Correlation between copy number variations of arm-level result and molecular subtypes
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
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/C10Z72SH
Overview
Introduction

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

Summary

Testing the association between copy number variation 82 arm-level events and 12 molecular subtypes across 539 patients, 696 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

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

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

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

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

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

  • 4q gain cnv correlated to 'CN_CNMF'.

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

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

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

  • 6q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 7q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 8p gain cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

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

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

  • 9q gain cnv correlated to 'RPPA_CHIERARCHICAL' and 'MIRSEQ_CNMF'.

  • 10p gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'RPPA_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 10q gain cnv correlated to 'MRNA_CNMF'.

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

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

  • 12p 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'.

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

  • 13q gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 15q gain cnv correlated to 'CN_CNMF'.

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

  • 16q gain cnv correlated to 'CN_CNMF'.

  • 17p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 17q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

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

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

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

  • xp gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • xq gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

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

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

  • 2p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

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

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

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

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

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

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

  • 7p loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 7q 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'.

  • 8p 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'.

  • 8q 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'.

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

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

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

  • 10q 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'.

  • 11p 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'.

  • 11q 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'.

  • 12p 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'.

  • 12q 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'.

  • 13q 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'.

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

  • 15q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16p 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'.

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

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

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

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

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

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

  • 19q 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'.

  • 20p loss cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 20q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 21q 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'.

  • 22q 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'.

  • xp 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'.

  • xq 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'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 696 significant findings detected.

Clinical
Features
MRNA
CNMF
MRNA
CHIERARCHICAL
CN
CNMF
METHLYATION
CNMF
RPPA
CNMF
RPPA
CHIERARCHICAL
MRNASEQ
CNMF
MRNASEQ
CHIERARCHICAL
MIRSEQ
CNMF
MIRSEQ
CHIERARCHICAL
MIRSEQ
MATURE
CNMF
MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
4p loss 106 (20%) 433 0.00366
(0.00655)
0.00181
(0.00342)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
4q loss 104 (19%) 435 0.0426
(0.0615)
0.00793
(0.0134)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
5p loss 53 (10%) 486 0.0429
(0.0617)
0.0402
(0.0585)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00035
(0.000733)
9e-05
(0.000208)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
5e-05
(0.00012)
0.00022
(0.00048)
5q loss 73 (14%) 466 0.0114
(0.0185)
0.0101
(0.0165)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
4e-05
(9.77e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
2e-05
(5.26e-05)
8p loss 78 (14%) 461 0.00872
(0.0145)
4e-05
(9.77e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
9p loss 99 (18%) 440 0.00126
(0.00244)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
9e-05
(0.000208)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00384
(0.00686)
0.0184
(0.0289)
9q loss 117 (22%) 422 5e-05
(0.00012)
2e-05
(5.26e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
2e-05
(5.26e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00012
(0.000272)
0.0013
(0.0025)
14q loss 62 (12%) 477 0.00252
(0.00467)
0.00055
(0.00112)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.0013
(0.0025)
5e-05
(0.00012)
15q loss 109 (20%) 430 0.00049
(0.00101)
4e-05
(9.77e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
16p loss 99 (18%) 440 0.00232
(0.00434)
0.00785
(0.0132)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00014
(0.000314)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.0003
(0.000638)
1e-05
(2.82e-05)
16q loss 140 (26%) 399 0.00088
(0.00176)
0.00143
(0.00272)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00028
(0.000603)
1e-05
(2.82e-05)
17p loss 129 (24%) 410 0.00319
(0.00577)
0.00017
(0.000376)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
4e-05
(9.77e-05)
0.00027
(0.000584)
17q loss 93 (17%) 446 0.00248
(0.00461)
2e-05
(5.26e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00552
(0.0096)
0.0221
(0.0344)
21q loss 54 (10%) 485 0.0363
(0.0534)
0.029
(0.0444)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.0171
(0.027)
0.00127
(0.00245)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
2e-05
(5.26e-05)
2e-05
(5.26e-05)
22q loss 110 (20%) 429 0.00261
(0.00481)
0.00711
(0.0121)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00969
(0.0159)
0.00122
(0.00237)
xp loss 86 (16%) 453 0.00059
(0.0012)
0.0009
(0.0018)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
3e-05
(7.55e-05)
3e-05
(7.55e-05)
xq loss 70 (13%) 469 0.00247
(0.0046)
0.00752
(0.0128)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
2e-05
(5.26e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00287
(0.00523)
1e-05
(2.82e-05)
8q gain 159 (29%) 380 0.0166
(0.0263)
0.0303
(0.046)
1e-05
(2.82e-05)
0.206
(0.258)
0.0155
(0.0246)
3e-05
(7.55e-05)
3e-05
(7.55e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00832
(0.0139)
0.00257
(0.00474)
0.00764
(0.013)
19p gain 55 (10%) 484 0.0362
(0.0534)
0.0291
(0.0445)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00279
(0.0051)
3e-05
(7.55e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
5e-05
(0.00012)
0.104
(0.14)
20p gain 109 (20%) 430 0.0353
(0.0524)
0.194
(0.245)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
5e-05
(0.00012)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00159
(0.00301)
0.00011
(0.000251)
20q gain 130 (24%) 409 0.00829
(0.0139)
0.0505
(0.0711)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
2e-05
(5.26e-05)
0.0001
(0.000229)
3p loss 52 (10%) 487 0.0365
(0.0536)
0.00071
(0.00143)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.0006
(0.00122)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.0645
(0.0895)
9e-05
(0.000208)
3q loss 31 (6%) 508 0.0361
(0.0533)
0.00068
(0.00138)
1e-05
(2.82e-05)
4e-05
(9.77e-05)
0.0342
(0.0511)
0.0005
(0.00103)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00075
(0.00151)
0.00016
(0.000356)
0.288
(0.351)
0.0468
(0.0665)
10p loss 44 (8%) 495 0.0358
(0.053)
0.0302
(0.0459)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
9e-05
(0.000208)
2e-05
(5.26e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.0691
(0.0956)
0.00087
(0.00174)
2p gain 93 (17%) 446 0.524
(0.599)
0.37
(0.44)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00426
(0.00754)
0.0248
(0.0383)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00019
(0.000419)
5e-05
(0.00012)
2q gain 78 (14%) 461 0.465
(0.54)
0.947
(1.00)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.0025
(0.00464)
0.00827
(0.0139)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.0001
(0.000229)
3e-05
(7.55e-05)
3q gain 85 (16%) 454 0.624
(0.699)
0.25
(0.309)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00765
(0.013)
0.00111
(0.00217)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00087
(0.00174)
3e-05
(7.55e-05)
5p gain 52 (10%) 487 1
(1.00)
0.515
(0.59)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.0125
(0.02)
0.0003
(0.000638)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00132
(0.00253)
2e-05
(5.26e-05)
6p gain 81 (15%) 458 0.689
(0.762)
0.738
(0.811)
1e-05
(2.82e-05)
2e-05
(5.26e-05)
0.00782
(0.0132)
0.00015
(0.000335)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
4e-05
(9.77e-05)
1e-05
(2.82e-05)
0.00091
(0.00181)
0.0121
(0.0194)
13q gain 30 (6%) 509 0.133
(0.175)
0.0064
(0.011)
1e-05
(2.82e-05)
8e-05
(0.000187)
0.0604
(0.0841)
0.00263
(0.00484)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
2e-05
(5.26e-05)
1e-05
(2.82e-05)
0.028
(0.0431)
0.01
(0.0165)
18p gain 73 (14%) 466 0.411
(0.484)
0.238
(0.296)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00013
(0.000293)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
2e-05
(5.26e-05)
1e-05
(2.82e-05)
18q gain 46 (9%) 493 0.109
(0.146)
0.18
(0.23)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
8e-05
(0.000187)
0.0119
(0.0192)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00546
(0.00951)
1e-05
(2.82e-05)
19q gain 58 (11%) 481 0.134
(0.175)
0.166
(0.214)
1e-05
(2.82e-05)
2e-05
(5.26e-05)
0.00306
(0.00556)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00016
(0.000356)
0.0199
(0.0313)
21q gain 39 (7%) 500 1e-05
(2.82e-05)
0.0001
(0.000229)
0.00017
(0.000376)
0.0003
(0.000638)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00414
(0.00734)
0.0446
(0.0638)
22q gain 30 (6%) 509 1e-05
(2.82e-05)
1e-05
(2.82e-05)
4e-05
(9.77e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00014
(0.000314)
1e-05
(2.82e-05)
4e-05
(9.77e-05)
6e-05
(0.000142)
6q loss 25 (5%) 514 0.348
(0.419)
0.0294
(0.045)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.0464
(0.0661)
0.108
(0.145)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00033
(0.000692)
1e-05
(2.82e-05)
0.00881
(0.0146)
0.0138
(0.022)
7q loss 45 (8%) 494 1e-05
(2.82e-05)
1e-05
(2.82e-05)
4e-05
(9.77e-05)
0.00093
(0.00184)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
6e-05
(0.000142)
0.00305
(0.00555)
8q loss 22 (4%) 517 1e-05
(2.82e-05)
2e-05
(5.26e-05)
0.00277
(0.00508)
0.00051
(0.00105)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
2e-05
(5.26e-05)
3e-05
(7.55e-05)
0.00126
(0.00244)
10q loss 40 (7%) 499 0.134
(0.175)
0.166
(0.214)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00655
(0.0113)
3e-05
(7.55e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00392
(0.00696)
0.0125
(0.02)
11p loss 76 (14%) 463 1e-05
(2.82e-05)
1e-05
(2.82e-05)
6e-05
(0.000142)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00011
(0.000251)
0.0002
(0.000439)
11q loss 73 (14%) 466 1e-05
(2.82e-05)
1e-05
(2.82e-05)
2e-05
(5.26e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
12p loss 45 (8%) 494 0.135
(0.176)
0.168
(0.216)
1e-05
(2.82e-05)
4e-05
(9.77e-05)
0.00027
(0.000584)
2e-05
(5.26e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00337
(0.00606)
0.00589
(0.0102)
12q loss 40 (7%) 499 1e-05
(2.82e-05)
5e-05
(0.00012)
0.0005
(0.00103)
3e-05
(7.55e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.0014
(0.00267)
0.00031
(0.000655)
13q loss 93 (17%) 446 1
(1.00)
0.194
(0.245)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
7e-05
(0.000165)
0.00149
(0.00282)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.0414
(0.0599)
0.0237
(0.0369)
18p loss 51 (9%) 488 1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.0271
(0.0418)
0.00101
(0.00198)
2e-05
(5.26e-05)
2e-05
(5.26e-05)
3e-05
(7.55e-05)
0.00319
(0.00577)
0.00897
(0.0149)
0.0109
(0.0177)
18q loss 63 (12%) 476 1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.0101
(0.0165)
0.00099
(0.00195)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
3e-05
(7.55e-05)
0.0114
(0.0185)
0.0113
(0.0183)
19p loss 57 (11%) 482 1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00013
(0.000293)
0.00012
(0.000272)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00385
(0.00686)
1e-05
(2.82e-05)
19q loss 54 (10%) 485 0.759
(0.831)
0.056
(0.0784)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
3e-05
(7.55e-05)
9e-05
(0.000208)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
4e-05
(9.77e-05)
0.00601
(0.0104)
0.00037
(0.000773)
12p gain 69 (13%) 470 0.579
(0.654)
0.688
(0.761)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.291
(0.353)
0.0492
(0.0695)
2e-05
(5.26e-05)
4e-05
(9.77e-05)
0.00136
(0.0026)
1e-05
(2.82e-05)
0.00676
(0.0116)
0.00092
(0.00183)
1p loss 27 (5%) 512 1e-05
(2.82e-05)
3e-05
(7.55e-05)
0.0481
(0.0682)
0.00014
(0.000314)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00044
(0.00091)
1e-05
(2.82e-05)
0.224
(0.279)
0.0413
(0.0599)
6p loss 20 (4%) 519 0.352
(0.422)
0.0299
(0.0456)
1e-05
(2.82e-05)
0.00033
(0.000692)
0.0377
(0.0552)
0.0563
(0.0785)
0.00011
(0.000251)
0.0003
(0.000638)
0.00352
(0.00631)
0.0004
(0.000829)
0.0102
(0.0167)
0.0799
(0.109)
7p loss 45 (8%) 494 0.0363
(0.0534)
0.194
(0.245)
1e-05
(2.82e-05)
3e-05
(7.55e-05)
0.00202
(0.00379)
0.0039
(0.00694)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.0552
(0.0774)
0.0538
(0.0755)
1p gain 54 (10%) 485 0.316
(0.382)
0.261
(0.321)
1e-05
(2.82e-05)
0.0184
(0.0289)
0.471
(0.546)
0.456
(0.53)
6e-05
(0.000142)
0.00029
(0.000622)
1e-05
(2.82e-05)
0.00021
(0.000459)
0.00326
(0.00588)
0.0395
(0.0577)
1q gain 189 (35%) 350 0.267
(0.327)
0.00928
(0.0153)
1e-05
(2.82e-05)
0.108
(0.144)
0.00021
(0.000459)
0.00094
(0.00185)
0.0116
(0.0187)
0.00028
(0.000603)
0.00017
(0.000376)
0.184
(0.234)
0.318
(0.383)
0.0144
(0.023)
9p gain 22 (4%) 517 0.00063
(0.00128)
0.0366
(0.0537)
0.00029
(0.000622)
0.00476
(0.00835)
0.00454
(0.00799)
0.0281
(0.0433)
0.00246
(0.00459)
0.0208
(0.0326)
0.506
(0.581)
0.296
(0.359)
17q gain 30 (6%) 509 1e-05
(2.82e-05)
1e-05
(2.82e-05)
0.00031
(0.000655)
0.326
(0.393)
2e-05
(5.26e-05)
1e-05
(2.82e-05)
6e-05
(0.000142)
1e-05
(2.82e-05)
0.0945
(0.127)
0.0344
(0.0512)
5q gain 20 (4%) 519 3e-05
(7.55e-05)
0.0147
(0.0234)
0.649
(0.724)
0.074
(0.102)
0.00213
(0.00399)
0.00663
(0.0114)
0.00444
(0.00784)
0.00093
(0.00184)
0.0562
(0.0785)
0.0004
(0.000829)
6q gain 66 (12%) 473 0.687
(0.761)
0.74
(0.812)
1e-05
(2.82e-05)
0.00052
(0.00106)
0.0836
(0.113)
0.0004
(0.000829)
6e-05
(0.000142)
0.0004
(0.000829)
0.0082
(0.0138)
0.00109
(0.00213)
0.247
(0.306)
0.19
(0.241)
11p gain 23 (4%) 516 0.0358
(0.053)
0.195
(0.245)
2e-05
(5.26e-05)
0.0392
(0.0573)
0.122
(0.162)
0.254
(0.314)
0.0002
(0.000439)
0.00138
(0.00264)
0.0146
(0.0232)
0.0117
(0.0189)
0.384
(0.456)
0.262
(0.321)
1q loss 16 (3%) 523 2e-05
(5.26e-05)
0.00635
(0.011)
0.365
(0.436)
0.0244
(0.0379)
0.00092
(0.00183)
0.00108
(0.00212)
0.0288
(0.0443)
0.00026
(0.000566)
0.799
(0.871)
0.246
(0.305)
3p gain 48 (9%) 491 1e-05
(2.82e-05)
0.00284
(0.00518)
0.615
(0.69)
0.132
(0.174)
3e-05
(7.55e-05)
0.00709
(0.0121)
0.0215
(0.0335)
0.0297
(0.0452)
0.258
(0.318)
0.154
(0.2)
14q gain 36 (7%) 503 1
(1.00)
0.842
(0.912)
1e-05
(2.82e-05)
0.0305
(0.0462)
0.188
(0.239)
0.2
(0.252)
1e-05
(2.82e-05)
0.0012
(0.00234)
0.00027
(0.000584)
0.00343
(0.00616)
0.362
(0.433)
0.309
(0.374)
16p gain 25 (5%) 514 1e-05
(2.82e-05)
0.00325
(0.00587)
0.0766
(0.105)
0.0821
(0.111)
0.00927
(0.0153)
0.049
(0.0694)
0.0209
(0.0326)
0.0478
(0.0678)
0.179
(0.228)
0.659
(0.734)
2q loss 18 (3%) 521 1e-05
(2.82e-05)
0.0411
(0.0598)
0.411
(0.484)
0.222
(0.277)
2e-05
(5.26e-05)
0.0072
(0.0123)
0.00873
(0.0145)
0.0426
(0.0615)
0.513
(0.588)
0.471
(0.546)
4p gain 14 (3%) 525 5e-05
(0.00012)
0.485
(0.561)
0.433
(0.507)
0.0322
(0.0487)
0.00142
(0.0027)
0.0435
(0.0625)
0.0732
(0.101)
0.0118
(0.019)
0.501
(0.577)
0.299
(0.363)
7p gain 68 (13%) 471 0.897
(0.962)
0.906
(0.971)
1e-05
(2.82e-05)
0.0051
(0.00891)
0.553
(0.629)
0.0503
(0.0711)
0.00865
(0.0144)
0.0505
(0.0711)
0.0314
(0.0475)
0.197
(0.249)
0.00032
(0.000674)
0.33
(0.397)
17p gain 13 (2%) 526 0.0385
(0.0563)
0.17
(0.217)
0.189
(0.239)
0.477
(0.552)
0.0084
(0.014)
0.017
(0.0269)
0.221
(0.276)
0.00461
(0.0081)
0.0341
(0.051)
0.716
(0.788)
20p loss 22 (4%) 517 0.849
(0.919)
0.165
(0.214)
1e-05
(2.82e-05)
0.141
(0.184)
0.154
(0.199)
0.0432
(0.0621)
0.0242
(0.0376)
0.0117
(0.0189)
0.0814
(0.111)
0.0102
(0.0167)
0.265
(0.325)
0.375
(0.446)
8p gain 116 (22%) 423 0.434
(0.508)
0.406
(0.479)
1e-05
(2.82e-05)
0.618
(0.692)
0.626
(0.7)
0.00276
(0.00507)
0.0467
(0.0665)
0.0517
(0.0727)
0.0344
(0.0512)
0.426
(0.501)
0.08
(0.109)
0.113
(0.15)
10p gain 116 (22%) 423 0.00499
(0.00874)
0.0881
(0.119)
0.0338
(0.0508)
0.571
(0.646)
0.0346
(0.0514)
0.553
(0.629)
0.218
(0.272)
0.117
(0.155)
0.146
(0.189)
0.224
(0.279)
0.0338
(0.0508)
0.0866
(0.117)
12q gain 51 (9%) 488 0.579
(0.654)
0.686
(0.761)
1e-05
(2.82e-05)
0.00121
(0.00235)
0.752
(0.824)
0.585
(0.66)
0.0337
(0.0507)
0.0782
(0.107)
0.26
(0.319)
0.0163
(0.0258)
0.364
(0.435)
0.0818
(0.111)
20q loss 11 (2%) 528 0.00187
(0.00353)
0.0162
(0.0257)
0.034
(0.0509)
0.186
(0.237)
0.0734
(0.101)
0.0638
(0.0887)
0.189
(0.239)
0.00545
(0.00951)
0.487
(0.562)
0.117
(0.156)
7q gain 65 (12%) 474 0.94
(1.00)
1
(1.00)
1e-05
(2.82e-05)
0.0592
(0.0826)
0.891
(0.957)
0.129
(0.17)
0.0813
(0.111)
0.034
(0.0509)
0.131
(0.173)
0.432
(0.507)
0.00735
(0.0125)
0.851
(0.92)
11q gain 20 (4%) 519 0.134
(0.175)
0.166
(0.214)
9e-05
(0.000208)
0.0254
(0.0393)
0.161
(0.208)
0.444
(0.518)
0.00189
(0.00356)
0.0647
(0.0897)
0.258
(0.318)
0.107
(0.144)
0.965
(1.00)
0.693
(0.765)
2p loss 12 (2%) 527 0.00031
(0.000655)
0.0884
(0.119)
0.289
(0.352)
0.424
(0.498)
0.0007
(0.00141)
0.0415
(0.06)
0.076
(0.104)
0.204
(0.256)
0.565
(0.641)
0.546
(0.623)
9q gain 10 (2%) 529 0.0935
(0.126)
0.367
(0.438)
0.593
(0.667)
0.0433
(0.0622)
0.391
(0.463)
0.372
(0.443)
0.0335
(0.0505)
0.394
(0.467)
0.837
(0.909)
0.331
(0.398)
xp gain 63 (12%) 476 0.861
(0.928)
0.926
(0.99)
1e-05
(2.82e-05)
0.675
(0.751)
0.876
(0.943)
0.774
(0.846)
0.551
(0.628)
0.803
(0.874)
0.704
(0.776)
0.913
(0.977)
0.0458
(0.0654)
0.41
(0.484)
xq gain 64 (12%) 475 0.731
(0.804)
0.478
(0.552)
1e-05
(2.82e-05)
1
(1.00)
0.696
(0.768)
0.456
(0.53)
0.388
(0.46)
0.933
(0.996)
0.588
(0.663)
0.97
(1.00)
0.00452
(0.00797)
0.853
(0.921)
4q gain 8 (1%) 531 0.00599
(0.0104)
0.861
(0.928)
0.57
(0.646)
0.146
(0.189)
0.175
(0.224)
0.442
(0.516)
0.565
(0.641)
0.281
(0.343)
0.268
(0.327)
0.673
(0.749)
10q gain 108 (20%) 431 0.00257
(0.00474)
0.0887
(0.12)
0.14
(0.183)
0.452
(0.527)
0.114
(0.152)
0.506
(0.581)
0.137
(0.179)
0.358
(0.429)
0.169
(0.217)
0.128
(0.169)
0.0779
(0.107)
0.0713
(0.0986)
15q gain 11 (2%) 528 0.00898
(0.0149)
0.764
(0.835)
0.0977
(0.131)
0.257
(0.317)
0.883
(0.949)
0.59
(0.664)
0.798
(0.871)
0.686
(0.761)
0.497
(0.573)
0.838
(0.909)
16q gain 10 (2%) 529 0.0438
(0.0627)
0.601
(0.675)
0.215
(0.27)
0.24
(0.298)
0.142
(0.185)
0.632
(0.706)
0.831
(0.904)
0.524
(0.599)
1
(1.00)
1
(1.00)
'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
1P GAIN MUTATED 39 4 4 7
1P GAIN WILD-TYPE 169 174 95 47

