479) 		0.0211
(0.0496) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.45
(0.547) 		0.298
(0.395) 		0.358
(0.46) 		0.0456
(0.09)
9p loss 319 (29%) 771 0.00802
(0.0226) 		0.152
(0.232) 		0.603
(0.683) 		0.438
(0.538) 		1e-05
(7e-05) 		4e-05
(0.00023) 		0.0626
(0.117) 		0.00595
(0.0176) 		0.00724
(0.0208) 		0.0109
(0.0293) 		0.948
(0.966) 		0.23
(0.324) 		0.451
(0.547) 		0.0785
(0.139)
12q loss 108 (10%) 982 0.0263
(0.0591) 		0.12
(0.192) 		0.597
(0.677) 		0.574
(0.658) 		7e-05
(0.000376) 		1e-05
(7e-05) 		0.39
(0.493) 		0.831
(0.87) 		0.703
(0.769) 		6e-05
(0.000328) 		0.0037
(0.0117) 		0.425
(0.529) 		0.421
(0.526) 		3e-05
(0.000178)
16p loss 78 (7%) 1012 0.524
(0.613) 		0.851
(0.885) 		0.56
(0.642) 		0.735
(0.797) 		1e-05
(7e-05) 		0.0155
(0.0389) 		0.0299
(0.0651) 		0.00707
(0.0203) 		0.00036
(0.00157) 		0.0005
(0.00208) 		0.931
(0.95) 		0.465
(0.562) 		0.496
(0.587) 		0.24
(0.335)
19p loss 57 (5%) 1033 0.00326
(0.0105) 		0.00705
(0.0203) 		0.0244
(0.0557) 		0.409
(0.511) 		0.00414
(0.0128) 		0.445
(0.543) 		0.125
(0.197) 		0.594
(0.676) 		0.536
(0.623) 		0.642
(0.717) 		0.096
(0.163) 		0.107
(0.176) 		0.0223
(0.052) 		0.018
(0.0435)
21q loss 78 (7%) 1012 0.0234
(0.054) 		0.00116
(0.00444) 		0.0836
(0.146) 		0.264
(0.363) 		0.0842
(0.147) 		0.00011
(0.000559) 		0.148
(0.227) 		0.524
(0.613) 		0.0881
(0.153) 		1e-05
(7e-05) 		0.374
(0.478) 		0.0268
(0.06) 		0.157
(0.237) 		0.0289
(0.0634)
2p gain 51 (5%) 1039 0.603
(0.683) 		0.734
(0.797) 		0.549
(0.632) 		0.227
(0.32) 		0.00355
(0.0113) 		0.21
(0.301) 		0.369
(0.472) 		0.486
(0.578) 		0.00562
(0.0168) 		0.00245
(0.00827) 		0.648
(0.722) 		0.0207
(0.0488) 		0.00412
(0.0128) 		0.066
(0.122)
3q gain 72 (7%) 1018 0.00123
(0.00466) 		0.0621
(0.117) 		0.576
(0.659) 		0.0638
(0.119) 		1e-05
(7e-05) 		0.00038
(0.00165) 		0.066
(0.122) 		0.17
(0.253) 		1e-05
(7e-05) 		1e-05
(7e-05) 		0.388
(0.491) 		0.135
(0.211) 		0.837
(0.875) 		0.117
(0.188)
9q gain 95 (9%) 995 0.115
(0.186) 		0.0534
(0.102) 		0.657
(0.731) 		0.0946
(0.161) 		7e-05
(0.000376) 		0.0177
(0.0432) 		0.47
(0.566) 		0.406
(0.509) 		0.00018
(0.000865) 		0.00413
(0.0128) 		0.618
(0.695) 		0.0101
(0.0274) 		0.741
(0.803) 		0.225
(0.318)
16p gain 54 (5%) 1036 0.0153
(0.0387) 		0.0662
(0.122) 		0.49
(0.581) 		0.272
(0.371) 		0.0711
(0.13) 		0.727
(0.791) 		0.671
(0.74) 		0.0448
(0.0893) 		0.0156
(0.0391) 		0.862
(0.893) 		0.153
(0.232) 		0.0201
(0.0479) 		0.344
(0.444) 		0.0371
(0.0763)
16q gain 57 (5%) 1033 0.0167
(0.0413) 		0.015
(0.038) 		0.342
(0.443) 		0.0476
(0.0931) 		0.193
(0.28) 		0.215
(0.307) 		0.974
(0.988) 		0.113
(0.185) 		0.424
(0.529) 		0.466
(0.562) 		0.048
(0.0938) 		0.101
(0.169) 		0.14
(0.216) 		0.031
(0.0668)
2p loss 54 (5%) 1036 0.0014
(0.0052) 		0.028
(0.0618) 		0.485
(0.578) 		0.77
(0.826) 		0.0939
(0.16) 		0.0135
(0.035) 		0.0203
(0.048) 		0.524
(0.613) 		0.146
(0.224) 		0.046
(0.0907) 		0.0751
(0.135) 		0.4
(0.503) 		0.161
(0.241) 		0.126
(0.2)
6q gain 28 (3%) 1062 0.00819
(0.023) 		0.0373
(0.0764) 		0.756
(0.813) 		0.104
(0.173) 		0.0504
(0.0975) 		0.0982
(0.165) 		0.165
(0.246) 		0.86
(0.891) 		0.227
(0.32) 		0.299
(0.395) 		0.00607
(0.0179) 		0.15
(0.228) 		0.222
(0.314) 		0.0378
(0.0772)
xq gain 58 (5%) 1032 0.299
(0.395) 		0.967
(0.982) 		0.986
(0.998) 		0.516
(0.607) 		0.0751
(0.135) 		1e-05
(7e-05) 		0.0465
(0.0914) 		0.175
(0.26) 		0.101
(0.169) 		0.0003
(0.00135) 		0.0624
(0.117) 		0.357
(0.46) 		0.141
(0.217) 		0.00351
(0.0112)
1q loss 46 (4%) 1044 0.786
(0.838) 		0.978
(0.991) 		0.796
(0.842) 		0.363
(0.466) 		0.0475
(0.0931) 		0.0101
(0.0274) 		0.677
(0.744) 		0.0486
(0.0947) 		0.0665
(0.122) 		0.014
(0.036) 		0.094
(0.16) 		0.146
(0.225) 		0.639
(0.715) 		0.362
(0.465)
9q loss 142 (13%) 948 0.27
(0.369) 		0.11
(0.18) 		0.166
(0.248) 		0.109
(0.179) 		0.0155
(0.0389) 		0.297
(0.394) 		0.0689
(0.126) 		0.0431
(0.0866) 		0.0057
(0.017) 		0.0335
(0.0709) 		0.462
(0.56) 		0.828
(0.868) 		0.863
(0.893) 		0.726
(0.791)
12p loss 84 (8%) 1006 0.0325
(0.069) 		0.152
(0.232) 		0.647
(0.722) 		0.848
(0.882) 		0.00193
(0.0068) 		0.0931
(0.16) 		0.799
(0.845) 		0.743
(0.804) 		0.111
(0.18) 		0.0237
(0.0546) 		0.0513
(0.0991) 		0.441
(0.539) 		0.791
(0.84) 		0.0436
(0.087)
18q loss 123 (11%) 967 0.0435
(0.087) 		0.00855
(0.0238) 		0.534
(0.622) 		0.328
(0.427) 		0.539
(0.624) 		0.00051
(0.0021) 		0.44
(0.539) 		0.479
(0.573) 		0.954
(0.971) 		0.288
(0.386) 		0.0187
(0.0449) 		0.712
(0.777) 		0.24
(0.335) 		0.29
(0.388)
20p loss 26 (2%) 1064 0.00018
(0.000865) 		5e-05
(0.000279) 		0.0463
(0.0912) 		0.0946
(0.161) 		0.0338
(0.0712) 		0.184
(0.27) 		0.321
(0.42) 		0.094
(0.16) 		0.748
(0.809) 		0.182
(0.268) 		0.428
(0.531) 		0.485
(0.578) 		0.75
(0.809) 		0.285
(0.384)
20q loss 21 (2%) 1069 0.00238
(0.00808) 		0.00012
(0.000607) 		0.475
(0.57) 		0.266
(0.366) 		0.00631
(0.0186) 		0.268
(0.367) 		0.478
(0.572) 		0.671
(0.74) 		0.8
(0.845) 		0.0124
(0.0326) 		0.832
(0.87) 		0.542
(0.627) 		0.382
(0.484) 		0.408
(0.511)
10q gain 12 (1%) 1078 0.786
(0.838) 		1
(1.00) 		0.0743
(0.134) 		0.796
(0.842) 		0.0453
(0.0899) 		0.00071
(0.00283) 		0.0914
(0.157) 		0.102
(0.171) 		0.853
(0.887) 		0.123
(0.196) 		0.136
(0.211) 		0.159
(0.24) 		0.588
(0.672) 		0.00407
(0.0127)
14q gain 26 (2%) 1064 0.392
(0.495) 		0.781
(0.835) 		0.0172
(0.0423) 		0.807
(0.851) 		0.00147
(0.00537) 		0.393
(0.495) 		1
(1.00) 		0.672
(0.74) 		0.0296
(0.0646) 		0.0779
(0.139) 		0.339
(0.439) 		0.684
(0.751) 		0.672
(0.74) 		0.24
(0.335)
3q loss 62 (6%) 1028 0.117
(0.189) 		0.124
(0.197) 		0.787
(0.838) 		0.712
(0.777) 		0.138
(0.214) 		0.138
(0.214) 		0.122
(0.195) 		0.0702
(0.128) 		0.101
(0.169) 		0.0347
(0.0727) 		0.0541
(0.104) 		0.0134
(0.0349) 		0.0873
(0.152) 		0.00642
(0.0188)
18p loss 137 (13%) 953 0.00948
(0.026) 		0.0321
(0.0685) 		0.304
(0.4) 		0.222
(0.314) 		0.355
(0.457) 		0.0158
(0.0395) 		0.304
(0.4) 		0.214
(0.306) 		0.548
(0.632) 		0.622
(0.699) 		0.24
(0.335) 		0.871
(0.9) 		0.618
(0.695) 		0.534
(0.622)
xp gain 35 (3%) 1055 0.194
(0.281) 		1
(1.00) 		0.819
(0.863) 		0.184
(0.27) 		0.903
(0.928) 		5e-05
(0.000279) 		0.146
(0.225) 		0.667
(0.738) 		0.844
(0.879) 		0.736
(0.798) 		0.661
(0.734) 		0.91
(0.932) 		0.886
(0.913) 		0.272
(0.371)
7p loss 10 (1%) 1080 0.0246
(0.056) 		0.0883
(0.153) 		0.197
(0.285) 		0.0611
(0.115) 		0.105
(0.173) 		0.21
(0.301) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
13q gain 17 (2%) 1073 0.0726
(0.132) 		0.496
(0.587) 		0.219
(0.311) 		0.827
(0.868) 		0.0856
(0.149) 		0.533
(0.621) 		0.507
(0.598) 		0.638
(0.715) 		0.29
(0.388) 		0.528
(0.616) 		0.294
(0.392) 		0.43
(0.532) 		0.376
(0.478) 		0.858
(0.89)
7q loss 9 (1%) 1081 0.0749
(0.135) 		0.611
(0.69) 		0.595
(0.677) 		0.213
(0.305) 		0.114
(0.185) 		0.0926
(0.159) 		0.0673
(0.123) 		0.371
(0.475) 		0.392
(0.495) 		1
(1.00) 		1
(1.00) 		0.833
(0.871) 		0.558
(0.642) 		0.906
(0.931)
'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S1.  Gene #1: '1p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
1P GAIN MUTATED 73 4 18
1P GAIN WILD-TYPE 456 466 73

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #5: 'CN_CNMF'

'1p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S2.  Gene #1: '1p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
1P GAIN MUTATED 19 5 1 0
1P GAIN WILD-TYPE 158 220 87 160

Figure S2.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'1p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00582 (Fisher's exact test), Q value = 0.017

Table S3.  Gene #1: '1p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
1P GAIN MUTATED 18 19 2
1P GAIN WILD-TYPE 216 235 156

Figure S3.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'1p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S4.  Gene #1: '1p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
1P GAIN MUTATED 38 0 1
1P GAIN WILD-TYPE 206 189 226

Figure S4.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S5.  Gene #1: '1p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
1P GAIN MUTATED 33 6 0
1P GAIN WILD-TYPE 170 184 267

Figure S5.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_CNMF'

P value = 0.0066 (Fisher's exact test), Q value = 0.019

Table S6.  Gene #1: '1p gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
1P GAIN MUTATED 8 4 0 1
1P GAIN WILD-TYPE 132 103 82 179

Figure S6.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S7.  Gene #1: '1p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
1P GAIN MUTATED 3 0 10
1P GAIN WILD-TYPE 219 184 93

Figure S7.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00292 (Fisher's exact test), Q value = 0.0096

Table S8.  Gene #1: '1p gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
1P GAIN MUTATED 4 8 0 1
1P GAIN WILD-TYPE 123 111 105 153

Figure S8.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0011 (Fisher's exact test), Q value = 0.0042

Table S9.  Gene #1: '1p gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
1P GAIN MUTATED 1 4 0 0 6 2
1P GAIN WILD-TYPE 98 73 118 56 57 90

Figure S9.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S10.  Gene #2: '1q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
1Q GAIN MUTATED 78 17 17
1Q GAIN WILD-TYPE 451 453 74

Figure S10.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S11.  Gene #2: '1q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
1Q GAIN MUTATED 24 9 3 2
1Q GAIN WILD-TYPE 153 216 85 158

Figure S11.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S12.  Gene #2: '1q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
1Q GAIN MUTATED 41 6 3
1Q GAIN WILD-TYPE 203 183 224

Figure S12.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S13.  Gene #2: '1q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
1Q GAIN MUTATED 35 9 6
1Q GAIN WILD-TYPE 168 181 261

Figure S13.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 0.0189 (Fisher's exact test), Q value = 0.045

Table S14.  Gene #2: '1q gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
1Q GAIN MUTATED 12 4 0 7
1Q GAIN WILD-TYPE 128 103 82 173

Figure S14.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0304 (Fisher's exact test), Q value = 0.066

Table S15.  Gene #2: '1q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
1Q GAIN MUTATED 7 6 10
1Q GAIN WILD-TYPE 215 178 93

Figure S15.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.03

Table S16.  Gene #2: '1q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
1Q GAIN MUTATED 5 10 0 8
1Q GAIN WILD-TYPE 122 109 105 146

Figure S16.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 0.00355 (Fisher's exact test), Q value = 0.011

Table S17.  Gene #3: '2p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
2P GAIN MUTATED 35 11 5
2P GAIN WILD-TYPE 494 459 86

Figure S17.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'CN_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.00562 (Fisher's exact test), Q value = 0.017

Table S18.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
2P GAIN MUTATED 17 3 5
2P GAIN WILD-TYPE 227 186 222

Figure S18.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00245 (Fisher's exact test), Q value = 0.0083

Table S19.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
2P GAIN MUTATED 16 4 5
2P GAIN WILD-TYPE 187 186 262

Figure S19.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0207 (Fisher's exact test), Q value = 0.049

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
2P GAIN MUTATED 5 2 7
2P GAIN WILD-TYPE 217 182 96

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

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00412 (Fisher's exact test), Q value = 0.013

Table S21.  Gene #3: '2p gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
2P GAIN MUTATED 2 9 0 3
2P GAIN WILD-TYPE 125 110 105 151

Figure S21.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'CN_CNMF'

P value = 0.00098 (Fisher's exact test), Q value = 0.0038

Table S22.  Gene #4: '2q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
2Q GAIN MUTATED 32 9 7
2Q GAIN WILD-TYPE 497 461 84

Figure S22.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.0353 (Fisher's exact test), Q value = 0.073

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
2Q GAIN MUTATED 10 4 0 3
2Q GAIN WILD-TYPE 167 221 88 157

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

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.00683 (Fisher's exact test), Q value = 0.02

