Correlation between copy number variations of arm-level result and molecular subtypes
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1K073C5
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1K073C5
Overview
Introduction

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

Summary

Testing the association between copy number variation 82 arm-level events and 12 molecular subtypes across 539 patients, 622 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p 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'.

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

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

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

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

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

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

  • 4q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

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

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

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

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

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

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

  • 8p gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 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 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 9q gain cnv correlated to 'CN_CNMF'.

  • 10p gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 10q gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

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

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

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

  • 15q gain cnv correlated to 'CN_CNMF'.

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

  • 16q gain cnv correlated to 'CN_CNMF'.

  • 17p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

  • 18p 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'.

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

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

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

  • 20q 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'.

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

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

  • xp gain cnv correlated to 'CN_CNMF'.

  • xq gain cnv correlated to 'CN_CNMF'.

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

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

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

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

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

  • 4p 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'.

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

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

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

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

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

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

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

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

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

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

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

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

  • 11p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  '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',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

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

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

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

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

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

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

  • 20q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 22q 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'.

  • xp 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'.

  • xq 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'.

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, 622 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
8q gain 159 (29%) 380 0.0104
(0.0191) 		0.031
(0.0524) 		1e-05
(2.95e-05) 		0.04
(0.065) 		0.0003
(0.000725) 		0.0219
(0.0382) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.00019
(0.000476) 		1e-05
(2.95e-05) 		0.00046
(0.00107) 		0.00745
(0.0142)
5q loss 74 (14%) 465 0.0132
(0.0238) 		0.00999
(0.0185) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.0012
(0.00261) 		0.00246
(0.00511) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.00014
(0.000355) 		3e-05
(8.22e-05)
8p loss 80 (15%) 459 0.00782
(0.0147) 		4e-05
(0.000108) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.0335
(0.0561) 		0.0251
(0.0433) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05)
14q loss 61 (11%) 478 0.0021
(0.00443) 		0.00045
(0.00105) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.0143
(0.0256) 		0.0499
(0.079) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.00497
(0.00972) 		2e-05
(5.64e-05)
20q gain 132 (24%) 407 0.00198
(0.00421) 		0.00711
(0.0135) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.0321
(0.054) 		0.673
(0.779) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05)
3p loss 51 (9%) 488 0.0383
(0.063) 		0.00073
(0.00164) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.0225
(0.0391) 		0.125
(0.18) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.0151
(0.027) 		0.0001
(0.000258)
4p loss 105 (19%) 434 0.0037
(0.00748) 		0.00163
(0.00349) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.00106
(0.00233) 		0.188
(0.259) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05)
9p loss 103 (19%) 436 0.00114
(0.00249) 		2e-05
(5.64e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.00379
(0.00761) 		0.562
(0.669) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.0091
(0.017) 		0.00062
(0.0014)
9q loss 122 (23%) 417 4e-05
(0.000108) 		3e-05
(8.22e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.00037
(0.000884) 		0.7
(0.806) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.00111
(0.00243) 		5e-05
(0.000133)
15q loss 109 (20%) 430 0.00074
(0.00165) 		7e-05
(0.000184) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.0009
(0.002) 		0.484
(0.589) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		2e-05
(5.64e-05) 		1e-05
(2.95e-05)
17p loss 130 (24%) 409 0.00328
(0.00672) 		0.00014
(0.000355) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.00361
(0.00732) 		0.369
(0.463) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05)
22q loss 109 (20%) 430 0.00196
(0.00417) 		0.00759
(0.0144) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.0388
(0.0638) 		0.279
(0.365) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.00382
(0.00766) 		0.00013
(0.000332)
xp loss 85 (16%) 454 0.00164
(0.00351) 		0.0004
(0.000946) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		2e-05
(5.64e-05) 		0.219
(0.295) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.00066
(0.00149) 		1e-05
(2.95e-05)
xq loss 71 (13%) 468 0.00831
(0.0156) 		0.0047
(0.00923) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.0002
(0.000498) 		0.214
(0.29) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.00576
(0.0111) 		1e-05
(2.95e-05)
13q gain 30 (6%) 509 0.138
(0.197) 		0.0068
(0.013) 		1e-05
(2.95e-05) 		6e-05
(0.000158) 		0.252
(0.334) 		0.0116
(0.0213) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.00707
(0.0135) 		0.0236
(0.041)
20p gain 112 (21%) 427 0.00803
(0.0151) 		0.0494
(0.0783) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.163
(0.23) 		0.743
(0.849) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.00025
(0.000613) 		1e-05
(2.95e-05)
4q loss 105 (19%) 434 0.151
(0.214) 		0.00513
(0.01) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.0135
(0.0243) 		0.19
(0.262) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05)
5p loss 55 (10%) 484 0.0517
(0.0811) 		0.0394
(0.0642) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.00378
(0.00761) 		0.104
(0.153) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		5e-05
(0.000133) 		0.00086
(0.00191)
7q loss 42 (8%) 497 1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.0462
(0.0736) 		0.014
(0.0251) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.00266
(0.00549) 		0.00034
(0.000816)
10p loss 43 (8%) 496 0.039
(0.0639) 		0.0295
(0.0504) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.0551
(0.0859) 		0.187
(0.259) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.0251
(0.0433) 		0.00406
(0.00809)
12p loss 43 (8%) 496 0.138
(0.197) 		0.165
(0.232) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.0416
(0.067) 		0.0376
(0.0622) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.00038
(0.000905) 		0.0025
(0.00518)
16p loss 97 (18%) 442 0.00232
(0.00485) 		0.00767
(0.0145) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.092
(0.138) 		0.321
(0.412) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.00416
(0.00825) 		1e-05
(2.95e-05)
16q loss 138 (26%) 401 0.0008
(0.00179) 		0.00135
(0.00292) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.345
(0.439) 		0.974
(1.00) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.00026
(0.000636) 		1e-05
(2.95e-05)
17q loss 93 (17%) 446 0.00199
(0.00422) 		2e-05
(5.64e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.107
(0.157) 		0.919
(1.00) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.00417
(0.00826) 		0.00052
(0.0012)
21q loss 54 (10%) 485 0.0401
(0.065) 		0.0299
(0.051) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.24
(0.321) 		0.425
(0.524) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.00364
(0.00737) 		2e-05
(5.64e-05)
1p gain 50 (9%) 489 0.535
(0.643) 		0.218
(0.295) 		1e-05
(2.95e-05) 		0.00046
(0.00107) 		0.0453
(0.0723) 		0.263
(0.347) 		1e-05
(2.95e-05) 		3e-05
(8.22e-05) 		2e-05
(5.64e-05) 		4e-05
(0.000108) 		0.00239
(0.00498) 		0.00294
(0.00605)
18p gain 72 (13%) 467 0.335
(0.429) 		0.241
(0.321) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.0121
(0.022) 		0.163
(0.231) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05)
18q gain 45 (8%) 494 0.255
(0.337) 		0.0432
(0.0693) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.279
(0.365) 		0.0953
(0.142) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		2e-05
(5.64e-05) 		0.0001
(0.000258)
19p gain 54 (10%) 485 0.0393
(0.0641) 		0.0302
(0.0513) 		1e-05
(2.95e-05) 		0.00027
(0.000659) 		0.908
(0.997) 		0.0752
(0.115) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.0004
(0.000946) 		0.0826
(0.125)
19q gain 57 (11%) 482 1e-05
(2.95e-05) 		3e-05
(8.22e-05) 		0.487
(0.592) 		0.0431
(0.0692) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.00021
(0.00052) 		0.0136
(0.0244)
3q loss 31 (6%) 508 0.0382
(0.0629) 		0.00072
(0.00162) 		1e-05
(2.95e-05) 		5e-05
(0.000133) 		0.0642
(0.0988) 		0.263
(0.347) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.00018
(0.000452) 		0.0124
(0.0226) 		0.0968
(0.144)
6q loss 25 (5%) 514 0.377
(0.471) 		0.0301
(0.0513) 		1e-05
(2.95e-05) 		3e-05
(8.22e-05) 		0.478
(0.583) 		0.804
(0.91) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.00018
(0.000452) 		2e-05
(5.64e-05) 		0.0124
(0.0226) 		0.00358
(0.00729)
12q loss 36 (7%) 503 1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.102
(0.151) 		0.0156
(0.0277) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		3e-05
(8.22e-05) 		0.00045
(0.00105)
19q loss 56 (10%) 483 0.255
(0.337) 		0.0167
(0.0296) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.25
(0.333) 		0.717
(0.823) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.0117
(0.0214) 		2e-05
(5.64e-05)
2p gain 95 (18%) 444 0.857
(0.956) 		0.372
(0.466) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.0567
(0.0881) 		0.244
(0.325) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		6e-05
(0.000158) 		0.00017
(0.000429)
2q gain 79 (15%) 460 0.343
(0.437) 		0.602
(0.71) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.0635
(0.0979) 		0.132
(0.191) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		9e-05
(0.000234) 		0.0003
(0.000725)
3p gain 49 (9%) 490 1e-05
(2.95e-05) 		0.00926
(0.0172) 		0.302
(0.391) 		0.947
(1.00) 		4e-05
(0.000108) 		0.00554
(0.0107) 		0.00111
(0.00243) 		0.00099
(0.00219) 		0.0149
(0.0266) 		0.0357
(0.0595)
3q gain 84 (16%) 455 0.617
(0.727) 		0.253
(0.335) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.105
(0.155) 		0.16
(0.227) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.00028
(0.00068) 		5e-05
(0.000133)
5p gain 51 (9%) 488 1
(1.00) 		0.514
(0.622) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.147
(0.21) 		0.705
(0.81) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.00021
(0.00052) 		1e-05
(2.95e-05)
6p gain 80 (15%) 459 0.208
(0.284) 		0.664
(0.771) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.0984
(0.146) 		0.833
(0.94) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.00211
(0.00445) 		0.0194
(0.0339)
12p gain 71 (13%) 468 0.387
(0.48) 		0.688
(0.795) 		1e-05
(2.95e-05) 		3e-05
(8.22e-05) 		0.915
(1.00) 		0.972
(1.00) 		1e-05
(2.95e-05) 		4e-05
(0.000108) 		0.00056
(0.00128) 		0.00062
(0.0014) 		0.00402
(0.00802) 		0.00346
(0.00706)
22q gain 31 (6%) 508 1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.372
(0.466) 		0.187
(0.259) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		4e-05
(0.000108) 		2e-05
(5.64e-05)
6p loss 18 (3%) 521 0.376
(0.47) 		0.029
(0.0498) 		1e-05
(2.95e-05) 		0.00127
(0.00276) 		0.364
(0.458) 		1
(1.00) 		0.00037
(0.000884) 		0.0002
(0.000498) 		0.00627
(0.0121) 		0.00397
(0.00794) 		0.0696
(0.107) 		0.0247
(0.0427)
7p loss 44 (8%) 495 0.0399
(0.0648) 		0.193
(0.266) 		1e-05
(2.95e-05) 		0.0004
(0.000946) 		0.0371
(0.0614) 		0.553
(0.661) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.062
(0.096) 		0.0619
(0.0959)
8q loss 25 (5%) 514 1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.327
(0.42) 		0.837
(0.944) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		3e-05
(8.22e-05) 		1e-05
(2.95e-05) 		0.00095
(0.00211) 		0.0087
(0.0163)
10q loss 40 (7%) 499 0.136
(0.195) 		0.167
(0.235) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.0546
(0.0852) 		0.17
(0.239) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.0316
(0.0531) 		0.00466
(0.00917)
11p loss 75 (14%) 464 1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.3
(0.39) 		0.331
(0.424) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.00046
(0.00107) 		2e-05
(5.64e-05)
11q loss 72 (13%) 467 1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.852
(0.954) 		0.789
(0.897) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05)
13q loss 93 (17%) 446 0.905
(0.996) 		0.196
(0.269) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.0245
(0.0425) 		0.5
(0.607) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		2e-05
(5.64e-05) 		1e-05
(2.95e-05) 		0.165
(0.232) 		0.00203
(0.0043)
18p loss 52 (10%) 487 1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.477
(0.583) 		0.567
(0.674) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.0001
(0.000258) 		8e-05
(0.000208) 		0.0174
(0.0306) 		0.00361
(0.00732)
18q loss 65 (12%) 474 0.535
(0.643) 		0.514
(0.622) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.531
(0.639) 		1
(1.00) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.0115
(0.0211) 		0.00041
(0.000967)
19p loss 59 (11%) 480 1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.097
(0.144) 		0.27
(0.354) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.00523
(0.0102) 		1e-05
(2.95e-05)
1q gain 188 (35%) 351 0.182
(0.253) 		0.0102
(0.0188) 		1e-05
(2.95e-05) 		0.187
(0.259) 		0.0935
(0.14) 		0.0157
(0.028) 		2e-05
(5.64e-05) 		0.00017
(0.000429) 		1e-05
(2.95e-05) 		0.017
(0.03) 		0.901
(0.995) 		0.077
(0.118)
5q gain 20 (4%) 519 1e-05
(2.95e-05) 		0.0357
(0.0595) 		0.368
(0.463) 		0.29
(0.377) 		0.00025
(0.000613) 		0.00652
(0.0125) 		0.00251
(0.00519) 		0.00014
(0.000355) 		0.23
(0.308) 		0.00012
(0.000307)
6q gain 64 (12%) 475 0.207
(0.283) 		0.661
(0.771) 		1e-05
(2.95e-05) 		0.00045
(0.00105) 		0.0515
(0.0809) 		0.758
(0.865) 		2e-05
(5.64e-05) 		0.00049
(0.00113) 		0.001
(0.00221) 		5e-05
(0.000133) 		0.0159
(0.0283) 		0.303
(0.392)
11p gain 23 (4%) 516 0.0392
(0.0641) 		0.197
(0.27) 		1e-05
(2.95e-05) 		0.0444
(0.071) 		0.055
(0.0857) 		0.114
(0.166) 		0.00327
(0.00672) 		0.00149
(0.00322) 		0.00223
(0.00467) 		0.00672
(0.0129) 		0.228
(0.307) 		0.362
(0.457)
17q gain 30 (6%) 509 1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.0412
(0.0665) 		1
(1.00) 		3e-05
(8.22e-05) 		1e-05
(2.95e-05) 		0.00012
(0.000307) 		0.0022
(0.00462) 		0.05
(0.079) 		0.0915
(0.137)
21q gain 39 (7%) 500 1e-05
(2.95e-05) 		0.00046
(0.00107) 		0.425
(0.524) 		0.454
(0.556) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.00034
(0.000816) 		0.234
(0.313)
1p loss 25 (5%) 514 1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		0.787
(0.897) 		0.362
(0.457) 		1e-05
(2.95e-05) 		1e-05
(2.95e-05) 		8e-05
(0.000208) 		1e-05
(2.95e-05) 		0.29
(0.377) 		0.0006
(0.00136)
1q loss 14 (3%) 525 1e-05
(2.95e-05) 		3e-05
(8.22e-05) 		8e-05
(0.000208) 		0.00108
(0.00237) 		0.00032
(0.000772) 		1e-05
(2.95e-05) 		0.526
(0.634) 		0.0075
(0.0142)
4p gain 14 (3%) 525 1e-05
(2.95e-05) 		0.846
(0.95) 		0.374
(0.467) 		0.0379
(0.0625) 		0.00055
(0.00126) 		0.0452
(0.0722) 		0.00407
(0.00809) 		0.00055
(0.00126) 		0.348
(0.441) 		0.435
(0.533)
14q gain 37 (7%) 502 1
(1.00) 		0.843
(0.948) 		1e-05
(2.95e-05) 		0.00215
(0.00452) 		0.0859
(0.13) 		0.691
(0.796) 		0.00023
(0.000569) 		0.00062
(0.0014) 		0.0062
(0.012) 		0.00049
(0.00113) 		0.0926
(0.139) 		0.312
(0.402)
7p gain 67 (12%) 472 0.853
(0.954) 		0.905
(0.996) 		1e-05
(2.95e-05) 		0.00134
(0.0029) 		0.846
(0.95) 		0.864
(0.963) 		0.039
(0.0639) 		0.0624
(0.0963) 		0.0132
(0.0238) 		0.431
(0.53) 		0.0311
(0.0525) 		0.0528
(0.0826)
9p gain 22 (4%) 517 7e-05
(0.000184) 		0.00379
(0.00761) 		0.0957
(0.142) 		0.327
(0.42) 		0.00501
(0.00978) 		0.0132
(0.0239) 		0.0107
(0.0197) 		0.111
(0.162) 		0.105
(0.155) 		0.369
(0.463)
12q gain 54 (10%) 485 0.386
(0.48) 		0.687
(0.794) 		1e-05
(2.95e-05) 		0.0088
(0.0164) 		0.963
(1.00) 		0.981
(1.00) 		0.00439
(0.00867) 		0.0422
(0.0678) 		0.0486
(0.0771) 		0.107
(0.157) 		0.2
(0.274) 		0.275
(0.36)
2q loss 17 (3%) 522 2e-05
(5.64e-05) 		0.116
(0.167) 		0.00028
(0.00068) 		0.0146
(0.0262) 		0.0185
(0.0324) 		0.0302
(0.0513) 		0.416
(0.515) 		0.801
(0.908)
20q loss 9 (2%) 530 0.0005
(0.00115) 		0.0864
(0.131) 		0.644
(0.752) 		1
(1.00) 		0.037
(0.0614) 		0.0307
(0.052) 		0.0405
(0.0655) 		0.047
(0.0747) 		0.174
(0.243) 		0.251
(0.333)
8p gain 118 (22%) 421 0.356
(0.451) 		0.402
(0.498) 		1e-05
(2.95e-05) 		0.883
(0.978) 		0.0214
(0.0373) 		0.217
(0.294) 		0.139
(0.199) 		0.0358
(0.0596) 		0.307
(0.396) 		0.0291
(0.05) 		0.116
(0.167) 		0.508
(0.616)
10p gain 117 (22%) 422 0.0077
(0.0145) 		0.09
(0.136) 		1e-05
(2.95e-05) 		0.872
(0.969) 		0.193
(0.266) 		0.814
(0.921) 		0.0932
(0.139) 		0.165
(0.232) 		0.575
(0.682) 		0.0185
(0.0325) 		0.537
(0.644) 		0.0359
(0.0597)
16p gain 27 (5%) 512 1e-05
(2.95e-05) 		0.00245
(0.0051) 		0.18
(0.25) 		0.634
(0.745) 		0.019
(0.0333) 		0.0523
(0.082) 		0.00337
(0.00689) 		0.237
(0.317) 		0.145
(0.207) 		0.358
(0.454)
20p loss 19 (4%) 520 1e-05
(2.95e-05) 		0.21
(0.286) 		0.465
(0.569) 		0.665
(0.771) 		0.0162
(0.0286) 		0.0103
(0.019) 		0.00707
(0.0135) 		0.0513
(0.0808) 		0.421
(0.52) 		0.43
(0.529)
7q gain 66 (12%) 473 0.854
(0.954) 		0.903
(0.996) 		1e-05
(2.95e-05) 		0.00151
(0.00324) 		0.854
(0.954) 		0.537
(0.644) 		0.178
(0.248) 		0.0274
(0.0471) 		0.0817
(0.124) 		0.476
(0.582) 		0.0898
(0.136) 		0.209
(0.285)
10q gain 109 (20%) 430 0.00495
(0.0097) 		0.0914
(0.137) 		4e-05
(0.000108) 		0.727
(0.832) 		0.123
(0.178) 		0.662
(0.771) 		0.14
(0.2) 		0.379
(0.472) 		0.34
(0.434) 		0.00195
(0.00416) 		0.565
(0.671) 		0.0603
(0.0936)
11q gain 19 (4%) 520 1e-05
(2.95e-05) 		0.115
(0.166) 		0.179
(0.249) 		0.0115
(0.0211) 		0.0333
(0.0559) 		0.102
(0.151) 		0.209
(0.285) 		0.0913
(0.137) 		0.885
(0.979) 		0.652
(0.761)
4q gain 8 (1%) 531 0.00457
(0.00901) 		0.618
(0.727) 		0.0293
(0.0502) 		0.547
(0.655) 		0.271
(0.356) 		0.0757
(0.116) 		0.796
(0.904) 		0.635
(0.745)
17p gain 12 (2%) 527 0.0015
(0.00323) 		0.16
(0.227) 		0.224
(0.302) 		1
(1.00) 		0.114
(0.166) 		0.0413
(0.0666) 		0.0774
(0.118) 		0.134
(0.193) 		0.347
(0.441) 		0.665
(0.771)
2p loss 11 (2%) 528 0.00024
(0.000592) 		0.301
(0.39) 		0.00533
(0.0103) 		0.0808
(0.123) 		0.401
(0.497) 		0.107
(0.157) 		0.559
(0.667) 		0.721
(0.826)
9q gain 9 (2%) 530 0.0308
(0.0521) 		0.167
(0.235) 		0.36
(0.455) 		0.305
(0.394) 		0.171
(0.24) 		0.511
(0.62) 		0.663
(0.771) 		0.263
(0.347)
15q gain 11 (2%) 528 0.00057
(0.0013) 		0.915
(1.00) 		0.691
(0.796) 		0.591
(0.699) 		0.638
(0.747) 		0.913
(1.00) 		1
(1.00) 		0.249
(0.332)
16q gain 10 (2%) 529 0.0121
(0.022) 		0.0511
(0.0805) 		0.944
(1.00) 		0.839
(0.945) 		0.111
(0.162) 		0.284
(0.37) 		0.0707
(0.109) 		0.211
(0.287) 		0.623
(0.732) 		0.796
(0.904)
xp gain 64 (12%) 475 0.576
(0.682) 		0.908
(0.997) 		1e-05
(2.95e-05) 		0.108
(0.158) 		0.874
(0.969) 		0.558
(0.665) 		0.525
(0.634) 		0.788
(0.897) 		0.266
(0.349) 		0.818
(0.924) 		0.227
(0.306) 		0.425
(0.524)
xq gain 64 (12%) 475 0.705
(0.81) 		0.927
(1.00) 		1e-05
(2.95e-05) 		0.587
(0.694) 		0.874
(0.969) 		0.337
(0.431) 		0.639
(0.747) 		0.885
(0.979) 		0.555
(0.663) 		0.981
(1.00) 		0.224
(0.302) 		0.87
(0.969)
'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
1P GAIN MUTATED 38 6 2 0 4
1P GAIN WILD-TYPE 131 299 17 9 33

