Correlation between copy number variations of arm-level result and molecular subtypes
Breast Invasive Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1G16058
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1G16058
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 'CN_CNMF',  'MRNASEQ_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',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 3q 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'.

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

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

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

  • 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', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • 8q 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'.

  • 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',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

  • 12p 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'.

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

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

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

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

  • 16p 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'.

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

  • 17p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

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

  • 1q loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • 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 'CN_CNMF',  'METHLYATION_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_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_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • 7q 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'.

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

  • 8q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 9p 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'.

  • 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', and 'MIRSEQ_CNMF'.

  • 10q 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'.

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

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

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

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

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

  • 16q 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'.

  • 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',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 18q 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'.

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

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

  • 20p 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'.

  • 20q 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'.

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

  • 22q loss cnv correlated to 'MRNA_CNMF',  'CN_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_CNMF',  '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 227 (21%) 853 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) 		0.00107
(0.00177)
2p gain 122 (11%) 958 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) 		2e-05
(4.45e-05)
2q gain 73 (7%) 1007 1e-05
(2.35e-05) 		2e-05
(4.45e-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) 		0.00835
(0.0116)
3q gain 213 (20%) 867 0.00515
(0.00745) 		0.0121
(0.0163) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		9e-05
(0.000178) 		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) 		0.00049
(0.000867)
6p gain 208 (19%) 872 1e-05
(2.35e-05) 		0.0002
(0.000371) 		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)
6q gain 149 (14%) 931 1e-05
(2.35e-05) 		0.00119
(0.00195) 		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)
8q gain 530 (49%) 550 0.00564
(0.00811) 		0.0392
(0.0482) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0105
(0.0143) 		0.00078
(0.00132) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
9p gain 139 (13%) 941 0.00022
(0.000405) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00016
(0.000303) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00013
(0.000252) 		1e-05
(2.35e-05) 		0.00066
(0.00114) 		0.049
(0.0595)
10p gain 208 (19%) 872 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)
12p gain 225 (21%) 855 0.00016
(0.000303) 		0.0249
(0.0316) 		1e-05
(2.35e-05) 		6e-05
(0.000122) 		0.00332
(0.00501) 		0.0116
(0.0157) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		6e-05
(0.000122) 		0.00465
(0.00679) 		0.00398
(0.00591)
16p gain 462 (43%) 618 0.00336
(0.00502) 		0.0102
(0.014) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00471
(0.00687) 		0.00123
(0.00201) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00051
(0.000898) 		1e-05
(2.35e-05) 		6e-05
(0.000122) 		0.00695
(0.00981)
18p gain 177 (16%) 903 0.00016
(0.000303) 		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)
18q gain 154 (14%) 926 0.00285
(0.00437) 		4e-05
(8.36e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00196
(0.00312) 		0.00633
(0.00904) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00015
(0.000287) 		0.00483
(0.00703)
21q gain 198 (18%) 882 1e-05
(2.35e-05) 		0.00054
(0.000942) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		2e-05
(4.45e-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)
22q gain 99 (9%) 981 1e-05
(2.35e-05) 		0.0079
(0.011) 		1e-05
(2.35e-05) 		4e-05
(8.36e-05) 		4e-05
(8.36e-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) 		7e-05
(0.000141) 		0.00391
(0.00581)
xq gain 137 (13%) 943 0.00453
(0.00663) 		0.00677
(0.00961) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0173
(0.0226) 		0.00049
(0.000867) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00014
(0.00027) 		7e-05
(0.000141) 		0.00423
(0.00624)
3p loss 188 (17%) 892 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) 		4e-05
(8.36e-05) 		0.0158
(0.0209)
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) 		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)
4q loss 311 (29%) 769 1e-05
(2.35e-05) 		0.00015
(0.000287) 		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) 		0.00022
(0.000405)
5p loss 142 (13%) 938 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)
9q loss 280 (26%) 800 1e-05
(2.35e-05) 		0.0217
(0.0278) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		2e-05
(4.45e-05) 		9e-05
(0.000178) 		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 loss 231 (21%) 849 0.00011
(0.000216) 		0.014
(0.0187) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		3e-05
(6.45e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0053
(0.00766) 		0.00079
(0.00133)
12p loss 153 (14%) 927 0.00017
(0.000321) 		0.00165
(0.00266) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		4e-05
(8.36e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		2e-05
(4.45e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05)
12q loss 137 (13%) 943 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)
14q loss 269 (25%) 811 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)
15q loss 318 (29%) 762 0.0007
(0.0012) 		0.00021
(0.000388) 		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)
17q loss 272 (25%) 808 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) 		2e-05
(4.45e-05) 		0.0134
(0.0179)
20p loss 93 (9%) 987 0.0299
(0.0372) 		0.00713
(0.01) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00042
(0.000751) 		0.00019
(0.000354) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		2e-05
(4.45e-05) 		1e-05
(2.35e-05) 		9e-05
(0.000178) 		0.00126
(0.00206)
xp loss 192 (18%) 888 0.0196
(0.0252) 		0.0195
(0.0251) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00019
(0.000354) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00081
(0.00136) 		0.00137
(0.00223) 		0.00101
(0.00167)
5q gain 211 (20%) 869 0.0182
(0.0235) 		0.00353
(0.00526) 		1e-05
(2.35e-05) 		0.0018
(0.00288) 		0.00302
(0.00461) 		0.00024
(0.000439) 		0.00647
(0.00923) 		0.00025
(0.000455) 		0.0157
(0.0209) 		1e-05
(2.35e-05) 		2e-05
(4.45e-05) 		0.0656
(0.0784)
7q gain 268 (25%) 812 0.0129
(0.0174) 		0.00869
(0.012) 		1e-05
(2.35e-05) 		0.00026
(0.000471) 		0.0454
(0.0555) 		0.00231
(0.00363) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		3e-05
(6.45e-05) 		0.00293
(0.00449) 		0.188
(0.208)
10q gain 114 (11%) 966 0.00307
(0.00468) 		0.0415
(0.0509) 		1e-05
(2.35e-05) 		0.00054
(0.000942) 		0.0106
(0.0144) 		0.0643
(0.0769) 		0.00073
(0.00124) 		7e-05
(0.000141) 		0.00021
(0.000388) 		3e-05
(6.45e-05) 		0.00266
(0.00412) 		0.0256
(0.0323)
11q gain 96 (9%) 984 0.0346
(0.0428) 		0.0916
(0.107) 		1e-05
(2.35e-05) 		0.00112
(0.00184) 		0.00145
(0.00235) 		0.00081
(0.00136) 		0.00038
(0.000686) 		0.0005
(0.000882) 		5e-05
(0.000103) 		0.00272
(0.0042) 		0.0298
(0.0372) 		0.0115
(0.0156)
19p gain 187 (17%) 893 0.00069
(0.00118) 		0.0033
(0.00499) 		1e-05
(2.35e-05) 		0.00025
(0.000455) 		0.00237
(0.0037) 		0.00418
(0.00619) 		1e-05
(2.35e-05) 		3e-05
(6.45e-05) 		0.00026
(0.000471) 		4e-05
(8.36e-05) 		4e-05
(8.36e-05) 		0.659
(0.67)
19q gain 219 (20%) 861 0.00233
(0.00366) 		0.00745
(0.0105) 		1e-05
(2.35e-05) 		4e-05
(8.36e-05) 		0.0157
(0.0209) 		0.0164
(0.0215) 		1e-05
(2.35e-05) 		2e-05
(4.45e-05) 		0.00015
(0.000287) 		2e-05
(4.45e-05) 		0.00045
(0.000804) 		0.177
(0.197)
20p gain 411 (38%) 669 0.00015
(0.000287) 		0.508
(0.526) 		1e-05
(2.35e-05) 		0.00185
(0.00295) 		0.0132
(0.0178) 		0.00463
(0.00677) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00858
(0.0119) 		0.00312
(0.00474)
xp gain 150 (14%) 930 0.0198
(0.0254) 		0.57
(0.583) 		1e-05
(2.35e-05) 		3e-05
(6.45e-05) 		0.00899
(0.0124) 		0.00833
(0.0116) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		6e-05
(0.000122) 		5e-05
(0.000103) 		0.00012
(0.000234)
2p loss 185 (17%) 895 0.00625
(0.00895) 		0.029
(0.0362) 		1e-05
(2.35e-05) 		9e-05
(0.000178) 		0.0299
(0.0372) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		3e-05
(6.45e-05) 		0.00039
(0.000703) 		0.0011
(0.00181) 		0.0593
(0.0711)
7p loss 111 (10%) 969 0.00559
(0.00805) 		0.881
(0.883) 		1e-05
(2.35e-05) 		2e-05
(4.45e-05) 		0.00018
(0.000337) 		0.00737
(0.0104) 		1e-05
(2.35e-05) 		2e-05
(4.45e-05) 		1e-05
(2.35e-05) 		4e-05
(8.36e-05) 		1e-05
(2.35e-05) 		0.00243
(0.00378)
9p loss 313 (29%) 767 5e-05
(0.000103) 		0.0402
(0.0494) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		5e-05
(0.000103) 		0.192
(0.211) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00014
(0.00027) 		1e-05
(2.35e-05)
13q loss 430 (40%) 650 0.0015
(0.00243) 		0.0664
(0.0789) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00435
(0.00639) 		0.00047
(0.000835) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00052
(0.000912) 		0.00067
(0.00115)
16q loss 591 (55%) 489 1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00011
(0.000216) 		0.0628
(0.0753) 		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) 		0.0011
(0.00181) 		3e-05
(6.45e-05)
19p loss 197 (18%) 883 0.00016
(0.000303) 		0.366
(0.386) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00023
(0.000421) 		8e-05
(0.00016) 		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)
19q loss 164 (15%) 916 0.0129
(0.0174) 		0.175
(0.195) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00542
(0.00782) 		0.00231
(0.00363) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		2e-05
(4.45e-05) 		0.00013
(0.000252) 		2e-05
(4.45e-05)
20q loss 57 (5%) 1023 0.475
(0.493) 		0.00078
(0.00132) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00067
(0.00115) 		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) 		0.00234
(0.00366)
xq loss 189 (18%) 891 0.0338
(0.0419) 		0.872
(0.875) 		1e-05
(2.35e-05) 		2e-05
(4.45e-05) 		0.00421
(0.00622) 		0.00056
(0.000975) 		1e-05
(2.35e-05) 		2e-05
(4.45e-05) 		3e-05
(6.45e-05) 		0.00241
(0.00375) 		0.0106
(0.0144) 		0.00283
(0.00436)
17q gain 221 (20%) 859 0.0554
(0.0669) 		0.0113
(0.0154) 		1e-05
(2.35e-05) 		0.00042
(0.000751) 		0.51
(0.528) 		4e-05
(8.36e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00154
(0.00249) 		0.00649
(0.00924)
1p loss 227 (21%) 853 0.0231
(0.0294) 		0.0019
(0.00303) 		1e-05
(2.35e-05) 		0.0005
(0.000882) 		0.0982
(0.114) 		0.0161
(0.0212) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00329
(0.00498) 		1e-05
(2.35e-05) 		0.0166
(0.0217) 		0.744
(0.75)
3q loss 105 (10%) 975 1e-05
(2.35e-05) 		0.0086
(0.0119) 		1e-05
(2.35e-05) 		4e-05
(8.36e-05) 		3e-05
(6.45e-05) 		0.00058
(0.00101) 		4e-05
(8.36e-05) 		7e-05
(0.000141) 		0.00203
(0.00322) 		0.0002
(0.000371) 		0.148
(0.166) 		0.0899
(0.105)
8p loss 395 (37%) 685 0.0201
(0.0258) 		0.196
(0.215) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00018
(0.000337) 		0.0323
(0.04) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		3e-05
(6.45e-05) 		0.0953
(0.111) 		0.00237
(0.0037)
11p loss 270 (25%) 810 0.333
(0.353) 		0.339
(0.36) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00316
(0.00479) 		0.00333
(0.00502) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		3e-05
(6.45e-05) 		2e-05
(4.45e-05) 		0.0179
(0.0232) 		0.0247
(0.0313)
17p loss 580 (54%) 500 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
(4.45e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.241
(0.261) 		0.313
(0.333)
18p loss 320 (30%) 760 0.00207
(0.00328) 		0.0219
(0.028) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00209
(0.00331) 		0.027
(0.0339) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.0147
(0.0196) 		1e-05
(2.35e-05) 		0.378
(0.398) 		0.802
(0.806)
18q loss 321 (30%) 759 0.00093
(0.00155) 		0.0042
(0.00621) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00063
(0.00109) 		0.00341
(0.00509) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00429
(0.00632) 		1e-05
(2.35e-05) 		0.27
(0.29) 		0.35
(0.371)
4q gain 71 (7%) 1009 0.124
(0.141) 		0.00491
(0.00712) 		1e-05
(2.35e-05) 		0.0162
(0.0213) 		0.0212
(0.0272) 		0.0284
(0.0355) 		0.0001
(0.000197) 		0.107
(0.122) 		0.0176
(0.0228) 		0.0423
(0.0518) 		0.518
(0.534) 		0.0394
(0.0485)
11p gain 141 (13%) 939 0.128
(0.144) 		0.392
(0.411) 		1e-05
(2.35e-05) 		0.00437
(0.00641) 		0.0455
(0.0555) 		0.512
(0.529) 		0.00019
(0.000354) 		0.00843
(0.0117) 		0.00011
(0.000216) 		3e-05
(6.45e-05) 		0.00212
(0.00335) 		1e-05
(2.35e-05)
20q gain 450 (42%) 630 9e-05
(0.000178) 		0.203
(0.222) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.122
(0.139) 		0.106
(0.121) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00062
(0.00107) 		3e-05
(6.45e-05)
6q loss 280 (26%) 800 0.202
(0.221) 		0.0256
(0.0323) 		1e-05
(2.35e-05) 		0.00094
(0.00157) 		0.712
(0.72) 		0.00079
(0.00133) 		2e-05
(4.45e-05) 		0.00037
(0.000669) 		0.00786
(0.011) 		2e-05
(4.45e-05) 		0.0105
(0.0143) 		0.205
(0.223)
7q loss 120 (11%) 960 0.0658
(0.0784) 		0.0767
(0.0906) 		2e-05
(4.45e-05) 		0.00334
(0.00502) 		0.0266
(0.0333) 		0.376
(0.396) 		0.00171
(0.00275) 		0.00023
(0.000421) 		0.00073
(0.00124) 		0.00015
(0.000287) 		0.00968
(0.0133) 		0.0169
(0.0221)
16p loss 174 (16%) 906 0.0929
(0.108) 		0.201
(0.22) 		0.00336
(0.00502) 		0.00041
(0.000736) 		0.00046
(0.00082) 		0.00247
(0.00383) 		0.00023
(0.000421) 		0.00225
(0.00355) 		0.00012
(0.000234) 		0.00434
(0.00638) 		3e-05
(6.45e-05) 		0.0661
(0.0787)
3p gain 137 (13%) 943 0.457
(0.476) 		0.297
(0.318) 		1e-05
(2.35e-05) 		5e-05
(0.000103) 		0.0255
(0.0323) 		0.00774
(0.0108) 		2e-05
(4.45e-05) 		1e-05
(2.35e-05) 		2e-05
(4.45e-05) 		6e-05
(0.000122) 		0.261
(0.282) 		0.178
(0.198)
4p gain 75 (7%) 1005 0.258
(0.278) 		0.0158
(0.0209) 		1e-05
(2.35e-05) 		0.00752
(0.0105) 		0.00162
(0.00261) 		0.0701
(0.0831) 		6e-05
(0.000122) 		0.0162
(0.0213) 		0.00696
(0.00981) 		0.0172
(0.0225) 		0.559
(0.573) 		0.121
(0.138)
8p gain 291 (27%) 789 0.0658
(0.0784) 		0.031
(0.0385) 		1e-05
(2.35e-05) 		0.00095
(0.00158) 		0.429
(0.448) 		0.0973
(0.113) 		0.00053
(0.000928) 		0.00138
(0.00224) 		0.0266
(0.0334) 		0.0386
(0.0477) 		0.0185
(0.0239) 		0.0832
(0.0978)
12q gain 186 (17%) 894 0.00063
(0.00109) 		0.141
(0.158) 		1e-05
(2.35e-05) 		0.00185
(0.00295) 		0.247
(0.268) 		0.026
(0.0327) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.00052
(0.000912) 		0.00234
(0.00366) 		0.119
(0.135) 		0.45
(0.47)
13q gain 93 (9%) 987 0.165
(0.184) 		0.604
(0.618) 		0.00142
(0.00231) 		0.00091
(0.00152) 		0.00599
(0.0086) 		0.00246
(0.00382) 		0.00604
(0.00866) 		0.00018
(0.000337) 		0.00844
(0.0117) 		0.00013
(0.000252) 		0.239
(0.26) 		0.0632
(0.0757)
14q gain 143 (13%) 937 0.641
(0.653) 		0.019
(0.0245) 		1e-05
(2.35e-05) 		0.00047
(0.000835) 		0.0793
(0.0934) 		0.0233
(0.0296) 		5e-05
(0.000103) 		7e-05
(0.000141) 		0.00066
(0.00114) 		3e-05
(6.45e-05) 		0.19
(0.209) 		0.308
(0.329)
2q loss 211 (20%) 869 0.106
(0.122) 		0.528
(0.543) 		1e-05
(2.35e-05) 		0.00335
(0.00502) 		0.0669
(0.0794) 		9e-05
(0.000178) 		0.00041
(0.000736) 		1e-05
(2.35e-05) 		0.00096
(0.00159) 		0.0197
(0.0254) 		0.00489
(0.0071) 		0.0888
(0.104)
22q loss 482 (45%) 598 0.0181
(0.0235) 		0.327
(0.348) 		1e-05
(2.35e-05) 		0.189
(0.208) 		0.184
(0.204) 		0.00018
(0.000337) 		0.0133
(0.0179) 		4e-05
(8.36e-05) 		0.00375
(0.00558) 		0.026
(0.0327) 		0.0369
(0.0456) 		0.272
(0.292)
5p gain 315 (29%) 765 0.238
(0.258) 		0.0402
(0.0494) 		1e-05
(2.35e-05) 		0.011
(0.0149) 		0.523
(0.538) 		0.686
(0.694) 		0.11
(0.126) 		0.0536
(0.0648) 		0.0119
(0.0161) 		0.0138
(0.0185) 		0.0164
(0.0215) 		0.302
(0.323)
7p gain 313 (29%) 767 0.122
(0.139) 		0.204
(0.223) 		1e-05
(2.35e-05) 		0.0001
(0.000197) 		0.148
(0.166) 		0.117
(0.134) 		1e-05
(2.35e-05) 		3e-05
(6.45e-05) 		0.00084
(0.00141) 		0.00284
(0.00437) 		0.0786
(0.0927) 		0.257
(0.277)
9q gain 122 (11%) 958 0.635
(0.647) 		0.139
(0.156) 		1e-05
(2.35e-05) 		0.00104
(0.00172) 		0.127
(0.143) 		0.00679
(0.00963) 		0.00334
(0.00502) 		0.0168
(0.022) 		0.796
(0.802) 		0.05
(0.0607) 		0.0426
(0.0521) 		0.059
(0.0709)
15q gain 88 (8%) 992 0.0142
(0.0189) 		0.213
(0.232) 		0.0128
(0.0173) 		0.0222
(0.0284) 		0.543
(0.557) 		0.0984
(0.114) 		0.0462
(0.0563) 		0.0148
(0.0197) 		0.0845
(0.0993) 		0.0118
(0.016) 		0.328
(0.349) 		0.345
(0.366)
6p loss 190 (18%) 890 0.329
(0.35) 		0.0477
(0.058) 		1e-05
(2.35e-05) 		0.115
(0.131) 		0.962
(0.962) 		0.00652
(0.00927) 		0.00312
(0.00474) 		0.00882
(0.0122) 		0.0523
(0.0633) 		0.00628
(0.00898) 		0.455
(0.474) 		0.646
(0.658)
11q loss 366 (34%) 714 0.091
(0.106) 		0.102
(0.118) 		1e-05
(2.35e-05) 		1e-05
(2.35e-05) 		0.413
(0.433) 		0.151
(0.169) 		1e-05
(2.35e-05) 		0.00299
(0.00458) 		0.0259
(0.0327) 		0.00823
(0.0115) 		0.632
(0.645) 		0.125
(0.142)
21q loss 179 (17%) 901 0.039
(0.0481) 		0.773
(0.779) 		1e-05
(2.35e-05) 		0.00072
(0.00123) 		0.543
(0.557) 		0.686
(0.694) 		0.058
(0.0699) 		0.00692
(0.00978) 		0.0241
(0.0306) 		0.00127
(0.00207) 		0.222
(0.241) 		0.0972
(0.113)
10p loss 175 (16%) 905 0.159
(0.178) 		0.884
(0.885) 		1e-05
(2.35e-05) 		0.00062
(0.00107) 		0.0868
(0.102) 		0.186
(0.206) 		0.00012
(0.000234) 		1e-05
(2.35e-05) 		0.00016
(0.000303) 		0.0789
(0.093) 		0.111
(0.127) 		0.235
(0.255)
1q gain 708 (66%) 372 0.385
(0.405) 		0.0965
(0.112) 		1e-05
(2.35e-05) 		0.19
(0.209) 		0.627
(0.64) 		0.111
(0.127) 		1e-05
(2.35e-05) 		0.00691
(0.00978) 		0.0583
(0.0702) 		0.00025
(0.000455) 		0.25
(0.27) 		0.302
(0.323)
17p gain 110 (10%) 970 0.169
(0.188) 		0.681
(0.69) 		1e-05
(2.35e-05) 		0.0708
(0.0839) 		0.845
(0.848) 		0.486
(0.504) 		0.0228
(0.029) 		0.0589
(0.0708) 		0.00488
(0.00709) 		0.139
(0.156) 		0.445
(0.464) 		0.00172
(0.00276)
1q loss 48 (4%) 1032 0.00269
(0.00416) 		0.203
(0.222) 		7e-05
(0.000141) 		0.475
(0.493) 		0.285
(0.305) 		0.516
(0.533) 		0.00175
(0.0028) 		0.105
(0.12) 		0.0158
(0.0209) 		0.138
(0.156) 		0.183
(0.204) 		0.422
(0.442)
16q gain 142 (13%) 938 0.0711
(0.0841) 		0.74
(0.748) 		0.00076
(0.00129) 		0.0529
(0.064) 		0.268
(0.288) 		0.172
(0.192) 		0.264
(0.284) 		0.00303
(0.00462) 		0.105
(0.12) 		0.00081
(0.00136) 		0.131
(0.148) 		0.103
(0.119)
8q loss 93 (9%) 987 0.228
(0.248) 		0.678
(0.689) 		5e-05
(0.000103) 		0.0917
(0.107) 		0.396
(0.416) 		0.52
(0.535) 		0.00923
(0.0127) 		0.0149
(0.0198) 		0.374
(0.395) 		0.447
(0.467) 		0.361
(0.382) 		0.802
(0.806)
'1p gain' versus 'MRNA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
1P GAIN MUTATED 27 21 58
1P GAIN WILD-TYPE 202 95 110