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 0.0184 (Fisher's exact test), Q value = 0.029

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
1P GAIN MUTATED 25 7 13
1P GAIN WILD-TYPE 129 71 180

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

'1p gain' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00014

Table S3.  Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
1P GAIN MUTATED 35 6 7 6
1P GAIN WILD-TYPE 153 117 86 127

Figure S3.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.00062

Table S4.  Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
1P GAIN MUTATED 26 2 7 4 9 4 2
1P GAIN WILD-TYPE 97 51 40 61 99 62 73

Figure S4.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S5.  Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
1P GAIN MUTATED 33 7 9 3 1
1P GAIN WILD-TYPE 131 73 97 130 46

Figure S5.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00046

Table S6.  Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
1P GAIN MUTATED 15 31 7
1P GAIN WILD-TYPE 203 141 133

Figure S6.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00326 (Fisher's exact test), Q value = 0.0059

Table S7.  Gene #1: '1p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
1P GAIN MUTATED 23 5 6 11
1P GAIN WILD-TYPE 93 93 86 81

Figure S7.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0395 (Fisher's exact test), Q value = 0.058

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
1P GAIN MUTATED 25 8 12
1P GAIN WILD-TYPE 138 124 91

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

'1q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00928 (Fisher's exact test), Q value = 0.015

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
1Q GAIN MUTATED 7 2 6 5 3
1Q GAIN WILD-TYPE 7 7 1 2 13

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

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S10.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
1Q GAIN MUTATED 77 24 37 51
1Q GAIN WILD-TYPE 131 154 62 3

Figure S10.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'RPPA_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00046

Table S11.  Gene #2: '1q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
1Q GAIN MUTATED 20 40 11 24 18 20 21
1Q GAIN WILD-TYPE 19 41 41 32 66 48 32

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

'1q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.0019

Table S12.  Gene #2: '1q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
1Q GAIN MUTATED 56 55 29 14
1Q GAIN WILD-TYPE 52 127 64 36

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.019

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
1Q GAIN MUTATED 69 52 36 32
1Q GAIN WILD-TYPE 119 71 57 101

Figure S13.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 6e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
1Q GAIN MUTATED 49 28 11 33 33 17 18
1Q GAIN WILD-TYPE 74 25 36 32 75 49 57

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

'1q gain' versus 'MIRSEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00038

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
1Q GAIN MUTATED 64 44 35 34 11
1Q GAIN WILD-TYPE 100 36 71 99 36

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

'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.023

Table S16.  Gene #2: '1q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
1Q GAIN MUTATED 61 33 43
1Q GAIN WILD-TYPE 102 99 60

Figure S16.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
2P GAIN MUTATED 68 2 17 6
2P GAIN WILD-TYPE 140 176 82 48

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S18.  Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
2P GAIN MUTATED 43 17 12
2P GAIN WILD-TYPE 111 61 181

Figure S18.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'RPPA_CNMF'

P value = 0.00426 (Fisher's exact test), Q value = 0.0075

Table S19.  Gene #3: '2p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
2P GAIN MUTATED 4 4 7 13 20 14 13
2P GAIN WILD-TYPE 35 77 45 43 64 54 40

Figure S19.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'2p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0248 (Fisher's exact test), Q value = 0.038

Table S20.  Gene #3: '2p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
2P GAIN MUTATED 10 42 15 8
2P GAIN WILD-TYPE 98 140 78 42

Figure S20.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S21.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
2P GAIN MUTATED 58 13 13 9
2P GAIN WILD-TYPE 130 110 80 124

Figure S21.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S22.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
2P GAIN MUTATED 48 7 10 4 14 6 4
2P GAIN WILD-TYPE 75 46 37 61 94 60 71

Figure S22.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S23.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
2P GAIN MUTATED 52 9 14 8 9
2P GAIN WILD-TYPE 112 71 92 125 38

Figure S23.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
2P GAIN MUTATED 25 57 10
2P GAIN WILD-TYPE 193 115 130

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

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00042

Table S25.  Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
2P GAIN MUTATED 33 6 17 13
2P GAIN WILD-TYPE 83 92 75 79

Figure S25.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00012

Table S26.  Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
2P GAIN MUTATED 36 8 25
2P GAIN WILD-TYPE 127 124 78

Figure S26.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S27.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
2Q GAIN MUTATED 56 1 16 5
2Q GAIN WILD-TYPE 152 177 83 49

Figure S27.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
2Q GAIN MUTATED 39 14 11
2Q GAIN WILD-TYPE 115 64 182

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

'2q gain' versus 'RPPA_CNMF'

P value = 0.0025 (Fisher's exact test), Q value = 0.0046

Table S29.  Gene #4: '2q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
2Q GAIN MUTATED 3 3 7 12 19 12 12
2Q GAIN WILD-TYPE 36 78 45 44 65 56 41

Figure S29.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'2q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00827 (Fisher's exact test), Q value = 0.014

Table S30.  Gene #4: '2q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
2Q GAIN MUTATED 7 38 16 7
2Q GAIN WILD-TYPE 101 144 77 43

Figure S30.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S31.  Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
2Q GAIN MUTATED 50 10 11 7
2Q GAIN WILD-TYPE 138 113 82 126

Figure S31.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S32.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
2Q GAIN MUTATED 41 5 8 3 12 5 4
2Q GAIN WILD-TYPE 82 48 39 62 96 61 71

Figure S32.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S33.  Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
2Q GAIN MUTATED 47 7 11 6 7
2Q GAIN WILD-TYPE 117 73 95 127 40

Figure S33.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S34.  Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
2Q GAIN MUTATED 21 49 8
2Q GAIN WILD-TYPE 197 123 132

Figure S34.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00023

Table S35.  Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
2Q GAIN MUTATED 32 5 13 12
2Q GAIN WILD-TYPE 84 93 79 80

Figure S35.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S36.  Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
2Q GAIN MUTATED 34 6 22
2Q GAIN WILD-TYPE 129 126 81

Figure S36.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
3P GAIN MUTATED 39 0 8 1
3P GAIN WILD-TYPE 169 178 91 53

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

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.00284 (Fisher's exact test), Q value = 0.0052

Table S38.  Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
3P GAIN MUTATED 25 7 10
3P GAIN WILD-TYPE 129 71 183

Figure S38.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
3P GAIN MUTATED 32 2 6 8
3P GAIN WILD-TYPE 156 121 87 125

Figure S39.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00709 (Fisher's exact test), Q value = 0.012

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
3P GAIN MUTATED 16 0 8 4 13 3 4
3P GAIN WILD-TYPE 107 53 39 61 95 63 71

Figure S40.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.034

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
3P GAIN MUTATED 25 4 6 8 5
3P GAIN WILD-TYPE 139 76 100 125 42

Figure S41.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0297 (Fisher's exact test), Q value = 0.045

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
3P GAIN MUTATED 14 24 10
3P GAIN WILD-TYPE 204 148 130

Figure S42.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
3Q GAIN MUTATED 74 0 10 1
3Q GAIN WILD-TYPE 134 178 89 53

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

'3q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S44.  Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
3Q GAIN MUTATED 48 16 11
3Q GAIN WILD-TYPE 106 62 182

Figure S44.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'RPPA_CNMF'

P value = 0.00765 (Fisher's exact test), Q value = 0.013

Table S45.  Gene #6: '3q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
3Q GAIN MUTATED 3 5 4 16 14 12 6
3Q GAIN WILD-TYPE 36 76 48 40 70 56 47

Figure S45.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'3q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00111 (Fisher's exact test), Q value = 0.0022

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
3Q GAIN MUTATED 5 36 15 4
3Q GAIN WILD-TYPE 103 146 78 46

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

'3q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S47.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
3Q GAIN MUTATED 60 2 14 9
3Q GAIN WILD-TYPE 128 121 79 124

Figure S47.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S48.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
3Q GAIN MUTATED 38 0 18 4 17 3 5
3Q GAIN WILD-TYPE 85 53 29 61 91 63 70

Figure S48.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S49.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
3Q GAIN MUTATED 50 4 13 9 9
3Q GAIN WILD-TYPE 114 76 93 124 38

Figure S49.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S50.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
3Q GAIN MUTATED 17 57 11
3Q GAIN WILD-TYPE 201 115 129

Figure S50.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0017

Table S51.  Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
3Q GAIN MUTATED 29 6 15 21
3Q GAIN WILD-TYPE 87 92 77 71

Figure S51.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S52.  Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
3Q GAIN MUTATED 42 9 20
3Q GAIN WILD-TYPE 121 123 83

Figure S52.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00012

Table S53.  Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
4P GAIN MUTATED 14 0 0 0
4P GAIN WILD-TYPE 194 178 99 54

Figure S53.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'4p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0322 (Fisher's exact test), Q value = 0.049

Table S54.  Gene #7: '4p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
4P GAIN MUTATED 0 9 4 0
4P GAIN WILD-TYPE 108 173 89 50

Figure S54.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.00142 (Fisher's exact test), Q value = 0.0027

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
4P GAIN MUTATED 12 1 0 1
4P GAIN WILD-TYPE 176 122 93 132

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

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0435 (Fisher's exact test), Q value = 0.062

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
4P GAIN MUTATED 8 0 2 0 3 1 0
4P GAIN WILD-TYPE 115 53 45 65 105 65 75

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

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0118 (Fisher's exact test), Q value = 0.019

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
4P GAIN MUTATED 3 10 1
4P GAIN WILD-TYPE 215 162 139

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

'4q gain' versus 'CN_CNMF'

P value = 0.00599 (Fisher's exact test), Q value = 0.01

Table S58.  Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
4Q GAIN MUTATED 8 0 0 0
4Q GAIN WILD-TYPE 200 178 99 54

Figure S58.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S59.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
5P GAIN MUTATED 47 0 3 2
5P GAIN WILD-TYPE 161 178 96 52

Figure S59.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S60.  Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
5P GAIN MUTATED 31 8 6
5P GAIN WILD-TYPE 123 70 187

Figure S60.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p gain' versus 'RPPA_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.02

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
5P GAIN MUTATED 1 5 3 11 16 5 5
5P GAIN WILD-TYPE 38 76 49 45 68 63 48

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

'5p gain' versus 'RPPA_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.00064

Table S62.  Gene #9: '5p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
5P GAIN MUTATED 5 33 7 1
5P GAIN WILD-TYPE 103 149 86 49

Figure S62.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S63.  Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
5P GAIN MUTATED 40 6 6 0
5P GAIN WILD-TYPE 148 117 87 133

Figure S63.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S64.  Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
5P GAIN MUTATED 28 3 12 1 6 2 0
5P GAIN WILD-TYPE 95 50 35 64 102 64 75

Figure S64.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S65.  Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
5P GAIN MUTATED 37 5 6 1 3
5P GAIN WILD-TYPE 127 75 100 132 44

Figure S65.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S66.  Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
5P GAIN MUTATED 13 38 1
5P GAIN WILD-TYPE 205 134 139

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

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00132 (Fisher's exact test), Q value = 0.0025

Table S67.  Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
5P GAIN MUTATED 20 2 9 12
5P GAIN WILD-TYPE 96 96 83 80

Figure S67.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S68.  Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
5P GAIN MUTATED 29 3 11
5P GAIN WILD-TYPE 134 129 92

Figure S68.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S69.  Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
5Q GAIN MUTATED 18 0 1 1
5Q GAIN WILD-TYPE 190 178 98 53

Figure S69.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.023

Table S70.  Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
5Q GAIN MUTATED 13 2 4
5Q GAIN WILD-TYPE 141 76 189

Figure S70.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.00213 (Fisher's exact test), Q value = 0.004

Table S71.  Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
5Q GAIN MUTATED 14 3 3 0
5Q GAIN WILD-TYPE 174 120 90 133

Figure S71.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00663 (Fisher's exact test), Q value = 0.011

Table S72.  Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
5Q GAIN MUTATED 7 2 6 1 4 0 0
5Q GAIN WILD-TYPE 116 51 41 64 104 66 75

Figure S72.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CNMF'

P value = 0.00444 (Fisher's exact test), Q value = 0.0078

Table S73.  Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
5Q GAIN MUTATED 12 4 2 0 2
5Q GAIN WILD-TYPE 152 76 104 133 45

Figure S73.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00093 (Fisher's exact test), Q value = 0.0018

Table S74.  Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
5Q GAIN MUTATED 7 13 0
5Q GAIN WILD-TYPE 211 159 140

Figure S74.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.00083

Table S75.  Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
5Q GAIN MUTATED 14 0 3
5Q GAIN WILD-TYPE 149 132 100

Figure S75.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S76.  Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
6P GAIN MUTATED 72 2 5 2
6P GAIN WILD-TYPE 136 176 94 52

Figure S76.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S77.  Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
6P GAIN MUTATED 42 15 14
6P GAIN WILD-TYPE 112 63 179

Figure S77.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p gain' versus 'RPPA_CNMF'

P value = 0.00782 (Fisher's exact test), Q value = 0.013

Table S78.  Gene #11: '6p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
6P GAIN MUTATED 2 6 4 13 20 10 9
6P GAIN WILD-TYPE 37 75 48 43 64 58 44

Figure S78.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'6p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00034

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
6P GAIN MUTATED 4 40 15 5
6P GAIN WILD-TYPE 104 142 78 45

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

'6p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S80.  Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
6P GAIN MUTATED 54 6 6 15
6P GAIN WILD-TYPE 134 117 87 118