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0011

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
1P GAIN MUTATED 30 5 10
1P GAIN WILD-TYPE 135 84 161

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

'1p gain' versus 'RPPA_CNMF'

P value = 0.0453 (Fisher's exact test), Q value = 0.072

Table S3.  Gene #1: '1p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
1P GAIN MUTATED 2 6 0 1 1 2
1P GAIN WILD-TYPE 39 31 39 11 40 22

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

'1p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S4.  Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
1P GAIN MUTATED 39 6 5
1P GAIN WILD-TYPE 195 147 145

Figure S4.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 8.2e-05

Table S5.  Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
1P GAIN MUTATED 26 2 7 2 7 4 2
1P GAIN WILD-TYPE 97 51 40 63 101 62 73

Figure S5.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.6e-05

Table S6.  Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
1P GAIN MUTATED 35 12 2
1P GAIN WILD-TYPE 188 138 155

Figure S6.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00011

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
1P GAIN MUTATED 21 1 4 23
1P GAIN WILD-TYPE 198 57 133 93

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

'1p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00239 (Fisher's exact test), Q value = 0.005

Table S8.  Gene #1: '1p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
1P GAIN MUTATED 30 6 8
1P GAIN WILD-TYPE 142 90 122

Figure S8.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00294 (Fisher's exact test), Q value = 0.0061

Table S9.  Gene #1: '1p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
1P GAIN MUTATED 26 6 12
1P GAIN WILD-TYPE 118 109 127

Figure S9.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.019

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
1Q GAIN MUTATED 6 2 6 5 3
1Q GAIN WILD-TYPE 8 7 1 2 13

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

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S11.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
1Q GAIN MUTATED 57 90 12 8 21
1Q GAIN WILD-TYPE 112 215 7 1 16

Figure S11.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0157 (Fisher's exact test), Q value = 0.028

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
1Q GAIN MUTATED 16 25 23 5
1Q GAIN WILD-TYPE 51 42 20 12

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.6e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
1Q GAIN MUTATED 76 75 37
1Q GAIN WILD-TYPE 158 78 113

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

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00043

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
1Q GAIN MUTATED 47 29 11 33 33 17 18
1Q GAIN WILD-TYPE 76 24 36 32 75 49 57

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

'1q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
1Q GAIN MUTATED 69 79 39
1Q GAIN WILD-TYPE 154 71 118

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

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.017 (Fisher's exact test), Q value = 0.03

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
1Q GAIN MUTATED 77 30 38 42
1Q GAIN WILD-TYPE 142 28 99 74

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

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
2P GAIN MUTATED 62 9 10 3 11
2P GAIN WILD-TYPE 107 296 9 6 26

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
2P GAIN MUTATED 53 9 11
2P GAIN WILD-TYPE 112 80 160

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S19.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
2P GAIN MUTATED 70 15 10
2P GAIN WILD-TYPE 164 138 140

Figure S19.  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 = 3e-05

Table S20.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
2P GAIN MUTATED 49 7 11 4 14 6 4
2P GAIN WILD-TYPE 74 46 36 61 94 60 71

Figure S20.  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 = 3e-05

Table S21.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
2P GAIN MUTATED 66 17 11
2P GAIN WILD-TYPE 157 133 146

Figure S21.  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 = 3e-05

Table S22.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
2P GAIN MUTATED 34 7 10 43
2P GAIN WILD-TYPE 185 51 127 73

Figure S22.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00016

Table S23.  Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
2P GAIN MUTATED 42 20 8
2P GAIN WILD-TYPE 130 76 122

Figure S23.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00043

Table S24.  Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
2P GAIN MUTATED 35 7 28
2P GAIN WILD-TYPE 109 108 111

Figure S24.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S25.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
2Q GAIN MUTATED 52 7 8 3 9
2Q GAIN WILD-TYPE 117 298 11 6 28

Figure S25.  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 = 3e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
2Q GAIN MUTATED 47 7 10
2Q GAIN WILD-TYPE 118 82 161

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

'2q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S27.  Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
2Q GAIN MUTATED 59 12 8
2Q GAIN WILD-TYPE 175 141 142

Figure S27.  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 = 3e-05

Table S28.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
2Q GAIN MUTATED 41 5 9 3 12 5 4
2Q GAIN WILD-TYPE 82 48 38 62 96 61 71

Figure S28.  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 = 3e-05

Table S29.  Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
2Q GAIN MUTATED 55 16 8
2Q GAIN WILD-TYPE 168 134 149

Figure S29.  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 = 3e-05

Table S30.  Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
2Q GAIN MUTATED 30 5 8 36
2Q GAIN WILD-TYPE 189 53 129 80

Figure S30.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00023

Table S31.  Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
2Q GAIN MUTATED 39 16 7
2Q GAIN WILD-TYPE 133 80 123

Figure S31.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.00073

Table S32.  Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
2Q GAIN MUTATED 31 6 25
2Q GAIN WILD-TYPE 113 109 114

Figure S32.  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 = 3e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
3P GAIN MUTATED 31 2 1 3 12
3P GAIN WILD-TYPE 138 303 18 6 25

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

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.00926 (Fisher's exact test), Q value = 0.017

Table S34.  Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
3P GAIN MUTATED 26 7 10
3P GAIN WILD-TYPE 139 82 161

Figure S34.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00011

Table S35.  Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
3P GAIN MUTATED 35 4 10
3P GAIN WILD-TYPE 199 149 140

Figure S35.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00554 (Fisher's exact test), Q value = 0.011

Table S36.  Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
3P GAIN MUTATED 16 0 8 4 14 3 4
3P GAIN WILD-TYPE 107 53 39 61 94 63 71

Figure S36.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0024

Table S37.  Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
3P GAIN MUTATED 33 8 8
3P GAIN WILD-TYPE 190 142 149

Figure S37.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00099 (Fisher's exact test), Q value = 0.0022

Table S38.  Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
3P GAIN MUTATED 18 0 11 20
3P GAIN WILD-TYPE 201 58 126 96

Figure S38.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.027

Table S39.  Gene #5: '3p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
3P GAIN MUTATED 25 9 6
3P GAIN WILD-TYPE 147 87 124

Figure S39.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0357 (Fisher's exact test), Q value = 0.06

Table S40.  Gene #5: '3p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
3P GAIN MUTATED 22 7 11
3P GAIN WILD-TYPE 122 108 128

Figure S40.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S41.  Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
3Q GAIN MUTATED 62 4 2 3 13
3Q GAIN WILD-TYPE 107 301 17 6 24

Figure S41.  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 = 3e-05

Table S42.  Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
3Q GAIN MUTATED 54 9 11
3Q GAIN WILD-TYPE 111 80 160

Figure S42.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S43.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
3Q GAIN MUTATED 68 5 11
3Q GAIN WILD-TYPE 166 148 139

Figure S43.  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 = 3e-05

Table S44.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
3Q GAIN MUTATED 37 0 18 4 17 3 5
3Q GAIN WILD-TYPE 86 53 29 61 91 63 70

Figure S44.  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 = 3e-05

Table S45.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
3Q GAIN MUTATED 63 12 9
3Q GAIN WILD-TYPE 160 138 148

Figure S45.  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 = 3e-05

Table S46.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
3Q GAIN MUTATED 30 0 12 42
3Q GAIN WILD-TYPE 189 58 125 74

Figure S46.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.00068

Table S47.  Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
3Q GAIN MUTATED 43 17 10
3Q GAIN WILD-TYPE 129 79 120

Figure S47.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00013

Table S48.  Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
3Q GAIN MUTATED 41 8 21
3Q GAIN WILD-TYPE 103 107 118

Figure S48.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S49.  Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
4P GAIN MUTATED 13 0 0 0 1
4P GAIN WILD-TYPE 156 305 19 9 36

Figure S49.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'4p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0379 (Fisher's exact test), Q value = 0.063

Table S50.  Gene #7: '4p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
4P GAIN MUTATED 5 0 0 0
4P GAIN WILD-TYPE 62 67 43 17

Figure S50.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0013

Table S51.  Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
4P GAIN MUTATED 13 0 1
4P GAIN WILD-TYPE 221 153 149

Figure S51.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0452 (Fisher's exact test), Q value = 0.072

Table S52.  Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

Figure S52.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CNMF'

P value = 0.00407 (Fisher's exact test), Q value = 0.0081

Table S53.  Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
4P GAIN MUTATED 12 1 1
4P GAIN WILD-TYPE 211 149 156