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 = 2.3e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
1P GAIN MUTATED 21 49 36
1P GAIN WILD-TYPE 138 217 52

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 = 2.3e-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 330 132 295 294 29
1P GAIN MUTATED 51 25 31 112 8
1P GAIN WILD-TYPE 279 107 264 182 21

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 = 2.3e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
1P GAIN MUTATED 34 36 33 53 8
1P GAIN WILD-TYPE 184 147 112 86 80

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 = 2.3e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
1P GAIN MUTATED 71 39 7 29 30 14 2
1P GAIN WILD-TYPE 123 198 23 175 101 53 8

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

'1p gain' versus 'RPPA_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
1P GAIN MUTATED 80 79 33
1P GAIN WILD-TYPE 140 319 222

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 = 2.3e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
1P GAIN MUTATED 39 43 20 32 84 5 3
1P GAIN WILD-TYPE 225 126 123 193 119 46 17

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 = 2.3e-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 41 37 8 44 77 19
1P GAIN WILD-TYPE 248 126 82 246 106 41

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 = 2.3e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
1P GAIN MUTATED 24 93 26 38 35 7
1P GAIN WILD-TYPE 115 177 182 178 147 39

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 = 2.3e-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 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
1P GAIN MUTATED 11 43 27 21 14 15 67 4 21
1P GAIN WILD-TYPE 55 80 157 165 60 98 92 69 62

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 = 2.3e-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 CLUS_6
ALL 133 92 59 119 145 114
1P GAIN MUTATED 17 13 10 19 62 22
1P GAIN WILD-TYPE 116 79 49 100 83 92

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 = 0.00107 (Fisher's exact test), Q value = 0.0018

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
1P GAIN MUTATED 87 39 17
1P GAIN WILD-TYPE 227 192 100

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

'1q gain' versus 'CN_CNMF'

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

Table S13.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
1Q GAIN MUTATED 204 125 160 199 20
1Q GAIN WILD-TYPE 126 7 135 95 9

Figure S13.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

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

Table S14.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
1Q GAIN MUTATED 135 118 85 187 134 36 11
1Q GAIN WILD-TYPE 129 51 58 38 69 15 9

Figure S14.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00691 (Fisher's exact test), Q value = 0.0098

Table S15.  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 169 123 56 200 121 37
1Q GAIN WILD-TYPE 120 40 34 90 62 23

Figure S15.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.00045

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
1Q GAIN MUTATED 35 87 125 99 58 85 106 48 53
1Q GAIN WILD-TYPE 31 36 59 87 16 28 53 25 30

Figure S16.  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 = 2.3e-05

Table S17.  Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
2P GAIN MUTATED 6 6 48
2P GAIN WILD-TYPE 223 110 120

Figure S17.  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 = 2.3e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
2P GAIN MUTATED 2 32 26
2P GAIN WILD-TYPE 157 234 62

Figure S18.  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 = 2.3e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
2P GAIN MUTATED 28 9 7 74 4
2P GAIN WILD-TYPE 302 123 288 220 25

Figure S19.  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 = 2.3e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
2P GAIN MUTATED 4 20 13 44 2
2P GAIN WILD-TYPE 214 163 132 95 86

Figure S20.  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 = 2.3e-05

Table S21.  Gene #3: '2p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
2P GAIN MUTATED 49 4 2 11 20 14 2
2P GAIN WILD-TYPE 145 233 28 193 111 53 8

Figure S21.  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 = 2.3e-05

Table S22.  Gene #3: '2p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
2P GAIN MUTATED 64 22 16
2P GAIN WILD-TYPE 156 376 239

Figure S22.  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 = 2.3e-05

Table S23.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
2P GAIN MUTATED 11 42 1 3 64 0 1
2P GAIN WILD-TYPE 253 127 142 222 139 51 19

Figure S23.  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 = 2.3e-05

Table S24.  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 8 27 1 5 58 23
2P GAIN WILD-TYPE 281 136 89 285 125 37

Figure S24.  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 = 2.3e-05

Table S25.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
2P GAIN MUTATED 14 79 3 7 11 3
2P GAIN WILD-TYPE 125 191 205 209 171 43

Figure S25.  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 = 2.3e-05

Table S26.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
2P GAIN MUTATED 7 23 4 3 4 3 47 1 25
2P GAIN WILD-TYPE 59 100 180 183 70 110 112 72 58

Figure S26.  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 = 2.3e-05

Table S27.  Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
2P GAIN MUTATED 11 5 3 3 47 10
2P GAIN WILD-TYPE 122 87 56 116 98 104

Figure S27.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S28.  Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
2P GAIN MUTATED 58 16 5
2P GAIN WILD-TYPE 256 215 112

Figure S28.  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 = 2.3e-05

Table S29.  Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
2Q GAIN MUTATED 5 5 28
2Q GAIN WILD-TYPE 224 111 140

Figure S29.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q gain' versus 'MRNA_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
2Q GAIN MUTATED 2 21 15
2Q GAIN WILD-TYPE 157 245 73

Figure S30.  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 = 2.3e-05

Table S31.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
2Q GAIN MUTATED 16 8 7 41 1
2Q GAIN WILD-TYPE 314 124 288 253 28

Figure S31.  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 = 2.3e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
2Q GAIN MUTATED 2 10 5 24 2
2Q GAIN WILD-TYPE 216 173 140 115 86

Figure S32.  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 = 2.3e-05

Table S33.  Gene #4: '2q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
2Q GAIN MUTATED 29 2 3 5 12 7 2
2Q GAIN WILD-TYPE 165 235 27 199 119 60 8

Figure S33.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'2q gain' versus 'RPPA_CHIERARCHICAL'

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

Table S34.  Gene #4: '2q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
2Q GAIN MUTATED 40 10 10
2Q GAIN WILD-TYPE 180 388 245

Figure S34.  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 = 2.3e-05

Table S35.  Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
2Q GAIN MUTATED 4 27 1 4 37 0 0
2Q GAIN WILD-TYPE 260 142 142 221 166 51 20

Figure S35.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S36.  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 4 21 1 3 33 11
2Q GAIN WILD-TYPE 285 142 89 287 150 49

Figure S36.  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 = 2.3e-05

Table S37.  Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
2Q GAIN MUTATED 6 44 3 5 8 3
2Q GAIN WILD-TYPE 133 226 205 211 174 43

Figure S37.  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 = 2.3e-05

Table S38.  Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
2Q GAIN MUTATED 3 15 4 1 3 3 22 0 18
2Q GAIN WILD-TYPE 63 108 180 185 71 110 137 73 65

Figure S38.  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 = 2.3e-05

Table S39.  Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
2Q GAIN MUTATED 6 4 3 2 30 6
2Q GAIN WILD-TYPE 127 88 56 117 115 108

Figure S39.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00835 (Fisher's exact test), Q value = 0.012

Table S40.  Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
2Q GAIN MUTATED 35 11 5
2Q GAIN WILD-TYPE 279 220 112

Figure S40.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
3P GAIN MUTATED 56 23 3 49 6
3P GAIN WILD-TYPE 274 109 292 245 23

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

'3p gain' versus 'METHLYATION_CNMF'

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

Table S42.  Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
3P GAIN MUTATED 18 19 7 31 5
3P GAIN WILD-TYPE 200 164 138 108 83

Figure S42.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p gain' versus 'RPPA_CNMF'

P value = 0.0255 (Fisher's exact test), Q value = 0.032

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
3P GAIN MUTATED 34 31 5 14 12 11 1
3P GAIN WILD-TYPE 160 206 25 190 119 56 9

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

'3p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00774 (Fisher's exact test), Q value = 0.011

Table S44.  Gene #5: '3p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
3P GAIN MUTATED 36 53 19
3P GAIN WILD-TYPE 184 345 236

Figure S44.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3p gain' versus 'MRNASEQ_CNMF'

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

Table S45.  Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
3P GAIN MUTATED 36 20 6 27 42 1 5
3P GAIN WILD-TYPE 228 149 137 198 161 50 15

Figure S45.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S46.  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 24 2 18 40 6
3P GAIN WILD-TYPE 242 139 88 272 143 54

Figure S46.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CNMF'

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

Table S47.  Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
3P GAIN MUTATED 23 55 20 12 20 3
3P GAIN WILD-TYPE 116 215 188 204 162 43

Figure S47.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00012

Table S48.  Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
3P GAIN MUTATED 9 15 8 17 11 18 37 6 12
3P GAIN WILD-TYPE 57 108 176 169 63 95 122 67 71

Figure S48.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MRNA_CNMF'

P value = 0.00515 (Fisher's exact test), Q value = 0.0075

Table S49.  Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
3Q GAIN MUTATED 47 16 50
3Q GAIN WILD-TYPE 182 100 118

Figure S49.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0121 (Fisher's exact test), Q value = 0.016

Table S50.  Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
3Q GAIN MUTATED 33 50 30
3Q GAIN WILD-TYPE 126 216 58

Figure S50.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
3Q GAIN MUTATED 72 29 10 95 7
3Q GAIN WILD-TYPE 258 103 285 199 22

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

'3q gain' versus 'METHLYATION_CNMF'

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

Table S52.  Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
3Q GAIN MUTATED 25 35 14 54 7
3Q GAIN WILD-TYPE 193 148 131 85 81

Figure S52.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'RPPA_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00018

Table S53.  Gene #6: '3q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
3Q GAIN MUTATED 62 38 5 24 28 15 1
3Q GAIN WILD-TYPE 132 199 25 180 103 52 9

Figure S53.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'3q gain' versus 'RPPA_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
3Q GAIN MUTATED 67 71 35
3Q GAIN WILD-TYPE 153 327 220

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

'3q gain' versus 'MRNASEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
3Q GAIN MUTATED 48 36 9 31 81 2 6
3Q GAIN WILD-TYPE 216 133 134 194 122 49 14

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 = 2.3e-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 54 37 3 30 75 14
3Q GAIN WILD-TYPE 235 126 87 260 108 46

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 = 2.3e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
3Q GAIN MUTATED 28 99 27 20 30 5
3Q GAIN WILD-TYPE 111 171 181 196 152 41

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 = 2.3e-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 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
3Q GAIN MUTATED 11 24 9 31 12 22 63 12 25
3Q GAIN WILD-TYPE 55 99 175 155 62 91 96 61 58

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 = 2.3e-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 CLUS_6
ALL 133 92 59 119 145 114
3Q GAIN MUTATED 17 11 8 17 55 15
3Q GAIN WILD-TYPE 116 81 51 102 90 99

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 = 0.00049 (Fisher's exact test), Q value = 0.00087

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
3Q GAIN MUTATED 78 29 16
3Q GAIN WILD-TYPE 236 202 101

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

'4p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0158 (Fisher's exact test), Q value = 0.021

Table S61.  Gene #7: '4p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
4P GAIN MUTATED 19 14 3
4P GAIN WILD-TYPE 140 252 85

Figure S61.  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 = 2.3e-05

Table S62.  Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
4P GAIN MUTATED 51 2 2 18 2
4P GAIN WILD-TYPE 279 130 293 276 27

Figure S62.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.00752 (Fisher's exact test), Q value = 0.011

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
4P GAIN MUTATED 10 24 7 8 3
4P GAIN WILD-TYPE 208 159 138 131 85

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

'4p gain' versus 'RPPA_CNMF'

P value = 0.00162 (Fisher's exact test), Q value = 0.0026

Table S64.  Gene #7: '4p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
4P GAIN MUTATED 9 23 7 7 14 6 0
4P GAIN WILD-TYPE 185 214 23 197 117 61 10

Figure S64.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00012

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
4P GAIN MUTATED 38 11 7 9 9 1 0
4P GAIN WILD-TYPE 226 158 136 216 194 50 20

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

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0162 (Fisher's exact test), Q value = 0.021

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 29 17 2 17 7 3
4P GAIN WILD-TYPE 260 146 88 273 176 57

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

'4p gain' versus 'MIRSEQ_CNMF'

P value = 0.00696 (Fisher's exact test), Q value = 0.0098

Table S67.  Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
4P GAIN MUTATED 19 17 16 7 10 5
4P GAIN WILD-TYPE 120 253 192 209 172 41

Figure S67.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0172 (Fisher's exact test), Q value = 0.022

Table S68.  Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
4P GAIN MUTATED 8 11 6 16 3 11 5 4 10
4P GAIN WILD-TYPE 58 112 178 170 71 102 154 69 73

Figure S68.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00491 (Fisher's exact test), Q value = 0.0071

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
4Q GAIN MUTATED 19 13 2
4Q GAIN WILD-TYPE 140 253 86

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 = 2.3e-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 330 132 295 294 29
4Q GAIN MUTATED 48 1 2 17 3
4Q GAIN WILD-TYPE 282 131 293 277 26

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

'4q gain' versus 'METHLYATION_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.021

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
4Q GAIN MUTATED 8 21 6 9 3
4Q GAIN WILD-TYPE 210 162 139 130 85

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

'4q gain' versus 'RPPA_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.027

Table S72.  Gene #8: '4q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
4Q GAIN MUTATED 7 22 6 11 13 4 0
4Q GAIN WILD-TYPE 187 215 24 193 118 63 10

Figure S72.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'4q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0284 (Fisher's exact test), Q value = 0.036

Table S73.  Gene #8: '4q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
4Q GAIN MUTATED 8 37 18
4Q GAIN WILD-TYPE 212 361 237

Figure S73.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4q gain' versus 'MRNASEQ_CNMF'

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

Table S74.  Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
4Q GAIN MUTATED 37 9 6 8 10 1 0
4Q GAIN WILD-TYPE 227 160 137 217 193 50 20

Figure S74.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q gain' versus 'MIRSEQ_CNMF'

P value = 0.0176 (Fisher's exact test), Q value = 0.023

Table S75.  Gene #8: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
4Q GAIN MUTATED 18 18 14 7 9 4
4Q GAIN WILD-TYPE 121 252 194 209 173 42

Figure S75.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0423 (Fisher's exact test), Q value = 0.052

Table S76.  Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
4Q GAIN MUTATED 9 8 6 14 2 12 8 3 8
4Q GAIN WILD-TYPE 57 115 178 172 72 101 151 70 75

Figure S76.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0394 (Fisher's exact test), Q value = 0.048

Table S77.  Gene #8: '4q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
4Q GAIN MUTATED 30 12 4
4Q GAIN WILD-TYPE 284 219 113

Figure S77.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0402 (Fisher's exact test), Q value = 0.049

Table S78.  Gene #9: '5p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
5P GAIN MUTATED 40 93 21
5P GAIN WILD-TYPE 119 173 67

Figure S78.  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 = 2.3e-05

Table S79.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
5P GAIN MUTATED 128 59 33 89 6
5P GAIN WILD-TYPE 202 73 262 205 23

Figure S79.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.015

Table S80.  Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
5P GAIN MUTATED 63 66 29 44 19
5P GAIN WILD-TYPE 155 117 116 95 69

Figure S80.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.016

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
5P GAIN MUTATED 43 92 60 42 57 15
5P GAIN WILD-TYPE 96 178 148 174 125 31

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

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0138 (Fisher's exact test), Q value = 0.018

Table S82.  Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
5P GAIN MUTATED 18 46 37 56 29 34 39 20 30
5P GAIN WILD-TYPE 48 77 147 130 45 79 120 53 53

Figure S82.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.022

Table S83.  Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
5P GAIN MUTATED 39 31 25 35 40 20
5P GAIN WILD-TYPE 94 61 34 84 105 94

Figure S83.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q gain' versus 'MRNA_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.024

Table S84.  Gene #10: '5q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
5Q GAIN MUTATED 53 28 22
5Q GAIN WILD-TYPE 176 88 146

Figure S84.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00353 (Fisher's exact test), Q value = 0.0053

Table S85.  Gene #10: '5q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
5Q GAIN MUTATED 35 61 7
5Q GAIN WILD-TYPE 124 205 81

Figure S85.  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 = 2.3e-05

Table S86.  Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
5Q GAIN MUTATED 99 52 28 26 6
5Q GAIN WILD-TYPE 231 80 267 268 23

Figure S86.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 0.0018 (Fisher's exact test), Q value = 0.0029

Table S87.  Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
5Q GAIN MUTATED 55 44 17 18 14
5Q GAIN WILD-TYPE 163 139 128 121 74

Figure S87.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q gain' versus 'RPPA_CNMF'

P value = 0.00302 (Fisher's exact test), Q value = 0.0046

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
5Q GAIN MUTATED 22 61 8 44 22 13 4
5Q GAIN WILD-TYPE 172 176 22 160 109 54 6

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

'5q gain' versus 'RPPA_CHIERARCHICAL'

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

Table S89.  Gene #10: '5q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
5Q GAIN MUTATED 24 95 55
5Q GAIN WILD-TYPE 196 303 200

Figure S89.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.00647 (Fisher's exact test), Q value = 0.0092

Table S90.  Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
5Q GAIN MUTATED 54 33 28 60 23 7 4
5Q GAIN WILD-TYPE 210 136 115 165 180 44 16

Figure S90.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.00045

Table S91.  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 72 38 16 59 16 8
5Q GAIN WILD-TYPE 217 125 74 231 167 52

Figure S91.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.021

Table S92.  Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
5Q GAIN MUTATED 30 36 47 38 44 13
5Q GAIN WILD-TYPE 109 234 161 178 138 33

Figure S92.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
5Q GAIN MUTATED 11 25 32 41 29 28 9 17 16
5Q GAIN WILD-TYPE 55 98 152 145 45 85 150 56 67

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

'5q gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S94.  Gene #10: '5q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
5Q GAIN MUTATED 32 20 22 29 12 15
5Q GAIN WILD-TYPE 101 72 37 90 133 99

Figure S94.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MRNA_CNMF'

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

Table S95.  Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
6P GAIN MUTATED 32 9 56
6P GAIN WILD-TYPE 197 107 112

Figure S95.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p gain' versus 'MRNA_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00037

Table S96.  Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
6P GAIN MUTATED 19 48 30
6P GAIN WILD-TYPE 140 218 58

Figure S96.  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 = 2.3e-05

Table S97.  Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
6P GAIN MUTATED 52 20 7 122 7
6P GAIN WILD-TYPE 278 112 288 172 22

Figure S97.  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 = 2.3e-05

Table S98.  Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
6P GAIN MUTATED 23 41 16 64 2
6P GAIN WILD-TYPE 195 142 129 75 86

Figure S98.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p gain' versus 'RPPA_CNMF'

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

Table S99.  Gene #11: '6p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
6P GAIN MUTATED 59 26 7 21 29 18 3
6P GAIN WILD-TYPE 135 211 23 183 102 49 7

Figure S99.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'6p gain' versus 'RPPA_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
6P GAIN MUTATED 67 62 34
6P GAIN WILD-TYPE 153 336 221

Figure S100.  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 = 2.3e-05

Table S101.  Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
6P GAIN MUTATED 38 39 7 21 89 4 9
6P GAIN WILD-TYPE 226 130 136 204 114 47 11

Figure S101.  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 = 2.3e-05

Table S102.  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 2 27 80 12
6P GAIN WILD-TYPE 253 113 88 263 103 48

Figure S102.  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 = 2.3e-05

Table S103.  Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
6P GAIN MUTATED 26 99 23 18 21 13
6P GAIN WILD-TYPE 113 171 185 198 161 33

Figure S103.  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 = 2.3e-05

Table S104.  Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
6P GAIN MUTATED 9 30 10 19 9 21 65 7 30
6P GAIN WILD-TYPE 57 93 174 167 65 92 94 66 53

Figure S104.  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 = 2.3e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
6P GAIN MUTATED 20 12 7 10 59 13
6P GAIN WILD-TYPE 113 80 52 109 86 101

Figure S105.  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 = 2.3e-05

Table S106.  Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
6P GAIN MUTATED 85 27 9
6P GAIN WILD-TYPE 229 204 108

Figure S106.  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 = 2.3e-05

Table S107.  Gene #12: '6q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
6Q GAIN MUTATED 17 8 45
6Q GAIN WILD-TYPE 212 108 123

Figure S107.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00119 (Fisher's exact test), Q value = 0.002

Table S108.  Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
6Q GAIN MUTATED 14 33 23
6Q GAIN WILD-TYPE 145 233 65

Figure S108.  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 = 2.3e-05

Table S109.  Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
6Q GAIN MUTATED 29 14 3 100 3
6Q GAIN WILD-TYPE 301 118 292 194 26

Figure S109.  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 = 2.3e-05

Table S110.  Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
6Q GAIN MUTATED 13 27 15 45 2
6Q GAIN WILD-TYPE 205 156 130 94 86

Figure S110.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q gain' versus 'RPPA_CNMF'

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

Table S111.  Gene #12: '6q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
6Q GAIN MUTATED 44 18 4 11 25 16 2
6Q GAIN WILD-TYPE 150 219 26 193 106 51 8

Figure S111.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'6q gain' versus 'RPPA_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
6Q GAIN MUTATED 54 45 21
6Q GAIN WILD-TYPE 166 353 234

Figure S112.  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 = 2.3e-05

Table S113.  Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
6Q GAIN MUTATED 23 26 4 17 66 4 8
6Q GAIN WILD-TYPE 241 143 139 208 137 47 12

Figure S113.  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 = 2.3e-05

Table S114.  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 2 20 58 8
6Q GAIN WILD-TYPE 265 127 88 270 125 52

