Correlation between copy number variations of arm-level result and molecular subtypes
Breast Invasive Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1W0953Z
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1W0953Z
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 1080 patients, 810 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

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

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

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

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

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

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

  • 5p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

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

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

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

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

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

  • 9q gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 10q gain cnv correlated to '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'.

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

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

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

  • 12q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • 15q gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

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

  • 18p gain cnv correlated to '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'.

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

  • 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 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  • 7q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  '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_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', and 'MRNASEQ_CNMF'.

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

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

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

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

  • 11p 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'.

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

  • 12p 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'.

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

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

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

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

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

  • 19p 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'.

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

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

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

  • 21q loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 22q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 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_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, 810 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
1p gain 206 (19%) 874 1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00031
(0.000555) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00018
(0.000337)
2p gain 123 (11%) 957 1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00014
(0.000267)
5q gain 212 (20%) 868 0.0113
(0.0151) 		0.00628
(0.00877) 		1e-05
(2.35e-05) 		0.00222
(0.00337) 		0.00233
(0.00352) 		0.00021
(0.000386) 		0.00474
(0.00676) 		0.00049
(0.000841) 		3e-05
(6.36e-05) 		2e-05
(4.34e-05) 		0.00035
(0.000616) 		0.0479
(0.0582)
6p gain 209 (19%) 871 1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00032
(0.000567) 		0.00322
(0.00474) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
6q gain 150 (14%) 930 1e-05
(2.35e-05) 		3e-05
(6.36e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		4e-05
(8.32e-05) 		0.01
(0.0135) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		2e-05
(4.34e-05)
10p gain 214 (20%) 866 1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		2e-05
(4.34e-05) 		2e-05
(4.34e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
10q gain 124 (11%) 956 0.0324
(0.0405) 		0.00071
(0.00119) 		1e-05
(2.35e-05) 		0.00076
(0.00128) 		0.0366
(0.0454) 		0.0335
(0.0418) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00035
(0.000616) 		1e-05
(2.35e-05) 		0.00014
(0.000267) 		0.00276
(0.0041)
18p gain 177 (16%) 903 1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00269
(0.004) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
21q gain 196 (18%) 884 1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00082
(0.00137) 		0.002
(0.00306) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		2e-05
(4.34e-05)
22q gain 99 (9%) 981 1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00013
(0.00025) 		0.0009
(0.00149) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00038
(0.000664) 		0.00603
(0.00844)
3p loss 186 (17%) 894 1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00232
(0.00351) 		3e-05
(6.36e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00735
(0.0102)
4p loss 353 (33%) 727 1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		2e-05
(4.34e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		2e-05
(4.34e-05)
4q loss 312 (29%) 768 1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00017
(0.000319) 		0.00267
(0.00398) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00808
(0.0111)
5p loss 140 (13%) 940 1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
5q loss 228 (21%) 852 1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
9p loss 313 (29%) 767 3e-05
(6.36e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00255
(0.00382) 		0.0405
(0.0501) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		5e-05
(0.000103) 		1e-05
(2.35e-05)
9q loss 283 (26%) 797 0.00013
(0.00025) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00151
(0.00238) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
11p loss 275 (25%) 805 0.00384
(0.00554) 		0.0157
(0.0207) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0405
(0.0501) 		0.00107
(0.00175) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00315
(0.00465) 		0.0042
(0.00603)
12p loss 151 (14%) 929 0.00154
(0.00242) 		0.00153
(0.00241) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00957
(0.013) 		0.00537
(0.00758) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
12q loss 131 (12%) 949 1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		6e-05
(0.000122) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
14q loss 266 (25%) 814 1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		2e-05
(4.34e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
15q loss 320 (30%) 760 9e-05
(0.000178) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0024
(0.00362) 		0.00889
(0.0121) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		2e-05
(4.34e-05)
16q loss 593 (55%) 487 1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00166
(0.00259) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00134
(0.00214) 		8e-05
(0.00016)
17q loss 275 (25%) 805 1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		8e-05
(0.00016) 		0.00222
(0.00337)
19p loss 193 (18%) 887 2e-05
(4.34e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0416
(0.0514) 		0.00096
(0.00158) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		2e-05
(4.34e-05) 		1e-05
(2.35e-05)
xp loss 190 (18%) 890 0.0001
(0.000196) 		0.00011
(0.000215) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00216
(0.0033) 		0.00033
(0.000584) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		3e-05
(6.36e-05) 		3e-05
(6.36e-05) 		0.0055
(0.00774) 		0.00309
(0.00457)
2q gain 73 (7%) 1007 1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		2e-05
(4.34e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0929
(0.107)
3q gain 212 (20%) 868 0.00032
(0.000567) 		0.00016
(0.000303) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.023
(0.0296) 		0.086
(0.1) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00013
(0.00025)
9p gain 141 (13%) 939 1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0001
(0.000196) 		0.00784
(0.0108) 		4e-05
(8.32e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00047
(0.000809) 		0.113
(0.128)
16p gain 464 (43%) 616 6e-05
(0.000122) 		0.00124
(0.00199) 		1e-05
(2.35e-05) 		2e-05
(4.34e-05) 		0.0572
(0.0686) 		3e-05
(6.36e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		2e-05
(4.34e-05) 		2e-05
(4.34e-05) 		0.00411
(0.00592)
17q gain 217 (20%) 863 1e-05
(2.35e-05) 		0.00011
(0.000215) 		1e-05
(2.35e-05) 		2e-05
(4.34e-05) 		0.615
(0.631) 		0.00017
(0.000319) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0124
(0.0164) 		1e-05
(2.35e-05) 		0.00111
(0.0018) 		0.00171
(0.00265)
18q gain 153 (14%) 927 1e-05
(2.35e-05) 		6e-05
(0.000122) 		1e-05
(2.35e-05) 		3e-05
(6.36e-05) 		0.16
(0.179) 		0.00363
(0.00529) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00087
(0.00145) 		0.00175
(0.00271)
19p gain 190 (18%) 890 0.00037
(0.000648) 		0.00512
(0.00726) 		1e-05
(2.35e-05) 		0.00203
(0.0031) 		0.0316
(0.0396) 		0.0239
(0.0306) 		1e-05
(2.35e-05) 		4e-05
(8.32e-05) 		1e-05
(2.35e-05) 		0.00012
(0.000233) 		0.0166
(0.0218) 		0.416
(0.437)
20p gain 416 (39%) 664 4e-05
(8.32e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0107
(0.0144) 		0.454
(0.475) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		2e-05
(4.34e-05) 		0.00469
(0.0067)
2p loss 182 (17%) 898 0.00753
(0.0104) 		0.0121
(0.0161) 		1e-05
(2.35e-05) 		2e-05
(4.34e-05) 		0.00167
(0.0026) 		0.00084
(0.0014) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00032
(0.000567) 		2e-05
(4.34e-05) 		2e-05
(4.34e-05) 		0.0522
(0.0631)
7p loss 112 (10%) 968 0.0198
(0.0257) 		0.00118
(0.00191) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.143
(0.161) 		0.0453
(0.0553) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00066
(0.00112) 		0.00029
(0.000523)
8p loss 399 (37%) 681 1e-05
(2.35e-05) 		9e-05
(0.000178) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0906
(0.105) 		0.00032
(0.000567) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		2e-05
(4.34e-05) 		0.00128
(0.00204) 		0.00078
(0.00131)
10q loss 229 (21%) 851 0.00292
(0.00433) 		0.00911
(0.0124) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00167
(0.0026) 		0.162
(0.18) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		9e-05
(0.000178) 		0.00978
(0.0133)
11q loss 365 (34%) 715 9e-05
(0.000178) 		2e-05
(4.34e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.956
(0.956) 		0.00248
(0.00373) 		0.00014
(0.000267) 		0.003
(0.00445) 		0.011
(0.0147) 		0.00085
(0.00142) 		0.0121
(0.0161) 		0.028
(0.0354)
13q loss 433 (40%) 647 6e-05
(0.000122) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.163
(0.181) 		0.00045
(0.000778) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00044
(0.000764)
19q loss 161 (15%) 919 0.00491
(0.00699) 		2e-05
(4.34e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.126
(0.142) 		0.0265
(0.0337) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0003
(0.000539) 		1e-05
(2.35e-05)
20q loss 55 (5%) 1025 0.0125
(0.0166) 		0.00502
(0.00714) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0443
(0.0542) 		0.0957
(0.11) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00016
(0.000303) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0002
(0.000371)
xq loss 190 (18%) 890 0.0887
(0.103) 		0.002
(0.00306) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0455
(0.0555) 		0.0153
(0.0202) 		0.00013
(0.00025) 		1e-05
(2.35e-05) 		2e-05
(4.34e-05) 		0.00068
(0.00115) 		0.0018
(0.00278) 		0.00167
(0.0026)
7q gain 266 (25%) 814 0.0035
(0.00512) 		0.0268
(0.0341) 		1e-05
(2.35e-05) 		5e-05
(0.000103) 		0.0161
(0.0212) 		0.36
(0.381) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00367
(0.00533) 		2e-05
(4.34e-05) 		0.00569
(0.008) 		0.564
(0.581)
8q gain 529 (49%) 551 2e-05
(4.34e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.212
(0.232) 		0.444
(0.465) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
12p gain 229 (21%) 851 0.00071
(0.00119) 		2e-05
(4.34e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0624
(0.0741) 		0.0573
(0.0686) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00054
(0.000924) 		0.0015
(0.00238) 		0.02
(0.0259)
19q gain 223 (21%) 857 0.00107
(0.00175) 		0.00376
(0.00545) 		1e-05
(2.35e-05) 		0.00267
(0.00398) 		0.0182
(0.0238) 		0.0813
(0.0951) 		2e-05
(4.34e-05) 		2e-05
(4.34e-05) 		1e-05
(2.35e-05) 		2e-05
(4.34e-05) 		0.016
(0.021) 		0.0697
(0.0827)
20q gain 451 (42%) 629 6e-05
(0.000122) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.119
(0.136) 		0.156
(0.175) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		2e-05
(4.34e-05) 		0.00019
(0.000354)
xp gain 151 (14%) 929 7e-05
(0.000141) 		0.00883
(0.0121) 		1e-05
(2.35e-05) 		6e-05
(0.000122) 		0.866
(0.871) 		0.508
(0.526) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00012
(0.000233) 		0.00014
(0.000267) 		0.00045
(0.000778)
xq gain 136 (13%) 944 0.0008
(0.00134) 		0.00229
(0.00347) 		1e-05
(2.35e-05) 		0.00013
(0.00025) 		0.333
(0.354) 		0.18
(0.2) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00046
(0.000793) 		0.0252
(0.0321)
2q loss 211 (20%) 869 0.085
(0.0988) 		0.0282
(0.0357) 		1e-05
(2.35e-05) 		6e-05
(0.000122) 		0.00359
(0.00524) 		0.00572
(0.00802) 		2e-05
(4.34e-05) 		1e-05
(2.35e-05) 		0.0033
(0.00484) 		0.00158
(0.00248) 		0.00025
(0.000453) 		0.0752
(0.0886)
17p loss 579 (54%) 501 1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0764
(0.09) 		0.12
(0.136)
20p loss 93 (9%) 987 0.00321
(0.00473) 		0.00019
(0.000354) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0534
(0.0644) 		0.215
(0.235) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		8e-05
(0.00016)
14q gain 143 (13%) 937 0.00113
(0.00183) 		0.0145
(0.0191) 		1e-05
(2.35e-05) 		0.00128
(0.00204) 		0.274
(0.295) 		0.356
(0.378) 		8e-05
(0.00016) 		0.00027
(0.000488) 		0.00024
(0.000436) 		1e-05
(2.35e-05) 		0.00155
(0.00244) 		0.32
(0.342)
1p loss 243 (22%) 837 0.00121
(0.00195) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.673
(0.687) 		0.517
(0.534) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0057
(0.008) 		2e-05
(4.34e-05) 		0.00187
(0.00288) 		0.696
(0.709)
3q loss 103 (10%) 977 0.00122
(0.00196) 		0.00017
(0.000319) 		1e-05
(2.35e-05) 		0.0011
(0.00179) 		0.185
(0.204) 		0.0303
(0.0382) 		0.00035
(0.000616) 		0.00021
(0.000386) 		0.0003
(0.000539) 		0.00016
(0.000303) 		0.0829
(0.0965) 		0.0771
(0.0906)
7q loss 120 (11%) 960 0.0365
(0.0453) 		0.0016
(0.00251) 		1e-05
(2.35e-05) 		0.0704
(0.0833) 		0.229
(0.249) 		0.469
(0.489) 		0.0006
(0.00102) 		0.00046
(0.000793) 		9e-05
(0.000178) 		5e-05
(0.000103) 		0.0259
(0.033) 		0.00414
(0.00596)
16p loss 173 (16%) 907 0.221
(0.241) 		0.096
(0.11) 		0.00032
(0.000567) 		0.00037
(0.000648) 		0.00993
(0.0135) 		0.116
(0.132) 		0.00056
(0.000953) 		0.00165
(0.00258) 		0.00148
(0.00235) 		0.00051
(0.000874) 		0.00019
(0.000354) 		0.0302
(0.0381)
18q loss 321 (30%) 759 0.00021
(0.000386) 		0.00022
(0.000403) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0104
(0.014) 		0.187
(0.207) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		3e-05
(6.36e-05) 		1e-05
(2.35e-05) 		0.206
(0.227) 		0.61
(0.627)
22q loss 482 (45%) 598 0.0539
(0.065) 		0.0052
(0.00736) 		1e-05
(2.35e-05) 		0.00011
(0.000215) 		0.109
(0.125) 		0.00253
(0.00379) 		0.0001
(0.000196) 		4e-05
(8.32e-05) 		0.00319
(0.00471) 		0.00056
(0.000953) 		0.00376
(0.00545) 		0.149
(0.168)
3p gain 135 (12%) 945 0.0286
(0.0361) 		0.044
(0.0539) 		1e-05
(2.35e-05) 		0.00017
(0.000319) 		0.495
(0.514) 		0.0581
(0.0692) 		2e-05
(4.34e-05) 		1e-05
(2.35e-05) 		0.00031
(0.000555) 		2e-05
(4.34e-05) 		0.0782
(0.0918) 		0.208
(0.228)
11p gain 138 (13%) 942 0.786
(0.796) 		0.0827
(0.0965) 		1e-05
(2.35e-05) 		0.00952
(0.013) 		0.694
(0.708) 		0.774
(0.784) 		0.00069
(0.00116) 		0.0113
(0.0151) 		8e-05
(0.00016) 		3e-05
(6.36e-05) 		0.00326
(0.00479) 		0.00017
(0.000319)
11q gain 94 (9%) 986 0.18
(0.199) 		0.0466
(0.0567) 		1e-05
(2.35e-05) 		0.00218
(0.00332) 		0.808
(0.817) 		0.641
(0.656) 		4e-05
(8.32e-05) 		0.00014
(0.000267) 		7e-05
(0.000141) 		0.00023
(0.000419) 		0.0574
(0.0686) 		0.0423
(0.0521)
12q gain 191 (18%) 889 0.00109
(0.00178) 		0.00146
(0.00232) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.247
(0.267) 		0.183
(0.203) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00023
(0.000419) 		0.0576
(0.0688) 		0.00104
(0.00171) 		0.709
(0.722)
6q loss 276 (26%) 804 0.0002
(0.000371) 		0.0135
(0.0179) 		1e-05
(2.35e-05) 		3e-05
(6.36e-05) 		0.483
(0.503) 		0.0793
(0.0931) 		0.00101
(0.00166) 		0.00088
(0.00146) 		0.369
(0.389) 		0.00056
(0.000953) 		0.00997
(0.0135) 		0.363
(0.383)
18p loss 320 (30%) 760 0.00021
(0.000386) 		0.00044
(0.000764) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.145
(0.163) 		0.182
(0.201) 		0.00029
(0.000523) 		1e-05
(2.35e-05) 		8e-05
(0.00016) 		1e-05
(2.35e-05) 		0.391
(0.412) 		0.941
(0.942)
21q loss 180 (17%) 900 0.0337
(0.042) 		0.149
(0.168) 		1e-05
(2.35e-05) 		0.00261
(0.0039) 		0.498
(0.516) 		0.453
(0.475) 		0.0173
(0.0226) 		0.00383
(0.00554) 		0.011
(0.0147) 		0.00632
(0.00881) 		0.0192
(0.0249) 		0.0507
(0.0613)
4p gain 76 (7%) 1004 0.00039
(0.00068) 		0.00111
(0.0018) 		1e-05
(2.35e-05) 		0.00036
(0.000633) 		0.861
(0.867) 		0.11
(0.125) 		0.043
(0.0527) 		0.012
(0.0159) 		0.43
(0.451) 		0.00021
(0.000386) 		0.309
(0.331) 		0.0944
(0.109)
4q gain 73 (7%) 1007 1e-05
(2.35e-05) 		0.00024
(0.000436) 		1e-05
(2.35e-05) 		0.00621
(0.00868) 		0.498
(0.516) 		0.0591
(0.0704) 		0.037
(0.0459) 		0.0569
(0.0684) 		0.593
(0.61) 		0.00063
(0.00107) 		0.106
(0.122) 		0.0205
(0.0265)
5p gain 316 (29%) 764 0.0218
(0.0281) 		0.0426
(0.0523) 		1e-05
(2.35e-05) 		0.019
(0.0247) 		0.9
(0.903) 		0.21
(0.231) 		0.0958
(0.11) 		0.0445
(0.0544) 		0.00443
(0.00634) 		0.0327
(0.0409) 		0.245
(0.265) 		0.311
(0.332)
7p gain 309 (29%) 771 0.00704
(0.00977) 		0.129
(0.146) 		1e-05
(2.35e-05) 		0.00023
(0.000419) 		0.158
(0.176) 		0.823
(0.83) 		0.00093
(0.00154) 		5e-05
(0.000103) 		0.0244
(0.0313) 		0.00137
(0.00218) 		0.0749
(0.0884) 		0.725
(0.737)
13q gain 92 (9%) 988 0.218
(0.239) 		0.283
(0.304) 		4e-05
(8.32e-05) 		0.00443
(0.00634) 		0.0903
(0.105) 		0.307
(0.328) 		0.00249
(0.00374) 		0.00044
(0.000764) 		0.00366
(0.00533) 		0.00852
(0.0117) 		0.0827
(0.0965) 		0.0262
(0.0334)
15q gain 87 (8%) 993 0.0423
(0.0521) 		0.279
(0.3) 		0.00184
(0.00284) 		0.0354
(0.0441) 		0.243
(0.263) 		0.156
(0.175) 		0.00507
(0.0072) 		0.0222
(0.0286) 		0.00807
(0.0111) 		0.0195
(0.0253) 		0.504
(0.522) 		0.133
(0.15)
17p gain 107 (10%) 973 0.0297
(0.0375) 		0.329
(0.35) 		1e-05
(2.35e-05) 		0.0244
(0.0312) 		0.46
(0.48) 		0.0814
(0.0951) 		0.0393
(0.0487) 		0.0166
(0.0217) 		0.355
(0.376) 		0.00428
(0.00614) 		0.48
(0.5) 		0.025
(0.0319)
6p loss 187 (17%) 893 0.0235
(0.0303) 		0.163
(0.181) 		1e-05
(2.35e-05) 		0.00759
(0.0105) 		0.667
(0.683) 		0.0612
(0.0728) 		0.00115
(0.00186) 		0.0104
(0.014) 		0.268
(0.289) 		0.0339
(0.0422) 		0.00703
(0.00977) 		0.525
(0.542)
1q gain 706 (65%) 374 0.0011
(0.00179) 		0.00541
(0.00763) 		1e-05
(2.35e-05) 		0.00022
(0.000403) 		0.81
(0.819) 		0.355
(0.376) 		0.912
(0.913) 		0.0035
(0.00512) 		0.133
(0.15) 		0.00384
(0.00554) 		0.121
(0.138) 		0.215
(0.235)
8p gain 290 (27%) 790 0.181
(0.2) 		0.109
(0.125) 		1e-05
(2.35e-05) 		0.00244
(0.00368) 		0.734
(0.745) 		0.0682
(0.081) 		0.00846
(0.0116) 		0.00124
(0.00199) 		0.0198
(0.0257) 		0.302
(0.324) 		0.00533
(0.00754) 		0.112
(0.128)
10p loss 173 (16%) 907 0.28
(0.301) 		0.235
(0.255) 		1e-05
(2.35e-05) 		4e-05
(8.32e-05) 		0.592
(0.609) 		0.888
(0.892) 		1e-05
(2.35e-05) 		4e-05
(8.32e-05) 		0.00189
(0.00291) 		0.00094
(0.00155) 		0.202
(0.222) 		0.612
(0.627)
9q gain 119 (11%) 961 0.276
(0.297) 		0.00121
(0.00195) 		1e-05
(2.35e-05) 		0.156
(0.175) 		0.764
(0.775) 		0.185
(0.204) 		0.00191
(0.00293) 		0.0304
(0.0382) 		0.0501
(0.0608) 		0.0735
(0.087) 		0.0957
(0.11) 		0.0459
(0.056)
16q gain 142 (13%) 938 0.486
(0.505) 		0.403
(0.424) 		0.0104
(0.014) 		0.0313
(0.0393) 		0.717
(0.729) 		0.414
(0.435) 		0.0572
(0.0686) 		0.00743
(0.0103) 		0.00176
(0.00272) 		0.00151
(0.00238) 		0.13
(0.147) 		0.247
(0.267)
1q loss 52 (5%) 1028 0.0745
(0.088) 		0.012
(0.016) 		6e-05
(0.000122) 		0.00704
(0.00977) 		0.242
(0.263) 		0.361
(0.382) 		0.0141
(0.0186) 		0.0529
(0.0638) 		0.0545
(0.0656) 		0.0269
(0.0341) 		0.0957
(0.11) 		0.477
(0.497)
8q loss 93 (9%) 987 0.0506
(0.0613) 		0.106
(0.121) 		0.00762
(0.0105) 		0.0108
(0.0145) 		0.882
(0.887) 		0.276
(0.297) 		0.0103
(0.0138) 		0.08
(0.0937) 		0.254
(0.274) 		0.837
(0.843) 		0.219
(0.239) 		0.387
(0.408)
'1p gain' versus 'MRNA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
1P GAIN MUTATED 2 4 16 39 6 19 6 5
1P GAIN WILD-TYPE 19 32 103 57 103 53 14 35