Figure S53.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.0013

Table S54.  Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
4P GAIN MUTATED 3 0 1 10
4P GAIN WILD-TYPE 216 58 136 106

Figure S54.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 0.00457 (Fisher's exact test), Q value = 0.009

Table S55.  Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
4Q GAIN MUTATED 7 0 0 0 1
4Q GAIN WILD-TYPE 162 305 19 9 36

Figure S55.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 0.0293 (Fisher's exact test), Q value = 0.05

Table S56.  Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
4Q GAIN MUTATED 7 0 1
4Q GAIN WILD-TYPE 227 153 149

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

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S57.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
5P GAIN MUTATED 43 3 4 1 0
5P GAIN WILD-TYPE 126 302 15 8 37

Figure S57.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S58.  Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
5P GAIN MUTATED 34 5 5
5P GAIN WILD-TYPE 131 84 166

Figure S58.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S59.  Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
5P GAIN MUTATED 45 5 1
5P GAIN WILD-TYPE 189 148 149

Figure S59.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S60.  Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
5P GAIN MUTATED 28 3 12 1 5 2 0
5P GAIN WILD-TYPE 95 50 35 64 103 64 75

Figure S60.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
5P GAIN MUTATED 40 10 1
5P GAIN WILD-TYPE 183 140 156

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

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S62.  Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
5P GAIN MUTATED 13 4 1 33
5P GAIN WILD-TYPE 206 54 136 83

Figure S62.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00052

Table S63.  Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
5P GAIN MUTATED 30 8 4
5P GAIN WILD-TYPE 142 88 126

Figure S63.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S64.  Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
5P GAIN MUTATED 32 1 9
5P GAIN WILD-TYPE 112 114 130

Figure S64.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S65.  Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
5Q GAIN MUTATED 15 1 3 1 0
5Q GAIN WILD-TYPE 154 304 16 8 37

Figure S65.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 0.06

Table S66.  Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
5Q GAIN MUTATED 13 2 4
5Q GAIN WILD-TYPE 152 87 167

Figure S66.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.00061

Table S67.  Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
5Q GAIN MUTATED 17 3 0
5Q GAIN WILD-TYPE 217 150 150

Figure S67.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00652 (Fisher's exact test), Q value = 0.013

Table S68.  Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

Figure S68.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CNMF'

P value = 0.00251 (Fisher's exact test), Q value = 0.0052

Table S69.  Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
5Q GAIN MUTATED 13 7 0
5Q GAIN WILD-TYPE 210 143 157

Figure S69.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00036

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
5Q GAIN MUTATED 6 2 0 12
5Q GAIN WILD-TYPE 213 56 137 104

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

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00031

Table S71.  Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
5Q GAIN MUTATED 14 0 3
5Q GAIN WILD-TYPE 130 115 136

Figure S71.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S72.  Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
6P GAIN MUTATED 61 5 1 1 12
6P GAIN WILD-TYPE 108 300 18 8 25

Figure S72.  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 = 3e-05

Table S73.  Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
6P GAIN MUTATED 49 12 11
6P GAIN WILD-TYPE 116 77 160

Figure S73.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S74.  Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
6P GAIN MUTATED 61 5 14
6P GAIN WILD-TYPE 173 148 136

Figure S74.  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 = 3e-05

Table S75.  Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
6P GAIN MUTATED 43 0 5 5 14 8 5
6P GAIN WILD-TYPE 80 53 42 60 94 58 70

Figure S75.  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 = 3e-05

Table S76.  Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
6P GAIN MUTATED 55 14 11
6P GAIN WILD-TYPE 168 136 146

Figure S76.  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 = 3e-05

Table S77.  Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
6P GAIN MUTATED 34 0 11 35
6P GAIN WILD-TYPE 185 58 126 81

Figure S77.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00211 (Fisher's exact test), Q value = 0.0044

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
6P GAIN MUTATED 42 15 12
6P GAIN WILD-TYPE 130 81 118

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

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0194 (Fisher's exact test), Q value = 0.034

Table S79.  Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
6P GAIN MUTATED 34 12 23
6P GAIN WILD-TYPE 110 103 116

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

'6q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S80.  Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
6Q GAIN MUTATED 46 5 1 1 11
6Q GAIN WILD-TYPE 123 300 18 8 26

Figure S80.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0011

Table S81.  Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
6Q GAIN MUTATED 35 9 12
6Q GAIN WILD-TYPE 130 80 159

Figure S81.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.6e-05

Table S82.  Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
6Q GAIN MUTATED 45 5 14
6Q GAIN WILD-TYPE 189 148 136

Figure S82.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.0011

Table S83.  Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
6Q GAIN MUTATED 28 0 6 5 12 7 6
6Q GAIN WILD-TYPE 95 53 41 60 96 59 69

Figure S83.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 0.001 (Fisher's exact test), Q value = 0.0022

Table S84.  Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
6Q GAIN MUTATED 41 12 11
6Q GAIN WILD-TYPE 182 138 146

Figure S84.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00013

Table S85.  Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
6Q GAIN MUTATED 29 0 11 24
6Q GAIN WILD-TYPE 190 58 126 92

Figure S85.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.028

Table S86.  Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
6Q GAIN MUTATED 31 13 9
6Q GAIN WILD-TYPE 141 83 121

Figure S86.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S87.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
7P GAIN MUTATED 33 9 12 2 11
7P GAIN WILD-TYPE 136 296 7 7 26

Figure S87.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.0029

Table S88.  Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
7P GAIN MUTATED 30 3 18
7P GAIN WILD-TYPE 135 86 153

Figure S88.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.039 (Fisher's exact test), Q value = 0.064

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
7P GAIN MUTATED 39 15 13
7P GAIN WILD-TYPE 195 138 137

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

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.0132 (Fisher's exact test), Q value = 0.024

Table S90.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
7P GAIN MUTATED 36 20 10
7P GAIN WILD-TYPE 187 130 147

Figure S90.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0311 (Fisher's exact test), Q value = 0.052

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
7P GAIN MUTATED 26 14 8
7P GAIN WILD-TYPE 146 82 122

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

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S92.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
7Q GAIN MUTATED 30 12 12 2 10
7Q GAIN WILD-TYPE 139 293 7 7 27

Figure S92.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.00151 (Fisher's exact test), Q value = 0.0032

Table S93.  Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
7Q GAIN MUTATED 27 2 21
7Q GAIN WILD-TYPE 138 87 150

Figure S93.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0274 (Fisher's exact test), Q value = 0.047

Table S94.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
7Q GAIN MUTATED 20 8 8 1 15 8 6
7Q GAIN WILD-TYPE 103 45 39 64 93 58 69

Figure S94.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S95.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
8P GAIN MUTATED 43 29 8 2 36
8P GAIN WILD-TYPE 126 276 11 7 1

Figure S95.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'RPPA_CNMF'

P value = 0.0214 (Fisher's exact test), Q value = 0.037

Table S96.  Gene #15: '8p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
8P GAIN MUTATED 7 10 4 2 2 8
8P GAIN WILD-TYPE 34 27 35 10 39 16

Figure S96.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0358 (Fisher's exact test), Q value = 0.06

Table S97.  Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
8P GAIN MUTATED 28 10 11 8 34 17 10
8P GAIN WILD-TYPE 95 43 36 57 74 49 65

Figure S97.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0291 (Fisher's exact test), Q value = 0.05

Table S98.  Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
8P GAIN MUTATED 60 6 27 24
8P GAIN WILD-TYPE 159 52 110 92

Figure S98.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MRNA_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.019

Table S99.  Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
8Q GAIN MUTATED 1 8 2 0
8Q GAIN WILD-TYPE 13 9 10 10

Figure S99.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.031 (Fisher's exact test), Q value = 0.052

Table S100.  Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S100.  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 = 3e-05

Table S101.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
8Q GAIN MUTATED 80 31 8 3 37
8Q GAIN WILD-TYPE 89 274 11 6 0

Figure S101.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.04 (Fisher's exact test), Q value = 0.065

Table S102.  Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
8Q GAIN MUTATED 64 24 46
8Q GAIN WILD-TYPE 101 65 125

Figure S102.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.00073

Table S103.  Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
8Q GAIN MUTATED 9 12 7 2 2 13
8Q GAIN WILD-TYPE 32 25 32 10 39 11

Figure S103.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0219 (Fisher's exact test), Q value = 0.038

Table S104.  Gene #16: '8q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
8Q GAIN MUTATED 15 15 6 9
8Q GAIN WILD-TYPE 52 52 37 8

Figure S104.  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 = 3e-05

Table S105.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
8Q GAIN MUTATED 97 28 34
8Q GAIN WILD-TYPE 137 125 116

Figure S105.  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 = 3e-05

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

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

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

'8q gain' versus 'MIRSEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00048

Table S107.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
8Q GAIN MUTATED 87 36 33
8Q GAIN WILD-TYPE 136 114 124

Figure S107.  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 = 3e-05

Table S108.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
8Q GAIN MUTATED 68 6 31 51
8Q GAIN WILD-TYPE 151 52 106 65

Figure S108.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0011

Table S109.  Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
8Q GAIN MUTATED 71 28 27
8Q GAIN WILD-TYPE 101 68 103

Figure S109.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00745 (Fisher's exact test), Q value = 0.014

Table S110.  Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
8Q GAIN MUTATED 59 27 40
8Q GAIN WILD-TYPE 85 88 99

Figure S110.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00018

Table S111.  Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
9P GAIN MUTATED 18 3 0 0 1
9P GAIN WILD-TYPE 151 302 19 9 36

Figure S111.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 0.00379 (Fisher's exact test), Q value = 0.0076

Table S112.  Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
9P GAIN MUTATED 15 2 3
9P GAIN WILD-TYPE 150 87 168

Figure S112.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 0.00501 (Fisher's exact test), Q value = 0.0098

Table S113.  Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
9P GAIN MUTATED 17 2 3
9P GAIN WILD-TYPE 217 151 147

Figure S113.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0132 (Fisher's exact test), Q value = 0.024

Table S114.  Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
9P GAIN MUTATED 11 0 1 1 7 2 0
9P GAIN WILD-TYPE 112 53 46 64 101 64 75

Figure S114.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.02

Table S115.  Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
9P GAIN MUTATED 16 4 2
9P GAIN WILD-TYPE 207 146 155

Figure S115.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.052

Table S116.  Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
9Q GAIN MUTATED 7 1 0 0 1
9Q GAIN WILD-TYPE 162 304 19 9 36

Figure S116.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'MRNA_CNMF'

P value = 0.0077 (Fisher's exact test), Q value = 0.015

Table S117.  Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
10P GAIN MUTATED 2 2 8 2
10P GAIN WILD-TYPE 12 15 4 8

Figure S117.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S118.  Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
10P GAIN MUTATED 41 46 7 4 19
10P GAIN WILD-TYPE 128 259 12 5 18

Figure S118.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0185 (Fisher's exact test), Q value = 0.033

Table S119.  Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
10P GAIN MUTATED 35 17 39 26
10P GAIN WILD-TYPE 184 41 98 90

Figure S119.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0359 (Fisher's exact test), Q value = 0.06

Table S120.  Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
10P GAIN MUTATED 24 33 24
10P GAIN WILD-TYPE 120 82 115

Figure S120.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'MRNA_CNMF'

P value = 0.00495 (Fisher's exact test), Q value = 0.0097

Table S121.  Gene #20: '10q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
10Q GAIN MUTATED 1 3 8 2
10Q GAIN WILD-TYPE 13 14 4 8

Figure S121.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00011

Table S122.  Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
10Q GAIN MUTATED 36 45 8 4 16
10Q GAIN WILD-TYPE 133 260 11 5 21

Figure S122.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00195 (Fisher's exact test), Q value = 0.0042

Table S123.  Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
10Q GAIN MUTATED 29 17 38 25
10Q GAIN WILD-TYPE 190 41 99 91

Figure S123.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'MRNA_CNMF'

P value = 0.0392 (Fisher's exact test), Q value = 0.064

Table S124.  Gene #21: '11p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
11P GAIN MUTATED 0 4 0 0
11P GAIN WILD-TYPE 14 13 12 10

Figure S124.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S125.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
11P GAIN MUTATED 17 0 4 0 2
11P GAIN WILD-TYPE 152 305 15 9 35

Figure S125.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.0444 (Fisher's exact test), Q value = 0.071

Table S126.  Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
11P GAIN MUTATED 12 4 3
11P GAIN WILD-TYPE 153 85 168

Figure S126.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CNMF'

P value = 0.00327 (Fisher's exact test), Q value = 0.0067

Table S127.  Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
11P GAIN MUTATED 18 2 3
11P GAIN WILD-TYPE 216 151 147

Figure S127.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00149 (Fisher's exact test), Q value = 0.0032

Table S128.  Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

Figure S128.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CNMF'

P value = 0.00223 (Fisher's exact test), Q value = 0.0047

Table S129.  Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
11P GAIN MUTATED 18 2 3
11P GAIN WILD-TYPE 205 148 154

Figure S129.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00672 (Fisher's exact test), Q value = 0.013

Table S130.  Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
11P GAIN MUTATED 8 1 2 12
11P GAIN WILD-TYPE 211 57 135 104

Figure S130.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S131.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
11Q GAIN MUTATED 13 0 3 0 3
11Q GAIN WILD-TYPE 156 305 16 9 34

Figure S131.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0115 (Fisher's exact test), Q value = 0.021

Table S132.  Gene #22: '11q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
11Q GAIN MUTATED 1 4 0 3
11Q GAIN WILD-TYPE 66 63 43 14

Figure S132.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 0.0333 (Fisher's exact test), Q value = 0.056

Table S133.  Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
11Q GAIN MUTATED 14 2 3
11Q GAIN WILD-TYPE 220 151 147

Figure S133.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S134.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
12P GAIN MUTATED 42 14 7 3 5
12P GAIN WILD-TYPE 127 291 12 6 32

Figure S134.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 8.2e-05

Table S135.  Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
12P GAIN MUTATED 35 14 8
12P GAIN WILD-TYPE 130 75 163

Figure S135.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S136.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
12P GAIN MUTATED 51 10 10
12P GAIN WILD-TYPE 183 143 140

Figure S136.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00011

Table S137.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
12P GAIN MUTATED 31 1 10 6 13 3 7
12P GAIN WILD-TYPE 92 52 37 59 95 63 68

Figure S137.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0013

Table S138.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
12P GAIN MUTATED 44 17 10
12P GAIN WILD-TYPE 179 133 147

Figure S138.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0014

Table S139.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
12P GAIN MUTATED 29 4 10 28
12P GAIN WILD-TYPE 190 54 127 88

Figure S139.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00402 (Fisher's exact test), Q value = 0.008

Table S140.  Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
12P GAIN MUTATED 34 11 9
12P GAIN WILD-TYPE 138 85 121

Figure S140.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00346 (Fisher's exact test), Q value = 0.0071

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
12P GAIN MUTATED 29 7 18
12P GAIN WILD-TYPE 115 108 121

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

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S142.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
12Q GAIN MUTATED 26 14 6 3 5
12Q GAIN WILD-TYPE 143 291 13 6 32

Figure S142.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 0.0088 (Fisher's exact test), Q value = 0.016

Table S143.  Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
12Q GAIN MUTATED 22 12 8
12Q GAIN WILD-TYPE 143 77 163

Figure S143.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.00439 (Fisher's exact test), Q value = 0.0087

Table S144.  Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
12Q GAIN MUTATED 35 9 10
12Q GAIN WILD-TYPE 199 144 140