Figure S114.  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 = 2.3e-05

Table S115.  Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
6Q GAIN MUTATED 19 76 15 13 13 7
6Q GAIN WILD-TYPE 120 194 193 203 169 39

Figure S115.  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 = 2.3e-05

Table S116.  Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
6Q GAIN MUTATED 5 23 7 12 5 16 44 6 25
6Q GAIN WILD-TYPE 61 100 177 174 69 97 115 67 58

Figure S116.  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 = 2.3e-05

Table S117.  Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
6Q GAIN MUTATED 13 10 4 9 47 11
6Q GAIN WILD-TYPE 120 82 55 110 98 103

Figure S117.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S118.  Gene #12: '6q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
6Q GAIN MUTATED 67 21 6
6Q GAIN WILD-TYPE 247 210 111

Figure S118.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-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 330 132 295 294 29
7P GAIN MUTATED 93 61 46 100 13
7P GAIN WILD-TYPE 237 71 249 194 16

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

'7p gain' versus 'METHLYATION_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
7P GAIN MUTATED 59 63 24 56 22
7P GAIN WILD-TYPE 159 120 121 83 66

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

'7p gain' versus 'MRNASEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
7P GAIN MUTATED 70 70 26 61 73 11 1
7P GAIN WILD-TYPE 194 99 117 164 130 40 19

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

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

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 65 27
7P GAIN WILD-TYPE 213 100 70 229 118 33

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

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.0014

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
7P GAIN MUTATED 40 98 43 53 50 20
7P GAIN WILD-TYPE 99 172 165 163 132 26

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

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00284 (Fisher's exact test), Q value = 0.0044

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 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
7P GAIN MUTATED 18 50 40 38 26 34 54 20 24
7P GAIN WILD-TYPE 48 73 144 148 48 79 105 53 59

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

'7q gain' versus 'MRNA_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.017

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
7Q GAIN MUTATED 48 23 55
7Q GAIN WILD-TYPE 181 93 113

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

'7q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00869 (Fisher's exact test), Q value = 0.012

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
7Q GAIN MUTATED 32 61 33
7Q GAIN WILD-TYPE 127 205 55

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 = 2.3e-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 330 132 295 294 29
7Q GAIN MUTATED 72 53 38 94 11
7Q GAIN WILD-TYPE 258 79 257 200 18

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

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.00047

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
7Q GAIN MUTATED 50 44 21 53 19
7Q GAIN WILD-TYPE 168 139 124 86 69

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

'7q gain' versus 'RPPA_CNMF'

P value = 0.0454 (Fisher's exact test), Q value = 0.055

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
7Q GAIN MUTATED 60 53 10 42 37 10 3
7Q GAIN WILD-TYPE 134 184 20 162 94 57 7

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

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00231 (Fisher's exact test), Q value = 0.0036

Table S130.  Gene #14: '7q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
7Q GAIN MUTATED 73 92 50
7Q GAIN WILD-TYPE 147 306 205

Figure S130.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7q gain' versus 'MRNASEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
7Q GAIN MUTATED 56 55 22 50 77 7 0
7Q GAIN WILD-TYPE 208 114 121 175 126 44 20

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

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S132.  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 61 48 16 48 72 22
7Q GAIN WILD-TYPE 228 115 74 242 111 38

Figure S132.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

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

Table S133.  Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
7Q GAIN MUTATED 26 97 33 47 40 18
7Q GAIN WILD-TYPE 113 173 175 169 142 28

Figure S133.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S134.  Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
7Q GAIN MUTATED 12 40 37 28 22 25 62 16 19
7Q GAIN WILD-TYPE 54 83 147 158 52 88 97 57 64

Figure S134.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00293 (Fisher's exact test), Q value = 0.0045

Table S135.  Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
7Q GAIN MUTATED 32 30 18 23 54 21
7Q GAIN WILD-TYPE 101 62 41 96 91 93

Figure S135.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.031 (Fisher's exact test), Q value = 0.038

Table S136.  Gene #15: '8p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
8P GAIN MUTATED 53 59 27
8P GAIN WILD-TYPE 106 207 61

Figure S136.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

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

Table S137.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
8P GAIN MUTATED 94 41 45 90 21
8P GAIN WILD-TYPE 236 91 250 204 8

Figure S137.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0016

Table S138.  Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
8P GAIN MUTATED 53 49 25 55 23
8P GAIN WILD-TYPE 165 134 120 84 65

Figure S138.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.00093

Table S139.  Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
8P GAIN MUTATED 82 36 31 61 71 5 3
8P GAIN WILD-TYPE 182 133 112 164 132 46 17

Figure S139.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00138 (Fisher's exact test), Q value = 0.0022

Table S140.  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 42 16 64 66 11
8P GAIN WILD-TYPE 199 121 74 226 117 49

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

'8p gain' versus 'MIRSEQ_CNMF'

P value = 0.0266 (Fisher's exact test), Q value = 0.033

Table S141.  Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
8P GAIN MUTATED 44 81 55 43 44 18
8P GAIN WILD-TYPE 95 189 153 173 138 28

Figure S141.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0386 (Fisher's exact test), Q value = 0.048

Table S142.  Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
8P GAIN MUTATED 17 29 32 51 22 35 55 22 22
8P GAIN WILD-TYPE 49 94 152 135 52 78 104 51 61

Figure S142.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.024

Table S143.  Gene #15: '8p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
8P GAIN MUTATED 36 16 15 23 52 29
8P GAIN WILD-TYPE 97 76 44 96 93 85

Figure S143.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MRNA_CNMF'

P value = 0.00564 (Fisher's exact test), Q value = 0.0081

Table S144.  Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
8Q GAIN MUTATED 116 49 103
8Q GAIN WILD-TYPE 113 67 65

Figure S144.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0392 (Fisher's exact test), Q value = 0.048

Table S145.  Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
8Q GAIN MUTATED 84 128 56
8Q GAIN WILD-TYPE 75 138 32

Figure S145.  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 = 2.3e-05

Table S146.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
8Q GAIN MUTATED 191 51 71 189 28
8Q GAIN WILD-TYPE 139 81 224 105 1

Figure S146.  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 = 2.3e-05

Table S147.  Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
8Q GAIN MUTATED 86 96 57 96 28
8Q GAIN WILD-TYPE 132 87 88 43 60

Figure S147.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.014

Table S148.  Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
8Q GAIN MUTATED 115 110 15 82 68 35 6
8Q GAIN WILD-TYPE 79 127 15 122 63 32 4

Figure S148.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.0013

Table S149.  Gene #16: '8q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
8Q GAIN MUTATED 126 202 103
8Q GAIN WILD-TYPE 94 196 152

Figure S149.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8q gain' versus 'MRNASEQ_CNMF'

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

Table S150.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
8Q GAIN MUTATED 160 76 51 76 135 16 13
8Q GAIN WILD-TYPE 104 93 92 149 68 35 7

Figure S150.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S151.  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 142 94 22 117 122 30
8Q GAIN WILD-TYPE 147 69 68 173 61 30

Figure S151.  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 = 2.3e-05

Table S152.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
8Q GAIN MUTATED 87 171 84 69 84 25
8Q GAIN WILD-TYPE 52 99 124 147 98 21

Figure S152.  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 = 2.3e-05

Table S153.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
8Q GAIN MUTATED 36 69 47 77 37 66 105 36 47
8Q GAIN WILD-TYPE 30 54 137 109 37 47 54 37 36

Figure S153.  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 = 2.3e-05

Table S154.  Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
8Q GAIN MUTATED 65 30 21 51 106 42
8Q GAIN WILD-TYPE 68 62 38 68 39 72

Figure S154.  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 = 2.3e-05

Table S155.  Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
8Q GAIN MUTATED 186 85 44
8Q GAIN WILD-TYPE 128 146 73

Figure S155.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'MRNA_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00041

Table S156.  Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
9P GAIN MUTATED 16 16 36
9P GAIN WILD-TYPE 213 100 132

Figure S156.  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 = 2.3e-05

Table S157.  Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
9P GAIN MUTATED 12 25 31
9P GAIN WILD-TYPE 147 241 57

Figure S157.  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 = 2.3e-05

Table S158.  Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
9P GAIN MUTATED 17 36 15 66 5
9P GAIN WILD-TYPE 313 96 280 228 24

Figure S158.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

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

Table S159.  Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
9P GAIN MUTATED 25 16 14 38 3
9P GAIN WILD-TYPE 193 167 131 101 85

Figure S159.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p gain' versus 'RPPA_CNMF'

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

Table S160.  Gene #17: '9p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
9P GAIN MUTATED 47 26 3 15 14 9 1
9P GAIN WILD-TYPE 147 211 27 189 117 58 9

Figure S160.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'9p gain' versus 'RPPA_CHIERARCHICAL'

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

Table S161.  Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
9P GAIN MUTATED 55 42 18
9P GAIN WILD-TYPE 165 356 237

Figure S161.  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 = 2.3e-05

Table S162.  Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
9P GAIN MUTATED 15 20 9 24 64 5 2
9P GAIN WILD-TYPE 249 149 134 201 139 46 18

Figure S162.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S163.  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 21 4 27 58 5
9P GAIN WILD-TYPE 265 142 86 263 125 55

Figure S163.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_CNMF'

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

Table S164.  Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
9P GAIN MUTATED 14 58 15 21 23 4
9P GAIN WILD-TYPE 125 212 193 195 159 42

Figure S164.  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 = 2.3e-05

Table S165.  Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
9P GAIN MUTATED 5 14 16 11 11 14 49 7 8
9P GAIN WILD-TYPE 61 109 168 175 63 99 110 66 75

Figure S165.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0011

Table S166.  Gene #17: '9p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
9P GAIN MUTATED 15 8 9 19 32 5
9P GAIN WILD-TYPE 118 84 50 100 113 109

Figure S166.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.049 (Fisher's exact test), Q value = 0.059

Table S167.  Gene #17: '9p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
9P GAIN MUTATED 47 21 20
9P GAIN WILD-TYPE 267 210 97

Figure S167.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

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

Table S168.  Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
9Q GAIN MUTATED 24 38 15 42 3
9Q GAIN WILD-TYPE 306 94 280 252 26

Figure S168.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.0017

Table S169.  Gene #18: '9q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
9Q GAIN MUTATED 28 22 10 25 2
9Q GAIN WILD-TYPE 190 161 135 114 86

Figure S169.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00679 (Fisher's exact test), Q value = 0.0096

Table S170.  Gene #18: '9q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
9Q GAIN MUTATED 37 45 19
9Q GAIN WILD-TYPE 183 353 236

Figure S170.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 0.00334 (Fisher's exact test), Q value = 0.005

Table S171.  Gene #18: '9q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
9Q GAIN MUTATED 19 24 10 25 38 4 2
9Q GAIN WILD-TYPE 245 145 133 200 165 47 18

Figure S171.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.022

Table S172.  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 25 33 8
9Q GAIN WILD-TYPE 259 142 85 265 150 52

Figure S172.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S173.  Gene #18: '9q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
9Q GAIN MUTATED 16 8 9 19 24 6
9Q GAIN WILD-TYPE 117 84 50 100 121 108

Figure S173.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p gain' versus 'MRNA_CNMF'

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

Table S174.  Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
10P GAIN MUTATED 29 16 64
10P GAIN WILD-TYPE 200 100 104

Figure S174.  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 = 2.3e-05

Table S175.  Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
10P GAIN MUTATED 15 56 38
10P GAIN WILD-TYPE 144 210 50

Figure S175.  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 = 2.3e-05

Table S176.  Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
10P GAIN MUTATED 53 24 11 117 3
10P GAIN WILD-TYPE 277 108 284 177 26

Figure S176.  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 = 2.3e-05

Table S177.  Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
10P GAIN MUTATED 16 35 24 61 2
10P GAIN WILD-TYPE 202 148 121 78 86

Figure S177.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p gain' versus 'RPPA_CNMF'

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

Table S178.  Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
10P GAIN MUTATED 68 24 8 24 27 20 4
10P GAIN WILD-TYPE 126 213 22 180 104 47 6

Figure S178.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p gain' versus 'RPPA_CHIERARCHICAL'

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

Table S179.  Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
10P GAIN MUTATED 79 67 29
10P GAIN WILD-TYPE 141 331 226

Figure S179.  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 = 2.3e-05

Table S180.  Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
10P GAIN MUTATED 41 40 13 18 86 4 6
10P GAIN WILD-TYPE 223 129 130 207 117 47 14

Figure S180.  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 = 2.3e-05

Table S181.  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 39 3 34 80 20
10P GAIN WILD-TYPE 257 124 87 256 103 40

Figure S181.  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 = 2.3e-05

Table S182.  Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
10P GAIN MUTATED 28 99 12 23 34 8
10P GAIN WILD-TYPE 111 171 196 193 148 38

Figure S182.  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 = 2.3e-05

Table S183.  Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
10P GAIN MUTATED 10 34 11 14 8 27 65 8 27
10P GAIN WILD-TYPE 56 89 173 172 66 86 94 65 56

Figure S183.  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 = 2.3e-05

Table S184.  Gene #19: '10p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
10P GAIN MUTATED 20 10 8 13 60 14
10P GAIN WILD-TYPE 113 82 51 106 85 100

Figure S184.  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 = 2.3e-05

Table S185.  Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
10P GAIN MUTATED 88 24 13
10P GAIN WILD-TYPE 226 207 104

Figure S185.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'MRNA_CNMF'

P value = 0.00307 (Fisher's exact test), Q value = 0.0047

Table S186.  Gene #20: '10q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
10Q GAIN MUTATED 19 12 33
10Q GAIN WILD-TYPE 210 104 135

Figure S186.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0415 (Fisher's exact test), Q value = 0.051

Table S187.  Gene #20: '10q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
10Q GAIN MUTATED 13 34 17
10Q GAIN WILD-TYPE 146 232 71

Figure S187.  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 = 2.3e-05

Table S188.  Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
10Q GAIN MUTATED 33 20 8 52 1
10Q GAIN WILD-TYPE 297 112 287 242 28

Figure S188.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'METHLYATION_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.00094

Table S189.  Gene #20: '10q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
10Q GAIN MUTATED 12 19 13 22 1
10Q GAIN WILD-TYPE 206 164 132 117 87

Figure S189.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q gain' versus 'RPPA_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.014

Table S190.  Gene #20: '10q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
10Q GAIN MUTATED 33 19 5 17 10 12 1
10Q GAIN WILD-TYPE 161 218 25 187 121 55 9

Figure S190.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.0012

Table S191.  Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
10Q GAIN MUTATED 27 23 8 16 32 2 6
10Q GAIN WILD-TYPE 237 146 135 209 171 49 14

Figure S191.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00014

Table S192.  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 25 2 20 29 12
10Q GAIN WILD-TYPE 263 138 88 270 154 48

Figure S192.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_CNMF'

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

Table S193.  Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
10Q GAIN MUTATED 19 43 9 15 19 7
10Q GAIN WILD-TYPE 120 227 199 201 163 39

Figure S193.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S194.  Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
10Q GAIN MUTATED 7 18 9 7 7 19 27 4 14
10Q GAIN WILD-TYPE 59 105 175 179 67 94 132 69 69

Figure S194.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00266 (Fisher's exact test), Q value = 0.0041

Table S195.  Gene #20: '10q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
10Q GAIN MUTATED 13 5 6 8 28 6
10Q GAIN WILD-TYPE 120 87 53 111 117 108

Figure S195.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0256 (Fisher's exact test), Q value = 0.032

Table S196.  Gene #20: '10q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
10Q GAIN MUTATED 41 14 11
10Q GAIN WILD-TYPE 273 217 106

Figure S196.  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 = 2.3e-05

Table S197.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
11P GAIN MUTATED 57 16 12 56 0
11P GAIN WILD-TYPE 273 116 283 238 29

Figure S197.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.00437 (Fisher's exact test), Q value = 0.0064

Table S198.  Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
11P GAIN MUTATED 29 23 8 28 8
11P GAIN WILD-TYPE 189 160 137 111 80

Figure S198.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p gain' versus 'RPPA_CNMF'

P value = 0.0455 (Fisher's exact test), Q value = 0.055

Table S199.  Gene #21: '11p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
11P GAIN MUTATED 39 23 3 25 14 11 0
11P GAIN WILD-TYPE 155 214 27 179 117 56 10

Figure S199.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'11p gain' versus 'MRNASEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00035

Table S200.  Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
11P GAIN MUTATED 43 30 9 16 37 4 1
11P GAIN WILD-TYPE 221 139 134 209 166 47 19

Figure S200.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00843 (Fisher's exact test), Q value = 0.012

Table S201.  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 37 29 7 25 34 8
11P GAIN WILD-TYPE 252 134 83 265 149 52

Figure S201.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00022

Table S202.  Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
11P GAIN MUTATED 23 48 24 10 26 8
11P GAIN WILD-TYPE 116 222 184 206 156 38

Figure S202.  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 S203.  Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
11P GAIN MUTATED 13 18 8 22 7 22 28 4 17
11P GAIN WILD-TYPE 53 105 176 164 67 91 131 69 66

Figure S203.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00212 (Fisher's exact test), Q value = 0.0033

Table S204.  Gene #21: '11p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
11P GAIN MUTATED 23 9 11 13 25 4
11P GAIN WILD-TYPE 110 83 48 106 120 110

Figure S204.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S205.  Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
11P GAIN MUTATED 58 11 16
11P GAIN WILD-TYPE 256 220 101

Figure S205.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'MRNA_CNMF'

P value = 0.0346 (Fisher's exact test), Q value = 0.043

Table S206.  Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
11Q GAIN MUTATED 14 12 23
11Q GAIN WILD-TYPE 215 104 145

Figure S206.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q gain' versus 'CN_CNMF'

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

Table S207.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
11Q GAIN MUTATED 28 12 7 48 1
11Q GAIN WILD-TYPE 302 120 288 246 28

Figure S207.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.0018

Table S208.  Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
11Q GAIN MUTATED 17 12 6 25 6
11Q GAIN WILD-TYPE 201 171 139 114 82

Figure S208.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q gain' versus 'RPPA_CNMF'

P value = 0.00145 (Fisher's exact test), Q value = 0.0024

Table S209.  Gene #22: '11q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
11Q GAIN MUTATED 29 10 3 16 9 11 0
11Q GAIN WILD-TYPE 165 227 27 188 122 56 10

Figure S209.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'11q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00081 (Fisher's exact test), Q value = 0.0014

Table S210.  Gene #22: '11q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
11Q GAIN MUTATED 34 26 18
11Q GAIN WILD-TYPE 186 372 237

Figure S210.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.00069

Table S211.  Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
11Q GAIN MUTATED 19 25 8 14 29 0 1
11Q GAIN WILD-TYPE 245 144 135 211 174 51 19

Figure S211.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.00088

Table S212.  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 19 18 5 16 27 11
11Q GAIN WILD-TYPE 270 145 85 274 156 49

Figure S212.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CNMF'

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

Table S213.  Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
11Q GAIN MUTATED 11 43 13 7 13 6
11Q GAIN WILD-TYPE 128 227 195 209 169 40

Figure S213.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00272 (Fisher's exact test), Q value = 0.0042

Table S214.  Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
11Q GAIN MUTATED 7 11 4 16 5 10 22 5 13
11Q GAIN WILD-TYPE 59 112 180 170 69 103 137 68 70

Figure S214.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.037

Table S215.  Gene #22: '11q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
11Q GAIN MUTATED 10 7 6 7 20 3
11Q GAIN WILD-TYPE 123 85 53 112 125 111

Figure S215.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0115 (Fisher's exact test), Q value = 0.016

Table S216.  Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
11Q GAIN MUTATED 33 9 11
11Q GAIN WILD-TYPE 281 222 106

Figure S216.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'MRNA_CNMF'

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

Table S217.  Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
12P GAIN MUTATED 49 12 51
12P GAIN WILD-TYPE 180 104 117

Figure S217.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'12p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0249 (Fisher's exact test), Q value = 0.032

Table S218.  Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
12P GAIN MUTATED 33 50 29
12P GAIN WILD-TYPE 126 216 59

Figure S218.  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 = 2.3e-05

Table S219.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
12P GAIN MUTATED 98 27 9 88 3
12P GAIN WILD-TYPE 232 105 286 206 26

Figure S219.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00012

Table S220.  Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
12P GAIN MUTATED 44 40 17 44 8
12P GAIN WILD-TYPE 174 143 128 95 80

Figure S220.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'RPPA_CNMF'

P value = 0.00332 (Fisher's exact test), Q value = 0.005

Table S221.  Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
12P GAIN MUTATED 61 53 3 35 26 8 2
12P GAIN WILD-TYPE 133 184 27 169 105 59 8

Figure S221.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'12p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0116 (Fisher's exact test), Q value = 0.016

Table S222.  Gene #23: '12p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
12P GAIN MUTATED 60 87 41
12P GAIN WILD-TYPE 160 311 214

Figure S222.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12p gain' versus 'MRNASEQ_CNMF'

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

Table S223.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
12P GAIN MUTATED 69 45 15 28 60 4 3
12P GAIN WILD-TYPE 195 124 128 197 143 47 17

Figure S223.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S224.  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 50 7 36 56 13
12P GAIN WILD-TYPE 227 113 83 254 127 47

Figure S224.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

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

Table S225.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
12P GAIN MUTATED 36 89 34 22 27 10
12P GAIN WILD-TYPE 103 181 174 194 155 36

Figure S225.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00012

Table S226.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
12P GAIN MUTATED 16 28 17 30 19 22 48 15 23
12P GAIN WILD-TYPE 50 95 167 156 55 91 111 58 60

Figure S226.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00465 (Fisher's exact test), Q value = 0.0068

Table S227.  Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
12P GAIN MUTATED 31 17 9 18 45 15
12P GAIN WILD-TYPE 102 75 50 101 100 99

Figure S227.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00398 (Fisher's exact test), Q value = 0.0059

Table S228.  Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
12P GAIN MUTATED 81 38 16
12P GAIN WILD-TYPE 233 193 101

Figure S228.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'MRNA_CNMF'

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

Table S229.  Gene #24: '12q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
12Q GAIN MUTATED 51 8 35
12Q GAIN WILD-TYPE 178 108 133

Figure S229.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'12q gain' versus 'CN_CNMF'

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

Table S230.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
12Q GAIN MUTATED 101 26 10 45 4
12Q GAIN WILD-TYPE 229 106 285 249 25

Figure S230.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 0.00185 (Fisher's exact test), Q value = 0.003