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

'1p gain' versus 'MRNA_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
1P GAIN MUTATED 13 17 27 35 5
1P GAIN WILD-TYPE 88 135 87 53 53

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

'1p gain' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
1P GAIN MUTATED 39 47 10 100 10
1P GAIN WILD-TYPE 236 360 88 157 33

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

'1p gain' versus 'METHLYATION_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
1P GAIN MUTATED 23 14 22 31 54 6
1P GAIN WILD-TYPE 121 85 191 92 81 53

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

'1p gain' versus 'RPPA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
1P GAIN MUTATED 50 14 18
1P GAIN WILD-TYPE 101 109 107

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

'1p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.00055

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
1P GAIN MUTATED 5 5 30 6 26 10
1P GAIN WILD-TYPE 59 41 60 46 90 21

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

'1p gain' versus 'MRNASEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
1P GAIN MUTATED 63 114 28
1P GAIN WILD-TYPE 496 190 184

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

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
1P GAIN MUTATED 30 33 10 37 77 18
1P GAIN WILD-TYPE 259 130 80 253 106 42

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

'1p gain' versus 'MIRSEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
1P GAIN MUTATED 100 32 30 41
1P GAIN WILD-TYPE 205 180 239 234

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

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
1P GAIN MUTATED 51 47 24 14 10 57
1P GAIN WILD-TYPE 243 105 221 126 86 77

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

'1p gain' versus 'MIRSEQ_MATURE_CNMF'

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

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

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

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

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00034

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

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

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

'1q gain' versus 'MRNA_CNMF'

P value = 0.0011 (Fisher's exact test), Q value = 0.0018

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
1Q GAIN MUTATED 14 20 60 66 86 50 12 28
1Q GAIN WILD-TYPE 7 16 59 30 23 22 8 12

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

'1q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00541 (Fisher's exact test), Q value = 0.0076

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
1Q GAIN MUTATED 50 102 82 60 42
1Q GAIN WILD-TYPE 51 50 32 28 16

Figure S14.  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 = 2.4e-05

Table S15.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
1Q GAIN MUTATED 177 241 94 166 28
1Q GAIN WILD-TYPE 98 166 4 91 15

Figure S15.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 4e-04

Table S16.  Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
1Q GAIN MUTATED 81 72 160 71 90 31
1Q GAIN WILD-TYPE 63 27 53 52 45 28

Figure S16.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0035 (Fisher's exact test), Q value = 0.0051

Table S17.  Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
1Q GAIN MUTATED 166 122 57 201 122 36
1Q GAIN WILD-TYPE 123 41 33 89 61 24

Figure S17.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00384 (Fisher's exact test), Q value = 0.0055

Table S18.  Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
1Q GAIN MUTATED 194 99 158 105 47 91
1Q GAIN WILD-TYPE 100 53 87 35 49 43

Figure S18.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MRNA_CNMF'

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

Table S19.  Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S19.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p gain' versus 'MRNA_CHIERARCHICAL'

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

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

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

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

'2p gain' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
2P GAIN MUTATED 24 15 8 71 5
2P GAIN WILD-TYPE 251 392 90 186 38

Figure S21.  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 = 2.4e-05

Table S22.  Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
2P GAIN MUTATED 19 7 2 15 39 3
2P GAIN WILD-TYPE 125 92 211 108 96 56

Figure S22.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'RPPA_CNMF'

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

Table S23.  Gene #3: '2p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
2P GAIN MUTATED 40 9 2
2P GAIN WILD-TYPE 111 114 123

Figure S23.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'2p gain' versus 'RPPA_CHIERARCHICAL'

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

Table S24.  Gene #3: '2p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
2P GAIN MUTATED 1 1 32 4 8 5
2P GAIN WILD-TYPE 63 45 58 48 108 26

Figure S24.  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 = 2.4e-05

Table S25.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
2P GAIN MUTATED 28 94 1
2P GAIN WILD-TYPE 531 210 211

Figure S25.  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 = 2.4e-05

Table S26.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
2P GAIN MUTATED 9 26 1 7 57 23
2P GAIN WILD-TYPE 280 137 89 283 126 37

Figure S26.  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 = 2.4e-05

Table S27.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
2P GAIN MUTATED 87 4 8 18
2P GAIN WILD-TYPE 218 208 261 257

Figure S27.  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 = 2.4e-05

Table S28.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
2P GAIN MUTATED 31 38 6 2 0 40
2P GAIN WILD-TYPE 263 114 239 138 96 94

Figure S28.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S29.  Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S29.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00027

Table S30.  Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S30.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'MRNA_CNMF'

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

Table S31.  Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S31.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q gain' versus 'MRNA_CHIERARCHICAL'

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

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

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

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

'2q gain' versus 'CN_CNMF'

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

Table S33.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
2Q GAIN MUTATED 12 11 7 42 1
2Q GAIN WILD-TYPE 263 396 91 215 42

Figure S33.  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 = 2.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
2Q GAIN MUTATED 8 6 2 6 21 2
2Q GAIN WILD-TYPE 136 93 211 117 114 57

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

'2q gain' versus 'RPPA_CNMF'

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

Table S35.  Gene #4: '2q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
2Q GAIN MUTATED 26 4 2
2Q GAIN WILD-TYPE 125 119 123

Figure S35.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'2q gain' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S36.  Gene #4: '2q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
2Q GAIN MUTATED 1 1 19 2 5 4
2Q GAIN WILD-TYPE 63 45 71 50 111 27

Figure S36.  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 = 2.4e-05

Table S37.  Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
2Q GAIN MUTATED 16 56 1
2Q GAIN WILD-TYPE 543 248 211

Figure S37.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S38.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
2Q GAIN MUTATED 5 19 1 3 33 12
2Q GAIN WILD-TYPE 284 144 89 287 150 48

Figure S38.  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 = 2.4e-05

Table S39.  Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
2Q GAIN MUTATED 46 4 5 13
2Q GAIN WILD-TYPE 259 208 264 262

Figure S39.  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 = 2.4e-05

Table S40.  Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
2Q GAIN MUTATED 19 26 4 2 0 17
2Q GAIN WILD-TYPE 275 126 241 138 96 117

Figure S40.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S41.  Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S41.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3p gain' versus 'MRNA_CNMF'

P value = 0.0286 (Fisher's exact test), Q value = 0.036

Table S42.  Gene #5: '3p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
3P GAIN MUTATED 4 6 23 18 16 12 6 0
3P GAIN WILD-TYPE 17 30 96 78 93 60 14 40

Figure S42.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.044 (Fisher's exact test), Q value = 0.054

Table S43.  Gene #5: '3p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
3P GAIN MUTATED 18 14 23 18 12
3P GAIN WILD-TYPE 83 138 91 70 46

Figure S43.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
3P GAIN MUTATED 49 13 19 44 10
3P GAIN WILD-TYPE 226 394 79 213 33

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

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00032

Table S45.  Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
3P GAIN MUTATED 15 10 17 7 29 1
3P GAIN WILD-TYPE 129 89 196 116 106 58

Figure S45.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S46.  Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
3P GAIN MUTATED 78 50 7
3P GAIN WILD-TYPE 481 254 205

Figure S46.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S47.  Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
3P GAIN MUTATED 47 25 2 18 38 5
3P GAIN WILD-TYPE 242 138 88 272 145 55

Figure S47.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.00055

Table S48.  Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
3P GAIN MUTATED 55 13 27 36
3P GAIN WILD-TYPE 250 199 242 239

Figure S48.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S49.  Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
3P GAIN MUTATED 38 24 11 17 12 29
3P GAIN WILD-TYPE 256 128 234 123 84 105

Figure S49.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MRNA_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.00057

Table S50.  Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S50.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 3e-04

Table S51.  Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S51.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
3Q GAIN MUTATED 62 23 24 92 11
3Q GAIN WILD-TYPE 213 384 74 165 32

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

'3q gain' versus 'METHLYATION_CNMF'

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

Table S53.  Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
3Q GAIN MUTATED 26 16 19 14 56 4
3Q GAIN WILD-TYPE 118 83 194 109 79 55

Figure S53.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'RPPA_CNMF'

P value = 0.023 (Fisher's exact test), Q value = 0.03

Table S54.  Gene #6: '3q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
3Q GAIN MUTATED 45 20 25
3Q GAIN WILD-TYPE 106 103 100

Figure S54.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

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

Table S55.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
3Q GAIN MUTATED 100 101 11
3Q GAIN WILD-TYPE 459 203 201

Figure S55.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S56.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
3Q GAIN MUTATED 53 38 3 30 75 13
3Q GAIN WILD-TYPE 236 125 87 260 108 47

Figure S56.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

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

Table S57.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
3Q GAIN MUTATED 108 19 34 47
3Q GAIN WILD-TYPE 197 193 235 228

Figure S57.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S58.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
3Q GAIN MUTATED 54 41 19 24 13 57
3Q GAIN WILD-TYPE 240 111 226 116 83 77

Figure S58.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S59.  Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S59.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00025

Table S60.  Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S60.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'MRNA_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.00068

Table S61.  Gene #7: '4p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S61.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00111 (Fisher's exact test), Q value = 0.0018

Table S62.  Gene #7: '4p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
4P GAIN MUTATED 18 7 7 3 2
4P GAIN WILD-TYPE 83 145 107 85 56

Figure S62.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

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

Table S63.  Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
4P GAIN MUTATED 47 7 3 15 4
4P GAIN WILD-TYPE 228 400 95 242 39

Figure S63.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.00063

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
4P GAIN MUTATED 23 8 7 4 7 4
4P GAIN WILD-TYPE 121 91 206 119 128 55

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

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.043 (Fisher's exact test), Q value = 0.053

Table S65.  Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
4P GAIN MUTATED 49 19 8
4P GAIN WILD-TYPE 510 285 204

Figure S65.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.016

Table S66.  Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
4P GAIN MUTATED 30 17 2 17 7 3
4P GAIN WILD-TYPE 259 146 88 273 176 57

Figure S66.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00039

Table S67.  Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
4P GAIN MUTATED 30 16 13 1 10 5
4P GAIN WILD-TYPE 264 136 232 139 86 129

Figure S67.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'MRNA_CNMF'

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

Table S68.  Gene #8: '4q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S68.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.00044

Table S69.  Gene #8: '4q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S69.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

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

Table S70.  Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
4Q GAIN MUTATED 45 7 2 14 5
4Q GAIN WILD-TYPE 230 400 96 243 38

Figure S70.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

'4q gain' versus 'METHLYATION_CNMF'

P value = 0.00621 (Fisher's exact test), Q value = 0.0087

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
4Q GAIN MUTATED 20 5 8 4 8 4
4Q GAIN WILD-TYPE 124 94 205 119 127 55

Figure S71.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 0.037 (Fisher's exact test), Q value = 0.046

Table S72.  Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
4Q GAIN MUTATED 48 17 8
4Q GAIN WILD-TYPE 511 287 204

Figure S72.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00063 (Fisher's exact test), Q value = 0.0011

Table S73.  Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
4Q GAIN MUTATED 33 10 12 1 8 8
4Q GAIN WILD-TYPE 261 142 233 139 88 126

Figure S73.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0205 (Fisher's exact test), Q value = 0.026

Table S74.  Gene #8: '4q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
4Q GAIN MUTATED 31 11 5
4Q GAIN WILD-TYPE 274 236 105

Figure S74.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p gain' versus 'MRNA_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.028

Table S75.  Gene #9: '5p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
5P GAIN MUTATED 5 14 33 24 31 29 12 8
5P GAIN WILD-TYPE 16 22 86 72 78 43 8 32

Figure S75.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'5p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0426 (Fisher's exact test), Q value = 0.052

Table S76.  Gene #9: '5p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
5P GAIN MUTATED 25 44 48 22 17
5P GAIN WILD-TYPE 76 108 66 66 41

Figure S76.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

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

Table S77.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
5P GAIN MUTATED 117 61 50 75 13
5P GAIN WILD-TYPE 158 346 48 182 30

Figure S77.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.019 (Fisher's exact test), Q value = 0.025

Table S78.  Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
5P GAIN MUTATED 46 36 58 23 45 12
5P GAIN WILD-TYPE 98 63 155 100 90 47

Figure S78.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0445 (Fisher's exact test), Q value = 0.054

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
5P GAIN MUTATED 87 60 20 74 50 23
5P GAIN WILD-TYPE 202 103 70 216 133 37

Figure S79.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 0.00443 (Fisher's exact test), Q value = 0.0063

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
5P GAIN MUTATED 92 43 79 96
5P GAIN WILD-TYPE 213 169 190 179

Figure S80.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0327 (Fisher's exact test), Q value = 0.041

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
5P GAIN MUTATED 91 51 53 50 29 36
5P GAIN WILD-TYPE 203 101 192 90 67 98

Figure S81.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'MRNA_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.015

Table S82.  Gene #10: '5q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
5Q GAIN MUTATED 5 9 24 8 29 17 6 4
5Q GAIN WILD-TYPE 16 27 95 88 80 55 14 36

Figure S82.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00628 (Fisher's exact test), Q value = 0.0088

Table S83.  Gene #10: '5q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
5Q GAIN MUTATED 17 33 29 7 16
5Q GAIN WILD-TYPE 84 119 85 81 42

Figure S83.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
5Q GAIN MUTATED 87 49 48 18 10
5Q GAIN WILD-TYPE 188 358 50 239 33

Figure S84.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 0.00222 (Fisher's exact test), Q value = 0.0034

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
5Q GAIN MUTATED 36 25 50 13 17 9
5Q GAIN WILD-TYPE 108 74 163 110 118 50

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

'5q gain' versus 'RPPA_CNMF'

P value = 0.00233 (Fisher's exact test), Q value = 0.0035

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
5Q GAIN MUTATED 18 30 34
5Q GAIN WILD-TYPE 133 93 91

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

'5q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00039

Table S87.  Gene #10: '5q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
5Q GAIN MUTATED 22 12 5 11 25 7
5Q GAIN WILD-TYPE 42 34 85 41 91 24

Figure S87.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.00474 (Fisher's exact test), Q value = 0.0068

Table S88.  Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
5Q GAIN MUTATED 126 41 43
5Q GAIN WILD-TYPE 433 263 169

Figure S88.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.00084

Table S89.  Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
5Q GAIN MUTATED 71 39 16 59 17 8
5Q GAIN WILD-TYPE 218 124 74 231 166 52

Figure S89.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 6.4e-05

Table S90.  Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
5Q GAIN MUTATED 36 38 64 71
5Q GAIN WILD-TYPE 269 174 205 204

Figure S90.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
5Q GAIN MUTATED 65 24 45 44 22 9
5Q GAIN WILD-TYPE 229 128 200 96 74 125

Figure S91.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.00062

Table S92.  Gene #10: '5q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S92.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0479 (Fisher's exact test), Q value = 0.058

Table S93.  Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
5Q GAIN MUTATED 52 49 31
5Q GAIN WILD-TYPE 253 198 79

Figure S93.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p gain' versus 'MRNA_CNMF'

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

Table S94.  Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S94.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p gain' versus 'MRNA_CHIERARCHICAL'

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

Table S95.  Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S95.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

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

Table S96.  Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
6P GAIN MUTATED 45 21 19 113 11
6P GAIN WILD-TYPE 230 386 79 144 32

Figure S96.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

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

Table S97.  Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
6P GAIN MUTATED 30 20 18 17 58 3
6P GAIN WILD-TYPE 114 79 195 106 77 56

Figure S97.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p gain' versus 'RPPA_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.00057

Table S98.  Gene #11: '6p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
6P GAIN MUTATED 46 17 16
6P GAIN WILD-TYPE 105 106 109

Figure S98.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'6p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00322 (Fisher's exact test), Q value = 0.0047

Table S99.  Gene #11: '6p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
6P GAIN MUTATED 12 5 32 9 17 4
6P GAIN WILD-TYPE 52 41 58 43 99 27

Figure S99.  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 = 2.4e-05

Table S100.  Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
6P GAIN MUTATED 84 110 14
6P GAIN WILD-TYPE 475 194 198

Figure S100.  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 = 2.4e-05

Table S101.  Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
6P GAIN MUTATED 36 50 3 27 80 12
6P GAIN WILD-TYPE 253 113 87 263 103 48

Figure S101.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

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

Table S102.  Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
6P GAIN MUTATED 110 19 36 36
6P GAIN WILD-TYPE 195 193 233 239

Figure S102.  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 = 2.4e-05

Table S103.  Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
6P GAIN MUTATED 53 46 19 12 12 59
6P GAIN WILD-TYPE 241 106 226 128 84 75

Figure S103.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S104.  Gene #11: '6p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S104.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S105.  Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S105.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'MRNA_CNMF'

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

Table S106.  Gene #12: '6q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S106.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6q gain' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.4e-05

Table S107.  Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S107.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

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

Table S108.  Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
6Q GAIN MUTATED 23 15 15 90 7
6Q GAIN WILD-TYPE 252 392 83 167 36

Figure S108.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

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

Table S109.  Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
6Q GAIN MUTATED 17 14 10 14 44 3
6Q GAIN WILD-TYPE 127 85 203 109 91 56

Figure S109.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q gain' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.3e-05

Table S110.  Gene #12: '6q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
6Q GAIN MUTATED 38 12 9
6Q GAIN WILD-TYPE 113 111 116

Figure S110.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'6q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.01 (Fisher's exact test), Q value = 0.014

Table S111.  Gene #12: '6q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
6Q GAIN MUTATED 8 3 25 7 12 4
6Q GAIN WILD-TYPE 56 43 65 45 104 27

Figure S111.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'6q gain' versus 'MRNASEQ_CNMF'

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

Table S112.  Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
6Q GAIN MUTATED 54 84 11
6Q GAIN WILD-TYPE 505 220 201

Figure S112.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S113.  Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
6Q GAIN MUTATED 24 36 3 20 58 8
6Q GAIN WILD-TYPE 265 127 87 270 125 52

Figure S113.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CNMF'

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

Table S114.  Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
6Q GAIN MUTATED 85 14 21 24
6Q GAIN WILD-TYPE 220 198 248 251

Figure S114.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S115.  Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
6Q GAIN MUTATED 38 38 14 6 8 40
6Q GAIN WILD-TYPE 256 114 231 134 88 94

Figure S115.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S116.  Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S116.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S117.  Gene #12: '6q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S117.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'MRNA_CNMF'

P value = 0.00704 (Fisher's exact test), Q value = 0.0098

Table S118.  Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
7P GAIN MUTATED 3 9 26 34 34 30 4 5
7P GAIN WILD-TYPE 18 27 93 62 75 42 16 35

Figure S118.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7p gain' versus 'CN_CNMF'

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

Table S119.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
7P GAIN MUTATED 81 77 49 88 14
7P GAIN WILD-TYPE 194 330 49 169 29

Figure S119.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00042

Table S120.  Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
7P GAIN MUTATED 49 31 57 22 54 9
7P GAIN WILD-TYPE 95 68 156 101 81 50

Figure S120.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.0015

Table S121.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
7P GAIN MUTATED 154 109 45
7P GAIN WILD-TYPE 405 195 167

Figure S121.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 1e-04

Table S122.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
7P GAIN MUTATED 76 63 20 61 61 27
7P GAIN WILD-TYPE 213 100 70 229 122 33

Figure S122.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 0.031

Table S123.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
7P GAIN MUTATED 102 45 77 76
7P GAIN WILD-TYPE 203 167 192 199

Figure S123.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00137 (Fisher's exact test), Q value = 0.0022

Table S124.  Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
7P GAIN MUTATED 91 51 53 47 15 43
7P GAIN WILD-TYPE 203 101 192 93 81 91

Figure S124.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MRNA_CNMF'

P value = 0.0035 (Fisher's exact test), Q value = 0.0051

Table S125.  Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
7Q GAIN MUTATED 2 7 22 34 30 22 3 3
7Q GAIN WILD-TYPE 19 29 97 62 79 50 17 37

Figure S125.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 0.034

Table S126.  Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
7Q GAIN MUTATED 18 30 30 32 13
7Q GAIN WILD-TYPE 83 122 84 56 45

Figure S126.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

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

Table S127.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
7Q GAIN MUTATED 65 63 43 83 12
7Q GAIN WILD-TYPE 210 344 55 174 31

Figure S127.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 1e-04

Table S128.  Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
7Q GAIN MUTATED 39 20 49 18 54 8
7Q GAIN WILD-TYPE 105 79 164 105 81 51