Figure S144.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0422 (Fisher's exact test), Q value = 0.068

Table S145.  Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
12Q GAIN MUTATED 19 1 8 6 10 3 7
12Q GAIN WILD-TYPE 104 52 39 59 98 63 68

Figure S145.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 0.0486 (Fisher's exact test), Q value = 0.077

Table S146.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
12Q GAIN MUTATED 31 13 10
12Q GAIN WILD-TYPE 192 137 147

Figure S146.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0068 (Fisher's exact test), Q value = 0.013

Table S147.  Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S147.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S148.  Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
13Q GAIN MUTATED 27 0 0 1 2
13Q GAIN WILD-TYPE 142 305 19 8 35

Figure S148.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00016

Table S149.  Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
13Q GAIN MUTATED 18 7 1
13Q GAIN WILD-TYPE 147 82 170

Figure S149.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0116 (Fisher's exact test), Q value = 0.021

Table S150.  Gene #25: '13q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
13Q GAIN MUTATED 4 1 0 3
13Q GAIN WILD-TYPE 63 66 43 14

Figure S150.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S151.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
13Q GAIN MUTATED 27 1 2
13Q GAIN WILD-TYPE 207 152 148

Figure S151.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S152.  Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

Figure S152.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S153.  Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
13Q GAIN MUTATED 27 1 2
13Q GAIN WILD-TYPE 196 149 155

Figure S153.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S154.  Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
13Q GAIN MUTATED 5 0 2 23
13Q GAIN WILD-TYPE 214 58 135 93

Figure S154.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00707 (Fisher's exact test), Q value = 0.013

Table S155.  Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
13Q GAIN MUTATED 17 6 2
13Q GAIN WILD-TYPE 155 90 128

Figure S155.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0236 (Fisher's exact test), Q value = 0.041

Table S156.  Gene #25: '13q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
13Q GAIN MUTATED 14 2 9
13Q GAIN WILD-TYPE 130 113 130

Figure S156.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S157.  Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
14Q GAIN MUTATED 26 4 1 0 6
14Q GAIN WILD-TYPE 143 301 18 9 31

Figure S157.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 0.00215 (Fisher's exact test), Q value = 0.0045

Table S158.  Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
14Q GAIN MUTATED 23 4 7
14Q GAIN WILD-TYPE 142 85 164

Figure S158.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00057

Table S159.  Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
14Q GAIN MUTATED 28 3 6
14Q GAIN WILD-TYPE 206 150 144

Figure S159.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0014

Table S160.  Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
14Q GAIN MUTATED 17 1 6 1 8 0 4
14Q GAIN WILD-TYPE 106 52 41 64 100 66 71

Figure S160.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 0.0062 (Fisher's exact test), Q value = 0.012

Table S161.  Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
14Q GAIN MUTATED 25 6 6
14Q GAIN WILD-TYPE 198 144 151

Figure S161.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.0011

Table S162.  Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
14Q GAIN MUTATED 10 1 7 19
14Q GAIN WILD-TYPE 209 57 130 97

Figure S162.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0013

Table S163.  Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
15Q GAIN MUTATED 8 0 1 0 2
15Q GAIN WILD-TYPE 161 305 18 9 35

Figure S163.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S164.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
16P GAIN MUTATED 22 1 1 0 3
16P GAIN WILD-TYPE 147 304 18 9 34

Figure S164.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 0.00245 (Fisher's exact test), Q value = 0.0051

Table S165.  Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
16P GAIN MUTATED 16 0 9
16P GAIN WILD-TYPE 149 89 162

Figure S165.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.019 (Fisher's exact test), Q value = 0.033

Table S166.  Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
16P GAIN MUTATED 19 4 4
16P GAIN WILD-TYPE 215 149 146

Figure S166.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.00337 (Fisher's exact test), Q value = 0.0069

Table S167.  Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
16P GAIN MUTATED 20 3 4
16P GAIN WILD-TYPE 203 147 153

Figure S167.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.022

Table S168.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
16Q GAIN MUTATED 8 1 0 0 1
16Q GAIN WILD-TYPE 161 304 19 9 36

Figure S168.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 0.0015 (Fisher's exact test), Q value = 0.0032

Table S169.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
17P GAIN MUTATED 8 1 0 1 2
17P GAIN WILD-TYPE 161 304 19 8 35

Figure S169.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0413 (Fisher's exact test), Q value = 0.067

Table S170.  Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
17P GAIN MUTATED 8 0 1 1 2 0 0
17P GAIN WILD-TYPE 115 53 46 64 106 66 75

Figure S170.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S171.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
17Q GAIN MUTATED 25 1 0 1 3
17Q GAIN WILD-TYPE 144 304 19 8 34

Figure S171.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S172.  Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
17Q GAIN MUTATED 23 2 2
17Q GAIN WILD-TYPE 142 87 169

Figure S172.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'RPPA_CNMF'

P value = 0.0412 (Fisher's exact test), Q value = 0.067

Table S173.  Gene #31: '17q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
17Q GAIN MUTATED 4 1 0 1 0 0
17Q GAIN WILD-TYPE 37 36 39 11 41 24

Figure S173.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 8.2e-05

Table S174.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
17Q GAIN MUTATED 25 2 3
17Q GAIN WILD-TYPE 209 151 147

Figure S174.  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 = 3e-05

Table S175.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
17Q GAIN MUTATED 19 0 5 1 3 2 0
17Q GAIN WILD-TYPE 104 53 42 64 105 64 75

Figure S175.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00031

Table S176.  Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
17Q GAIN MUTATED 24 3 3
17Q GAIN WILD-TYPE 199 147 154

Figure S176.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0022 (Fisher's exact test), Q value = 0.0046

Table S177.  Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
17Q GAIN MUTATED 11 1 3 15
17Q GAIN WILD-TYPE 208 57 134 101

Figure S177.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S178.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
18P GAIN MUTATED 65 3 3 0 1
18P GAIN WILD-TYPE 104 302 16 9 36

Figure S178.  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 = 3e-05

Table S179.  Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
18P GAIN MUTATED 45 13 4
18P GAIN WILD-TYPE 120 76 167

Figure S179.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'RPPA_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.022

Table S180.  Gene #32: '18p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
18P GAIN MUTATED 7 3 0 0 1 4
18P GAIN WILD-TYPE 34 34 39 12 40 20

Figure S180.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S181.  Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
18P GAIN MUTATED 65 3 4
18P GAIN WILD-TYPE 169 150 146

Figure S181.  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 = 3e-05

Table S182.  Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
18P GAIN MUTATED 47 1 13 1 7 2 1
18P GAIN WILD-TYPE 76 52 34 64 101 64 74

Figure S182.  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 = 3e-05

Table S183.  Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
18P GAIN MUTATED 60 9 3
18P GAIN WILD-TYPE 163 141 154

Figure S183.  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 = 3e-05

Table S184.  Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
18P GAIN MUTATED 24 1 2 45
18P GAIN WILD-TYPE 195 57 135 71

Figure S184.  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 = 3e-05

Table S185.  Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
18P GAIN MUTATED 40 16 3
18P GAIN WILD-TYPE 132 80 127

Figure S185.  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 = 3e-05

Table S186.  Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
18P GAIN MUTATED 33 2 24
18P GAIN WILD-TYPE 111 113 115

Figure S186.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0432 (Fisher's exact test), Q value = 0.069

Table S187.  Gene #33: '18q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
18Q GAIN MUTATED 0 3 0 0 1
18Q GAIN WILD-TYPE 14 6 7 7 15

Figure S187.  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 = 3e-05

Table S188.  Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
18Q GAIN MUTATED 39 3 2 0 1
18Q GAIN WILD-TYPE 130 302 17 9 36

Figure S188.  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 = 3e-05

Table S189.  Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
18Q GAIN MUTATED 29 7 3
18Q GAIN WILD-TYPE 136 82 168

Figure S189.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S190.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
18Q GAIN MUTATED 40 2 3
18Q GAIN WILD-TYPE 194 151 147

Figure S190.  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 = 3e-05

Table S191.  Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
18Q GAIN MUTATED 30 1 5 0 6 2 1
18Q GAIN WILD-TYPE 93 52 42 65 102 64 74

Figure S191.  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 = 3e-05

Table S192.  Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
18Q GAIN MUTATED 35 9 1
18Q GAIN WILD-TYPE 188 141 156

Figure S192.  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 = 3e-05

Table S193.  Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
18Q GAIN MUTATED 19 1 1 24
18Q GAIN WILD-TYPE 200 57 136 92

Figure S193.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.6e-05

Table S194.  Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
18Q GAIN MUTATED 27 8 1
18Q GAIN WILD-TYPE 145 88 129

Figure S194.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00026

Table S195.  Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
18Q GAIN MUTATED 22 1 13
18Q GAIN WILD-TYPE 122 114 126

Figure S195.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'MRNA_CNMF'

P value = 0.0393 (Fisher's exact test), Q value = 0.064

Table S196.  Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
19P GAIN MUTATED 0 4 0 0
19P GAIN WILD-TYPE 14 13 12 10

Figure S196.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0302 (Fisher's exact test), Q value = 0.051

Table S197.  Gene #34: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
19P GAIN MUTATED 1 3 0 0 0
19P GAIN WILD-TYPE 13 6 7 7 16

Figure S197.  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 = 3e-05

Table S198.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
19P GAIN MUTATED 49 0 1 0 4
19P GAIN WILD-TYPE 120 305 18 9 33

Figure S198.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.00066

Table S199.  Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
19P GAIN MUTATED 30 11 8
19P GAIN WILD-TYPE 135 78 163

Figure S199.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S200.  Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
19P GAIN MUTATED 47 2 4
19P GAIN WILD-TYPE 187 151 146

Figure S200.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S201.  Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
19P GAIN MUTATED 36 1 3 2 8 2 1
19P GAIN WILD-TYPE 87 52 44 63 100 64 74

Figure S201.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S202.  Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
19P GAIN MUTATED 45 4 5
19P GAIN WILD-TYPE 178 146 152

Figure S202.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S203.  Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
19P GAIN MUTATED 17 1 6 30
19P GAIN WILD-TYPE 202 57 131 86

Figure S203.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.00095

Table S204.  Gene #34: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
19P GAIN MUTATED 28 14 4
19P GAIN WILD-TYPE 144 82 126

Figure S204.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S205.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
19Q GAIN MUTATED 51 0 2 0 4
19Q GAIN WILD-TYPE 118 305 17 9 33

Figure S205.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 8.2e-05

Table S206.  Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
19Q GAIN MUTATED 33 11 7
19Q GAIN WILD-TYPE 132 78 164

Figure S206.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0431 (Fisher's exact test), Q value = 0.069

Table S207.  Gene #35: '19q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
19Q GAIN MUTATED 5 1 0 2
19Q GAIN WILD-TYPE 62 66 43 15

Figure S207.  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 = 3e-05

Table S208.  Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
19Q GAIN MUTATED 52 2 3
19Q GAIN WILD-TYPE 182 151 147

Figure S208.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S209.  Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
19Q GAIN MUTATED 39 1 6 1 8 1 1
19Q GAIN WILD-TYPE 84 52 41 64 100 65 74

Figure S209.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S210.  Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
19Q GAIN MUTATED 48 5 4
19Q GAIN WILD-TYPE 175 145 153

Figure S210.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S211.  Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
19Q GAIN MUTATED 14 1 5 37
19Q GAIN WILD-TYPE 205 57 132 79

Figure S211.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00052

Table S212.  Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
19Q GAIN MUTATED 29 15 4
19Q GAIN WILD-TYPE 143 81 126

Figure S212.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.024

Table S213.  Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
19Q GAIN MUTATED 24 6 18
19Q GAIN WILD-TYPE 120 109 121

Figure S213.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'MRNA_CNMF'

P value = 0.00803 (Fisher's exact test), Q value = 0.015

Table S214.  Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
20P GAIN MUTATED 0 5 0 0
20P GAIN WILD-TYPE 14 12 12 10

Figure S214.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0494 (Fisher's exact test), Q value = 0.078

Table S215.  Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
20P GAIN MUTATED 2 3 0 0 0
20P GAIN WILD-TYPE 12 6 7 7 16

Figure S215.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S216.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
20P GAIN MUTATED 85 7 12 2 6
20P GAIN WILD-TYPE 84 298 7 7 31

Figure S216.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S217.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
20P GAIN MUTATED 73 13 17
20P GAIN WILD-TYPE 92 76 154

Figure S217.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S218.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
20P GAIN MUTATED 89 9 14
20P GAIN WILD-TYPE 145 144 136

Figure S218.  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 = 3e-05

Table S219.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
20P GAIN MUTATED 62 4 15 2 15 12 2
20P GAIN WILD-TYPE 61 49 32 63 93 54 73

Figure S219.  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 = 3e-05

Table S220.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
20P GAIN MUTATED 81 16 14
20P GAIN WILD-TYPE 142 134 143

Figure S220.  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 = 3e-05

Table S221.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
20P GAIN MUTATED 36 5 13 57
20P GAIN WILD-TYPE 183 53 124 59

Figure S221.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.00061

Table S222.  Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
20P GAIN MUTATED 58 20 18
20P GAIN WILD-TYPE 114 76 112

Figure S222.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S223.  Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
20P GAIN MUTATED 56 15 25
20P GAIN WILD-TYPE 88 100 114

Figure S223.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 0.00198 (Fisher's exact test), Q value = 0.0042

Table S224.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
20Q GAIN MUTATED 0 6 0 0
20Q GAIN WILD-TYPE 14 11 12 10

Figure S224.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00711 (Fisher's exact test), Q value = 0.014

Table S225.  Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
20Q GAIN MUTATED 2 4 0 0 0
20Q GAIN WILD-TYPE 12 5 7 7 16

Figure S225.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S226.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
20Q GAIN MUTATED 103 8 12 2 7
20Q GAIN WILD-TYPE 66 297 7 7 30

Figure S226.  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 = 3e-05

Table S227.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
20Q GAIN MUTATED 83 16 21
20Q GAIN WILD-TYPE 82 73 150

Figure S227.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.0321 (Fisher's exact test), Q value = 0.054

Table S228.  Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
20Q GAIN MUTATED 6 8 2 0 2 6
20Q GAIN WILD-TYPE 35 29 37 12 39 18

Figure S228.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S229.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
20Q GAIN MUTATED 104 10 18
20Q GAIN WILD-TYPE 130 143 132

Figure S229.  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 = 3e-05

Table S230.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
20Q GAIN MUTATED 71 4 19 3 18 14 3
20Q GAIN WILD-TYPE 52 49 28 62 90 52 72

Figure S230.  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 = 3e-05

Table S231.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
20Q GAIN MUTATED 95 17 18
20Q GAIN WILD-TYPE 128 133 139

Figure S231.  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 = 3e-05

Table S232.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
20Q GAIN MUTATED 43 5 17 65
20Q GAIN WILD-TYPE 176 53 120 51

Figure S232.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S233.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
20Q GAIN MUTATED 70 23 19
20Q GAIN WILD-TYPE 102 73 111

Figure S233.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S234.  Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
20Q GAIN MUTATED 64 18 30
20Q GAIN WILD-TYPE 80 97 109

Figure S234.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S235.  Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
21Q GAIN MUTATED 35 1 0 0 3
21Q GAIN WILD-TYPE 134 304 19 9 34

Figure S235.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0011

Table S236.  Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
21Q GAIN MUTATED 24 7 5
21Q GAIN WILD-TYPE 141 82 166

Figure S236.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S237.  Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
21Q GAIN MUTATED 33 2 4
21Q GAIN WILD-TYPE 201 151 146