Table S231.  Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
12Q GAIN MUTATED 46 39 13 20 8
12Q GAIN WILD-TYPE 172 144 132 119 80

Figure S231.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.026 (Fisher's exact test), Q value = 0.033

Table S232.  Gene #24: '12q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
12Q GAIN MUTATED 32 88 39
12Q GAIN WILD-TYPE 188 310 216

Figure S232.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12q gain' versus 'MRNASEQ_CNMF'

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

Table S233.  Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
12Q GAIN MUTATED 67 44 15 30 23 4 2
12Q GAIN WILD-TYPE 197 125 128 195 180 47 18

Figure S233.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S234.  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 66 49 6 34 21 9
12Q GAIN WILD-TYPE 223 114 84 256 162 51

Figure S234.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.00091

Table S235.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
12Q GAIN MUTATED 35 54 34 18 31 9
12Q GAIN WILD-TYPE 104 216 174 198 151 37

Figure S235.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00234 (Fisher's exact test), Q value = 0.0037

Table S236.  Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
12Q GAIN MUTATED 16 28 17 33 18 19 17 16 17
12Q GAIN WILD-TYPE 50 95 167 153 56 94 142 57 66

Figure S236.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 0.00142 (Fisher's exact test), Q value = 0.0023

Table S237.  Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
13Q GAIN MUTATED 31 7 14 40 1
13Q GAIN WILD-TYPE 299 125 281 254 28

Figure S237.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.0015

Table S238.  Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
13Q GAIN MUTATED 9 19 9 20 2
13Q GAIN WILD-TYPE 209 164 136 119 86

Figure S238.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'RPPA_CNMF'

P value = 0.00599 (Fisher's exact test), Q value = 0.0086

Table S239.  Gene #25: '13q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
13Q GAIN MUTATED 24 20 1 7 16 10 1
13Q GAIN WILD-TYPE 170 217 29 197 115 57 9

Figure S239.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'13q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00246 (Fisher's exact test), Q value = 0.0038

Table S240.  Gene #25: '13q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
13Q GAIN MUTATED 30 37 12
13Q GAIN WILD-TYPE 190 361 243

Figure S240.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 0.00604 (Fisher's exact test), Q value = 0.0087

Table S241.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
13Q GAIN MUTATED 22 19 6 16 29 1 0
13Q GAIN WILD-TYPE 242 150 137 209 174 50 20

Figure S241.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S242.  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 24 11
13Q GAIN WILD-TYPE 263 146 87 278 159 49

Figure S242.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 0.00844 (Fisher's exact test), Q value = 0.012

Table S243.  Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
13Q GAIN MUTATED 13 37 14 9 14 4
13Q GAIN WILD-TYPE 126 233 194 207 168 42

Figure S243.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S244.  Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
13Q GAIN MUTATED 9 11 5 7 9 9 18 8 15
13Q GAIN WILD-TYPE 57 112 179 179 65 104 141 65 68

Figure S244.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MRNA_CHIERARCHICAL'

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

Table S245.  Gene #26: '14q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
14Q GAIN MUTATED 24 46 5
14Q GAIN WILD-TYPE 135 220 83

Figure S245.  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 = 2.3e-05

Table S246.  Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
14Q GAIN MUTATED 69 25 20 26 3
14Q GAIN WILD-TYPE 261 107 275 268 26

Figure S246.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.00083

Table S247.  Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
14Q GAIN MUTATED 27 38 8 12 8
14Q GAIN WILD-TYPE 191 145 137 127 80

Figure S247.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0233 (Fisher's exact test), Q value = 0.03

Table S248.  Gene #26: '14q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
14Q GAIN MUTATED 27 65 23
14Q GAIN WILD-TYPE 193 333 232

Figure S248.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q gain' versus 'MRNASEQ_CNMF'

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

Table S249.  Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
14Q GAIN MUTATED 38 39 11 35 15 2 2
14Q GAIN WILD-TYPE 226 130 132 190 188 49 18

Figure S249.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00014

Table S250.  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 34 7 32 11 14
14Q GAIN WILD-TYPE 245 129 83 258 172 46

Figure S250.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0011

Table S251.  Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
14Q GAIN MUTATED 24 32 22 18 32 14
14Q GAIN WILD-TYPE 115 238 186 198 150 32

Figure S251.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S252.  Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
14Q GAIN MUTATED 14 23 14 18 17 23 9 9 15
14Q GAIN WILD-TYPE 52 100 170 168 57 90 150 64 68

Figure S252.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q gain' versus 'MRNA_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.019

Table S253.  Gene #27: '15q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
15Q GAIN MUTATED 16 6 24
15Q GAIN WILD-TYPE 213 110 144

Figure S253.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q gain' versus 'CN_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.017

Table S254.  Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
15Q GAIN MUTATED 33 10 12 32 1
15Q GAIN WILD-TYPE 297 122 283 262 28

Figure S254.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

'15q gain' versus 'METHLYATION_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 0.028

Table S255.  Gene #27: '15q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
15Q GAIN MUTATED 10 14 6 17 10
15Q GAIN WILD-TYPE 208 169 139 122 78

Figure S255.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 0.0462 (Fisher's exact test), Q value = 0.056

Table S256.  Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
15Q GAIN MUTATED 23 16 8 12 26 1 2
15Q GAIN WILD-TYPE 241 153 135 213 177 50 18

Figure S256.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0148 (Fisher's exact test), Q value = 0.02

Table S257.  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 23 7
15Q GAIN WILD-TYPE 263 148 87 276 160 53

Figure S257.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0118 (Fisher's exact test), Q value = 0.016

Table S258.  Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
15Q GAIN MUTATED 6 14 4 12 7 10 16 6 12
15Q GAIN WILD-TYPE 60 109 180 174 67 103 143 67 71

Figure S258.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MRNA_CNMF'

P value = 0.00336 (Fisher's exact test), Q value = 0.005

Table S259.  Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
16P GAIN MUTATED 126 43 73
16P GAIN WILD-TYPE 103 73 95

Figure S259.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.014

Table S260.  Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
16P GAIN MUTATED 83 130 29
16P GAIN WILD-TYPE 76 136 59

Figure S260.  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 = 2.3e-05

Table S261.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
16P GAIN MUTATED 150 86 104 108 14
16P GAIN WILD-TYPE 180 46 191 186 15

Figure S261.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

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

Table S262.  Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
16P GAIN MUTATED 113 85 38 42 28
16P GAIN WILD-TYPE 105 98 107 97 60

Figure S262.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p gain' versus 'RPPA_CNMF'

P value = 0.00471 (Fisher's exact test), Q value = 0.0069

Table S263.  Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
16P GAIN MUTATED 60 118 13 85 58 34 5
16P GAIN WILD-TYPE 134 119 17 119 73 33 5

Figure S263.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'16p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00123 (Fisher's exact test), Q value = 0.002

Table S264.  Gene #28: '16p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
16P GAIN MUTATED 71 184 118
16P GAIN WILD-TYPE 149 214 137

Figure S264.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16p gain' versus 'MRNASEQ_CNMF'

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

Table S265.  Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
16P GAIN MUTATED 103 80 58 135 53 22 10
16P GAIN WILD-TYPE 161 89 85 90 150 29 10

Figure S265.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S266.  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 142 80 34 133 47 25
16P GAIN WILD-TYPE 147 83 56 157 136 35

Figure S266.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 9e-04

Table S267.  Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
16P GAIN MUTATED 59 94 92 83 94 29
16P GAIN WILD-TYPE 80 176 116 133 88 17

Figure S267.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S268.  Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
16P GAIN MUTATED 25 56 75 78 43 64 36 32 42
16P GAIN WILD-TYPE 41 67 109 108 31 49 123 41 41

Figure S268.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00012

Table S269.  Gene #28: '16p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
16P GAIN MUTATED 62 42 27 64 38 42
16P GAIN WILD-TYPE 71 50 32 55 107 72

Figure S269.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00695 (Fisher's exact test), Q value = 0.0098

Table S270.  Gene #28: '16p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
16P GAIN MUTATED 116 96 63
16P GAIN WILD-TYPE 198 135 54

Figure S270.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

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

Table S271.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
16Q GAIN MUTATED 54 18 21 48 1
16Q GAIN WILD-TYPE 276 114 274 246 28

Figure S271.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00303 (Fisher's exact test), Q value = 0.0046

Table S272.  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 41 26 4 29 26 15
16Q GAIN WILD-TYPE 248 137 86 261 157 45

Figure S272.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00081 (Fisher's exact test), Q value = 0.0014

Table S273.  Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
16Q GAIN MUTATED 12 19 13 24 5 14 20 8 24
16Q GAIN WILD-TYPE 54 104 171 162 69 99 139 65 59

Figure S273.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

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

Table S274.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
17P GAIN MUTATED 55 11 10 30 4
17P GAIN WILD-TYPE 275 121 285 264 25

Figure S274.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.029

Table S275.  Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
17P GAIN MUTATED 38 17 10 12 24 5 3
17P GAIN WILD-TYPE 226 152 133 213 179 46 17

Figure S275.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 0.00488 (Fisher's exact test), Q value = 0.0071

Table S276.  Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
17P GAIN MUTATED 27 29 20 16 11 4
17P GAIN WILD-TYPE 112 241 188 200 171 42

Figure S276.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00172 (Fisher's exact test), Q value = 0.0028

Table S277.  Gene #30: '17p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
17P GAIN MUTATED 47 17 6
17P GAIN WILD-TYPE 267 214 111

Figure S277.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'MRNA_CHIERARCHICAL'

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

Table S278.  Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
17Q GAIN MUTATED 38 53 8
17Q GAIN WILD-TYPE 121 213 80

Figure S278.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

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

Table S279.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
17Q GAIN MUTATED 138 14 18 41 10
17Q GAIN WILD-TYPE 192 118 277 253 19

Figure S279.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.00075

Table S280.  Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
17Q GAIN MUTATED 46 58 22 19 15
17Q GAIN WILD-TYPE 172 125 123 120 73

Figure S280.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.4e-05

Table S281.  Gene #31: '17q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
17Q GAIN MUTATED 26 108 51
17Q GAIN WILD-TYPE 194 290 204

Figure S281.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17q gain' versus 'MRNASEQ_CNMF'

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

Table S282.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
17Q GAIN MUTATED 101 35 20 25 26 7 6
17Q GAIN WILD-TYPE 163 134 123 200 177 44 14

Figure S282.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S283.  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 91 40 6 54 21 8
17Q GAIN WILD-TYPE 198 123 84 236 162 52

Figure S283.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

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

Table S284.  Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
17Q GAIN MUTATED 53 46 48 29 33 7
17Q GAIN WILD-TYPE 86 224 160 187 149 39

Figure S284.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S285.  Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
17Q GAIN MUTATED 27 21 22 50 9 27 17 22 21
17Q GAIN WILD-TYPE 39 102 162 136 65 86 142 51 62

Figure S285.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00154 (Fisher's exact test), Q value = 0.0025

Table S286.  Gene #31: '17q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
17Q GAIN MUTATED 36 9 12 37 25 20
17Q GAIN WILD-TYPE 97 83 47 82 120 94

Figure S286.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00649 (Fisher's exact test), Q value = 0.0092

Table S287.  Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
17Q GAIN MUTATED 82 35 22
17Q GAIN WILD-TYPE 232 196 95

Figure S287.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'MRNA_CNMF'

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

Table S288.  Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
18P GAIN MUTATED 34 9 44
18P GAIN WILD-TYPE 195 107 124

Figure S288.  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 = 2.3e-05

Table S289.  Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
18P GAIN MUTATED 26 29 32
18P GAIN WILD-TYPE 133 237 56

Figure S289.  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 = 2.3e-05

Table S290.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
18P GAIN MUTATED 50 24 10 83 10
18P GAIN WILD-TYPE 280 108 285 211 19

Figure S290.  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 = 2.3e-05

Table S291.  Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
18P GAIN MUTATED 28 16 12 53 4
18P GAIN WILD-TYPE 190 167 133 86 84

Figure S291.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'RPPA_CNMF'

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

Table S292.  Gene #32: '18p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
18P GAIN MUTATED 58 29 3 19 18 15 1
18P GAIN WILD-TYPE 136 208 27 185 113 52 9

Figure S292.  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 = 2.3e-05

Table S293.  Gene #32: '18p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
18P GAIN MUTATED 61 59 23
18P GAIN WILD-TYPE 159 339 232

Figure S293.  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 = 2.3e-05

Table S294.  Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
18P GAIN MUTATED 39 22 5 35 73 0 3
18P GAIN WILD-TYPE 225 147 138 190 130 51 17

Figure S294.  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 = 2.3e-05

Table S295.  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 50 21 3 20 69 14
18P GAIN WILD-TYPE 239 142 87 270 114 46

Figure S295.  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 = 2.3e-05

Table S296.  Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
18P GAIN MUTATED 22 82 22 11 27 6
18P GAIN WILD-TYPE 117 188 186 205 155 40

Figure S296.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S297.  Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
18P GAIN MUTATED 12 20 10 18 11 12 59 9 19
18P GAIN WILD-TYPE 54 103 174 168 63 101 100 64 64

Figure S297.  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 = 2.3e-05

Table S298.  Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
18P GAIN MUTATED 19 5 7 14 56 8
18P GAIN WILD-TYPE 114 87 52 105 89 106

Figure S298.  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 = 2.3e-05

Table S299.  Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
18P GAIN MUTATED 74 20 15
18P GAIN WILD-TYPE 240 211 102

Figure S299.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'MRNA_CNMF'

P value = 0.00285 (Fisher's exact test), Q value = 0.0044

Table S300.  Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
18Q GAIN MUTATED 37 8 36
18Q GAIN WILD-TYPE 192 108 132

Figure S300.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q gain' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.4e-05

Table S301.  Gene #33: '18q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
18Q GAIN MUTATED 28 26 27
18Q GAIN WILD-TYPE 131 240 61

Figure S301.  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 = 2.3e-05

Table S302.  Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
18Q GAIN MUTATED 47 24 7 67 9
18Q GAIN WILD-TYPE 283 108 288 227 20

Figure S302.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

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

Table S303.  Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
18Q GAIN MUTATED 29 16 10 37 4
18Q GAIN WILD-TYPE 189 167 135 102 84

Figure S303.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'RPPA_CNMF'

P value = 0.00196 (Fisher's exact test), Q value = 0.0031

Table S304.  Gene #33: '18q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
18Q GAIN MUTATED 46 29 2 19 18 11 0
18Q GAIN WILD-TYPE 148 208 28 185 113 56 10

Figure S304.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'18q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00633 (Fisher's exact test), Q value = 0.009

Table S305.  Gene #33: '18q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
18Q GAIN MUTATED 43 58 24
18Q GAIN WILD-TYPE 177 340 231

Figure S305.  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 = 2.3e-05

Table S306.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
18Q GAIN MUTATED 41 11 5 36 57 1 3
18Q GAIN WILD-TYPE 223 158 138 189 146 50 17

Figure S306.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S307.  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 51 17 3 24 53 6
18Q GAIN WILD-TYPE 238 146 87 266 130 54

Figure S307.  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 = 2.3e-05

Table S308.  Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
18Q GAIN MUTATED 26 60 21 11 25 5
18Q GAIN WILD-TYPE 113 210 187 205 157 41

Figure S308.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S309.  Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
18Q GAIN MUTATED 14 14 10 20 11 12 45 9 13
18Q GAIN WILD-TYPE 52 109 174 166 63 101 114 64 70

Figure S309.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00029

Table S310.  Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
18Q GAIN MUTATED 19 5 5 12 36 9
18Q GAIN WILD-TYPE 114 87 54 107 109 105

Figure S310.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00483 (Fisher's exact test), Q value = 0.007

Table S311.  Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
18Q GAIN MUTATED 54 18 14
18Q GAIN WILD-TYPE 260 213 103

Figure S311.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'MRNA_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0012

Table S312.  Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
19P GAIN MUTATED 27 19 45
19P GAIN WILD-TYPE 202 97 123

Figure S312.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0033 (Fisher's exact test), Q value = 0.005

Table S313.  Gene #34: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
19P GAIN MUTATED 19 46 26
19P GAIN WILD-TYPE 140 220 62

Figure S313.  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 = 2.3e-05

Table S314.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
19P GAIN MUTATED 45 35 19 82 6
19P GAIN WILD-TYPE 285 97 276 212 23

Figure S314.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.00045

Table S315.  Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
19P GAIN MUTATED 24 31 19 41 12
19P GAIN WILD-TYPE 194 152 126 98 76

Figure S315.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'RPPA_CNMF'

P value = 0.00237 (Fisher's exact test), Q value = 0.0037

Table S316.  Gene #34: '19p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
19P GAIN MUTATED 52 32 4 26 31 11 1
19P GAIN WILD-TYPE 142 205 26 178 100 56 9

Figure S316.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'19p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00418 (Fisher's exact test), Q value = 0.0062

Table S317.  Gene #34: '19p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
19P GAIN MUTATED 56 59 42
19P GAIN WILD-TYPE 164 339 213

Figure S317.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19p gain' versus 'MRNASEQ_CNMF'

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

Table S318.  Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
19P GAIN MUTATED 32 29 19 28 64 5 8
19P GAIN WILD-TYPE 232 140 124 197 139 46 12

Figure S318.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S319.  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 24 10 40 56 16
19P GAIN WILD-TYPE 250 139 80 250 127 44

Figure S319.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.00047

Table S320.  Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
19P GAIN MUTATED 25 72 31 25 23 8
19P GAIN WILD-TYPE 114 198 177 191 159 38

Figure S320.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.4e-05

Table S321.  Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
19P GAIN MUTATED 5 30 23 19 11 19 45 13 19
19P GAIN WILD-TYPE 61 93 161 167 63 94 114 60 64

Figure S321.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.4e-05

Table S322.  Gene #34: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
19P GAIN MUTATED 13 13 17 12 43 15
19P GAIN WILD-TYPE 120 79 42 107 102 99

Figure S322.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'MRNA_CNMF'

P value = 0.00233 (Fisher's exact test), Q value = 0.0037

Table S323.  Gene #35: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
19Q GAIN MUTATED 36 24 51
19Q GAIN WILD-TYPE 193 92 117

Figure S323.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00745 (Fisher's exact test), Q value = 0.01

Table S324.  Gene #35: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
19Q GAIN MUTATED 27 54 30
19Q GAIN WILD-TYPE 132 212 58

Figure S324.  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 = 2.3e-05

Table S325.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
19Q GAIN MUTATED 60 39 22 90 8
19Q GAIN WILD-TYPE 270 93 273 204 21

Figure S325.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.4e-05

Table S326.  Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
19Q GAIN MUTATED 28 37 19 46 14
19Q GAIN WILD-TYPE 190 146 126 93 74

Figure S326.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'RPPA_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.021

Table S327.  Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
19Q GAIN MUTATED 57 39 6 35 30 13 0
19Q GAIN WILD-TYPE 137 198 24 169 101 54 10

Figure S327.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'19q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.021

Table S328.  Gene #35: '19q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
19Q GAIN MUTATED 60 70 50
19Q GAIN WILD-TYPE 160 328 205

Figure S328.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19q gain' versus 'MRNASEQ_CNMF'

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

Table S329.  Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
19Q GAIN MUTATED 46 37 23 28 69 6 8
19Q GAIN WILD-TYPE 218 132 120 197 134 45 12

Figure S329.  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 = 4.5e-05

Table S330.  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 33 13 44 62 17
19Q GAIN WILD-TYPE 241 130 77 246 121 43

Figure S330.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00029

Table S331.  Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
19Q GAIN MUTATED 31 82 35 30 30 9
19Q GAIN WILD-TYPE 108 188 173 186 152 37

Figure S331.  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 = 4.5e-05

Table S332.  Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
19Q GAIN MUTATED 7 37 27 24 10 24 50 14 24
19Q GAIN WILD-TYPE 59 86 157 162 64 89 109 59 59

Figure S332.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 8e-04

Table S333.  Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
19Q GAIN MUTATED 24 14 17 15 47 17
19Q GAIN WILD-TYPE 109 78 42 104 98 97

Figure S333.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MRNA_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00029

Table S334.  Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
20P GAIN MUTATED 87 34 89
20P GAIN WILD-TYPE 142 82 79

Figure S334.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'CN_CNMF'

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

Table S335.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
20P GAIN MUTATED 172 62 24 141 12
20P GAIN WILD-TYPE 158 70 271 153 17

Figure S335.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.00185 (Fisher's exact test), Q value = 0.003

Table S336.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
20P GAIN MUTATED 81 83 43 55 20
20P GAIN WILD-TYPE 137 100 102 84 68

Figure S336.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 0.0132 (Fisher's exact test), Q value = 0.018

Table S337.  Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
20P GAIN MUTATED 85 85 17 62 46 32 4
20P GAIN WILD-TYPE 109 152 13 142 85 35 6

Figure S337.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00463 (Fisher's exact test), Q value = 0.0068

Table S338.  Gene #36: '20p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
20P GAIN MUTATED 87 168 76
20P GAIN WILD-TYPE 133 230 179

Figure S338.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNASEQ_CNMF'

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

Table S339.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
20P GAIN MUTATED 113 85 34 70 86 11 10
20P GAIN WILD-TYPE 151 84 109 155 117 40 10

Figure S339.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S340.  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 112 86 7 104 76 24
20P GAIN WILD-TYPE 177 77 83 186 107 36

Figure S340.  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 = 2.3e-05

Table S341.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
20P GAIN MUTATED 66 128 63 47 74 27
20P GAIN WILD-TYPE 73 142 145 169 108 19

Figure S341.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S342.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
20P GAIN MUTATED 24 60 44 58 46 47 60 21 45
20P GAIN WILD-TYPE 42 63 140 128 28 66 99 52 38

Figure S342.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00858 (Fisher's exact test), Q value = 0.012

Table S343.  Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
20P GAIN MUTATED 52 29 26 46 72 32
20P GAIN WILD-TYPE 81 63 33 73 73 82

Figure S343.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00312 (Fisher's exact test), Q value = 0.0047

Table S344.  Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
20P GAIN MUTATED 140 70 47
20P GAIN WILD-TYPE 174 161 70

Figure S344.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00018

Table S345.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
20Q GAIN MUTATED 97 35 94
20Q GAIN WILD-TYPE 132 81 74

Figure S345.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'CN_CNMF'