Figure S128.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.021

Table S129.  Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
7Q GAIN MUTATED 48 23 24
7Q GAIN WILD-TYPE 103 100 101

Figure S129.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

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

Table S130.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
7Q GAIN MUTATED 121 106 38
7Q GAIN WILD-TYPE 438 198 174

Figure S130.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S131.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
7Q GAIN MUTATED 63 48 16 48 70 20
7Q GAIN WILD-TYPE 226 115 74 242 113 40

Figure S131.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.00367 (Fisher's exact test), Q value = 0.0053

Table S132.  Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
7Q GAIN MUTATED 96 42 66 55
7Q GAIN WILD-TYPE 209 170 203 220

Figure S132.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S133.  Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
7Q GAIN MUTATED 66 43 45 39 12 54
7Q GAIN WILD-TYPE 228 109 200 101 84 80

Figure S133.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00569 (Fisher's exact test), Q value = 0.008

Table S134.  Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
7Q GAIN MUTATED 42 54 27 29 26
7Q GAIN WILD-TYPE 138 85 72 82 107

Figure S134.  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 = 2.4e-05

Table S135.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
8P GAIN MUTATED 75 77 36 76 26
8P GAIN WILD-TYPE 200 330 62 181 17

Figure S135.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.00244 (Fisher's exact test), Q value = 0.0037

Table S136.  Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
8P GAIN MUTATED 42 28 44 24 53 15
8P GAIN WILD-TYPE 102 71 169 99 82 44

Figure S136.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.00846 (Fisher's exact test), Q value = 0.012

Table S137.  Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
8P GAIN MUTATED 155 93 40
8P GAIN WILD-TYPE 404 211 172

Figure S137.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00124 (Fisher's exact test), Q value = 0.002

Table S138.  Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
8P GAIN MUTATED 90 41 15 64 66 12
8P GAIN WILD-TYPE 199 122 75 226 117 48

Figure S138.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CNMF'

P value = 0.0198 (Fisher's exact test), Q value = 0.026

Table S139.  Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
8P GAIN MUTATED 98 42 72 72
8P GAIN WILD-TYPE 207 170 197 203

Figure S139.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00533 (Fisher's exact test), Q value = 0.0075

Table S140.  Gene #15: '8p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
8P GAIN MUTATED 51 52 19 22 30
8P GAIN WILD-TYPE 129 87 80 89 103

Figure S140.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S141.  Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S141.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8q gain' versus 'MRNA_CHIERARCHICAL'

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

Table S142.  Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S142.  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 = 2.4e-05

Table S143.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
8Q GAIN MUTATED 164 124 39 163 39
8Q GAIN WILD-TYPE 111 283 59 94 4

Figure S143.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

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

Table S144.  Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
8Q GAIN MUTATED 85 46 64 51 93 22
8Q GAIN WILD-TYPE 59 53 149 72 42 37

Figure S144.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

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

Table S145.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
8Q GAIN MUTATED 274 183 69
8Q GAIN WILD-TYPE 285 121 143

Figure S145.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S146.  Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
8Q GAIN MUTATED 143 93 22 117 121 30
8Q GAIN WILD-TYPE 146 70 68 173 62 30

Figure S146.  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 = 2.4e-05

Table S147.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
8Q GAIN MUTATED 196 67 109 147
8Q GAIN WILD-TYPE 109 145 160 128

Figure S147.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S148.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
8Q GAIN MUTATED 161 86 80 56 44 92
8Q GAIN WILD-TYPE 133 66 165 84 52 42

Figure S148.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S149.  Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S149.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S150.  Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S150.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'MRNA_CNMF'

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

Table S151.  Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S151.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p gain' versus 'MRNA_CHIERARCHICAL'

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

Table S152.  Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S152.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

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

Table S153.  Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
9P GAIN MUTATED 16 26 28 64 7
9P GAIN WILD-TYPE 259 381 70 193 36

Figure S153.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 2e-04

Table S154.  Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
9P GAIN MUTATED 16 9 21 15 35 2
9P GAIN WILD-TYPE 128 90 192 108 100 57

Figure S154.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p gain' versus 'RPPA_CNMF'

P value = 0.00784 (Fisher's exact test), Q value = 0.011

Table S155.  Gene #17: '9p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
9P GAIN MUTATED 31 11 12
9P GAIN WILD-TYPE 120 112 113

Figure S155.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'9p gain' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.3e-05

Table S156.  Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
9P GAIN MUTATED 9 3 26 6 4 6
9P GAIN WILD-TYPE 55 43 64 46 112 25

Figure S156.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9p gain' versus 'MRNASEQ_CNMF'

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

Table S157.  Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
9P GAIN MUTATED 47 78 16
9P GAIN WILD-TYPE 512 226 196

Figure S157.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S158.  Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
9P GAIN MUTATED 24 22 4 27 58 6
9P GAIN WILD-TYPE 265 141 86 263 125 54

Figure S158.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_CNMF'

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

Table S159.  Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
9P GAIN MUTATED 69 19 19 30
9P GAIN WILD-TYPE 236 193 250 245

Figure S159.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S160.  Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
9P GAIN MUTATED 29 19 21 18 7 43
9P GAIN WILD-TYPE 265 133 224 122 89 91

Figure S160.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.00081

Table S161.  Gene #17: '9p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S161.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00121 (Fisher's exact test), Q value = 0.0019

Table S162.  Gene #18: '9q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
9Q GAIN MUTATED 2 16 11 15 11
9Q GAIN WILD-TYPE 99 136 103 73 47

Figure S162.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

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

Table S163.  Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
9Q GAIN MUTATED 22 25 28 40 4
9Q GAIN WILD-TYPE 253 382 70 217 39

Figure S163.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 0.00191 (Fisher's exact test), Q value = 0.0029

Table S164.  Gene #18: '9q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
9Q GAIN MUTATED 56 49 14
9Q GAIN WILD-TYPE 503 255 198

Figure S164.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0304 (Fisher's exact test), Q value = 0.038

Table S165.  Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
9Q GAIN MUTATED 30 21 5 24 31 8
9Q GAIN WILD-TYPE 259 142 85 266 152 52

Figure S165.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0459 (Fisher's exact test), Q value = 0.056

Table S166.  Gene #18: '9q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
9Q GAIN MUTATED 38 22 20
9Q GAIN WILD-TYPE 267 225 90

Figure S166.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p gain' versus 'MRNA_CNMF'

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

Table S167.  Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S167.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p gain' versus 'MRNA_CHIERARCHICAL'

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

Table S168.  Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S168.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

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

Table S169.  Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
10P GAIN MUTATED 50 29 16 112 7
10P GAIN WILD-TYPE 225 378 82 145 36

Figure S169.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

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

Table S170.  Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
10P GAIN MUTATED 28 17 12 24 59 2
10P GAIN WILD-TYPE 116 82 201 99 76 57

Figure S170.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p gain' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S171.  Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
10P GAIN MUTATED 53 21 16
10P GAIN WILD-TYPE 98 102 109

Figure S171.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p gain' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S172.  Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
10P GAIN MUTATED 7 11 40 7 19 6
10P GAIN WILD-TYPE 57 35 50 45 97 25

Figure S172.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10p gain' versus 'MRNASEQ_CNMF'

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

Table S173.  Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
10P GAIN MUTATED 75 122 17
10P GAIN WILD-TYPE 484 182 195

Figure S173.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S174.  Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
10P GAIN MUTATED 32 41 3 35 81 22
10P GAIN WILD-TYPE 257 122 87 255 102 38

Figure S174.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CNMF'

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

Table S175.  Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
10P GAIN MUTATED 109 23 30 48
10P GAIN WILD-TYPE 196 189 239 227

Figure S175.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S176.  Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
10P GAIN MUTATED 67 49 17 14 6 57
10P GAIN WILD-TYPE 227 103 228 126 90 77

Figure S176.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S177.  Gene #19: '10p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S177.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S178.  Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S178.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'MRNA_CNMF'

P value = 0.0324 (Fisher's exact test), Q value = 0.041

Table S179.  Gene #20: '10q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
10Q GAIN MUTATED 2 3 13 19 9 16 5 3
10Q GAIN WILD-TYPE 19 33 106 77 100 56 15 37

Figure S179.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00071 (Fisher's exact test), Q value = 0.0012

Table S180.  Gene #20: '10q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
10Q GAIN MUTATED 10 11 25 19 5
10Q GAIN WILD-TYPE 91 141 89 69 53

Figure S180.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

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

Table S181.  Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
10Q GAIN MUTATED 29 22 14 54 5
10Q GAIN WILD-TYPE 246 385 84 203 38

Figure S181.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'METHLYATION_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0013

Table S182.  Gene #20: '10q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
10Q GAIN MUTATED 15 12 8 15 22 2
10Q GAIN WILD-TYPE 129 87 205 108 113 57

Figure S182.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q gain' versus 'RPPA_CNMF'

P value = 0.0366 (Fisher's exact test), Q value = 0.045

Table S183.  Gene #20: '10q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
10Q GAIN MUTATED 31 14 13
10Q GAIN WILD-TYPE 120 109 112

Figure S183.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'10q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0335 (Fisher's exact test), Q value = 0.042

Table S184.  Gene #20: '10q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
10Q GAIN MUTATED 6 8 22 3 16 3
10Q GAIN WILD-TYPE 58 38 68 49 100 28

Figure S184.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10q gain' versus 'MRNASEQ_CNMF'

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

Table S185.  Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
10Q GAIN MUTATED 54 59 11
10Q GAIN WILD-TYPE 505 245 201

Figure S185.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S186.  Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
10Q GAIN MUTATED 26 27 2 22 32 15
10Q GAIN WILD-TYPE 263 136 88 268 151 45

Figure S186.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.00062

Table S187.  Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
10Q GAIN MUTATED 55 15 22 30
10Q GAIN WILD-TYPE 250 197 247 245

Figure S187.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S188.  Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
10Q GAIN MUTATED 41 29 12 11 4 25
10Q GAIN WILD-TYPE 253 123 233 129 92 109

Figure S188.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00027

Table S189.  Gene #20: '10q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S189.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00276 (Fisher's exact test), Q value = 0.0041

Table S190.  Gene #20: '10q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
10Q GAIN MUTATED 46 15 11
10Q GAIN WILD-TYPE 259 232 99

Figure S190.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

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

Table S191.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
11P GAIN MUTATED 50 18 14 51 5
11P GAIN WILD-TYPE 225 389 84 206 38

Figure S191.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.00952 (Fisher's exact test), Q value = 0.013

Table S192.  Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
11P GAIN MUTATED 24 8 23 10 26 3
11P GAIN WILD-TYPE 120 91 190 113 109 56

Figure S192.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0012

Table S193.  Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
11P GAIN MUTATED 69 54 14
11P GAIN WILD-TYPE 490 250 198

Figure S193.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.015

Table S194.  Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
11P GAIN MUTATED 35 29 7 25 33 8
11P GAIN WILD-TYPE 254 134 83 265 150 52

Figure S194.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00016

Table S195.  Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
11P GAIN MUTATED 55 11 28 42
11P GAIN WILD-TYPE 250 201 241 233

Figure S195.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.4e-05

Table S196.  Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
11P GAIN MUTATED 49 26 11 17 10 23
11P GAIN WILD-TYPE 245 126 234 123 86 111

Figure S196.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00326 (Fisher's exact test), Q value = 0.0048

Table S197.  Gene #21: '11p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
11P GAIN MUTATED 32 24 6 12 9
11P GAIN WILD-TYPE 148 115 93 99 124

Figure S197.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00032

Table S198.  Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S198.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0466 (Fisher's exact test), Q value = 0.057

Table S199.  Gene #22: '11q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
11Q GAIN MUTATED 7 12 19 8 2
11Q GAIN WILD-TYPE 94 140 95 80 56

Figure S199.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

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

Table S200.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
11Q GAIN MUTATED 21 11 10 46 6
11Q GAIN WILD-TYPE 254 396 88 211 37

Figure S200.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 0.00218 (Fisher's exact test), Q value = 0.0033

Table S201.  Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
11Q GAIN MUTATED 9 6 16 8 24 1
11Q GAIN WILD-TYPE 135 93 197 115 111 58

Figure S201.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.3e-05

Table S202.  Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
11Q GAIN MUTATED 38 46 10
11Q GAIN WILD-TYPE 521 258 202

Figure S202.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00027

Table S203.  Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
11Q GAIN MUTATED 18 19 5 14 27 11
11Q GAIN WILD-TYPE 271 144 85 276 156 49

Figure S203.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00014

Table S204.  Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
11Q GAIN MUTATED 45 7 19 20
11Q GAIN WILD-TYPE 260 205 250 255

Figure S204.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.00042

Table S205.  Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
11Q GAIN MUTATED 24 22 8 10 7 20
11Q GAIN WILD-TYPE 270 130 237 130 89 114

Figure S205.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0423 (Fisher's exact test), Q value = 0.052

Table S206.  Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
11Q GAIN MUTATED 30 11 10
11Q GAIN WILD-TYPE 275 236 100

Figure S206.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'MRNA_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0012

Table S207.  Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
12P GAIN MUTATED 2 4 33 32 16 22 3 3
12P GAIN WILD-TYPE 19 32 86 64 93 50 17 37

Figure S207.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'12p gain' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S208.  Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
12P GAIN MUTATED 27 16 33 30 9
12P GAIN WILD-TYPE 74 136 81 58 49

Figure S208.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

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

Table S209.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
12P GAIN MUTATED 89 20 25 85 10
12P GAIN WILD-TYPE 186 387 73 172 33

Figure S209.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

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

Table S210.  Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
12P GAIN MUTATED 54 20 25 14 39 4
12P GAIN WILD-TYPE 90 79 188 109 96 55

Figure S210.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

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

Table S211.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
12P GAIN MUTATED 123 86 19
12P GAIN WILD-TYPE 436 218 193

Figure S211.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S212.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
12P GAIN MUTATED 62 51 7 37 58 13
12P GAIN WILD-TYPE 227 112 83 253 125 47

Figure S212.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

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

Table S213.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
12P GAIN MUTATED 100 20 52 50
12P GAIN WILD-TYPE 205 192 217 225

Figure S213.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.00092

Table S214.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
12P GAIN MUTATED 66 36 35 25 15 45
12P GAIN WILD-TYPE 228 116 210 115 81 89

Figure S214.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0015 (Fisher's exact test), Q value = 0.0024

Table S215.  Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
12P GAIN MUTATED 46 39 15 11 25
12P GAIN WILD-TYPE 134 100 84 100 108

Figure S215.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.02 (Fisher's exact test), Q value = 0.026

Table S216.  Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
12P GAIN MUTATED 77 43 16
12P GAIN WILD-TYPE 228 204 94

Figure S216.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'MRNA_CNMF'

P value = 0.00109 (Fisher's exact test), Q value = 0.0018

Table S217.  Gene #24: '12q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
12Q GAIN MUTATED 1 6 33 12 17 23 2 3
12Q GAIN WILD-TYPE 20 30 86 84 92 49 18 37

Figure S217.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'12q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00146 (Fisher's exact test), Q value = 0.0023

Table S218.  Gene #24: '12q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
12Q GAIN MUTATED 26 17 32 11 11
12Q GAIN WILD-TYPE 75 135 82 77 47

Figure S218.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

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

Table S219.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
12Q GAIN MUTATED 96 19 26 41 9
12Q GAIN WILD-TYPE 179 388 72 216 34

Figure S219.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

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

Table S220.  Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
12Q GAIN MUTATED 54 18 29 9 15 5
12Q GAIN WILD-TYPE 90 81 184 114 120 54

Figure S220.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

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

Table S221.  Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
12Q GAIN MUTATED 127 47 16
12Q GAIN WILD-TYPE 432 257 196

Figure S221.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S222.  Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
12Q GAIN MUTATED 68 50 6 35 22 9
12Q GAIN WILD-TYPE 221 113 84 255 161 51

Figure S222.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00042

Table S223.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
12Q GAIN MUTATED 58 17 53 58
12Q GAIN WILD-TYPE 247 195 216 217

Figure S223.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.0017

Table S224.  Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
12Q GAIN MUTATED 47 19 17 9 19
12Q GAIN WILD-TYPE 133 120 82 102 114

Figure S224.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.3e-05

Table S225.  Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
13Q GAIN MUTATED 27 15 8 39 3
13Q GAIN WILD-TYPE 248 392 90 218 40

Figure S225.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.00443 (Fisher's exact test), Q value = 0.0063

Table S226.  Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
13Q GAIN MUTATED 14 7 11 7 19 0
13Q GAIN WILD-TYPE 130 92 202 116 116 59

Figure S226.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 0.00249 (Fisher's exact test), Q value = 0.0037

Table S227.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
13Q GAIN MUTATED 47 37 8
13Q GAIN WILD-TYPE 512 267 204

Figure S227.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.00076

Table S228.  Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
13Q GAIN MUTATED 26 17 3 12 23 11
13Q GAIN WILD-TYPE 263 146 87 278 160 49

Figure S228.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 0.00366 (Fisher's exact test), Q value = 0.0053

Table S229.  Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
13Q GAIN MUTATED 41 11 21 17
13Q GAIN WILD-TYPE 264 201 248 258

Figure S229.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00852 (Fisher's exact test), Q value = 0.012

Table S230.  Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
13Q GAIN MUTATED 26 23 11 8 8 14
13Q GAIN WILD-TYPE 268 129 234 132 88 120

Figure S230.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0262 (Fisher's exact test), Q value = 0.033

Table S231.  Gene #25: '13q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
13Q GAIN MUTATED 34 13 6
13Q GAIN WILD-TYPE 271 234 104

Figure S231.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q gain' versus 'MRNA_CNMF'

P value = 0.00113 (Fisher's exact test), Q value = 0.0018

Table S232.  Gene #26: '14q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
14Q GAIN MUTATED 3 8 15 6 18 20 3 1
14Q GAIN WILD-TYPE 18 28 104 90 91 52 17 39

Figure S232.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0145 (Fisher's exact test), Q value = 0.019

Table S233.  Gene #26: '14q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
14Q GAIN MUTATED 15 21 26 5 7
14Q GAIN WILD-TYPE 86 131 88 83 51

Figure S233.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

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

Table S234.  Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
14Q GAIN MUTATED 61 32 18 27 5
14Q GAIN WILD-TYPE 214 375 80 230 38

Figure S234.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 0.00128 (Fisher's exact test), Q value = 0.002

Table S235.  Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
14Q GAIN MUTATED 29 18 23 6 14 4
14Q GAIN WILD-TYPE 115 81 190 117 121 55

Figure S235.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00016

Table S236.  Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
14Q GAIN MUTATED 95 35 12
14Q GAIN WILD-TYPE 464 269 200

Figure S236.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.00049

Table S237.  Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
14Q GAIN MUTATED 44 33 7 32 12 14
14Q GAIN WILD-TYPE 245 130 83 258 171 46

Figure S237.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00044

Table S238.  Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
14Q GAIN MUTATED 36 13 42 51
14Q GAIN WILD-TYPE 269 199 227 224

Figure S238.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S239.  Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
14Q GAIN MUTATED 63 28 20 20 7 4
14Q GAIN WILD-TYPE 231 124 225 120 89 130

Figure S239.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00155 (Fisher's exact test), Q value = 0.0024

Table S240.  Gene #26: '14q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
14Q GAIN MUTATED 41 12 12 10 14
14Q GAIN WILD-TYPE 139 127 87 101 119

Figure S240.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q gain' versus 'MRNA_CNMF'

P value = 0.0423 (Fisher's exact test), Q value = 0.052

Table S241.  Gene #27: '15q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
15Q GAIN MUTATED 2 4 11 11 3 9 4 1
15Q GAIN WILD-TYPE 19 32 108 85 106 63 16 39

Figure S241.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q gain' versus 'CN_CNMF'

P value = 0.00184 (Fisher's exact test), Q value = 0.0028

Table S242.  Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
15Q GAIN MUTATED 31 21 4 30 1
15Q GAIN WILD-TYPE 244 386 94 227 42

Figure S242.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

'15q gain' versus 'METHLYATION_CNMF'

P value = 0.0354 (Fisher's exact test), Q value = 0.044

Table S243.  Gene #27: '15q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
15Q GAIN MUTATED 11 9 10 4 16 7
15Q GAIN WILD-TYPE 133 90 203 119 119 52

Figure S243.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 0.00507 (Fisher's exact test), Q value = 0.0072

Table S244.  Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
15Q GAIN MUTATED 44 35 8
15Q GAIN WILD-TYPE 515 269 204

Figure S244.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0222 (Fisher's exact test), Q value = 0.029

Table S245.  Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
15Q GAIN MUTATED 26 15 3 14 22 7
15Q GAIN WILD-TYPE 263 148 87 276 161 53

Figure S245.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_CNMF'

P value = 0.00807 (Fisher's exact test), Q value = 0.011

Table S246.  Gene #27: '15q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
15Q GAIN MUTATED 33 11 13 29
15Q GAIN WILD-TYPE 272 201 256 246

Figure S246.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0195 (Fisher's exact test), Q value = 0.025

Table S247.  Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
15Q GAIN MUTATED 27 19 9 9 8 14
15Q GAIN WILD-TYPE 267 133 236 131 88 120

Figure S247.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MRNA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00012

Table S248.  Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S248.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00124 (Fisher's exact test), Q value = 0.002

Table S249.  Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
16P GAIN MUTATED 44 75 58 29 39
16P GAIN WILD-TYPE 57 77 56 59 19