Figure S237.  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 = 3e-05

Table S238.  Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
21Q GAIN MUTATED 24 0 7 1 3 1 3
21Q GAIN WILD-TYPE 99 53 40 64 105 65 72

Figure S238.  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 = 3e-05

Table S239.  Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
21Q GAIN MUTATED 34 2 3
21Q GAIN WILD-TYPE 189 148 154

Figure S239.  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 = 3e-05

Table S240.  Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
21Q GAIN MUTATED 9 1 4 25
21Q GAIN WILD-TYPE 210 57 133 91

Figure S240.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.00082

Table S241.  Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
21Q GAIN MUTATED 23 10 2
21Q GAIN WILD-TYPE 149 86 128

Figure S241.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S242.  Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
22Q GAIN MUTATED 27 3 0 1 0
22Q GAIN WILD-TYPE 142 302 19 8 37

Figure S242.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S243.  Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
22Q GAIN MUTATED 26 1 1
22Q GAIN WILD-TYPE 139 88 170

Figure S243.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S244.  Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
22Q GAIN MUTATED 31 0 0
22Q GAIN WILD-TYPE 203 153 150

Figure S244.  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 = 3e-05

Table S245.  Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
22Q GAIN MUTATED 16 0 12 0 3 0 0
22Q GAIN WILD-TYPE 107 53 35 65 105 66 75

Figure S245.  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 = 3e-05

Table S246.  Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
22Q GAIN MUTATED 28 1 1
22Q GAIN WILD-TYPE 195 149 156

Figure S246.  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 = 3e-05

Table S247.  Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
22Q GAIN MUTATED 9 0 1 20
22Q GAIN WILD-TYPE 210 58 136 96

Figure S247.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00011

Table S248.  Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
22Q GAIN MUTATED 24 2 2
22Q GAIN WILD-TYPE 148 94 128

Figure S248.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.6e-05

Table S249.  Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
22Q GAIN MUTATED 22 1 5
22Q GAIN WILD-TYPE 122 114 134

Figure S249.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S250.  Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
XP GAIN MUTATED 23 7 8 3 23
XP GAIN WILD-TYPE 146 298 11 6 14

Figure S250.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S251.  Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
XQ GAIN MUTATED 24 7 8 3 22
XQ GAIN WILD-TYPE 145 298 11 6 15

Figure S251.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S252.  Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
1P LOSS MUTATED 18 0 3 4 0
1P LOSS WILD-TYPE 151 305 16 5 37

Figure S252.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S253.  Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
1P LOSS MUTATED 20 1 0
1P LOSS WILD-TYPE 145 88 171

Figure S253.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S254.  Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
1P LOSS MUTATED 23 1 1
1P LOSS WILD-TYPE 211 152 149

Figure S254.  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 = 3e-05

Table S255.  Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
1P LOSS MUTATED 13 1 7 0 4 0 0
1P LOSS WILD-TYPE 110 52 40 65 104 66 75

Figure S255.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00021

Table S256.  Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
1P LOSS MUTATED 21 3 1
1P LOSS WILD-TYPE 202 147 156

Figure S256.  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 = 3e-05

Table S257.  Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
1P LOSS MUTATED 6 0 0 19
1P LOSS WILD-TYPE 213 58 137 97

Figure S257.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.0014

Table S258.  Gene #42: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
1P LOSS MUTATED 14 0 8
1P LOSS WILD-TYPE 130 115 131

Figure S258.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S259.  Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
1Q LOSS MUTATED 12 0 1 1 0
1Q LOSS WILD-TYPE 157 305 18 8 37

Figure S259.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 8.2e-05

Table S260.  Gene #43: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
1Q LOSS MUTATED 12 0 0
1Q LOSS WILD-TYPE 153 89 171

Figure S260.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00021

Table S261.  Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
1Q LOSS MUTATED 14 0 0
1Q LOSS WILD-TYPE 220 153 150

Figure S261.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00108 (Fisher's exact test), Q value = 0.0024

Table S262.  Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
1Q LOSS MUTATED 7 0 5 0 2 0 0
1Q LOSS WILD-TYPE 116 53 42 65 106 66 75

Figure S262.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.00077

Table S263.  Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
1Q LOSS MUTATED 13 1 0
1Q LOSS WILD-TYPE 210 149 157

Figure S263.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S264.  Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
1Q LOSS MUTATED 2 0 0 12
1Q LOSS WILD-TYPE 217 58 137 104

Figure S264.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0075 (Fisher's exact test), Q value = 0.014

Table S265.  Gene #43: '1q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
1Q LOSS MUTATED 9 0 3
1Q LOSS WILD-TYPE 135 115 136

Figure S265.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00059

Table S266.  Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
2P LOSS MUTATED 10 0 1 0 0
2P LOSS WILD-TYPE 159 305 18 9 37

Figure S266.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 0.00533 (Fisher's exact test), Q value = 0.01

Table S267.  Gene #44: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
2P LOSS MUTATED 10 0 1
2P LOSS WILD-TYPE 224 153 149

Figure S267.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.6e-05

Table S268.  Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
2Q LOSS MUTATED 16 0 1 0 0
2Q LOSS WILD-TYPE 153 305 18 9 37

Figure S268.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.00068

Table S269.  Gene #45: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
2Q LOSS MUTATED 15 0 2
2Q LOSS WILD-TYPE 219 153 148

Figure S269.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0146 (Fisher's exact test), Q value = 0.026

Table S270.  Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
2Q LOSS MUTATED 9 0 1 0 6 1 0
2Q LOSS WILD-TYPE 114 53 46 65 102 65 75

Figure S270.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.032

Table S271.  Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
2Q LOSS MUTATED 13 2 2
2Q LOSS WILD-TYPE 210 148 155

Figure S271.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0302 (Fisher's exact test), Q value = 0.051

Table S272.  Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
2Q LOSS MUTATED 5 0 3 9
2Q LOSS WILD-TYPE 214 58 134 107

Figure S272.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MRNA_CNMF'

P value = 0.0383 (Fisher's exact test), Q value = 0.063

Table S273.  Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
3P LOSS MUTATED 0 4 0 0
3P LOSS WILD-TYPE 14 13 12 10

Figure S273.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.0016

Table S274.  Gene #46: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
3P LOSS MUTATED 0 4 0 0 0
3P LOSS WILD-TYPE 14 5 7 7 16

Figure S274.  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 = 3e-05

Table S275.  Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
3P LOSS MUTATED 45 0 3 2 1
3P LOSS WILD-TYPE 124 305 16 7 36

Figure S275.  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 = 3e-05

Table S276.  Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
3P LOSS MUTATED 33 6 3
3P LOSS WILD-TYPE 132 83 168

Figure S276.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.039

Table S277.  Gene #46: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
3P LOSS MUTATED 2 8 1 0 1 2
3P LOSS WILD-TYPE 39 29 38 12 40 22

Figure S277.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S278.  Gene #46: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
3P LOSS MUTATED 47 1 2
3P LOSS WILD-TYPE 187 152 148

Figure S278.  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 = 3e-05

Table S279.  Gene #46: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
3P LOSS MUTATED 36 0 6 0 6 2 0
3P LOSS WILD-TYPE 87 53 41 65 102 64 75

Figure S279.  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 = 3e-05

Table S280.  Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
3P LOSS MUTATED 38 8 3
3P LOSS WILD-TYPE 185 142 154

Figure S280.  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 = 3e-05

Table S281.  Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
3P LOSS MUTATED 19 1 2 27
3P LOSS WILD-TYPE 200 57 135 89

Figure S281.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0151 (Fisher's exact test), Q value = 0.027

Table S282.  Gene #46: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
3P LOSS MUTATED 25 9 6
3P LOSS WILD-TYPE 147 87 124

Figure S282.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00026

Table S283.  Gene #46: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
3P LOSS MUTATED 26 3 11
3P LOSS WILD-TYPE 118 112 128

Figure S283.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'MRNA_CNMF'

P value = 0.0382 (Fisher's exact test), Q value = 0.063

Table S284.  Gene #47: '3q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
3Q LOSS MUTATED 0 4 0 0
3Q LOSS WILD-TYPE 14 13 12 10

Figure S284.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00072 (Fisher's exact test), Q value = 0.0016

Table S285.  Gene #47: '3q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
3Q LOSS MUTATED 0 4 0 0 0
3Q LOSS WILD-TYPE 14 5 7 7 16

Figure S285.  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 = 3e-05

Table S286.  Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
3Q LOSS MUTATED 27 0 1 2 1
3Q LOSS WILD-TYPE 142 305 18 7 36

Figure S286.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00013

Table S287.  Gene #47: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
3Q LOSS MUTATED 20 3 2
3Q LOSS WILD-TYPE 145 86 169

Figure S287.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S288.  Gene #47: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
3Q LOSS MUTATED 28 0 2
3Q LOSS WILD-TYPE 206 153 148

Figure S288.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S289.  Gene #47: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
3Q LOSS MUTATED 21 0 4 0 3 2 0
3Q LOSS WILD-TYPE 102 53 43 65 105 64 75

Figure S289.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S290.  Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
3Q LOSS MUTATED 25 1 3
3Q LOSS WILD-TYPE 198 149 154

Figure S290.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00045

Table S291.  Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
3Q LOSS MUTATED 12 0 2 15
3Q LOSS WILD-TYPE 207 58 135 101

Figure S291.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.023

Table S292.  Gene #47: '3q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
3Q LOSS MUTATED 16 7 2
3Q LOSS WILD-TYPE 156 89 128

Figure S292.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MRNA_CNMF'

P value = 0.0037 (Fisher's exact test), Q value = 0.0075

Table S293.  Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
4P LOSS MUTATED 1 7 0 0
4P LOSS WILD-TYPE 13 10 12 10

Figure S293.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00163 (Fisher's exact test), Q value = 0.0035

Table S294.  Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
4P LOSS MUTATED 3 5 0 0 0
4P LOSS WILD-TYPE 11 4 7 7 16

Figure S294.  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 = 3e-05

Table S295.  Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
4P LOSS MUTATED 91 4 4 4 2
4P LOSS WILD-TYPE 78 301 15 5 35

Figure S295.  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 = 3e-05

Table S296.  Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
4P LOSS MUTATED 72 16 6
4P LOSS WILD-TYPE 93 73 165

Figure S296.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.0023

Table S297.  Gene #48: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
4P LOSS MUTATED 5 8 0 1 1 6
4P LOSS WILD-TYPE 36 29 39 11 40 18

Figure S297.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S298.  Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
4P LOSS MUTATED 91 6 8
4P LOSS WILD-TYPE 143 147 142

Figure S298.  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 = 3e-05

Table S299.  Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
4P LOSS MUTATED 62 2 15 2 18 5 1
4P LOSS WILD-TYPE 61 51 32 63 90 61 74

Figure S299.  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 = 3e-05

Table S300.  Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
4P LOSS MUTATED 81 14 8
4P LOSS WILD-TYPE 142 136 149

Figure S300.  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 = 3e-05

Table S301.  Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
4P LOSS MUTATED 38 1 5 59
4P LOSS WILD-TYPE 181 57 132 57

Figure S301.  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 = 3e-05

Table S302.  Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
4P LOSS MUTATED 55 26 12
4P LOSS WILD-TYPE 117 70 118

Figure S302.  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 = 3e-05

Table S303.  Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
4P LOSS MUTATED 52 9 32
4P LOSS WILD-TYPE 92 106 107

Figure S303.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00513 (Fisher's exact test), Q value = 0.01

Table S304.  Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
4Q LOSS MUTATED 1 4 0 0 0
4Q LOSS WILD-TYPE 13 5 7 7 16

Figure S304.  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 = 3e-05

Table S305.  Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
4Q LOSS MUTATED 92 3 4 4 2
4Q LOSS WILD-TYPE 77 302 15 5 35

Figure S305.  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 = 3e-05

Table S306.  Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
4Q LOSS MUTATED 73 15 5
4Q LOSS WILD-TYPE 92 74 166

Figure S306.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'RPPA_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.024

Table S307.  Gene #49: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
4Q LOSS MUTATED 5 7 1 1 1 6
4Q LOSS WILD-TYPE 36 30 38 11 40 18

Figure S307.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S308.  Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
4Q LOSS MUTATED 91 6 8
4Q LOSS WILD-TYPE 143 147 142

Figure S308.  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 = 3e-05

Table S309.  Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
4Q LOSS MUTATED 65 2 13 2 17 6 0
4Q LOSS WILD-TYPE 58 51 34 63 91 60 75

Figure S309.  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 = 3e-05

Table S310.  Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
4Q LOSS MUTATED 82 13 8
4Q LOSS WILD-TYPE 141 137 149

Figure S310.  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 = 3e-05

Table S311.  Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
4Q LOSS MUTATED 39 1 4 59
4Q LOSS WILD-TYPE 180 57 133 57

Figure S311.  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 = 3e-05

Table S312.  Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
4Q LOSS MUTATED 53 28 11
4Q LOSS WILD-TYPE 119 68 119

Figure S312.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S313.  Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
4Q LOSS MUTATED 49 8 35
4Q LOSS WILD-TYPE 95 107 104

Figure S313.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0394 (Fisher's exact test), Q value = 0.064

Table S314.  Gene #50: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
5P LOSS MUTATED 3 3 0 0 0
5P LOSS WILD-TYPE 11 6 7 7 16

Figure S314.  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 = 3e-05

Table S315.  Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
5P LOSS MUTATED 46 0 3 2 4
5P LOSS WILD-TYPE 123 305 16 7 33

Figure S315.  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 = 3e-05

Table S316.  Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
5P LOSS MUTATED 38 5 2
5P LOSS WILD-TYPE 127 84 169

Figure S316.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'RPPA_CNMF'

P value = 0.00378 (Fisher's exact test), Q value = 0.0076

Table S317.  Gene #50: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
5P LOSS MUTATED 5 6 0 1 0 4
5P LOSS WILD-TYPE 36 31 39 11 41 20

Figure S317.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S318.  Gene #50: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
5P LOSS MUTATED 47 4 4
5P LOSS WILD-TYPE 187 149 146

Figure S318.  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 = 3e-05

Table S319.  Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
5P LOSS MUTATED 33 0 8 1 9 4 0
5P LOSS WILD-TYPE 90 53 39 64 99 62 75

Figure S319.  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 = 3e-05

Table S320.  Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
5P LOSS MUTATED 43 6 5
5P LOSS WILD-TYPE 180 144 152

Figure S320.  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 = 3e-05

Table S321.  Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
5P LOSS MUTATED 20 0 2 32
5P LOSS WILD-TYPE 199 58 135 84

Figure S321.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00013

Table S322.  Gene #50: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
5P LOSS MUTATED 30 10 3
5P LOSS WILD-TYPE 142 86 127

Figure S322.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00086 (Fisher's exact test), Q value = 0.0019

Table S323.  Gene #50: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
5P LOSS MUTATED 22 3 18
5P LOSS WILD-TYPE 122 112 121

Figure S323.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'MRNA_CNMF'

P value = 0.0132 (Fisher's exact test), Q value = 0.024

Table S324.  Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
5Q LOSS MUTATED 1 6 0 0
5Q LOSS WILD-TYPE 13 11 12 10

Figure S324.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00999 (Fisher's exact test), Q value = 0.019

Table S325.  Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
5Q LOSS MUTATED 3 4 0 0 0
5Q LOSS WILD-TYPE 11 5 7 7 16

Figure S325.  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 = 3e-05

Table S326.  Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
5Q LOSS MUTATED 66 0 2 2 4
5Q LOSS WILD-TYPE 103 305 17 7 33