Table S24.  Gene #4: '2q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
2Q GAIN MUTATED 16 3 4
2Q GAIN WILD-TYPE 228 186 223

Figure S24.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0021

Table S25.  Gene #4: '2q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
2Q GAIN MUTATED 16 3 4
2Q GAIN WILD-TYPE 187 187 263

Figure S25.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0175 (Fisher's exact test), Q value = 0.043

Table S26.  Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
2Q GAIN MUTATED 4 2 7
2Q GAIN WILD-TYPE 218 182 96

Figure S26.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.031

Table S27.  Gene #4: '2q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
2Q GAIN MUTATED 2 8 0 3
2Q GAIN WILD-TYPE 125 111 105 151

Figure S27.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0271 (Fisher's exact test), Q value = 0.06

Table S28.  Gene #4: '2q gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
2Q GAIN MUTATED 2 4 1 0 5 1
2Q GAIN WILD-TYPE 97 73 117 56 58 91

Figure S28.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p gain' versus 'MRNA_CNMF'

P value = 0.00174 (Fisher's exact test), Q value = 0.0062

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
3P GAIN MUTATED 16 18 5 15
3P GAIN WILD-TYPE 142 78 132 102

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

'3p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0283 (Fisher's exact test), Q value = 0.062

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
3P GAIN MUTATED 13 18 5 18
3P GAIN WILD-TYPE 135 84 95 140

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

'3p gain' versus 'MIR_CHIERARCHICAL'

P value = 0.0257 (Fisher's exact test), Q value = 0.058

Table S31.  Gene #5: '3p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
3P GAIN MUTATED 35 5 15
3P GAIN WILD-TYPE 258 119 114

Figure S31.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
3P GAIN MUTATED 46 12 10
3P GAIN WILD-TYPE 483 458 81

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

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.04

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
3P GAIN MUTATED 13 5 1 3
3P GAIN WILD-TYPE 164 220 87 157

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

'3p gain' versus 'MRNASEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0016

Table S34.  Gene #5: '3p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
3P GAIN MUTATED 21 3 5
3P GAIN WILD-TYPE 223 186 222

Figure S34.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.0013

Table S35.  Gene #5: '3p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
3P GAIN MUTATED 19 6 4
3P GAIN WILD-TYPE 184 184 263

Figure S35.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MRNA_CNMF'

P value = 0.00123 (Fisher's exact test), Q value = 0.0047

Table S36.  Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
3Q GAIN MUTATED 18 20 6 16
3Q GAIN WILD-TYPE 140 76 131 101

Figure S36.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S37.  Gene #6: '3q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
3Q GAIN MUTATED 50 11 11
3Q GAIN WILD-TYPE 479 459 80

Figure S37.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0016

Table S38.  Gene #6: '3q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
3Q GAIN MUTATED 15 3 1 2
3Q GAIN WILD-TYPE 162 222 87 158

Figure S38.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S39.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
3Q GAIN MUTATED 26 3 2
3Q GAIN WILD-TYPE 218 186 225

Figure S39.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S40.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
3Q GAIN MUTATED 24 4 3
3Q GAIN WILD-TYPE 179 186 264

Figure S40.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 0.00511 (Fisher's exact test), Q value = 0.015

Table S41.  Gene #7: '4p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
4P GAIN MUTATED 27 12 9
4P GAIN WILD-TYPE 502 458 82

Figure S41.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #5: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.0466 (Fisher's exact test), Q value = 0.091

Table S42.  Gene #7: '4p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
4P GAIN MUTATED 6 8 3 0
4P GAIN WILD-TYPE 171 217 85 160

Figure S42.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'4p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0408 (Fisher's exact test), Q value = 0.083

Table S43.  Gene #7: '4p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
4P GAIN MUTATED 15 5 5
4P GAIN WILD-TYPE 219 249 153

Figure S43.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.00307 (Fisher's exact test), Q value = 0.01

Table S44.  Gene #7: '4p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
4P GAIN MUTATED 16 2 4
4P GAIN WILD-TYPE 228 187 223

Figure S44.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00084 (Fisher's exact test), Q value = 0.0033

Table S45.  Gene #7: '4p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
4P GAIN MUTATED 14 6 2
4P GAIN WILD-TYPE 189 184 265

Figure S45.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0243 (Fisher's exact test), Q value = 0.056

Table S46.  Gene #7: '4p gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
4P GAIN MUTATED 4 7 0 2
4P GAIN WILD-TYPE 123 112 105 152

Figure S46.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'4q gain' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0015

Table S47.  Gene #8: '4q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
4Q GAIN MUTATED 26 8 9
4Q GAIN WILD-TYPE 503 462 82

Figure S47.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #5: 'CN_CNMF'

'4q gain' versus 'METHLYATION_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.03

Table S48.  Gene #8: '4q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
4Q GAIN MUTATED 8 3 3 0
4Q GAIN WILD-TYPE 169 222 85 160

Figure S48.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00018

Table S49.  Gene #8: '4q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
4Q GAIN MUTATED 15 2 0
4Q GAIN WILD-TYPE 229 187 227

Figure S49.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00033

Table S50.  Gene #8: '4q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
4Q GAIN MUTATED 14 1 2
4Q GAIN WILD-TYPE 189 189 265

Figure S50.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0204 (Fisher's exact test), Q value = 0.048

Table S51.  Gene #8: '4q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
4Q GAIN MUTATED 1 3 5
4Q GAIN WILD-TYPE 221 181 98

Figure S51.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0263 (Fisher's exact test), Q value = 0.059

Table S52.  Gene #8: '4q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
4Q GAIN MUTATED 1 6 0 2
4Q GAIN WILD-TYPE 126 113 105 152

Figure S52.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'4q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0149 (Fisher's exact test), Q value = 0.038

Table S53.  Gene #8: '4q gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
4Q GAIN MUTATED 1 1 2 0 5 0
4Q GAIN WILD-TYPE 98 76 116 56 58 92

Figure S53.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S54.  Gene #9: '5p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
5P GAIN MUTATED 44 8 8
5P GAIN WILD-TYPE 485 462 83

Figure S54.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.00975 (Fisher's exact test), Q value = 0.027

Table S55.  Gene #9: '5p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
5P GAIN MUTATED 9 4 3 0
5P GAIN WILD-TYPE 168 221 85 160

Figure S55.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'5p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00796 (Fisher's exact test), Q value = 0.022

Table S56.  Gene #9: '5p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
5P GAIN MUTATED 6 12 0
5P GAIN WILD-TYPE 228 242 158

Figure S56.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S57.  Gene #9: '5p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
5P GAIN MUTATED 18 1 2
5P GAIN WILD-TYPE 226 188 225

Figure S57.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00023

Table S58.  Gene #9: '5p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
5P GAIN MUTATED 17 3 1
5P GAIN WILD-TYPE 186 187 266

Figure S58.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 0.0259 (Fisher's exact test), Q value = 0.059

Table S59.  Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
5P GAIN MUTATED 5 5 0 1
5P GAIN WILD-TYPE 135 102 82 179

Figure S59.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0269 (Fisher's exact test), Q value = 0.06

Table S60.  Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
5P GAIN MUTATED 3 2 6
5P GAIN WILD-TYPE 219 182 97

Figure S60.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S61.  Gene #9: '5p gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
5P GAIN MUTATED 0 10 0 1
5P GAIN WILD-TYPE 127 109 105 153

Figure S61.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-04 (Fisher's exact test), Q value = 0.0035

Table S62.  Gene #9: '5p gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
5P GAIN MUTATED 1 3 0 0 6 1
5P GAIN WILD-TYPE 98 74 118 56 57 91

Figure S62.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
5Q GAIN MUTATED 39 4 7
5Q GAIN WILD-TYPE 490 466 84

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

'5q gain' versus 'METHLYATION_CNMF'

P value = 0.00088 (Fisher's exact test), Q value = 0.0035

Table S64.  Gene #10: '5q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
5Q GAIN MUTATED 10 2 3 0
5Q GAIN WILD-TYPE 167 223 85 160

Figure S64.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'5q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.013 (Fisher's exact test), Q value = 0.034

Table S65.  Gene #10: '5q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
5Q GAIN MUTATED 4 10 0
5Q GAIN WILD-TYPE 230 244 158

Figure S65.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S66.  Gene #10: '5q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
5Q GAIN MUTATED 17 1 1
5Q GAIN WILD-TYPE 227 188 226

Figure S66.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
5Q GAIN MUTATED 17 1 1
5Q GAIN WILD-TYPE 186 189 266

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

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00558 (Fisher's exact test), Q value = 0.017

Table S68.  Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
5Q GAIN MUTATED 2 1 6
5Q GAIN WILD-TYPE 220 183 97

Figure S68.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00047

Table S69.  Gene #10: '5q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
5Q GAIN MUTATED 0 8 0 1
5Q GAIN WILD-TYPE 127 111 105 153

Figure S69.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.0025

Table S70.  Gene #10: '5q gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
5Q GAIN MUTATED 1 1 0 0 6 1
5Q GAIN WILD-TYPE 98 76 118 56 57 91

Figure S70.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p gain' versus 'MRNA_CNMF'

P value = 0.0351 (Fisher's exact test), Q value = 0.073

Table S71.  Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
6P GAIN MUTATED 5 9 2 5
6P GAIN WILD-TYPE 153 87 135 112

Figure S71.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.029

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
6P GAIN MUTATED 6 9 0 0
6P GAIN WILD-TYPE 171 216 88 160

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

'6p gain' versus 'RPPA_CNMF'

P value = 0.00656 (Fisher's exact test), Q value = 0.019

Table S73.  Gene #11: '6p gain' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
6P GAIN MUTATED 3 1 10 2
6P GAIN WILD-TYPE 210 167 146 107

Figure S73.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'RPPA_CNMF'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.034

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
6P GAIN MUTATED 4 5 1 0
6P GAIN WILD-TYPE 136 102 81 180

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

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.024 (Fisher's exact test), Q value = 0.055

Table S75.  Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
6P GAIN MUTATED 6 0 4
6P GAIN WILD-TYPE 216 184 99

Figure S75.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0312 (Fisher's exact test), Q value = 0.067

Table S76.  Gene #11: '6p gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
6P GAIN MUTATED 4 4 0 0 0 2
6P GAIN WILD-TYPE 95 73 118 56 63 90

Figure S76.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'MRNA_CNMF'

P value = 0.00819 (Fisher's exact test), Q value = 0.023

Table S77.  Gene #12: '6q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
6Q GAIN MUTATED 4 10 2 4
6Q GAIN WILD-TYPE 154 86 135 113

Figure S77.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0373 (Fisher's exact test), Q value = 0.076

Table S78.  Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
6Q GAIN MUTATED 5 7 0 8
6Q GAIN WILD-TYPE 143 95 100 150

Figure S78.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 0.00607 (Fisher's exact test), Q value = 0.018

Table S79.  Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
6Q GAIN MUTATED 0 4 1 0
6Q GAIN WILD-TYPE 140 103 81 180

Figure S79.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0378 (Fisher's exact test), Q value = 0.077

Table S80.  Gene #12: '6q gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
6Q GAIN MUTATED 0 3 0 0 0 2
6Q GAIN WILD-TYPE 99 74 118 56 63 90

Figure S80.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S81.  Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
7P GAIN MUTATED 146 66 115 85
7P GAIN WILD-TYPE 12 30 22 32

Figure S81.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S82.  Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
7P GAIN MUTATED 132 55 86 139
7P GAIN WILD-TYPE 16 47 14 19

Figure S82.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7p gain' versus 'MIR_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0021

Table S83.  Gene #13: '7p gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
7P GAIN MUTATED 128 143 65 110
7P GAIN WILD-TYPE 15 44 25 16

Figure S83.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'MIR_CNMF'

'7p gain' versus 'MIR_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S84.  Gene #13: '7p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
7P GAIN MUTATED 215 113 118
7P GAIN WILD-TYPE 78 11 11

Figure S84.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S85.  Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
7P GAIN MUTATED 481 61 52
7P GAIN WILD-TYPE 48 409 39

Figure S85.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S86.  Gene #13: '7p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
7P GAIN MUTATED 150 44 30 15
7P GAIN WILD-TYPE 27 181 58 145

Figure S86.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0021

Table S87.  Gene #13: '7p gain' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
7P GAIN MUTATED 96 51 81 50
7P GAIN WILD-TYPE 117 117 75 59

Figure S87.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'RPPA_CNMF'

'7p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00086

Table S88.  Gene #13: '7p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
7P GAIN MUTATED 116 116 46
7P GAIN WILD-TYPE 118 138 112

Figure S88.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S89.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
7P GAIN MUTATED 172 36 36
7P GAIN WILD-TYPE 72 153 191

Figure S89.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S90.  Gene #13: '7p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
7P GAIN MUTATED 166 31 47
7P GAIN WILD-TYPE 37 159 220

Figure S90.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.00145 (Fisher's exact test), Q value = 0.0053

Table S91.  Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
7P GAIN MUTATED 44 34 12 32
7P GAIN WILD-TYPE 96 73 70 148

Figure S91.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S92.  Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
7P GAIN MUTATED 39 28 55
7P GAIN WILD-TYPE 183 156 48

Figure S92.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
7P GAIN MUTATED 33 45 11 32
7P GAIN WILD-TYPE 94 74 94 122

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

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S94.  Gene #13: '7p gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
7P GAIN MUTATED 16 11 19 7 47 21
7P GAIN WILD-TYPE 83 66 99 49 16 71

Figure S94.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S95.  Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
7Q GAIN MUTATED 145 65 116 90
7Q GAIN WILD-TYPE 13 31 21 27

Figure S95.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S96.  Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
7Q GAIN MUTATED 130 61 86 139
7Q GAIN WILD-TYPE 18 41 14 19

Figure S96.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7q gain' versus 'MIR_CNMF'

P value = 0.00358 (Fisher's exact test), Q value = 0.011

Table S97.  Gene #14: '7q gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
7Q GAIN MUTATED 129 143 70 108
7Q GAIN WILD-TYPE 14 44 20 18

Figure S97.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'MIR_CNMF'

'7q gain' versus 'MIR_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00051

Table S98.  Gene #14: '7q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
7Q GAIN MUTATED 222 112 116
7Q GAIN WILD-TYPE 71 12 13

Figure S98.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S99.  Gene #14: '7q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
7Q GAIN MUTATED 487 92 52
7Q GAIN WILD-TYPE 42 378 39

Figure S99.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S100.  Gene #14: '7q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
7Q GAIN MUTATED 155 61 34 23
7Q GAIN WILD-TYPE 22 164 54 137

Figure S100.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0138 (Fisher's exact test), Q value = 0.035

Table S101.  Gene #14: '7q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
7Q GAIN MUTATED 121 126 59
7Q GAIN WILD-TYPE 113 128 99

Figure S101.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S102.  Gene #14: '7q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
7Q GAIN MUTATED 178 50 50
7Q GAIN WILD-TYPE 66 139 177

Figure S102.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S103.  Gene #14: '7q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
7Q GAIN MUTATED 171 43 64
7Q GAIN WILD-TYPE 32 147 203

Figure S103.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.00755 (Fisher's exact test), Q value = 0.022

Table S104.  Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
7Q GAIN MUTATED 49 41 15 47
7Q GAIN WILD-TYPE 91 66 67 133

Figure S104.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S105.  Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
7Q GAIN MUTATED 50 43 59
7Q GAIN WILD-TYPE 172 141 44

Figure S105.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S106.  Gene #14: '7q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
7Q GAIN MUTATED 38 53 14 46
7Q GAIN WILD-TYPE 89 66 91 108

Figure S106.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
7Q GAIN MUTATED 21 15 29 7 50 29
7Q GAIN WILD-TYPE 78 62 89 49 13 63

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

'8p gain' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S108.  Gene #15: '8p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
8P GAIN MUTATED 7 19 5 17
8P GAIN WILD-TYPE 151 77 132 100

Figure S108.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00059 (Fisher's exact test), Q value = 0.0024

Table S109.  Gene #15: '8p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
8P GAIN MUTATED 10 21 4 13
8P GAIN WILD-TYPE 138 81 96 145

Figure S109.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8p gain' versus 'MIR_CNMF'