Figure S249.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

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

Table S250.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
16P GAIN MUTATED 128 156 66 95 19
16P GAIN WILD-TYPE 147 251 32 162 24

Figure S250.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S251.  Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
16P GAIN MUTATED 58 44 112 33 42 15
16P GAIN WILD-TYPE 86 55 101 90 93 44

Figure S251.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p gain' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.4e-05

Table S252.  Gene #28: '16p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
16P GAIN MUTATED 48 26 31 25 49 11
16P GAIN WILD-TYPE 16 20 59 27 67 20

Figure S252.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16p gain' versus 'MRNASEQ_CNMF'

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

Table S253.  Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
16P GAIN MUTATED 281 99 83
16P GAIN WILD-TYPE 278 205 129

Figure S253.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S254.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
16P GAIN MUTATED 144 81 33 132 47 26
16P GAIN WILD-TYPE 145 82 57 158 136 34

Figure S254.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

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

Table S255.  Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
16P GAIN MUTATED 103 72 132 146
16P GAIN WILD-TYPE 202 140 137 129

Figure S255.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S256.  Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
16P GAIN MUTATED 143 65 97 73 45 30
16P GAIN WILD-TYPE 151 87 148 67 51 104

Figure S256.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S257.  Gene #28: '16p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

Figure S257.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00411 (Fisher's exact test), Q value = 0.0059

Table S258.  Gene #28: '16p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
16P GAIN MUTATED 114 98 61
16P GAIN WILD-TYPE 191 149 49

Figure S258.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.014

Table S259.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
16Q GAIN MUTATED 45 36 12 44 5
16Q GAIN WILD-TYPE 230 371 86 213 38

Figure S259.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.039

Table S260.  Gene #29: '16q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
16Q GAIN MUTATED 25 11 20 17 22 2
16Q GAIN WILD-TYPE 119 88 193 106 113 57

Figure S260.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00743 (Fisher's exact test), Q value = 0.01

Table S261.  Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
16Q GAIN MUTATED 38 25 5 31 26 16
16Q GAIN WILD-TYPE 251 138 85 259 157 44

Figure S261.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 0.00176 (Fisher's exact test), Q value = 0.0027

Table S262.  Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
16Q GAIN MUTATED 58 17 29 35
16Q GAIN WILD-TYPE 247 195 240 240

Figure S262.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00151 (Fisher's exact test), Q value = 0.0024

Table S263.  Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
16Q GAIN MUTATED 37 37 22 15 13 15
16Q GAIN WILD-TYPE 257 115 223 125 83 119

Figure S263.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MRNA_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.037

Table S264.  Gene #30: '17p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
17P GAIN MUTATED 1 5 22 8 7 5 3 1
17P GAIN WILD-TYPE 20 31 97 88 102 67 17 39

Figure S264.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p gain' versus 'CN_CNMF'

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

Table S265.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
17P GAIN MUTATED 48 21 10 21 7
17P GAIN WILD-TYPE 227 386 88 236 36

Figure S265.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 0.031

Table S266.  Gene #30: '17p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
17P GAIN MUTATED 23 12 12 12 16 3
17P GAIN WILD-TYPE 121 87 201 111 119 56

Figure S266.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 0.0393 (Fisher's exact test), Q value = 0.049

Table S267.  Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
17P GAIN MUTATED 65 29 12
17P GAIN WILD-TYPE 494 275 200

Figure S267.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.022

Table S268.  Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
17P GAIN MUTATED 40 19 2 25 16 4
17P GAIN WILD-TYPE 249 144 88 265 167 56

Figure S268.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00428 (Fisher's exact test), Q value = 0.0061

Table S269.  Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
17P GAIN MUTATED 38 16 16 7 17 10
17P GAIN WILD-TYPE 256 136 229 133 79 124

Figure S269.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.025 (Fisher's exact test), Q value = 0.032

Table S270.  Gene #30: '17p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
17P GAIN MUTATED 41 18 7
17P GAIN WILD-TYPE 264 229 103

Figure S270.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'MRNA_CNMF'

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

Table S271.  Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
17Q GAIN MUTATED 3 8 46 8 10 11 5 4
17Q GAIN WILD-TYPE 18 28 73 88 99 61 15 36

Figure S271.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00021

Table S272.  Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
17Q GAIN MUTATED 34 23 24 7 7
17Q GAIN WILD-TYPE 67 129 90 81 51

Figure S272.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

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

Table S273.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
17Q GAIN MUTATED 115 39 15 35 13
17Q GAIN WILD-TYPE 160 368 83 222 30

Figure S273.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S274.  Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
17Q GAIN MUTATED 53 25 36 18 18 8
17Q GAIN WILD-TYPE 91 74 177 105 117 51

Figure S274.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00032

Table S275.  Gene #31: '17q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
17Q GAIN MUTATED 6 12 8 9 37 4
17Q GAIN WILD-TYPE 58 34 82 43 79 27

Figure S275.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17q gain' versus 'MRNASEQ_CNMF'

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

Table S276.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
17Q GAIN MUTATED 148 42 26
17Q GAIN WILD-TYPE 411 262 186

Figure S276.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S277.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
17Q GAIN MUTATED 89 40 7 54 19 7
17Q GAIN WILD-TYPE 200 123 83 236 164 53

Figure S277.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.016

Table S278.  Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
17Q GAIN MUTATED 56 30 55 71
17Q GAIN WILD-TYPE 249 182 214 204

Figure S278.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S279.  Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
17Q GAIN MUTATED 82 25 33 30 29 13
17Q GAIN WILD-TYPE 212 127 212 110 67 121

Figure S279.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0018

Table S280.  Gene #31: '17q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
17Q GAIN MUTATED 57 22 15 18 23
17Q GAIN WILD-TYPE 123 117 84 93 110

Figure S280.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00171 (Fisher's exact test), Q value = 0.0027

Table S281.  Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
17Q GAIN MUTATED 80 35 20
17Q GAIN WILD-TYPE 225 212 90

Figure S281.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'MRNA_CNMF'

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

Table S282.  Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
18P GAIN MUTATED 1 1 19 35 16 10 4 1
18P GAIN WILD-TYPE 20 35 100 61 93 62 16 39

Figure S282.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p gain' versus 'MRNA_CHIERARCHICAL'

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

Table S283.  Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
18P GAIN MUTATED 20 13 17 32 5
18P GAIN WILD-TYPE 81 139 97 56 53

Figure S283.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

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

Table S284.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
18P GAIN MUTATED 44 22 19 81 11
18P GAIN WILD-TYPE 231 385 79 176 32

Figure S284.  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 = 2.4e-05

Table S285.  Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
18P GAIN MUTATED 21 10 15 14 51 2
18P GAIN WILD-TYPE 123 89 198 109 84 57

Figure S285.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'RPPA_CNMF'

P value = 0.00269 (Fisher's exact test), Q value = 0.004

Table S286.  Gene #32: '18p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
18P GAIN MUTATED 39 13 18
18P GAIN WILD-TYPE 112 110 107

Figure S286.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'18p gain' versus 'RPPA_CHIERARCHICAL'

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

Table S287.  Gene #32: '18p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
18P GAIN MUTATED 13 5 34 3 11 4
18P GAIN WILD-TYPE 51 41 56 49 105 27

Figure S287.  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 = 2.4e-05

Table S288.  Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
18P GAIN MUTATED 83 88 6
18P GAIN WILD-TYPE 476 216 206

Figure S288.  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 = 2.4e-05

Table S289.  Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
18P GAIN MUTATED 49 21 3 20 70 14
18P GAIN WILD-TYPE 240 142 87 270 113 46

Figure S289.  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 = 2.4e-05

Table S290.  Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
18P GAIN MUTATED 90 14 26 40
18P GAIN WILD-TYPE 215 198 243 235

Figure S290.  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 = 2.4e-05

Table S291.  Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
18P GAIN MUTATED 33 36 19 14 14 54
18P GAIN WILD-TYPE 261 116 226 126 82 80

Figure S291.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S292.  Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
18P GAIN MUTATED 26 51 10 11 11
18P GAIN WILD-TYPE 154 88 89 100 122

Figure S292.  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 = 2.4e-05

Table S293.  Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
18P GAIN MUTATED 72 21 16
18P GAIN WILD-TYPE 233 226 94

Figure S293.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'MRNA_CNMF'

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

Table S294.  Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
18Q GAIN MUTATED 2 1 21 30 17 5 4 1
18Q GAIN WILD-TYPE 19 35 98 66 92 67 16 39

Figure S294.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q gain' versus 'MRNA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00012

Table S295.  Gene #33: '18q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
18Q GAIN MUTATED 22 13 14 27 5
18Q GAIN WILD-TYPE 79 139 100 61 53

Figure S295.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

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

Table S296.  Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
18Q GAIN MUTATED 40 16 20 66 11
18Q GAIN WILD-TYPE 235 391 78 191 32

Figure S296.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 6.4e-05

Table S297.  Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
18Q GAIN MUTATED 20 10 16 11 35 3
18Q GAIN WILD-TYPE 124 89 197 112 100 56

Figure S297.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00363 (Fisher's exact test), Q value = 0.0053

Table S298.  Gene #33: '18q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
18Q GAIN MUTATED 13 6 26 5 12 2
18Q GAIN WILD-TYPE 51 40 64 47 104 29

Figure S298.  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 = 2.4e-05

Table S299.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
18Q GAIN MUTATED 83 63 7
18Q GAIN WILD-TYPE 476 241 205

Figure S299.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S300.  Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
18Q GAIN MUTATED 50 17 3 24 53 6
18Q GAIN WILD-TYPE 239 146 87 266 130 54

Figure S300.  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 = 2.4e-05

Table S301.  Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
18Q GAIN MUTATED 69 13 25 40
18Q GAIN WILD-TYPE 236 199 244 235

Figure S301.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S302.  Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
18Q GAIN MUTATED 38 23 18 15 13 40
18Q GAIN WILD-TYPE 256 129 227 125 83 94

Figure S302.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0014

Table S303.  Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
18Q GAIN MUTATED 25 32 9 8 11
18Q GAIN WILD-TYPE 155 107 90 103 122

Figure S303.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00175 (Fisher's exact test), Q value = 0.0027

Table S304.  Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
18Q GAIN MUTATED 53 18 14
18Q GAIN WILD-TYPE 252 229 96

Figure S304.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'MRNA_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.00065

Table S305.  Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
19P GAIN MUTATED 6 3 15 29 15 11 9 4
19P GAIN WILD-TYPE 15 33 104 67 94 61 11 36

Figure S305.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00512 (Fisher's exact test), Q value = 0.0073

Table S306.  Gene #34: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
19P GAIN MUTATED 12 18 26 25 11
19P GAIN WILD-TYPE 89 134 88 63 47

Figure S306.  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 = 2.4e-05

Table S307.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
19P GAIN MUTATED 41 40 28 73 8
19P GAIN WILD-TYPE 234 367 70 184 35

Figure S307.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.00203 (Fisher's exact test), Q value = 0.0031

Table S308.  Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
19P GAIN MUTATED 20 20 25 19 38 6
19P GAIN WILD-TYPE 124 79 188 104 97 53

Figure S308.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'RPPA_CNMF'

P value = 0.0316 (Fisher's exact test), Q value = 0.04

Table S309.  Gene #34: '19p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
19P GAIN MUTATED 39 18 19
19P GAIN WILD-TYPE 112 105 106

Figure S309.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'19p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0239 (Fisher's exact test), Q value = 0.031

Table S310.  Gene #34: '19p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
19P GAIN MUTATED 13 9 27 4 17 6
19P GAIN WILD-TYPE 51 37 63 48 99 25

Figure S310.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19p gain' versus 'MRNASEQ_CNMF'

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

Table S311.  Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
19P GAIN MUTATED 80 82 26
19P GAIN WILD-TYPE 479 222 186

Figure S311.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.3e-05

Table S312.  Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
19P GAIN MUTATED 39 27 10 41 55 16
19P GAIN WILD-TYPE 250 136 80 249 128 44

Figure S312.  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 = 2.4e-05

Table S313.  Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
19P GAIN MUTATED 85 24 41 37
19P GAIN WILD-TYPE 220 188 228 238

Figure S313.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00023

Table S314.  Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
19P GAIN MUTATED 46 39 30 20 13 39
19P GAIN WILD-TYPE 248 113 215 120 83 95

Figure S314.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.022

Table S315.  Gene #34: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
19P GAIN MUTATED 24 38 15 21 19
19P GAIN WILD-TYPE 156 101 84 90 114

Figure S315.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'MRNA_CNMF'

P value = 0.00107 (Fisher's exact test), Q value = 0.0018

Table S316.  Gene #35: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
19Q GAIN MUTATED 5 3 26 34 15 17 8 5
19Q GAIN WILD-TYPE 16 33 93 62 94 55 12 35

Figure S316.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00376 (Fisher's exact test), Q value = 0.0054

Table S317.  Gene #35: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
19Q GAIN MUTATED 18 22 33 29 11
19Q GAIN WILD-TYPE 83 130 81 59 47

Figure S317.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

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

Table S318.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
19Q GAIN MUTATED 50 45 30 87 11
19Q GAIN WILD-TYPE 225 362 68 170 32

Figure S318.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 0.00267 (Fisher's exact test), Q value = 0.004

Table S319.  Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
19Q GAIN MUTATED 30 18 31 18 42 7
19Q GAIN WILD-TYPE 114 81 182 105 93 52

Figure S319.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'RPPA_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.024

Table S320.  Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
19Q GAIN MUTATED 44 22 20
19Q GAIN WILD-TYPE 107 101 105

Figure S320.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S321.  Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
19Q GAIN MUTATED 97 92 32
19Q GAIN WILD-TYPE 462 212 180

Figure S321.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S322.  Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
19Q GAIN MUTATED 48 34 13 45 62 19
19Q GAIN WILD-TYPE 241 129 77 245 121 41

Figure S322.  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 = 2.4e-05

Table S323.  Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
19Q GAIN MUTATED 96 30 46 49
19Q GAIN WILD-TYPE 209 182 223 226

Figure S323.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S324.  Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
19Q GAIN MUTATED 61 50 35 21 14 40
19Q GAIN WILD-TYPE 233 102 210 119 82 94

Figure S324.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.021

Table S325.  Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
19Q GAIN MUTATED 35 43 15 24 21
19Q GAIN WILD-TYPE 145 96 84 87 112

Figure S325.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.3e-05

Table S326.  Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
20P GAIN MUTATED 8 13 49 42 34 42 15 7
20P GAIN WILD-TYPE 13 23 70 54 75 30 5 33

Figure S326.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

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

Table S327.  Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
20P GAIN MUTATED 42 45 68 38 17
20P GAIN WILD-TYPE 59 107 46 50 41

Figure S327.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

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

Table S328.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
20P GAIN MUTATED 153 61 55 127 20
20P GAIN WILD-TYPE 122 346 43 130 23

Figure S328.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

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

Table S329.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
20P GAIN MUTATED 78 43 56 41 56 15
20P GAIN WILD-TYPE 66 56 157 82 79 44

Figure S329.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.014

Table S330.  Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
20P GAIN MUTATED 78 46 44
20P GAIN WILD-TYPE 73 77 81

Figure S330.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

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

Table S331.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
20P GAIN MUTATED 229 138 47
20P GAIN WILD-TYPE 330 166 165

Figure S331.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S332.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
20P GAIN MUTATED 111 90 7 105 77 24
20P GAIN WILD-TYPE 178 73 83 185 106 36

Figure S332.  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 = 2.4e-05

Table S333.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
20P GAIN MUTATED 146 45 90 129
20P GAIN WILD-TYPE 159 167 179 146

Figure S333.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S334.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
20P GAIN MUTATED 129 76 63 59 28 55
20P GAIN WILD-TYPE 165 76 182 81 68 79

Figure S334.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S335.  Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
20P GAIN MUTATED 90 68 32 37 35
20P GAIN WILD-TYPE 90 71 67 74 98

Figure S335.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00469 (Fisher's exact test), Q value = 0.0067

Table S336.  Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
20P GAIN MUTATED 136 78 48
20P GAIN WILD-TYPE 169 169 62

Figure S336.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00012

Table S337.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
20Q GAIN MUTATED 7 13 61 40 35 42 15 10
20Q GAIN WILD-TYPE 14 23 58 56 74 30 5 30

Figure S337.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

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

Table S338.  Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
20Q GAIN MUTATED 52 49 71 34 17
20Q GAIN WILD-TYPE 49 103 43 54 41

Figure S338.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

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

Table S339.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
20Q GAIN MUTATED 178 63 55 133 22
20Q GAIN WILD-TYPE 97 344 43 124 21

Figure S339.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

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

Table S340.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
20Q GAIN MUTATED 93 48 60 41 60 14
20Q GAIN WILD-TYPE 51 51 153 82 75 45

Figure S340.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

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

Table S341.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
20Q GAIN MUTATED 258 143 48
20Q GAIN WILD-TYPE 301 161 164

Figure S341.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S342.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
20Q GAIN MUTATED 131 95 7 111 78 27
20Q GAIN WILD-TYPE 158 68 83 179 105 33

Figure S342.  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 = 2.4e-05

Table S343.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
20Q GAIN MUTATED 155 46 104 141
20Q GAIN WILD-TYPE 150 166 165 134

Figure S343.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S344.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
20Q GAIN MUTATED 155 76 67 58 32 58
20Q GAIN WILD-TYPE 139 76 178 82 64 76

Figure S344.  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 = 4.3e-05

Table S345.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
20Q GAIN MUTATED 103 72 37 40 39
20Q GAIN WILD-TYPE 77 67 62 71 94

Figure S345.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00035

Table S346.  Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
20Q GAIN MUTATED 158 84 49
20Q GAIN WILD-TYPE 147 163 61

Figure S346.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'MRNA_CNMF'

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

Table S347.  Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
21Q GAIN MUTATED 2 2 16 31 11 31 8 3
21Q GAIN WILD-TYPE 19 34 103 65 98 41 12 37

Figure S347.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q gain' versus 'MRNA_CHIERARCHICAL'

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

Table S348.  Gene #38: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
21Q GAIN MUTATED 12 15 44 27 6
21Q GAIN WILD-TYPE 89 137 70 61 52

Figure S348.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

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

Table S349.  Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
21Q GAIN MUTATED 42 32 21 89 12
21Q GAIN WILD-TYPE 233 375 77 168 31

Figure S349.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

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

Table S350.  Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
21Q GAIN MUTATED 25 18 19 14 49 3
21Q GAIN WILD-TYPE 119 81 194 109 86 56

Figure S350.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q gain' versus 'RPPA_CNMF'

P value = 0.00082 (Fisher's exact test), Q value = 0.0014

Table S351.  Gene #38: '21q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
21Q GAIN MUTATED 47 23 16
21Q GAIN WILD-TYPE 104 100 109

Figure S351.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'21q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.002 (Fisher's exact test), Q value = 0.0031

Table S352.  Gene #38: '21q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
21Q GAIN MUTATED 7 8 30 8 21 12
21Q GAIN WILD-TYPE 57 38 60 44 95 19

Figure S352.  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 = 2.4e-05

Table S353.  Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
21Q GAIN MUTATED 75 106 14
21Q GAIN WILD-TYPE 484 198 198

Figure S353.  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 = 2.4e-05

Table S354.  Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
21Q GAIN MUTATED 38 42 4 25 61 25
21Q GAIN WILD-TYPE 251 121 86 265 122 35

Figure S354.  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 = 2.4e-05

Table S355.  Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
21Q GAIN MUTATED 93 23 27 48
21Q GAIN WILD-TYPE 212 189 242 227

Figure S355.  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 = 2.4e-05

Table S356.  Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
21Q GAIN MUTATED 53 47 24 14 9 44
21Q GAIN WILD-TYPE 241 105 221 126 87 90

Figure S356.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S357.  Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
21Q GAIN MUTATED 29 51 6 12 19
21Q GAIN WILD-TYPE 151 88 93 99 114

Figure S357.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S358.  Gene #38: '21q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
21Q GAIN MUTATED 78 30 9
21Q GAIN WILD-TYPE 227 217 101

Figure S358.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q gain' versus 'MRNA_CNMF'

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

Table S359.  Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
22Q GAIN MUTATED 3 0 12 18 2 15 2 0
22Q GAIN WILD-TYPE 18 36 107 78 107 57 18 40

Figure S359.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q gain' versus 'MRNA_CHIERARCHICAL'

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

Table S360.  Gene #39: '22q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
22Q GAIN MUTATED 9 3 24 15 1
22Q GAIN WILD-TYPE 92 149 90 73 57

Figure S360.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

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

Table S361.  Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
22Q GAIN MUTATED 29 9 3 53 5
22Q GAIN WILD-TYPE 246 398 95 204 38

Figure S361.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

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

Table S362.  Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
22Q GAIN MUTATED 13 14 6 9 22 0
22Q GAIN WILD-TYPE 131 85 207 114 113 59

Figure S362.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'RPPA_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00025

Table S363.  Gene #39: '22q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
22Q GAIN MUTATED 30 9 6
22Q GAIN WILD-TYPE 121 114 119

Figure S363.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'22q gain' versus 'RPPA_CHIERARCHICAL'

P value = 9e-04 (Fisher's exact test), Q value = 0.0015

Table S364.  Gene #39: '22q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
22Q GAIN MUTATED 1 1 17 4 16 6
22Q GAIN WILD-TYPE 63 45 73 48 100 25

Figure S364.  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 = 2.4e-05

Table S365.  Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
22Q GAIN MUTATED 35 61 1
22Q GAIN WILD-TYPE 524 243 211