Figure S326.  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 = 3e-05

Table S327.  Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
5Q LOSS MUTATED 54 6 2
5Q LOSS WILD-TYPE 111 83 169

Figure S327.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'RPPA_CNMF'

P value = 0.0012 (Fisher's exact test), Q value = 0.0026

Table S328.  Gene #51: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
5Q LOSS MUTATED 5 7 1 0 0 6
5Q LOSS WILD-TYPE 36 30 38 12 41 18

Figure S328.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00246 (Fisher's exact test), Q value = 0.0051

Table S329.  Gene #51: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
5Q LOSS MUTATED 11 4 0 4
5Q LOSS WILD-TYPE 56 63 43 13

Figure S329.  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 = 3e-05

Table S330.  Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
5Q LOSS MUTATED 65 4 5
5Q LOSS WILD-TYPE 169 149 145

Figure S330.  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 = 3e-05

Table S331.  Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
5Q LOSS MUTATED 50 0 7 1 11 5 0
5Q LOSS WILD-TYPE 73 53 40 64 97 61 75

Figure S331.  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 = 3e-05

Table S332.  Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
5Q LOSS MUTATED 61 7 5
5Q LOSS WILD-TYPE 162 143 152

Figure S332.  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 = 3e-05

Table S333.  Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
5Q LOSS MUTATED 29 0 3 41
5Q LOSS WILD-TYPE 190 58 134 75

Figure S333.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00036

Table S334.  Gene #51: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
5Q LOSS MUTATED 38 14 7
5Q LOSS WILD-TYPE 134 82 123

Figure S334.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 8.2e-05

Table S335.  Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
5Q LOSS MUTATED 31 4 24
5Q LOSS WILD-TYPE 113 111 115

Figure S335.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.029 (Fisher's exact test), Q value = 0.05

Table S336.  Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
6P LOSS MUTATED 1 3 0 0 0
6P LOSS WILD-TYPE 13 6 7 7 16

Figure S336.  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 = 3e-05

Table S337.  Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
6P LOSS MUTATED 15 0 2 1 0
6P LOSS WILD-TYPE 154 305 17 8 37

Figure S337.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.00127 (Fisher's exact test), Q value = 0.0028

Table S338.  Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
6P LOSS MUTATED 10 2 0
6P LOSS WILD-TYPE 155 87 171

Figure S338.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.00088

Table S339.  Gene #52: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
6P LOSS MUTATED 16 1 1
6P LOSS WILD-TYPE 218 152 149

Figure S339.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 5e-04

Table S340.  Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
6P LOSS MUTATED 13 1 2 0 2 0 0
6P LOSS WILD-TYPE 110 52 45 65 106 66 75

Figure S340.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CNMF'

P value = 0.00627 (Fisher's exact test), Q value = 0.012

Table S341.  Gene #52: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
6P LOSS MUTATED 13 2 1
6P LOSS WILD-TYPE 210 148 156

Figure S341.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00397 (Fisher's exact test), Q value = 0.0079

Table S342.  Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
6P LOSS MUTATED 8 0 0 8
6P LOSS WILD-TYPE 211 58 137 108

Figure S342.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0247 (Fisher's exact test), Q value = 0.043

Table S343.  Gene #52: '6p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
6P LOSS MUTATED 8 0 4
6P LOSS WILD-TYPE 136 115 135

Figure S343.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0301 (Fisher's exact test), Q value = 0.051

Table S344.  Gene #53: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
6Q LOSS MUTATED 1 3 0 0 0
6Q LOSS WILD-TYPE 13 6 7 7 16

Figure S344.  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 = 3e-05

Table S345.  Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
6Q LOSS MUTATED 22 0 2 1 0
6Q LOSS WILD-TYPE 147 305 17 8 37

Figure S345.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 8.2e-05

Table S346.  Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
6Q LOSS MUTATED 15 4 0
6Q LOSS WILD-TYPE 150 85 171

Figure S346.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S347.  Gene #53: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
6Q LOSS MUTATED 23 1 1
6Q LOSS WILD-TYPE 211 152 149

Figure S347.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S348.  Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
6Q LOSS MUTATED 20 1 2 0 2 0 0
6Q LOSS WILD-TYPE 103 52 45 65 106 66 75

Figure S348.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00045

Table S349.  Gene #53: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
6Q LOSS MUTATED 19 3 1
6Q LOSS WILD-TYPE 204 147 156

Figure S349.  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 = 5.6e-05

Table S350.  Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
6Q LOSS MUTATED 10 0 0 13
6Q LOSS WILD-TYPE 209 58 137 103

Figure S350.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.023

Table S351.  Gene #53: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
6Q LOSS MUTATED 13 5 1
6Q LOSS WILD-TYPE 159 91 129

Figure S351.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00358 (Fisher's exact test), Q value = 0.0073

Table S352.  Gene #53: '6q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
6Q LOSS MUTATED 11 0 8
6Q LOSS WILD-TYPE 133 115 131

Figure S352.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p loss' versus 'MRNA_CNMF'

P value = 0.0399 (Fisher's exact test), Q value = 0.065

Table S353.  Gene #54: '7p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
7P LOSS MUTATED 0 4 0 0
7P LOSS WILD-TYPE 14 13 12 10

Figure S353.  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 = 3e-05

Table S354.  Gene #54: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
7P LOSS MUTATED 39 3 1 1 0
7P LOSS WILD-TYPE 130 302 18 8 37

Figure S354.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.00095

Table S355.  Gene #54: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
7P LOSS MUTATED 24 10 5
7P LOSS WILD-TYPE 141 79 166

Figure S355.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p loss' versus 'RPPA_CNMF'

P value = 0.0371 (Fisher's exact test), Q value = 0.061

Table S356.  Gene #54: '7p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
7P LOSS MUTATED 3 4 0 1 0 0
7P LOSS WILD-TYPE 38 33 39 11 41 24

Figure S356.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S357.  Gene #54: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
7P LOSS MUTATED 39 1 4
7P LOSS WILD-TYPE 195 152 146

Figure S357.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S358.  Gene #54: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
7P LOSS MUTATED 30 0 2 0 8 4 0
7P LOSS WILD-TYPE 93 53 45 65 100 62 75

Figure S358.  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 = 3e-05

Table S359.  Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
7P LOSS MUTATED 35 3 6
7P LOSS WILD-TYPE 188 147 151

Figure S359.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S360.  Gene #54: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
7P LOSS MUTATED 14 0 3 27
7P LOSS WILD-TYPE 205 58 134 89

Figure S360.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S361.  Gene #55: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
7Q LOSS MUTATED 41 0 0 1 0
7Q LOSS WILD-TYPE 128 305 19 8 37

Figure S361.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

'7q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S362.  Gene #55: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
7Q LOSS MUTATED 29 9 1
7Q LOSS WILD-TYPE 136 80 170

Figure S362.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q loss' versus 'RPPA_CNMF'

P value = 0.0462 (Fisher's exact test), Q value = 0.074

Table S363.  Gene #55: '7q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
7Q LOSS MUTATED 4 4 0 0 0 2
7Q LOSS WILD-TYPE 37 33 39 12 41 22

Figure S363.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'7q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.025

Table S364.  Gene #55: '7q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
7Q LOSS MUTATED 8 1 0 1
7Q LOSS WILD-TYPE 59 66 43 16

Figure S364.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S365.  Gene #55: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
7Q LOSS MUTATED 41 0 1
7Q LOSS WILD-TYPE 193 153 149

Figure S365.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S366.  Gene #55: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
7Q LOSS MUTATED 32 0 4 0 4 2 0
7Q LOSS WILD-TYPE 91 53 43 65 104 64 75

Figure S366.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S367.  Gene #55: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
7Q LOSS MUTATED 38 2 2
7Q LOSS WILD-TYPE 185 148 155

Figure S367.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S368.  Gene #55: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
7Q LOSS MUTATED 10 0 1 31
7Q LOSS WILD-TYPE 209 58 136 85

Figure S368.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00266 (Fisher's exact test), Q value = 0.0055

Table S369.  Gene #55: '7q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
7Q LOSS MUTATED 25 8 4
7Q LOSS WILD-TYPE 147 88 126

Figure S369.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.00082

Table S370.  Gene #55: '7q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
7Q LOSS MUTATED 22 2 13
7Q LOSS WILD-TYPE 122 113 126

Figure S370.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'MRNA_CNMF'

P value = 0.00782 (Fisher's exact test), Q value = 0.015

Table S371.  Gene #56: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
8P LOSS MUTATED 0 5 0 0
8P LOSS WILD-TYPE 14 12 12 10

Figure S371.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p loss' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00011

Table S372.  Gene #56: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
8P LOSS MUTATED 0 5 0 0 0
8P LOSS WILD-TYPE 14 4 7 7 16

Figure S372.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S373.  Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
8P LOSS MUTATED 75 3 1 1 0
8P LOSS WILD-TYPE 94 302 18 8 37

Figure S373.  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 = 3e-05

Table S374.  Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
8P LOSS MUTATED 58 11 2
8P LOSS WILD-TYPE 107 78 169

Figure S374.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'RPPA_CNMF'

P value = 0.0335 (Fisher's exact test), Q value = 0.056

Table S375.  Gene #56: '8p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
8P LOSS MUTATED 5 2 3 0 0 5
8P LOSS WILD-TYPE 36 35 36 12 41 19

Figure S375.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0251 (Fisher's exact test), Q value = 0.043

Table S376.  Gene #56: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
8P LOSS MUTATED 8 4 0 3
8P LOSS WILD-TYPE 59 63 43 14

Figure S376.  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 = 3e-05

Table S377.  Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
8P LOSS MUTATED 73 3 3
8P LOSS WILD-TYPE 161 150 147

Figure S377.  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 = 3e-05

Table S378.  Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
8P LOSS MUTATED 57 0 11 1 6 3 1
8P LOSS WILD-TYPE 66 53 36 64 102 63 74

Figure S378.  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 = 3e-05

Table S379.  Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
8P LOSS MUTATED 68 5 4
8P LOSS WILD-TYPE 155 145 153

Figure S379.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S380.  Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
8P LOSS MUTATED 19 0 4 54
8P LOSS WILD-TYPE 200 58 133 62

Figure S380.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S381.  Gene #56: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
8P LOSS MUTATED 45 15 6
8P LOSS WILD-TYPE 127 81 124

Figure S381.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S382.  Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
8P LOSS MUTATED 41 3 22
8P LOSS WILD-TYPE 103 112 117

Figure S382.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S383.  Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
8Q LOSS MUTATED 23 1 1 0 0
8Q LOSS WILD-TYPE 146 304 18 9 37

Figure S383.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S384.  Gene #57: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
8Q LOSS MUTATED 20 3 0
8Q LOSS WILD-TYPE 145 86 171

Figure S384.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S385.  Gene #57: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
8Q LOSS MUTATED 23 0 2
8Q LOSS WILD-TYPE 211 153 148

Figure S385.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S386.  Gene #57: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
8Q LOSS MUTATED 19 0 3 0 1 1 1
8Q LOSS WILD-TYPE 104 53 44 65 107 65 74

Figure S386.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 8.2e-05

Table S387.  Gene #57: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
8Q LOSS MUTATED 21 1 2
8Q LOSS WILD-TYPE 202 149 155

Figure S387.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S388.  Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
8Q LOSS MUTATED 6 0 2 16
8Q LOSS WILD-TYPE 213 58 135 100

Figure S388.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0021

Table S389.  Gene #57: '8q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
8Q LOSS MUTATED 17 3 1
8Q LOSS WILD-TYPE 155 93 129

Figure S389.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0087 (Fisher's exact test), Q value = 0.016

Table S390.  Gene #57: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
8Q LOSS MUTATED 13 1 7
8Q LOSS WILD-TYPE 131 114 132

Figure S390.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'MRNA_CNMF'

P value = 0.00114 (Fisher's exact test), Q value = 0.0025

Table S391.  Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
9P LOSS MUTATED 1 8 0 0
9P LOSS WILD-TYPE 13 9 12 10

Figure S391.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.6e-05

Table S392.  Gene #58: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
9P LOSS MUTATED 2 7 0 0 0
9P LOSS WILD-TYPE 12 2 7 7 16

Figure S392.  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 = 3e-05

Table S393.  Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
9P LOSS MUTATED 90 2 6 1 4
9P LOSS WILD-TYPE 79 303 13 8 33

Figure S393.  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 = 3e-05

Table S394.  Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
9P LOSS MUTATED 59 20 9
9P LOSS WILD-TYPE 106 69 162

Figure S394.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CNMF'

P value = 0.00379 (Fisher's exact test), Q value = 0.0076

Table S395.  Gene #58: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
9P LOSS MUTATED 5 9 1 1 1 6
9P LOSS WILD-TYPE 36 28 38 11 40 18

Figure S395.  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 = 3e-05

Table S396.  Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
9P LOSS MUTATED 84 6 13
9P LOSS WILD-TYPE 150 147 137

Figure S396.  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 = 3e-05

Table S397.  Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
9P LOSS MUTATED 58 0 18 2 13 11 1
9P LOSS WILD-TYPE 65 53 29 63 95 55 74

Figure S397.  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 = 3e-05

Table S398.  Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
9P LOSS MUTATED 74 12 14
9P LOSS WILD-TYPE 149 138 143

Figure S398.  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 = 3e-05

Table S399.  Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
9P LOSS MUTATED 30 1 11 58
9P LOSS WILD-TYPE 189 57 126 58

Figure S399.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0091 (Fisher's exact test), Q value = 0.017

Table S400.  Gene #58: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
9P LOSS MUTATED 47 22 17
9P LOSS WILD-TYPE 125 74 113

Figure S400.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0014

Table S401.  Gene #58: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
9P LOSS MUTATED 44 13 29
9P LOSS WILD-TYPE 100 102 110

Figure S401.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00011

Table S402.  Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
9Q LOSS MUTATED 0 9 0 0
9Q LOSS WILD-TYPE 14 8 12 10

Figure S402.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 8.2e-05

Table S403.  Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
9Q LOSS MUTATED 2 7 0 0 0
9Q LOSS WILD-TYPE 12 2 7 7 16

Figure S403.  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 = 3e-05

Table S404.  Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
9Q LOSS MUTATED 105 3 7 2 5
9Q LOSS WILD-TYPE 64 302 12 7 32

Figure S404.  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 = 3e-05

Table S405.  Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
9Q LOSS MUTATED 71 22 13
9Q LOSS WILD-TYPE 94 67 158

Figure S405.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.00088

Table S406.  Gene #59: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
9Q LOSS MUTATED 6 12 1 2 1 6
9Q LOSS WILD-TYPE 35 25 38 10 40 18

Figure S406.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S407.  Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
9Q LOSS MUTATED 99 8 15
9Q LOSS WILD-TYPE 135 145 135

Figure S407.  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 = 3e-05

Table S408.  Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
9Q LOSS MUTATED 70 0 18 3 17 13 1
9Q LOSS WILD-TYPE 53 53 29 62 91 53 74

Figure S408.  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 = 3e-05

Table S409.  Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
9Q LOSS MUTATED 86 17 16
9Q LOSS WILD-TYPE 137 133 141

Figure S409.  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 = 3e-05

Table S410.  Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
9Q LOSS MUTATED 43 1 12 63
9Q LOSS WILD-TYPE 176 57 125 53

Figure S410.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0024

Table S411.  Gene #59: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
9Q LOSS MUTATED 56 28 19
9Q LOSS WILD-TYPE 116 68 111