P value = 0.0379 (Fisher's exact test), Q value = 0.077

Table S110.  Gene #15: '8p gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
8P GAIN MUTATED 7 21 13 8
8P GAIN WILD-TYPE 136 166 77 118

Figure S110.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'MIR_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 0.00896 (Fisher's exact test), Q value = 0.025

Table S111.  Gene #15: '8p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
8P GAIN MUTATED 42 42 17
8P GAIN WILD-TYPE 487 428 74

Figure S111.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #5: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00033

Table S112.  Gene #15: '8p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
8P GAIN MUTATED 10 37 3 8
8P GAIN WILD-TYPE 167 188 85 152

Figure S112.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'8p gain' versus 'RPPA_CNMF'

P value = 0.00888 (Fisher's exact test), Q value = 0.025

Table S113.  Gene #15: '8p gain' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
8P GAIN MUTATED 21 6 18 15
8P GAIN WILD-TYPE 192 162 138 94

Figure S113.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'RPPA_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00178 (Fisher's exact test), Q value = 0.0064

Table S114.  Gene #15: '8p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
8P GAIN MUTATED 20 31 16
8P GAIN WILD-TYPE 183 159 251

Figure S114.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.049 (Fisher's exact test), Q value = 0.095

Table S115.  Gene #15: '8p gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
8P GAIN MUTATED 19 12 9 8
8P GAIN WILD-TYPE 108 107 96 146

Figure S115.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00286 (Fisher's exact test), Q value = 0.0095

Table S116.  Gene #15: '8p gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
8P GAIN MUTATED 18 7 5 2 3 13
8P GAIN WILD-TYPE 81 70 113 54 60 79

Figure S116.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S117.  Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
8Q GAIN MUTATED 7 20 6 21
8Q GAIN WILD-TYPE 151 76 131 96

Figure S117.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8q gain' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S118.  Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
8Q GAIN MUTATED 9 26 4 15
8Q GAIN WILD-TYPE 139 76 96 143

Figure S118.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8q gain' versus 'MIR_CNMF'

P value = 0.04 (Fisher's exact test), Q value = 0.081

Table S119.  Gene #16: '8q gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
8Q GAIN MUTATED 9 26 12 8
8Q GAIN WILD-TYPE 134 161 78 118

Figure S119.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'MIR_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 0.00245 (Fisher's exact test), Q value = 0.0083

Table S120.  Gene #16: '8q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
8Q GAIN MUTATED 44 54 19
8Q GAIN WILD-TYPE 485 416 72

Figure S120.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S121.  Gene #16: '8q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
8Q GAIN MUTATED 11 43 6 8
8Q GAIN WILD-TYPE 166 182 82 152

Figure S121.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 0.0202 (Fisher's exact test), Q value = 0.048

Table S122.  Gene #16: '8q gain' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
8Q GAIN MUTATED 22 8 20 16
8Q GAIN WILD-TYPE 191 160 136 93

Figure S122.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'RPPA_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0019

Table S123.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
8Q GAIN MUTATED 21 37 20
8Q GAIN WILD-TYPE 182 153 247

Figure S123.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0434 (Fisher's exact test), Q value = 0.087

Table S124.  Gene #16: '8q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
8Q GAIN MUTATED 22 13 12 10
8Q GAIN WILD-TYPE 105 106 93 144

Figure S124.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0011

Table S125.  Gene #16: '8q gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
8Q GAIN MUTATED 21 9 6 2 3 16
8Q GAIN WILD-TYPE 78 68 112 54 60 76

Figure S125.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'MRNA_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.03

Table S126.  Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
9P GAIN MUTATED 16 15 5 8
9P GAIN WILD-TYPE 142 81 132 109

Figure S126.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0304 (Fisher's exact test), Q value = 0.066

Table S127.  Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
9P GAIN MUTATED 15 12 2 15
9P GAIN WILD-TYPE 133 90 98 143

Figure S127.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00042

Table S128.  Gene #17: '9p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
9P GAIN MUTATED 38 13 13
9P GAIN WILD-TYPE 491 457 78

Figure S128.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #5: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.044

Table S129.  Gene #17: '9p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
9P GAIN MUTATED 14 9 2 2
9P GAIN WILD-TYPE 163 216 86 158

Figure S129.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00018

Table S130.  Gene #17: '9p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
9P GAIN MUTATED 25 4 5
9P GAIN WILD-TYPE 219 185 222

Figure S130.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0019

Table S131.  Gene #17: '9p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
9P GAIN MUTATED 21 7 6
9P GAIN WILD-TYPE 182 183 261

Figure S131.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0277 (Fisher's exact test), Q value = 0.061

Table S132.  Gene #17: '9p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
9P GAIN MUTATED 4 5 8
9P GAIN WILD-TYPE 218 179 95

Figure S132.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00038

Table S133.  Gene #18: '9q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
9Q GAIN MUTATED 58 22 15
9Q GAIN WILD-TYPE 471 448 76

Figure S133.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #5: 'CN_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.043

Table S134.  Gene #18: '9q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
9Q GAIN MUTATED 17 15 2 4
9Q GAIN WILD-TYPE 160 210 86 156

Figure S134.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00086

Table S135.  Gene #18: '9q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
9Q GAIN MUTATED 29 6 8
9Q GAIN WILD-TYPE 215 183 219

Figure S135.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00413 (Fisher's exact test), Q value = 0.013

Table S136.  Gene #18: '9q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
9Q GAIN MUTATED 23 10 10
9Q GAIN WILD-TYPE 180 180 257

Figure S136.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.027

Table S137.  Gene #18: '9q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
9Q GAIN MUTATED 6 7 11
9Q GAIN WILD-TYPE 216 177 92

Figure S137.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'10p gain' versus 'MRNA_CNMF'

P value = 0.00137 (Fisher's exact test), Q value = 0.0051

Table S138.  Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
10P GAIN MUTATED 1 6 0 5
10P GAIN WILD-TYPE 157 90 137 112

Figure S138.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00051

Table S139.  Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
10P GAIN MUTATED 2 9 0 1
10P GAIN WILD-TYPE 146 93 100 157

Figure S139.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S140.  Gene #19: '10p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
10P GAIN MUTATED 2 61 7
10P GAIN WILD-TYPE 527 409 84

Figure S140.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S141.  Gene #19: '10p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
10P GAIN MUTATED 0 56 2 0
10P GAIN WILD-TYPE 177 169 86 160

Figure S141.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'10p gain' versus 'RPPA_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0013

Table S142.  Gene #19: '10p gain' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
10P GAIN MUTATED 17 4 10 18
10P GAIN WILD-TYPE 196 164 146 91

Figure S142.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'RPPA_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0019

Table S143.  Gene #19: '10p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
10P GAIN MUTATED 12 13 34
10P GAIN WILD-TYPE 232 176 193

Figure S143.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S144.  Gene #19: '10p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
10P GAIN MUTATED 2 43 14
10P GAIN WILD-TYPE 201 147 253

Figure S144.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CNMF'

P value = 0.0277 (Fisher's exact test), Q value = 0.061

Table S145.  Gene #19: '10p gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
10P GAIN MUTATED 16 20 5 15
10P GAIN WILD-TYPE 124 87 77 165

Figure S145.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'10p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.045

Table S146.  Gene #19: '10p gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
10P GAIN MUTATED 18 20 6 12
10P GAIN WILD-TYPE 109 99 99 142

Figure S146.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S147.  Gene #19: '10p gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
10P GAIN MUTATED 21 17 7 0 0 11
10P GAIN WILD-TYPE 78 60 111 56 63 81

Figure S147.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 0.0453 (Fisher's exact test), Q value = 0.09

Table S148.  Gene #20: '10q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
10Q GAIN MUTATED 2 8 2
10Q GAIN WILD-TYPE 527 462 89

Figure S148.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #5: 'CN_CNMF'

'10q gain' versus 'METHLYATION_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0028

Table S149.  Gene #20: '10q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
10Q GAIN MUTATED 0 9 0 0
10Q GAIN WILD-TYPE 177 216 88 160

Figure S149.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'10q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00407 (Fisher's exact test), Q value = 0.013

Table S150.  Gene #20: '10q gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
10Q GAIN MUTATED 0 6 2 0 0 1
10Q GAIN WILD-TYPE 99 71 116 56 63 91

Figure S150.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.052

Table S151.  Gene #21: '11p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
11P GAIN MUTATED 18 30 1
11P GAIN WILD-TYPE 511 440 90

Figure S151.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #5: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00083

Table S152.  Gene #21: '11p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
11P GAIN MUTATED 3 10 2 20
11P GAIN WILD-TYPE 174 215 86 140

Figure S152.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00989 (Fisher's exact test), Q value = 0.027

Table S153.  Gene #21: '11p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
11P GAIN MUTATED 6 8 25
11P GAIN WILD-TYPE 197 182 242

Figure S153.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CNMF'

P value = 0.045 (Fisher's exact test), Q value = 0.089

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
11P GAIN MUTATED 6 4 11 11
11P GAIN WILD-TYPE 134 103 71 169

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

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.032

Table S155.  Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
11P GAIN MUTATED 14 17 1
11P GAIN WILD-TYPE 208 167 102

Figure S155.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00424 (Fisher's exact test), Q value = 0.013

Table S156.  Gene #21: '11p gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
11P GAIN MUTATED 4 2 8 8 0 10
11P GAIN WILD-TYPE 95 75 110 48 63 82

Figure S156.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S157.  Gene #22: '11q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
11Q GAIN MUTATED 14 54 6
11Q GAIN WILD-TYPE 515 416 85

Figure S157.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #5: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S158.  Gene #22: '11q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
11Q GAIN MUTATED 4 31 2 24
11Q GAIN WILD-TYPE 173 194 86 136

Figure S158.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'11q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0491 (Fisher's exact test), Q value = 0.095

Table S159.  Gene #22: '11q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
11Q GAIN MUTATED 29 17 10
11Q GAIN WILD-TYPE 205 237 148

Figure S159.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S160.  Gene #22: '11q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
11Q GAIN MUTATED 8 19 35
11Q GAIN WILD-TYPE 236 170 192

Figure S160.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S161.  Gene #22: '11q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
11Q GAIN MUTATED 3 23 36
11Q GAIN WILD-TYPE 200 167 231

Figure S161.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0378 (Fisher's exact test), Q value = 0.077

Table S162.  Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
11Q GAIN MUTATED 31 23 5
11Q GAIN WILD-TYPE 191 161 98

Figure S162.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0265 (Fisher's exact test), Q value = 0.059

Table S163.  Gene #22: '11q gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
11Q GAIN MUTATED 13 8 12 10 1 15
11Q GAIN WILD-TYPE 86 69 106 46 62 77

Figure S163.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 0.0219 (Fisher's exact test), Q value = 0.051

Table S164.  Gene #23: '12p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
12P GAIN MUTATED 57 28 8
12P GAIN WILD-TYPE 472 442 83

Figure S164.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 0.00423 (Fisher's exact test), Q value = 0.013

Table S165.  Gene #23: '12p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
12P GAIN MUTATED 15 23 2 4
12P GAIN WILD-TYPE 162 202 86 156

Figure S165.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'12p gain' versus 'RPPA_CNMF'

P value = 0.0307 (Fisher's exact test), Q value = 0.066

Table S166.  Gene #23: '12p gain' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
12P GAIN MUTATED 9 8 18 9
12P GAIN WILD-TYPE 204 160 138 100

Figure S166.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'RPPA_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.05

Table S167.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
12P GAIN MUTATED 24 6 18
12P GAIN WILD-TYPE 220 183 209

Figure S167.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0234 (Fisher's exact test), Q value = 0.054

Table S168.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
12P GAIN MUTATED 21 16 11
12P GAIN WILD-TYPE 182 174 256

Figure S168.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 0.0394 (Fisher's exact test), Q value = 0.08

Table S169.  Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
12P GAIN MUTATED 12 11 5 5
12P GAIN WILD-TYPE 128 96 77 175

Figure S169.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 0.038

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
12P GAIN MUTATED 17 5 11
12P GAIN WILD-TYPE 205 179 92

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

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0227 (Fisher's exact test), Q value = 0.053

Table S171.  Gene #23: '12p gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
12P GAIN MUTATED 7 7 1 3 5 10
12P GAIN WILD-TYPE 92 70 117 53 58 82

Figure S171.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'MIR_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.028

Table S172.  Gene #24: '12q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
12Q GAIN MUTATED 16 15 17
12Q GAIN WILD-TYPE 277 109 112

Figure S172.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00018

Table S173.  Gene #24: '12q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
12Q GAIN MUTATED 50 12 3
12Q GAIN WILD-TYPE 479 458 88

Figure S173.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.048

Table S174.  Gene #24: '12q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
12Q GAIN MUTATED 14 8 1 3
12Q GAIN WILD-TYPE 163 217 87 157

Figure S174.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'12q gain' versus 'RPPA_CNMF'

P value = 0.00262 (Fisher's exact test), Q value = 0.0087

Table S175.  Gene #24: '12q gain' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
12Q GAIN MUTATED 3 6 15 5
12Q GAIN WILD-TYPE 210 162 141 104

Figure S175.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'RPPA_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.00302 (Fisher's exact test), Q value = 0.0099

Table S176.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
12Q GAIN MUTATED 19 3 6
12Q GAIN WILD-TYPE 225 186 221

Figure S176.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00072 (Fisher's exact test), Q value = 0.0029

Table S177.  Gene #24: '12q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
12Q GAIN MUTATED 18 5 5
12Q GAIN WILD-TYPE 185 185 262

Figure S177.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 0.0367 (Fisher's exact test), Q value = 0.075

Table S178.  Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
12Q GAIN MUTATED 7 4 4 1
12Q GAIN WILD-TYPE 133 103 78 179

Figure S178.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00923 (Fisher's exact test), Q value = 0.025

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
12Q GAIN MUTATED 6 2 8
12Q GAIN WILD-TYPE 216 182 95

Figure S179.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0203 (Fisher's exact test), Q value = 0.048

Table S180.  Gene #24: '12q gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
12Q GAIN MUTATED 3 2 0 2 6 3
12Q GAIN WILD-TYPE 96 75 118 54 57 89

Figure S180.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q gain' versus 'MIR_CNMF'

P value = 0.0172 (Fisher's exact test), Q value = 0.042

Table S181.  Gene #26: '14q gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
14Q GAIN MUTATED 9 5 7 1
14Q GAIN WILD-TYPE 134 182 83 125

Figure S181.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'MIR_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 0.00147 (Fisher's exact test), Q value = 0.0054

Table S182.  Gene #26: '14q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
14Q GAIN MUTATED 19 3 4
14Q GAIN WILD-TYPE 510 467 87

Figure S182.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #5: 'CN_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 0.065

Table S183.  Gene #26: '14q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
14Q GAIN MUTATED 8 1 1
14Q GAIN WILD-TYPE 236 188 226

Figure S183.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'15q gain' versus 'CN_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.053

Table S184.  Gene #27: '15q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
15Q GAIN MUTATED 20 10 7
15Q GAIN WILD-TYPE 509 460 84

Figure S184.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #5: 'CN_CNMF'

'15q gain' versus 'METHLYATION_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.035

Table S185.  Gene #27: '15q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
15Q GAIN MUTATED 5 9 0 0
15Q GAIN WILD-TYPE 172 216 88 160

Figure S185.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'15q gain' versus 'RPPA_CNMF'

P value = 0.0172 (Fisher's exact test), Q value = 0.042

Table S186.  Gene #27: '15q gain' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
15Q GAIN MUTATED 8 0 7 2
15Q GAIN WILD-TYPE 205 168 149 107

Figure S186.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #7: 'RPPA_CNMF'

'15q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00322 (Fisher's exact test), Q value = 0.01

Table S187.  Gene #27: '15q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
15Q GAIN MUTATED 12 5 0
15Q GAIN WILD-TYPE 222 249 158

Figure S187.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 0.0299 (Fisher's exact test), Q value = 0.065

Table S188.  Gene #27: '15q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
15Q GAIN MUTATED 13 2 5
15Q GAIN WILD-TYPE 231 187 222