Figure S365.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S366.  Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
22Q GAIN MUTATED 20 23 0 8 33 13
22Q GAIN WILD-TYPE 269 140 90 282 150 47

Figure S366.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CNMF'

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

Table S367.  Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
22Q GAIN MUTATED 54 3 17 22
22Q GAIN WILD-TYPE 251 209 252 253

Figure S367.  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 = 2.4e-05

Table S368.  Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
22Q GAIN MUTATED 31 28 6 3 6 22
22Q GAIN WILD-TYPE 263 124 239 137 90 112

Figure S368.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.00066

Table S369.  Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
22Q GAIN MUTATED 13 25 6 4 6
22Q GAIN WILD-TYPE 167 114 93 107 127

Figure S369.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00603 (Fisher's exact test), Q value = 0.0084

Table S370.  Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
22Q GAIN MUTATED 36 14 4
22Q GAIN WILD-TYPE 269 233 106

Figure S370.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp gain' versus 'MRNA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00014

Table S371.  Gene #40: 'xp gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
XP GAIN MUTATED 1 1 17 18 17 21 9 2
XP GAIN WILD-TYPE 20 35 102 78 92 51 11 38

Figure S371.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00883 (Fisher's exact test), Q value = 0.012

Table S372.  Gene #40: 'xp gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
XP GAIN MUTATED 12 17 31 16 10
XP GAIN WILD-TYPE 89 135 83 72 48

Figure S372.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xp gain' versus 'CN_CNMF'

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

Table S373.  Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
XP GAIN MUTATED 42 22 24 55 8
XP GAIN WILD-TYPE 233 385 74 202 35

Figure S373.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00012

Table S374.  Gene #40: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
XP GAIN MUTATED 26 15 19 6 29 2
XP GAIN WILD-TYPE 118 84 194 117 106 57

Figure S374.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp gain' versus 'MRNASEQ_CNMF'

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

Table S375.  Gene #40: 'xp gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
XP GAIN MUTATED 79 62 9
XP GAIN WILD-TYPE 480 242 203

Figure S375.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xp gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S376.  Gene #40: 'xp gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
XP GAIN MUTATED 38 37 1 28 37 9
XP GAIN WILD-TYPE 251 126 89 262 146 51

Figure S376.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_CNMF'

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

Table S377.  Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
XP GAIN MUTATED 64 7 28 45
XP GAIN WILD-TYPE 241 205 241 230

Figure S377.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xp gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00023

Table S378.  Gene #40: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
XP GAIN MUTATED 46 26 13 18 13 28
XP GAIN WILD-TYPE 248 126 232 122 83 106

Figure S378.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00027

Table S379.  Gene #40: 'xp gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
XP GAIN MUTATED 24 32 9 5 11
XP GAIN WILD-TYPE 156 107 90 106 122

Figure S379.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.00078

Table S380.  Gene #40: 'xp gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
XP GAIN MUTATED 54 20 7
XP GAIN WILD-TYPE 251 227 103

Figure S380.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'MRNA_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0013

Table S381.  Gene #41: 'xq gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
XQ GAIN MUTATED 2 1 17 24 13 18 4 1
XQ GAIN WILD-TYPE 19 35 102 72 96 54 16 39

Figure S381.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'xq gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00229 (Fisher's exact test), Q value = 0.0035

Table S382.  Gene #41: 'xq gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
XQ GAIN MUTATED 11 15 26 22 6
XQ GAIN WILD-TYPE 90 137 88 66 52

Figure S382.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

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

Table S383.  Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
XQ GAIN MUTATED 41 17 20 50 8
XQ GAIN WILD-TYPE 234 390 78 207 35

Figure S383.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00025

Table S384.  Gene #41: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
XQ GAIN MUTATED 19 11 17 4 28 3
XQ GAIN WILD-TYPE 125 88 196 119 107 56

Figure S384.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

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

Table S385.  Gene #41: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
XQ GAIN MUTATED 69 60 6
XQ GAIN WILD-TYPE 490 244 206

Figure S385.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S386.  Gene #41: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
XQ GAIN MUTATED 37 25 0 22 43 8
XQ GAIN WILD-TYPE 252 138 90 268 140 52

Figure S386.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CNMF'

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

Table S387.  Gene #41: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
XQ GAIN MUTATED 63 6 25 35
XQ GAIN WILD-TYPE 242 206 244 240

Figure S387.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S388.  Gene #41: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
XQ GAIN MUTATED 35 22 12 14 14 32
XQ GAIN WILD-TYPE 259 130 233 126 82 102

Figure S388.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.00079

Table S389.  Gene #41: 'xq gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
XQ GAIN MUTATED 15 30 8 6 11
XQ GAIN WILD-TYPE 165 109 91 105 122

Figure S389.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0252 (Fisher's exact test), Q value = 0.032

Table S390.  Gene #41: 'xq gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
XQ GAIN MUTATED 43 20 7
XQ GAIN WILD-TYPE 262 227 103

Figure S390.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'MRNA_CNMF'

P value = 0.00121 (Fisher's exact test), Q value = 0.0019

Table S391.  Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
1P LOSS MUTATED 3 6 33 11 29 29 3 7
1P LOSS WILD-TYPE 18 30 86 85 80 43 17 33

Figure S391.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

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

Table S392.  Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
1P LOSS MUTATED 33 22 42 10 14
1P LOSS WILD-TYPE 68 130 72 78 44

Figure S392.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

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

Table S393.  Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
1P LOSS MUTATED 97 38 47 50 11
1P LOSS WILD-TYPE 178 369 51 207 32

Figure S393.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

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

Table S394.  Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
1P LOSS MUTATED 51 33 36 16 19 9
1P LOSS WILD-TYPE 93 66 177 107 116 50

Figure S394.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

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

Table S395.  Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
1P LOSS MUTATED 161 53 27
1P LOSS WILD-TYPE 398 251 185

Figure S395.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S396.  Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
1P LOSS MUTATED 83 66 5 55 22 10
1P LOSS WILD-TYPE 206 97 85 235 161 50

Figure S396.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.0057 (Fisher's exact test), Q value = 0.008

Table S397.  Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
1P LOSS MUTATED 65 31 73 69
1P LOSS WILD-TYPE 240 181 196 206

Figure S397.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S398.  Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
1P LOSS MUTATED 90 29 39 40 24 16
1P LOSS WILD-TYPE 204 123 206 100 72 118

Figure S398.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00187 (Fisher's exact test), Q value = 0.0029

Table S399.  Gene #42: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
1P LOSS MUTATED 46 17 23 11 27
1P LOSS WILD-TYPE 134 122 76 100 106

Figure S399.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.016

Table S400.  Gene #43: '1q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
1Q LOSS MUTATED 11 2 8 4 2
1Q LOSS WILD-TYPE 90 150 106 84 56

Figure S400.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00012

Table S401.  Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
1Q LOSS MUTATED 22 5 4 17 4
1Q LOSS WILD-TYPE 253 402 94 240 39

Figure S401.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 0.00704 (Fisher's exact test), Q value = 0.0098

Table S402.  Gene #43: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
1Q LOSS MUTATED 14 6 3 3 7 2
1Q LOSS WILD-TYPE 130 93 210 120 128 57

Figure S402.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.019

Table S403.  Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
1Q LOSS MUTATED 34 14 3
1Q LOSS WILD-TYPE 525 290 209

Figure S403.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0269 (Fisher's exact test), Q value = 0.034

Table S404.  Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
1Q LOSS MUTATED 24 7 5 4 5 5
1Q LOSS WILD-TYPE 270 145 240 136 91 129

Figure S404.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MRNA_CNMF'

P value = 0.00753 (Fisher's exact test), Q value = 0.01

Table S405.  Gene #44: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
2P LOSS MUTATED 3 9 31 9 24 14 2 2
2P LOSS WILD-TYPE 18 27 88 87 85 58 18 38

Figure S405.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0121 (Fisher's exact test), Q value = 0.016

Table S406.  Gene #44: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
2P LOSS MUTATED 28 21 25 9 11
2P LOSS WILD-TYPE 73 131 89 79 47

Figure S406.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

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

Table S407.  Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
2P LOSS MUTATED 83 31 24 35 9
2P LOSS WILD-TYPE 192 376 74 222 34

Figure S407.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S408.  Gene #44: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
2P LOSS MUTATED 39 17 37 7 13 5
2P LOSS WILD-TYPE 105 82 176 116 122 54

Figure S408.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p loss' versus 'RPPA_CNMF'

P value = 0.00167 (Fisher's exact test), Q value = 0.0026

Table S409.  Gene #44: '2p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
2P LOSS MUTATED 25 13 35
2P LOSS WILD-TYPE 126 110 90

Figure S409.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'2p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00084 (Fisher's exact test), Q value = 0.0014

Table S410.  Gene #44: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
2P LOSS MUTATED 18 3 8 7 31 6
2P LOSS WILD-TYPE 46 43 82 45 85 25

Figure S410.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2p loss' versus 'MRNASEQ_CNMF'

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

Table S411.  Gene #44: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
2P LOSS MUTATED 133 28 19
2P LOSS WILD-TYPE 426 276 193

Figure S411.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S412.  Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
2P LOSS MUTATED 76 42 8 36 16 2
2P LOSS WILD-TYPE 213 121 82 254 167 58

Figure S412.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.00057

Table S413.  Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
2P LOSS MUTATED 41 23 47 67
2P LOSS WILD-TYPE 264 189 222 208

Figure S413.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S414.  Gene #44: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
2P LOSS MUTATED 68 19 26 30 22 13
2P LOSS WILD-TYPE 226 133 219 110 74 121

Figure S414.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S415.  Gene #44: '2p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
2P LOSS MUTATED 49 10 10 16 15
2P LOSS WILD-TYPE 131 129 89 95 118

Figure S415.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0282 (Fisher's exact test), Q value = 0.036

Table S416.  Gene #45: '2q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
2Q LOSS MUTATED 28 21 31 16 11
2Q LOSS WILD-TYPE 73 131 83 72 47

Figure S416.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

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

Table S417.  Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
2Q LOSS MUTATED 89 34 26 50 12
2Q LOSS WILD-TYPE 186 373 72 207 31

Figure S417.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00012

Table S418.  Gene #45: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
2Q LOSS MUTATED 45 17 37 11 24 5
2Q LOSS WILD-TYPE 99 82 176 112 111 54

Figure S418.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q loss' versus 'RPPA_CNMF'

P value = 0.00359 (Fisher's exact test), Q value = 0.0052

Table S419.  Gene #45: '2q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
2Q LOSS MUTATED 33 14 35
2Q LOSS WILD-TYPE 118 109 90

Figure S419.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'2q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00572 (Fisher's exact test), Q value = 0.008

Table S420.  Gene #45: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
2Q LOSS MUTATED 18 3 15 6 33 7
2Q LOSS WILD-TYPE 46 43 75 46 83 24

Figure S420.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S421.  Gene #45: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
2Q LOSS MUTATED 135 53 21
2Q LOSS WILD-TYPE 424 251 191

Figure S421.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S422.  Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
2Q LOSS MUTATED 77 46 9 40 33 4
2Q LOSS WILD-TYPE 212 117 81 250 150 56

Figure S422.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.0033 (Fisher's exact test), Q value = 0.0048

Table S423.  Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
2Q LOSS MUTATED 62 26 49 70
2Q LOSS WILD-TYPE 243 186 220 205

Figure S423.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00158 (Fisher's exact test), Q value = 0.0025

Table S424.  Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
2Q LOSS MUTATED 70 24 28 30 25 30
2Q LOSS WILD-TYPE 224 128 217 110 71 104

Figure S424.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.00045

Table S425.  Gene #45: '2q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
2Q LOSS MUTATED 53 22 11 18 16
2Q LOSS WILD-TYPE 127 117 88 93 117

Figure S425.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MRNA_CNMF'

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

Table S426.  Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
3P LOSS MUTATED 0 7 19 29 4 17 6 4
3P LOSS WILD-TYPE 21 29 100 67 105 55 14 36

Figure S426.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p loss' versus 'MRNA_CHIERARCHICAL'

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

Table S427.  Gene #46: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
3P LOSS MUTATED 15 18 27 26 0
3P LOSS WILD-TYPE 86 134 87 62 58

Figure S427.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

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

Table S428.  Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
3P LOSS MUTATED 55 28 15 84 4
3P LOSS WILD-TYPE 220 379 83 173 39

Figure S428.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

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

Table S429.  Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
3P LOSS MUTATED 35 21 12 16 40 7
3P LOSS WILD-TYPE 109 78 201 107 95 52

Figure S429.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CNMF'

P value = 0.00232 (Fisher's exact test), Q value = 0.0035

Table S430.  Gene #46: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
3P LOSS MUTATED 41 16 16
3P LOSS WILD-TYPE 110 107 109

Figure S430.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.4e-05

Table S431.  Gene #46: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
3P LOSS MUTATED 2 3 31 10 20 7
3P LOSS WILD-TYPE 62 43 59 42 96 24

Figure S431.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

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

Table S432.  Gene #46: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
3P LOSS MUTATED 73 92 20
3P LOSS WILD-TYPE 486 212 192

Figure S432.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S433.  Gene #46: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
3P LOSS MUTATED 31 43 5 36 55 15
3P LOSS WILD-TYPE 258 120 85 254 128 45

Figure S433.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

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

Table S434.  Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
3P LOSS MUTATED 87 20 26 47
3P LOSS WILD-TYPE 218 192 243 228

Figure S434.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S435.  Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
3P LOSS MUTATED 63 36 27 8 7 39
3P LOSS WILD-TYPE 231 116 218 132 89 95

Figure S435.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S436.  Gene #46: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
3P LOSS MUTATED 27 48 9 9 24
3P LOSS WILD-TYPE 153 91 90 102 109

Figure S436.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00735 (Fisher's exact test), Q value = 0.01

Table S437.  Gene #46: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
3P LOSS MUTATED 68 38 11
3P LOSS WILD-TYPE 237 209 99

Figure S437.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'MRNA_CNMF'

P value = 0.00122 (Fisher's exact test), Q value = 0.002

Table S438.  Gene #47: '3q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
3Q LOSS MUTATED 0 3 13 14 2 11 4 1
3Q LOSS WILD-TYPE 21 33 106 82 107 61 16 39

Figure S438.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00032

Table S439.  Gene #47: '3q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
3Q LOSS MUTATED 10 7 19 12 0
3Q LOSS WILD-TYPE 91 145 95 76 58

Figure S439.  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 = 2.4e-05

Table S440.  Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
3Q LOSS MUTATED 34 13 9 43 4
3Q LOSS WILD-TYPE 241 394 89 214 39

Figure S440.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 0.0011 (Fisher's exact test), Q value = 0.0018

Table S441.  Gene #47: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
3Q LOSS MUTATED 21 12 10 7 21 3
3Q LOSS WILD-TYPE 123 87 203 116 114 56

Figure S441.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0303 (Fisher's exact test), Q value = 0.038

Table S442.  Gene #47: '3q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
3Q LOSS MUTATED 1 4 16 5 11 4
3Q LOSS WILD-TYPE 63 42 74 47 105 27

Figure S442.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.00062

Table S443.  Gene #47: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
3Q LOSS MUTATED 46 46 11
3Q LOSS WILD-TYPE 513 258 201

Figure S443.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00039

Table S444.  Gene #47: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
3Q LOSS MUTATED 21 28 3 18 24 9
3Q LOSS WILD-TYPE 268 135 87 272 159 51

Figure S444.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.00054

Table S445.  Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
3Q LOSS MUTATED 42 10 15 32
3Q LOSS WILD-TYPE 263 202 254 243

Figure S445.  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 = 3e-04

Table S446.  Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
3Q LOSS MUTATED 40 20 12 5 5 17
3Q LOSS WILD-TYPE 254 132 233 135 91 117

Figure S446.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MRNA_CNMF'

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

Table S447.  Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
4P LOSS MUTATED 4 7 25 60 22 41 8 7
4P LOSS WILD-TYPE 17 29 94 36 87 31 12 33

Figure S447.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p loss' versus 'MRNA_CHIERARCHICAL'

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

Table S448.  Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
4P LOSS MUTATED 24 28 57 54 11
4P LOSS WILD-TYPE 77 124 57 34 47

Figure S448.  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 = 2.4e-05

Table S449.  Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
4P LOSS MUTATED 78 54 45 165 11
4P LOSS WILD-TYPE 197 353 53 92 32

Figure S449.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

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

Table S450.  Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
4P LOSS MUTATED 40 31 43 33 90 6
4P LOSS WILD-TYPE 104 68 170 90 45 53

Figure S450.  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 = 2.4e-05

Table S451.  Gene #48: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
4P LOSS MUTATED 79 26 36
4P LOSS WILD-TYPE 72 97 89

Figure S451.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p loss' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S452.  Gene #48: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
4P LOSS MUTATED 18 10 53 18 29 13
4P LOSS WILD-TYPE 46 36 37 34 87 18

Figure S452.  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 = 2.4e-05

Table S453.  Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
4P LOSS MUTATED 141 183 28
4P LOSS WILD-TYPE 418 121 184

Figure S453.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S454.  Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
4P LOSS MUTATED 67 69 9 55 120 32
4P LOSS WILD-TYPE 222 94 81 235 63 28

Figure S454.  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 = 2.4e-05

Table S455.  Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
4P LOSS MUTATED 168 39 43 92
4P LOSS WILD-TYPE 137 173 226 183

Figure S455.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S456.  Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
4P LOSS MUTATED 91 70 30 45 17 89
4P LOSS WILD-TYPE 203 82 215 95 79 45

Figure S456.  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 = 2.4e-05

Table S457.  Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
4P LOSS MUTATED 49 93 19 27 25
4P LOSS WILD-TYPE 131 46 80 84 108

Figure S457.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S458.  Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
4P LOSS MUTATED 124 56 33
4P LOSS WILD-TYPE 181 191 77

Figure S458.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'MRNA_CNMF'

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

Table S459.  Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
4Q LOSS MUTATED 4 7 24 46 21 36 7 7
4Q LOSS WILD-TYPE 17 29 95 50 88 36 13 33

Figure S459.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q loss' versus 'MRNA_CHIERARCHICAL'

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

Table S460.  Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
4Q LOSS MUTATED 24 26 50 41 11
4Q LOSS WILD-TYPE 77 126 64 47 47

Figure S460.  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 = 2.4e-05

Table S461.  Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
4Q LOSS MUTATED 69 50 45 137 11
4Q LOSS WILD-TYPE 206 357 53 120 32

Figure S461.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

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

Table S462.  Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
4Q LOSS MUTATED 37 28 42 33 73 5
4Q LOSS WILD-TYPE 107 71 171 90 62 54

Figure S462.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'RPPA_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00032

Table S463.  Gene #49: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
4Q LOSS MUTATED 66 26 32
4Q LOSS WILD-TYPE 85 97 93

Figure S463.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00267 (Fisher's exact test), Q value = 0.004

Table S464.  Gene #49: '4q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
4Q LOSS MUTATED 16 10 44 17 28 9
4Q LOSS WILD-TYPE 48 36 46 35 88 22

Figure S464.  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 = 2.4e-05

Table S465.  Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
4Q LOSS MUTATED 135 151 25
4Q LOSS WILD-TYPE 424 153 187

Figure S465.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S466.  Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
4Q LOSS MUTATED 64 66 9 51 94 27
4Q LOSS WILD-TYPE 225 97 81 239 89 33

Figure S466.  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 = 2.4e-05

Table S467.  Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
4Q LOSS MUTATED 133 36 46 86
4Q LOSS WILD-TYPE 172 176 223 189

Figure S467.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S468.  Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
4Q LOSS MUTATED 82 62 29 43 17 68
4Q LOSS WILD-TYPE 212 90 216 97 79 66

Figure S468.  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 = 2.4e-05

Table S469.  Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
4Q LOSS MUTATED 46 69 19 27 21
4Q LOSS WILD-TYPE 134 70 80 84 112

Figure S469.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00808 (Fisher's exact test), Q value = 0.011

Table S470.  Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
4Q LOSS MUTATED 98 51 33
4Q LOSS WILD-TYPE 207 196 77

Figure S470.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'MRNA_CNMF'

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

Table S471.  Gene #50: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
5P LOSS MUTATED 1 1 8 40 5 11 1 2
5P LOSS WILD-TYPE 20 35 111 56 104 61 19 38

Figure S471.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5p loss' versus 'MRNA_CHIERARCHICAL'

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

Table S472.  Gene #50: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
5P LOSS MUTATED 9 5 17 37 1
5P LOSS WILD-TYPE 92 147 97 51 57

Figure S472.  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 = 2.4e-05

Table S473.  Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
5P LOSS MUTATED 20 14 4 96 6
5P LOSS WILD-TYPE 255 393 94 161 37

Figure S473.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

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

Table S474.  Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
5P LOSS MUTATED 14 8 4 18 53 2
5P LOSS WILD-TYPE 130 91 209 105 82 57

Figure S474.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'RPPA_CNMF'

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

Table S475.  Gene #50: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
5P LOSS MUTATED 43 10 8
5P LOSS WILD-TYPE 108 113 117

Figure S475.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5p loss' versus 'RPPA_CHIERARCHICAL'

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

Table S476.  Gene #50: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
5P LOSS MUTATED 1 1 38 6 12 3
5P LOSS WILD-TYPE 63 45 52 46 104 28

Figure S476.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5p loss' versus 'MRNASEQ_CNMF'

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

Table S477.  Gene #50: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
5P LOSS MUTATED 40 92 7
5P LOSS WILD-TYPE 519 212 205