Figure S411.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00013

Table S412.  Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
9Q LOSS MUTATED 55 15 33
9Q LOSS WILD-TYPE 89 100 106

Figure S412.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'MRNA_CNMF'

P value = 0.039 (Fisher's exact test), Q value = 0.064

Table S413.  Gene #60: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
10P LOSS MUTATED 0 4 0 0
10P LOSS WILD-TYPE 14 13 12 10

Figure S413.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0295 (Fisher's exact test), Q value = 0.05

Table S414.  Gene #60: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
10P LOSS MUTATED 1 3 0 0 0
10P LOSS WILD-TYPE 13 6 7 7 16

Figure S414.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S415.  Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
10P LOSS MUTATED 42 0 1 0 0
10P LOSS WILD-TYPE 127 305 18 9 37

Figure S415.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S416.  Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
10P LOSS MUTATED 31 5 1
10P LOSS WILD-TYPE 134 84 170

Figure S416.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S417.  Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
10P LOSS MUTATED 39 1 3
10P LOSS WILD-TYPE 195 152 147

Figure S417.  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 = 3e-05

Table S418.  Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
10P LOSS MUTATED 28 0 7 1 4 3 0
10P LOSS WILD-TYPE 95 53 40 64 104 63 75

Figure S418.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S419.  Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
10P LOSS MUTATED 35 4 2
10P LOSS WILD-TYPE 188 146 155

Figure S419.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S420.  Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
10P LOSS MUTATED 12 0 2 27
10P LOSS WILD-TYPE 207 58 135 89

Figure S420.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0251 (Fisher's exact test), Q value = 0.043

Table S421.  Gene #60: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
10P LOSS MUTATED 21 10 5
10P LOSS WILD-TYPE 151 86 125

Figure S421.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00406 (Fisher's exact test), Q value = 0.0081

Table S422.  Gene #60: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
10P LOSS MUTATED 20 3 13
10P LOSS WILD-TYPE 124 112 126

Figure S422.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S423.  Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
10Q LOSS MUTATED 38 1 1 0 0
10Q LOSS WILD-TYPE 131 304 18 9 37

Figure S423.  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 = 3e-05

Table S424.  Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
10Q LOSS MUTATED 28 6 1
10Q LOSS WILD-TYPE 137 83 170

Figure S424.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S425.  Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
10Q LOSS MUTATED 35 1 4
10Q LOSS WILD-TYPE 199 152 146

Figure S425.  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 = 3e-05

Table S426.  Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
10Q LOSS MUTATED 25 0 5 1 5 4 0
10Q LOSS WILD-TYPE 98 53 42 64 103 62 75

Figure S426.  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 = 3e-05

Table S427.  Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
10Q LOSS MUTATED 32 4 3
10Q LOSS WILD-TYPE 191 146 154

Figure S427.  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 = 3e-05

Table S428.  Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
10Q LOSS MUTATED 14 0 3 22
10Q LOSS WILD-TYPE 205 58 134 94

Figure S428.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0316 (Fisher's exact test), Q value = 0.053

Table S429.  Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
10Q LOSS MUTATED 22 6 6
10Q LOSS WILD-TYPE 150 90 124

Figure S429.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00466 (Fisher's exact test), Q value = 0.0092

Table S430.  Gene #61: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
10Q LOSS MUTATED 21 4 9
10Q LOSS WILD-TYPE 123 111 130

Figure S430.  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 = 3e-05

Table S431.  Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
11P LOSS MUTATED 66 0 3 4 2
11P LOSS WILD-TYPE 103 305 16 5 35

Figure S431.  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 = 3e-05

Table S432.  Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
11P LOSS MUTATED 53 12 5
11P LOSS WILD-TYPE 112 77 166

Figure S432.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S433.  Gene #62: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
11P LOSS MUTATED 65 3 7
11P LOSS WILD-TYPE 169 150 143

Figure S433.  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 = 3e-05

Table S434.  Gene #62: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
11P LOSS MUTATED 44 1 11 1 11 7 0
11P LOSS WILD-TYPE 79 52 36 64 97 59 75

Figure S434.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S435.  Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
11P LOSS MUTATED 57 9 8
11P LOSS WILD-TYPE 166 141 149

Figure S435.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S436.  Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
11P LOSS MUTATED 28 0 6 40
11P LOSS WILD-TYPE 191 58 131 76

Figure S436.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0011

Table S437.  Gene #62: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
11P LOSS MUTATED 44 15 11
11P LOSS WILD-TYPE 128 81 119

Figure S437.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.6e-05

Table S438.  Gene #62: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
11P LOSS MUTATED 44 8 18
11P LOSS WILD-TYPE 100 107 121

Figure S438.  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 = 3e-05

Table S439.  Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
11Q LOSS MUTATED 62 0 4 4 2
11Q LOSS WILD-TYPE 107 305 15 5 35

Figure S439.  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 = 3e-05

Table S440.  Gene #63: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
11Q LOSS MUTATED 52 11 6
11Q LOSS WILD-TYPE 113 78 165

Figure S440.  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 = 3e-05

Table S441.  Gene #63: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
11Q LOSS MUTATED 60 3 9
11Q LOSS WILD-TYPE 174 150 141

Figure S441.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S442.  Gene #63: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
11Q LOSS MUTATED 44 1 10 1 10 6 0
11Q LOSS WILD-TYPE 79 52 37 64 98 60 75

Figure S442.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S443.  Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
11Q LOSS MUTATED 55 8 9
11Q LOSS WILD-TYPE 168 142 148

Figure S443.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S444.  Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
11Q LOSS MUTATED 26 0 7 39
11Q LOSS WILD-TYPE 193 58 130 77

Figure S444.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S445.  Gene #63: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
11Q LOSS MUTATED 49 10 10
11Q LOSS WILD-TYPE 123 86 120

Figure S445.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S446.  Gene #63: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
11Q LOSS MUTATED 46 8 15
11Q LOSS WILD-TYPE 98 107 124

Figure S446.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S447.  Gene #64: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
12P LOSS MUTATED 41 0 0 0 2
12P LOSS WILD-TYPE 128 305 19 9 35

Figure S447.  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 = 3e-05

Table S448.  Gene #64: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
12P LOSS MUTATED 29 3 4
12P LOSS WILD-TYPE 136 86 167

Figure S448.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p loss' versus 'RPPA_CNMF'

P value = 0.0416 (Fisher's exact test), Q value = 0.067

Table S449.  Gene #64: '12p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
12P LOSS MUTATED 2 6 1 0 0 2
12P LOSS WILD-TYPE 39 31 38 12 41 22

Figure S449.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'12p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0376 (Fisher's exact test), Q value = 0.062

Table S450.  Gene #64: '12p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
12P LOSS MUTATED 7 2 0 2
12P LOSS WILD-TYPE 60 65 43 15

Figure S450.  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 = 3e-05

Table S451.  Gene #64: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
12P LOSS MUTATED 38 0 5
12P LOSS WILD-TYPE 196 153 145

Figure S451.  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 = 3e-05

Table S452.  Gene #64: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
12P LOSS MUTATED 27 0 7 1 3 5 0
12P LOSS WILD-TYPE 96 53 40 64 105 61 75

Figure S452.  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 = 3e-05

Table S453.  Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
12P LOSS MUTATED 35 2 4
12P LOSS WILD-TYPE 188 148 153

Figure S453.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S454.  Gene #64: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
12P LOSS MUTATED 9 0 3 29
12P LOSS WILD-TYPE 210 58 134 87

Figure S454.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.00091

Table S455.  Gene #64: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
12P LOSS MUTATED 26 5 4
12P LOSS WILD-TYPE 146 91 126

Figure S455.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0025 (Fisher's exact test), Q value = 0.0052

Table S456.  Gene #64: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
12P LOSS MUTATED 22 4 9
12P LOSS WILD-TYPE 122 111 130

Figure S456.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S457.  Gene #65: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
12Q LOSS MUTATED 34 0 0 0 2
12Q LOSS WILD-TYPE 135 305 19 9 35

Figure S457.  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 = 3e-05

Table S458.  Gene #65: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
12Q LOSS MUTATED 27 1 2
12Q LOSS WILD-TYPE 138 88 169

Figure S458.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0156 (Fisher's exact test), Q value = 0.028

Table S459.  Gene #65: '12q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
12Q LOSS MUTATED 7 1 0 2
12Q LOSS WILD-TYPE 60 66 43 15

Figure S459.  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 = 3e-05

Table S460.  Gene #65: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
12Q LOSS MUTATED 33 0 3
12Q LOSS WILD-TYPE 201 153 147

Figure S460.  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 = 3e-05

Table S461.  Gene #65: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
12Q LOSS MUTATED 25 0 6 0 2 3 0
12Q LOSS WILD-TYPE 98 53 41 65 106 63 75

Figure S461.  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 = 3e-05

Table S462.  Gene #65: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
12Q LOSS MUTATED 29 3 2
12Q LOSS WILD-TYPE 194 147 155

Figure S462.  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 = 3e-05

Table S463.  Gene #65: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
12Q LOSS MUTATED 9 0 1 24
12Q LOSS WILD-TYPE 210 58 136 92

Figure S463.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 8.2e-05

Table S464.  Gene #65: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
12Q LOSS MUTATED 24 3 2
12Q LOSS WILD-TYPE 148 93 128

Figure S464.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0011

Table S465.  Gene #65: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
12Q LOSS MUTATED 20 2 7
12Q LOSS WILD-TYPE 124 113 132

Figure S465.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S466.  Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
13Q LOSS MUTATED 71 6 8 3 5
13Q LOSS WILD-TYPE 98 299 11 6 32

Figure S466.  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 = 3e-05

Table S467.  Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
13Q LOSS MUTATED 51 17 13
13Q LOSS WILD-TYPE 114 72 158

Figure S467.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CNMF'

P value = 0.0245 (Fisher's exact test), Q value = 0.042

Table S468.  Gene #66: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
13Q LOSS MUTATED 4 8 0 1 3 4
13Q LOSS WILD-TYPE 37 29 39 11 38 20

Figure S468.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S469.  Gene #66: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
13Q LOSS MUTATED 68 9 16
13Q LOSS WILD-TYPE 166 144 134

Figure S469.  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 = 3e-05

Table S470.  Gene #66: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
13Q LOSS MUTATED 38 4 14 0 24 12 1
13Q LOSS WILD-TYPE 85 49 33 65 84 54 74

Figure S470.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.6e-05

Table S471.  Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
13Q LOSS MUTATED 60 18 14
13Q LOSS WILD-TYPE 163 132 143

Figure S471.  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 = 3e-05

Table S472.  Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
13Q LOSS MUTATED 44 3 11 34
13Q LOSS WILD-TYPE 175 55 126 82

Figure S472.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00203 (Fisher's exact test), Q value = 0.0043

Table S473.  Gene #66: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
13Q LOSS MUTATED 43 16 22
13Q LOSS WILD-TYPE 101 99 117

Figure S473.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

P value = 0.0021 (Fisher's exact test), Q value = 0.0044

Table S474.  Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
14Q LOSS MUTATED 0 6 0 0
14Q LOSS WILD-TYPE 14 11 12 10

Figure S474.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0011

Table S475.  Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
14Q LOSS MUTATED 1 5 0 0 0
14Q LOSS WILD-TYPE 13 4 7 7 16

Figure S475.  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 = 3e-05

Table S476.  Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
14Q LOSS MUTATED 54 0 2 3 2
14Q LOSS WILD-TYPE 115 305 17 6 35

Figure S476.  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 = 3e-05

Table S477.  Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
14Q LOSS MUTATED 40 7 1
14Q LOSS WILD-TYPE 125 82 170

Figure S477.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 0.0143 (Fisher's exact test), Q value = 0.026

Table S478.  Gene #67: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
14Q LOSS MUTATED 5 6 0 0 1 4
14Q LOSS WILD-TYPE 36 31 39 12 40 20

Figure S478.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0499 (Fisher's exact test), Q value = 0.079

Table S479.  Gene #67: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 67 43 17
14Q LOSS MUTATED 9 3 1 3
14Q LOSS WILD-TYPE 58 64 42 14

Figure S479.  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 = 3e-05

Table S480.  Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
14Q LOSS MUTATED 54 3 4
14Q LOSS WILD-TYPE 180 150 146

Figure S480.  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 = 3e-05

Table S481.  Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
14Q LOSS MUTATED 45 1 4 0 7 4 0
14Q LOSS WILD-TYPE 78 52 43 65 101 62 75

Figure S481.  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 = 3e-05

Table S482.  Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
14Q LOSS MUTATED 49 8 2
14Q LOSS WILD-TYPE 174 142 155

Figure S482.  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 = 3e-05

Table S483.  Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
14Q LOSS MUTATED 20 0 2 37
14Q LOSS WILD-TYPE 199 58 135 79

Figure S483.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00497 (Fisher's exact test), Q value = 0.0097

Table S484.  Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
14Q LOSS MUTATED 30 10 7
14Q LOSS WILD-TYPE 142 86 123

Figure S484.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.6e-05

Table S485.  Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
14Q LOSS MUTATED 31 3 13
14Q LOSS WILD-TYPE 113 112 126

Figure S485.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'MRNA_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.0017

Table S486.  Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
15Q LOSS MUTATED 0 7 0 0
15Q LOSS WILD-TYPE 14 10 12 10

Figure S486.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00018

Table S487.  Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
15Q LOSS MUTATED 1 6 0 0 0
15Q LOSS WILD-TYPE 13 3 7 7 16

Figure S487.  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 = 3e-05

Table S488.  Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
15Q LOSS MUTATED 91 4 6 5 3
15Q LOSS WILD-TYPE 78 301 13 4 34

Figure S488.  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 = 3e-05

Table S489.  Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
15Q LOSS MUTATED 70 18 8
15Q LOSS WILD-TYPE 95 71 163

Figure S489.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'RPPA_CNMF'

P value = 9e-04 (Fisher's exact test), Q value = 0.002

Table S490.  Gene #68: '15q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
15Q LOSS MUTATED 1 11 2 1 1 3
15Q LOSS WILD-TYPE 40 26 37 11 40 21

Figure S490.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S491.  Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
15Q LOSS MUTATED 94 6 9
15Q LOSS WILD-TYPE 140 147 141

Figure S491.  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 = 3e-05

Table S492.  Gene #68: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
15Q LOSS MUTATED 71 1 9 2 18 7 1
15Q LOSS WILD-TYPE 52 52 38 63 90 59 74

Figure S492.  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 = 3e-05

Table S493.  Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
15Q LOSS MUTATED 86 13 8
15Q LOSS WILD-TYPE 137 137 149

Figure S493.  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 = 3e-05

Table S494.  Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
15Q LOSS MUTATED 41 0 5 61
15Q LOSS WILD-TYPE 178 58 132 55

Figure S494.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.6e-05

Table S495.  Gene #68: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
15Q LOSS MUTATED 58 23 13
15Q LOSS WILD-TYPE 114 73 117

Figure S495.  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 = 3e-05

Table S496.  Gene #68: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
15Q LOSS MUTATED 55 8 31
15Q LOSS WILD-TYPE 89 107 108

Figure S496.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'MRNA_CNMF'

P value = 0.00232 (Fisher's exact test), Q value = 0.0048

Table S497.  Gene #69: '16p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
16P LOSS MUTATED 0 6 0 0
16P LOSS WILD-TYPE 14 11 12 10

Figure S497.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00767 (Fisher's exact test), Q value = 0.014