Figure S188.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00421 (Fisher's exact test), Q value = 0.013

Table S189.  Gene #27: '15q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
15Q GAIN MUTATED 12 6 2
15Q GAIN WILD-TYPE 191 184 265

Figure S189.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MRNA_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.039

Table S190.  Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
16P GAIN MUTATED 11 10 3 13
16P GAIN WILD-TYPE 147 86 134 104

Figure S190.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0448 (Fisher's exact test), Q value = 0.089

Table S191.  Gene #28: '16p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
16P GAIN MUTATED 14 5 9
16P GAIN WILD-TYPE 220 249 149

Figure S191.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.039

Table S192.  Gene #28: '16p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
16P GAIN MUTATED 13 8 2
16P GAIN WILD-TYPE 231 181 225

Figure S192.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0201 (Fisher's exact test), Q value = 0.048

Table S193.  Gene #28: '16p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
16P GAIN MUTATED 2 10 4
16P GAIN WILD-TYPE 220 174 99

Figure S193.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0371 (Fisher's exact test), Q value = 0.076

Table S194.  Gene #28: '16p gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
16P GAIN MUTATED 1 5 4 0 0 6
16P GAIN WILD-TYPE 98 72 114 56 63 86

Figure S194.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'MRNA_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.041

Table S195.  Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
16Q GAIN MUTATED 9 12 4 12
16Q GAIN WILD-TYPE 149 84 133 105

Figure S195.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 0.038

Table S196.  Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
16Q GAIN MUTATED 10 15 3 9
16Q GAIN WILD-TYPE 138 87 97 149

Figure S196.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q gain' versus 'MIR_CHIERARCHICAL'

P value = 0.0476 (Fisher's exact test), Q value = 0.093

Table S197.  Gene #29: '16q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
16Q GAIN MUTATED 27 6 4
16Q GAIN WILD-TYPE 266 118 125

Figure S197.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 0.048 (Fisher's exact test), Q value = 0.094

Table S198.  Gene #29: '16q gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
16Q GAIN MUTATED 1 7 2 9
16Q GAIN WILD-TYPE 139 100 80 171

Figure S198.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.031 (Fisher's exact test), Q value = 0.067

Table S199.  Gene #29: '16q gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
16Q GAIN MUTATED 2 7 5 0 0 5
16Q GAIN WILD-TYPE 97 70 113 56 63 87

Figure S199.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'MRNA_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00083

Table S200.  Gene #30: '17p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
17P GAIN MUTATED 9 17 4 15
17P GAIN WILD-TYPE 149 79 133 102

Figure S200.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0141 (Fisher's exact test), Q value = 0.036

Table S201.  Gene #30: '17p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
17P GAIN MUTATED 10 17 4 14
17P GAIN WILD-TYPE 138 85 96 144

Figure S201.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p gain' versus 'MIR_CNMF'

P value = 0.0426 (Fisher's exact test), Q value = 0.086

Table S202.  Gene #30: '17p gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
17P GAIN MUTATED 5 21 8 14
17P GAIN WILD-TYPE 138 166 82 112

Figure S202.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'MIR_CNMF'

'17p gain' versus 'MIR_CHIERARCHICAL'

P value = 0.0153 (Fisher's exact test), Q value = 0.039

Table S203.  Gene #30: '17p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
17P GAIN MUTATED 35 8 5
17P GAIN WILD-TYPE 258 116 124

Figure S203.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 0.056

Table S204.  Gene #30: '17p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
17P GAIN MUTATED 46 21 6
17P GAIN WILD-TYPE 483 449 85

Figure S204.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #5: 'CN_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 0.0273 (Fisher's exact test), Q value = 0.06

Table S205.  Gene #30: '17p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
17P GAIN MUTATED 19 4 11
17P GAIN WILD-TYPE 225 185 216

Figure S205.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNA_CNMF'

P value = 0.00137 (Fisher's exact test), Q value = 0.0051

Table S206.  Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
17Q GAIN MUTATED 13 18 6 17
17Q GAIN WILD-TYPE 145 78 131 100

Figure S206.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q gain' versus 'MIR_CHIERARCHICAL'

P value = 0.0241 (Fisher's exact test), Q value = 0.055

Table S207.  Gene #31: '17q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
17Q GAIN MUTATED 41 9 8
17Q GAIN WILD-TYPE 252 115 121

Figure S207.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 0.00683 (Fisher's exact test), Q value = 0.02

Table S208.  Gene #31: '17q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
17Q GAIN MUTATED 55 24 8
17Q GAIN WILD-TYPE 474 446 83

Figure S208.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #5: 'CN_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 0.00131 (Fisher's exact test), Q value = 0.0049

Table S209.  Gene #31: '17q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
17Q GAIN MUTATED 26 4 14
17Q GAIN WILD-TYPE 218 185 213

Figure S209.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0167 (Fisher's exact test), Q value = 0.041

Table S210.  Gene #31: '17q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
17Q GAIN MUTATED 22 11 11
17Q GAIN WILD-TYPE 181 179 256

Figure S210.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 0.027 (Fisher's exact test), Q value = 0.06

Table S211.  Gene #31: '17q gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
17Q GAIN MUTATED 6 11 5 4
17Q GAIN WILD-TYPE 134 96 77 176

Figure S211.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'18p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S212.  Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
18P GAIN MUTATED 12 23 4 16
18P GAIN WILD-TYPE 146 73 133 101

Figure S212.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.0021

Table S213.  Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
18P GAIN MUTATED 11 22 4 18
18P GAIN WILD-TYPE 137 80 96 140

Figure S213.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S214.  Gene #32: '18p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
18P GAIN MUTATED 44 17 17
18P GAIN WILD-TYPE 485 453 74

Figure S214.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #5: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 0.0183 (Fisher's exact test), Q value = 0.044

Table S215.  Gene #32: '18p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
18P GAIN MUTATED 10 14 3 1
18P GAIN WILD-TYPE 167 211 85 159

Figure S215.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00047

Table S216.  Gene #32: '18p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
18P GAIN MUTATED 26 4 7
18P GAIN WILD-TYPE 218 185 220

Figure S216.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.0011

Table S217.  Gene #32: '18p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
18P GAIN MUTATED 21 11 5
18P GAIN WILD-TYPE 182 179 262

Figure S217.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00592 (Fisher's exact test), Q value = 0.018

Table S218.  Gene #32: '18p gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
18P GAIN MUTATED 2 9 2 0 4 3
18P GAIN WILD-TYPE 97 68 116 56 59 89

Figure S218.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S219.  Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
18Q GAIN MUTATED 11 22 5 18
18Q GAIN WILD-TYPE 147 74 132 99

Figure S219.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00098

Table S220.  Gene #33: '18q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
18Q GAIN MUTATED 10 24 6 16
18Q GAIN WILD-TYPE 138 78 94 142

Figure S220.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S221.  Gene #33: '18q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
18Q GAIN MUTATED 46 14 15
18Q GAIN WILD-TYPE 483 456 76

Figure S221.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #5: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 0.0015 (Fisher's exact test), Q value = 0.0054

Table S222.  Gene #33: '18q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
18Q GAIN MUTATED 13 10 3 0
18Q GAIN WILD-TYPE 164 215 85 160

Figure S222.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'18q gain' versus 'RPPA_CNMF'

P value = 0.0405 (Fisher's exact test), Q value = 0.082

Table S223.  Gene #33: '18q gain' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
18Q GAIN MUTATED 14 6 17 4
18Q GAIN WILD-TYPE 199 162 139 105

Figure S223.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'RPPA_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S224.  Gene #33: '18q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
18Q GAIN MUTATED 28 1 5
18Q GAIN WILD-TYPE 216 188 222

Figure S224.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S225.  Gene #33: '18q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
18Q GAIN MUTATED 23 9 2
18Q GAIN WILD-TYPE 180 181 265

Figure S225.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00959 (Fisher's exact test), Q value = 0.026

Table S226.  Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
18Q GAIN MUTATED 6 2 8
18Q GAIN WILD-TYPE 216 182 95

Figure S226.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0348 (Fisher's exact test), Q value = 0.073

Table S227.  Gene #33: '18q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
18Q GAIN MUTATED 3 9 2 2
18Q GAIN WILD-TYPE 124 110 103 152

Figure S227.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.0016

Table S228.  Gene #33: '18q gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
18Q GAIN MUTATED 1 8 1 0 5 1
18Q GAIN WILD-TYPE 98 69 117 56 58 91

Figure S228.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S229.  Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
19P GAIN MUTATED 58 34 85 21
19P GAIN WILD-TYPE 100 62 52 96

Figure S229.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p gain' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00023

Table S230.  Gene #34: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
19P GAIN MUTATED 62 26 58 52
19P GAIN WILD-TYPE 86 76 42 106

Figure S230.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p gain' versus 'MIR_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0019

Table S231.  Gene #34: '19p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
19P GAIN MUTATED 95 49 68
19P GAIN WILD-TYPE 198 75 61

Figure S231.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S232.  Gene #34: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
19P GAIN MUTATED 229 76 19
19P GAIN WILD-TYPE 300 394 72

Figure S232.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S233.  Gene #34: '19p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
19P GAIN MUTATED 72 12 6 57
19P GAIN WILD-TYPE 105 213 82 103

Figure S233.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'19p gain' versus 'RPPA_CNMF'

P value = 0.0359 (Fisher's exact test), Q value = 0.074

Table S234.  Gene #34: '19p gain' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
19P GAIN MUTATED 62 30 47 29
19P GAIN WILD-TYPE 151 138 109 80

Figure S234.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'RPPA_CNMF'

'19p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00144 (Fisher's exact test), Q value = 0.0053

Table S235.  Gene #34: '19p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
19P GAIN MUTATED 63 80 25
19P GAIN WILD-TYPE 171 174 133

Figure S235.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00023

Table S236.  Gene #34: '19p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
19P GAIN MUTATED 77 37 33
19P GAIN WILD-TYPE 167 152 194

Figure S236.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S237.  Gene #34: '19p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
19P GAIN MUTATED 72 12 63
19P GAIN WILD-TYPE 131 178 204

Figure S237.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.033

Table S238.  Gene #34: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
19P GAIN MUTATED 22 17 27 32
19P GAIN WILD-TYPE 118 90 55 148

Figure S238.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0312 (Fisher's exact test), Q value = 0.067

Table S239.  Gene #34: '19p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
19P GAIN MUTATED 33 37 28
19P GAIN WILD-TYPE 189 147 75

Figure S239.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0021

Table S240.  Gene #34: '19p gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
19P GAIN MUTATED 14 25 34 25
19P GAIN WILD-TYPE 113 94 71 129

Figure S240.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'19p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S241.  Gene #34: '19p gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
19P GAIN MUTATED 9 10 21 20 23 15
19P GAIN WILD-TYPE 90 67 97 36 40 77

Figure S241.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S242.  Gene #35: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
19Q GAIN MUTATED 51 28 79 13
19Q GAIN WILD-TYPE 107 68 58 104

Figure S242.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S243.  Gene #35: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
19Q GAIN MUTATED 55 18 55 43
19Q GAIN WILD-TYPE 93 84 45 115

Figure S243.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q gain' versus 'MIR_CHIERARCHICAL'

P value = 0.00456 (Fisher's exact test), Q value = 0.014

Table S244.  Gene #35: '19q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
19Q GAIN MUTATED 81 46 56
19Q GAIN WILD-TYPE 212 78 73

Figure S244.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S245.  Gene #35: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
19Q GAIN MUTATED 197 6 20
19Q GAIN WILD-TYPE 332 464 71

Figure S245.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S246.  Gene #35: '19q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
19Q GAIN MUTATED 59 3 5 0
19Q GAIN WILD-TYPE 118 222 83 160

Figure S246.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'19q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0039 (Fisher's exact test), Q value = 0.012

Table S247.  Gene #35: '19q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
19Q GAIN MUTATED 30 46 11
19Q GAIN WILD-TYPE 204 208 147

Figure S247.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S248.  Gene #35: '19q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
19Q GAIN MUTATED 67 5 1
19Q GAIN WILD-TYPE 177 184 226

Figure S248.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S249.  Gene #35: '19q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
19Q GAIN MUTATED 65 4 4
19Q GAIN WILD-TYPE 138 186 263

Figure S249.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 0.00116 (Fisher's exact test), Q value = 0.0044

Table S250.  Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
19Q GAIN MUTATED 8 13 0 6
19Q GAIN WILD-TYPE 132 94 82 174

Figure S250.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S251.  Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
19Q GAIN MUTATED 4 2 21
19Q GAIN WILD-TYPE 218 182 82

Figure S251.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00018

Table S252.  Gene #35: '19q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
19Q GAIN MUTATED 7 16 0 4
19Q GAIN WILD-TYPE 120 103 105 150

Figure S252.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S253.  Gene #35: '19q gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
19Q GAIN MUTATED 3 0 3 0 20 1
19Q GAIN WILD-TYPE 96 77 115 56 43 91

Figure S253.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S254.  Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
20P GAIN MUTATED 53 29 80 30
20P GAIN WILD-TYPE 105 67 57 87

Figure S254.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S255.  Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
20P GAIN MUTATED 55 21 64 52
20P GAIN WILD-TYPE 93 81 36 106

Figure S255.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'MIR_CNMF'

P value = 0.00359 (Fisher's exact test), Q value = 0.011

Table S256.  Gene #36: '20p gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
20P GAIN MUTATED 60 76 20 56
20P GAIN WILD-TYPE 83 111 70 70

Figure S256.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'MIR_CNMF'

'20p gain' versus 'MIR_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S257.  Gene #36: '20p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
20P GAIN MUTATED 85 58 69
20P GAIN WILD-TYPE 208 66 60

Figure S257.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S258.  Gene #36: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
20P GAIN MUTATED 221 19 26
20P GAIN WILD-TYPE 308 451 65

Figure S258.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S259.  Gene #36: '20p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
20P GAIN MUTATED 65 8 10 7
20P GAIN WILD-TYPE 112 217 78 153

Figure S259.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 0.00975 (Fisher's exact test), Q value = 0.027

Table S260.  Gene #36: '20p gain' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
20P GAIN MUTATED 41 17 37 19
20P GAIN WILD-TYPE 172 151 119 90

Figure S260.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'RPPA_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00023

Table S261.  Gene #36: '20p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
20P GAIN MUTATED 46 58 10
20P GAIN WILD-TYPE 188 196 148

Figure S261.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S262.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
20P GAIN MUTATED 78 13 6
20P GAIN WILD-TYPE 166 176 221

Figure S262.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S263.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
20P GAIN MUTATED 73 9 15
20P GAIN WILD-TYPE 130 181 252

Figure S263.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S264.  Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
20P GAIN MUTATED 8 10 26
20P GAIN WILD-TYPE 214 174 77

Figure S264.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0012

Table S265.  Gene #36: '20p gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
20P GAIN MUTATED 13 19 1 11
20P GAIN WILD-TYPE 114 100 104 143

Figure S265.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S266.  Gene #36: '20p gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
20P GAIN MUTATED 3 4 9 2 21 5
20P GAIN WILD-TYPE 96 73 109 54 42 87

Figure S266.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S267.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
20Q GAIN MUTATED 53 30 80 28
20Q GAIN WILD-TYPE 105 66 57 89

Figure S267.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S268.  Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
20Q GAIN MUTATED 58 22 62 49
20Q GAIN WILD-TYPE 90 80 38 109

Figure S268.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'MIR_CNMF'

P value = 0.00211 (Fisher's exact test), Q value = 0.0073

Table S269.  Gene #37: '20q gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
20Q GAIN MUTATED 61 75 19 55
20Q GAIN WILD-TYPE 82 112 71 71

Figure S269.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'MIR_CNMF'

'20q gain' versus 'MIR_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00018

Table S270.  Gene #37: '20q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
20Q GAIN MUTATED 85 57 68
20Q GAIN WILD-TYPE 208 67 61

Figure S270.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S271.  Gene #37: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
20Q GAIN MUTATED 220 19 24
20Q GAIN WILD-TYPE 309 451 67

Figure S271.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S272.  Gene #37: '20q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
20Q GAIN MUTATED 66 8 9 6
20Q GAIN WILD-TYPE 111 217 79 154