Figure S477.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S478.  Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
5P LOSS MUTATED 15 25 1 12 78 8
5P LOSS WILD-TYPE 274 138 89 278 105 52

Figure S478.  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 = 2.4e-05

Table S479.  Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
5P LOSS MUTATED 86 14 12 25
5P LOSS WILD-TYPE 219 198 257 250

Figure S479.  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 = 2.4e-05

Table S480.  Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
5P LOSS MUTATED 34 28 7 3 4 61
5P LOSS WILD-TYPE 260 124 238 137 92 73

Figure S480.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S481.  Gene #50: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
5P LOSS MUTATED 12 56 5 4 9
5P LOSS WILD-TYPE 168 83 94 107 124

Figure S481.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S482.  Gene #50: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
5P LOSS MUTATED 70 12 4
5P LOSS WILD-TYPE 235 235 106

Figure S482.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'MRNA_CNMF'

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

Table S483.  Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
5Q LOSS MUTATED 2 3 14 60 4 21 5 3
5Q LOSS WILD-TYPE 19 33 105 36 105 51 15 37

Figure S483.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'MRNA_CHIERARCHICAL'

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

Table S484.  Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
5Q LOSS MUTATED 14 10 32 55 1
5Q LOSS WILD-TYPE 87 142 82 33 57

Figure S484.  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 = 2.4e-05

Table S485.  Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
5Q LOSS MUTATED 32 20 5 162 9
5Q LOSS WILD-TYPE 243 387 93 95 34

Figure S485.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

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

Table S486.  Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
5Q LOSS MUTATED 23 11 6 30 88 4
5Q LOSS WILD-TYPE 121 88 207 93 47 55

Figure S486.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'RPPA_CNMF'

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

Table S487.  Gene #51: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
5Q LOSS MUTATED 68 19 9
5Q LOSS WILD-TYPE 83 104 116

Figure S487.  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 = 2.4e-05

Table S488.  Gene #51: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
5Q LOSS MUTATED 3 3 55 10 19 6
5Q LOSS WILD-TYPE 61 43 35 42 97 25

Figure S488.  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 = 2.4e-05

Table S489.  Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
5Q LOSS MUTATED 59 156 12
5Q LOSS WILD-TYPE 500 148 200

Figure S489.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S490.  Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
5Q LOSS MUTATED 25 38 1 24 119 20
5Q LOSS WILD-TYPE 264 125 89 266 64 40

Figure S490.  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 = 2.4e-05

Table S491.  Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
5Q LOSS MUTATED 150 18 19 36
5Q LOSS WILD-TYPE 155 194 250 239

Figure S491.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S492.  Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
5Q LOSS MUTATED 51 58 11 4 5 94
5Q LOSS WILD-TYPE 243 94 234 136 91 40

Figure S492.  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 = 2.4e-05

Table S493.  Gene #51: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
5Q LOSS MUTATED 16 88 13 9 14
5Q LOSS WILD-TYPE 164 51 86 102 119

Figure S493.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S494.  Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
5Q LOSS MUTATED 107 25 8
5Q LOSS WILD-TYPE 198 222 102

Figure S494.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'MRNA_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 0.03

Table S495.  Gene #52: '6p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
6P LOSS MUTATED 5 10 30 9 19 10 1 9
6P LOSS WILD-TYPE 16 26 89 87 90 62 19 31

Figure S495.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p loss' versus 'CN_CNMF'

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

Table S496.  Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
6P LOSS MUTATED 88 46 15 29 9
6P LOSS WILD-TYPE 187 361 83 228 34

Figure S496.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.00759 (Fisher's exact test), Q value = 0.01

Table S497.  Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
6P LOSS MUTATED 40 14 30 19 18 6
6P LOSS WILD-TYPE 104 85 183 104 117 53

Figure S497.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 0.00115 (Fisher's exact test), Q value = 0.0019

Table S498.  Gene #52: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
6P LOSS MUTATED 119 38 29
6P LOSS WILD-TYPE 440 266 183

Figure S498.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.014

Table S499.  Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
6P LOSS MUTATED 68 30 14 45 19 10
6P LOSS WILD-TYPE 221 133 76 245 164 50

Figure S499.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0339 (Fisher's exact test), Q value = 0.042

Table S500.  Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
6P LOSS MUTATED 63 21 36 29 21 15
6P LOSS WILD-TYPE 231 131 209 111 75 119

Figure S500.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00703 (Fisher's exact test), Q value = 0.0098

Table S501.  Gene #52: '6p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
6P LOSS MUTATED 45 15 12 20 28
6P LOSS WILD-TYPE 135 124 87 91 105

Figure S501.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MRNA_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.00037

Table S502.  Gene #53: '6q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
6Q LOSS MUTATED 6 13 44 13 23 14 1 14
6Q LOSS WILD-TYPE 15 23 75 83 86 58 19 26

Figure S502.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'6q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0135 (Fisher's exact test), Q value = 0.018

Table S503.  Gene #53: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
6Q LOSS MUTATED 36 42 24 13 13
6Q LOSS WILD-TYPE 65 110 90 75 45

Figure S503.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

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

Table S504.  Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
6Q LOSS MUTATED 124 78 21 37 16
6Q LOSS WILD-TYPE 151 329 77 220 27

Figure S504.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 6.4e-05

Table S505.  Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
6Q LOSS MUTATED 61 22 58 21 24 12
6Q LOSS WILD-TYPE 83 77 155 102 111 47

Figure S505.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.00101 (Fisher's exact test), Q value = 0.0017

Table S506.  Gene #53: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
6Q LOSS MUTATED 167 56 52
6Q LOSS WILD-TYPE 392 248 160

Figure S506.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00088 (Fisher's exact test), Q value = 0.0015

Table S507.  Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
6Q LOSS MUTATED 93 42 22 75 26 17
6Q LOSS WILD-TYPE 196 121 68 215 157 43

Figure S507.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.00095

Table S508.  Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
6Q LOSS MUTATED 86 29 60 48 31 20
6Q LOSS WILD-TYPE 208 123 185 92 65 114

Figure S508.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00997 (Fisher's exact test), Q value = 0.013

Table S509.  Gene #53: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
6Q LOSS MUTATED 56 22 21 33 39
6Q LOSS WILD-TYPE 124 117 78 78 94

Figure S509.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p loss' versus 'MRNA_CNMF'

P value = 0.0198 (Fisher's exact test), Q value = 0.026

Table S510.  Gene #54: '7p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
7P LOSS MUTATED 3 3 20 14 4 9 4 2
7P LOSS WILD-TYPE 18 33 99 82 105 63 16 38

Figure S510.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'7p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00118 (Fisher's exact test), Q value = 0.0019

Table S511.  Gene #54: '7p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
7P LOSS MUTATED 16 7 21 12 3
7P LOSS WILD-TYPE 85 145 93 76 55

Figure S511.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

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

Table S512.  Gene #54: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
7P LOSS MUTATED 40 10 6 53 3
7P LOSS WILD-TYPE 235 397 92 204 40

Figure S512.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

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

Table S513.  Gene #54: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
7P LOSS MUTATED 19 9 10 6 26 1
7P LOSS WILD-TYPE 125 90 203 117 109 58

Figure S513.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0453 (Fisher's exact test), Q value = 0.055

Table S514.  Gene #54: '7p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
7P LOSS MUTATED 4 3 15 2 17 1
7P LOSS WILD-TYPE 60 43 75 50 99 30

Figure S514.  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 = 2.4e-05

Table S515.  Gene #54: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
7P LOSS MUTATED 53 52 6
7P LOSS WILD-TYPE 506 252 206

Figure S515.  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 = 2.4e-05

Table S516.  Gene #54: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
7P LOSS MUTATED 31 25 0 19 31 5
7P LOSS WILD-TYPE 258 138 90 271 152 55

Figure S516.  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 = 2.4e-05

Table S517.  Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
7P LOSS MUTATED 56 4 26 24
7P LOSS WILD-TYPE 249 208 243 251

Figure S517.  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 = 2.4e-05

Table S518.  Gene #54: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
7P LOSS MUTATED 41 22 7 6 8 26
7P LOSS WILD-TYPE 253 130 238 134 88 108

Figure S518.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0011

Table S519.  Gene #54: '7p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
7P LOSS MUTATED 18 25 8 3 8
7P LOSS WILD-TYPE 162 114 91 108 125

Figure S519.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.00052

Table S520.  Gene #54: '7p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
7P LOSS MUTATED 44 13 5
7P LOSS WILD-TYPE 261 234 105

Figure S520.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q loss' versus 'MRNA_CNMF'

P value = 0.0365 (Fisher's exact test), Q value = 0.045

Table S521.  Gene #55: '7q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
7Q LOSS MUTATED 5 4 18 7 8 14 5 4
7Q LOSS WILD-TYPE 16 32 101 89 101 58 15 36

Figure S521.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'7q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0016 (Fisher's exact test), Q value = 0.0025

Table S522.  Gene #55: '7q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
7Q LOSS MUTATED 14 12 27 6 6
7Q LOSS WILD-TYPE 87 140 87 82 52

Figure S522.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

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

Table S523.  Gene #55: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
7Q LOSS MUTATED 47 18 11 41 3
7Q LOSS WILD-TYPE 228 389 87 216 40

Figure S523.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.001

Table S524.  Gene #55: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
7Q LOSS MUTATED 74 36 9
7Q LOSS WILD-TYPE 485 268 203

Figure S524.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.00079

Table S525.  Gene #55: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
7Q LOSS MUTATED 38 31 2 24 17 7
7Q LOSS WILD-TYPE 251 132 88 266 166 53

Figure S525.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00018

Table S526.  Gene #55: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
7Q LOSS MUTATED 47 7 28 36
7Q LOSS WILD-TYPE 258 205 241 239

Figure S526.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 1e-04

Table S527.  Gene #55: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
7Q LOSS MUTATED 49 24 10 10 12 13
7Q LOSS WILD-TYPE 245 128 235 130 84 121

Figure S527.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0259 (Fisher's exact test), Q value = 0.033

Table S528.  Gene #55: '7q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
7Q LOSS MUTATED 26 17 9 5 8
7Q LOSS WILD-TYPE 154 122 90 106 125

Figure S528.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00414 (Fisher's exact test), Q value = 0.006

Table S529.  Gene #55: '7q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
7Q LOSS MUTATED 41 13 11
7Q LOSS WILD-TYPE 264 234 99

Figure S529.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'MRNA_CNMF'

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

Table S530.  Gene #56: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
8P LOSS MUTATED 5 10 56 45 22 37 11 17
8P LOSS WILD-TYPE 16 26 63 51 87 35 9 23

Figure S530.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p loss' versus 'MRNA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00018

Table S531.  Gene #56: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
8P LOSS MUTATED 48 45 58 39 13
8P LOSS WILD-TYPE 53 107 56 49 45

Figure S531.  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 = 2.4e-05

Table S532.  Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
8P LOSS MUTATED 134 98 19 133 15
8P LOSS WILD-TYPE 141 309 79 124 28

Figure S532.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

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

Table S533.  Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
8P LOSS MUTATED 74 37 50 44 57 11
8P LOSS WILD-TYPE 70 62 163 79 78 48

Figure S533.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.00057

Table S534.  Gene #56: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
8P LOSS MUTATED 11 17 40 28 55 15
8P LOSS WILD-TYPE 53 29 50 24 61 16

Figure S534.  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 = 2.4e-05

Table S535.  Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
8P LOSS MUTATED 199 142 55
8P LOSS WILD-TYPE 360 162 157

Figure S535.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S536.  Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
8P LOSS MUTATED 98 84 18 88 74 34
8P LOSS WILD-TYPE 191 79 72 202 109 26

Figure S536.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

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

Table S537.  Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
8P LOSS MUTATED 142 57 84 110
8P LOSS WILD-TYPE 163 155 185 165

Figure S537.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S538.  Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
8P LOSS MUTATED 124 73 67 40 30 59
8P LOSS WILD-TYPE 170 79 178 100 66 75

Figure S538.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00128 (Fisher's exact test), Q value = 0.002

Table S539.  Gene #56: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
8P LOSS MUTATED 77 61 34 26 39
8P LOSS WILD-TYPE 103 78 65 85 94

Figure S539.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.0013

Table S540.  Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
8P LOSS MUTATED 131 78 28
8P LOSS WILD-TYPE 174 169 82

Figure S540.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 0.00762 (Fisher's exact test), Q value = 0.011

Table S541.  Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
8Q LOSS MUTATED 33 20 11 26 3
8Q LOSS WILD-TYPE 242 387 87 231 40

Figure S541.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.014

Table S542.  Gene #57: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
8Q LOSS MUTATED 21 11 9 10 12 2
8Q LOSS WILD-TYPE 123 88 204 113 123 57

Figure S542.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.014

Table S543.  Gene #57: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
8Q LOSS MUTATED 54 31 8
8Q LOSS WILD-TYPE 505 273 204

Figure S543.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 6.4e-05

Table S544.  Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
9P LOSS MUTATED 7 10 53 30 18 33 10 6
9P LOSS WILD-TYPE 14 26 66 66 91 39 10 34

Figure S544.  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 = 2.4e-05

Table S545.  Gene #58: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
9P LOSS MUTATED 43 31 59 25 9
9P LOSS WILD-TYPE 58 121 55 63 49

Figure S545.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

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

Table S546.  Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
9P LOSS MUTATED 149 42 16 97 9
9P LOSS WILD-TYPE 126 365 82 160 34

Figure S546.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

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

Table S547.  Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
9P LOSS MUTATED 71 36 24 21 47 9
9P LOSS WILD-TYPE 73 63 189 102 88 50

Figure S547.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CNMF'

P value = 0.00255 (Fisher's exact test), Q value = 0.0038

Table S548.  Gene #58: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
9P LOSS MUTATED 67 35 33
9P LOSS WILD-TYPE 84 88 92

Figure S548.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0405 (Fisher's exact test), Q value = 0.05

Table S549.  Gene #58: '9p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
9P LOSS MUTATED 13 14 32 14 50 12
9P LOSS WILD-TYPE 51 32 58 38 66 19

Figure S549.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9p loss' versus 'MRNASEQ_CNMF'

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

Table S550.  Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
9P LOSS MUTATED 180 103 28
9P LOSS WILD-TYPE 379 201 184

Figure S550.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S551.  Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
9P LOSS MUTATED 96 76 5 59 50 25
9P LOSS WILD-TYPE 193 87 85 231 133 35

Figure S551.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

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

Table S552.  Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
9P LOSS MUTATED 117 29 61 100
9P LOSS WILD-TYPE 188 183 208 175

Figure S552.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S553.  Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
9P LOSS MUTATED 124 67 29 30 21 36
9P LOSS WILD-TYPE 170 85 216 110 75 98

Figure S553.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 1e-04

Table S554.  Gene #58: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
9P LOSS MUTATED 65 52 21 19 28
9P LOSS WILD-TYPE 115 87 78 92 105

Figure S554.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S555.  Gene #58: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
9P LOSS MUTATED 119 48 18
9P LOSS WILD-TYPE 186 199 92

Figure S555.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'MRNA_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00025

Table S556.  Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
9Q LOSS MUTATED 7 5 41 41 19 23 8 5
9Q LOSS WILD-TYPE 14 31 78 55 90 49 12 35

Figure S556.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

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

Table S557.  Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
9Q LOSS MUTATED 36 23 47 35 8
9Q LOSS WILD-TYPE 65 129 67 53 50

Figure S557.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

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

Table S558.  Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
9Q LOSS MUTATED 115 37 15 105 11
9Q LOSS WILD-TYPE 160 370 83 152 32

Figure S558.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

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

Table S559.  Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
9Q LOSS MUTATED 58 26 24 21 56 5
9Q LOSS WILD-TYPE 86 73 189 102 79 54

Figure S559.  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 = 2.4e-05

Table S560.  Gene #59: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
9Q LOSS MUTATED 67 27 24
9Q LOSS WILD-TYPE 84 96 101

Figure S560.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00151 (Fisher's exact test), Q value = 0.0024

Table S561.  Gene #59: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
9Q LOSS MUTATED 11 10 40 10 35 12
9Q LOSS WILD-TYPE 53 36 50 42 81 19

Figure S561.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9q loss' versus 'MRNASEQ_CNMF'

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

Table S562.  Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
9Q LOSS MUTATED 148 113 20
9Q LOSS WILD-TYPE 411 191 192

Figure S562.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S563.  Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
9Q LOSS MUTATED 81 60 3 49 68 20
9Q LOSS WILD-TYPE 208 103 87 241 115 40

Figure S563.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

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

Table S564.  Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
9Q LOSS MUTATED 121 24 52 77
9Q LOSS WILD-TYPE 184 188 217 198

Figure S564.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S565.  Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
9Q LOSS MUTATED 102 58 20 21 20 53
9Q LOSS WILD-TYPE 192 94 225 119 76 81

Figure S565.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S566.  Gene #59: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
9Q LOSS MUTATED 51 57 19 15 24
9Q LOSS WILD-TYPE 129 82 80 96 109

Figure S566.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S567.  Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
9Q LOSS MUTATED 111 41 14
9Q LOSS WILD-TYPE 194 206 96

Figure S567.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

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

Table S568.  Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
10P LOSS MUTATED 61 30 19 53 10
10P LOSS WILD-TYPE 214 377 79 204 33

Figure S568.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.3e-05

Table S569.  Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
10P LOSS MUTATED 35 17 25 9 35 8
10P LOSS WILD-TYPE 109 82 188 114 100 51

Figure S569.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

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

Table S570.  Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
10P LOSS MUTATED 97 63 13
10P LOSS WILD-TYPE 462 241 199

Figure S570.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.3e-05

Table S571.  Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
10P LOSS MUTATED 52 41 4 33 32 11
10P LOSS WILD-TYPE 237 122 86 257 151 49

Figure S571.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.00189 (Fisher's exact test), Q value = 0.0029

Table S572.  Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
10P LOSS MUTATED 58 18 40 54
10P LOSS WILD-TYPE 247 194 229 221

Figure S572.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.0016

Table S573.  Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
10P LOSS MUTATED 56 34 20 21 14 25
10P LOSS WILD-TYPE 238 118 225 119 82 109

Figure S573.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MRNA_CNMF'

P value = 0.00292 (Fisher's exact test), Q value = 0.0043

Table S574.  Gene #61: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
10Q LOSS MUTATED 6 5 28 31 14 16 3 2
10Q LOSS WILD-TYPE 15 31 91 65 95 56 17 38

Figure S574.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00911 (Fisher's exact test), Q value = 0.012

Table S575.  Gene #61: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
10Q LOSS MUTATED 21 21 30 26 7
10Q LOSS WILD-TYPE 80 131 84 62 51

Figure S575.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

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

Table S576.  Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
10Q LOSS MUTATED 74 34 19 89 13
10Q LOSS WILD-TYPE 201 373 79 168 30

Figure S576.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

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

Table S577.  Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
10Q LOSS MUTATED 50 22 26 14 55 7
10Q LOSS WILD-TYPE 94 77 187 109 80 52

Figure S577.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CNMF'

P value = 0.00167 (Fisher's exact test), Q value = 0.0026

Table S578.  Gene #61: '10q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
10Q LOSS MUTATED 47 20 19
10Q LOSS WILD-TYPE 104 103 106

Figure S578.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

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

Table S579.  Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
10Q LOSS MUTATED 114 100 15
10Q LOSS WILD-TYPE 445 204 197

Figure S579.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S580.  Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
10Q LOSS MUTATED 58 54 4 39 60 14
10Q LOSS WILD-TYPE 231 109 86 251 123 46

Figure S580.  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 = 2.4e-05

Table S581.  Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
10Q LOSS MUTATED 93 25 42 64
10Q LOSS WILD-TYPE 212 187 227 211

Figure S581.  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 = 2.4e-05

Table S582.  Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
10Q LOSS MUTATED 74 48 28 17 15 42
10Q LOSS WILD-TYPE 220 104 217 123 81 92

Figure S582.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00018

Table S583.  Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
10Q LOSS MUTATED 47 45 17 10 28
10Q LOSS WILD-TYPE 133 94 82 101 105

Figure S583.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00978 (Fisher's exact test), Q value = 0.013

Table S584.  Gene #61: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
10Q LOSS MUTATED 83 48 16
10Q LOSS WILD-TYPE 222 199 94

Figure S584.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'MRNA_CNMF'

P value = 0.00384 (Fisher's exact test), Q value = 0.0055

Table S585.  Gene #62: '11p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
11P LOSS MUTATED 2 10 42 28 18 28 6 7
11P LOSS WILD-TYPE 19 26 77 68 91 44 14 33

Figure S585.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0157 (Fisher's exact test), Q value = 0.021

Table S586.  Gene #62: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
11P LOSS MUTATED 34 33 40 25 9
11P LOSS WILD-TYPE 67 119 74 63 49

Figure S586.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

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

Table S587.  Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
11P LOSS MUTATED 108 33 28 98 8
11P LOSS WILD-TYPE 167 374 70 159 35

Figure S587.  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 = 2.4e-05

Table S588.  Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
11P LOSS MUTATED 59 31 26 18 45 10
11P LOSS WILD-TYPE 85 68 187 105 90 49

Figure S588.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'RPPA_CNMF'

P value = 0.0405 (Fisher's exact test), Q value = 0.05

Table S589.  Gene #62: '11p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
11P LOSS MUTATED 53 32 27
11P LOSS WILD-TYPE 98 91 98