Figure S80.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S81.  Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
6P GAIN MUTATED 42 0 6 5 14 8 6
6P GAIN WILD-TYPE 81 53 41 60 94 58 69

Figure S81.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 9.8e-05

Table S82.  Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
6P GAIN MUTATED 45 6 10 12 8
6P GAIN WILD-TYPE 119 74 96 121 39

Figure S82.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S83.  Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
6P GAIN MUTATED 21 48 12
6P GAIN WILD-TYPE 197 124 128

Figure S83.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.0018

Table S84.  Gene #11: '6p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
6P GAIN MUTATED 34 10 11 13
6P GAIN WILD-TYPE 82 88 81 79

Figure S84.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0121 (Fisher's exact test), Q value = 0.019

Table S85.  Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
6P GAIN MUTATED 37 13 18
6P GAIN WILD-TYPE 126 119 85

Figure S85.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S86.  Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
6Q GAIN MUTATED 59 1 5 1
6Q GAIN WILD-TYPE 149 177 94 53

Figure S86.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0011

Table S87.  Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
6Q GAIN MUTATED 33 10 14
6Q GAIN WILD-TYPE 121 68 179

Figure S87.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q gain' versus 'RPPA_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.00083

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
6Q GAIN MUTATED 3 33 12 4
6Q GAIN WILD-TYPE 105 149 81 46

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

'6q gain' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00014

Table S89.  Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
6Q GAIN MUTATED 40 6 6 14
6Q GAIN WILD-TYPE 148 117 87 119

Figure S89.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.00083

Table S90.  Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
6Q GAIN MUTATED 28 0 7 5 12 8 6
6Q GAIN WILD-TYPE 95 53 40 60 96 58 69

Figure S90.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 0.0082 (Fisher's exact test), Q value = 0.014

Table S91.  Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
6Q GAIN MUTATED 33 6 9 11 7
6Q GAIN WILD-TYPE 131 74 97 122 40

Figure S91.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00109 (Fisher's exact test), Q value = 0.0021

Table S92.  Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
6Q GAIN MUTATED 20 35 11
6Q GAIN WILD-TYPE 198 137 129

Figure S92.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S93.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
7P GAIN MUTATED 43 2 15 8
7P GAIN WILD-TYPE 165 176 84 46

Figure S93.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.0051 (Fisher's exact test), Q value = 0.0089

Table S94.  Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
7P GAIN MUTATED 29 4 19
7P GAIN WILD-TYPE 125 74 174

Figure S94.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.00865 (Fisher's exact test), Q value = 0.014

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
7P GAIN MUTATED 36 14 6 12
7P GAIN WILD-TYPE 152 109 87 121

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

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.0314 (Fisher's exact test), Q value = 0.048

Table S96.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
7P GAIN MUTATED 30 13 9 10 5
7P GAIN WILD-TYPE 134 67 97 123 42

Figure S96.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.00067

Table S97.  Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
7P GAIN MUTATED 26 4 12 7
7P GAIN WILD-TYPE 90 94 80 85

Figure S97.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S98.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
7Q GAIN MUTATED 37 4 15 9
7Q GAIN WILD-TYPE 171 174 84 45

Figure S98.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.034 (Fisher's exact test), Q value = 0.051

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
7Q GAIN MUTATED 19 8 8 1 15 8 6
7Q GAIN WILD-TYPE 104 45 39 64 93 58 69

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

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00735 (Fisher's exact test), Q value = 0.013

Table S100.  Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
7Q GAIN MUTATED 22 5 13 7
7Q GAIN WILD-TYPE 94 93 79 85

Figure S100.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
8P GAIN MUTATED 64 7 40 5
8P GAIN WILD-TYPE 144 171 59 49

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

'8p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00276 (Fisher's exact test), Q value = 0.0051

Table S102.  Gene #15: '8p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
8P GAIN MUTATED 14 33 31 13
8P GAIN WILD-TYPE 94 149 62 37

Figure S102.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8p gain' versus 'MRNASEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
8P GAIN MUTATED 50 29 12 25
8P GAIN WILD-TYPE 138 94 81 108

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

'8p gain' versus 'MIRSEQ_CNMF'

P value = 0.0344 (Fisher's exact test), Q value = 0.051

Table S104.  Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
8P GAIN MUTATED 44 23 14 25 9
8P GAIN WILD-TYPE 120 57 92 108 38

Figure S104.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MRNA_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.026

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 17 14 7
8Q GAIN MUTATED 1 8 2 0
8Q GAIN WILD-TYPE 14 9 12 7

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

'8q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0303 (Fisher's exact test), Q value = 0.046

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
8Q GAIN MUTATED 4 5 0 0 2
8Q GAIN WILD-TYPE 10 4 7 7 14

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

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
8Q GAIN MUTATED 106 6 42 5
8Q GAIN WILD-TYPE 102 172 57 49

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

'8q gain' versus 'RPPA_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 0.025

Table S108.  Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
8Q GAIN MUTATED 9 13 15 23 31 16 18
8Q GAIN WILD-TYPE 30 68 37 33 53 52 35

Figure S108.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8q gain' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S109.  Gene #16: '8q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
8Q GAIN MUTATED 14 55 39 17
8Q GAIN WILD-TYPE 94 127 54 33

Figure S109.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S110.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
8Q GAIN MUTATED 81 31 18 29
8Q GAIN WILD-TYPE 107 92 75 104

Figure S110.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
8Q GAIN MUTATED 53 10 18 8 37 23 10
8Q GAIN WILD-TYPE 70 43 29 57 71 43 65

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

'8q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S112.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
8Q GAIN MUTATED 74 24 16 31 11
8Q GAIN WILD-TYPE 90 56 90 102 36

Figure S112.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00832 (Fisher's exact test), Q value = 0.014

Table S113.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
8Q GAIN MUTATED 60 65 31
8Q GAIN WILD-TYPE 158 107 109

Figure S113.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00257 (Fisher's exact test), Q value = 0.0047

Table S114.  Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
8Q GAIN MUTATED 53 24 25 24
8Q GAIN WILD-TYPE 63 74 67 68

Figure S114.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00764 (Fisher's exact test), Q value = 0.013

Table S115.  Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
8Q GAIN MUTATED 66 34 26
8Q GAIN WILD-TYPE 97 98 77

Figure S115.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.0013

Table S116.  Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
9P GAIN MUTATED 18 3 1 0
9P GAIN WILD-TYPE 190 175 98 54

Figure S116.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 0.0366 (Fisher's exact test), Q value = 0.054

Table S117.  Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
9P GAIN MUTATED 12 4 4
9P GAIN WILD-TYPE 142 74 189

Figure S117.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p gain' versus 'RPPA_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.00062

Table S118.  Gene #17: '9p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
9P GAIN MUTATED 0 0 1 10 5 3 2
9P GAIN WILD-TYPE 39 81 51 46 79 65 51

Figure S118.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'9p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00476 (Fisher's exact test), Q value = 0.0083

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
9P GAIN MUTATED 0 12 8 1
9P GAIN WILD-TYPE 108 170 85 49

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

'9p gain' versus 'MRNASEQ_CNMF'

P value = 0.00454 (Fisher's exact test), Q value = 0.008

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
9P GAIN MUTATED 15 2 4 1
9P GAIN WILD-TYPE 173 121 89 132

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

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0281 (Fisher's exact test), Q value = 0.043

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
9P GAIN MUTATED 10 0 2 1 7 2 0
9P GAIN WILD-TYPE 113 53 45 64 101 64 75

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

'9p gain' versus 'MIRSEQ_CNMF'

P value = 0.00246 (Fisher's exact test), Q value = 0.0046

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
9P GAIN MUTATED 16 2 2 2 0
9P GAIN WILD-TYPE 148 78 104 131 47

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

'9p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0208 (Fisher's exact test), Q value = 0.033

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
9P GAIN MUTATED 7 13 2
9P GAIN WILD-TYPE 211 159 138

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

'9q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0433 (Fisher's exact test), Q value = 0.062

Table S124.  Gene #18: '9q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
9Q GAIN MUTATED 0 4 5 0
9Q GAIN WILD-TYPE 108 178 88 50

Figure S124.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_CNMF'

P value = 0.0335 (Fisher's exact test), Q value = 0.051

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
9Q GAIN MUTATED 8 1 0 1 0
9Q GAIN WILD-TYPE 156 79 106 132 47

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

'10p gain' versus 'MRNA_CNMF'

P value = 0.00499 (Fisher's exact test), Q value = 0.0087

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 17 14 7
10P GAIN MUTATED 2 2 9 1
10P GAIN WILD-TYPE 13 15 5 6

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

'10p gain' versus 'CN_CNMF'

P value = 0.0338 (Fisher's exact test), Q value = 0.051

Table S127.  Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
10P GAIN MUTATED 53 26 26 11
10P GAIN WILD-TYPE 155 152 73 43

Figure S127.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'RPPA_CNMF'

P value = 0.0346 (Fisher's exact test), Q value = 0.051

Table S128.  Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
10P GAIN MUTATED 6 25 6 11 12 17 16
10P GAIN WILD-TYPE 33 56 46 45 72 51 37

Figure S128.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0338 (Fisher's exact test), Q value = 0.051

Table S129.  Gene #19: '10p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
10P GAIN MUTATED 25 27 18 10
10P GAIN WILD-TYPE 91 71 74 82

Figure S129.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q gain' versus 'MRNA_CNMF'

P value = 0.00257 (Fisher's exact test), Q value = 0.0047

Table S130.  Gene #20: '10q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 17 14 7
10Q GAIN MUTATED 1 3 9 1
10Q GAIN WILD-TYPE 14 14 5 6

Figure S130.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p gain' versus 'MRNA_CNMF'

P value = 0.0358 (Fisher's exact test), Q value = 0.053

Table S131.  Gene #21: '11p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 17 14 7
11P GAIN MUTATED 0 4 0 0
11P GAIN WILD-TYPE 15 13 14 7

Figure S131.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S132.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
11P GAIN MUTATED 21 0 1 1
11P GAIN WILD-TYPE 187 178 98 53

Figure S132.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.0392 (Fisher's exact test), Q value = 0.057

Table S133.  Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
11P GAIN MUTATED 12 3 4
11P GAIN WILD-TYPE 142 75 189

Figure S133.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.00044

Table S134.  Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
11P GAIN MUTATED 18 2 0 3
11P GAIN WILD-TYPE 170 121 93 130

Figure S134.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00138 (Fisher's exact test), Q value = 0.0026

Table S135.  Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
11P GAIN MUTATED 14 1 1 0 5 2 0
11P GAIN WILD-TYPE 109 52 46 65 103 64 75

Figure S135.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 0.023

Table S136.  Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
11P GAIN MUTATED 15 2 1 4 1
11P GAIN WILD-TYPE 149 78 105 129 46

Figure S136.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0117 (Fisher's exact test), Q value = 0.019

Table S137.  Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
11P GAIN MUTATED 7 14 2
11P GAIN WILD-TYPE 211 158 138

Figure S137.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00021

Table S138.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
11Q GAIN MUTATED 17 0 2 1
11Q GAIN WILD-TYPE 191 178 97 53

Figure S138.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 0.0254 (Fisher's exact test), Q value = 0.039

Table S139.  Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
11Q GAIN MUTATED 11 1 4
11Q GAIN WILD-TYPE 143 77 189

Figure S139.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 0.00189 (Fisher's exact test), Q value = 0.0036

Table S140.  Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
11Q GAIN MUTATED 15 2 0 3
11Q GAIN WILD-TYPE 173 121 93 130

Figure S140.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S141.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
12P GAIN MUTATED 53 4 5 7
12P GAIN WILD-TYPE 155 174 94 47

Figure S141.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S142.  Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
12P GAIN MUTATED 32 15 8
12P GAIN WILD-TYPE 122 63 185

Figure S142.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0492 (Fisher's exact test), Q value = 0.07

Table S143.  Gene #23: '12p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
12P GAIN MUTATED 10 34 8 5
12P GAIN WILD-TYPE 98 148 85 45

Figure S143.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S144.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
12P GAIN MUTATED 44 8 9 8
12P GAIN WILD-TYPE 144 115 84 125

Figure S144.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 9.8e-05

Table S145.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
12P GAIN MUTATED 31 1 10 6 11 3 7
12P GAIN WILD-TYPE 92 52 37 59 97 63 68

Figure S145.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 0.00136 (Fisher's exact test), Q value = 0.0026

Table S146.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
12P GAIN MUTATED 33 7 11 8 10
12P GAIN WILD-TYPE 131 73 95 125 37

Figure S146.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S147.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
12P GAIN MUTATED 18 41 10
12P GAIN WILD-TYPE 200 131 130

Figure S147.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00676 (Fisher's exact test), Q value = 0.012

Table S148.  Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
12P GAIN MUTATED 25 6 9 12
12P GAIN WILD-TYPE 91 92 83 80

Figure S148.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00092 (Fisher's exact test), Q value = 0.0018

Table S149.  Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
12P GAIN MUTATED 32 7 13
12P GAIN WILD-TYPE 131 125 90

Figure S149.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S150.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
12Q GAIN MUTATED 35 4 5 7
12Q GAIN WILD-TYPE 173 174 94 47

Figure S150.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 0.00121 (Fisher's exact test), Q value = 0.0024

Table S151.  Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
12Q GAIN MUTATED 20 12 8
12Q GAIN WILD-TYPE 134 66 185

Figure S151.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.0337 (Fisher's exact test), Q value = 0.051

Table S152.  Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
12Q GAIN MUTATED 27 7 9 8
12Q GAIN WILD-TYPE 161 116 84 125

Figure S152.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0163 (Fisher's exact test), Q value = 0.026

Table S153.  Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
12Q GAIN MUTATED 15 26 10
12Q GAIN WILD-TYPE 203 146 130

Figure S153.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0064 (Fisher's exact test), Q value = 0.011

Table S154.  Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
13Q GAIN MUTATED 0 3 0 0 0
13Q GAIN WILD-TYPE 14 6 7 7 16

Figure S154.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S155.  Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
13Q GAIN MUTATED 28 0 1 1
13Q GAIN WILD-TYPE 180 178 98 53

Figure S155.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00019

Table S156.  Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
13Q GAIN MUTATED 16 8 2
13Q GAIN WILD-TYPE 138 70 191

Figure S156.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00263 (Fisher's exact test), Q value = 0.0048

Table S157.  Gene #25: '13q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
13Q GAIN MUTATED 0 17 6 3
13Q GAIN WILD-TYPE 108 165 87 47

Figure S157.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S158.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
13Q GAIN MUTATED 26 0 2 2
13Q GAIN WILD-TYPE 162 123 91 131

Figure S158.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S159.  Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
13Q GAIN MUTATED 26 0 1 0 1 1 1
13Q GAIN WILD-TYPE 97 53 46 65 107 65 74

Figure S159.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S160.  Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
13Q GAIN MUTATED 23 0 3 2 2
13Q GAIN WILD-TYPE 141 80 103 131 45

Figure S160.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S161.  Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
13Q GAIN MUTATED 2 26 2
13Q GAIN WILD-TYPE 216 146 138

Figure S161.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.043

Table S162.  Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
13Q GAIN MUTATED 12 1 6 6
13Q GAIN WILD-TYPE 104 97 86 86

Figure S162.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.01 (Fisher's exact test), Q value = 0.016

Table S163.  Gene #25: '13q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
13Q GAIN MUTATED 14 2 9
13Q GAIN WILD-TYPE 149 130 94

Figure S163.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S164.  Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
14Q GAIN MUTATED 28 1 2 5
14Q GAIN WILD-TYPE 180 177 97 49

Figure S164.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 0.0305 (Fisher's exact test), Q value = 0.046

Table S165.  Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
14Q GAIN MUTATED 19 5 9
14Q GAIN WILD-TYPE 135 73 184

Figure S165.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S166.  Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
14Q GAIN MUTATED 26 4 0 6
14Q GAIN WILD-TYPE 162 119 93 127

Figure S166.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0012 (Fisher's exact test), Q value = 0.0023

Table S167.  Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
14Q GAIN MUTATED 16 1 6 1 8 0 4
14Q GAIN WILD-TYPE 107 52 41 64 100 66 71

Figure S167.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.00058

Table S168.  Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
14Q GAIN MUTATED 21 4 0 7 4
14Q GAIN WILD-TYPE 143 76 106 126 43

Figure S168.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00343 (Fisher's exact test), Q value = 0.0062

Table S169.  Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
14Q GAIN MUTATED 8 21 7
14Q GAIN WILD-TYPE 210 151 133

Figure S169.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 0.00898 (Fisher's exact test), Q value = 0.015

Table S170.  Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
15Q GAIN MUTATED 10 1 0 0
15Q GAIN WILD-TYPE 198 177 99 54

Figure S170.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S171.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
16P GAIN MUTATED 22 1 1 1
16P GAIN WILD-TYPE 186 177 98 53

Figure S171.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 0.00325 (Fisher's exact test), Q value = 0.0059

Table S172.  Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
16P GAIN MUTATED 15 0 8
16P GAIN WILD-TYPE 139 78 185

Figure S172.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.00927 (Fisher's exact test), Q value = 0.015

Table S173.  Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
16P GAIN MUTATED 17 2 2 4
16P GAIN WILD-TYPE 171 121 91 129

Figure S173.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.049 (Fisher's exact test), Q value = 0.069

Table S174.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
16P GAIN MUTATED 12 2 2 1 5 3 0
16P GAIN WILD-TYPE 111 51 45 64 103 63 75

Figure S174.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.0209 (Fisher's exact test), Q value = 0.033

Table S175.  Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
16P GAIN MUTATED 16 2 3 3 1
16P GAIN WILD-TYPE 148 78 103 130 46

Figure S175.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0478 (Fisher's exact test), Q value = 0.068

Table S176.  Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
16P GAIN MUTATED 7 14 4
16P GAIN WILD-TYPE 211 158 136

Figure S176.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 0.0438 (Fisher's exact test), Q value = 0.063

Table S177.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
16Q GAIN MUTATED 8 1 0 1
16Q GAIN WILD-TYPE 200 177 99 53