Figure S272.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.00246 (Fisher's exact test), Q value = 0.0083

Table S273.  Gene #37: '20q gain' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
20Q GAIN MUTATED 42 15 37 20
20Q GAIN WILD-TYPE 171 153 119 89

Figure S273.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'RPPA_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S274.  Gene #37: '20q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
20Q GAIN MUTATED 46 59 9
20Q GAIN WILD-TYPE 188 195 149

Figure S274.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S275.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
20Q GAIN MUTATED 79 11 6
20Q GAIN WILD-TYPE 165 178 221

Figure S275.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S276.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
20Q GAIN MUTATED 74 9 13
20Q GAIN WILD-TYPE 129 181 254

Figure S276.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 0.032 (Fisher's exact test), Q value = 0.068

Table S277.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
20Q GAIN MUTATED 17 13 3 10
20Q GAIN WILD-TYPE 123 94 79 170

Figure S277.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S278.  Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
20Q GAIN MUTATED 9 8 26
20Q GAIN WILD-TYPE 213 176 77

Figure S278.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00083

Table S279.  Gene #37: '20q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
20Q GAIN MUTATED 15 18 1 9
20Q GAIN WILD-TYPE 112 101 104 145

Figure S279.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S280.  Gene #37: '20q gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
20Q GAIN MUTATED 6 3 7 2 21 4
20Q GAIN WILD-TYPE 93 74 111 54 42 88

Figure S280.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'MRNA_CNMF'

P value = 0.00276 (Fisher's exact test), Q value = 0.0092

Table S281.  Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
21Q GAIN MUTATED 29 10 8 8
21Q GAIN WILD-TYPE 129 86 129 109

Figure S281.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00764 (Fisher's exact test), Q value = 0.022

Table S282.  Gene #38: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
21Q GAIN MUTATED 25 6 5 19
21Q GAIN WILD-TYPE 123 96 95 139

Figure S282.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q gain' versus 'MIR_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 0.042

Table S283.  Gene #38: '21q gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
21Q GAIN MUTATED 23 15 5 19
21Q GAIN WILD-TYPE 120 172 85 107

Figure S283.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'MIR_CNMF'

'21q gain' versus 'MIR_CHIERARCHICAL'

P value = 0.00411 (Fisher's exact test), Q value = 0.013

Table S284.  Gene #38: '21q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
21Q GAIN MUTATED 26 25 11
21Q GAIN WILD-TYPE 267 99 118

Figure S284.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S285.  Gene #38: '21q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
21Q GAIN MUTATED 61 14 13
21Q GAIN WILD-TYPE 468 456 78

Figure S285.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'CN_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00075

Table S286.  Gene #38: '21q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
21Q GAIN MUTATED 31 8 8
21Q GAIN WILD-TYPE 213 181 219

Figure S286.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S287.  Gene #38: '21q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
21Q GAIN MUTATED 30 5 12
21Q GAIN WILD-TYPE 173 185 255

Figure S287.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S288.  Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
22Q GAIN MUTATED 6 13 0 11
22Q GAIN WILD-TYPE 152 83 137 106

Figure S288.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00545 (Fisher's exact test), Q value = 0.016

Table S289.  Gene #39: '22q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
22Q GAIN MUTATED 11 10 0 9
22Q GAIN WILD-TYPE 137 92 100 149

Figure S289.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00018

Table S290.  Gene #39: '22q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
22Q GAIN MUTATED 7 3 0 18
22Q GAIN WILD-TYPE 170 222 88 142

Figure S290.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0362 (Fisher's exact test), Q value = 0.075

Table S291.  Gene #39: '22q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
22Q GAIN MUTATED 13 4 19
22Q GAIN WILD-TYPE 190 186 248

Figure S291.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00249 (Fisher's exact test), Q value = 0.0084

Table S292.  Gene #39: '22q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
22Q GAIN MUTATED 2 2 12 8
22Q GAIN WILD-TYPE 125 117 93 146

Figure S292.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00491 (Fisher's exact test), Q value = 0.015

Table S293.  Gene #39: '22q gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
22Q GAIN MUTATED 2 1 3 7 2 9
22Q GAIN WILD-TYPE 97 76 115 49 61 83

Figure S293.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp gain' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00028

Table S294.  Gene #40: 'xp gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
XP GAIN MUTATED 4 18 1 0
XP GAIN WILD-TYPE 173 207 87 160

Figure S294.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S295.  Gene #41: 'xq gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
XQ GAIN MUTATED 4 36 4 0
XQ GAIN WILD-TYPE 173 189 84 160

Figure S295.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'xq gain' versus 'RPPA_CNMF'

P value = 0.0465 (Fisher's exact test), Q value = 0.091

Table S296.  Gene #41: 'xq gain' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
XQ GAIN MUTATED 14 4 8 11
XQ GAIN WILD-TYPE 199 164 148 98

Figure S296.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #7: 'RPPA_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0013

Table S297.  Gene #41: 'xq gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
XQ GAIN MUTATED 9 26 12
XQ GAIN WILD-TYPE 194 164 255

Figure S297.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00351 (Fisher's exact test), Q value = 0.011

Table S298.  Gene #41: 'xq gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
XQ GAIN MUTATED 15 7 5 0 3 10
XQ GAIN WILD-TYPE 84 70 113 56 60 82

Figure S298.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S299.  Gene #42: '1p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
1P LOSS MUTATED 15 184 1
1P LOSS WILD-TYPE 514 286 90

Figure S299.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S300.  Gene #42: '1p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
1P LOSS MUTATED 6 6 19 157
1P LOSS WILD-TYPE 171 219 69 3

Figure S300.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'1p loss' versus 'RPPA_CNMF'

P value = 0.00205 (Fisher's exact test), Q value = 0.0071

Table S301.  Gene #42: '1p loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
1P LOSS MUTATED 48 62 37 20
1P LOSS WILD-TYPE 165 106 119 89

Figure S301.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'1p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S302.  Gene #42: '1p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
1P LOSS MUTATED 53 49 65
1P LOSS WILD-TYPE 181 205 93

Figure S302.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S303.  Gene #42: '1p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
1P LOSS MUTATED 10 97 82
1P LOSS WILD-TYPE 234 92 145

Figure S303.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S304.  Gene #42: '1p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
1P LOSS MUTATED 6 11 172
1P LOSS WILD-TYPE 197 179 95

Figure S304.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S305.  Gene #42: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
1P LOSS MUTATED 28 8 67 82
1P LOSS WILD-TYPE 112 99 15 98

Figure S305.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S306.  Gene #42: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
1P LOSS MUTATED 80 98 7
1P LOSS WILD-TYPE 142 86 96

Figure S306.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S307.  Gene #42: '1p loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
1P LOSS MUTATED 17 17 82 69
1P LOSS WILD-TYPE 110 102 23 85

Figure S307.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S308.  Gene #42: '1p loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
1P LOSS MUTATED 7 25 60 54 4 35
1P LOSS WILD-TYPE 92 52 58 2 59 57

Figure S308.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 0.0475 (Fisher's exact test), Q value = 0.093

Table S309.  Gene #43: '1q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
1Q LOSS MUTATED 15 28 3
1Q LOSS WILD-TYPE 514 442 88

Figure S309.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #5: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.027

Table S310.  Gene #43: '1q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
1Q LOSS MUTATED 6 7 5 17
1Q LOSS WILD-TYPE 171 218 83 143

Figure S310.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'1q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0486 (Fisher's exact test), Q value = 0.095

Table S311.  Gene #43: '1q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
1Q LOSS MUTATED 15 7 12
1Q LOSS WILD-TYPE 219 247 146

Figure S311.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.036

Table S312.  Gene #43: '1q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
1Q LOSS MUTATED 6 7 23
1Q LOSS WILD-TYPE 197 183 244

Figure S312.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MRNA_CNMF'

P value = 0.0014 (Fisher's exact test), Q value = 0.0052

Table S313.  Gene #44: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
2P LOSS MUTATED 7 14 3 5
2P LOSS WILD-TYPE 151 82 134 112

Figure S313.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.028 (Fisher's exact test), Q value = 0.062

Table S314.  Gene #44: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
2P LOSS MUTATED 8 12 2 7
2P LOSS WILD-TYPE 140 90 98 151

Figure S314.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p loss' versus 'METHLYATION_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.035

Table S315.  Gene #44: '2p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
2P LOSS MUTATED 11 17 2 2
2P LOSS WILD-TYPE 166 208 86 158

Figure S315.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'2p loss' versus 'RPPA_CNMF'

P value = 0.0203 (Fisher's exact test), Q value = 0.048

Table S316.  Gene #44: '2p loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
2P LOSS MUTATED 11 5 15 2
2P LOSS WILD-TYPE 202 163 141 107

Figure S316.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.046 (Fisher's exact test), Q value = 0.091

Table S317.  Gene #44: '2p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
2P LOSS MUTATED 10 13 6
2P LOSS WILD-TYPE 193 177 261

Figure S317.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MRNA_CNMF'

P value = 0.00198 (Fisher's exact test), Q value = 0.0069

Table S318.  Gene #45: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
2Q LOSS MUTATED 7 14 3 6
2Q LOSS WILD-TYPE 151 82 134 111

Figure S318.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 0.034

Table S319.  Gene #45: '2q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
2Q LOSS MUTATED 8 13 2 7
2Q LOSS WILD-TYPE 140 89 98 151

Figure S319.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.00789 (Fisher's exact test), Q value = 0.022

Table S320.  Gene #45: '2q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
2Q LOSS MUTATED 9 17 1 2
2Q LOSS WILD-TYPE 168 208 87 158

Figure S320.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'2q loss' versus 'RPPA_CNMF'

P value = 0.00208 (Fisher's exact test), Q value = 0.0072

Table S321.  Gene #45: '2q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
2Q LOSS MUTATED 9 3 16 2
2Q LOSS WILD-TYPE 204 165 140 107

Figure S321.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.0355 (Fisher's exact test), Q value = 0.074

Table S322.  Gene #45: '2q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
2Q LOSS MUTATED 4 9 2 3
2Q LOSS WILD-TYPE 136 98 80 177

Figure S322.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00443 (Fisher's exact test), Q value = 0.014

Table S323.  Gene #45: '2q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
2Q LOSS MUTATED 2 9 2 1 0 3
2Q LOSS WILD-TYPE 97 68 116 55 63 89

Figure S323.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'RPPA_CNMF'

P value = 0.00262 (Fisher's exact test), Q value = 0.0087

Table S324.  Gene #46: '3p loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
3P LOSS MUTATED 11 4 16 13
3P LOSS WILD-TYPE 202 164 140 96

Figure S324.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0336 (Fisher's exact test), Q value = 0.071

Table S325.  Gene #46: '3p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
3P LOSS MUTATED 23 16 5
3P LOSS WILD-TYPE 211 238 153

Figure S325.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.0301 (Fisher's exact test), Q value = 0.065

Table S326.  Gene #46: '3p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
3P LOSS MUTATED 21 5 14
3P LOSS WILD-TYPE 223 184 213

Figure S326.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0422 (Fisher's exact test), Q value = 0.085

Table S327.  Gene #46: '3p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
3P LOSS MUTATED 17 14 9
3P LOSS WILD-TYPE 186 176 258

Figure S327.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.0014 (Fisher's exact test), Q value = 0.0052

Table S328.  Gene #46: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
3P LOSS MUTATED 9 14 4 3
3P LOSS WILD-TYPE 131 93 78 177

Figure S328.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0023

Table S329.  Gene #46: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
3P LOSS MUTATED 18 2 10
3P LOSS WILD-TYPE 204 182 93

Figure S329.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0347 (Fisher's exact test), Q value = 0.073

Table S330.  Gene #47: '3q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
3Q LOSS MUTATED 12 16 8
3Q LOSS WILD-TYPE 191 174 259

Figure S330.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.035

Table S331.  Gene #47: '3q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
3Q LOSS MUTATED 15 4 10
3Q LOSS WILD-TYPE 207 180 93

Figure S331.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00642 (Fisher's exact test), Q value = 0.019

Table S332.  Gene #47: '3q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
3Q LOSS MUTATED 8 11 2 2 2 3
3Q LOSS WILD-TYPE 91 66 116 54 61 89

Figure S332.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00164 (Fisher's exact test), Q value = 0.0059

Table S333.  Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
4P LOSS MUTATED 10 20 4 17
4P LOSS WILD-TYPE 138 82 96 141

Figure S333.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p loss' versus 'MIR_CNMF'

P value = 0.0325 (Fisher's exact test), Q value = 0.069

Table S334.  Gene #48: '4p loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
4P LOSS MUTATED 6 25 10 12
4P LOSS WILD-TYPE 137 162 80 114

Figure S334.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'MIR_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 0.00869 (Fisher's exact test), Q value = 0.024

Table S335.  Gene #48: '4p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
4P LOSS MUTATED 47 71 9
4P LOSS WILD-TYPE 482 399 82

Figure S335.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S336.  Gene #48: '4p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
4P LOSS MUTATED 14 24 1 44
4P LOSS WILD-TYPE 163 201 87 116

Figure S336.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CNMF'

P value = 0.00654 (Fisher's exact test), Q value = 0.019

Table S337.  Gene #48: '4p loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
4P LOSS MUTATED 33 15 27 6
4P LOSS WILD-TYPE 180 153 129 103

Figure S337.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.0356 (Fisher's exact test), Q value = 0.074

Table S338.  Gene #48: '4p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
4P LOSS MUTATED 23 29 39
4P LOSS WILD-TYPE 221 160 188

Figure S338.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00335 (Fisher's exact test), Q value = 0.011

Table S339.  Gene #48: '4p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
4P LOSS MUTATED 20 19 52
4P LOSS WILD-TYPE 183 171 215

Figure S339.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00042

Table S340.  Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
4P LOSS MUTATED 12 12 26 21
4P LOSS WILD-TYPE 128 95 56 159

Figure S340.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00149 (Fisher's exact test), Q value = 0.0054

Table S341.  Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
4P LOSS MUTATED 38 29 4
4P LOSS WILD-TYPE 184 155 99

Figure S341.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0017

Table S342.  Gene #48: '4p loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
4P LOSS MUTATED 10 11 28 22
4P LOSS WILD-TYPE 117 108 77 132

Figure S342.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S343.  Gene #48: '4p loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
4P LOSS MUTATED 6 13 13 18 1 20
4P LOSS WILD-TYPE 93 64 105 38 62 72

Figure S343.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'MRNA_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.0036

Table S344.  Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
4Q LOSS MUTATED 12 18 5 14
4Q LOSS WILD-TYPE 146 78 132 103

Figure S344.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0025

Table S345.  Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
4Q LOSS MUTATED 10 20 3 16
4Q LOSS WILD-TYPE 138 82 97 142

Figure S345.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q loss' versus 'MIR_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.043

Table S346.  Gene #49: '4q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
4Q LOSS MUTATED 5 24 10 13
4Q LOSS WILD-TYPE 138 163 80 113

Figure S346.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S347.  Gene #49: '4q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
4Q LOSS MUTATED 44 95 10
4Q LOSS WILD-TYPE 485 375 81

Figure S347.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S348.  Gene #49: '4q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
4Q LOSS MUTATED 14 43 4 47
4Q LOSS WILD-TYPE 163 182 84 113

Figure S348.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'4q loss' versus 'RPPA_CNMF'

P value = 0.00341 (Fisher's exact test), Q value = 0.011

Table S349.  Gene #49: '4q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
4Q LOSS MUTATED 37 23 34 7
4Q LOSS WILD-TYPE 176 145 122 102

Figure S349.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.00401 (Fisher's exact test), Q value = 0.013

Table S350.  Gene #49: '4q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
4Q LOSS MUTATED 27 36 50
4Q LOSS WILD-TYPE 217 153 177

Figure S350.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00086

Table S351.  Gene #49: '4q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
4Q LOSS MUTATED 19 30 64
4Q LOSS WILD-TYPE 184 160 203

Figure S351.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0014

Table S352.  Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
4Q LOSS MUTATED 13 19 27 34
4Q LOSS WILD-TYPE 127 88 55 146