Figure S589.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'11p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00107 (Fisher's exact test), Q value = 0.0018

Table S590.  Gene #62: '11p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
11P LOSS MUTATED 8 9 33 12 35 15
11P LOSS WILD-TYPE 56 37 57 40 81 16

Figure S590.  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 = 2.4e-05

Table S591.  Gene #62: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
11P LOSS MUTATED 144 104 27
11P LOSS WILD-TYPE 415 200 185

Figure S591.  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 = 2.4e-05

Table S592.  Gene #62: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
11P LOSS MUTATED 78 60 7 53 57 20
11P LOSS WILD-TYPE 211 103 83 237 126 40

Figure S592.  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 = 2.4e-05

Table S593.  Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
11P LOSS MUTATED 107 32 57 71
11P LOSS WILD-TYPE 198 180 212 204

Figure S593.  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 = 2.4e-05

Table S594.  Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
11P LOSS MUTATED 95 52 36 25 17 42
11P LOSS WILD-TYPE 199 100 209 115 79 92

Figure S594.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00315 (Fisher's exact test), Q value = 0.0047

Table S595.  Gene #62: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
11P LOSS MUTATED 49 48 21 18 24
11P LOSS WILD-TYPE 131 91 78 93 109

Figure S595.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0042 (Fisher's exact test), Q value = 0.006

Table S596.  Gene #62: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
11P LOSS MUTATED 92 47 21
11P LOSS WILD-TYPE 213 200 89

Figure S596.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'MRNA_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00018

Table S597.  Gene #63: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
11Q LOSS MUTATED 5 16 65 26 25 27 6 15
11Q LOSS WILD-TYPE 16 20 54 70 84 45 14 25

Figure S597.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S598.  Gene #63: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
11Q LOSS MUTATED 58 49 41 24 13
11Q LOSS WILD-TYPE 43 103 73 64 45

Figure S598.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

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

Table S599.  Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
11Q LOSS MUTATED 168 64 34 89 10
11Q LOSS WILD-TYPE 107 343 64 168 33

Figure S599.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

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

Table S600.  Gene #63: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
11Q LOSS MUTATED 79 44 52 27 41 14
11Q LOSS WILD-TYPE 65 55 161 96 94 45

Figure S600.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00248 (Fisher's exact test), Q value = 0.0037

Table S601.  Gene #63: '11q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
11Q LOSS MUTATED 12 15 31 17 57 13
11Q LOSS WILD-TYPE 52 31 59 35 59 18

Figure S601.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00027

Table S602.  Gene #63: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
11Q LOSS MUTATED 219 93 51
11Q LOSS WILD-TYPE 340 211 161

Figure S602.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.003 (Fisher's exact test), Q value = 0.0044

Table S603.  Gene #63: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
11Q LOSS MUTATED 117 63 18 94 53 18
11Q LOSS WILD-TYPE 172 100 72 196 130 42

Figure S603.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.015

Table S604.  Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
11Q LOSS MUTATED 107 52 93 105
11Q LOSS WILD-TYPE 198 160 176 170

Figure S604.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00085 (Fisher's exact test), Q value = 0.0014

Table S605.  Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
11Q LOSS MUTATED 127 53 62 46 29 40
11Q LOSS WILD-TYPE 167 99 183 94 67 94

Figure S605.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.016

Table S606.  Gene #63: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
11Q LOSS MUTATED 74 49 32 25 37
11Q LOSS WILD-TYPE 106 90 67 86 96

Figure S606.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.028 (Fisher's exact test), Q value = 0.035

Table S607.  Gene #63: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
11Q LOSS MUTATED 116 71 30
11Q LOSS WILD-TYPE 189 176 80

Figure S607.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p loss' versus 'MRNA_CNMF'

P value = 0.00154 (Fisher's exact test), Q value = 0.0024

Table S608.  Gene #64: '12p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
12P LOSS MUTATED 3 7 12 27 8 10 4 3
12P LOSS WILD-TYPE 18 29 107 69 101 62 16 37

Figure S608.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'12p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00153 (Fisher's exact test), Q value = 0.0024

Table S609.  Gene #64: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
12P LOSS MUTATED 9 14 22 23 6
12P LOSS WILD-TYPE 92 138 92 65 52

Figure S609.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

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

Table S610.  Gene #64: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
12P LOSS MUTATED 38 34 11 67 1
12P LOSS WILD-TYPE 237 373 87 190 42

Figure S610.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

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

Table S611.  Gene #64: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
12P LOSS MUTATED 16 10 16 12 43 9
12P LOSS WILD-TYPE 128 89 197 111 92 50

Figure S611.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p loss' versus 'RPPA_CNMF'

P value = 0.00957 (Fisher's exact test), Q value = 0.013

Table S612.  Gene #64: '12p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
12P LOSS MUTATED 34 16 12
12P LOSS WILD-TYPE 117 107 113

Figure S612.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'12p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00537 (Fisher's exact test), Q value = 0.0076

Table S613.  Gene #64: '12p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
12P LOSS MUTATED 12 4 21 9 8 8
12P LOSS WILD-TYPE 52 42 69 43 108 23

Figure S613.  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 = 2.4e-05

Table S614.  Gene #64: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
12P LOSS MUTATED 52 80 18
12P LOSS WILD-TYPE 507 224 194

Figure S614.  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 = 2.4e-05

Table S615.  Gene #64: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
12P LOSS MUTATED 29 25 5 26 50 15
12P LOSS WILD-TYPE 260 138 85 264 133 45

Figure S615.  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 = 2.4e-05

Table S616.  Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
12P LOSS MUTATED 70 17 20 42
12P LOSS WILD-TYPE 235 195 249 233

Figure S616.  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 = 2.4e-05

Table S617.  Gene #64: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
12P LOSS MUTATED 41 34 15 15 7 37
12P LOSS WILD-TYPE 253 118 230 125 89 97

Figure S617.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S618.  Gene #64: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
12P LOSS MUTATED 22 45 9 11 9
12P LOSS WILD-TYPE 158 94 90 100 124

Figure S618.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S619.  Gene #64: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
12P LOSS MUTATED 69 16 11
12P LOSS WILD-TYPE 236 231 99

Figure S619.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'MRNA_CNMF'

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

Table S620.  Gene #65: '12q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
12Q LOSS MUTATED 2 3 7 33 5 5 2 3
12Q LOSS WILD-TYPE 19 33 112 63 104 67 18 37

Figure S620.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'12q loss' versus 'MRNA_CHIERARCHICAL'

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

Table S621.  Gene #65: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
12Q LOSS MUTATED 5 8 15 28 4
12Q LOSS WILD-TYPE 96 144 99 60 54

Figure S621.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

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

Table S622.  Gene #65: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
12Q LOSS MUTATED 20 22 9 78 2
12Q LOSS WILD-TYPE 255 385 89 179 41

Figure S622.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

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

Table S623.  Gene #65: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
12Q LOSS MUTATED 11 9 10 9 55 3
12Q LOSS WILD-TYPE 133 90 203 114 80 56

Figure S623.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q loss' versus 'RPPA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00012

Table S624.  Gene #65: '12q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
12Q LOSS MUTATED 33 9 7
12Q LOSS WILD-TYPE 118 114 118

Figure S624.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'12q loss' versus 'RPPA_CHIERARCHICAL'

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

Table S625.  Gene #65: '12q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
12Q LOSS MUTATED 8 2 28 3 4 4
12Q LOSS WILD-TYPE 56 44 62 49 112 27

Figure S625.  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 = 2.4e-05

Table S626.  Gene #65: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
12Q LOSS MUTATED 32 85 13
12Q LOSS WILD-TYPE 527 219 199

Figure S626.  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 = 2.4e-05

Table S627.  Gene #65: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
12Q LOSS MUTATED 16 16 3 19 63 13
12Q LOSS WILD-TYPE 273 147 87 271 120 47

Figure S627.  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 = 2.4e-05

Table S628.  Gene #65: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
12Q LOSS MUTATED 77 15 11 25
12Q LOSS WILD-TYPE 228 197 258 250

Figure S628.  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 = 2.4e-05

Table S629.  Gene #65: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
12Q LOSS MUTATED 30 30 11 6 4 47
12Q LOSS WILD-TYPE 264 122 234 134 92 87

Figure S629.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S630.  Gene #65: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
12Q LOSS MUTATED 15 53 6 10 11
12Q LOSS WILD-TYPE 165 86 93 101 122

Figure S630.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S631.  Gene #65: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
12Q LOSS MUTATED 72 16 7
12Q LOSS WILD-TYPE 233 231 103

Figure S631.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'MRNA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00012

Table S632.  Gene #66: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
13Q LOSS MUTATED 7 14 62 51 30 38 9 8
13Q LOSS WILD-TYPE 14 22 57 45 79 34 11 32

Figure S632.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q loss' versus 'MRNA_CHIERARCHICAL'

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

Table S633.  Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
13Q LOSS MUTATED 58 40 62 47 12
13Q LOSS WILD-TYPE 43 112 52 41 46

Figure S633.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

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

Table S634.  Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
13Q LOSS MUTATED 148 77 49 133 26
13Q LOSS WILD-TYPE 127 330 49 124 17

Figure S634.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

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

Table S635.  Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
13Q LOSS MUTATED 67 48 64 39 73 12
13Q LOSS WILD-TYPE 77 51 149 84 62 47

Figure S635.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.00078

Table S636.  Gene #66: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
13Q LOSS MUTATED 17 21 50 15 59 10
13Q LOSS WILD-TYPE 47 25 40 37 57 21

Figure S636.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'13q loss' versus 'MRNASEQ_CNMF'

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

Table S637.  Gene #66: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
13Q LOSS MUTATED 220 161 51
13Q LOSS WILD-TYPE 339 143 161

Figure S637.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S638.  Gene #66: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
13Q LOSS MUTATED 117 83 18 92 98 24
13Q LOSS WILD-TYPE 172 80 72 198 85 36

Figure S638.  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 = 2.4e-05

Table S639.  Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
13Q LOSS MUTATED 159 52 98 117
13Q LOSS WILD-TYPE 146 160 171 158

Figure S639.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S640.  Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
13Q LOSS MUTATED 147 68 66 43 30 72
13Q LOSS WILD-TYPE 147 84 179 97 66 62

Figure S640.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S641.  Gene #66: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
13Q LOSS MUTATED 78 74 29 24 44
13Q LOSS WILD-TYPE 102 65 70 87 89

Figure S641.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.00076

Table S642.  Gene #66: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
13Q LOSS MUTATED 139 78 32
13Q LOSS WILD-TYPE 166 169 78

Figure S642.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

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

Table S643.  Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
14Q LOSS MUTATED 3 1 30 50 7 14 9 5
14Q LOSS WILD-TYPE 18 35 89 46 102 58 11 35

Figure S643.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

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

Table S644.  Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
14Q LOSS MUTATED 24 17 29 47 2
14Q LOSS WILD-TYPE 77 135 85 41 56

Figure S644.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

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

Table S645.  Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
14Q LOSS MUTATED 61 36 21 138 10
14Q LOSS WILD-TYPE 214 371 77 119 33

Figure S645.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

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

Table S646.  Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
14Q LOSS MUTATED 36 26 21 27 80 6
14Q LOSS WILD-TYPE 108 73 192 96 55 53

Figure S646.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S647.  Gene #67: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
14Q LOSS MUTATED 55 24 16
14Q LOSS WILD-TYPE 96 99 109

Figure S647.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

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

Table S648.  Gene #67: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
14Q LOSS MUTATED 4 9 44 10 23 5
14Q LOSS WILD-TYPE 60 37 46 42 93 26

Figure S648.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

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

Table S649.  Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
14Q LOSS MUTATED 100 144 21
14Q LOSS WILD-TYPE 459 160 191

Figure S649.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S650.  Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
14Q LOSS MUTATED 42 55 3 44 109 12
14Q LOSS WILD-TYPE 247 108 87 246 74 48

Figure S650.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

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

Table S651.  Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
14Q LOSS MUTATED 143 29 35 52
14Q LOSS WILD-TYPE 162 183 234 223

Figure S651.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S652.  Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
14Q LOSS MUTATED 61 54 30 19 9 86
14Q LOSS WILD-TYPE 233 98 215 121 87 48

Figure S652.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S653.  Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
14Q LOSS MUTATED 35 78 19 17 24
14Q LOSS WILD-TYPE 145 61 80 94 109

Figure S653.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S654.  Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
14Q LOSS MUTATED 113 44 16
14Q LOSS WILD-TYPE 192 203 94

Figure S654.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'MRNA_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00018

Table S655.  Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
15Q LOSS MUTATED 4 9 32 45 22 33 8 6
15Q LOSS WILD-TYPE 17 27 87 51 87 39 12 34

Figure S655.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

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

Table S656.  Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
15Q LOSS MUTATED 27 29 48 43 12
15Q LOSS WILD-TYPE 74 123 66 45 46

Figure S656.  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 = 2.4e-05

Table S657.  Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
15Q LOSS MUTATED 87 41 42 136 14
15Q LOSS WILD-TYPE 188 366 56 121 29

Figure S657.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

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

Table S658.  Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
15Q LOSS MUTATED 51 29 35 29 74 9
15Q LOSS WILD-TYPE 93 70 178 94 61 50

Figure S658.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'RPPA_CNMF'

P value = 0.0024 (Fisher's exact test), Q value = 0.0036

Table S659.  Gene #68: '15q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
15Q LOSS MUTATED 67 32 36
15Q LOSS WILD-TYPE 84 91 89

Figure S659.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'15q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00889 (Fisher's exact test), Q value = 0.012

Table S660.  Gene #68: '15q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
15Q LOSS MUTATED 19 8 44 16 38 10
15Q LOSS WILD-TYPE 45 38 46 36 78 21

Figure S660.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'15q loss' versus 'MRNASEQ_CNMF'

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

Table S661.  Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
15Q LOSS MUTATED 153 139 25
15Q LOSS WILD-TYPE 406 165 187

Figure S661.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S662.  Gene #68: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
15Q LOSS MUTATED 74 66 8 58 94 17
15Q LOSS WILD-TYPE 215 97 82 232 89 43

Figure S662.  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 = 2.4e-05

Table S663.  Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
15Q LOSS MUTATED 135 28 56 92
15Q LOSS WILD-TYPE 170 184 213 183

Figure S663.  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 = 2.4e-05

Table S664.  Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
15Q LOSS MUTATED 94 63 28 39 16 71
15Q LOSS WILD-TYPE 200 89 217 101 80 63

Figure S664.  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 = 2.4e-05

Table S665.  Gene #68: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
15Q LOSS MUTATED 55 71 23 21 21
15Q LOSS WILD-TYPE 125 68 76 90 112

Figure S665.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S666.  Gene #68: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
15Q LOSS MUTATED 114 47 30
15Q LOSS WILD-TYPE 191 200 80

Figure S666.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.00057

Table S667.  Gene #69: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
16P LOSS MUTATED 41 49 11 64 8
16P LOSS WILD-TYPE 234 358 87 193 35

Figure S667.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.00065

Table S668.  Gene #69: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
16P LOSS MUTATED 19 16 26 24 39 4
16P LOSS WILD-TYPE 125 83 187 99 96 55

Figure S668.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'RPPA_CNMF'

P value = 0.00993 (Fisher's exact test), Q value = 0.013

Table S669.  Gene #69: '16p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
16P LOSS MUTATED 30 9 19
16P LOSS WILD-TYPE 121 114 106

Figure S669.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.00095

Table S670.  Gene #69: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
16P LOSS MUTATED 77 70 25
16P LOSS WILD-TYPE 482 234 187

Figure S670.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00165 (Fisher's exact test), Q value = 0.0026

Table S671.  Gene #69: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
16P LOSS MUTATED 37 23 14 41 50 7
16P LOSS WILD-TYPE 252 140 76 249 133 53

Figure S671.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 0.00148 (Fisher's exact test), Q value = 0.0023

Table S672.  Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
16P LOSS MUTATED 70 30 40 31
16P LOSS WILD-TYPE 235 182 229 244

Figure S672.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.00087

Table S673.  Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
16P LOSS MUTATED 41 25 32 21 11 41
16P LOSS WILD-TYPE 253 127 213 119 85 93

Figure S673.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00035

Table S674.  Gene #69: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
16P LOSS MUTATED 22 42 12 13 21
16P LOSS WILD-TYPE 158 97 87 98 112

Figure S674.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0302 (Fisher's exact test), Q value = 0.038

Table S675.  Gene #69: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
16P LOSS MUTATED 62 37 11
16P LOSS WILD-TYPE 243 210 99

Figure S675.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'MRNA_CNMF'

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

Table S676.  Gene #70: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
16Q LOSS MUTATED 12 21 63 28 81 38 11 30
16Q LOSS WILD-TYPE 9 15 56 68 28 34 9 10

Figure S676.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q loss' versus 'MRNA_CHIERARCHICAL'

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

Table S677.  Gene #70: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
16Q LOSS MUTATED 58 102 58 24 42
16Q LOSS WILD-TYPE 43 50 56 64 16

Figure S677.  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 = 2.4e-05

Table S678.  Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
16Q LOSS MUTATED 141 243 75 108 26
16Q LOSS WILD-TYPE 134 164 23 149 17

Figure S678.  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 = 2.4e-05

Table S679.  Gene #70: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
16Q LOSS MUTATED 65 66 153 55 58 28
16Q LOSS WILD-TYPE 79 33 60 68 77 31

Figure S679.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'RPPA_CNMF'

P value = 0.00166 (Fisher's exact test), Q value = 0.0026

Table S680.  Gene #70: '16q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
16Q LOSS MUTATED 63 68 79
16Q LOSS WILD-TYPE 88 55 46

Figure S680.  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 = 2.4e-05

Table S681.  Gene #70: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
16Q LOSS MUTATED 47 25 28 29 70 11
16Q LOSS WILD-TYPE 17 21 62 23 46 20

Figure S681.  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 = 2.4e-05

Table S682.  Gene #70: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
16Q LOSS MUTATED 343 115 133
16Q LOSS WILD-TYPE 216 189 79

Figure S682.  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 = 2.4e-05

Table S683.  Gene #70: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
16Q LOSS MUTATED 167 86 64 193 64 17
16Q LOSS WILD-TYPE 122 77 26 97 119 43

Figure S683.  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 = 2.4e-05

Table S684.  Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
16Q LOSS MUTATED 113 129 181 160
16Q LOSS WILD-TYPE 192 83 88 115

Figure S684.  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 = 2.4e-05

Table S685.  Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
16Q LOSS MUTATED 162 51 158 109 48 55
16Q LOSS WILD-TYPE 132 101 87 31 48 79

Figure S685.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.0021

Table S686.  Gene #70: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
16Q LOSS MUTATED 103 55 63 61 80
16Q LOSS WILD-TYPE 77 84 36 50 53

Figure S686.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00016

Table S687.  Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
16Q LOSS MUTATED 139 153 70
16Q LOSS WILD-TYPE 166 94 40

Figure S687.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

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

Table S688.  Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
17P LOSS MUTATED 13 23 66 61 30 57 12 21
17P LOSS WILD-TYPE 8 13 53 35 79 15 8 19

Figure S688.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

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

Table S689.  Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
17P LOSS MUTATED 57 76 85 54 11
17P LOSS WILD-TYPE 44 76 29 34 47

Figure S689.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

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

Table S690.  Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
17P LOSS MUTATED 182 144 42 191 20
17P LOSS WILD-TYPE 93 263 56 66 23

Figure S690.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

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

Table S691.  Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
17P LOSS MUTATED 101 63 84 51 83 23
17P LOSS WILD-TYPE 43 36 129 72 52 36

Figure S691.  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 = 2.4e-05

Table S692.  Gene #71: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
17P LOSS MUTATED 111 59 50
17P LOSS WILD-TYPE 40 64 75

Figure S692.  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 = 2.4e-05

Table S693.  Gene #71: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
17P LOSS MUTATED 21 15 61 29 71 23
17P LOSS WILD-TYPE 43 31 29 23 45 8

Figure S693.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17p loss' versus 'MRNASEQ_CNMF'

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

Table S694.  Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
17P LOSS MUTATED 281 205 90
17P LOSS WILD-TYPE 278 99 122

Figure S694.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S695.  Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
17P LOSS MUTATED 125 122 41 135 109 44
17P LOSS WILD-TYPE 164 41 49 155 74 16

Figure S695.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

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

Table S696.  Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
17P LOSS MUTATED 202 86 131 150
17P LOSS WILD-TYPE 103 126 138 125

Figure S696.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S697.  Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
17P LOSS MUTATED 178 92 104 78 27 90
17P LOSS WILD-TYPE 116 60 141 62 69 44

Figure S697.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MRNA_CNMF'

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

Table S698.  Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
17Q LOSS MUTATED 4 4 23 50 12 35 4 12
17Q LOSS WILD-TYPE 17 32 96 46 97 37 16 28

Figure S698.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q loss' versus 'MRNA_CHIERARCHICAL'

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

Table S699.  Gene #72: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
17Q LOSS MUTATED 21 26 48 44 5
17Q LOSS WILD-TYPE 80 126 66 44 53

Figure S699.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

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

Table S700.  Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
17Q LOSS MUTATED 62 53 25 130 5
17Q LOSS WILD-TYPE 213 354 73 127 38

Figure S700.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

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

Table S701.  Gene #72: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
17Q LOSS MUTATED 40 18 17 34 64 4
17Q LOSS WILD-TYPE 104 81 196 89 71 55