Figure S177.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 0.0385 (Fisher's exact test), Q value = 0.056

Table S178.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
17P GAIN MUTATED 10 1 1 1
17P GAIN WILD-TYPE 198 177 98 53

Figure S178.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 0.0084 (Fisher's exact test), Q value = 0.014

Table S179.  Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
17P GAIN MUTATED 10 1 2 0
17P GAIN WILD-TYPE 178 122 91 133

Figure S179.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.017 (Fisher's exact test), Q value = 0.027

Table S180.  Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
17P GAIN MUTATED 9 0 1 1 2 0 0
17P GAIN WILD-TYPE 114 53 46 64 106 66 75

Figure S180.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00461 (Fisher's exact test), Q value = 0.0081

Table S181.  Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
17P GAIN MUTATED 2 10 1
17P GAIN WILD-TYPE 216 162 139

Figure S181.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0341 (Fisher's exact test), Q value = 0.051

Table S182.  Gene #30: '17p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
17P GAIN MUTATED 7 2 1 0
17P GAIN WILD-TYPE 109 96 91 92

Figure S182.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S183.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
17Q GAIN MUTATED 26 1 2 1
17Q GAIN WILD-TYPE 182 177 97 53

Figure S183.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S184.  Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
17Q GAIN MUTATED 21 3 2
17Q GAIN WILD-TYPE 133 75 191

Figure S184.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'RPPA_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.00065

Table S185.  Gene #31: '17q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
17Q GAIN MUTATED 1 0 0 5 10 8 1
17Q GAIN WILD-TYPE 38 81 52 51 74 60 52

Figure S185.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S186.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
17Q GAIN MUTATED 23 1 4 2
17Q GAIN WILD-TYPE 165 122 89 131

Figure S186.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S187.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
17Q GAIN MUTATED 19 0 5 1 3 2 0
17Q GAIN WILD-TYPE 104 53 42 64 105 64 75

Figure S187.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00014

Table S188.  Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
17Q GAIN MUTATED 22 1 2 3 2
17Q GAIN WILD-TYPE 142 79 104 130 45

Figure S188.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S189.  Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
17Q GAIN MUTATED 3 24 3
17Q GAIN WILD-TYPE 215 148 137

Figure S189.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0344 (Fisher's exact test), Q value = 0.051

Table S190.  Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
17Q GAIN MUTATED 15 3 7
17Q GAIN WILD-TYPE 148 129 96

Figure S190.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S191.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
18P GAIN MUTATED 68 1 2 2
18P GAIN WILD-TYPE 140 177 97 52

Figure S191.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S192.  Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
18P GAIN MUTATED 41 17 5
18P GAIN WILD-TYPE 113 61 188

Figure S192.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S193.  Gene #32: '18p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
18P GAIN MUTATED 1 1 4 13 22 11 7
18P GAIN WILD-TYPE 38 80 48 43 62 57 46

Figure S193.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'18p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00029

Table S194.  Gene #32: '18p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
18P GAIN MUTATED 4 39 12 4
18P GAIN WILD-TYPE 104 143 81 46

Figure S194.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S195.  Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
18P GAIN MUTATED 59 2 8 4
18P GAIN WILD-TYPE 129 121 85 129

Figure S195.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S196.  Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
18P GAIN MUTATED 48 1 13 1 7 2 1
18P GAIN WILD-TYPE 75 52 34 64 101 64 74

Figure S196.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S197.  Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
18P GAIN MUTATED 52 5 6 2 8
18P GAIN WILD-TYPE 112 75 100 131 39

Figure S197.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S198.  Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
18P GAIN MUTATED 12 59 2
18P GAIN WILD-TYPE 206 113 138

Figure S198.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S199.  Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
18P GAIN MUTATED 30 3 16 11
18P GAIN WILD-TYPE 86 95 76 81

Figure S199.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S200.  Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
18P GAIN MUTATED 34 2 24
18P GAIN WILD-TYPE 129 130 79

Figure S200.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S201.  Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
18Q GAIN MUTATED 41 1 2 2
18Q GAIN WILD-TYPE 167 177 97 52

Figure S201.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S202.  Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
18Q GAIN MUTATED 24 12 4
18Q GAIN WILD-TYPE 130 66 189

Figure S202.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'RPPA_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00019

Table S203.  Gene #33: '18q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
18Q GAIN MUTATED 0 1 1 8 16 6 4
18Q GAIN WILD-TYPE 39 80 51 48 68 62 49

Figure S203.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'18q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0119 (Fisher's exact test), Q value = 0.019

Table S204.  Gene #33: '18q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
18Q GAIN MUTATED 2 21 10 3
18Q GAIN WILD-TYPE 106 161 83 47

Figure S204.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S205.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
18Q GAIN MUTATED 38 2 3 3
18Q GAIN WILD-TYPE 150 121 90 130

Figure S205.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S206.  Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
18Q GAIN MUTATED 32 1 4 0 6 2 1
18Q GAIN WILD-TYPE 91 52 43 65 102 64 74

Figure S206.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S207.  Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
18Q GAIN MUTATED 33 5 2 1 5
18Q GAIN WILD-TYPE 131 75 104 132 42

Figure S207.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S208.  Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
18Q GAIN MUTATED 10 35 1
18Q GAIN WILD-TYPE 208 137 139

Figure S208.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00546 (Fisher's exact test), Q value = 0.0095

Table S209.  Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
18Q GAIN MUTATED 18 2 9 8
18Q GAIN WILD-TYPE 98 96 83 84

Figure S209.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S210.  Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
18Q GAIN MUTATED 24 1 12
18Q GAIN WILD-TYPE 139 131 91

Figure S210.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'MRNA_CNMF'

P value = 0.0362 (Fisher's exact test), Q value = 0.053

Table S211.  Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 17 14 7
19P GAIN MUTATED 0 4 0 0
19P GAIN WILD-TYPE 15 13 14 7

Figure S211.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0291 (Fisher's exact test), Q value = 0.045

Table S212.  Gene #34: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
19P GAIN MUTATED 1 3 0 0 0
19P GAIN WILD-TYPE 13 6 7 7 16

Figure S212.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S213.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
19P GAIN MUTATED 53 0 1 1
19P GAIN WILD-TYPE 155 178 98 53

Figure S213.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S214.  Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
19P GAIN MUTATED 26 16 8
19P GAIN WILD-TYPE 128 62 185

Figure S214.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'RPPA_CNMF'

P value = 0.00279 (Fisher's exact test), Q value = 0.0051

Table S215.  Gene #34: '19p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
19P GAIN MUTATED 1 3 1 10 14 5 7
19P GAIN WILD-TYPE 38 78 51 46 70 63 46

Figure S215.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'19p gain' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S216.  Gene #34: '19p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
19P GAIN MUTATED 2 31 4 4
19P GAIN WILD-TYPE 106 151 89 46

Figure S216.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S217.  Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
19P GAIN MUTATED 44 3 3 4
19P GAIN WILD-TYPE 144 120 90 129

Figure S217.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S218.  Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
19P GAIN MUTATED 37 1 3 2 8 2 1
19P GAIN WILD-TYPE 86 52 44 63 100 64 74

Figure S218.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S219.  Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
19P GAIN MUTATED 37 3 3 5 7
19P GAIN WILD-TYPE 127 77 103 128 40

Figure S219.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S220.  Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
19P GAIN MUTATED 12 37 6
19P GAIN WILD-TYPE 206 135 134

Figure S220.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00012

Table S221.  Gene #34: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
19P GAIN MUTATED 26 4 12 5
19P GAIN WILD-TYPE 90 94 80 87

Figure S221.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S222.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
19Q GAIN MUTATED 56 0 1 1
19Q GAIN WILD-TYPE 152 178 98 53

Figure S222.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S223.  Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
19Q GAIN MUTATED 28 17 7
19Q GAIN WILD-TYPE 126 61 186

Figure S223.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'RPPA_CNMF'

P value = 0.00306 (Fisher's exact test), Q value = 0.0056

Table S224.  Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
19Q GAIN MUTATED 1 3 2 10 15 5 8
19Q GAIN WILD-TYPE 38 78 50 46 69 63 45

Figure S224.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'19q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S225.  Gene #35: '19q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
19Q GAIN MUTATED 2 32 4 6
19Q GAIN WILD-TYPE 106 150 89 44

Figure S225.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S226.  Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
19Q GAIN MUTATED 48 3 4 3
19Q GAIN WILD-TYPE 140 120 89 130

Figure S226.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S227.  Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
19Q GAIN MUTATED 40 1 6 1 8 1 1
19Q GAIN WILD-TYPE 83 52 41 64 100 65 74

Figure S227.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S228.  Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
19Q GAIN MUTATED 42 3 3 4 6
19Q GAIN WILD-TYPE 122 77 103 129 41

Figure S228.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S229.  Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
19Q GAIN MUTATED 9 44 5
19Q GAIN WILD-TYPE 209 128 135

Figure S229.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00036

Table S230.  Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
19Q GAIN MUTATED 26 3 12 8
19Q GAIN WILD-TYPE 90 95 80 84

Figure S230.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0199 (Fisher's exact test), Q value = 0.031

Table S231.  Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
19Q GAIN MUTATED 26 8 15
19Q GAIN WILD-TYPE 137 124 88

Figure S231.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'MRNA_CNMF'

P value = 0.0353 (Fisher's exact test), Q value = 0.052

Table S232.  Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 17 14 7
20P GAIN MUTATED 0 4 0 0
20P GAIN WILD-TYPE 15 13 14 7

Figure S232.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S233.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
20P GAIN MUTATED 99 3 2 5
20P GAIN WILD-TYPE 109 175 97 49

Figure S233.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S234.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
20P GAIN MUTATED 63 20 18
20P GAIN WILD-TYPE 91 58 175

Figure S234.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S235.  Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
20P GAIN MUTATED 1 6 3 17 30 15 13
20P GAIN WILD-TYPE 38 75 49 39 54 53 40

Figure S235.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00012

Table S236.  Gene #36: '20p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
20P GAIN MUTATED 7 51 19 8
20P GAIN WILD-TYPE 101 131 74 42

Figure S236.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S237.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
20P GAIN MUTATED 76 7 12 14
20P GAIN WILD-TYPE 112 116 81 119

Figure S237.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S238.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
20P GAIN MUTATED 60 4 15 2 14 12 2
20P GAIN WILD-TYPE 63 49 32 63 94 54 73

Figure S238.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S239.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
20P GAIN MUTATED 70 8 7 14 10
20P GAIN WILD-TYPE 94 72 99 119 37

Figure S239.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S240.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
20P GAIN MUTATED 24 72 13
20P GAIN WILD-TYPE 194 100 127

Figure S240.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00159 (Fisher's exact test), Q value = 0.003

Table S241.  Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
20P GAIN MUTATED 41 14 16 23
20P GAIN WILD-TYPE 75 84 76 69

Figure S241.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00025

Table S242.  Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
20P GAIN MUTATED 56 18 20
20P GAIN WILD-TYPE 107 114 83

Figure S242.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 0.00829 (Fisher's exact test), Q value = 0.014

Table S243.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 17 14 7
20Q GAIN MUTATED 0 5 0 0
20Q GAIN WILD-TYPE 15 12 14 7

Figure S243.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S244.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
20Q GAIN MUTATED 119 3 3 5
20Q GAIN WILD-TYPE 89 175 96 49

Figure S244.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S245.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
20Q GAIN MUTATED 73 22 24
20Q GAIN WILD-TYPE 81 56 169

Figure S245.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S246.  Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
20Q GAIN MUTATED 1 7 5 22 34 17 14
20Q GAIN WILD-TYPE 38 74 47 34 50 51 39

Figure S246.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S247.  Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
20Q GAIN MUTATED 8 62 22 8
20Q GAIN WILD-TYPE 100 120 71 42

Figure S247.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S248.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
20Q GAIN MUTATED 91 8 14 17
20Q GAIN WILD-TYPE 97 115 79 116

Figure S248.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S249.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
20Q GAIN MUTATED 69 4 19 3 18 14 3
20Q GAIN WILD-TYPE 54 49 28 62 90 52 72

Figure S249.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S250.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
20Q GAIN MUTATED 84 8 10 17 10
20Q GAIN WILD-TYPE 80 72 96 116 37

Figure S250.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S251.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
20Q GAIN MUTATED 30 82 17
20Q GAIN WILD-TYPE 188 90 123

Figure S251.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S252.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
20Q GAIN MUTATED 52 15 19 25
20Q GAIN WILD-TYPE 64 83 73 67

Figure S252.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00023

Table S253.  Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
20Q GAIN MUTATED 64 22 25
20Q GAIN WILD-TYPE 99 110 78

Figure S253.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S254.  Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
21Q GAIN MUTATED 38 1 0 0
21Q GAIN WILD-TYPE 170 177 99 54

Figure S254.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00023

Table S255.  Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
21Q GAIN MUTATED 20 11 5
21Q GAIN WILD-TYPE 134 67 188

Figure S255.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q gain' versus 'RPPA_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00038

Table S256.  Gene #38: '21q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
21Q GAIN MUTATED 0 1 0 10 10 6 5
21Q GAIN WILD-TYPE 39 80 52 46 74 62 48

Figure S256.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'21q gain' versus 'RPPA_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.00064

Table S257.  Gene #38: '21q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
21Q GAIN MUTATED 0 21 8 3
21Q GAIN WILD-TYPE 108 161 85 47

Figure S257.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S258.  Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
21Q GAIN MUTATED 31 1 3 4
21Q GAIN WILD-TYPE 157 122 90 129

Figure S258.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S259.  Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
21Q GAIN MUTATED 24 0 7 1 3 1 3
21Q GAIN WILD-TYPE 99 53 40 64 105 65 72

Figure S259.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S260.  Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
21Q GAIN MUTATED 29 0 2 3 5
21Q GAIN WILD-TYPE 135 80 104 130 42

Figure S260.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S261.  Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
21Q GAIN MUTATED 5 30 4
21Q GAIN WILD-TYPE 213 142 136

Figure S261.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00414 (Fisher's exact test), Q value = 0.0073

Table S262.  Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
21Q GAIN MUTATED 18 3 10 4
21Q GAIN WILD-TYPE 98 95 82 88

Figure S262.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0446 (Fisher's exact test), Q value = 0.064

Table S263.  Gene #38: '21q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
21Q GAIN MUTATED 15 6 14
21Q GAIN WILD-TYPE 148 126 89

Figure S263.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S264.  Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
22Q GAIN MUTATED 27 0 1 2
22Q GAIN WILD-TYPE 181 178 98 52

Figure S264.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S265.  Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
22Q GAIN MUTATED 23 3 1
22Q GAIN WILD-TYPE 131 75 192

Figure S265.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 9.8e-05

Table S266.  Gene #39: '22q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
22Q GAIN MUTATED 0 0 1 7 13 4 1
22Q GAIN WILD-TYPE 39 81 51 49 71 64 52

Figure S266.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'22q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S267.  Gene #39: '22q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
22Q GAIN MUTATED 1 24 1 0
22Q GAIN WILD-TYPE 107 158 92 50

Figure S267.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S268.  Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
22Q GAIN MUTATED 26 0 4 0
22Q GAIN WILD-TYPE 162 123 89 133

Figure S268.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S269.  Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
22Q GAIN MUTATED 15 0 12 0 3 0 0
22Q GAIN WILD-TYPE 108 53 35 65 105 66 75

Figure S269.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00031

Table S270.  Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
22Q GAIN MUTATED 18 0 7 1 3
22Q GAIN WILD-TYPE 146 80 99 132 44

Figure S270.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S271.  Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
22Q GAIN MUTATED 1 27 1
22Q GAIN WILD-TYPE 217 145 139

Figure S271.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 9.8e-05

Table S272.  Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
22Q GAIN MUTATED 12 1 1 13
22Q GAIN WILD-TYPE 104 97 91 79

Figure S272.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00014

Table S273.  Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
22Q GAIN MUTATED 21 1 5
22Q GAIN WILD-TYPE 142 131 98

Figure S273.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S274.  Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
XP GAIN MUTATED 34 2 20 7
XP GAIN WILD-TYPE 174 176 79 47

Figure S274.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

'xp gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0458 (Fisher's exact test), Q value = 0.065

Table S275.  Gene #40: 'xp gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
XP GAIN MUTATED 22 9 7 8
XP GAIN WILD-TYPE 94 89 85 84

Figure S275.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S276.  Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
XQ GAIN MUTATED 37 2 19 6
XQ GAIN WILD-TYPE 171 176 80 48

Figure S276.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00452 (Fisher's exact test), Q value = 0.008

Table S277.  Gene #41: 'xq gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
XQ GAIN MUTATED 24 11 7 5
XQ GAIN WILD-TYPE 92 87 85 87

Figure S277.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S278.  Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
1P LOSS MUTATED 26 0 0 1
1P LOSS WILD-TYPE 182 178 99 53

Figure S278.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S279.  Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
1P LOSS MUTATED 18 5 1
1P LOSS WILD-TYPE 136 73 192

Figure S279.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'RPPA_CNMF'

P value = 0.0481 (Fisher's exact test), Q value = 0.068

Table S280.  Gene #42: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
1P LOSS MUTATED 0 0 2 5 5 2 4
1P LOSS WILD-TYPE 39 81 50 51 79 66 49

Figure S280.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'1p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00031

Table S281.  Gene #42: '1p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
1P LOSS MUTATED 0 16 0 2
1P LOSS WILD-TYPE 108 166 93 48

Figure S281.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S282.  Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
1P LOSS MUTATED 23 0 3 1
1P LOSS WILD-TYPE 165 123 90 132

Figure S282.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S283.  Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
1P LOSS MUTATED 15 0 7 0 5 0 0
1P LOSS WILD-TYPE 108 53 40 65 103 66 75

Figure S283.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.00091

Table S284.  Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
1P LOSS MUTATED 19 1 3 2 2
1P LOSS WILD-TYPE 145 79 103 131 45

Figure S284.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S285.  Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
1P LOSS MUTATED 3 23 1
1P LOSS WILD-TYPE 215 149 139