Figure S352.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0115 (Fisher's exact test), Q value = 0.03

Table S353.  Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
4Q LOSS MUTATED 44 40 9
4Q LOSS WILD-TYPE 178 144 94

Figure S353.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00703 (Fisher's exact test), Q value = 0.02

Table S354.  Gene #49: '4q loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
4Q LOSS MUTATED 15 17 30 31
4Q LOSS WILD-TYPE 112 102 75 123

Figure S354.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S355.  Gene #49: '4q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
4Q LOSS MUTATED 8 19 19 18 2 27
4Q LOSS WILD-TYPE 91 58 99 38 61 65

Figure S355.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S356.  Gene #50: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
5P LOSS MUTATED 5 22 5 9
5P LOSS WILD-TYPE 153 74 132 108

Figure S356.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S357.  Gene #50: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
5P LOSS MUTATED 6 23 5 7
5P LOSS WILD-TYPE 142 79 95 151

Figure S357.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5p loss' versus 'MIR_CNMF'

P value = 0.00207 (Fisher's exact test), Q value = 0.0072

Table S358.  Gene #50: '5p loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
5P LOSS MUTATED 4 25 6 6
5P LOSS WILD-TYPE 139 162 84 120

Figure S358.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #3: 'MIR_CNMF'

'5p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S359.  Gene #50: '5p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
5P LOSS MUTATED 22 39 19
5P LOSS WILD-TYPE 507 431 72

Figure S359.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00028

Table S360.  Gene #50: '5p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
5P LOSS MUTATED 12 29 3 2
5P LOSS WILD-TYPE 165 196 85 158

Figure S360.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0249 (Fisher's exact test), Q value = 0.056

Table S361.  Gene #50: '5p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
5P LOSS MUTATED 14 23 14
5P LOSS WILD-TYPE 189 167 253

Figure S361.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00042

Table S362.  Gene #50: '5p loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
5P LOSS MUTATED 3 15 6 0 2 10
5P LOSS WILD-TYPE 96 62 112 56 61 82

Figure S362.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S363.  Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
5Q LOSS MUTATED 6 21 5 11
5Q LOSS WILD-TYPE 152 75 132 106

Figure S363.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S364.  Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
5Q LOSS MUTATED 9 23 4 7
5Q LOSS WILD-TYPE 139 79 96 151

Figure S364.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5q loss' versus 'MIR_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0023

Table S365.  Gene #51: '5q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
5Q LOSS MUTATED 4 27 6 6
5Q LOSS WILD-TYPE 139 160 84 120

Figure S365.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S366.  Gene #51: '5q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
5Q LOSS MUTATED 22 41 17
5Q LOSS WILD-TYPE 507 429 74

Figure S366.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #5: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00018

Table S367.  Gene #51: '5q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
5Q LOSS MUTATED 12 28 2 2
5Q LOSS WILD-TYPE 165 197 86 158

Figure S367.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'5q loss' versus 'RPPA_CNMF'

P value = 0.0316 (Fisher's exact test), Q value = 0.068

Table S368.  Gene #51: '5q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
5Q LOSS MUTATED 17 6 19 7
5Q LOSS WILD-TYPE 196 162 137 102

Figure S368.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 0.0412 (Fisher's exact test), Q value = 0.083

Table S369.  Gene #51: '5q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
5Q LOSS MUTATED 27 10 13
5Q LOSS WILD-TYPE 217 179 214

Figure S369.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00319 (Fisher's exact test), Q value = 0.01

Table S370.  Gene #51: '5q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
5Q LOSS MUTATED 15 24 11
5Q LOSS WILD-TYPE 188 166 256

Figure S370.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00091

Table S371.  Gene #51: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
5Q LOSS MUTATED 5 18 2 9
5Q LOSS WILD-TYPE 135 89 80 171

Figure S371.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0168 (Fisher's exact test), Q value = 0.041

Table S372.  Gene #51: '5q loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
5Q LOSS MUTATED 13 12 2 7
5Q LOSS WILD-TYPE 114 107 103 147

Figure S372.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00028

Table S373.  Gene #51: '5q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
5Q LOSS MUTATED 4 14 3 0 2 11
5Q LOSS WILD-TYPE 95 63 115 56 61 81

Figure S373.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S374.  Gene #52: '6p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
6P LOSS MUTATED 81 27 9
6P LOSS WILD-TYPE 448 443 82

Figure S374.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #5: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.00189 (Fisher's exact test), Q value = 0.0067

Table S375.  Gene #52: '6p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
6P LOSS MUTATED 19 12 14 6
6P LOSS WILD-TYPE 158 213 74 154

Figure S375.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'6p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0211 (Fisher's exact test), Q value = 0.05

Table S376.  Gene #52: '6p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
6P LOSS MUTATED 33 20 10
6P LOSS WILD-TYPE 201 234 148

Figure S376.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S377.  Gene #52: '6p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
6P LOSS MUTATED 42 11 11
6P LOSS WILD-TYPE 202 178 216

Figure S377.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S378.  Gene #52: '6p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
6P LOSS MUTATED 38 13 13
6P LOSS WILD-TYPE 165 177 254

Figure S378.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0456 (Fisher's exact test), Q value = 0.09

Table S379.  Gene #52: '6p loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
6P LOSS MUTATED 7 2 5 3 10 4
6P LOSS WILD-TYPE 92 75 113 53 53 88

Figure S379.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00038

Table S380.  Gene #53: '6q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
6Q LOSS MUTATED 119 59 11
6Q LOSS WILD-TYPE 410 411 80

Figure S380.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #5: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.0041

Table S381.  Gene #53: '6q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
6Q LOSS MUTATED 33 36 16 9
6Q LOSS WILD-TYPE 144 189 72 151

Figure S381.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'6q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00195 (Fisher's exact test), Q value = 0.0068

Table S382.  Gene #53: '6q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
6Q LOSS MUTATED 51 37 14
6Q LOSS WILD-TYPE 183 217 144

Figure S382.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00028

Table S383.  Gene #53: '6q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
6Q LOSS MUTATED 60 19 27
6Q LOSS WILD-TYPE 184 170 200

Figure S383.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00018

Table S384.  Gene #53: '6q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
6Q LOSS MUTATED 52 31 23
6Q LOSS WILD-TYPE 151 159 244

Figure S384.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 0.00107 (Fisher's exact test), Q value = 0.0041

Table S385.  Gene #53: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
6Q LOSS MUTATED 30 14 4 16
6Q LOSS WILD-TYPE 110 93 78 164

Figure S385.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.029 (Fisher's exact test), Q value = 0.063

Table S386.  Gene #53: '6q loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
6Q LOSS MUTATED 22 18 6 16
6Q LOSS WILD-TYPE 105 101 99 138

Figure S386.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00233 (Fisher's exact test), Q value = 0.0079

Table S387.  Gene #53: '6q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
6Q LOSS MUTATED 21 5 11 4 14 7
6Q LOSS WILD-TYPE 78 72 107 52 49 85

Figure S387.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p loss' versus 'MRNA_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 0.056

Table S388.  Gene #54: '7p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
7P LOSS MUTATED 0 4 1 2
7P LOSS WILD-TYPE 158 92 136 115

Figure S388.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00033

Table S389.  Gene #56: '8p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
8P LOSS MUTATED 51 15 9
8P LOSS WILD-TYPE 478 455 82

Figure S389.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #5: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S390.  Gene #56: '8p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
8P LOSS MUTATED 21 7 1 0
8P LOSS WILD-TYPE 156 218 87 160

Figure S390.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S391.  Gene #56: '8p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
8P LOSS MUTATED 26 4 2
8P LOSS WILD-TYPE 218 185 225

Figure S391.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00023

Table S392.  Gene #56: '8p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
8P LOSS MUTATED 22 6 4
8P LOSS WILD-TYPE 181 184 263

Figure S392.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00143 (Fisher's exact test), Q value = 0.0053

Table S393.  Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
8P LOSS MUTATED 7 1 9
8P LOSS WILD-TYPE 215 183 94

Figure S393.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00735 (Fisher's exact test), Q value = 0.021

Table S394.  Gene #56: '8p loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
8P LOSS MUTATED 2 10 1 3
8P LOSS WILD-TYPE 125 109 104 151

Figure S394.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S395.  Gene #56: '8p loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
8P LOSS MUTATED 1 6 1 0 8 0
8P LOSS WILD-TYPE 98 71 117 56 55 92

Figure S395.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'MIR_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.071

Table S396.  Gene #57: '8q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
8Q LOSS MUTATED 19 10 6 6
8Q LOSS WILD-TYPE 124 177 84 120

Figure S396.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'8q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S397.  Gene #57: '8q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
8Q LOSS MUTATED 41 5 6
8Q LOSS WILD-TYPE 488 465 85

Figure S397.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #5: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S398.  Gene #57: '8q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
8Q LOSS MUTATED 17 2 1 0
8Q LOSS WILD-TYPE 160 223 87 160

Figure S398.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00018

Table S399.  Gene #57: '8q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
8Q LOSS MUTATED 19 3 1
8Q LOSS WILD-TYPE 225 186 226

Figure S399.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S400.  Gene #57: '8q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
8Q LOSS MUTATED 18 3 2
8Q LOSS WILD-TYPE 185 187 265

Figure S400.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00071 (Fisher's exact test), Q value = 0.0028

Table S401.  Gene #57: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
8Q LOSS MUTATED 4 0 7
8Q LOSS WILD-TYPE 218 184 96

Figure S401.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0489 (Fisher's exact test), Q value = 0.095

Table S402.  Gene #57: '8q loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
8Q LOSS MUTATED 2 6 0 2
8Q LOSS WILD-TYPE 125 113 105 152

Figure S402.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S403.  Gene #57: '8q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
8Q LOSS MUTATED 0 3 0 0 7 0
8Q LOSS WILD-TYPE 99 74 118 56 56 92

Figure S403.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'MRNA_CNMF'

P value = 0.00802 (Fisher's exact test), Q value = 0.023

Table S404.  Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
9P LOSS MUTATED 53 21 59 43
9P LOSS WILD-TYPE 105 75 78 74

Figure S404.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S405.  Gene #58: '9p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
9P LOSS MUTATED 192 108 19
9P LOSS WILD-TYPE 337 362 72

Figure S405.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00023

Table S406.  Gene #58: '9p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
9P LOSS MUTATED 64 64 16 24
9P LOSS WILD-TYPE 113 161 72 136

Figure S406.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00595 (Fisher's exact test), Q value = 0.018

Table S407.  Gene #58: '9p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
9P LOSS MUTATED 77 77 30
9P LOSS WILD-TYPE 157 177 128

Figure S407.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 0.00724 (Fisher's exact test), Q value = 0.021

Table S408.  Gene #58: '9p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
9P LOSS MUTATED 78 43 45
9P LOSS WILD-TYPE 166 146 182

Figure S408.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.029

Table S409.  Gene #58: '9p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
9P LOSS MUTATED 65 48 53
9P LOSS WILD-TYPE 138 142 214

Figure S409.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 0.039

Table S410.  Gene #59: '9q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
9Q LOSS MUTATED 84 46 12
9Q LOSS WILD-TYPE 445 424 79

Figure S410.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'CN_CNMF'

'9q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0431 (Fisher's exact test), Q value = 0.087

Table S411.  Gene #59: '9q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
9Q LOSS MUTATED 30 38 11
9Q LOSS WILD-TYPE 204 216 147

Figure S411.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 0.0057 (Fisher's exact test), Q value = 0.017

Table S412.  Gene #59: '9q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
9Q LOSS MUTATED 42 17 19
9Q LOSS WILD-TYPE 202 172 208

Figure S412.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0335 (Fisher's exact test), Q value = 0.071

Table S413.  Gene #59: '9q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
9Q LOSS MUTATED 34 20 24
9Q LOSS WILD-TYPE 169 170 243

Figure S413.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S414.  Gene #60: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
10P LOSS MUTATED 141 63 128 87
10P LOSS WILD-TYPE 17 33 9 30

Figure S414.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S415.  Gene #60: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
10P LOSS MUTATED 127 62 93 137
10P LOSS WILD-TYPE 21 40 7 21

Figure S415.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p loss' versus 'MIR_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.037

Table S416.  Gene #60: '10p loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
10P LOSS MUTATED 129 150 68 107
10P LOSS WILD-TYPE 14 37 22 19

Figure S416.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #3: 'MIR_CNMF'

'10p loss' versus 'MIR_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00056

Table S417.  Gene #60: '10p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
10P LOSS MUTATED 226 108 120
10P LOSS WILD-TYPE 67 16 9

Figure S417.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S418.  Gene #60: '10p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
10P LOSS MUTATED 476 27 60
10P LOSS WILD-TYPE 53 443 31

Figure S418.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #5: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S419.  Gene #60: '10p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
10P LOSS MUTATED 165 7 27 7
10P LOSS WILD-TYPE 12 218 61 153

Figure S419.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'10p loss' versus 'RPPA_CNMF'

P value = 0.00217 (Fisher's exact test), Q value = 0.0075

Table S420.  Gene #60: '10p loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
10P LOSS MUTATED 91 49 75 37
10P LOSS WILD-TYPE 122 119 81 72

Figure S420.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'10p loss' versus 'RPPA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00038

Table S421.  Gene #60: '10p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
10P LOSS MUTATED 101 112 39
10P LOSS WILD-TYPE 133 142 119

Figure S421.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S422.  Gene #60: '10p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
10P LOSS MUTATED 189 21 4
10P LOSS WILD-TYPE 55 168 223

Figure S422.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S423.  Gene #60: '10p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
10P LOSS MUTATED 181 10 23
10P LOSS WILD-TYPE 22 180 244

Figure S423.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00091

Table S424.  Gene #60: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
10P LOSS MUTATED 32 26 5 20
10P LOSS WILD-TYPE 108 81 77 160

Figure S424.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S425.  Gene #60: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
10P LOSS MUTATED 11 12 60
10P LOSS WILD-TYPE 211 172 43

Figure S425.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S426.  Gene #60: '10p loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
10P LOSS MUTATED 26 37 3 17
10P LOSS WILD-TYPE 101 82 102 137

Figure S426.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S427.  Gene #60: '10p loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
10P LOSS MUTATED 4 6 12 1 55 5
10P LOSS WILD-TYPE 95 71 106 55 8 87

Figure S427.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S428.  Gene #61: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
10Q LOSS MUTATED 142 69 131 91
10Q LOSS WILD-TYPE 16 27 6 26

Figure S428.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S429.  Gene #61: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
10Q LOSS MUTATED 128 69 97 139
10Q LOSS WILD-TYPE 20 33 3 19

Figure S429.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10q loss' versus 'MIR_CNMF'

P value = 0.00465 (Fisher's exact test), Q value = 0.014

Table S430.  Gene #61: '10q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
10Q LOSS MUTATED 132 158 68 110
10Q LOSS WILD-TYPE 11 29 22 16

Figure S430.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'10q loss' versus 'MIR_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00056

Table S431.  Gene #61: '10q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
10Q LOSS MUTATED 236 109 123
10Q LOSS WILD-TYPE 57 15 6

Figure S431.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S432.  Gene #61: '10q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
10Q LOSS MUTATED 483 45 63
10Q LOSS WILD-TYPE 46 425 28

Figure S432.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S433.  Gene #61: '10q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
10Q LOSS MUTATED 165 21 27 7
10Q LOSS WILD-TYPE 12 204 61 153

Figure S433.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0011

Table S434.  Gene #61: '10q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
10Q LOSS MUTATED 96 51 82 38
10Q LOSS WILD-TYPE 117 117 74 71

Figure S434.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'10q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00065

Table S435.  Gene #61: '10q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
10Q LOSS MUTATED 108 117 42
10Q LOSS WILD-TYPE 126 137 116

Figure S435.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S436.  Gene #61: '10q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
10Q LOSS MUTATED 197 23 10
10Q LOSS WILD-TYPE 47 166 217

Figure S436.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S437.  Gene #61: '10q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
10Q LOSS MUTATED 184 21 25
10Q LOSS WILD-TYPE 19 169 242