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

Table S346.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
20Q GAIN MUTATED 202 61 26 149 12
20Q GAIN WILD-TYPE 128 71 269 145 17

Figure S346.  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 = 2.3e-05

Table S347.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
20Q GAIN MUTATED 89 100 42 62 19
20Q GAIN WILD-TYPE 129 83 103 77 69

Figure S347.  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 = 2.3e-05

Table S348.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
20Q GAIN MUTATED 144 87 35 69 88 13 12
20Q GAIN WILD-TYPE 120 82 108 156 115 38 8

Figure S348.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S349.  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 132 94 7 111 76 28
20Q GAIN WILD-TYPE 157 69 83 179 107 32

Figure S349.  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 = 2.3e-05

Table S350.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
20Q GAIN MUTATED 79 134 78 48 77 28
20Q GAIN WILD-TYPE 60 136 130 168 105 18

Figure S350.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S351.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
20Q GAIN MUTATED 31 66 45 68 44 59 61 23 47
20Q GAIN WILD-TYPE 35 57 139 118 30 54 98 50 36

Figure S351.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.0011

Table S352.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
20Q GAIN MUTATED 66 31 29 52 76 32
20Q GAIN WILD-TYPE 67 61 30 67 69 82

Figure S352.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S353.  Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
20Q GAIN MUTATED 163 74 49
20Q GAIN WILD-TYPE 151 157 68

Figure S353.  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 = 2.3e-05

Table S354.  Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
21Q GAIN MUTATED 31 17 57
21Q GAIN WILD-TYPE 198 99 111

Figure S354.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.00094

Table S355.  Gene #38: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
21Q GAIN MUTATED 18 60 27
21Q GAIN WILD-TYPE 141 206 61

Figure S355.  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 = 2.3e-05

Table S356.  Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
21Q GAIN MUTATED 49 25 17 100 7
21Q GAIN WILD-TYPE 281 107 278 194 22

Figure S356.  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 = 2.3e-05

Table S357.  Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
21Q GAIN MUTATED 16 37 17 51 8
21Q GAIN WILD-TYPE 202 146 128 88 80

Figure S357.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q gain' versus 'RPPA_CNMF'

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

Table S358.  Gene #38: '21q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
21Q GAIN MUTATED 55 29 5 23 32 14 4
21Q GAIN WILD-TYPE 139 208 25 181 99 53 6

Figure S358.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'21q gain' versus 'RPPA_CHIERARCHICAL'

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

Table S359.  Gene #38: '21q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
21Q GAIN MUTATED 72 56 34
21Q GAIN WILD-TYPE 148 342 221

Figure S359.  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 = 2.3e-05

Table S360.  Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
21Q GAIN MUTATED 34 49 10 23 72 4 5
21Q GAIN WILD-TYPE 230 120 133 202 131 47 15

Figure S360.  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 = 2.3e-05

Table S361.  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 43 4 25 62 25
21Q GAIN WILD-TYPE 251 120 86 265 121 35

Figure S361.  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 = 2.3e-05

Table S362.  Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
21Q GAIN MUTATED 28 84 18 26 27 10
21Q GAIN WILD-TYPE 111 186 190 190 155 36

Figure S362.  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 = 2.3e-05

Table S363.  Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
21Q GAIN MUTATED 7 36 12 19 12 19 53 10 25
21Q GAIN WILD-TYPE 59 87 172 167 62 94 106 63 58

Figure S363.  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 = 2.3e-05

Table S364.  Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
21Q GAIN MUTATED 18 8 9 16 52 15
21Q GAIN WILD-TYPE 115 84 50 103 93 99

Figure S364.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S365.  Gene #38: '21q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
21Q GAIN MUTATED 81 28 9
21Q GAIN WILD-TYPE 233 203 108

Figure S365.  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 = 2.3e-05

Table S366.  Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
22Q GAIN MUTATED 12 5 35
22Q GAIN WILD-TYPE 217 111 133

Figure S366.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0079 (Fisher's exact test), Q value = 0.011

Table S367.  Gene #39: '22q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
22Q GAIN MUTATED 8 29 15
22Q GAIN WILD-TYPE 151 237 73

Figure S367.  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 = 2.3e-05

Table S368.  Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
22Q GAIN MUTATED 32 2 4 59 2
22Q GAIN WILD-TYPE 298 130 291 235 27

Figure S368.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.4e-05

Table S369.  Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
22Q GAIN MUTATED 11 22 10 21 0
22Q GAIN WILD-TYPE 207 161 135 118 88

Figure S369.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.4e-05

Table S370.  Gene #39: '22q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
22Q GAIN MUTATED 30 10 4 10 17 12 1
22Q GAIN WILD-TYPE 164 227 26 194 114 55 9

Figure S370.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'22q gain' versus 'RPPA_CHIERARCHICAL'

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

Table S371.  Gene #39: '22q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
22Q GAIN MUTATED 42 30 12
22Q GAIN WILD-TYPE 178 368 243

Figure S371.  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 = 2.3e-05

Table S372.  Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
22Q GAIN MUTATED 23 29 1 5 37 0 2
22Q GAIN WILD-TYPE 241 140 142 220 166 51 18

Figure S372.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S373.  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 21 23 0 8 32 13
22Q GAIN WILD-TYPE 268 140 90 282 151 47

Figure S373.  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 = 2.3e-05

Table S374.  Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
22Q GAIN MUTATED 11 48 13 5 15 4
22Q GAIN WILD-TYPE 128 222 195 211 167 42

Figure S374.  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 = 2.3e-05

Table S375.  Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
22Q GAIN MUTATED 5 17 3 10 0 10 28 7 16
22Q GAIN WILD-TYPE 61 106 181 176 74 103 131 66 67

Figure S375.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00014

Table S376.  Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
22Q GAIN MUTATED 10 3 6 5 27 4
22Q GAIN WILD-TYPE 123 89 53 114 118 110

Figure S376.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00391 (Fisher's exact test), Q value = 0.0058

Table S377.  Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
22Q GAIN MUTATED 38 12 5
22Q GAIN WILD-TYPE 276 219 112

Figure S377.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp gain' versus 'MRNA_CNMF'

P value = 0.0198 (Fisher's exact test), Q value = 0.025

Table S378.  Gene #40: 'xp gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
XP GAIN MUTATED 35 12 38
XP GAIN WILD-TYPE 194 104 130

Figure S378.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp gain' versus 'CN_CNMF'

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

Table S379.  Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
XP GAIN MUTATED 43 22 14 66 5
XP GAIN WILD-TYPE 287 110 281 228 24

Figure S379.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

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

Table S380.  Gene #40: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
XP GAIN MUTATED 24 28 6 34 6
XP GAIN WILD-TYPE 194 155 139 105 82

Figure S380.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp gain' versus 'RPPA_CNMF'

P value = 0.00899 (Fisher's exact test), Q value = 0.012

Table S381.  Gene #40: 'xp gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
XP GAIN MUTATED 35 32 0 18 23 13 1
XP GAIN WILD-TYPE 159 205 30 186 108 54 9

Figure S381.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'xp gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00833 (Fisher's exact test), Q value = 0.012

Table S382.  Gene #40: 'xp gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
XP GAIN MUTATED 44 52 26
XP GAIN WILD-TYPE 176 346 229

Figure S382.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xp gain' versus 'MRNASEQ_CNMF'

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

Table S383.  Gene #40: 'xp gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
XP GAIN MUTATED 36 28 7 24 45 3 6
XP GAIN WILD-TYPE 228 141 136 201 158 48 14

Figure S383.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xp gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S384.  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 27 39 7
XP GAIN WILD-TYPE 251 126 89 263 144 53

Figure S384.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_CNMF'

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

Table S385.  Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
XP GAIN MUTATED 24 58 18 9 23 11
XP GAIN WILD-TYPE 115 212 190 207 159 35

Figure S385.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xp gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00012

Table S386.  Gene #40: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
XP GAIN MUTATED 7 22 9 20 15 16 32 5 17
XP GAIN WILD-TYPE 59 101 175 166 59 97 127 68 66

Figure S386.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S387.  Gene #40: 'xp gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
XP GAIN MUTATED 17 8 5 12 35 4
XP GAIN WILD-TYPE 116 84 54 107 110 110

Figure S387.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00023

Table S388.  Gene #40: 'xp gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
XP GAIN MUTATED 56 15 10
XP GAIN WILD-TYPE 258 216 107

Figure S388.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'MRNA_CNMF'

P value = 0.00453 (Fisher's exact test), Q value = 0.0066

Table S389.  Gene #41: 'xq gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
XQ GAIN MUTATED 32 10 38
XQ GAIN WILD-TYPE 197 106 130

Figure S389.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'xq gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00677 (Fisher's exact test), Q value = 0.0096

Table S390.  Gene #41: 'xq gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
XQ GAIN MUTATED 21 35 24
XQ GAIN WILD-TYPE 138 231 64

Figure S390.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

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

Table S391.  Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
XQ GAIN MUTATED 39 20 12 62 4
XQ GAIN WILD-TYPE 291 112 283 232 25

Figure S391.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

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

Table S392.  Gene #41: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
XQ GAIN MUTATED 23 20 4 33 5
XQ GAIN WILD-TYPE 195 163 141 106 83

Figure S392.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq gain' versus 'RPPA_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 0.023

Table S393.  Gene #41: 'xq gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
XQ GAIN MUTATED 37 28 0 19 18 9 2
XQ GAIN WILD-TYPE 157 209 30 185 113 58 8

Figure S393.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'xq gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.00087

Table S394.  Gene #41: 'xq gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
XQ GAIN MUTATED 46 43 24
XQ GAIN WILD-TYPE 174 355 231

Figure S394.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xq gain' versus 'MRNASEQ_CNMF'

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

Table S395.  Gene #41: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
XQ GAIN MUTATED 32 22 5 20 50 3 4
XQ GAIN WILD-TYPE 232 147 138 205 153 48 16

Figure S395.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S396.  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 23 45 6
XQ GAIN WILD-TYPE 252 138 90 267 138 54

Figure S396.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CNMF'

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

Table S397.  Gene #41: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
XQ GAIN MUTATED 20 61 18 7 16 8
XQ GAIN WILD-TYPE 119 209 190 209 166 38

Figure S397.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S398.  Gene #41: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
XQ GAIN MUTATED 3 17 11 22 13 12 36 4 12
XQ GAIN WILD-TYPE 63 106 173 164 61 101 123 69 71

Figure S398.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00014

Table S399.  Gene #41: 'xq gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
XQ GAIN MUTATED 13 7 6 8 33 4
XQ GAIN WILD-TYPE 120 85 53 111 112 110

Figure S399.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00423 (Fisher's exact test), Q value = 0.0062

Table S400.  Gene #41: 'xq gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
XQ GAIN MUTATED 47 16 8
XQ GAIN WILD-TYPE 267 215 109

Figure S400.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'MRNA_CNMF'

P value = 0.0231 (Fisher's exact test), Q value = 0.029

Table S401.  Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
1P LOSS MUTATED 64 19 32
1P LOSS WILD-TYPE 165 97 136

Figure S401.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0019 (Fisher's exact test), Q value = 0.003

Table S402.  Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
1P LOSS MUTATED 39 68 8
1P LOSS WILD-TYPE 120 198 80

Figure S402.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

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

Table S403.  Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
1P LOSS MUTATED 108 46 16 52 5
1P LOSS WILD-TYPE 222 86 279 242 24

Figure S403.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.00088

Table S404.  Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
1P LOSS MUTATED 41 57 22 21 12
1P LOSS WILD-TYPE 177 126 123 118 76

Figure S404.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'RPPA_CHIERARCHICAL'

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

Table S405.  Gene #42: '1p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
1P LOSS MUTATED 34 97 45
1P LOSS WILD-TYPE 186 301 210

Figure S405.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'1p loss' versus 'MRNASEQ_CNMF'

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

Table S406.  Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
1P LOSS MUTATED 74 56 13 47 22 8 5
1P LOSS WILD-TYPE 190 113 130 178 181 43 15

Figure S406.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S407.  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 79 60 7 51 20 8
1P LOSS WILD-TYPE 210 103 83 239 163 52

Figure S407.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.00329 (Fisher's exact test), Q value = 0.005

Table S408.  Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
1P LOSS MUTATED 34 55 49 26 42 15
1P LOSS WILD-TYPE 105 215 159 190 140 31

Figure S408.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S409.  Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
1P LOSS MUTATED 20 29 21 38 27 32 17 18 19
1P LOSS WILD-TYPE 46 94 163 148 47 81 142 55 64

Figure S409.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.022

Table S410.  Gene #42: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
1P LOSS MUTATED 33 16 6 22 14 21
1P LOSS WILD-TYPE 100 76 53 97 131 93

Figure S410.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1q loss' versus 'MRNA_CNMF'

P value = 0.00269 (Fisher's exact test), Q value = 0.0042

Table S411.  Gene #43: '1q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
1Q LOSS MUTATED 17 0 11
1Q LOSS WILD-TYPE 212 116 157

Figure S411.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1q loss' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00014

Table S412.  Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
1Q LOSS MUTATED 26 3 2 15 2
1Q LOSS WILD-TYPE 304 129 293 279 27

Figure S412.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 0.00175 (Fisher's exact test), Q value = 0.0028

Table S413.  Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
1Q LOSS MUTATED 22 11 2 4 7 0 1
1Q LOSS WILD-TYPE 242 158 141 221 196 51 19

Figure S413.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q loss' versus 'MIRSEQ_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.021

Table S414.  Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
1Q LOSS MUTATED 12 16 8 3 5 2
1Q LOSS WILD-TYPE 127 254 200 213 177 44

Figure S414.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p loss' versus 'MRNA_CNMF'

P value = 0.00625 (Fisher's exact test), Q value = 0.009

Table S415.  Gene #44: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
2P LOSS MUTATED 57 15 24
2P LOSS WILD-TYPE 172 101 144

Figure S415.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.029 (Fisher's exact test), Q value = 0.036

Table S416.  Gene #44: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
2P LOSS MUTATED 38 49 9
2P LOSS WILD-TYPE 121 217 79

Figure S416.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

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

Table S417.  Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
2P LOSS MUTATED 92 36 10 43 4
2P LOSS WILD-TYPE 238 96 285 251 25

Figure S417.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00018

Table S418.  Gene #44: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
2P LOSS MUTATED 51 35 12 12 10
2P LOSS WILD-TYPE 167 148 133 127 78

Figure S418.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p loss' versus 'RPPA_CNMF'

P value = 0.0299 (Fisher's exact test), Q value = 0.037

Table S419.  Gene #44: '2p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
2P LOSS MUTATED 33 56 1 27 20 12 1
2P LOSS WILD-TYPE 161 181 29 177 111 55 9

Figure S419.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'2p loss' versus 'RPPA_CHIERARCHICAL'

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

Table S420.  Gene #44: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
2P LOSS MUTATED 24 96 30
2P LOSS WILD-TYPE 196 302 225

Figure S420.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2p loss' versus 'MRNASEQ_CNMF'

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

Table S421.  Gene #44: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
2P LOSS MUTATED 71 28 16 44 20 2 2
2P LOSS WILD-TYPE 193 141 127 181 183 49 18

Figure S421.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S422.  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 43 8 38 16 2
2P LOSS WILD-TYPE 213 120 82 252 167 58

Figure S422.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

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

Table S423.  Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
2P LOSS MUTATED 41 35 40 20 36 9
2P LOSS WILD-TYPE 98 235 168 196 146 37

Figure S423.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 7e-04

Table S424.  Gene #44: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
2P LOSS MUTATED 18 23 18 38 16 28 14 13 13
2P LOSS WILD-TYPE 48 100 166 148 58 85 145 60 70

Figure S424.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S425.  Gene #44: '2p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
2P LOSS MUTATED 34 7 11 22 14 14
2P LOSS WILD-TYPE 99 85 48 97 131 100

Figure S425.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q loss' versus 'CN_CNMF'

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

Table S426.  Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
2Q LOSS MUTATED 98 39 11 57 6
2Q LOSS WILD-TYPE 232 93 284 237 23

Figure S426.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.00335 (Fisher's exact test), Q value = 0.005

Table S427.  Gene #45: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
2Q LOSS MUTATED 52 38 15 26 9
2Q LOSS WILD-TYPE 166 145 130 113 79

Figure S427.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q loss' versus 'RPPA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00018

Table S428.  Gene #45: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
2Q LOSS MUTATED 39 100 31
2Q LOSS WILD-TYPE 181 298 224

Figure S428.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.00074

Table S429.  Gene #45: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
2Q LOSS MUTATED 73 34 17 44 36 3 2
2Q LOSS WILD-TYPE 191 135 126 181 167 48 18

Figure S429.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S430.  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 41 32 4
2Q LOSS WILD-TYPE 212 117 81 249 151 56

Figure S430.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.0016

Table S431.  Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
2Q LOSS MUTATED 42 54 38 24 39 10
2Q LOSS WILD-TYPE 97 216 170 192 143 36

Figure S431.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0197 (Fisher's exact test), Q value = 0.025

Table S432.  Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
2Q LOSS MUTATED 18 29 19 38 18 26 31 15 13
2Q LOSS WILD-TYPE 48 94 165 148 56 87 128 58 70

Figure S432.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00489 (Fisher's exact test), Q value = 0.0071

Table S433.  Gene #45: '2q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
2Q LOSS MUTATED 38 9 12 23 25 14
2Q LOSS WILD-TYPE 95 83 47 96 120 100

Figure S433.  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 = 2.3e-05

Table S434.  Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
3P LOSS MUTATED 23 11 53
3P LOSS WILD-TYPE 206 105 115

Figure S434.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p loss' versus 'MRNA_CHIERARCHICAL'

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

Table S435.  Gene #46: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
3P LOSS MUTATED 11 50 26
3P LOSS WILD-TYPE 148 216 62

Figure S435.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

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

Table S436.  Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
3P LOSS MUTATED 66 16 9 94 3
3P LOSS WILD-TYPE 264 116 286 200 26

Figure S436.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

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

Table S437.  Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
3P LOSS MUTATED 20 47 19 41 5
3P LOSS WILD-TYPE 198 136 126 98 83

Figure S437.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CNMF'

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

Table S438.  Gene #46: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
3P LOSS MUTATED 60 21 8 25 26 17 2
3P LOSS WILD-TYPE 134 216 22 179 105 50 8

Figure S438.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

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

Table S439.  Gene #46: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
3P LOSS MUTATED 69 56 34
3P LOSS WILD-TYPE 151 342 221

Figure S439.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

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

Table S440.  Gene #46: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
3P LOSS MUTATED 41 50 14 14 59 5 4
3P LOSS WILD-TYPE 223 119 129 211 144 46 16

Figure S440.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S441.  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 44 5 36 56 15
3P LOSS WILD-TYPE 258 119 85 254 127 45

Figure S441.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

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

Table S442.  Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
3P LOSS MUTATED 26 80 24 20 23 9
3P LOSS WILD-TYPE 113 190 184 196 159 37

Figure S442.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S443.  Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
3P LOSS MUTATED 13 29 16 20 2 18 45 16 23
3P LOSS WILD-TYPE 53 94 168 166 72 95 114 57 60

Figure S443.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.4e-05

Table S444.  Gene #46: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
3P LOSS MUTATED 22 10 7 12 48 18
3P LOSS WILD-TYPE 111 82 52 107 97 96

Figure S444.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0158 (Fisher's exact test), Q value = 0.021

Table S445.  Gene #46: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
3P LOSS MUTATED 69 35 13
3P LOSS WILD-TYPE 245 196 104

Figure S445.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'MRNA_CNMF'

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

Table S446.  Gene #47: '3q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
3Q LOSS MUTATED 13 5 30
3Q LOSS WILD-TYPE 216 111 138

Figure S446.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0086 (Fisher's exact test), Q value = 0.012

Table S447.  Gene #47: '3q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
3Q LOSS MUTATED 6 31 11
3Q LOSS WILD-TYPE 153 235 77

Figure S447.  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 = 2.3e-05

Table S448.  Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
3Q LOSS MUTATED 40 11 2 49 3
3Q LOSS WILD-TYPE 290 121 293 245 26

Figure S448.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.4e-05

Table S449.  Gene #47: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
3Q LOSS MUTATED 14 28 8 24 2
3Q LOSS WILD-TYPE 204 155 137 115 86

Figure S449.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q loss' versus 'RPPA_CNMF'

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

Table S450.  Gene #47: '3q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
3Q LOSS MUTATED 35 14 4 11 9 13 1
3Q LOSS WILD-TYPE 159 223 26 193 122 54 9

Figure S450.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'3q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.001

Table S451.  Gene #47: '3q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
3Q LOSS MUTATED 36 36 15
3Q LOSS WILD-TYPE 184 362 240

Figure S451.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.4e-05

Table S452.  Gene #47: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
3Q LOSS MUTATED 26 31 7 8 27 4 2
3Q LOSS WILD-TYPE 238 138 136 217 176 47 18

Figure S452.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00014

Table S453.  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 29 3 18 25 9
3Q LOSS WILD-TYPE 268 134 87 272 158 51

Figure S453.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 0.00203 (Fisher's exact test), Q value = 0.0032

Table S454.  Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
3Q LOSS MUTATED 17 40 13 11 14 6
3Q LOSS WILD-TYPE 122 230 195 205 168 40

Figure S454.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00037

Table S455.  Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
3Q LOSS MUTATED 11 17 11 8 1 10 22 9 12
3Q LOSS WILD-TYPE 55 106 173 178 73 103 137 64 71

Figure S455.  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 = 2.3e-05

Table S456.  Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
4P LOSS MUTATED 55 28 90
4P LOSS WILD-TYPE 174 88 78

Figure S456.  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 = 2.3e-05

Table S457.  Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
4P LOSS MUTATED 32 87 54
4P LOSS WILD-TYPE 127 179 34

Figure S457.  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 = 2.3e-05

Table S458.  Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
4P LOSS MUTATED 78 56 26 187 6
4P LOSS WILD-TYPE 252 76 269 107 23

Figure S458.  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 = 2.3e-05

Table S459.  Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
4P LOSS MUTATED 50 54 35 93 12
4P LOSS WILD-TYPE 168 129 110 46 76

Figure S459.  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 = 2.3e-05

Table S460.  Gene #48: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
4P LOSS MUTATED 114 49 7 44 42 31 2
4P LOSS WILD-TYPE 80 188 23 160 89 36 8