Figure S285.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0413 (Fisher's exact test), Q value = 0.06

Table S286.  Gene #42: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
1P LOSS MUTATED 15 3 6
1P LOSS WILD-TYPE 148 129 97

Figure S286.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S287.  Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
1Q LOSS MUTATED 16 0 0 0
1Q LOSS WILD-TYPE 192 178 99 54

Figure S287.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 0.00635 (Fisher's exact test), Q value = 0.011

Table S288.  Gene #43: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
1Q LOSS MUTATED 9 4 1
1Q LOSS WILD-TYPE 145 74 192

Figure S288.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0244 (Fisher's exact test), Q value = 0.038

Table S289.  Gene #43: '1q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
1Q LOSS MUTATED 0 8 0 1
1Q LOSS WILD-TYPE 108 174 93 49

Figure S289.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.0018

Table S290.  Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
1Q LOSS MUTATED 13 0 2 1
1Q LOSS WILD-TYPE 175 123 91 132

Figure S290.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00108 (Fisher's exact test), Q value = 0.0021

Table S291.  Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
1Q LOSS MUTATED 8 0 5 0 3 0 0
1Q LOSS WILD-TYPE 115 53 42 65 105 66 75

Figure S291.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CNMF'

P value = 0.0288 (Fisher's exact test), Q value = 0.044

Table S292.  Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
1Q LOSS MUTATED 11 0 2 2 1
1Q LOSS WILD-TYPE 153 80 104 131 46

Figure S292.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.00057

Table S293.  Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
1Q LOSS MUTATED 2 13 1
1Q LOSS WILD-TYPE 216 159 139

Figure S293.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.00065

Table S294.  Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
2P LOSS MUTATED 12 0 0 0
2P LOSS WILD-TYPE 196 178 99 54

Figure S294.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 7e-04 (Fisher's exact test), Q value = 0.0014

Table S295.  Gene #44: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
2P LOSS MUTATED 11 0 0 1
2P LOSS WILD-TYPE 177 123 93 132

Figure S295.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0415 (Fisher's exact test), Q value = 0.06

Table S296.  Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
2P LOSS MUTATED 7 0 1 0 4 0 0
2P LOSS WILD-TYPE 116 53 46 65 104 66 75

Figure S296.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S297.  Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
2Q LOSS MUTATED 18 0 0 0
2Q LOSS WILD-TYPE 190 178 99 54

Figure S297.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.0411 (Fisher's exact test), Q value = 0.06

Table S298.  Gene #45: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
2Q LOSS MUTATED 9 5 3
2Q LOSS WILD-TYPE 145 73 190

Figure S298.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S299.  Gene #45: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
2Q LOSS MUTATED 16 0 0 2
2Q LOSS WILD-TYPE 172 123 93 131

Figure S299.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0072 (Fisher's exact test), Q value = 0.012

Table S300.  Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
2Q LOSS MUTATED 10 0 1 0 6 1 0
2Q LOSS WILD-TYPE 113 53 46 65 102 65 75

Figure S300.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.00873 (Fisher's exact test), Q value = 0.015

Table S301.  Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
2Q LOSS MUTATED 13 2 1 2 0
2Q LOSS WILD-TYPE 151 78 105 131 47

Figure S301.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0426 (Fisher's exact test), Q value = 0.061

Table S302.  Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
2Q LOSS MUTATED 4 11 3
2Q LOSS WILD-TYPE 214 161 137

Figure S302.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MRNA_CNMF'

P value = 0.0365 (Fisher's exact test), Q value = 0.054

Table S303.  Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 17 14 7
3P LOSS MUTATED 0 4 0 0
3P LOSS WILD-TYPE 15 13 14 7

Figure S303.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00071 (Fisher's exact test), Q value = 0.0014

Table S304.  Gene #46: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
3P LOSS MUTATED 0 4 0 0 0
3P LOSS WILD-TYPE 14 5 7 7 16

Figure S304.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S305.  Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
3P LOSS MUTATED 49 0 0 3
3P LOSS WILD-TYPE 159 178 99 51

Figure S305.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S306.  Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
3P LOSS MUTATED 28 11 4
3P LOSS WILD-TYPE 126 67 189

Figure S306.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0012

Table S307.  Gene #46: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
3P LOSS MUTATED 2 1 3 8 18 7 4
3P LOSS WILD-TYPE 37 80 49 48 66 61 49

Figure S307.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S308.  Gene #46: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
3P LOSS MUTATED 1 30 10 2
3P LOSS WILD-TYPE 107 152 83 48

Figure S308.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S309.  Gene #46: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
3P LOSS MUTATED 43 3 3 2
3P LOSS WILD-TYPE 145 120 90 131

Figure S309.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S310.  Gene #46: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
3P LOSS MUTATED 36 0 6 0 7 2 0
3P LOSS WILD-TYPE 87 53 41 65 101 64 75

Figure S310.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S311.  Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
3P LOSS MUTATED 37 3 5 3 2
3P LOSS WILD-TYPE 127 77 101 130 45

Figure S311.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S312.  Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
3P LOSS MUTATED 12 36 2
3P LOSS WILD-TYPE 206 136 138

Figure S312.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00021

Table S313.  Gene #46: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
3P LOSS MUTATED 28 3 10
3P LOSS WILD-TYPE 135 129 93

Figure S313.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'MRNA_CNMF'

P value = 0.0361 (Fisher's exact test), Q value = 0.053

Table S314.  Gene #47: '3q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 17 14 7
3Q LOSS MUTATED 0 4 0 0
3Q LOSS WILD-TYPE 15 13 14 7

Figure S314.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00068 (Fisher's exact test), Q value = 0.0014

Table S315.  Gene #47: '3q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
3Q LOSS MUTATED 0 4 0 0 0
3Q LOSS WILD-TYPE 14 5 7 7 16

Figure S315.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S316.  Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
3Q LOSS MUTATED 28 0 0 3
3Q LOSS WILD-TYPE 180 178 99 51

Figure S316.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 9.8e-05

Table S317.  Gene #47: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
3Q LOSS MUTATED 19 3 3
3Q LOSS WILD-TYPE 135 75 190

Figure S317.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q loss' versus 'RPPA_CNMF'

P value = 0.0342 (Fisher's exact test), Q value = 0.051

Table S318.  Gene #47: '3q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
3Q LOSS MUTATED 0 1 3 4 11 5 3
3Q LOSS WILD-TYPE 39 80 49 52 73 63 50

Figure S318.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'3q loss' versus 'RPPA_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.001

Table S319.  Gene #47: '3q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
3Q LOSS MUTATED 0 20 5 2
3Q LOSS WILD-TYPE 108 162 88 48

Figure S319.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S320.  Gene #47: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
3Q LOSS MUTATED 26 1 1 2
3Q LOSS WILD-TYPE 162 122 92 131

Figure S320.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S321.  Gene #47: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
3Q LOSS MUTATED 20 0 4 0 4 2 0
3Q LOSS WILD-TYPE 103 53 43 65 104 64 75

Figure S321.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 0.00075 (Fisher's exact test), Q value = 0.0015

Table S322.  Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
3Q LOSS MUTATED 20 1 3 3 2
3Q LOSS WILD-TYPE 144 79 103 130 45

Figure S322.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00036

Table S323.  Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
3Q LOSS MUTATED 7 20 2
3Q LOSS WILD-TYPE 211 152 138

Figure S323.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0468 (Fisher's exact test), Q value = 0.066

Table S324.  Gene #47: '3q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
3Q LOSS MUTATED 14 3 8
3Q LOSS WILD-TYPE 149 129 95

Figure S324.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'MRNA_CNMF'

P value = 0.00366 (Fisher's exact test), Q value = 0.0065

Table S325.  Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 17 14 7
4P LOSS MUTATED 1 7 0 0
4P LOSS WILD-TYPE 14 10 14 7

Figure S325.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00181 (Fisher's exact test), Q value = 0.0034

Table S326.  Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
4P LOSS MUTATED 3 5 0 0 0
4P LOSS WILD-TYPE 11 4 7 7 16

Figure S326.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S327.  Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
4P LOSS MUTATED 102 1 1 2
4P LOSS WILD-TYPE 106 177 98 52

Figure S327.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S328.  Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
4P LOSS MUTATED 62 23 10
4P LOSS WILD-TYPE 92 55 183

Figure S328.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S329.  Gene #48: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
4P LOSS MUTATED 3 1 5 21 31 10 14
4P LOSS WILD-TYPE 36 80 47 35 53 58 39

Figure S329.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S330.  Gene #48: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
4P LOSS MUTATED 4 55 17 9
4P LOSS WILD-TYPE 104 127 76 41

Figure S330.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S331.  Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
4P LOSS MUTATED 83 5 11 7
4P LOSS WILD-TYPE 105 118 82 126

Figure S331.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S332.  Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
4P LOSS MUTATED 63 2 15 2 18 5 1
4P LOSS WILD-TYPE 60 51 32 63 90 61 74

Figure S332.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S333.  Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
4P LOSS MUTATED 78 7 4 7 8
4P LOSS WILD-TYPE 86 73 102 126 39

Figure S333.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S334.  Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
4P LOSS MUTATED 26 73 5
4P LOSS WILD-TYPE 192 99 135

Figure S334.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S335.  Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
4P LOSS MUTATED 48 8 22 16
4P LOSS WILD-TYPE 68 90 70 76

Figure S335.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S336.  Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
4P LOSS MUTATED 52 12 30
4P LOSS WILD-TYPE 111 120 73

Figure S336.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'MRNA_CNMF'

P value = 0.0426 (Fisher's exact test), Q value = 0.061

Table S337.  Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 17 14 7
4Q LOSS MUTATED 1 5 0 0
4Q LOSS WILD-TYPE 14 12 14 7

Figure S337.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00793 (Fisher's exact test), Q value = 0.013

Table S338.  Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
4Q LOSS MUTATED 2 4 0 0 0
4Q LOSS WILD-TYPE 12 5 7 7 16

Figure S338.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S339.  Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
4Q LOSS MUTATED 101 0 1 2
4Q LOSS WILD-TYPE 107 178 98 52

Figure S339.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S340.  Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
4Q LOSS MUTATED 60 25 8
4Q LOSS WILD-TYPE 94 53 185

Figure S340.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S341.  Gene #49: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
4Q LOSS MUTATED 3 2 4 16 32 11 16
4Q LOSS WILD-TYPE 36 79 48 40 52 57 37

Figure S341.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S342.  Gene #49: '4q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
4Q LOSS MUTATED 4 52 18 10
4Q LOSS WILD-TYPE 104 130 75 40

Figure S342.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S343.  Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
4Q LOSS MUTATED 84 5 8 7
4Q LOSS WILD-TYPE 104 118 85 126

Figure S343.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S344.  Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
4Q LOSS MUTATED 65 2 12 2 17 6 0
4Q LOSS WILD-TYPE 58 51 35 63 91 60 75

Figure S344.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S345.  Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
4Q LOSS MUTATED 73 7 5 7 10
4Q LOSS WILD-TYPE 91 73 101 126 37

Figure S345.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S346.  Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
4Q LOSS MUTATED 26 72 4
4Q LOSS WILD-TYPE 192 100 136

Figure S346.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S347.  Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
4Q LOSS MUTATED 46 8 22 16
4Q LOSS WILD-TYPE 70 90 70 76

Figure S347.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S348.  Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
4Q LOSS MUTATED 50 11 31
4Q LOSS WILD-TYPE 113 121 72

Figure S348.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'MRNA_CNMF'

P value = 0.0429 (Fisher's exact test), Q value = 0.062

Table S349.  Gene #50: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 17 14 7
5P LOSS MUTATED 1 5 0 0
5P LOSS WILD-TYPE 14 12 14 7

Figure S349.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0402 (Fisher's exact test), Q value = 0.059

Table S350.  Gene #50: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
5P LOSS MUTATED 3 3 0 0 0
5P LOSS WILD-TYPE 11 6 7 7 16

Figure S350.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S351.  Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
5P LOSS MUTATED 51 0 0 2
5P LOSS WILD-TYPE 157 178 99 52

Figure S351.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S352.  Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
5P LOSS MUTATED 33 7 3
5P LOSS WILD-TYPE 121 71 190

Figure S352.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'RPPA_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.00073

Table S353.  Gene #50: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
5P LOSS MUTATED 1 2 2 13 14 6 6
5P LOSS WILD-TYPE 38 79 50 43 70 62 47

Figure S353.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5p loss' versus 'RPPA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00021

Table S354.  Gene #50: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
5P LOSS MUTATED 1 29 9 5
5P LOSS WILD-TYPE 107 153 84 45

Figure S354.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S355.  Gene #50: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
5P LOSS MUTATED 40 4 5 4
5P LOSS WILD-TYPE 148 119 88 129

Figure S355.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S356.  Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
5P LOSS MUTATED 32 0 8 1 8 4 0
5P LOSS WILD-TYPE 91 53 39 64 100 62 75

Figure S356.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S357.  Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
5P LOSS MUTATED 36 3 5 4 4
5P LOSS WILD-TYPE 128 77 101 129 43

Figure S357.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S358.  Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
5P LOSS MUTATED 12 38 2
5P LOSS WILD-TYPE 206 134 138

Figure S358.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00012

Table S359.  Gene #50: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
5P LOSS MUTATED 25 3 7 6
5P LOSS WILD-TYPE 91 95 85 86

Figure S359.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.00048

Table S360.  Gene #50: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
5P LOSS MUTATED 24 3 14
5P LOSS WILD-TYPE 139 129 89

Figure S360.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'MRNA_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.018

Table S361.  Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 17 14 7
5Q LOSS MUTATED 1 6 0 0
5Q LOSS WILD-TYPE 14 11 14 7

Figure S361.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'MRNA_CHIERARCHICAL'

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

Table S362.  Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
5Q LOSS MUTATED 3 4 0 0 0
5Q LOSS WILD-TYPE 11 5 7 7 16

Figure S362.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S363.  Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
5Q LOSS MUTATED 71 0 0 2
5Q LOSS WILD-TYPE 137 178 99 52

Figure S363.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S364.  Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
5Q LOSS MUTATED 48 10 3
5Q LOSS WILD-TYPE 106 68 190

Figure S364.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 9.8e-05

Table S365.  Gene #51: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
5Q LOSS MUTATED 1 2 3 13 19 9 11
5Q LOSS WILD-TYPE 38 79 49 43 65 59 42

Figure S365.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S366.  Gene #51: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
5Q LOSS MUTATED 0 39 12 7
5Q LOSS WILD-TYPE 108 143 81 43

Figure S366.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S367.  Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
5Q LOSS MUTATED 59 3 6 5
5Q LOSS WILD-TYPE 129 120 87 128

Figure S367.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S368.  Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
5Q LOSS MUTATED 49 0 7 1 11 5 0
5Q LOSS WILD-TYPE 74 53 40 64 97 61 75

Figure S368.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S369.  Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
5Q LOSS MUTATED 51 3 6 4 8
5Q LOSS WILD-TYPE 113 77 100 129 39

Figure S369.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S370.  Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
5Q LOSS MUTATED 15 54 3
5Q LOSS WILD-TYPE 203 118 137

Figure S370.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S371.  Gene #51: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
5Q LOSS MUTATED 36 3 10 9
5Q LOSS WILD-TYPE 80 95 82 83

Figure S371.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S372.  Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
5Q LOSS MUTATED 33 5 20
5Q LOSS WILD-TYPE 130 127 83

Figure S372.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0299 (Fisher's exact test), Q value = 0.046

Table S373.  Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
6P LOSS MUTATED 1 3 0 0 0
6P LOSS WILD-TYPE 13 6 7 7 16

Figure S373.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S374.  Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
6P LOSS MUTATED 19 0 0 1
6P LOSS WILD-TYPE 189 178 99 53

Figure S374.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.00069

Table S375.  Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
6P LOSS MUTATED 10 4 0
6P LOSS WILD-TYPE 144 74 193

Figure S375.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p loss' versus 'RPPA_CNMF'

P value = 0.0377 (Fisher's exact test), Q value = 0.055

Table S376.  Gene #52: '6p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
6P LOSS MUTATED 1 0 1 3 7 2 0
6P LOSS WILD-TYPE 38 81 51 53 77 66 53

Figure S376.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00025

Table S377.  Gene #52: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
6P LOSS MUTATED 17 1 1 1
6P LOSS WILD-TYPE 171 122 92 132

Figure S377.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.00064

Table S378.  Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
6P LOSS MUTATED 14 1 2 0 2 1 0
6P LOSS WILD-TYPE 109 52 45 65 106 65 75

Figure S378.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CNMF'

P value = 0.00352 (Fisher's exact test), Q value = 0.0063

Table S379.  Gene #52: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
6P LOSS MUTATED 13 1 1 1 2
6P LOSS WILD-TYPE 151 79 105 132 45

Figure S379.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.00083

Table S380.  Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
6P LOSS MUTATED 5 13 0
6P LOSS WILD-TYPE 213 159 140

Figure S380.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.017

Table S381.  Gene #52: '6p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
6P LOSS MUTATED 10 1 2 1
6P LOSS WILD-TYPE 106 97 90 91

Figure S381.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0294 (Fisher's exact test), Q value = 0.045

Table S382.  Gene #53: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
6Q LOSS MUTATED 1 3 0 0 0
6Q LOSS WILD-TYPE 13 6 7 7 16

Figure S382.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S383.  Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
6Q LOSS MUTATED 24 0 0 1
6Q LOSS WILD-TYPE 184 178 99 53

Figure S383.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S384.  Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
6Q LOSS MUTATED 14 5 0
6Q LOSS WILD-TYPE 140 73 193

Figure S384.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'RPPA_CNMF'

P value = 0.0464 (Fisher's exact test), Q value = 0.066

Table S385.  Gene #53: '6q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
6Q LOSS MUTATED 1 0 1 4 8 2 2
6Q LOSS WILD-TYPE 38 81 51 52 76 66 51

Figure S385.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S386.  Gene #53: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
6Q LOSS MUTATED 22 1 1 1
6Q LOSS WILD-TYPE 166 122 92 132