Figure S437.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S438.  Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
10Q LOSS MUTATED 35 32 6 24
10Q LOSS WILD-TYPE 105 75 76 156

Figure S438.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S439.  Gene #61: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
10Q LOSS MUTATED 15 15 67
10Q LOSS WILD-TYPE 207 169 36

Figure S439.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S440.  Gene #61: '10q loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
10Q LOSS MUTATED 31 42 5 19
10Q LOSS WILD-TYPE 96 77 100 135

Figure S440.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S441.  Gene #61: '10q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
10Q LOSS MUTATED 8 9 12 1 56 11
10Q LOSS WILD-TYPE 91 68 106 55 7 81

Figure S441.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S442.  Gene #62: '11p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
11P LOSS MUTATED 27 32 8 23
11P LOSS WILD-TYPE 131 64 129 94

Figure S442.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S443.  Gene #62: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
11P LOSS MUTATED 26 36 4 24
11P LOSS WILD-TYPE 122 66 96 134

Figure S443.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11p loss' versus 'MIR_CHIERARCHICAL'

P value = 0.0179 (Fisher's exact test), Q value = 0.043

Table S444.  Gene #62: '11p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
11P LOSS MUTATED 62 20 13
11P LOSS WILD-TYPE 231 104 116

Figure S444.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S445.  Gene #62: '11p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
11P LOSS MUTATED 70 55 37
11P LOSS WILD-TYPE 459 415 54

Figure S445.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #5: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S446.  Gene #62: '11p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
11P LOSS MUTATED 20 51 6 0
11P LOSS WILD-TYPE 157 174 82 160

Figure S446.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S447.  Gene #62: '11p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
11P LOSS MUTATED 55 16 19
11P LOSS WILD-TYPE 189 173 208

Figure S447.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S448.  Gene #62: '11p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
11P LOSS MUTATED 33 43 14
11P LOSS WILD-TYPE 170 147 253

Figure S448.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00018

Table S449.  Gene #62: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
11P LOSS MUTATED 14 29 4 17
11P LOSS WILD-TYPE 126 78 78 163

Figure S449.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00028

Table S450.  Gene #62: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
11P LOSS MUTATED 23 14 27
11P LOSS WILD-TYPE 199 170 76

Figure S450.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0026

Table S451.  Gene #62: '11p loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
11P LOSS MUTATED 20 24 4 15
11P LOSS WILD-TYPE 107 95 101 139

Figure S451.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S452.  Gene #62: '11p loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
11P LOSS MUTATED 11 27 10 0 8 7
11P LOSS WILD-TYPE 88 50 108 56 55 85

Figure S452.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00018

Table S453.  Gene #63: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
11Q LOSS MUTATED 31 28 9 17
11Q LOSS WILD-TYPE 127 68 128 100

Figure S453.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00094

Table S454.  Gene #63: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
11Q LOSS MUTATED 28 27 5 25
11Q LOSS WILD-TYPE 120 75 95 133

Figure S454.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S455.  Gene #63: '11q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
11Q LOSS MUTATED 74 16 22
11Q LOSS WILD-TYPE 455 454 69

Figure S455.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #5: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00047

Table S456.  Gene #63: '11q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
11Q LOSS MUTATED 18 11 4 0
11Q LOSS WILD-TYPE 159 214 84 160

Figure S456.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S457.  Gene #63: '11q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
11Q LOSS MUTATED 39 4 3
11Q LOSS WILD-TYPE 205 185 224

Figure S457.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S458.  Gene #63: '11q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
11Q LOSS MUTATED 32 10 4
11Q LOSS WILD-TYPE 171 180 263

Figure S458.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00086

Table S459.  Gene #63: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
11Q LOSS MUTATED 6 3 13
11Q LOSS WILD-TYPE 216 181 90

Figure S459.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00493 (Fisher's exact test), Q value = 0.015

Table S460.  Gene #63: '11q loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
11Q LOSS MUTATED 7 10 0 4
11Q LOSS WILD-TYPE 120 109 105 150

Figure S460.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00376 (Fisher's exact test), Q value = 0.012

Table S461.  Gene #63: '11q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
11Q LOSS MUTATED 2 6 3 0 8 2
11Q LOSS WILD-TYPE 97 71 115 56 55 90

Figure S461.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p loss' versus 'MRNA_CNMF'

P value = 0.0325 (Fisher's exact test), Q value = 0.069

Table S462.  Gene #64: '12p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
12P LOSS MUTATED 15 17 8 14
12P LOSS WILD-TYPE 143 79 129 103

Figure S462.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'12p loss' versus 'CN_CNMF'

P value = 0.00193 (Fisher's exact test), Q value = 0.0068

Table S463.  Gene #64: '12p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
12P LOSS MUTATED 40 28 16
12P LOSS WILD-TYPE 489 442 75

Figure S463.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #5: 'CN_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0237 (Fisher's exact test), Q value = 0.055

Table S464.  Gene #64: '12p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
12P LOSS MUTATED 16 17 9
12P LOSS WILD-TYPE 187 173 258

Figure S464.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0436 (Fisher's exact test), Q value = 0.087

Table S465.  Gene #64: '12p loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
12P LOSS MUTATED 5 9 6 1 0 6
12P LOSS WILD-TYPE 94 68 112 55 63 86

Figure S465.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'MRNA_CNMF'

P value = 0.0263 (Fisher's exact test), Q value = 0.059

Table S466.  Gene #65: '12q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
12Q LOSS MUTATED 12 16 8 15
12Q LOSS WILD-TYPE 146 80 129 102

Figure S466.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00038

Table S467.  Gene #65: '12q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
12Q LOSS MUTATED 39 47 22
12Q LOSS WILD-TYPE 490 423 69

Figure S467.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #5: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S468.  Gene #65: '12q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
12Q LOSS MUTATED 7 43 8 5
12Q LOSS WILD-TYPE 170 182 80 155

Figure S468.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00033

Table S469.  Gene #65: '12q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
12Q LOSS MUTATED 16 36 16
12Q LOSS WILD-TYPE 187 154 251

Figure S469.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 0.0037 (Fisher's exact test), Q value = 0.012

Table S470.  Gene #65: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
12Q LOSS MUTATED 9 22 6 16
12Q LOSS WILD-TYPE 131 85 76 164

Figure S470.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00018

Table S471.  Gene #65: '12q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
12Q LOSS MUTATED 12 19 11 1 0 10
12Q LOSS WILD-TYPE 87 58 107 55 63 82

Figure S471.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S472.  Gene #66: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
13Q LOSS MUTATED 58 35 22 48
13Q LOSS WILD-TYPE 100 61 115 69

Figure S472.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00159 (Fisher's exact test), Q value = 0.0058

Table S473.  Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
13Q LOSS MUTATED 50 41 17 55
13Q LOSS WILD-TYPE 98 61 83 103

Figure S473.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 0.00329 (Fisher's exact test), Q value = 0.011

Table S474.  Gene #66: '13q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
13Q LOSS MUTATED 161 105 32
13Q LOSS WILD-TYPE 368 365 59

Figure S474.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #5: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.039

Table S475.  Gene #66: '13q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
13Q LOSS MUTATED 52 56 14 27
13Q LOSS WILD-TYPE 125 169 74 133

Figure S475.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0014

Table S476.  Gene #66: '13q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
13Q LOSS MUTATED 78 30 50
13Q LOSS WILD-TYPE 166 159 177

Figure S476.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00048 (Fisher's exact test), Q value = 0.002

Table S477.  Gene #66: '13q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
13Q LOSS MUTATED 59 56 43
13Q LOSS WILD-TYPE 144 134 224

Figure S477.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00933 (Fisher's exact test), Q value = 0.026

Table S478.  Gene #66: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
13Q LOSS MUTATED 52 28 31
13Q LOSS WILD-TYPE 170 156 72

Figure S478.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0349 (Fisher's exact test), Q value = 0.073

Table S479.  Gene #66: '13q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
13Q LOSS MUTATED 16 23 19 9 18 26
13Q LOSS WILD-TYPE 83 54 99 47 45 66

Figure S479.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S480.  Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
14Q LOSS MUTATED 48 33 13 41
14Q LOSS WILD-TYPE 110 63 124 76

Figure S480.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00075

Table S481.  Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
14Q LOSS MUTATED 43 35 10 47
14Q LOSS WILD-TYPE 105 67 90 111

Figure S481.  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 = 7e-05

Table S482.  Gene #67: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
14Q LOSS MUTATED 130 62 35
14Q LOSS WILD-TYPE 399 408 56

Figure S482.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 0.00181 (Fisher's exact test), Q value = 0.0065

Table S483.  Gene #67: '14q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
14Q LOSS MUTATED 48 32 18 20
14Q LOSS WILD-TYPE 129 193 70 140

Figure S483.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S484.  Gene #67: '14q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
14Q LOSS MUTATED 79 29 23
14Q LOSS WILD-TYPE 165 160 204

Figure S484.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S485.  Gene #67: '14q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
14Q LOSS MUTATED 66 31 34
14Q LOSS WILD-TYPE 137 159 233

Figure S485.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 0.00845 (Fisher's exact test), Q value = 0.024

Table S486.  Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
14Q LOSS MUTATED 35 12 11 22
14Q LOSS WILD-TYPE 105 95 71 158

Figure S486.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0012 (Fisher's exact test), Q value = 0.0046

Table S487.  Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
14Q LOSS MUTATED 29 22 29
14Q LOSS WILD-TYPE 193 162 74

Figure S487.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.042

Table S488.  Gene #67: '14q loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
14Q LOSS MUTATED 23 28 10 19
14Q LOSS WILD-TYPE 104 91 95 135

Figure S488.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00229 (Fisher's exact test), Q value = 0.0078

Table S489.  Gene #67: '14q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
14Q LOSS MUTATED 15 15 15 6 21 8
14Q LOSS WILD-TYPE 84 62 103 50 42 84

Figure S489.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'MRNA_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00042

Table S490.  Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
15Q LOSS MUTATED 25 24 11 33
15Q LOSS WILD-TYPE 133 72 126 84

Figure S490.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S491.  Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
15Q LOSS MUTATED 20 37 7 29
15Q LOSS WILD-TYPE 128 65 93 129

Figure S491.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'MIR_CNMF'

P value = 0.00144 (Fisher's exact test), Q value = 0.0053

Table S492.  Gene #68: '15q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
15Q LOSS MUTATED 16 48 17 15
15Q LOSS WILD-TYPE 127 139 73 111

Figure S492.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'15q loss' versus 'MIR_CHIERARCHICAL'

P value = 0.00192 (Fisher's exact test), Q value = 0.0068

Table S493.  Gene #68: '15q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
15Q LOSS MUTATED 64 10 22
15Q LOSS WILD-TYPE 229 114 107

Figure S493.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00098

Table S494.  Gene #68: '15q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
15Q LOSS MUTATED 23 19 1 28
15Q LOSS WILD-TYPE 154 206 87 132

Figure S494.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'15q loss' versus 'RPPA_CNMF'

P value = 0.0336 (Fisher's exact test), Q value = 0.071

Table S495.  Gene #68: '15q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
15Q LOSS MUTATED 28 15 29 9
15Q LOSS WILD-TYPE 185 153 127 100

Figure S495.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.0293 (Fisher's exact test), Q value = 0.064

Table S496.  Gene #68: '15q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
15Q LOSS MUTATED 39 15 24
15Q LOSS WILD-TYPE 205 174 203

Figure S496.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0018

Table S497.  Gene #68: '15q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
15Q LOSS MUTATED 7 13 6 14 2 8
15Q LOSS WILD-TYPE 92 64 112 42 61 84

Figure S497.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S498.  Gene #69: '16p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
16P LOSS MUTATED 54 10 14
16P LOSS WILD-TYPE 475 460 77

Figure S498.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 0.039

Table S499.  Gene #69: '16p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
16P LOSS MUTATED 16 8 3 3
16P LOSS WILD-TYPE 161 217 85 157

Figure S499.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'16p loss' versus 'RPPA_CNMF'

P value = 0.0299 (Fisher's exact test), Q value = 0.065

Table S500.  Gene #69: '16p loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
16P LOSS MUTATED 14 4 14 3
16P LOSS WILD-TYPE 199 164 142 106

Figure S500.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'16p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00707 (Fisher's exact test), Q value = 0.02

Table S501.  Gene #69: '16p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
16P LOSS MUTATED 19 14 2
16P LOSS WILD-TYPE 215 240 156

Figure S501.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0016

Table S502.  Gene #69: '16p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
16P LOSS MUTATED 26 6 6
16P LOSS WILD-TYPE 218 183 221

Figure S502.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.0021

Table S503.  Gene #69: '16p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
16P LOSS MUTATED 23 5 10
16P LOSS WILD-TYPE 180 185 257

Figure S503.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MRNA_CNMF'

P value = 0.0342 (Fisher's exact test), Q value = 0.072

Table S504.  Gene #70: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
16Q LOSS MUTATED 26 18 10 18
16Q LOSS WILD-TYPE 132 78 127 99

Figure S504.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S505.  Gene #70: '16q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
16Q LOSS MUTATED 72 17 15
16Q LOSS WILD-TYPE 457 453 76

Figure S505.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #5: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S506.  Gene #70: '16q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
16Q LOSS MUTATED 28 10 4 4
16Q LOSS WILD-TYPE 149 215 84 156

Figure S506.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'16q loss' versus 'RPPA_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.043

Table S507.  Gene #70: '16q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
16Q LOSS MUTATED 20 6 19 6
16Q LOSS WILD-TYPE 193 162 137 103

Figure S507.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'16q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 8e-04

Table S508.  Gene #70: '16q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
16Q LOSS MUTATED 31 17 3
16Q LOSS WILD-TYPE 203 237 155

Figure S508.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S509.  Gene #70: '16q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
16Q LOSS MUTATED 35 7 8
16Q LOSS WILD-TYPE 209 182 219

Figure S509.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S510.  Gene #70: '16q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
16Q LOSS MUTATED 32 7 11
16Q LOSS WILD-TYPE 171 183 256

Figure S510.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00328 (Fisher's exact test), Q value = 0.011

Table S511.  Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
16Q LOSS MUTATED 7 4 11
16Q LOSS WILD-TYPE 215 180 92

Figure S511.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0269 (Fisher's exact test), Q value = 0.06

Table S512.  Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
17P LOSS MUTATED 23 15 8 10
17P LOSS WILD-TYPE 125 87 92 148

Figure S512.  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 = 7e-05

Table S513.  Gene #71: '17p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
17P LOSS MUTATED 49 13 16
17P LOSS WILD-TYPE 480 457 75

Figure S513.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #5: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00098

Table S514.  Gene #71: '17p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
17P LOSS MUTATED 19 6 3 2
17P LOSS WILD-TYPE 158 219 85 158

Figure S514.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S515.  Gene #71: '17p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
17P LOSS MUTATED 28 3 4
17P LOSS WILD-TYPE 216 186 223

Figure S515.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S516.  Gene #71: '17p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
17P LOSS MUTATED 24 7 4
17P LOSS WILD-TYPE 179 183 263

Figure S516.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00202 (Fisher's exact test), Q value = 0.007

Table S517.  Gene #71: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
17P LOSS MUTATED 5 1 8
17P LOSS WILD-TYPE 217 183 95

Figure S517.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0454 (Fisher's exact test), Q value = 0.09

Table S518.  Gene #71: '17p loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
17P LOSS MUTATED 3 2 0 1 5 2
17P LOSS WILD-TYPE 96 75 118 55 58 90

Figure S518.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'MRNA_CNMF'

P value = 0.00874 (Fisher's exact test), Q value = 0.024

Table S519.  Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
17Q LOSS MUTATED 19 7 9 2
17Q LOSS WILD-TYPE 139 89 128 115

Figure S519.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q loss' versus 'MIR_CHIERARCHICAL'

P value = 0.0433 (Fisher's exact test), Q value = 0.087

Table S520.  Gene #72: '17q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
17Q LOSS MUTATED 15 15 11
17Q LOSS WILD-TYPE 278 109 118