Figure S460.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p loss' versus 'RPPA_CHIERARCHICAL'

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

Table S461.  Gene #48: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
4P LOSS MUTATED 128 101 60
4P LOSS WILD-TYPE 92 297 195

Figure S461.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p loss' versus 'MRNASEQ_CNMF'

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

Table S462.  Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
4P LOSS MUTATED 58 80 16 54 129 7 8
4P LOSS WILD-TYPE 206 89 127 171 74 44 12

Figure S462.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S463.  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 S463.  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 = 2.3e-05

Table S464.  Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
4P LOSS MUTATED 38 158 31 40 62 13
4P LOSS WILD-TYPE 101 112 177 176 120 33

Figure S464.  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 = 2.3e-05

Table S465.  Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
4P LOSS MUTATED 17 54 27 40 25 27 102 8 42
4P LOSS WILD-TYPE 49 69 157 146 49 86 57 65 41

Figure S465.  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 = 2.3e-05

Table S466.  Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
4P LOSS MUTATED 24 21 19 31 96 22
4P LOSS WILD-TYPE 109 71 40 88 49 92

Figure S466.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S467.  Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
4P LOSS MUTATED 131 47 35
4P LOSS WILD-TYPE 183 184 82

Figure S467.  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 = 2.3e-05

Table S468.  Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
4Q LOSS MUTATED 51 23 77
4Q LOSS WILD-TYPE 178 93 91

Figure S468.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00029

Table S469.  Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
4Q LOSS MUTATED 33 77 41
4Q LOSS WILD-TYPE 126 189 47

Figure S469.  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 = 2.3e-05

Table S470.  Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
4Q LOSS MUTATED 72 56 22 155 6
4Q LOSS WILD-TYPE 258 76 273 139 23

Figure S470.  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 = 2.3e-05

Table S471.  Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
4Q LOSS MUTATED 49 49 33 75 12
4Q LOSS WILD-TYPE 169 134 112 64 76

Figure S471.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'RPPA_CNMF'

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

Table S472.  Gene #49: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
4Q LOSS MUTATED 96 42 10 35 43 29 1
4Q LOSS WILD-TYPE 98 195 20 169 88 38 9

Figure S472.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4q loss' versus 'RPPA_CHIERARCHICAL'

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

Table S473.  Gene #49: '4q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
4Q LOSS MUTATED 106 99 51
4Q LOSS WILD-TYPE 114 299 204

Figure S473.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4q loss' versus 'MRNASEQ_CNMF'

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

Table S474.  Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
4Q LOSS MUTATED 54 73 15 54 102 5 7
4Q LOSS WILD-TYPE 210 96 128 171 101 46 13

Figure S474.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S475.  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 63 66 9 51 94 27
4Q LOSS WILD-TYPE 226 97 81 239 89 33

Figure S475.  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 = 2.3e-05

Table S476.  Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
4Q LOSS MUTATED 34 123 34 37 58 14
4Q LOSS WILD-TYPE 105 147 174 179 124 32

Figure S476.  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 = 2.3e-05

Table S477.  Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
4Q LOSS MUTATED 15 43 26 39 26 27 76 8 40
4Q LOSS WILD-TYPE 51 80 158 147 48 86 83 65 43

Figure S477.  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 = 2.3e-05

Table S478.  Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
4Q LOSS MUTATED 26 18 18 27 73 20
4Q LOSS WILD-TYPE 107 74 41 92 72 94

Figure S478.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.00041

Table S479.  Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
4Q LOSS MUTATED 106 42 34
4Q LOSS WILD-TYPE 208 189 83

Figure S479.  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 = 2.3e-05

Table S480.  Gene #50: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
5P LOSS MUTATED 14 9 50
5P LOSS WILD-TYPE 215 107 118

Figure S480.  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 = 2.3e-05

Table S481.  Gene #50: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
5P LOSS MUTATED 6 30 37
5P LOSS WILD-TYPE 153 236 51

Figure S481.  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 = 2.3e-05

Table S482.  Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
5P LOSS MUTATED 26 4 6 103 3
5P LOSS WILD-TYPE 304 128 289 191 26

Figure S482.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

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

Table S483.  Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
5P LOSS MUTATED 8 14 20 56 1
5P LOSS WILD-TYPE 210 169 125 83 87

Figure S483.  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 = 2.3e-05

Table S484.  Gene #50: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
5P LOSS MUTATED 64 9 1 15 23 13 1
5P LOSS WILD-TYPE 130 228 29 189 108 54 9

Figure S484.  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 = 2.3e-05

Table S485.  Gene #50: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
5P LOSS MUTATED 72 35 19
5P LOSS WILD-TYPE 148 363 236

Figure S485.  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 = 2.3e-05

Table S486.  Gene #50: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
5P LOSS MUTATED 20 25 4 7 82 2 1
5P LOSS WILD-TYPE 244 144 139 218 121 49 19

Figure S486.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S487.  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 14 25 1 12 78 11
5P LOSS WILD-TYPE 275 138 89 278 105 49

Figure S487.  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 = 2.3e-05

Table S488.  Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
5P LOSS MUTATED 19 81 3 16 14 6
5P LOSS WILD-TYPE 120 189 205 200 168 40

Figure S488.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S489.  Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
5P LOSS MUTATED 8 20 3 7 4 9 69 5 14
5P LOSS WILD-TYPE 58 103 181 179 70 104 90 68 69

Figure S489.  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 = 2.3e-05

Table S490.  Gene #50: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
5P LOSS MUTATED 10 3 2 6 57 7
5P LOSS WILD-TYPE 123 89 57 113 88 107

Figure S490.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S491.  Gene #50: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
5P LOSS MUTATED 73 8 4
5P LOSS WILD-TYPE 241 223 113

Figure S491.  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 = 2.3e-05

Table S492.  Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
5Q LOSS MUTATED 16 16 79
5Q LOSS WILD-TYPE 213 100 89

Figure S492.  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 = 2.3e-05

Table S493.  Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
5Q LOSS MUTATED 7 49 55
5Q LOSS WILD-TYPE 152 217 33

Figure S493.  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 = 2.3e-05

Table S494.  Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
5Q LOSS MUTATED 34 7 8 175 4
5Q LOSS WILD-TYPE 296 125 287 119 25

Figure S494.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

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

Table S495.  Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
5Q LOSS MUTATED 13 22 32 93 3
5Q LOSS WILD-TYPE 205 161 113 46 85

Figure S495.  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 = 2.3e-05

Table S496.  Gene #51: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
5Q LOSS MUTATED 98 13 6 23 34 24 2
5Q LOSS WILD-TYPE 96 224 24 181 97 43 8

Figure S496.  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 = 2.3e-05

Table S497.  Gene #51: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
5Q LOSS MUTATED 116 53 31
5Q LOSS WILD-TYPE 104 345 224

Figure S497.  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 = 2.3e-05

Table S498.  Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
5Q LOSS MUTATED 34 42 7 8 128 3 5
5Q LOSS WILD-TYPE 230 127 136 217 75 48 15

Figure S498.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S499.  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 23 38 1 23 121 21
5Q LOSS WILD-TYPE 266 125 89 267 62 39

Figure S499.  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 = 2.3e-05

Table S500.  Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
5Q LOSS MUTATED 28 145 5 18 19 8
5Q LOSS WILD-TYPE 111 125 203 198 163 38

Figure S500.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S501.  Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
5Q LOSS MUTATED 10 39 4 10 5 11 106 7 31
5Q LOSS WILD-TYPE 56 84 180 176 69 102 53 66 52

Figure S501.  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 = 2.3e-05

Table S502.  Gene #51: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
5Q LOSS MUTATED 16 10 4 8 92 11
5Q LOSS WILD-TYPE 117 82 55 111 53 103

Figure S502.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S503.  Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
5Q LOSS MUTATED 114 19 8
5Q LOSS WILD-TYPE 200 212 109

Figure S503.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0477 (Fisher's exact test), Q value = 0.058

Table S504.  Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
6P LOSS MUTATED 36 51 9
6P LOSS WILD-TYPE 123 215 79

Figure S504.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

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

Table S505.  Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
6P LOSS MUTATED 103 27 26 29 5
6P LOSS WILD-TYPE 227 105 269 265 24

Figure S505.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00652 (Fisher's exact test), Q value = 0.0093

Table S506.  Gene #52: '6p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
6P LOSS MUTATED 28 89 40
6P LOSS WILD-TYPE 192 309 215

Figure S506.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 0.00312 (Fisher's exact test), Q value = 0.0047

Table S507.  Gene #52: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
6P LOSS MUTATED 65 31 23 41 21 7 1
6P LOSS WILD-TYPE 199 138 120 184 182 44 19

Figure S507.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00882 (Fisher's exact test), Q value = 0.012

Table S508.  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 15 48 18 10
6P LOSS WILD-TYPE 221 133 75 242 165 50

Figure S508.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00628 (Fisher's exact test), Q value = 0.009

Table S509.  Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
6P LOSS MUTATED 17 19 26 43 17 24 15 16 11
6P LOSS WILD-TYPE 49 104 158 143 57 89 144 57 72

Figure S509.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0256 (Fisher's exact test), Q value = 0.032

Table S510.  Gene #53: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
6Q LOSS MUTATED 47 72 13
6Q LOSS WILD-TYPE 112 194 75

Figure S510.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

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

Table S511.  Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
6Q LOSS MUTATED 149 39 45 37 10
6Q LOSS WILD-TYPE 181 93 250 257 19

Figure S511.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.00094 (Fisher's exact test), Q value = 0.0016

Table S512.  Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
6Q LOSS MUTATED 73 57 28 26 17
6Q LOSS WILD-TYPE 145 126 117 113 71

Figure S512.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.0013

Table S513.  Gene #53: '6q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
6Q LOSS MUTATED 40 127 62
6Q LOSS WILD-TYPE 180 271 193

Figure S513.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'6q loss' versus 'MRNASEQ_CNMF'

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

Table S514.  Gene #53: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
6Q LOSS MUTATED 98 43 37 58 30 11 2
6Q LOSS WILD-TYPE 166 126 106 167 173 40 18

Figure S514.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.00067

Table S515.  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 94 42 23 78 25 17
6Q LOSS WILD-TYPE 195 121 67 212 158 43

Figure S515.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 0.00786 (Fisher's exact test), Q value = 0.011

Table S516.  Gene #53: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
6Q LOSS MUTATED 43 52 67 53 46 17
6Q LOSS WILD-TYPE 96 218 141 163 136 29

Figure S516.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S517.  Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
6Q LOSS MUTATED 25 27 43 62 27 36 21 22 15
6Q LOSS WILD-TYPE 41 96 141 124 47 77 138 51 68

Figure S517.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.014

Table S518.  Gene #53: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
6Q LOSS MUTATED 40 19 21 35 23 33
6Q LOSS WILD-TYPE 93 73 38 84 122 81

Figure S518.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p loss' versus 'MRNA_CNMF'

P value = 0.00559 (Fisher's exact test), Q value = 0.0081

Table S519.  Gene #54: '7p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
7P LOSS MUTATED 24 6 29
7P LOSS WILD-TYPE 205 110 139

Figure S519.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'7p loss' versus 'CN_CNMF'

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

Table S520.  Gene #54: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
7P LOSS MUTATED 46 9 5 51 0
7P LOSS WILD-TYPE 284 123 290 243 29

Figure S520.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

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

Table S521.  Gene #54: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
7P LOSS MUTATED 12 23 6 28 2
7P LOSS WILD-TYPE 206 160 139 111 86

Figure S521.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p loss' versus 'RPPA_CNMF'

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

Table S522.  Gene #54: '7p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
7P LOSS MUTATED 37 17 5 12 10 10 0
7P LOSS WILD-TYPE 157 220 25 192 121 57 10

Figure S522.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00737 (Fisher's exact test), Q value = 0.01

Table S523.  Gene #54: '7p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
7P LOSS MUTATED 33 42 16
7P LOSS WILD-TYPE 187 356 239

Figure S523.  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 = 2.3e-05

Table S524.  Gene #54: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
7P LOSS MUTATED 33 22 4 10 35 2 4
7P LOSS WILD-TYPE 231 147 139 215 168 49 16

Figure S524.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S525.  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 29 6
7P LOSS WILD-TYPE 258 138 90 271 154 54

Figure S525.  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 = 2.3e-05

Table S526.  Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
7P LOSS MUTATED 18 47 20 4 16 4
7P LOSS WILD-TYPE 121 223 188 212 166 42

Figure S526.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.4e-05

Table S527.  Gene #54: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
7P LOSS MUTATED 9 16 6 15 3 15 27 4 14
7P LOSS WILD-TYPE 57 107 178 171 71 98 132 69 69

Figure S527.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S528.  Gene #54: '7p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
7P LOSS MUTATED 15 5 3 7 29 2
7P LOSS WILD-TYPE 118 87 56 112 116 112

Figure S528.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00243 (Fisher's exact test), Q value = 0.0038

Table S529.  Gene #54: '7p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
7P LOSS MUTATED 42 13 6
7P LOSS WILD-TYPE 272 218 111

Figure S529.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

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

Table S530.  Gene #55: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
7Q LOSS MUTATED 54 14 13 39 0
7Q LOSS WILD-TYPE 276 118 282 255 29

Figure S530.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

'7q loss' versus 'METHLYATION_CNMF'

P value = 0.00334 (Fisher's exact test), Q value = 0.005

Table S531.  Gene #55: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
7Q LOSS MUTATED 17 27 6 19 5
7Q LOSS WILD-TYPE 201 156 139 120 83

Figure S531.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q loss' versus 'RPPA_CNMF'

P value = 0.0266 (Fisher's exact test), Q value = 0.033

Table S532.  Gene #55: '7q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
7Q LOSS MUTATED 26 23 3 15 14 16 1
7Q LOSS WILD-TYPE 168 214 27 189 117 51 9

Figure S532.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 0.00171 (Fisher's exact test), Q value = 0.0027

Table S533.  Gene #55: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
7Q LOSS MUTATED 32 30 6 20 22 4 5
7Q LOSS WILD-TYPE 232 139 137 205 181 47 15

Figure S533.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S534.  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 39 31 2 24 16 7
7Q LOSS WILD-TYPE 250 132 88 266 167 53

Figure S534.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.0012

Table S535.  Gene #55: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
7Q LOSS MUTATED 22 38 23 8 21 6
7Q LOSS WILD-TYPE 117 232 185 208 161 40

Figure S535.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00029

Table S536.  Gene #55: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
7Q LOSS MUTATED 11 23 6 19 6 17 15 6 15
7Q LOSS WILD-TYPE 55 100 178 167 68 96 144 67 68

Figure S536.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00968 (Fisher's exact test), Q value = 0.013

Table S537.  Gene #55: '7q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
7Q LOSS MUTATED 17 6 6 12 22 3
7Q LOSS WILD-TYPE 116 86 53 107 123 111

Figure S537.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0169 (Fisher's exact test), Q value = 0.022

Table S538.  Gene #55: '7q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
7Q LOSS MUTATED 40 13 13
7Q LOSS WILD-TYPE 274 218 104

Figure S538.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'MRNA_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.026

Table S539.  Gene #56: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
8P LOSS MUTATED 79 41 80
8P LOSS WILD-TYPE 150 75 88

Figure S539.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p loss' versus 'CN_CNMF'

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

Table S540.  Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
8P LOSS MUTATED 156 23 61 148 7
8P LOSS WILD-TYPE 174 109 234 146 22

Figure S540.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

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

Table S541.  Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
8P LOSS MUTATED 61 85 49 60 15
8P LOSS WILD-TYPE 157 98 96 79 73

Figure S541.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'RPPA_CNMF'

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

Table S542.  Gene #56: '8p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
8P LOSS MUTATED 88 74 12 60 53 37 6
8P LOSS WILD-TYPE 106 163 18 144 78 30 4

Figure S542.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0323 (Fisher's exact test), Q value = 0.04

Table S543.  Gene #56: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
8P LOSS MUTATED 99 145 86
8P LOSS WILD-TYPE 121 253 169

Figure S543.  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 = 2.3e-05

Table S544.  Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
8P LOSS MUTATED 113 87 36 44 82 18 12
8P LOSS WILD-TYPE 151 82 107 181 121 33 8

Figure S544.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S545.  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 80 19 89 72 34
8P LOSS WILD-TYPE 191 83 71 201 111 26

Figure S545.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

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

Table S546.  Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
8P LOSS MUTATED 61 127 65 53 66 17
8P LOSS WILD-TYPE 78 143 143 163 116 29

Figure S546.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S547.  Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
8P LOSS MUTATED 29 53 45 55 26 40 65 30 46
8P LOSS WILD-TYPE 37 70 139 131 48 73 94 43 37

Figure S547.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00237 (Fisher's exact test), Q value = 0.0037

Table S548.  Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
8P LOSS MUTATED 133 75 30
8P LOSS WILD-TYPE 181 156 87

Figure S548.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

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

Table S549.  Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
8Q LOSS MUTATED 47 10 10 25 1
8Q LOSS WILD-TYPE 283 122 285 269 28

Figure S549.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 0.00923 (Fisher's exact test), Q value = 0.013

Table S550.  Gene #57: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
8Q LOSS MUTATED 26 27 6 17 14 2 1
8Q LOSS WILD-TYPE 238 142 137 208 189 49 19

Figure S550.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0149 (Fisher's exact test), Q value = 0.02

Table S551.  Gene #57: '8q 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
8Q LOSS MUTATED 29 18 1 22 14 9
8Q LOSS WILD-TYPE 260 145 89 268 169 51

Figure S551.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MRNA_CNMF'

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

Table S552.  Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
9P LOSS MUTATED 69 22 74
9P LOSS WILD-TYPE 160 94 94

Figure S552.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0402 (Fisher's exact test), Q value = 0.049

Table S553.  Gene #58: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
9P LOSS MUTATED 42 99 24
9P LOSS WILD-TYPE 117 167 64

Figure S553.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

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

Table S554.  Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
9P LOSS MUTATED 169 14 17 106 7
9P LOSS WILD-TYPE 161 118 278 188 22

Figure S554.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

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

Table S555.  Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
9P LOSS MUTATED 54 73 24 49 10
9P LOSS WILD-TYPE 164 110 121 90 78

Figure S555.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CNMF'

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

Table S556.  Gene #58: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
9P LOSS MUTATED 74 52 11 50 38 28 7
9P LOSS WILD-TYPE 120 185 19 154 93 39 3

Figure S556.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

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

Table S557.  Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
9P LOSS MUTATED 111 72 17 38 57 8 8
9P LOSS WILD-TYPE 153 97 126 187 146 43 12

Figure S557.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S558.  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 49 26
9P LOSS WILD-TYPE 193 87 85 231 134 34

Figure S558.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

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

Table S559.  Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
9P LOSS MUTATED 68 103 46 27 51 12
9P LOSS WILD-TYPE 71 167 162 189 131 34

Figure S559.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S560.  Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
9P LOSS MUTATED 27 52 19 47 19 40 44 18 41
9P LOSS WILD-TYPE 39 71 165 139 55 73 115 55 42

Figure S560.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S561.  Gene #58: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
9P LOSS MUTATED 51 19 14 23 56 23
9P LOSS WILD-TYPE 82 73 45 96 89 91

Figure S561.  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 = 2.3e-05

Table S562.  Gene #58: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
9P LOSS MUTATED 120 47 19
9P LOSS WILD-TYPE 194 184 98

Figure S562.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'MRNA_CNMF'

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

Table S563.  Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
9Q LOSS MUTATED 57 18 71
9Q LOSS WILD-TYPE 172 98 97

Figure S563.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0217 (Fisher's exact test), Q value = 0.028

Table S564.  Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
9Q LOSS MUTATED 35 77 34
9Q LOSS WILD-TYPE 124 189 54

Figure S564.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

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

Table S565.  Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
9Q LOSS MUTATED 136 12 13 111 8
9Q LOSS WILD-TYPE 194 120 282 183 21

Figure S565.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

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

Table S566.  Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
9Q LOSS MUTATED 47 53 24 58 7
9Q LOSS WILD-TYPE 171 130 121 81 81

Figure S566.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CNMF'

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

Table S567.  Gene #59: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
9Q LOSS MUTATED 71 43 11 38 35 23 5
9Q LOSS WILD-TYPE 123 194 19 166 96 44 5

Figure S567.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q loss' versus 'RPPA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00018

Table S568.  Gene #59: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
9Q LOSS MUTATED 80 98 48
9Q LOSS WILD-TYPE 140 300 207

Figure S568.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9q loss' versus 'MRNASEQ_CNMF'

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

Table S569.  Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
9Q LOSS MUTATED 93 48 11 38 75 5 8
9Q LOSS WILD-TYPE 171 121 132 187 128 46 12

Figure S569.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S570.  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 61 3 47 66 20
9Q LOSS WILD-TYPE 208 102 87 243 117 40

Figure S570.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

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

Table S571.  Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
9Q LOSS MUTATED 53 111 38 22 38 9
9Q LOSS WILD-TYPE 86 159 170 194 144 37

Figure S571.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S572.  Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
9Q LOSS MUTATED 18 47 15 35 15 37 58 14 32
9Q LOSS WILD-TYPE 48 76 169 151 59 76 101 59 51

Figure S572.  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 = 2.3e-05

Table S573.  Gene #59: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
9Q LOSS MUTATED 43 17 10 16 59 18
9Q LOSS WILD-TYPE 90 75 49 103 86 96

Figure S573.  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 = 2.3e-05

Table S574.  Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
9Q LOSS MUTATED 110 41 12
9Q LOSS WILD-TYPE 204 190 105

Figure S574.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

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

Table S575.  Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
10P LOSS MUTATED 71 20 14 66 4
10P LOSS WILD-TYPE 259 112 281 228 25

Figure S575.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.0011

Table S576.  Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
10P LOSS MUTATED 39 37 11 33 9
10P LOSS WILD-TYPE 179 146 134 106 79

Figure S576.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00023

Table S577.  Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
10P LOSS MUTATED 52 41 10 27 39 4 2
10P LOSS WILD-TYPE 212 128 133 198 164 47 18

Figure S577.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S578.  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 51 42 4 33 33 12
10P LOSS WILD-TYPE 238 121 86 257 150 48

Figure S578.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

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

Table S579.  Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
10P LOSS MUTATED 35 53 33 16 28 7
10P LOSS WILD-TYPE 104 217 175 200 154 39