Figure S386.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S387.  Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
6Q LOSS MUTATED 20 1 2 0 2 0 0
6Q LOSS WILD-TYPE 103 52 45 65 106 66 75

Figure S387.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.00069

Table S388.  Gene #53: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
6Q LOSS MUTATED 17 2 1 1 2
6Q LOSS WILD-TYPE 147 78 105 132 45

Figure S388.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S389.  Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
6Q LOSS MUTATED 5 18 0
6Q LOSS WILD-TYPE 213 154 140

Figure S389.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00881 (Fisher's exact test), Q value = 0.015

Table S390.  Gene #53: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
6Q LOSS MUTATED 12 1 4 2
6Q LOSS WILD-TYPE 104 97 88 90

Figure S390.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0138 (Fisher's exact test), Q value = 0.022

Table S391.  Gene #53: '6q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
6Q LOSS MUTATED 10 1 8
6Q LOSS WILD-TYPE 153 131 95

Figure S391.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p loss' versus 'MRNA_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.053

Table S392.  Gene #54: '7p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 17 14 7
7P LOSS MUTATED 0 4 0 0
7P LOSS WILD-TYPE 15 13 14 7

Figure S392.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'7p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S393.  Gene #54: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
7P LOSS MUTATED 42 3 0 0
7P LOSS WILD-TYPE 166 175 99 54

Figure S393.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S394.  Gene #54: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
7P LOSS MUTATED 21 13 6
7P LOSS WILD-TYPE 133 65 187

Figure S394.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p loss' versus 'RPPA_CNMF'

P value = 0.00202 (Fisher's exact test), Q value = 0.0038

Table S395.  Gene #54: '7p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
7P LOSS MUTATED 1 2 1 8 14 4 7
7P LOSS WILD-TYPE 38 79 51 48 70 64 46

Figure S395.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0039 (Fisher's exact test), Q value = 0.0069

Table S396.  Gene #54: '7p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
7P LOSS MUTATED 2 24 6 5
7P LOSS WILD-TYPE 106 158 87 45

Figure S396.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S397.  Gene #54: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
7P LOSS MUTATED 39 2 1 3
7P LOSS WILD-TYPE 149 121 92 130

Figure S397.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S398.  Gene #54: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
7P LOSS MUTATED 31 0 2 0 8 4 0
7P LOSS WILD-TYPE 92 53 45 65 100 62 75

Figure S398.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S399.  Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
7P LOSS MUTATED 31 2 2 6 4
7P LOSS WILD-TYPE 133 78 104 127 43

Figure S399.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S400.  Gene #54: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
7P LOSS MUTATED 11 31 3
7P LOSS WILD-TYPE 207 141 137

Figure S400.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S401.  Gene #55: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
7Q LOSS MUTATED 45 0 0 0
7Q LOSS WILD-TYPE 163 178 99 54

Figure S401.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

'7q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S402.  Gene #55: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
7Q LOSS MUTATED 26 12 3
7Q LOSS WILD-TYPE 128 66 190

Figure S402.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q loss' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 9.8e-05

Table S403.  Gene #55: '7q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
7Q LOSS MUTATED 0 1 2 7 17 4 6
7Q LOSS WILD-TYPE 39 80 50 49 67 64 47

Figure S403.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'7q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00093 (Fisher's exact test), Q value = 0.0018

Table S404.  Gene #55: '7q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
7Q LOSS MUTATED 1 24 7 5
7Q LOSS WILD-TYPE 107 158 86 45

Figure S404.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S405.  Gene #55: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
7Q LOSS MUTATED 43 0 1 1
7Q LOSS WILD-TYPE 145 123 92 132

Figure S405.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S406.  Gene #55: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
7Q LOSS MUTATED 34 0 4 0 5 2 0
7Q LOSS WILD-TYPE 89 53 43 65 103 64 75

Figure S406.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S407.  Gene #55: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
7Q LOSS MUTATED 37 1 2 2 3
7Q LOSS WILD-TYPE 127 79 104 131 44

Figure S407.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S408.  Gene #55: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
7Q LOSS MUTATED 8 36 1
7Q LOSS WILD-TYPE 210 136 139

Figure S408.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00014

Table S409.  Gene #55: '7q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
7Q LOSS MUTATED 24 2 6 7
7Q LOSS WILD-TYPE 92 96 86 85

Figure S409.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00305 (Fisher's exact test), Q value = 0.0055

Table S410.  Gene #55: '7q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
7Q LOSS MUTATED 21 4 14
7Q LOSS WILD-TYPE 142 128 89

Figure S410.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'MRNA_CNMF'

P value = 0.00872 (Fisher's exact test), Q value = 0.015

Table S411.  Gene #56: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 17 14 7
8P LOSS MUTATED 0 5 0 0
8P LOSS WILD-TYPE 15 12 14 7

Figure S411.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p loss' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 9.8e-05

Table S412.  Gene #56: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
8P LOSS MUTATED 0 5 0 0 0
8P LOSS WILD-TYPE 14 4 7 7 16

Figure S412.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S413.  Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
8P LOSS MUTATED 75 1 1 1
8P LOSS WILD-TYPE 133 177 98 53

Figure S413.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S414.  Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
8P LOSS MUTATED 48 19 2
8P LOSS WILD-TYPE 106 59 191

Figure S414.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S415.  Gene #56: '8p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
8P LOSS MUTATED 1 2 5 11 24 11 11
8P LOSS WILD-TYPE 38 79 47 45 60 57 42

Figure S415.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S416.  Gene #56: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
8P LOSS MUTATED 1 47 10 7
8P LOSS WILD-TYPE 107 135 83 43

Figure S416.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S417.  Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
8P LOSS MUTATED 64 2 9 2
8P LOSS WILD-TYPE 124 121 84 131

Figure S417.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S418.  Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
8P LOSS MUTATED 56 0 11 1 7 1 1
8P LOSS WILD-TYPE 67 53 36 64 101 65 74

Figure S418.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S419.  Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
8P LOSS MUTATED 59 2 6 3 5
8P LOSS WILD-TYPE 105 78 100 130 42

Figure S419.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S420.  Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
8P LOSS MUTATED 9 63 3
8P LOSS WILD-TYPE 209 109 137

Figure S420.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S421.  Gene #56: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
8P LOSS MUTATED 34 2 13 16
8P LOSS WILD-TYPE 82 96 79 76

Figure S421.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S422.  Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
8P LOSS MUTATED 37 4 24
8P LOSS WILD-TYPE 126 128 79

Figure S422.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S423.  Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
8Q LOSS MUTATED 20 0 1 1
8Q LOSS WILD-TYPE 188 178 98 53

Figure S423.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S424.  Gene #57: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
8Q LOSS MUTATED 15 5 0
8Q LOSS WILD-TYPE 139 73 193

Figure S424.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q loss' versus 'RPPA_CNMF'

P value = 0.00277 (Fisher's exact test), Q value = 0.0051

Table S425.  Gene #57: '8q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
8Q LOSS MUTATED 0 1 2 3 12 1 2
8Q LOSS WILD-TYPE 39 80 50 53 72 67 51

Figure S425.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'8q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.001

Table S426.  Gene #57: '8q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
8Q LOSS MUTATED 1 18 1 1
8Q LOSS WILD-TYPE 107 164 92 49

Figure S426.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S427.  Gene #57: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
8Q LOSS MUTATED 18 0 3 1
8Q LOSS WILD-TYPE 170 123 90 132

Figure S427.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S428.  Gene #57: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
8Q LOSS MUTATED 18 0 2 0 1 0 1
8Q LOSS WILD-TYPE 105 53 45 65 107 66 74

Figure S428.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S429.  Gene #57: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
8Q LOSS MUTATED 18 0 2 1 0
8Q LOSS WILD-TYPE 146 80 104 132 47

Figure S429.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S430.  Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
8Q LOSS MUTATED 1 19 1
8Q LOSS WILD-TYPE 217 153 139

Figure S430.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S431.  Gene #57: '8q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
8Q LOSS MUTATED 14 0 1 4
8Q LOSS WILD-TYPE 102 98 91 88

Figure S431.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00126 (Fisher's exact test), Q value = 0.0024

Table S432.  Gene #57: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
8Q LOSS MUTATED 12 0 7
8Q LOSS WILD-TYPE 151 132 96

Figure S432.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'MRNA_CNMF'

P value = 0.00126 (Fisher's exact test), Q value = 0.0024

Table S433.  Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 17 14 7
9P LOSS MUTATED 1 8 0 0
9P LOSS WILD-TYPE 14 9 14 7

Figure S433.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S434.  Gene #58: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
9P LOSS MUTATED 2 7 0 0 0
9P LOSS WILD-TYPE 12 2 7 7 16

Figure S434.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S435.  Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
9P LOSS MUTATED 94 1 0 4
9P LOSS WILD-TYPE 114 177 99 50

Figure S435.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S436.  Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
9P LOSS MUTATED 53 21 10
9P LOSS WILD-TYPE 101 57 183

Figure S436.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S437.  Gene #58: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
9P LOSS MUTATED 4 2 6 12 26 10 13
9P LOSS WILD-TYPE 35 79 46 44 58 58 40

Figure S437.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9p loss' versus 'RPPA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00021

Table S438.  Gene #58: '9p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
9P LOSS MUTATED 5 44 17 7
9P LOSS WILD-TYPE 103 138 76 43

Figure S438.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S439.  Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
9P LOSS MUTATED 73 5 8 13
9P LOSS WILD-TYPE 115 118 85 120

Figure S439.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S440.  Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
9P LOSS MUTATED 56 0 17 2 12 11 1
9P LOSS WILD-TYPE 67 53 30 63 96 55 74

Figure S440.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S441.  Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
9P LOSS MUTATED 65 5 5 12 9
9P LOSS WILD-TYPE 99 75 101 121 38

Figure S441.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S442.  Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
9P LOSS MUTATED 19 65 12
9P LOSS WILD-TYPE 199 107 128

Figure S442.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00384 (Fisher's exact test), Q value = 0.0069

Table S443.  Gene #58: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
9P LOSS MUTATED 37 13 18 14
9P LOSS WILD-TYPE 79 85 74 78

Figure S443.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0184 (Fisher's exact test), Q value = 0.029

Table S444.  Gene #58: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
9P LOSS MUTATED 42 17 23
9P LOSS WILD-TYPE 121 115 80

Figure S444.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'MRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00012

Table S445.  Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 17 14 7
9Q LOSS MUTATED 0 9 0 0
9Q LOSS WILD-TYPE 15 8 14 7

Figure S445.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S446.  Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
9Q LOSS MUTATED 2 7 0 0 0
9Q LOSS WILD-TYPE 12 2 7 7 16

Figure S446.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S447.  Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
9Q LOSS MUTATED 111 1 1 4
9Q LOSS WILD-TYPE 97 177 98 50

Figure S447.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S448.  Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
9Q LOSS MUTATED 61 25 15
9Q LOSS WILD-TYPE 93 53 178

Figure S448.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S449.  Gene #59: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
9Q LOSS MUTATED 5 2 6 19 30 14 13
9Q LOSS WILD-TYPE 34 79 46 37 54 54 40

Figure S449.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q loss' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S450.  Gene #59: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
9Q LOSS MUTATED 7 54 21 7
9Q LOSS WILD-TYPE 101 128 72 43

Figure S450.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S451.  Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
9Q LOSS MUTATED 87 8 8 14
9Q LOSS WILD-TYPE 101 115 85 119

Figure S451.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S452.  Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
9Q LOSS MUTATED 68 0 17 3 15 13 1
9Q LOSS WILD-TYPE 55 53 30 62 93 53 74

Figure S452.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S453.  Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
9Q LOSS MUTATED 79 6 5 14 10
9Q LOSS WILD-TYPE 85 74 101 119 37

Figure S453.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S454.  Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
9Q LOSS MUTATED 27 74 13
9Q LOSS WILD-TYPE 191 98 127

Figure S454.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00027

Table S455.  Gene #59: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
9Q LOSS MUTATED 46 14 21 17
9Q LOSS WILD-TYPE 70 84 71 75

Figure S455.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0013 (Fisher's exact test), Q value = 0.0025

Table S456.  Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
9Q LOSS MUTATED 53 19 26
9Q LOSS WILD-TYPE 110 113 77

Figure S456.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'MRNA_CNMF'

P value = 0.0358 (Fisher's exact test), Q value = 0.053

Table S457.  Gene #60: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 17 14 7
10P LOSS MUTATED 0 4 0 0
10P LOSS WILD-TYPE 15 13 14 7

Figure S457.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0302 (Fisher's exact test), Q value = 0.046

Table S458.  Gene #60: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
10P LOSS MUTATED 1 3 0 0 0
10P LOSS WILD-TYPE 13 6 7 7 16

Figure S458.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S459.  Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
10P LOSS MUTATED 43 0 0 1
10P LOSS WILD-TYPE 165 178 99 53

Figure S459.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S460.  Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
10P LOSS MUTATED 26 10 2
10P LOSS WILD-TYPE 128 68 191

Figure S460.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'RPPA_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00021

Table S461.  Gene #60: '10p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
10P LOSS MUTATED 0 0 3 6 15 5 7
10P LOSS WILD-TYPE 39 81 49 50 69 63 46

Figure S461.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p loss' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S462.  Gene #60: '10p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
10P LOSS MUTATED 0 27 6 3
10P LOSS WILD-TYPE 108 155 87 47

Figure S462.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S463.  Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
10P LOSS MUTATED 38 0 3 3
10P LOSS WILD-TYPE 150 123 90 130

Figure S463.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S464.  Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
10P LOSS MUTATED 28 0 8 1 4 3 0
10P LOSS WILD-TYPE 95 53 39 64 104 63 75

Figure S464.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S465.  Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
10P LOSS MUTATED 33 3 2 1 3
10P LOSS WILD-TYPE 131 77 104 132 44

Figure S465.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S466.  Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
10P LOSS MUTATED 8 32 2
10P LOSS WILD-TYPE 210 140 138

Figure S466.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00087 (Fisher's exact test), Q value = 0.0017

Table S467.  Gene #60: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
10P LOSS MUTATED 21 3 13
10P LOSS WILD-TYPE 142 129 90

Figure S467.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S468.  Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
10Q LOSS MUTATED 39 0 0 1
10Q LOSS WILD-TYPE 169 178 99 53

Figure S468.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S469.  Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
10Q LOSS MUTATED 22 11 2
10Q LOSS WILD-TYPE 132 67 191

Figure S469.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CNMF'

P value = 0.00655 (Fisher's exact test), Q value = 0.011

Table S470.  Gene #61: '10q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
10Q LOSS MUTATED 0 1 4 4 13 6 6
10Q LOSS WILD-TYPE 39 80 48 52 71 62 47

Figure S470.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'10q loss' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S471.  Gene #61: '10q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
10Q LOSS MUTATED 0 25 5 4
10Q LOSS WILD-TYPE 108 157 88 46

Figure S471.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S472.  Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
10Q LOSS MUTATED 33 0 3 4
10Q LOSS WILD-TYPE 155 123 90 129

Figure S472.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S473.  Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
10Q LOSS MUTATED 25 0 5 1 5 4 0
10Q LOSS WILD-TYPE 98 53 42 64 103 62 75

Figure S473.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S474.  Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
10Q LOSS MUTATED 29 3 2 2 3
10Q LOSS WILD-TYPE 135 77 104 131 44

Figure S474.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S475.  Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
10Q LOSS MUTATED 9 27 3
10Q LOSS WILD-TYPE 209 145 137

Figure S475.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00392 (Fisher's exact test), Q value = 0.007

Table S476.  Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
10Q LOSS MUTATED 19 3 5 7
10Q LOSS WILD-TYPE 97 95 87 85

Figure S476.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0125 (Fisher's exact test), Q value = 0.02

Table S477.  Gene #61: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
10Q LOSS MUTATED 19 4 11
10Q LOSS WILD-TYPE 144 128 92

Figure S477.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S478.  Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
11P LOSS MUTATED 71 0 0 5
11P LOSS WILD-TYPE 137 178 99 49

Figure S478.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S479.  Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
11P LOSS MUTATED 41 23 7
11P LOSS WILD-TYPE 113 55 186

Figure S479.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'RPPA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00014

Table S480.  Gene #62: '11p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
11P LOSS MUTATED 2 3 5 10 25 8 6
11P LOSS WILD-TYPE 37 78 47 46 59 60 47

Figure S480.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'11p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S481.  Gene #62: '11p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
11P LOSS MUTATED 3 42 11 3
11P LOSS WILD-TYPE 105 140 82 47

Figure S481.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S482.  Gene #62: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
11P LOSS MUTATED 57 4 8 7
11P LOSS WILD-TYPE 131 119 85 126

Figure S482.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S483.  Gene #62: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
11P LOSS MUTATED 44 1 11 1 11 8 0
11P LOSS WILD-TYPE 79 52 36 64 97 58 75

Figure S483.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S484.  Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
11P LOSS MUTATED 54 4 2 9 6
11P LOSS WILD-TYPE 110 76 104 124 41

Figure S484.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S485.  Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
11P LOSS MUTATED 17 50 8
11P LOSS WILD-TYPE 201 122 132

Figure S485.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00025

Table S486.  Gene #62: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
11P LOSS MUTATED 37 9 14 11
11P LOSS WILD-TYPE 79 89 78 81

Figure S486.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00044

Table S487.  Gene #62: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
11P LOSS MUTATED 44 12 15
11P LOSS WILD-TYPE 119 120 88

Figure S487.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S488.  Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
11Q LOSS MUTATED 69 0 0 4
11Q LOSS WILD-TYPE 139 178 99 50

Figure S488.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S489.  Gene #63: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
11Q LOSS MUTATED 40 22 8
11Q LOSS WILD-TYPE 114 56 185

Figure S489.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S490.  Gene #63: '11q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
11Q LOSS MUTATED 3 3 5 9 27 9 4
11Q LOSS WILD-TYPE 36 78 47 47 57 59 49