Figure S520.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S521.  Gene #72: '17q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
17Q LOSS MUTATED 33 7 11
17Q LOSS WILD-TYPE 496 463 80

Figure S521.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #5: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 0.00288 (Fisher's exact test), Q value = 0.0095

Table S522.  Gene #72: '17q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
17Q LOSS MUTATED 12 3 2 1
17Q LOSS WILD-TYPE 165 222 86 159

Figure S522.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'17q loss' versus 'RPPA_CNMF'

P value = 0.05 (Fisher's exact test), Q value = 0.097

Table S523.  Gene #72: '17q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
17Q LOSS MUTATED 13 2 7 2
17Q LOSS WILD-TYPE 200 166 149 107

Figure S523.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'17q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0141 (Fisher's exact test), Q value = 0.036

Table S524.  Gene #72: '17q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
17Q LOSS MUTATED 14 9 1
17Q LOSS WILD-TYPE 220 245 157

Figure S524.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 0.00126 (Fisher's exact test), Q value = 0.0048

Table S525.  Gene #72: '17q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
17Q LOSS MUTATED 16 2 3
17Q LOSS WILD-TYPE 228 187 224

Figure S525.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00094

Table S526.  Gene #72: '17q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
17Q LOSS MUTATED 15 4 2
17Q LOSS WILD-TYPE 188 186 265

Figure S526.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MRNA_CNMF'

P value = 0.00948 (Fisher's exact test), Q value = 0.026

Table S527.  Gene #73: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
18P LOSS MUTATED 22 15 6 16
18P LOSS WILD-TYPE 136 81 131 101

Figure S527.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0321 (Fisher's exact test), Q value = 0.068

Table S528.  Gene #73: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
18P LOSS MUTATED 19 16 4 20
18P LOSS WILD-TYPE 129 86 96 138

Figure S528.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p loss' versus 'METHLYATION_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.039

Table S529.  Gene #73: '18p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
18P LOSS MUTATED 28 20 9 31
18P LOSS WILD-TYPE 149 205 79 129

Figure S529.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'18q loss' versus 'MRNA_CNMF'

P value = 0.0435 (Fisher's exact test), Q value = 0.087

Table S530.  Gene #74: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
18Q LOSS MUTATED 20 11 6 15
18Q LOSS WILD-TYPE 138 85 131 102

Figure S530.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00855 (Fisher's exact test), Q value = 0.024

Table S531.  Gene #74: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
18Q LOSS MUTATED 18 12 2 20
18Q LOSS WILD-TYPE 130 90 98 138

Figure S531.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q loss' versus 'METHLYATION_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0021

Table S532.  Gene #74: '18q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
18Q LOSS MUTATED 18 18 6 34
18Q LOSS WILD-TYPE 159 207 82 126

Figure S532.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 0.0187 (Fisher's exact test), Q value = 0.045

Table S533.  Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
18Q LOSS MUTATED 17 7 18 20
18Q LOSS WILD-TYPE 123 100 64 160

Figure S533.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'19p loss' versus 'MRNA_CNMF'

P value = 0.00326 (Fisher's exact test), Q value = 0.011

Table S534.  Gene #75: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
19P LOSS MUTATED 3 9 2 9
19P LOSS WILD-TYPE 155 87 135 108

Figure S534.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00705 (Fisher's exact test), Q value = 0.02

Table S535.  Gene #75: '19p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
19P LOSS MUTATED 4 11 1 7
19P LOSS WILD-TYPE 144 91 99 151

Figure S535.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p loss' versus 'MIR_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 0.056

Table S536.  Gene #75: '19p loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
19P LOSS MUTATED 3 16 2 4
19P LOSS WILD-TYPE 140 171 88 122

Figure S536.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #3: 'MIR_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 0.00414 (Fisher's exact test), Q value = 0.013

Table S537.  Gene #75: '19p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
19P LOSS MUTATED 16 35 6
19P LOSS WILD-TYPE 513 435 85

Figure S537.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #5: 'CN_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0223 (Fisher's exact test), Q value = 0.052

Table S538.  Gene #75: '19p loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
19P LOSS MUTATED 5 8 13 5
19P LOSS WILD-TYPE 122 111 92 149

Figure S538.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.018 (Fisher's exact test), Q value = 0.044

Table S539.  Gene #75: '19p loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
19P LOSS MUTATED 4 8 4 9 2 4
19P LOSS WILD-TYPE 95 69 114 47 61 88

Figure S539.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'MRNA_CNMF'

P value = 0.00233 (Fisher's exact test), Q value = 0.0079

Table S540.  Gene #76: '19q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
19Q LOSS MUTATED 6 10 2 12
19Q LOSS WILD-TYPE 152 86 135 105

Figure S540.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0107 (Fisher's exact test), Q value = 0.029

Table S541.  Gene #76: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
19Q LOSS MUTATED 7 12 1 10
19Q LOSS WILD-TYPE 141 90 99 148

Figure S541.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S542.  Gene #76: '19q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
19Q LOSS MUTATED 24 216 4
19Q LOSS WILD-TYPE 505 254 87

Figure S542.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #5: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S543.  Gene #76: '19q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
19Q LOSS MUTATED 11 31 18 158
19Q LOSS WILD-TYPE 166 194 70 2

Figure S543.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'19q loss' versus 'RPPA_CNMF'

P value = 0.00292 (Fisher's exact test), Q value = 0.0096

Table S544.  Gene #76: '19q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
19Q LOSS MUTATED 52 66 52 24
19Q LOSS WILD-TYPE 161 102 104 85

Figure S544.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'19q loss' versus 'RPPA_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00094

Table S545.  Gene #76: '19q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
19Q LOSS MUTATED 60 65 69
19Q LOSS WILD-TYPE 174 189 89

Figure S545.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S546.  Gene #76: '19q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
19Q LOSS MUTATED 22 102 97
19Q LOSS WILD-TYPE 222 87 130

Figure S546.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S547.  Gene #76: '19q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
19Q LOSS MUTATED 12 30 179
19Q LOSS WILD-TYPE 191 160 88

Figure S547.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S548.  Gene #76: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
19Q LOSS MUTATED 33 21 70 86
19Q LOSS WILD-TYPE 107 86 12 94

Figure S548.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S549.  Gene #76: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
19Q LOSS MUTATED 97 103 10
19Q LOSS WILD-TYPE 125 81 93

Figure S549.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S550.  Gene #76: '19q loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
19Q LOSS MUTATED 22 26 87 74
19Q LOSS WILD-TYPE 105 93 18 80

Figure S550.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S551.  Gene #76: '19q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
19Q LOSS MUTATED 11 39 62 55 2 40
19Q LOSS WILD-TYPE 88 38 56 1 61 52

Figure S551.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'MRNA_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00086

Table S552.  Gene #77: '20p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
20P LOSS MUTATED 4 10 0 3
20P LOSS WILD-TYPE 154 86 137 114

Figure S552.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p loss' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00028

Table S553.  Gene #77: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
20P LOSS MUTATED 5 11 0 1
20P LOSS WILD-TYPE 143 91 100 157

Figure S553.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p loss' versus 'MIR_CNMF'

P value = 0.0463 (Fisher's exact test), Q value = 0.091

Table S554.  Gene #77: '20p loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
20P LOSS MUTATED 2 7 7 2
20P LOSS WILD-TYPE 141 180 83 124

Figure S554.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #3: 'MIR_CNMF'

'20p loss' versus 'CN_CNMF'

P value = 0.0338 (Fisher's exact test), Q value = 0.071

Table S555.  Gene #77: '20p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
20P LOSS MUTATED 12 8 6
20P LOSS WILD-TYPE 517 462 85

Figure S555.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #5: 'CN_CNMF'

'20q loss' versus 'MRNA_CNMF'

P value = 0.00238 (Fisher's exact test), Q value = 0.0081

Table S556.  Gene #78: '20q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
20Q LOSS MUTATED 4 8 0 3
20Q LOSS WILD-TYPE 154 88 137 114

Figure S556.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00061

Table S557.  Gene #78: '20q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
20Q LOSS MUTATED 4 10 0 1
20Q LOSS WILD-TYPE 144 92 100 157

Figure S557.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q loss' versus 'CN_CNMF'

P value = 0.00631 (Fisher's exact test), Q value = 0.019

Table S558.  Gene #78: '20q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
20Q LOSS MUTATED 14 3 4
20Q LOSS WILD-TYPE 515 467 87

Figure S558.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #5: 'CN_CNMF'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0124 (Fisher's exact test), Q value = 0.033

Table S559.  Gene #78: '20q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
20Q LOSS MUTATED 2 5 0
20Q LOSS WILD-TYPE 201 185 267

Figure S559.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MRNA_CNMF'

P value = 0.0234 (Fisher's exact test), Q value = 0.054

Table S560.  Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
21Q LOSS MUTATED 5 12 8 11
21Q LOSS WILD-TYPE 153 84 129 106

Figure S560.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00116 (Fisher's exact test), Q value = 0.0044

Table S561.  Gene #79: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
21Q LOSS MUTATED 5 17 6 8
21Q LOSS WILD-TYPE 143 85 94 150

Figure S561.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00056

Table S562.  Gene #79: '21q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
21Q LOSS MUTATED 9 29 4 3
21Q LOSS WILD-TYPE 168 196 84 157

Figure S562.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S563.  Gene #79: '21q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
21Q LOSS MUTATED 10 28 7
21Q LOSS WILD-TYPE 193 162 260

Figure S563.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 0.06

Table S564.  Gene #79: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
21Q LOSS MUTATED 20 6 10
21Q LOSS WILD-TYPE 202 178 93

Figure S564.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0289 (Fisher's exact test), Q value = 0.063

Table S565.  Gene #79: '21q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
21Q LOSS MUTATED 10 11 4 1 3 6
21Q LOSS WILD-TYPE 89 66 114 55 60 86

Figure S565.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S566.  Gene #80: '22q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 529 470 91
22Q LOSS MUTATED 168 36 36
22Q LOSS WILD-TYPE 361 434 55

Figure S566.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #5: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S567.  Gene #80: '22q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
22Q LOSS MUTATED 54 27 18 5
22Q LOSS WILD-TYPE 123 198 70 155

Figure S567.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CNMF'

P value = 0.00784 (Fisher's exact test), Q value = 0.022

Table S568.  Gene #80: '22q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
22Q LOSS MUTATED 37 23 44 18
22Q LOSS WILD-TYPE 176 145 112 91

Figure S568.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0322 (Fisher's exact test), Q value = 0.069

Table S569.  Gene #80: '22q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
22Q LOSS MUTATED 51 52 19
22Q LOSS WILD-TYPE 183 202 139

Figure S569.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S570.  Gene #80: '22q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
22Q LOSS MUTATED 77 17 16
22Q LOSS WILD-TYPE 167 172 211

Figure S570.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S571.  Gene #80: '22q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
22Q LOSS MUTATED 68 23 19
22Q LOSS WILD-TYPE 135 167 248

Figure S571.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.0014

Table S572.  Gene #80: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
22Q LOSS MUTATED 18 15 24
22Q LOSS WILD-TYPE 204 169 79

Figure S572.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00171 (Fisher's exact test), Q value = 0.0062

Table S573.  Gene #80: '22q loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
22Q LOSS MUTATED 17 23 5 11
22Q LOSS WILD-TYPE 110 96 100 143

Figure S573.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00018

Table S574.  Gene #80: '22q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
22Q LOSS MUTATED 3 15 10 3 17 8
22Q LOSS WILD-TYPE 96 62 108 53 46 84

Figure S574.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'MRNA_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.029

Table S575.  Gene #81: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
XP LOSS MUTATED 23 30 23 25
XP LOSS WILD-TYPE 135 66 114 92

Figure S575.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00821 (Fisher's exact test), Q value = 0.023

Table S576.  Gene #81: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
XP LOSS MUTATED 20 32 19 30
XP LOSS WILD-TYPE 128 70 81 128

Figure S576.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xp loss' versus 'MIR_CNMF'

P value = 0.0453 (Fisher's exact test), Q value = 0.09

Table S577.  Gene #81: 'xp loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 187 90 126
XP LOSS MUTATED 22 48 18 18
XP LOSS WILD-TYPE 121 139 72 108

Figure S577.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #3: 'MIR_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 0.0078 (Fisher's exact test), Q value = 0.022

Table S578.  Gene #81: 'xp loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
XP LOSS MUTATED 39 54 7 33
XP LOSS WILD-TYPE 138 171 81 127

Figure S578.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'xp loss' versus 'RPPA_CNMF'

P value = 0.00252 (Fisher's exact test), Q value = 0.0084

Table S579.  Gene #81: 'xp loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
XP LOSS MUTATED 47 23 48 20
XP LOSS WILD-TYPE 166 145 108 89

Figure S579.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'xp loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0138 (Fisher's exact test), Q value = 0.035

Table S580.  Gene #81: 'xp loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 254 158
XP LOSS MUTATED 61 55 22
XP LOSS WILD-TYPE 173 199 136

Figure S580.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 0.0243 (Fisher's exact test), Q value = 0.056

Table S581.  Gene #81: 'xp loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
XP LOSS MUTATED 62 28 48
XP LOSS WILD-TYPE 182 161 179

Figure S581.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0193 (Fisher's exact test), Q value = 0.046

Table S582.  Gene #81: 'xp loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 203 190 267
XP LOSS MUTATED 44 51 43
XP LOSS WILD-TYPE 159 139 224

Figure S582.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.051

Table S583.  Gene #81: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
XP LOSS MUTATED 23 24 25 27
XP LOSS WILD-TYPE 117 83 57 153

Figure S583.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00122 (Fisher's exact test), Q value = 0.0046

Table S584.  Gene #81: 'xp loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
XP LOSS MUTATED 33 19 29 17
XP LOSS WILD-TYPE 94 100 76 137

Figure S584.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0013

Table S585.  Gene #81: 'xp loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
XP LOSS MUTATED 20 23 9 13 8 25
XP LOSS WILD-TYPE 79 54 109 43 55 67

Figure S585.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'MRNA_CNMF'

P value = 0.035 (Fisher's exact test), Q value = 0.073

Table S586.  Gene #82: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 96 137 117
XQ LOSS MUTATED 22 27 21 22
XQ LOSS WILD-TYPE 136 69 116 95

Figure S586.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xq loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0251 (Fisher's exact test), Q value = 0.057

Table S587.  Gene #82: 'xq loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
XQ LOSS MUTATED 18 28 18 28
XQ LOSS WILD-TYPE 130 74 82 130

Figure S587.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0011

Table S588.  Gene #82: 'xq loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 177 225 88 160
XQ LOSS MUTATED 39 29 4 32
XQ LOSS WILD-TYPE 138 196 84 128

Figure S588.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0021

Table S589.  Gene #82: 'xq loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 213 168 156 109
XQ LOSS MUTATED 34 19 44 14
XQ LOSS WILD-TYPE 179 149 112 95

Figure S589.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.00191 (Fisher's exact test), Q value = 0.0068

Table S590.  Gene #82: 'xq loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 244 189 227
XQ LOSS MUTATED 55 21 29
XQ LOSS WILD-TYPE 189 168 198

Figure S590.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00023

Table S591.  Gene #82: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
XQ LOSS MUTATED 12 16 25 17
XQ LOSS WILD-TYPE 128 91 57 163

Figure S591.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0015

Table S592.  Gene #82: 'xq loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
XQ LOSS MUTATED 19 11 27 12
XQ LOSS WILD-TYPE 108 108 78 142

Figure S592.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-04 (Fisher's exact test), Q value = 0.0035

Table S593.  Gene #82: 'xq loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
XQ LOSS MUTATED 9 17 6 13 7 17
XQ LOSS WILD-TYPE 90 60 112 43 56 75

Figure S593.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #14: '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/GBMLGG-TP/22534382/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/GBMLGG-TP/22573865/GBMLGG-TP.transferedmergedcluster.txt

  • Number of patients = 1090

  • Number of significantly arm-level cnvs = 82

  • Number of molecular subtypes = 14

  • 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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