Figure S579.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MRNA_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00022

Table S580.  Gene #61: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
10Q LOSS MUTATED 37 17 55
10Q LOSS WILD-TYPE 192 99 113

Figure S580.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.019

Table S581.  Gene #61: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
10Q LOSS MUTATED 25 56 28
10Q LOSS WILD-TYPE 134 210 60

Figure S581.  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 = 2.3e-05

Table S582.  Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
10Q LOSS MUTATED 84 23 15 102 7
10Q LOSS WILD-TYPE 246 109 280 192 22

Figure S582.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

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

Table S583.  Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
10Q LOSS MUTATED 42 50 17 55 10
10Q LOSS WILD-TYPE 176 133 128 84 78

Figure S583.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CNMF'

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

Table S584.  Gene #61: '10q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
10Q LOSS MUTATED 63 39 11 27 38 20 2
10Q LOSS WILD-TYPE 131 198 19 177 93 47 8

Figure S584.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'10q loss' versus 'RPPA_CHIERARCHICAL'

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

Table S585.  Gene #61: '10q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
10Q LOSS MUTATED 74 84 42
10Q LOSS WILD-TYPE 146 314 213

Figure S585.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10q loss' versus 'MRNASEQ_CNMF'

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

Table S586.  Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
10Q LOSS MUTATED 64 53 12 28 69 2 3
10Q LOSS WILD-TYPE 200 116 131 197 134 49 17

Figure S586.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S587.  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 56 55 4 39 62 15
10Q LOSS WILD-TYPE 233 108 86 251 121 45

Figure S587.  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 = 2.3e-05

Table S588.  Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
10Q LOSS MUTATED 42 83 33 23 38 7
10Q LOSS WILD-TYPE 97 187 175 193 144 39

Figure S588.  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 = 2.3e-05

Table S589.  Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
10Q LOSS MUTATED 20 36 21 26 10 23 48 13 29
10Q LOSS WILD-TYPE 46 87 163 160 64 90 111 60 54

Figure S589.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0053 (Fisher's exact test), Q value = 0.0077

Table S590.  Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
10Q LOSS MUTATED 32 16 12 20 49 18
10Q LOSS WILD-TYPE 101 76 47 99 96 96

Figure S590.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.0013

Table S591.  Gene #61: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
10Q LOSS MUTATED 90 39 18
10Q LOSS WILD-TYPE 224 192 99

Figure S591.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

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

Table S592.  Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
11P LOSS MUTATED 120 25 15 105 5
11P LOSS WILD-TYPE 210 107 280 189 24

Figure S592.  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 = 2.3e-05

Table S593.  Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
11P LOSS MUTATED 40 64 22 52 8
11P LOSS WILD-TYPE 178 119 123 87 80

Figure S593.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'RPPA_CNMF'

P value = 0.00316 (Fisher's exact test), Q value = 0.0048

Table S594.  Gene #62: '11p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
11P LOSS MUTATED 64 52 9 36 40 18 5
11P LOSS WILD-TYPE 130 185 21 168 91 49 5

Figure S594.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'11p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00333 (Fisher's exact test), Q value = 0.005

Table S595.  Gene #62: '11p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
11P LOSS MUTATED 72 103 49
11P LOSS WILD-TYPE 148 295 206

Figure S595.  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 = 2.3e-05

Table S596.  Gene #62: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
11P LOSS MUTATED 86 58 20 26 63 11 6
11P LOSS WILD-TYPE 178 111 123 199 140 40 14

Figure S596.  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 = 2.3e-05

Table S597.  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 74 61 7 52 57 19
11P LOSS WILD-TYPE 215 102 83 238 126 41

Figure S597.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

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

Table S598.  Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
11P LOSS MUTATED 41 94 41 37 40 9
11P LOSS WILD-TYPE 98 176 167 179 142 37

Figure S598.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S599.  Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
11P LOSS MUTATED 23 40 21 40 17 29 49 17 26
11P LOSS WILD-TYPE 43 83 163 146 57 84 110 56 57

Figure S599.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.023

Table S600.  Gene #62: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
11P LOSS MUTATED 34 14 13 26 50 23
11P LOSS WILD-TYPE 99 78 46 93 95 91

Figure S600.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0247 (Fisher's exact test), Q value = 0.031

Table S601.  Gene #62: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
11P LOSS MUTATED 91 45 24
11P LOSS WILD-TYPE 223 186 93

Figure S601.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

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

Table S602.  Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
11Q LOSS MUTATED 190 36 34 101 5
11Q LOSS WILD-TYPE 140 96 261 193 24

Figure S602.  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 = 2.3e-05

Table S603.  Gene #63: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
11Q LOSS MUTATED 73 85 31 50 19
11Q LOSS WILD-TYPE 145 98 114 89 69

Figure S603.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

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

Table S604.  Gene #63: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
11Q LOSS MUTATED 140 58 39 47 59 17 4
11Q LOSS WILD-TYPE 124 111 104 178 144 34 16

Figure S604.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00299 (Fisher's exact test), Q value = 0.0046

Table S605.  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 115 66 18 93 54 18
11Q LOSS WILD-TYPE 174 97 72 197 129 42

Figure S605.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.0259 (Fisher's exact test), Q value = 0.033

Table S606.  Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
11Q LOSS MUTATED 60 93 76 57 60 12
11Q LOSS WILD-TYPE 79 177 132 159 122 34

Figure S606.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00823 (Fisher's exact test), Q value = 0.011

Table S607.  Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
11Q LOSS MUTATED 28 45 40 69 25 47 48 26 30
11Q LOSS WILD-TYPE 38 78 144 117 49 66 111 47 53

Figure S607.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MRNA_CNMF'

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

Table S608.  Gene #64: '12p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
12P LOSS MUTATED 21 14 40
12P LOSS WILD-TYPE 208 102 128

Figure S608.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'12p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00165 (Fisher's exact test), Q value = 0.0027

Table S609.  Gene #64: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
12P LOSS MUTATED 14 38 23
12P LOSS WILD-TYPE 145 228 65

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 = 2.3e-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 330 132 295 294 29
12P LOSS MUTATED 44 17 19 72 1
12P LOSS WILD-TYPE 286 115 276 222 28

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 = 2.3e-05

Table S611.  Gene #64: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
12P LOSS MUTATED 20 22 14 42 9
12P LOSS WILD-TYPE 198 161 131 97 79

Figure S611.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p loss' versus 'RPPA_CNMF'

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

Table S612.  Gene #64: '12p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
12P LOSS MUTATED 34 20 8 18 25 20 2
12P LOSS WILD-TYPE 160 217 22 186 106 47 8

Figure S612.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'12p loss' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.4e-05

Table S613.  Gene #64: '12p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
12P LOSS MUTATED 54 46 27
12P LOSS WILD-TYPE 166 352 228

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 = 2.3e-05

Table S614.  Gene #64: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
12P LOSS MUTATED 31 27 10 19 59 3 3
12P LOSS WILD-TYPE 233 142 133 206 144 48 17

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 = 2.3e-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 26 6 26 50 15
12P LOSS WILD-TYPE 260 137 84 264 133 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 = 2.3e-05

Table S616.  Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
12P LOSS MUTATED 26 65 12 16 25 7
12P LOSS WILD-TYPE 113 205 196 200 157 39

Figure S616.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-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 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
12P LOSS MUTATED 7 23 11 21 7 14 42 10 16
12P LOSS WILD-TYPE 59 100 173 165 67 99 117 63 67

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 = 2.3e-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 CLUS_6
ALL 133 92 59 119 145 114
12P LOSS MUTATED 16 8 7 12 46 7
12P LOSS WILD-TYPE 117 84 52 107 99 107

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 = 2.3e-05

Table S619.  Gene #64: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
12P LOSS MUTATED 70 16 10
12P LOSS WILD-TYPE 244 215 107

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 = 2.3e-05

Table S620.  Gene #65: '12q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
12Q LOSS MUTATED 11 16 38
12Q LOSS WILD-TYPE 218 100 130

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 = 2.3e-05

Table S621.  Gene #65: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
12Q LOSS MUTATED 7 28 30
12Q LOSS WILD-TYPE 152 238 58

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 = 2.3e-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 330 132 295 294 29
12Q LOSS MUTATED 27 14 10 85 1
12Q LOSS WILD-TYPE 303 118 285 209 28

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 = 2.3e-05

Table S623.  Gene #65: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
12Q LOSS MUTATED 13 19 11 54 4
12Q LOSS WILD-TYPE 205 164 134 85 84

Figure S623.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q loss' versus 'RPPA_CNMF'

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

Table S624.  Gene #65: '12q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
12Q LOSS MUTATED 43 13 5 13 21 14 2
12Q LOSS WILD-TYPE 151 224 25 191 110 53 8

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 = 2.3e-05

Table S625.  Gene #65: '12q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
12Q LOSS MUTATED 56 36 19
12Q LOSS WILD-TYPE 164 362 236

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 = 2.3e-05

Table S626.  Gene #65: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
12Q LOSS MUTATED 19 20 7 13 73 3 1
12Q LOSS WILD-TYPE 245 149 136 212 130 48 19

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 = 2.3e-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 17 18 4 20 64 13
12Q LOSS WILD-TYPE 272 145 86 270 119 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 = 2.3e-05

Table S628.  Gene #65: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
12Q LOSS MUTATED 18 74 7 16 13 6
12Q LOSS WILD-TYPE 121 196 201 200 169 40

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 = 2.3e-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 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
12Q LOSS MUTATED 5 15 7 11 6 12 54 8 16
12Q LOSS WILD-TYPE 61 108 177 175 68 101 105 65 67

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 = 2.3e-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 CLUS_6
ALL 133 92 59 119 145 114
12Q LOSS MUTATED 11 6 7 12 53 7
12Q LOSS WILD-TYPE 122 86 52 107 92 107

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 = 2.3e-05

Table S631.  Gene #65: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
12Q LOSS MUTATED 72 16 8
12Q LOSS WILD-TYPE 242 215 109

Figure S631.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'MRNA_CNMF'

P value = 0.0015 (Fisher's exact test), Q value = 0.0024

Table S632.  Gene #66: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
13Q LOSS MUTATED 93 36 88
13Q LOSS WILD-TYPE 136 80 80

Figure S632.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q loss' versus 'CN_CNMF'

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

Table S633.  Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
13Q LOSS MUTATED 174 61 35 146 14
13Q LOSS WILD-TYPE 156 71 260 148 15

Figure S633.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

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

Table S634.  Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
13Q LOSS MUTATED 86 84 42 75 14
13Q LOSS WILD-TYPE 132 99 103 64 74

Figure S634.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CNMF'

P value = 0.00435 (Fisher's exact test), Q value = 0.0064

Table S635.  Gene #66: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
13Q LOSS MUTATED 102 87 13 69 56 27 2
13Q LOSS WILD-TYPE 92 150 17 135 75 40 8

Figure S635.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.00083

Table S636.  Gene #66: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
13Q LOSS MUTATED 115 147 94
13Q LOSS WILD-TYPE 105 251 161

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 = 2.3e-05

Table S637.  Gene #66: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
13Q LOSS MUTATED 115 81 38 65 105 14 11
13Q LOSS WILD-TYPE 149 88 105 160 98 37 9

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 = 2.3e-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 118 82 18 91 96 24
13Q LOSS WILD-TYPE 171 81 72 199 87 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 = 2.3e-05

Table S639.  Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
13Q LOSS MUTATED 64 135 84 54 68 18
13Q LOSS WILD-TYPE 75 135 124 162 114 28

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 = 2.3e-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 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
13Q LOSS MUTATED 24 63 41 73 20 55 79 30 38
13Q LOSS WILD-TYPE 42 60 143 113 54 58 80 43 45

Figure S640.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.00091

Table S641.  Gene #66: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
13Q LOSS MUTATED 55 25 18 40 75 34
13Q LOSS WILD-TYPE 78 67 41 79 70 80

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 = 0.00067 (Fisher's exact test), Q value = 0.0011

Table S642.  Gene #66: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
13Q LOSS MUTATED 141 71 35
13Q LOSS WILD-TYPE 173 160 82

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 = 2.3e-05

Table S643.  Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
14Q LOSS MUTATED 35 20 66
14Q LOSS WILD-TYPE 194 96 102

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 = 2.3e-05

Table S644.  Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
14Q LOSS MUTATED 18 56 47
14Q LOSS WILD-TYPE 141 210 41

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 = 2.3e-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 330 132 295 294 29
14Q LOSS MUTATED 74 21 11 156 7
14Q LOSS WILD-TYPE 256 111 284 138 22

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 = 2.3e-05

Table S646.  Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
14Q LOSS MUTATED 27 45 31 88 7
14Q LOSS WILD-TYPE 191 138 114 51 81

Figure S646.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

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

Table S647.  Gene #67: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
14Q LOSS MUTATED 93 29 6 40 30 19 2
14Q LOSS WILD-TYPE 101 208 24 164 101 48 8

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 = 2.3e-05

Table S648.  Gene #67: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
14Q LOSS MUTATED 93 69 57
14Q LOSS WILD-TYPE 127 329 198

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 = 2.3e-05

Table S649.  Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
14Q LOSS MUTATED 66 42 14 17 115 7 7
14Q LOSS WILD-TYPE 198 127 129 208 88 44 13

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 = 2.3e-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 56 3 45 110 12
14Q LOSS WILD-TYPE 247 107 87 245 73 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 = 2.3e-05

Table S651.  Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
14Q LOSS MUTATED 34 136 31 31 26 4
14Q LOSS WILD-TYPE 105 134 177 185 156 42

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 = 2.3e-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 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
14Q LOSS MUTATED 14 35 20 24 9 22 92 12 34
14Q LOSS WILD-TYPE 52 88 164 162 65 91 67 61 49

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 = 2.3e-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 CLUS_6
ALL 133 92 59 119 145 114
14Q LOSS MUTATED 23 20 13 17 82 18
14Q LOSS WILD-TYPE 110 72 46 102 63 96

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 = 2.3e-05

Table S654.  Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
14Q LOSS MUTATED 114 39 20
14Q LOSS WILD-TYPE 200 192 97

Figure S654.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'MRNA_CNMF'

P value = 7e-04 (Fisher's exact test), Q value = 0.0012

Table S655.  Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
15Q LOSS MUTATED 60 26 70
15Q LOSS WILD-TYPE 169 90 98

Figure S655.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

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

Table S656.  Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
15Q LOSS MUTATED 35 79 42
15Q LOSS WILD-TYPE 124 187 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 = 2.3e-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 330 132 295 294 29
15Q LOSS MUTATED 94 55 14 148 7
15Q LOSS WILD-TYPE 236 77 281 146 22

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 = 2.3e-05

Table S658.  Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
15Q LOSS MUTATED 46 59 32 81 10
15Q LOSS WILD-TYPE 172 124 113 58 78

Figure S658.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'RPPA_CNMF'

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

Table S659.  Gene #68: '15q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
15Q LOSS MUTATED 89 58 14 33 47 28 2
15Q LOSS WILD-TYPE 105 179 16 171 84 39 8

Figure S659.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'15q loss' versus 'RPPA_CHIERARCHICAL'

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

Table S660.  Gene #68: '15q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
15Q LOSS MUTATED 101 116 54
15Q LOSS WILD-TYPE 119 282 201

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 = 2.3e-05

Table S661.  Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
15Q LOSS MUTATED 73 70 16 47 99 4 6
15Q LOSS WILD-TYPE 191 99 127 178 104 47 14

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 = 2.3e-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 73 65 8 57 95 17
15Q LOSS WILD-TYPE 216 98 82 233 88 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 = 2.3e-05

Table S663.  Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
15Q LOSS MUTATED 43 126 37 30 56 18
15Q LOSS WILD-TYPE 96 144 171 186 126 28

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 = 2.3e-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 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
15Q LOSS MUTATED 17 42 22 33 28 35 81 11 41
15Q LOSS WILD-TYPE 49 81 162 153 46 78 78 62 42

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 = 2.3e-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 CLUS_6
ALL 133 92 59 119 145 114
15Q LOSS MUTATED 39 22 20 21 75 15
15Q LOSS WILD-TYPE 94 70 39 98 70 99

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

Table S666.  Gene #68: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
15Q LOSS MUTATED 122 41 29
15Q LOSS WILD-TYPE 192 190 88

Figure S666.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 0.00336 (Fisher's exact test), Q value = 0.005

Table S667.  Gene #69: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
16P LOSS MUTATED 46 15 39 68 6
16P LOSS WILD-TYPE 284 117 256 226 23

Figure S667.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.00074

Table S668.  Gene #69: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
16P LOSS MUTATED 24 27 25 40 10
16P LOSS WILD-TYPE 194 156 120 99 78

Figure S668.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'RPPA_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.00082

Table S669.  Gene #69: '16p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
16P LOSS MUTATED 53 37 4 24 17 5 2
16P LOSS WILD-TYPE 141 200 26 180 114 62 8

Figure S669.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'16p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00247 (Fisher's exact test), Q value = 0.0038

Table S670.  Gene #69: '16p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
16P LOSS MUTATED 51 62 29
16P LOSS WILD-TYPE 169 336 226

Figure S670.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16p loss' versus 'MRNASEQ_CNMF'

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

Table S671.  Gene #69: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
16P LOSS MUTATED 38 26 17 29 56 3 4
16P LOSS WILD-TYPE 226 143 126 196 147 48 16

Figure S671.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00225 (Fisher's exact test), Q value = 0.0035

Table S672.  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 38 24 13 40 50 8
16P LOSS WILD-TYPE 251 139 77 250 133 52

Figure S672.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00023

Table S673.  Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
16P LOSS MUTATED 20 67 27 26 20 12
16P LOSS WILD-TYPE 119 203 181 190 162 34

Figure S673.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00434 (Fisher's exact test), Q value = 0.0064

Table S674.  Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
16P LOSS MUTATED 6 17 26 24 14 17 45 8 15
16P LOSS WILD-TYPE 60 106 158 162 60 96 114 65 68

Figure S674.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S675.  Gene #69: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
16P LOSS MUTATED 16 13 4 12 44 20
16P LOSS WILD-TYPE 117 79 55 107 101 94

Figure S675.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MRNA_CNMF'

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

Table S676.  Gene #70: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
16Q LOSS MUTATED 149 69 64
16Q LOSS WILD-TYPE 80 47 104

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 = 2.3e-05

Table S677.  Gene #70: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
16Q LOSS MUTATED 105 154 23
16Q LOSS WILD-TYPE 54 112 65

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 = 2.3e-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 330 132 295 294 29
16Q LOSS MUTATED 169 94 180 125 23
16Q LOSS WILD-TYPE 161 38 115 169 6

Figure S678.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00022

Table S679.  Gene #70: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
16Q LOSS MUTATED 136 107 68 56 54
16Q LOSS WILD-TYPE 82 76 77 83 34

Figure S679.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'RPPA_CHIERARCHICAL'

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

Table S680.  Gene #70: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
16Q LOSS MUTATED 83 239 151
16Q LOSS WILD-TYPE 137 159 104

Figure S680.  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 = 2.3e-05

Table S681.  Gene #70: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
16Q LOSS MUTATED 127 82 94 171 70 35 10
16Q LOSS WILD-TYPE 137 87 49 54 133 16 10

Figure S681.  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 = 2.3e-05

Table S682.  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 164 85 65 195 63 17
16Q LOSS WILD-TYPE 125 78 25 95 120 43

Figure S682.  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 = 2.3e-05

Table S683.  Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
16Q LOSS MUTATED 66 104 128 131 113 39
16Q LOSS WILD-TYPE 73 166 80 85 69 7

Figure S683.  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 = 2.3e-05

Table S684.  Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
16Q LOSS MUTATED 23 58 129 106 64 75 57 40 29
16Q LOSS WILD-TYPE 43 65 55 80 10 38 102 33 54

Figure S684.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S685.  Gene #70: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
16Q LOSS MUTATED 69 60 28 71 61 73
16Q LOSS WILD-TYPE 64 32 31 48 84 41

Figure S685.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S686.  Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
16Q LOSS MUTATED 140 148 74
16Q LOSS WILD-TYPE 174 83 43

Figure S686.  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 = 2.3e-05

Table S687.  Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
17P LOSS MUTATED 100 64 118
17P LOSS WILD-TYPE 129 52 50

Figure S687.  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 = 2.3e-05

Table S688.  Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
17P LOSS MUTATED 62 167 53
17P LOSS WILD-TYPE 97 99 35

Figure S688.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

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

Table S689.  Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
17P LOSS MUTATED 201 69 86 210 14
17P LOSS WILD-TYPE 129 63 209 84 15

Figure S689.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

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

Table S690.  Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
17P LOSS MUTATED 103 119 58 89 35
17P LOSS WILD-TYPE 115 64 87 50 53

Figure S690.  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 = 2.3e-05

Table S691.  Gene #71: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
17P LOSS MUTATED 132 105 23 82 81 46 5
17P LOSS WILD-TYPE 62 132 7 122 50 21 5

Figure S691.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'17p loss' versus 'RPPA_CHIERARCHICAL'

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

Table S692.  Gene #71: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
17P LOSS MUTATED 151 201 122
17P LOSS WILD-TYPE 69 197 133

Figure S692.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17p loss' versus 'MRNASEQ_CNMF'

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

Table S693.  Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
17P LOSS MUTATED 155 127 66 75 119 22 13
17P LOSS WILD-TYPE 109 42 77 150 84 29 7

Figure S693.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S694.  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 128 122 41 135 108 43
17P LOSS WILD-TYPE 161 41 49 155 75 17

Figure S694.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

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

Table S695.  Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
17P LOSS MUTATED 84 180 92 89 97 28
17P LOSS WILD-TYPE 55 90 116 127 85 18

Figure S695.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S696.  Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
17P LOSS MUTATED 36 91 70 81 43 60 95 43 51
17P LOSS WILD-TYPE 30 32 114 105 31 53 64 30 32

Figure S696.  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 = 2.3e-05

Table S697.  Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
17Q LOSS MUTATED 40 29 72
17Q LOSS WILD-TYPE 189 87 96

Figure S697.  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 = 2.3e-05

Table S698.  Gene #72: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
17Q LOSS MUTATED 21 76 44
17Q LOSS WILD-TYPE 138 190 44

Figure S698.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

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

Table S699.  Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
17Q LOSS MUTATED 68 39 26 139 0
17Q LOSS WILD-TYPE 262 93 269 155 29