Figure S701.  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 = 2.4e-05

Table S702.  Gene #72: '17q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
17Q LOSS MUTATED 72 29 17
17Q LOSS WILD-TYPE 79 94 108

Figure S702.  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 = 2.4e-05

Table S703.  Gene #72: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
17Q LOSS MUTATED 8 10 50 11 24 15
17Q LOSS WILD-TYPE 56 36 40 41 92 16

Figure S703.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17q loss' versus 'MRNASEQ_CNMF'

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

Table S704.  Gene #72: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
17Q LOSS MUTATED 98 141 34
17Q LOSS WILD-TYPE 461 163 178

Figure S704.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S705.  Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
17Q LOSS MUTATED 32 58 14 53 83 33
17Q LOSS WILD-TYPE 257 105 76 237 100 27

Figure S705.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

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

Table S706.  Gene #72: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
17Q LOSS MUTATED 126 38 46 60
17Q LOSS WILD-TYPE 179 174 223 215

Figure S706.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S707.  Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
17Q LOSS MUTATED 73 59 41 24 5 68
17Q LOSS WILD-TYPE 221 93 204 116 91 66

Figure S707.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00016

Table S708.  Gene #72: '17q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
17Q LOSS MUTATED 37 58 16 23 32
17Q LOSS WILD-TYPE 143 81 83 88 101

Figure S708.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00222 (Fisher's exact test), Q value = 0.0034

Table S709.  Gene #72: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
17Q LOSS MUTATED 95 53 18
17Q LOSS WILD-TYPE 210 194 92

Figure S709.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'MRNA_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00039

Table S710.  Gene #73: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
18P LOSS MUTATED 6 11 35 27 19 38 9 13
18P LOSS WILD-TYPE 15 25 84 69 90 34 11 27

Figure S710.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.00076

Table S711.  Gene #73: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
18P LOSS MUTATED 28 39 55 24 12
18P LOSS WILD-TYPE 73 113 59 64 46

Figure S711.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

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

Table S712.  Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
18P LOSS MUTATED 109 65 38 97 11
18P LOSS WILD-TYPE 166 342 60 160 32

Figure S712.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

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

Table S713.  Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
18P LOSS MUTATED 63 42 43 33 39 10
18P LOSS WILD-TYPE 81 57 170 90 96 49

Figure S713.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.00052

Table S714.  Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
18P LOSS MUTATED 161 114 45
18P LOSS WILD-TYPE 398 190 167

Figure S714.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S715.  Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
18P LOSS MUTATED 66 87 14 79 50 24
18P LOSS WILD-TYPE 223 76 76 211 133 36

Figure S715.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00016

Table S716.  Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
18P LOSS MUTATED 111 45 64 97
18P LOSS WILD-TYPE 194 167 205 178

Figure S716.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S717.  Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
18P LOSS MUTATED 119 53 56 38 17 34
18P LOSS WILD-TYPE 175 99 189 102 79 100

Figure S717.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MRNA_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00039

Table S718.  Gene #74: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
18Q LOSS MUTATED 5 11 34 26 19 38 7 9
18Q LOSS WILD-TYPE 16 25 85 70 90 34 13 31

Figure S718.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 4e-04

Table S719.  Gene #74: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
18Q LOSS MUTATED 27 34 53 24 11
18Q LOSS WILD-TYPE 74 118 61 64 47

Figure S719.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

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

Table S720.  Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
18Q LOSS MUTATED 107 64 39 101 10
18Q LOSS WILD-TYPE 168 343 59 156 33

Figure S720.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

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

Table S721.  Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
18Q LOSS MUTATED 64 41 44 31 46 9
18Q LOSS WILD-TYPE 80 58 169 92 89 50

Figure S721.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.014

Table S722.  Gene #74: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
18Q LOSS MUTATED 57 27 32
18Q LOSS WILD-TYPE 94 96 93

Figure S722.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

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

Table S723.  Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
18Q LOSS MUTATED 160 118 42
18Q LOSS WILD-TYPE 399 186 170

Figure S723.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S724.  Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
18Q LOSS MUTATED 61 88 15 74 56 26
18Q LOSS WILD-TYPE 228 75 75 216 127 34

Figure S724.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 6.4e-05

Table S725.  Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
18Q LOSS MUTATED 115 45 64 92
18Q LOSS WILD-TYPE 190 167 205 183

Figure S725.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S726.  Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
18Q LOSS MUTATED 112 60 55 35 15 39
18Q LOSS WILD-TYPE 182 92 190 105 81 95

Figure S726.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S727.  Gene #75: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
19P LOSS MUTATED 2 6 30 20 8 25 1 2
19P LOSS WILD-TYPE 19 30 89 76 101 47 19 38

Figure S727.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p loss' versus 'MRNA_CHIERARCHICAL'

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

Table S728.  Gene #75: '19p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
19P LOSS MUTATED 29 13 32 18 2
19P LOSS WILD-TYPE 72 139 82 70 56

Figure S728.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

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

Table S729.  Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
19P LOSS MUTATED 93 20 9 66 5
19P LOSS WILD-TYPE 182 387 89 191 38

Figure S729.  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 = 2.4e-05

Table S730.  Gene #75: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
19P LOSS MUTATED 53 13 15 15 34 3
19P LOSS WILD-TYPE 91 86 198 108 101 56

Figure S730.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'RPPA_CNMF'

P value = 0.0416 (Fisher's exact test), Q value = 0.051

Table S731.  Gene #75: '19p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
19P LOSS MUTATED 38 17 20
19P LOSS WILD-TYPE 113 106 105

Figure S731.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'19p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00096 (Fisher's exact test), Q value = 0.0016

Table S732.  Gene #75: '19p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
19P LOSS MUTATED 3 6 21 7 27 11
19P LOSS WILD-TYPE 61 40 69 45 89 20

Figure S732.  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 = 2.4e-05

Table S733.  Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
19P LOSS MUTATED 102 79 11
19P LOSS WILD-TYPE 457 225 201

Figure S733.  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 = 2.4e-05

Table S734.  Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
19P LOSS MUTATED 54 56 3 25 44 10
19P LOSS WILD-TYPE 235 107 87 265 139 50

Figure S734.  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 = 2.4e-05

Table S735.  Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
19P LOSS MUTATED 87 13 42 46
19P LOSS WILD-TYPE 218 199 227 229

Figure S735.  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 = 2.4e-05

Table S736.  Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
19P LOSS MUTATED 71 38 13 14 19 33
19P LOSS WILD-TYPE 223 114 232 126 77 101

Figure S736.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S737.  Gene #75: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
19P LOSS MUTATED 37 41 13 6 20
19P LOSS WILD-TYPE 143 98 86 105 113

Figure S737.  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 = 2.4e-05

Table S738.  Gene #75: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
19P LOSS MUTATED 77 34 6
19P LOSS WILD-TYPE 228 213 104

Figure S738.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'MRNA_CNMF'

P value = 0.00491 (Fisher's exact test), Q value = 0.007

Table S739.  Gene #76: '19q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
19Q LOSS MUTATED 3 6 20 13 8 21 2 2
19Q LOSS WILD-TYPE 18 30 99 83 101 51 18 38

Figure S739.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S740.  Gene #76: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
19Q LOSS MUTATED 23 10 29 11 2
19Q LOSS WILD-TYPE 78 142 85 77 56

Figure S740.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

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

Table S741.  Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
19Q LOSS MUTATED 84 15 6 50 6
19Q LOSS WILD-TYPE 191 392 92 207 37

Figure S741.  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 = 2.4e-05

Table S742.  Gene #76: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
19Q LOSS MUTATED 41 15 12 17 27 2
19Q LOSS WILD-TYPE 103 84 201 106 108 57

Figure S742.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0265 (Fisher's exact test), Q value = 0.034

Table S743.  Gene #76: '19q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
19Q LOSS MUTATED 3 4 15 6 22 8
19Q LOSS WILD-TYPE 61 42 75 46 94 23

Figure S743.  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 = 2.4e-05

Table S744.  Gene #76: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
19Q LOSS MUTATED 87 65 8
19Q LOSS WILD-TYPE 472 239 204

Figure S744.  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 = 2.4e-05

Table S745.  Gene #76: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
19Q LOSS MUTATED 53 42 2 18 34 11
19Q LOSS WILD-TYPE 236 121 88 272 149 49

Figure S745.  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 = 2.4e-05

Table S746.  Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
19Q LOSS MUTATED 71 11 35 40
19Q LOSS WILD-TYPE 234 201 234 235

Figure S746.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S747.  Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
19Q LOSS MUTATED 59 25 12 12 20 29
19Q LOSS WILD-TYPE 235 127 233 128 76 105

Figure S747.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.00054

Table S748.  Gene #76: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
19Q LOSS MUTATED 30 34 10 6 16
19Q LOSS WILD-TYPE 150 105 89 105 117

Figure S748.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S749.  Gene #76: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
19Q LOSS MUTATED 65 27 4
19Q LOSS WILD-TYPE 240 220 106

Figure S749.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'MRNA_CNMF'

P value = 0.00321 (Fisher's exact test), Q value = 0.0047

Table S750.  Gene #77: '20p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
20P LOSS MUTATED 1 2 10 16 2 7 1 0
20P LOSS WILD-TYPE 20 34 109 80 107 65 19 40

Figure S750.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00035

Table S751.  Gene #77: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
20P LOSS MUTATED 9 4 12 14 0
20P LOSS WILD-TYPE 92 148 102 74 58

Figure S751.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

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

Table S752.  Gene #77: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
20P LOSS MUTATED 28 8 6 48 3
20P LOSS WILD-TYPE 247 399 92 209 40

Figure S752.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

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

Table S753.  Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
20P LOSS MUTATED 12 9 11 3 33 1
20P LOSS WILD-TYPE 132 90 202 120 102 58

Figure S753.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p loss' versus 'MRNASEQ_CNMF'

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

Table S754.  Gene #77: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
20P LOSS MUTATED 36 54 3
20P LOSS WILD-TYPE 523 250 209

Figure S754.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S755.  Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
20P LOSS MUTATED 19 22 2 5 41 4
20P LOSS WILD-TYPE 270 141 88 285 142 56

Figure S755.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_CNMF'

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

Table S756.  Gene #77: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
20P LOSS MUTATED 49 7 16 15
20P LOSS WILD-TYPE 256 205 253 260

Figure S756.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S757.  Gene #77: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
20P LOSS MUTATED 27 12 7 4 5 32
20P LOSS WILD-TYPE 267 140 238 136 91 102

Figure S757.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S758.  Gene #77: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
20P LOSS MUTATED 8 28 6 4 5
20P LOSS WILD-TYPE 172 111 93 107 128

Figure S758.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00016

Table S759.  Gene #77: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
20P LOSS MUTATED 37 13 1
20P LOSS WILD-TYPE 268 234 109

Figure S759.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q loss' versus 'MRNA_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.017

Table S760.  Gene #78: '20q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
20Q LOSS MUTATED 1 2 3 11 1 4 0 0
20Q LOSS WILD-TYPE 20 34 116 85 108 68 20 40

Figure S760.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00502 (Fisher's exact test), Q value = 0.0071

Table S761.  Gene #78: '20q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
20Q LOSS MUTATED 3 3 6 10 0
20Q LOSS WILD-TYPE 98 149 108 78 58

Figure S761.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q loss' versus 'CN_CNMF'

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

Table S762.  Gene #78: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
20Q LOSS MUTATED 13 3 5 32 2
20Q LOSS WILD-TYPE 262 404 93 225 41

Figure S762.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

'20q loss' versus 'METHLYATION_CNMF'

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

Table S763.  Gene #78: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
20Q LOSS MUTATED 5 2 6 2 26 0
20Q LOSS WILD-TYPE 139 97 207 121 109 59

Figure S763.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q loss' versus 'RPPA_CNMF'

P value = 0.0443 (Fisher's exact test), Q value = 0.054

Table S764.  Gene #78: '20q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
20Q LOSS MUTATED 10 2 2
20Q LOSS WILD-TYPE 141 121 123

Figure S764.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q loss' versus 'MRNASEQ_CNMF'

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

Table S765.  Gene #78: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
20Q LOSS MUTATED 16 36 3
20Q LOSS WILD-TYPE 543 268 209

Figure S765.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S766.  Gene #78: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
20Q LOSS MUTATED 8 9 2 3 31 2
20Q LOSS WILD-TYPE 281 154 88 287 152 58

Figure S766.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 3e-04

Table S767.  Gene #78: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
20Q LOSS MUTATED 30 6 8 8
20Q LOSS WILD-TYPE 275 206 261 267

Figure S767.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S768.  Gene #78: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
20Q LOSS MUTATED 11 10 6 1 1 23
20Q LOSS WILD-TYPE 283 142 239 139 95 111

Figure S768.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S769.  Gene #78: '20q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
20Q LOSS MUTATED 2 22 2 2 3
20Q LOSS WILD-TYPE 178 117 97 109 130

Figure S769.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00037

Table S770.  Gene #78: '20q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
20Q LOSS MUTATED 25 6 0
20Q LOSS WILD-TYPE 280 241 110

Figure S770.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'MRNA_CNMF'

P value = 0.0337 (Fisher's exact test), Q value = 0.042

Table S771.  Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
21Q LOSS MUTATED 2 9 28 13 10 17 2 5
21Q LOSS WILD-TYPE 19 27 91 83 99 55 18 35

Figure S771.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q loss' versus 'CN_CNMF'

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

Table S772.  Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
21Q LOSS MUTATED 79 22 17 53 9
21Q LOSS WILD-TYPE 196 385 81 204 34

Figure S772.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.00261 (Fisher's exact test), Q value = 0.0039

Table S773.  Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
21Q LOSS MUTATED 37 20 24 15 24 5
21Q LOSS WILD-TYPE 107 79 189 108 111 54

Figure S773.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 0.023

Table S774.  Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
21Q LOSS MUTATED 103 54 22
21Q LOSS WILD-TYPE 456 250 190

Figure S774.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00383 (Fisher's exact test), Q value = 0.0055

Table S775.  Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
21Q LOSS MUTATED 50 41 6 40 33 9
21Q LOSS WILD-TYPE 239 122 84 250 150 51

Figure S775.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.015

Table S776.  Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
21Q LOSS MUTATED 64 22 40 48
21Q LOSS WILD-TYPE 241 190 229 227

Figure S776.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00632 (Fisher's exact test), Q value = 0.0088

Table S777.  Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
21Q LOSS MUTATED 63 29 25 23 10 24
21Q LOSS WILD-TYPE 231 123 220 117 86 110

Figure S777.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.025

Table S778.  Gene #79: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
21Q LOSS MUTATED 41 24 13 10 17
21Q LOSS WILD-TYPE 139 115 86 101 116

Figure S778.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0052 (Fisher's exact test), Q value = 0.0074

Table S779.  Gene #80: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
22Q LOSS MUTATED 62 72 46 34 22
22Q LOSS WILD-TYPE 39 80 68 54 36

Figure S779.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

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

Table S780.  Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
22Q LOSS MUTATED 150 137 61 113 21
22Q LOSS WILD-TYPE 125 270 37 144 22

Figure S780.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00021

Table S781.  Gene #80: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
22Q LOSS MUTATED 88 45 85 44 62 18
22Q LOSS WILD-TYPE 56 54 128 79 73 41

Figure S781.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00253 (Fisher's exact test), Q value = 0.0038

Table S782.  Gene #80: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
22Q LOSS MUTATED 37 26 33 23 62 7
22Q LOSS WILD-TYPE 27 20 57 29 54 24

Figure S782.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 2e-04

Table S783.  Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
22Q LOSS MUTATED 285 113 83
22Q LOSS WILD-TYPE 274 191 129

Figure S783.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.3e-05

Table S784.  Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
22Q LOSS MUTATED 137 92 33 135 70 14
22Q LOSS WILD-TYPE 152 71 57 155 113 46

Figure S784.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 0.00319 (Fisher's exact test), Q value = 0.0047

Table S785.  Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
22Q LOSS MUTATED 129 75 138 130
22Q LOSS WILD-TYPE 176 137 131 145

Figure S785.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.00095

Table S786.  Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
22Q LOSS MUTATED 160 60 92 69 38 53
22Q LOSS WILD-TYPE 134 92 153 71 58 81

Figure S786.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00376 (Fisher's exact test), Q value = 0.0054

Table S787.  Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
22Q LOSS MUTATED 102 58 45 40 53
22Q LOSS WILD-TYPE 78 81 54 71 80

Figure S787.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'MRNA_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 2e-04

Table S788.  Gene #81: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
XP LOSS MUTATED 2 7 29 29 9 17 0 3
XP LOSS WILD-TYPE 19 29 90 67 100 55 20 37

Figure S788.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00021

Table S789.  Gene #81: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
XP LOSS MUTATED 28 17 21 26 4
XP LOSS WILD-TYPE 73 135 93 62 54

Figure S789.  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 = 2.4e-05

Table S790.  Gene #81: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
XP LOSS MUTATED 75 23 14 73 5
XP LOSS WILD-TYPE 200 384 84 184 38

Figure S790.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

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

Table S791.  Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
XP LOSS MUTATED 39 21 19 10 32 8
XP LOSS WILD-TYPE 105 78 194 113 103 51

Figure S791.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp loss' versus 'RPPA_CNMF'

P value = 0.00216 (Fisher's exact test), Q value = 0.0033

Table S792.  Gene #81: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
XP LOSS MUTATED 42 14 21
XP LOSS WILD-TYPE 109 109 104

Figure S792.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'xp loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.00058

Table S793.  Gene #81: 'xp loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
XP LOSS MUTATED 7 1 27 9 25 8
XP LOSS WILD-TYPE 57 45 63 43 91 23

Figure S793.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xp loss' versus 'MRNASEQ_CNMF'

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

Table S794.  Gene #81: 'xp loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
XP LOSS MUTATED 96 76 16
XP LOSS WILD-TYPE 463 228 196

Figure S794.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S795.  Gene #81: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
XP LOSS MUTATED 59 36 3 32 50 8
XP LOSS WILD-TYPE 230 127 87 258 133 52

Figure S795.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 6.4e-05

Table S796.  Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
XP LOSS MUTATED 76 17 43 48
XP LOSS WILD-TYPE 229 195 226 227

Figure S796.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.4e-05

Table S797.  Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
XP LOSS MUTATED 64 24 24 16 17 39
XP LOSS WILD-TYPE 230 128 221 124 79 95

Figure S797.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0055 (Fisher's exact test), Q value = 0.0077

Table S798.  Gene #81: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
XP LOSS MUTATED 36 34 13 9 20
XP LOSS WILD-TYPE 144 105 86 102 113

Figure S798.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00309 (Fisher's exact test), Q value = 0.0046

Table S799.  Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
XP LOSS MUTATED 68 32 12
XP LOSS WILD-TYPE 237 215 98

Figure S799.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.002 (Fisher's exact test), Q value = 0.0031

Table S800.  Gene #82: 'xq loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 101 152 114 88 58
XQ LOSS MUTATED 29 15 24 17 7
XQ LOSS WILD-TYPE 72 137 90 71 51

Figure S800.  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 = 2.4e-05

Table S801.  Gene #82: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 275 407 98 257 43
XQ LOSS MUTATED 73 25 16 71 5
XQ LOSS WILD-TYPE 202 382 82 186 38

Figure S801.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

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

Table S802.  Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 144 99 213 123 135 59
XQ LOSS MUTATED 42 25 22 8 31 7
XQ LOSS WILD-TYPE 102 74 191 115 104 52

Figure S802.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CNMF'

P value = 0.0455 (Fisher's exact test), Q value = 0.056

Table S803.  Gene #82: 'xq loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 123 125
XQ LOSS MUTATED 36 15 24
XQ LOSS WILD-TYPE 115 108 101

Figure S803.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0153 (Fisher's exact test), Q value = 0.02

Table S804.  Gene #82: 'xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 64 46 90 52 116 31
XQ LOSS MUTATED 8 2 22 8 28 7
XQ LOSS WILD-TYPE 56 44 68 44 88 24

Figure S804.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00025

Table S805.  Gene #82: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 559 304 212
XQ LOSS MUTATED 102 69 18
XQ LOSS WILD-TYPE 457 235 194

Figure S805.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S806.  Gene #82: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 289 163 90 290 183 60
XQ LOSS MUTATED 58 44 4 36 41 6
XQ LOSS WILD-TYPE 231 119 86 254 142 54

Figure S806.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.3e-05

Table S807.  Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 305 212 269 275
XQ LOSS MUTATED 71 16 47 53
XQ LOSS WILD-TYPE 234 196 222 222

Figure S807.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00068 (Fisher's exact test), Q value = 0.0011

Table S808.  Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 152 245 140 96 134
XQ LOSS MUTATED 69 23 26 19 18 32
XQ LOSS WILD-TYPE 225 129 219 121 78 102

Figure S808.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0018 (Fisher's exact test), Q value = 0.0028

Table S809.  Gene #82: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 180 139 99 111 133
XQ LOSS MUTATED 41 32 15 8 19
XQ LOSS WILD-TYPE 139 107 84 103 114

Figure S809.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00167 (Fisher's exact test), Q value = 0.0026

Table S810.  Gene #82: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 305 247 110
XQ LOSS MUTATED 70 34 11
XQ LOSS WILD-TYPE 235 213 99

Figure S810.  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/BRCA-TP/20146428/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BRCA-TP/20125499/BRCA-TP.transferedmergedcluster.txt

  • Number of patients = 1080

  • Number of significantly arm-level cnvs = 82

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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