Figure S490.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'11q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S491.  Gene #63: '11q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
11Q LOSS MUTATED 4 46 9 1
11Q LOSS WILD-TYPE 104 136 84 49

Figure S491.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S492.  Gene #63: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
11Q LOSS MUTATED 53 4 7 9
11Q LOSS WILD-TYPE 135 119 86 124

Figure S492.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S493.  Gene #63: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
11Q LOSS MUTATED 44 1 10 1 10 7 0
11Q LOSS WILD-TYPE 79 52 37 64 98 59 75

Figure S493.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S494.  Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
11Q LOSS MUTATED 55 4 2 10 2
11Q LOSS WILD-TYPE 109 76 104 123 45

Figure S494.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S495.  Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
11Q LOSS MUTATED 15 49 9
11Q LOSS WILD-TYPE 203 123 131

Figure S495.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S496.  Gene #63: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
11Q LOSS MUTATED 39 10 9 12
11Q LOSS WILD-TYPE 77 88 83 80

Figure S496.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S497.  Gene #63: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
11Q LOSS MUTATED 47 11 12
11Q LOSS WILD-TYPE 116 121 91

Figure S497.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S498.  Gene #64: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
12P LOSS MUTATED 44 0 0 1
12P LOSS WILD-TYPE 164 178 99 53

Figure S498.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 9.8e-05

Table S499.  Gene #64: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
12P LOSS MUTATED 24 10 5
12P LOSS WILD-TYPE 130 68 188

Figure S499.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p loss' versus 'RPPA_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.00058

Table S500.  Gene #64: '12p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
12P LOSS MUTATED 1 1 0 7 13 6 8
12P LOSS WILD-TYPE 38 80 52 49 71 62 45

Figure S500.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'12p loss' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S501.  Gene #64: '12p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
12P LOSS MUTATED 0 27 5 4
12P LOSS WILD-TYPE 108 155 88 46

Figure S501.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S502.  Gene #64: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
12P LOSS MUTATED 38 1 1 5
12P LOSS WILD-TYPE 150 122 92 128

Figure S502.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S503.  Gene #64: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
12P LOSS MUTATED 28 0 7 1 4 5 0
12P LOSS WILD-TYPE 95 53 40 64 104 61 75

Figure S503.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S504.  Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
12P LOSS MUTATED 32 1 3 4 3
12P LOSS WILD-TYPE 132 79 103 129 44

Figure S504.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S505.  Gene #64: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
12P LOSS MUTATED 7 33 3
12P LOSS WILD-TYPE 211 139 137

Figure S505.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00337 (Fisher's exact test), Q value = 0.0061

Table S506.  Gene #64: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
12P LOSS MUTATED 21 4 5 8
12P LOSS WILD-TYPE 95 94 87 84

Figure S506.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00589 (Fisher's exact test), Q value = 0.01

Table S507.  Gene #64: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
12P LOSS MUTATED 24 5 9
12P LOSS WILD-TYPE 139 127 94

Figure S507.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S508.  Gene #65: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
12Q LOSS MUTATED 39 0 0 1
12Q LOSS WILD-TYPE 169 178 99 53

Figure S508.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00012

Table S509.  Gene #65: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
12Q LOSS MUTATED 23 8 3
12Q LOSS WILD-TYPE 131 70 190

Figure S509.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q loss' versus 'RPPA_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.001

Table S510.  Gene #65: '12q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
12Q LOSS MUTATED 1 1 0 7 12 5 8
12Q LOSS WILD-TYPE 38 80 52 49 72 63 45

Figure S510.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'12q loss' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S511.  Gene #65: '12q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
12Q LOSS MUTATED 0 25 5 4
12Q LOSS WILD-TYPE 108 157 88 46

Figure S511.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S512.  Gene #65: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
12Q LOSS MUTATED 35 1 1 3
12Q LOSS WILD-TYPE 153 122 92 130

Figure S512.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S513.  Gene #65: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
12Q LOSS MUTATED 27 0 7 0 3 3 0
12Q LOSS WILD-TYPE 96 53 40 65 105 63 75

Figure S513.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S514.  Gene #65: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
12Q LOSS MUTATED 28 1 3 2 4
12Q LOSS WILD-TYPE 136 79 103 131 43

Figure S514.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S515.  Gene #65: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
12Q LOSS MUTATED 5 32 1
12Q LOSS WILD-TYPE 213 140 139

Figure S515.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0014 (Fisher's exact test), Q value = 0.0027

Table S516.  Gene #65: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
12Q LOSS MUTATED 19 2 5 7
12Q LOSS WILD-TYPE 97 96 87 85

Figure S516.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.00065

Table S517.  Gene #65: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
12Q LOSS MUTATED 22 2 9
12Q LOSS WILD-TYPE 141 130 94

Figure S517.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S518.  Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
13Q LOSS MUTATED 86 3 2 2
13Q LOSS WILD-TYPE 122 175 97 52

Figure S518.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S519.  Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
13Q LOSS MUTATED 47 17 17
13Q LOSS WILD-TYPE 107 61 176

Figure S519.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00016

Table S520.  Gene #66: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
13Q LOSS MUTATED 4 4 4 15 26 9 10
13Q LOSS WILD-TYPE 35 77 48 41 58 59 43

Figure S520.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00149 (Fisher's exact test), Q value = 0.0028

Table S521.  Gene #66: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
13Q LOSS MUTATED 6 40 17 9
13Q LOSS WILD-TYPE 102 142 76 41

Figure S521.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S522.  Gene #66: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
13Q LOSS MUTATED 61 12 6 14
13Q LOSS WILD-TYPE 127 111 87 119

Figure S522.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S523.  Gene #66: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
13Q LOSS MUTATED 39 4 14 0 23 12 1
13Q LOSS WILD-TYPE 84 49 33 65 85 54 74

Figure S523.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S524.  Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
13Q LOSS MUTATED 55 12 6 14 5
13Q LOSS WILD-TYPE 109 68 100 119 42

Figure S524.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S525.  Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
13Q LOSS MUTATED 30 50 12
13Q LOSS WILD-TYPE 188 122 128

Figure S525.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0414 (Fisher's exact test), Q value = 0.06

Table S526.  Gene #66: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
13Q LOSS MUTATED 34 18 16 13
13Q LOSS WILD-TYPE 82 80 76 79

Figure S526.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0237 (Fisher's exact test), Q value = 0.037

Table S527.  Gene #66: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
13Q LOSS MUTATED 43 18 20
13Q LOSS WILD-TYPE 120 114 83

Figure S527.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

P value = 0.00252 (Fisher's exact test), Q value = 0.0047

Table S528.  Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 17 14 7
14Q LOSS MUTATED 0 6 0 0
14Q LOSS WILD-TYPE 15 11 14 7

Figure S528.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.0011

Table S529.  Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
14Q LOSS MUTATED 1 5 0 0 0
14Q LOSS WILD-TYPE 13 4 7 7 16

Figure S529.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S530.  Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
14Q LOSS MUTATED 60 0 0 2
14Q LOSS WILD-TYPE 148 178 99 52

Figure S530.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S531.  Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
14Q LOSS MUTATED 36 12 1
14Q LOSS WILD-TYPE 118 66 192

Figure S531.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S532.  Gene #67: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
14Q LOSS MUTATED 1 0 4 5 20 11 9
14Q LOSS WILD-TYPE 38 81 48 51 64 57 44

Figure S532.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S533.  Gene #67: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
14Q LOSS MUTATED 1 33 11 5
14Q LOSS WILD-TYPE 107 149 82 45

Figure S533.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S534.  Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
14Q LOSS MUTATED 53 2 3 4
14Q LOSS WILD-TYPE 135 121 90 129

Figure S534.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S535.  Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
14Q LOSS MUTATED 46 1 4 0 7 4 0
14Q LOSS WILD-TYPE 77 52 43 65 101 62 75

Figure S535.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S536.  Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
14Q LOSS MUTATED 42 6 7 2 3
14Q LOSS WILD-TYPE 122 74 99 131 44

Figure S536.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S537.  Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
14Q LOSS MUTATED 12 46 2
14Q LOSS WILD-TYPE 206 126 138

Figure S537.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0013 (Fisher's exact test), Q value = 0.0025

Table S538.  Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
14Q LOSS MUTATED 23 3 10 12
14Q LOSS WILD-TYPE 93 95 82 80

Figure S538.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00012

Table S539.  Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
14Q LOSS MUTATED 31 4 13
14Q LOSS WILD-TYPE 132 128 90

Figure S539.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'MRNA_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.001

Table S540.  Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 17 14 7
15Q LOSS MUTATED 0 7 0 0
15Q LOSS WILD-TYPE 15 10 14 7

Figure S540.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 9.8e-05

Table S541.  Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
15Q LOSS MUTATED 1 6 0 0 0
15Q LOSS WILD-TYPE 13 3 7 7 16

Figure S541.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S542.  Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
15Q LOSS MUTATED 103 0 2 4
15Q LOSS WILD-TYPE 105 178 97 50

Figure S542.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S543.  Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
15Q LOSS MUTATED 59 27 10
15Q LOSS WILD-TYPE 95 51 183

Figure S543.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S544.  Gene #68: '15q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
15Q LOSS MUTATED 3 2 6 19 31 12 12
15Q LOSS WILD-TYPE 36 79 46 37 53 56 41

Figure S544.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'15q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S545.  Gene #68: '15q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
15Q LOSS MUTATED 3 53 20 9
15Q LOSS WILD-TYPE 105 129 73 41

Figure S545.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S546.  Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
15Q LOSS MUTATED 88 9 6 6
15Q LOSS WILD-TYPE 100 114 87 127

Figure S546.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S547.  Gene #68: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
15Q LOSS MUTATED 72 1 9 2 17 7 1
15Q LOSS WILD-TYPE 51 52 38 63 91 59 74

Figure S547.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S548.  Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
15Q LOSS MUTATED 79 6 4 8 10
15Q LOSS WILD-TYPE 85 74 102 125 37

Figure S548.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S549.  Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
15Q LOSS MUTATED 28 74 5
15Q LOSS WILD-TYPE 190 98 135

Figure S549.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S550.  Gene #68: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
15Q LOSS MUTATED 48 8 22 16
15Q LOSS WILD-TYPE 68 90 70 76

Figure S550.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S551.  Gene #68: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
15Q LOSS MUTATED 55 11 28
15Q LOSS WILD-TYPE 108 121 75

Figure S551.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'MRNA_CNMF'

P value = 0.00232 (Fisher's exact test), Q value = 0.0043

Table S552.  Gene #69: '16p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 17 14 7
16P LOSS MUTATED 0 6 0 0
16P LOSS WILD-TYPE 15 11 14 7

Figure S552.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00785 (Fisher's exact test), Q value = 0.013

Table S553.  Gene #69: '16p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
16P LOSS MUTATED 2 4 0 0 0
16P LOSS WILD-TYPE 12 5 7 7 16

Figure S553.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S554.  Gene #69: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
16P LOSS MUTATED 94 0 3 2
16P LOSS WILD-TYPE 114 178 96 52

Figure S554.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S555.  Gene #69: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
16P LOSS MUTATED 51 30 8
16P LOSS WILD-TYPE 103 48 185

Figure S555.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'RPPA_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00031

Table S556.  Gene #69: '16p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
16P LOSS MUTATED 2 5 7 16 24 15 13
16P LOSS WILD-TYPE 37 76 45 40 60 53 40

Figure S556.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'16p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S557.  Gene #69: '16p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
16P LOSS MUTATED 4 53 16 9
16P LOSS WILD-TYPE 104 129 77 41

Figure S557.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S558.  Gene #69: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
16P LOSS MUTATED 78 8 6 7
16P LOSS WILD-TYPE 110 115 87 126

Figure S558.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S559.  Gene #69: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
16P LOSS MUTATED 60 4 11 1 15 7 1
16P LOSS WILD-TYPE 63 49 36 64 93 59 74

Figure S559.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S560.  Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
16P LOSS MUTATED 67 7 5 9 8
16P LOSS WILD-TYPE 97 73 101 124 39

Figure S560.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S561.  Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
16P LOSS MUTATED 23 67 6
16P LOSS WILD-TYPE 195 105 134

Figure S561.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.00064

Table S562.  Gene #69: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
16P LOSS MUTATED 38 9 19 21
16P LOSS WILD-TYPE 78 89 73 71

Figure S562.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S563.  Gene #69: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
16P LOSS MUTATED 48 9 30
16P LOSS WILD-TYPE 115 123 73

Figure S563.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'MRNA_CNMF'

P value = 0.00088 (Fisher's exact test), Q value = 0.0018

Table S564.  Gene #70: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 17 14 7
16Q LOSS MUTATED 0 8 1 0
16Q LOSS WILD-TYPE 15 9 13 7

Figure S564.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00143 (Fisher's exact test), Q value = 0.0027

Table S565.  Gene #70: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
16Q LOSS MUTATED 2 6 0 0 1
16Q LOSS WILD-TYPE 12 3 7 7 15

Figure S565.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S566.  Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
16Q LOSS MUTATED 124 3 9 4
16Q LOSS WILD-TYPE 84 175 90 50

Figure S566.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S567.  Gene #70: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
16Q LOSS MUTATED 71 36 16
16Q LOSS WILD-TYPE 83 42 177

Figure S567.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S568.  Gene #70: '16q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
16Q LOSS MUTATED 4 7 9 20 38 16 18
16Q LOSS WILD-TYPE 35 74 43 36 46 52 35

Figure S568.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'16q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S569.  Gene #70: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
16Q LOSS MUTATED 10 73 18 11
16Q LOSS WILD-TYPE 98 109 75 39

Figure S569.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S570.  Gene #70: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
16Q LOSS MUTATED 103 14 10 13
16Q LOSS WILD-TYPE 85 109 83 120

Figure S570.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S571.  Gene #70: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
16Q LOSS MUTATED 79 7 16 3 22 9 4
16Q LOSS WILD-TYPE 44 46 31 62 86 57 71

Figure S571.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S572.  Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
16Q LOSS MUTATED 87 12 12 13 12
16Q LOSS WILD-TYPE 77 68 94 120 35

Figure S572.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S573.  Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
16Q LOSS MUTATED 35 89 12
16Q LOSS WILD-TYPE 183 83 128

Figure S573.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 6e-04

Table S574.  Gene #70: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
16Q LOSS MUTATED 49 15 27 29
16Q LOSS WILD-TYPE 67 83 65 63

Figure S574.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S575.  Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
16Q LOSS MUTATED 63 18 39
16Q LOSS WILD-TYPE 100 114 64

Figure S575.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 0.00319 (Fisher's exact test), Q value = 0.0058

Table S576.  Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 17 14 7
17P LOSS MUTATED 0 7 1 0
17P LOSS WILD-TYPE 15 10 13 7

Figure S576.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00038

Table S577.  Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
17P LOSS MUTATED 1 6 1 0 0
17P LOSS WILD-TYPE 13 3 6 7 16

Figure S577.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S578.  Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
17P LOSS MUTATED 125 1 2 1
17P LOSS WILD-TYPE 83 177 97 53

Figure S578.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S579.  Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
17P LOSS MUTATED 69 31 14
17P LOSS WILD-TYPE 85 47 179

Figure S579.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S580.  Gene #71: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
17P LOSS MUTATED 3 2 7 20 37 14 18
17P LOSS WILD-TYPE 36 79 45 36 47 54 35

Figure S580.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'17p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S581.  Gene #71: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
17P LOSS MUTATED 4 68 19 10
17P LOSS WILD-TYPE 104 114 74 40

Figure S581.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S582.  Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
17P LOSS MUTATED 101 5 9 13
17P LOSS WILD-TYPE 87 118 84 120

Figure S582.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S583.  Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
17P LOSS MUTATED 83 1 10 3 17 13 1
17P LOSS WILD-TYPE 40 52 37 62 91 53 74

Figure S583.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S584.  Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
17P LOSS MUTATED 90 6 7 14 9
17P LOSS WILD-TYPE 74 74 99 119 38

Figure S584.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S585.  Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
17P LOSS MUTATED 29 84 13
17P LOSS WILD-TYPE 189 88 127

Figure S585.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 9.8e-05

Table S586.  Gene #71: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
17P LOSS MUTATED 50 14 25 20
17P LOSS WILD-TYPE 66 84 67 72

Figure S586.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.00058

Table S587.  Gene #71: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
17P LOSS MUTATED 56 20 33
17P LOSS WILD-TYPE 107 112 70

Figure S587.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'MRNA_CNMF'

P value = 0.00248 (Fisher's exact test), Q value = 0.0046

Table S588.  Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 17 14 7
17Q LOSS MUTATED 0 6 0 0
17Q LOSS WILD-TYPE 15 11 14 7

Figure S588.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S589.  Gene #72: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
17Q LOSS MUTATED 0 6 0 0 0
17Q LOSS WILD-TYPE 14 3 7 7 16

Figure S589.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S590.  Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
17Q LOSS MUTATED 90 1 1 1
17Q LOSS WILD-TYPE 118 177 98 53

Figure S590.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S591.  Gene #72: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
17Q LOSS MUTATED 42 27 13
17Q LOSS WILD-TYPE 112 51 180

Figure S591.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S592.  Gene #72: '17q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
17Q LOSS MUTATED 3 2 5 14 29 8 11
17Q LOSS WILD-TYPE 36 79 47 42 55 60 42

Figure S592.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'17q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S593.  Gene #72: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
17Q LOSS MUTATED 2 49 15 6
17Q LOSS WILD-TYPE 106 133 78 44

Figure S593.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S594.  Gene #72: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
17Q LOSS MUTATED 70 5 6 11
17Q LOSS WILD-TYPE 118 118 87 122

Figure S594.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S595.  Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
17Q LOSS MUTATED 55 1 6 3 15 12 0
17Q LOSS WILD-TYPE 68 52 41 62 93 54 75

Figure S595.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S596.  Gene #72: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
17Q LOSS MUTATED 59 6 6 12 7
17Q LOSS WILD-TYPE 105 74 100 121 40