Figure S699.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

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

Table S700.  Gene #72: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
17Q LOSS MUTATED 31 37 33 67 8
17Q LOSS WILD-TYPE 187 146 112 72 80

Figure S700.  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 = 2.3e-05

Table S701.  Gene #72: '17q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
17Q LOSS MUTATED 81 32 12 34 44 21 1
17Q LOSS WILD-TYPE 113 205 18 170 87 46 9

Figure S701.  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 = 2.3e-05

Table S702.  Gene #72: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
17Q LOSS MUTATED 108 64 53
17Q LOSS WILD-TYPE 112 334 202

Figure S702.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17q loss' versus 'MRNASEQ_CNMF'

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

Table S703.  Gene #72: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
17Q LOSS MUTATED 40 75 18 30 90 11 6
17Q LOSS WILD-TYPE 224 94 125 195 113 40 14

Figure S703.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S704.  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 29 57 15 53 84 32
17Q LOSS WILD-TYPE 260 106 75 237 99 28

Figure S704.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

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

Table S705.  Gene #72: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
17Q LOSS MUTATED 28 117 28 41 39 14
17Q LOSS WILD-TYPE 111 153 180 175 143 32

Figure S705.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S706.  Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
17Q LOSS MUTATED 11 51 29 17 21 20 74 14 30
17Q LOSS WILD-TYPE 55 72 155 169 53 93 85 59 53

Figure S706.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S707.  Gene #72: '17q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
17Q LOSS MUTATED 28 18 16 18 60 26
17Q LOSS WILD-TYPE 105 74 43 101 85 88

Figure S707.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.018

Table S708.  Gene #72: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
17Q LOSS MUTATED 95 49 22
17Q LOSS WILD-TYPE 219 182 95

Figure S708.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'MRNA_CNMF'

P value = 0.00207 (Fisher's exact test), Q value = 0.0033

Table S709.  Gene #73: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
18P LOSS MUTATED 57 32 69
18P LOSS WILD-TYPE 172 84 99

Figure S709.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0219 (Fisher's exact test), Q value = 0.028

Table S710.  Gene #73: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
18P LOSS MUTATED 38 96 24
18P LOSS WILD-TYPE 121 170 64

Figure S710.  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 = 2.3e-05

Table S711.  Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
18P LOSS MUTATED 121 46 42 106 5
18P LOSS WILD-TYPE 209 86 253 188 24

Figure S711.  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 = 2.3e-05

Table S712.  Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
18P LOSS MUTATED 50 87 37 42 13
18P LOSS WILD-TYPE 168 96 108 97 75

Figure S712.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'RPPA_CNMF'

P value = 0.00209 (Fisher's exact test), Q value = 0.0033

Table S713.  Gene #73: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
18P LOSS MUTATED 75 54 13 51 43 21 5
18P LOSS WILD-TYPE 119 183 17 153 88 46 5

Figure S713.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.027 (Fisher's exact test), Q value = 0.034

Table S714.  Gene #73: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
18P LOSS MUTATED 78 122 62
18P LOSS WILD-TYPE 142 276 193

Figure S714.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18p loss' versus 'MRNASEQ_CNMF'

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

Table S715.  Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
18P LOSS MUTATED 84 91 26 38 55 16 10
18P LOSS WILD-TYPE 180 78 117 187 148 35 10

Figure S715.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S716.  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 65 88 14 79 50 24
18P LOSS WILD-TYPE 224 75 76 211 133 36

Figure S716.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.02

Table S717.  Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
18P LOSS MUTATED 50 95 50 51 55 16
18P LOSS WILD-TYPE 89 175 158 165 127 30

Figure S717.  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 = 2.3e-05

Table S718.  Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
18P LOSS MUTATED 21 58 36 46 20 39 39 25 33
18P LOSS WILD-TYPE 45 65 148 140 54 74 120 48 50

Figure S718.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MRNA_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.0016

Table S719.  Gene #74: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
18Q LOSS MUTATED 53 29 67
18Q LOSS WILD-TYPE 176 87 101

Figure S719.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0042 (Fisher's exact test), Q value = 0.0062

Table S720.  Gene #74: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
18Q LOSS MUTATED 32 93 24
18Q LOSS WILD-TYPE 127 173 64

Figure S720.  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 = 2.3e-05

Table S721.  Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
18Q LOSS MUTATED 119 48 41 108 5
18Q LOSS WILD-TYPE 211 84 254 186 24

Figure S721.  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 = 2.3e-05

Table S722.  Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
18Q LOSS MUTATED 54 86 34 48 13
18Q LOSS WILD-TYPE 164 97 111 91 75

Figure S722.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CNMF'

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

Table S723.  Gene #74: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
18Q LOSS MUTATED 73 56 14 48 43 24 6
18Q LOSS WILD-TYPE 121 181 16 156 88 43 4

Figure S723.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00341 (Fisher's exact test), Q value = 0.0051

Table S724.  Gene #74: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
18Q LOSS MUTATED 82 123 59
18Q LOSS WILD-TYPE 138 275 196

Figure S724.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18q loss' versus 'MRNASEQ_CNMF'

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

Table S725.  Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
18Q LOSS MUTATED 83 88 28 39 61 12 9
18Q LOSS WILD-TYPE 181 81 115 186 142 39 11

Figure S725.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S726.  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 60 88 15 75 56 26
18Q LOSS WILD-TYPE 229 75 75 215 127 34

Figure S726.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 0.00429 (Fisher's exact test), Q value = 0.0063

Table S727.  Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
18Q LOSS MUTATED 44 104 49 52 53 14
18Q LOSS WILD-TYPE 95 166 159 164 129 32

Figure S727.  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 = 2.3e-05

Table S728.  Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
18Q LOSS MUTATED 20 57 37 42 18 38 45 22 37
18Q LOSS WILD-TYPE 46 66 147 144 56 75 114 51 46

Figure S728.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MRNA_CNMF'

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

Table S729.  Gene #75: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
19P LOSS MUTATED 39 10 47
19P LOSS WILD-TYPE 190 106 121

Figure S729.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p loss' versus 'CN_CNMF'

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

Table S730.  Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
19P LOSS MUTATED 101 13 6 76 1
19P LOSS WILD-TYPE 229 119 289 218 28

Figure S730.  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 = 2.3e-05

Table S731.  Gene #75: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
19P LOSS MUTATED 28 49 17 40 2
19P LOSS WILD-TYPE 190 134 128 99 86

Figure S731.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'RPPA_CNMF'

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

Table S732.  Gene #75: '19p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
19P LOSS MUTATED 51 35 6 21 24 20 2
19P LOSS WILD-TYPE 143 202 24 183 107 47 8

Figure S732.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'19p loss' versus 'RPPA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00016

Table S733.  Gene #75: '19p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
19P LOSS MUTATED 55 78 26
19P LOSS WILD-TYPE 165 320 229

Figure S733.  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 = 2.3e-05

Table S734.  Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
19P LOSS MUTATED 71 50 7 15 49 3 1
19P LOSS WILD-TYPE 193 119 136 210 154 48 19

Figure S734.  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 = 2.3e-05

Table S735.  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 55 58 3 24 44 12
19P LOSS WILD-TYPE 234 105 87 266 139 48

Figure S735.  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 = 2.3e-05

Table S736.  Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
19P LOSS MUTATED 43 80 23 12 25 9
19P LOSS WILD-TYPE 96 190 185 204 157 37

Figure S736.  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 = 2.3e-05

Table S737.  Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
19P LOSS MUTATED 21 29 5 27 11 19 38 16 26
19P LOSS WILD-TYPE 45 94 179 159 63 94 121 57 57

Figure S737.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S738.  Gene #75: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
19P LOSS MUTATED 40 11 3 10 44 12
19P LOSS WILD-TYPE 93 81 56 109 101 102

Figure S738.  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 = 2.3e-05

Table S739.  Gene #75: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
19P LOSS MUTATED 83 31 6
19P LOSS WILD-TYPE 231 200 111

Figure S739.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'MRNA_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.017

Table S740.  Gene #76: '19q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
19Q LOSS MUTATED 33 9 34
19Q LOSS WILD-TYPE 196 107 134

Figure S740.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-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 330 132 295 294 29
19Q LOSS MUTATED 88 11 6 58 1
19Q LOSS WILD-TYPE 242 121 289 236 28

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 = 2.3e-05

Table S742.  Gene #76: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
19Q LOSS MUTATED 26 41 17 30 2
19Q LOSS WILD-TYPE 192 142 128 109 86

Figure S742.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'RPPA_CNMF'

P value = 0.00542 (Fisher's exact test), Q value = 0.0078

Table S743.  Gene #76: '19q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
19Q LOSS MUTATED 42 30 4 20 16 17 1
19Q LOSS WILD-TYPE 152 207 26 184 115 50 9

Figure S743.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'19q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00231 (Fisher's exact test), Q value = 0.0036

Table S744.  Gene #76: '19q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
19Q LOSS MUTATED 44 63 23
19Q LOSS WILD-TYPE 176 335 232

Figure S744.  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 = 2.3e-05

Table S745.  Gene #76: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
19Q LOSS MUTATED 57 47 6 14 37 2 0
19Q LOSS WILD-TYPE 207 122 137 211 166 49 20

Figure S745.  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 = 2.3e-05

Table S746.  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 54 42 2 17 35 13
19Q LOSS WILD-TYPE 235 121 88 273 148 47

Figure S746.  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 = 2.3e-05

Table S747.  Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
19Q LOSS MUTATED 32 65 22 12 22 7
19Q LOSS WILD-TYPE 107 205 186 204 160 39

Figure S747.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S748.  Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
19Q LOSS MUTATED 17 24 6 29 10 17 31 11 15
19Q LOSS WILD-TYPE 49 99 178 157 64 96 128 62 68

Figure S748.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S749.  Gene #76: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
19Q LOSS MUTATED 25 8 3 12 38 12
19Q LOSS WILD-TYPE 108 84 56 107 107 102

Figure S749.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S750.  Gene #76: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
19Q LOSS MUTATED 69 25 4
19Q LOSS WILD-TYPE 245 206 113

Figure S750.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'MRNA_CNMF'

P value = 0.0299 (Fisher's exact test), Q value = 0.037

Table S751.  Gene #77: '20p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
20P LOSS MUTATED 13 5 20
20P LOSS WILD-TYPE 216 111 148

Figure S751.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00713 (Fisher's exact test), Q value = 0.01

Table S752.  Gene #77: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
20P LOSS MUTATED 8 16 14
20P LOSS WILD-TYPE 151 250 74

Figure S752.  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 = 2.3e-05

Table S753.  Gene #77: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
20P LOSS MUTATED 30 5 7 49 2
20P LOSS WILD-TYPE 300 127 288 245 27

Figure S753.  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 = 2.3e-05

Table S754.  Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
20P LOSS MUTATED 7 17 7 35 4
20P LOSS WILD-TYPE 211 166 138 104 84

Figure S754.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p loss' versus 'RPPA_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.00075

Table S755.  Gene #77: '20p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
20P LOSS MUTATED 32 11 2 11 15 8 0
20P LOSS WILD-TYPE 162 226 28 193 116 59 10

Figure S755.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'20p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00035

Table S756.  Gene #77: '20p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
20P LOSS MUTATED 36 28 15
20P LOSS WILD-TYPE 184 370 240

Figure S756.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20p loss' versus 'MRNASEQ_CNMF'

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

Table S757.  Gene #77: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
20P LOSS MUTATED 26 13 4 6 43 0 1
20P LOSS WILD-TYPE 238 156 139 219 160 51 19

Figure S757.  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 = 2.3e-05

Table S758.  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 18 22 2 6 41 4
20P LOSS WILD-TYPE 271 141 88 284 142 56

Figure S758.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_CNMF'

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

Table S759.  Gene #77: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
20P LOSS MUTATED 9 47 11 10 7 3
20P LOSS WILD-TYPE 130 223 197 206 175 43

Figure S759.  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 = 2.3e-05

Table S760.  Gene #77: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
20P LOSS MUTATED 6 8 4 7 3 12 37 3 7
20P LOSS WILD-TYPE 60 115 180 179 71 101 122 70 76

Figure S760.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00018

Table S761.  Gene #77: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
20P LOSS MUTATED 6 4 2 6 28 6
20P LOSS WILD-TYPE 127 88 57 113 117 108

Figure S761.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00126 (Fisher's exact test), Q value = 0.0021

Table S762.  Gene #77: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
20P LOSS MUTATED 37 12 3
20P LOSS WILD-TYPE 277 219 114

Figure S762.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.0013

Table S763.  Gene #78: '20q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
20Q LOSS MUTATED 3 9 11
20Q LOSS WILD-TYPE 156 257 77

Figure S763.  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 = 2.3e-05

Table S764.  Gene #78: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
20Q LOSS MUTATED 13 5 4 33 2
20Q LOSS WILD-TYPE 317 127 291 261 27

Figure S764.  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 = 2.3e-05

Table S765.  Gene #78: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
20Q LOSS MUTATED 5 5 6 24 2
20Q LOSS WILD-TYPE 213 178 139 115 86

Figure S765.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q loss' versus 'RPPA_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0011

Table S766.  Gene #78: '20q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
20Q LOSS MUTATED 24 8 0 5 4 4 0
20Q LOSS WILD-TYPE 170 229 30 199 127 63 10

Figure S766.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q loss' versus 'RPPA_CHIERARCHICAL'

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

Table S767.  Gene #78: '20q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
20Q LOSS MUTATED 25 16 4
20Q LOSS WILD-TYPE 195 382 251

Figure S767.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20q loss' versus 'MRNASEQ_CNMF'

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

Table S768.  Gene #78: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
20Q LOSS MUTATED 9 6 4 4 34 0 0
20Q LOSS WILD-TYPE 255 163 139 221 169 51 20

Figure S768.  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 = 2.3e-05

Table S769.  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 4 33 1
20Q LOSS WILD-TYPE 281 154 88 286 150 59

Figure S769.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_CNMF'

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

Table S770.  Gene #78: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
20Q LOSS MUTATED 2 32 4 10 5 1
20Q LOSS WILD-TYPE 137 238 204 206 177 45

Figure S770.  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 = 2.3e-05

Table S771.  Gene #78: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
20Q LOSS MUTATED 2 6 3 2 1 3 30 3 4
20Q LOSS WILD-TYPE 64 117 181 184 73 110 129 70 79

Figure S771.  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 = 2.3e-05

Table S772.  Gene #78: '20q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
20Q LOSS MUTATED 2 2 1 2 22 4
20Q LOSS WILD-TYPE 131 90 58 117 123 110

Figure S772.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00234 (Fisher's exact test), Q value = 0.0037

Table S773.  Gene #78: '20q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
20Q LOSS MUTATED 25 7 1
20Q LOSS WILD-TYPE 289 224 116

Figure S773.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'MRNA_CNMF'

P value = 0.039 (Fisher's exact test), Q value = 0.048

Table S774.  Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
21Q LOSS MUTATED 34 13 37
21Q LOSS WILD-TYPE 195 103 131

Figure S774.  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 = 2.3e-05

Table S775.  Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
21Q LOSS MUTATED 86 18 12 55 8
21Q LOSS WILD-TYPE 244 114 283 239 21

Figure S775.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.0012

Table S776.  Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
21Q LOSS MUTATED 41 40 14 26 5
21Q LOSS WILD-TYPE 177 143 131 113 83

Figure S776.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00692 (Fisher's exact test), Q value = 0.0098

Table S777.  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 49 40 6 41 33 9
21Q LOSS WILD-TYPE 240 123 84 249 150 51

Figure S777.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.031

Table S778.  Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
21Q LOSS MUTATED 29 54 27 23 34 6
21Q LOSS WILD-TYPE 110 216 181 193 148 40

Figure S778.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00127 (Fisher's exact test), Q value = 0.0021

Table S779.  Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
21Q LOSS MUTATED 19 24 13 26 12 23 27 11 18
21Q LOSS WILD-TYPE 47 99 171 160 62 90 132 62 65

Figure S779.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MRNA_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.023

Table S780.  Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
22Q LOSS MUTATED 120 52 64
22Q LOSS WILD-TYPE 109 64 104

Figure S780.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'CN_CNMF'

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

Table S781.  Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 330 132 295 294 29
22Q LOSS MUTATED 180 86 77 129 10
22Q LOSS WILD-TYPE 150 46 218 165 19

Figure S781.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

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

Table S782.  Gene #80: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
22Q LOSS MUTATED 73 200 120
22Q LOSS WILD-TYPE 147 198 135

Figure S782.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.018

Table S783.  Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
22Q LOSS MUTATED 143 69 61 104 77 19 8
22Q LOSS WILD-TYPE 121 100 82 121 126 32 12

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 = 8.4e-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 136 92 33 135 71 14
22Q LOSS WILD-TYPE 153 71 57 155 112 46

Figure S784.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 0.00375 (Fisher's exact test), Q value = 0.0056

Table S785.  Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
22Q LOSS MUTATED 77 115 99 80 74 27
22Q LOSS WILD-TYPE 62 155 109 136 108 19

Figure S785.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.026 (Fisher's exact test), Q value = 0.033

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 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
22Q LOSS MUTATED 34 53 71 79 43 61 60 31 40
22Q LOSS WILD-TYPE 32 70 113 107 31 52 99 42 43

Figure S786.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0369 (Fisher's exact test), Q value = 0.046

Table S787.  Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
22Q LOSS MUTATED 73 41 28 57 58 40
22Q LOSS WILD-TYPE 60 51 31 62 87 74

Figure S787.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'MRNA_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.025

Table S788.  Gene #81: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
XP LOSS MUTATED 39 15 43
XP LOSS WILD-TYPE 190 101 125

Figure S788.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0195 (Fisher's exact test), Q value = 0.025

Table S789.  Gene #81: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 266 88
XP LOSS MUTATED 29 42 26
XP LOSS WILD-TYPE 130 224 62

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 = 2.3e-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 330 132 295 294 29
XP LOSS MUTATED 81 21 6 81 3
XP LOSS WILD-TYPE 249 111 289 213 26

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 = 2.3e-05

Table S791.  Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
XP LOSS MUTATED 37 39 11 37 6
XP LOSS WILD-TYPE 181 144 134 102 82

Figure S791.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp loss' versus 'RPPA_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00035

Table S792.  Gene #81: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
XP LOSS MUTATED 56 37 10 24 21 11 2
XP LOSS WILD-TYPE 138 200 20 180 110 56 8

Figure S792.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'xp loss' versus 'RPPA_CHIERARCHICAL'

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

Table S793.  Gene #81: 'xp loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
XP LOSS MUTATED 61 72 28
XP LOSS WILD-TYPE 159 326 227

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 = 2.3e-05

Table S794.  Gene #81: 'xp loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
XP LOSS MUTATED 66 35 11 20 53 5 0
XP LOSS WILD-TYPE 198 134 132 205 150 46 20

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 = 2.3e-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 51 9
XP LOSS WILD-TYPE 230 127 87 258 132 51

Figure S795.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

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

Table S796.  Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
XP LOSS MUTATED 28 70 38 15 29 6
XP LOSS WILD-TYPE 111 200 170 201 153 40

Figure S796.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00081 (Fisher's exact test), Q value = 0.0014

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 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
XP LOSS MUTATED 13 23 14 33 11 21 44 14 13
XP LOSS WILD-TYPE 53 100 170 153 63 92 115 59 70

Figure S797.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S798.  Gene #81: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
XP LOSS MUTATED 30 10 6 14 39 15
XP LOSS WILD-TYPE 103 82 53 105 106 99

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 = 0.00101 (Fisher's exact test), Q value = 0.0017

Table S799.  Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
XP LOSS MUTATED 72 29 13
XP LOSS WILD-TYPE 242 202 104

Figure S799.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'MRNA_CNMF'

P value = 0.0338 (Fisher's exact test), Q value = 0.042

Table S800.  Gene #82: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 229 116 168
XQ LOSS MUTATED 41 13 39
XQ LOSS WILD-TYPE 188 103 129

Figure S800.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-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 330 132 295 294 29
XQ LOSS MUTATED 83 21 7 74 4
XQ LOSS WILD-TYPE 247 111 288 220 25

Figure S801.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

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

Table S802.  Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 218 183 145 139 88
XQ LOSS MUTATED 37 47 10 32 7
XQ LOSS WILD-TYPE 181 136 135 107 81

Figure S802.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CNMF'

P value = 0.00421 (Fisher's exact test), Q value = 0.0062

Table S803.  Gene #82: 'xq loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 194 237 30 204 131 67 10
XQ LOSS MUTATED 50 40 10 24 20 12 1
XQ LOSS WILD-TYPE 144 197 20 180 111 55 9

Figure S803.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.00098

Table S804.  Gene #82: 'xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 220 398 255
XQ LOSS MUTATED 52 77 28
XQ LOSS WILD-TYPE 168 321 227

Figure S804.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xq loss' versus 'MRNASEQ_CNMF'

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

Table S805.  Gene #82: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 264 169 143 225 203 51 20
XQ LOSS MUTATED 67 37 13 23 42 6 0
XQ LOSS WILD-TYPE 197 132 130 202 161 45 20

Figure S805.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-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 35 40 7
XQ LOSS WILD-TYPE 231 119 86 255 143 53

Figure S806.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

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

Table S807.  Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 139 270 208 216 182 46
XQ LOSS MUTATED 29 60 39 14 35 9
XQ LOSS WILD-TYPE 110 210 169 202 147 37

Figure S807.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00241 (Fisher's exact test), Q value = 0.0038

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 CLUS_7 CLUS_8 CLUS_9
ALL 66 123 184 186 74 113 159 73 83
XQ LOSS MUTATED 15 25 13 34 11 24 35 16 13
XQ LOSS WILD-TYPE 51 98 171 152 63 89 124 57 70

Figure S808.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.014

Table S809.  Gene #82: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 133 92 59 119 145 114
XQ LOSS MUTATED 32 12 5 17 34 14
XQ LOSS WILD-TYPE 101 80 54 102 111 100

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 = 0.00283 (Fisher's exact test), Q value = 0.0044

Table S810.  Gene #82: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 314 231 117
XQ LOSS MUTATED 71 29 14
XQ LOSS WILD-TYPE 243 202 103

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/22531238/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BRCA-TP/22595637/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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