Figure S596.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S597.  Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
17Q LOSS MUTATED 25 54 11
17Q LOSS WILD-TYPE 193 118 129

Figure S597.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00552 (Fisher's exact test), Q value = 0.0096

Table S598.  Gene #72: '17q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
17Q LOSS MUTATED 36 12 16 16
17Q LOSS WILD-TYPE 80 86 76 76

Figure S598.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0221 (Fisher's exact test), Q value = 0.034

Table S599.  Gene #72: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
17Q LOSS MUTATED 43 18 19
17Q LOSS WILD-TYPE 120 114 84

Figure S599.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S600.  Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
18P LOSS MUTATED 49 0 1 1
18P LOSS WILD-TYPE 159 178 98 53

Figure S600.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S601.  Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
18P LOSS MUTATED 29 11 5
18P LOSS WILD-TYPE 125 67 188

Figure S601.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'RPPA_CNMF'

P value = 0.0271 (Fisher's exact test), Q value = 0.042

Table S602.  Gene #73: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
18P LOSS MUTATED 3 3 6 4 16 4 8
18P LOSS WILD-TYPE 36 78 46 52 68 64 45

Figure S602.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00101 (Fisher's exact test), Q value = 0.002

Table S603.  Gene #73: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
18P LOSS MUTATED 2 28 10 4
18P LOSS WILD-TYPE 106 154 83 46

Figure S603.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S604.  Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
18P LOSS MUTATED 35 6 4 6
18P LOSS WILD-TYPE 153 117 89 127

Figure S604.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S605.  Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
18P LOSS MUTATED 21 1 6 1 16 6 0
18P LOSS WILD-TYPE 102 52 41 64 92 60 75

Figure S605.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S606.  Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
18P LOSS MUTATED 32 6 1 7 4
18P LOSS WILD-TYPE 132 74 105 126 43

Figure S606.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00319 (Fisher's exact test), Q value = 0.0058

Table S607.  Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
18P LOSS MUTATED 20 25 5
18P LOSS WILD-TYPE 198 147 135

Figure S607.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00897 (Fisher's exact test), Q value = 0.015

Table S608.  Gene #73: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
18P LOSS MUTATED 22 5 7 11
18P LOSS WILD-TYPE 94 93 85 81

Figure S608.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.018

Table S609.  Gene #73: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
18P LOSS MUTATED 28 10 7
18P LOSS WILD-TYPE 135 122 96

Figure S609.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S610.  Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
18Q LOSS MUTATED 61 0 1 1
18Q LOSS WILD-TYPE 147 178 98 53

Figure S610.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S611.  Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
18Q LOSS MUTATED 35 14 7
18Q LOSS WILD-TYPE 119 64 186

Figure S611.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.017

Table S612.  Gene #74: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
18Q LOSS MUTATED 5 3 5 9 20 7 6
18Q LOSS WILD-TYPE 34 78 47 47 64 61 47

Figure S612.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00099 (Fisher's exact test), Q value = 0.0019

Table S613.  Gene #74: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
18Q LOSS MUTATED 5 35 12 3
18Q LOSS WILD-TYPE 103 147 81 47

Figure S613.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S614.  Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
18Q LOSS MUTATED 42 7 7 7
18Q LOSS WILD-TYPE 146 116 86 126

Figure S614.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S615.  Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
18Q LOSS MUTATED 26 1 12 1 18 5 0
18Q LOSS WILD-TYPE 97 52 35 64 90 61 75

Figure S615.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S616.  Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
18Q LOSS MUTATED 38 6 3 9 6
18Q LOSS WILD-TYPE 126 74 103 124 41

Figure S616.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S617.  Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
18Q LOSS MUTATED 20 36 6
18Q LOSS WILD-TYPE 198 136 134

Figure S617.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.018

Table S618.  Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
18Q LOSS MUTATED 26 7 10 13
18Q LOSS WILD-TYPE 90 91 82 79

Figure S618.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.018

Table S619.  Gene #74: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
18Q LOSS MUTATED 33 11 12
18Q LOSS WILD-TYPE 130 121 91

Figure S619.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S620.  Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
19P LOSS MUTATED 55 0 0 2
19P LOSS WILD-TYPE 153 178 99 52

Figure S620.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S621.  Gene #75: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
19P LOSS MUTATED 42 8 2
19P LOSS WILD-TYPE 112 70 191

Figure S621.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'RPPA_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00029

Table S622.  Gene #75: '19p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
19P LOSS MUTATED 1 0 7 9 16 8 7
19P LOSS WILD-TYPE 38 81 45 47 68 60 46

Figure S622.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'19p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00027

Table S623.  Gene #75: '19p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
19P LOSS MUTATED 2 31 12 3
19P LOSS WILD-TYPE 106 151 81 47

Figure S623.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S624.  Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
19P LOSS MUTATED 44 4 5 4
19P LOSS WILD-TYPE 144 119 88 129

Figure S624.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S625.  Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
19P LOSS MUTATED 34 1 8 1 10 3 0
19P LOSS WILD-TYPE 89 52 39 64 98 63 75

Figure S625.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S626.  Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
19P LOSS MUTATED 42 3 2 5 4
19P LOSS WILD-TYPE 122 77 104 128 43

Figure S626.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S627.  Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
19P LOSS MUTATED 15 38 3
19P LOSS WILD-TYPE 203 134 137

Figure S627.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00385 (Fisher's exact test), Q value = 0.0069

Table S628.  Gene #75: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
19P LOSS MUTATED 24 5 8 13
19P LOSS WILD-TYPE 92 93 84 79

Figure S628.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S629.  Gene #75: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
19P LOSS MUTATED 36 4 10
19P LOSS WILD-TYPE 127 128 93

Figure S629.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S630.  Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
19Q LOSS MUTATED 51 0 1 2
19Q LOSS WILD-TYPE 157 178 98 52

Figure S630.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S631.  Gene #76: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
19Q LOSS MUTATED 32 12 4
19Q LOSS WILD-TYPE 122 66 189

Figure S631.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S632.  Gene #76: '19q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
19Q LOSS MUTATED 1 0 5 6 20 6 7
19Q LOSS WILD-TYPE 38 81 47 50 64 62 46

Figure S632.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'19q loss' versus 'RPPA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00021

Table S633.  Gene #76: '19q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
19Q LOSS MUTATED 2 31 10 2
19Q LOSS WILD-TYPE 106 151 83 48

Figure S633.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S634.  Gene #76: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
19Q LOSS MUTATED 39 4 5 5
19Q LOSS WILD-TYPE 149 119 88 128

Figure S634.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S635.  Gene #76: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
19Q LOSS MUTATED 34 1 5 1 8 4 0
19Q LOSS WILD-TYPE 89 52 42 64 100 62 75

Figure S635.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S636.  Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
19Q LOSS MUTATED 37 3 3 6 4
19Q LOSS WILD-TYPE 127 77 103 127 43

Figure S636.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 9.8e-05

Table S637.  Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
19Q LOSS MUTATED 16 33 4
19Q LOSS WILD-TYPE 202 139 136

Figure S637.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00601 (Fisher's exact test), Q value = 0.01

Table S638.  Gene #76: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
19Q LOSS MUTATED 24 6 8 8
19Q LOSS WILD-TYPE 92 92 84 84

Figure S638.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.00077

Table S639.  Gene #76: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
19Q LOSS MUTATED 30 5 11
19Q LOSS WILD-TYPE 133 127 92

Figure S639.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S640.  Gene #77: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
20P LOSS MUTATED 20 0 1 1
20P LOSS WILD-TYPE 188 178 98 53

Figure S640.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0432 (Fisher's exact test), Q value = 0.062

Table S641.  Gene #77: '20p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
20P LOSS MUTATED 1 13 2 1
20P LOSS WILD-TYPE 107 169 91 49

Figure S641.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 0.0242 (Fisher's exact test), Q value = 0.038

Table S642.  Gene #77: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
20P LOSS MUTATED 14 2 3 2
20P LOSS WILD-TYPE 174 121 90 131

Figure S642.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0117 (Fisher's exact test), Q value = 0.019

Table S643.  Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
20P LOSS MUTATED 11 2 3 0 4 1 0
20P LOSS WILD-TYPE 112 51 44 65 104 65 75

Figure S643.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.017

Table S644.  Gene #77: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
20P LOSS MUTATED 5 13 2
20P LOSS WILD-TYPE 213 159 138

Figure S644.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q loss' versus 'CN_CNMF'

P value = 0.00187 (Fisher's exact test), Q value = 0.0035

Table S645.  Gene #78: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
20Q LOSS MUTATED 10 0 0 1
20Q LOSS WILD-TYPE 198 178 99 53

Figure S645.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

'20q loss' versus 'METHLYATION_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.026

Table S646.  Gene #78: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
20Q LOSS MUTATED 4 3 0
20Q LOSS WILD-TYPE 150 75 193

Figure S646.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q loss' versus 'RPPA_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.051

Table S647.  Gene #78: '20q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
20Q LOSS MUTATED 2 0 0 4 3 1 0
20Q LOSS WILD-TYPE 37 81 52 52 81 67 53

Figure S647.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00545 (Fisher's exact test), Q value = 0.0095

Table S648.  Gene #78: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
20Q LOSS MUTATED 2 8 0
20Q LOSS WILD-TYPE 216 164 140

Figure S648.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MRNA_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.053

Table S649.  Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 17 14 7
21Q LOSS MUTATED 0 4 0 0
21Q LOSS WILD-TYPE 15 13 14 7

Figure S649.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.029 (Fisher's exact test), Q value = 0.044

Table S650.  Gene #79: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
21Q LOSS MUTATED 1 3 0 0 0
21Q LOSS WILD-TYPE 13 6 7 7 16

Figure S650.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S651.  Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
21Q LOSS MUTATED 47 2 2 3
21Q LOSS WILD-TYPE 161 176 97 51

Figure S651.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S652.  Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
21Q LOSS MUTATED 31 10 5
21Q LOSS WILD-TYPE 123 68 188

Figure S652.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'RPPA_CNMF'

P value = 0.0171 (Fisher's exact test), Q value = 0.027

Table S653.  Gene #79: '21q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
21Q LOSS MUTATED 2 3 4 6 18 6 6
21Q LOSS WILD-TYPE 37 78 48 50 66 62 47

Figure S653.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'21q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00127 (Fisher's exact test), Q value = 0.0025

Table S654.  Gene #79: '21q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
21Q LOSS MUTATED 3 30 8 4
21Q LOSS WILD-TYPE 105 152 85 46

Figure S654.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S655.  Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
21Q LOSS MUTATED 42 3 8 1
21Q LOSS WILD-TYPE 146 120 85 132

Figure S655.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S656.  Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
21Q LOSS MUTATED 30 1 7 4 10 2 0
21Q LOSS WILD-TYPE 93 52 40 61 98 64 75

Figure S656.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S657.  Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
21Q LOSS MUTATED 38 5 6 1 2
21Q LOSS WILD-TYPE 126 75 100 132 45

Figure S657.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S658.  Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
21Q LOSS MUTATED 15 36 1
21Q LOSS WILD-TYPE 203 136 139

Figure S658.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S659.  Gene #79: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
21Q LOSS MUTATED 21 0 9 16
21Q LOSS WILD-TYPE 95 98 83 76

Figure S659.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S660.  Gene #79: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
21Q LOSS MUTATED 31 3 12
21Q LOSS WILD-TYPE 132 129 91

Figure S660.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'MRNA_CNMF'

P value = 0.00261 (Fisher's exact test), Q value = 0.0048

Table S661.  Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 17 14 7
22Q LOSS MUTATED 0 6 0 0
22Q LOSS WILD-TYPE 15 11 14 7

Figure S661.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00711 (Fisher's exact test), Q value = 0.012

Table S662.  Gene #80: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
22Q LOSS MUTATED 2 4 0 0 0
22Q LOSS WILD-TYPE 12 5 7 7 16

Figure S662.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S663.  Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
22Q LOSS MUTATED 106 1 2 1
22Q LOSS WILD-TYPE 102 177 97 53

Figure S663.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S664.  Gene #80: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
22Q LOSS MUTATED 58 27 16
22Q LOSS WILD-TYPE 96 51 177

Figure S664.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S665.  Gene #80: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
22Q LOSS MUTATED 3 3 7 19 29 9 15
22Q LOSS WILD-TYPE 36 78 45 37 55 59 38

Figure S665.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S666.  Gene #80: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
22Q LOSS MUTATED 3 50 21 11
22Q LOSS WILD-TYPE 105 132 72 39

Figure S666.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S667.  Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
22Q LOSS MUTATED 81 7 6 15
22Q LOSS WILD-TYPE 107 116 87 118

Figure S667.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S668.  Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
22Q LOSS MUTATED 63 1 7 1 22 13 2
22Q LOSS WILD-TYPE 60 52 40 64 86 53 73

Figure S668.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S669.  Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
22Q LOSS MUTATED 76 6 2 16 8
22Q LOSS WILD-TYPE 88 74 104 117 39

Figure S669.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S670.  Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
22Q LOSS MUTATED 29 66 13
22Q LOSS WILD-TYPE 189 106 127

Figure S670.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00969 (Fisher's exact test), Q value = 0.016

Table S671.  Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
22Q LOSS MUTATED 40 16 22 17
22Q LOSS WILD-TYPE 76 82 70 75

Figure S671.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00122 (Fisher's exact test), Q value = 0.0024

Table S672.  Gene #80: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
22Q LOSS MUTATED 51 18 26
22Q LOSS WILD-TYPE 112 114 77

Figure S672.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'MRNA_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.0012

Table S673.  Gene #81: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 17 14 7
XP LOSS MUTATED 0 7 0 0
XP LOSS WILD-TYPE 15 10 14 7

Figure S673.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp loss' versus 'MRNA_CHIERARCHICAL'

P value = 9e-04 (Fisher's exact test), Q value = 0.0018

Table S674.  Gene #81: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
XP LOSS MUTATED 2 5 0 0 0
XP LOSS WILD-TYPE 12 4 7 7 16

Figure S674.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S675.  Gene #81: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
XP LOSS MUTATED 84 1 0 1
XP LOSS WILD-TYPE 124 177 99 53

Figure S675.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S676.  Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
XP LOSS MUTATED 37 25 9
XP LOSS WILD-TYPE 117 53 184

Figure S676.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S677.  Gene #81: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
XP LOSS MUTATED 3 2 7 14 30 6 10
XP LOSS WILD-TYPE 36 79 45 42 54 62 43

Figure S677.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'xp loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S678.  Gene #81: 'xp loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
XP LOSS MUTATED 3 54 11 4
XP LOSS WILD-TYPE 105 128 82 46

Figure S678.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S679.  Gene #81: 'xp loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
XP LOSS MUTATED 68 7 5 5
XP LOSS WILD-TYPE 120 116 88 128

Figure S679.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S680.  Gene #81: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
XP LOSS MUTATED 53 2 6 1 19 4 0
XP LOSS WILD-TYPE 70 51 41 64 89 62 75

Figure S680.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S681.  Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
XP LOSS MUTATED 57 6 7 8 5
XP LOSS WILD-TYPE 107 74 99 125 42

Figure S681.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S682.  Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
XP LOSS MUTATED 22 57 4
XP LOSS WILD-TYPE 196 115 136

Figure S682.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S683.  Gene #81: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
XP LOSS MUTATED 38 9 12 11
XP LOSS WILD-TYPE 78 89 80 81

Figure S683.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S684.  Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
XP LOSS MUTATED 42 8 20
XP LOSS WILD-TYPE 121 124 83

Figure S684.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'MRNA_CNMF'

P value = 0.00247 (Fisher's exact test), Q value = 0.0046

Table S685.  Gene #82: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 17 14 7
XQ LOSS MUTATED 0 6 0 0
XQ LOSS WILD-TYPE 15 11 14 7

Figure S685.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xq loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00752 (Fisher's exact test), Q value = 0.013

Table S686.  Gene #82: 'xq loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
XQ LOSS MUTATED 2 4 0 0 0
XQ LOSS WILD-TYPE 12 5 7 7 16

Figure S686.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S687.  Gene #82: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 178 99 54
XQ LOSS MUTATED 67 1 0 2
XQ LOSS WILD-TYPE 141 177 99 52

Figure S687.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S688.  Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 78 193
XQ LOSS MUTATED 33 20 6
XQ LOSS WILD-TYPE 121 58 187

Figure S688.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S689.  Gene #82: 'xq loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 39 81 52 56 84 68 53
XQ LOSS MUTATED 3 1 6 13 22 6 7
XQ LOSS WILD-TYPE 36 80 46 43 62 62 46

Figure S689.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S690.  Gene #82: 'xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 182 93 50
XQ LOSS MUTATED 2 45 7 4
XQ LOSS WILD-TYPE 106 137 86 46

Figure S690.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S691.  Gene #82: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 188 123 93 133
XQ LOSS MUTATED 55 5 5 4
XQ LOSS WILD-TYPE 133 118 88 129

Figure S691.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S692.  Gene #82: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
XQ LOSS MUTATED 40 2 7 1 15 4 0
XQ LOSS WILD-TYPE 83 51 40 64 93 62 75

Figure S692.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S693.  Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 164 80 106 133 47
XQ LOSS MUTATED 47 5 5 7 3
XQ LOSS WILD-TYPE 117 75 101 126 44

Figure S693.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S694.  Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 218 172 140
XQ LOSS MUTATED 17 46 4
XQ LOSS WILD-TYPE 201 126 136

Figure S694.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00287 (Fisher's exact test), Q value = 0.0052

Table S695.  Gene #82: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 98 92 92
XQ LOSS MUTATED 28 8 8 14
XQ LOSS WILD-TYPE 88 90 84 78

Figure S695.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S696.  Gene #82: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 132 103
XQ LOSS MUTATED 38 5 15
XQ LOSS WILD-TYPE 125 127 88

Figure S696.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input
  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UCEC-TP/22534123/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UCEC-TP/22553827/UCEC-TP.transferedmergedcluster.txt

  • Number of patients = 539

  • Number of significantly arm-level cnvs = 82

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)