Table S498.  Gene #69: '16p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
16P LOSS MUTATED 2 4 0 0 0
16P LOSS WILD-TYPE 12 5 7 7 16

Figure S498.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S499.  Gene #69: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
16P LOSS MUTATED 85 4 4 1 3
16P LOSS WILD-TYPE 84 301 15 8 34

Figure S499.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S500.  Gene #69: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
16P LOSS MUTATED 61 20 6
16P LOSS WILD-TYPE 104 69 165

Figure S500.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S501.  Gene #69: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
16P LOSS MUTATED 85 4 8
16P LOSS WILD-TYPE 149 149 142

Figure S501.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S502.  Gene #69: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
16P LOSS MUTATED 60 3 11 1 14 7 1
16P LOSS WILD-TYPE 63 50 36 64 94 59 74

Figure S502.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S503.  Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
16P LOSS MUTATED 74 11 9
16P LOSS WILD-TYPE 149 139 148

Figure S503.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S504.  Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
16P LOSS MUTATED 34 1 6 53
16P LOSS WILD-TYPE 185 57 131 63

Figure S504.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00416 (Fisher's exact test), Q value = 0.0083

Table S505.  Gene #69: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
16P LOSS MUTATED 47 23 16
16P LOSS WILD-TYPE 125 73 114

Figure S505.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S506.  Gene #69: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
16P LOSS MUTATED 46 7 33
16P LOSS WILD-TYPE 98 108 106

Figure S506.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'MRNA_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0018

Table S507.  Gene #70: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
16Q LOSS MUTATED 0 8 1 0
16Q LOSS WILD-TYPE 14 9 11 10

Figure S507.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00135 (Fisher's exact test), Q value = 0.0029

Table S508.  Gene #70: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
16Q LOSS MUTATED 2 6 0 0 1
16Q LOSS WILD-TYPE 12 3 7 7 15

Figure S508.  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 = 3e-05

Table S509.  Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
16Q LOSS MUTATED 112 14 7 1 4
16Q LOSS WILD-TYPE 57 291 12 8 33

Figure S509.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S510.  Gene #70: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
16Q LOSS MUTATED 80 26 15
16Q LOSS WILD-TYPE 85 63 156

Figure S510.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S511.  Gene #70: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
16Q LOSS MUTATED 110 14 14
16Q LOSS WILD-TYPE 124 139 136

Figure S511.  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 = 3e-05

Table S512.  Gene #70: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
16Q LOSS MUTATED 78 7 16 3 21 9 4
16Q LOSS WILD-TYPE 45 46 31 62 87 57 71

Figure S512.  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 = 3e-05

Table S513.  Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
16Q LOSS MUTATED 96 23 15
16Q LOSS WILD-TYPE 127 127 142

Figure S513.  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 = 3e-05

Table S514.  Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
16Q LOSS MUTATED 49 6 12 67
16Q LOSS WILD-TYPE 170 52 125 49

Figure S514.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.00064

Table S515.  Gene #70: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
16Q LOSS MUTATED 66 30 22
16Q LOSS WILD-TYPE 106 66 108

Figure S515.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S516.  Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
16Q LOSS MUTATED 61 13 44
16Q LOSS WILD-TYPE 83 102 95

Figure S516.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 0.00328 (Fisher's exact test), Q value = 0.0067

Table S517.  Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
17P LOSS MUTATED 0 7 1 0
17P LOSS WILD-TYPE 14 10 11 10

Figure S517.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00036

Table S518.  Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
17P LOSS MUTATED 1 6 1 0 0
17P LOSS WILD-TYPE 13 3 6 7 16

Figure S518.  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 = 3e-05

Table S519.  Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
17P LOSS MUTATED 120 3 4 1 2
17P LOSS WILD-TYPE 49 302 15 8 35

Figure S519.  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 = 3e-05

Table S520.  Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
17P LOSS MUTATED 83 21 11
17P LOSS WILD-TYPE 82 68 160

Figure S520.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'RPPA_CNMF'

P value = 0.00361 (Fisher's exact test), Q value = 0.0073

Table S521.  Gene #71: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
17P LOSS MUTATED 5 8 3 0 1 8
17P LOSS WILD-TYPE 36 29 36 12 40 16

Figure S521.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S522.  Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
17P LOSS MUTATED 110 4 15
17P LOSS WILD-TYPE 124 149 135

Figure S522.  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 = 3e-05

Table S523.  Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
17P LOSS MUTATED 84 1 10 3 17 13 1
17P LOSS WILD-TYPE 39 52 37 62 91 53 74

Figure S523.  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 = 3e-05

Table S524.  Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
17P LOSS MUTATED 99 12 16
17P LOSS WILD-TYPE 124 138 141

Figure S524.  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 = 3e-05

Table S525.  Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
17P LOSS MUTATED 45 0 13 69
17P LOSS WILD-TYPE 174 58 124 47

Figure S525.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S526.  Gene #71: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
17P LOSS MUTATED 66 28 16
17P LOSS WILD-TYPE 106 68 114

Figure S526.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S527.  Gene #71: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
17P LOSS MUTATED 59 16 35
17P LOSS WILD-TYPE 85 99 104

Figure S527.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'MRNA_CNMF'

P value = 0.00199 (Fisher's exact test), Q value = 0.0042

Table S528.  Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
17Q LOSS MUTATED 0 6 0 0
17Q LOSS WILD-TYPE 14 11 12 10

Figure S528.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.6e-05

Table S529.  Gene #72: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
17Q LOSS MUTATED 0 6 0 0 0
17Q LOSS WILD-TYPE 14 3 7 7 16

Figure S529.  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 = 3e-05

Table S530.  Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
17Q LOSS MUTATED 84 2 4 1 2
17Q LOSS WILD-TYPE 85 303 15 8 35

Figure S530.  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 = 3e-05

Table S531.  Gene #72: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
17Q LOSS MUTATED 54 18 10
17Q LOSS WILD-TYPE 111 71 161

Figure S531.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S532.  Gene #72: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
17Q LOSS MUTATED 75 4 13
17Q LOSS WILD-TYPE 159 149 137

Figure S532.  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 = 3e-05

Table S533.  Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
17Q LOSS MUTATED 55 1 6 3 15 12 0
17Q LOSS WILD-TYPE 68 52 41 62 93 54 75

Figure S533.  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 = 3e-05

Table S534.  Gene #72: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
17Q LOSS MUTATED 66 10 14
17Q LOSS WILD-TYPE 157 140 143

Figure S534.  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 = 3e-05

Table S535.  Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
17Q LOSS MUTATED 34 0 11 45
17Q LOSS WILD-TYPE 185 58 126 71

Figure S535.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00417 (Fisher's exact test), Q value = 0.0083

Table S536.  Gene #72: '17q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
17Q LOSS MUTATED 46 19 15
17Q LOSS WILD-TYPE 126 77 115

Figure S536.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0012

Table S537.  Gene #72: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
17Q LOSS MUTATED 44 14 22
17Q LOSS WILD-TYPE 100 101 117

Figure S537.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S538.  Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
18P LOSS MUTATED 38 1 6 4 3
18P LOSS WILD-TYPE 131 304 13 5 34

Figure S538.  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 = 3e-05

Table S539.  Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
18P LOSS MUTATED 34 8 4
18P LOSS WILD-TYPE 131 81 167

Figure S539.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S540.  Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
18P LOSS MUTATED 40 5 7
18P LOSS WILD-TYPE 194 148 143

Figure S540.  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 = 3e-05

Table S541.  Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
18P LOSS MUTATED 21 1 6 1 17 6 0
18P LOSS WILD-TYPE 102 52 41 64 91 60 75

Figure S541.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00026

Table S542.  Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
18P LOSS MUTATED 36 8 7
18P LOSS WILD-TYPE 187 142 150

Figure S542.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00021

Table S543.  Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
18P LOSS MUTATED 24 1 5 21
18P LOSS WILD-TYPE 195 57 132 95

Figure S543.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.031

Table S544.  Gene #73: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
18P LOSS MUTATED 29 8 9
18P LOSS WILD-TYPE 143 88 121

Figure S544.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00361 (Fisher's exact test), Q value = 0.0073

Table S545.  Gene #73: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
18P LOSS MUTATED 27 7 12
18P LOSS WILD-TYPE 117 108 127

Figure S545.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S546.  Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
18Q LOSS MUTATED 50 1 7 4 3
18Q LOSS WILD-TYPE 119 304 12 5 34

Figure S546.  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 = 3e-05

Table S547.  Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
18Q LOSS MUTATED 42 11 6
18Q LOSS WILD-TYPE 123 78 165

Figure S547.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S548.  Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
18Q LOSS MUTATED 52 5 8
18Q LOSS WILD-TYPE 182 148 142

Figure S548.  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 = 3e-05

Table S549.  Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
18Q LOSS MUTATED 27 1 11 1 19 6 0
18Q LOSS WILD-TYPE 96 52 36 64 89 60 75

Figure S549.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S550.  Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
18Q LOSS MUTATED 48 7 9
18Q LOSS WILD-TYPE 175 143 148

Figure S550.  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 = 3e-05

Table S551.  Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
18Q LOSS MUTATED 25 0 6 33
18Q LOSS WILD-TYPE 194 58 131 83

Figure S551.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.021

Table S552.  Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
18Q LOSS MUTATED 36 11 12
18Q LOSS WILD-TYPE 136 85 118

Figure S552.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.00097

Table S553.  Gene #74: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
18Q LOSS MUTATED 34 8 17
18Q LOSS WILD-TYPE 110 107 122

Figure S553.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S554.  Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
19P LOSS MUTATED 51 0 5 2 1
19P LOSS WILD-TYPE 118 305 14 7 36

Figure S554.  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 = 3e-05

Table S555.  Gene #75: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
19P LOSS MUTATED 45 6 2
19P LOSS WILD-TYPE 120 83 169

Figure S555.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S556.  Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
19P LOSS MUTATED 50 4 5
19P LOSS WILD-TYPE 184 149 145

Figure S556.  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 = 3e-05

Table S557.  Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
19P LOSS MUTATED 34 1 9 1 11 3 0
19P LOSS WILD-TYPE 89 52 38 64 97 63 75

Figure S557.  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 = 3e-05

Table S558.  Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
19P LOSS MUTATED 44 7 6
19P LOSS WILD-TYPE 179 143 151

Figure S558.  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 = 3e-05

Table S559.  Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
19P LOSS MUTATED 23 0 3 31
19P LOSS WILD-TYPE 196 58 134 85

Figure S559.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00523 (Fisher's exact test), Q value = 0.01

Table S560.  Gene #75: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
19P LOSS MUTATED 33 8 10
19P LOSS WILD-TYPE 139 88 120

Figure S560.  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 = 3e-05

Table S561.  Gene #75: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
19P LOSS MUTATED 37 3 11
19P LOSS WILD-TYPE 107 112 128

Figure S561.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0167 (Fisher's exact test), Q value = 0.03

Table S562.  Gene #76: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
19Q LOSS MUTATED 0 3 1 0 0
19Q LOSS WILD-TYPE 14 6 6 7 16

Figure S562.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S563.  Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
19Q LOSS MUTATED 49 1 4 1 1
19Q LOSS WILD-TYPE 120 304 15 8 36

Figure S563.  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 = 3e-05

Table S564.  Gene #76: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
19Q LOSS MUTATED 37 8 4
19Q LOSS WILD-TYPE 128 81 167

Figure S564.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S565.  Gene #76: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
19Q LOSS MUTATED 45 4 6
19Q LOSS WILD-TYPE 189 149 144

Figure S565.  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 = 3e-05

Table S566.  Gene #76: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
19Q LOSS MUTATED 34 1 6 1 9 4 0
19Q LOSS WILD-TYPE 89 52 41 64 99 62 75

Figure S566.  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 = 3e-05

Table S567.  Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
19Q LOSS MUTATED 41 6 7
19Q LOSS WILD-TYPE 182 144 150

Figure S567.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S568.  Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
19Q LOSS MUTATED 25 0 4 25
19Q LOSS WILD-TYPE 194 58 133 91

Figure S568.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.021

Table S569.  Gene #76: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
19Q LOSS MUTATED 30 8 9
19Q LOSS WILD-TYPE 142 88 121

Figure S569.  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 = 5.6e-05

Table S570.  Gene #76: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
19Q LOSS MUTATED 31 4 12
19Q LOSS WILD-TYPE 113 111 127

Figure S570.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S571.  Gene #77: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
20P LOSS MUTATED 16 1 1 1 0
20P LOSS WILD-TYPE 153 304 18 8 37

Figure S571.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.029

Table S572.  Gene #77: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
20P LOSS MUTATED 14 2 2
20P LOSS WILD-TYPE 220 151 148

Figure S572.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.019

Table S573.  Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
20P LOSS MUTATED 10 2 3 0 2 1 0
20P LOSS WILD-TYPE 113 51 44 65 106 65 75

Figure S573.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_CNMF'

P value = 0.00707 (Fisher's exact test), Q value = 0.013

Table S574.  Gene #77: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
20P LOSS MUTATED 14 3 1
20P LOSS WILD-TYPE 209 147 156

Figure S574.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q loss' versus 'CN_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0012

Table S575.  Gene #78: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
20Q LOSS MUTATED 7 0 1 1 0
20Q LOSS WILD-TYPE 162 305 18 8 37

Figure S575.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

'20q loss' versus 'MRNASEQ_CNMF'

P value = 0.037 (Fisher's exact test), Q value = 0.061

Table S576.  Gene #78: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
20Q LOSS MUTATED 7 1 0
20Q LOSS WILD-TYPE 227 152 150

Figure S576.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0307 (Fisher's exact test), Q value = 0.052

Table S577.  Gene #78: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
20Q LOSS MUTATED 5 1 2 0 0 0 0
20Q LOSS WILD-TYPE 118 52 45 65 108 66 75

Figure S577.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_CNMF'

P value = 0.0405 (Fisher's exact test), Q value = 0.066

Table S578.  Gene #78: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
20Q LOSS MUTATED 7 2 0
20Q LOSS WILD-TYPE 216 148 157

Figure S578.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.047 (Fisher's exact test), Q value = 0.075

Table S579.  Gene #78: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
20Q LOSS MUTATED 4 0 0 5
20Q LOSS WILD-TYPE 215 58 137 111

Figure S579.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MRNA_CNMF'

P value = 0.0401 (Fisher's exact test), Q value = 0.065

Table S580.  Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
21Q LOSS MUTATED 0 4 0 0
21Q LOSS WILD-TYPE 14 13 12 10

Figure S580.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0299 (Fisher's exact test), Q value = 0.051

Table S581.  Gene #79: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
21Q LOSS MUTATED 1 3 0 0 0
21Q LOSS WILD-TYPE 13 6 7 7 16

Figure S581.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S582.  Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
21Q LOSS MUTATED 44 4 2 4 0
21Q LOSS WILD-TYPE 125 301 17 5 37

Figure S582.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S583.  Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
21Q LOSS MUTATED 34 7 5
21Q LOSS WILD-TYPE 131 82 166

Figure S583.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S584.  Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
21Q LOSS MUTATED 46 7 1
21Q LOSS WILD-TYPE 188 146 149

Figure S584.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S585.  Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
21Q LOSS MUTATED 30 1 7 4 10 2 0
21Q LOSS WILD-TYPE 93 52 40 61 98 64 75

Figure S585.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S586.  Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
21Q LOSS MUTATED 43 7 2
21Q LOSS WILD-TYPE 180 143 155

Figure S586.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S587.  Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
21Q LOSS MUTATED 21 1 1 29
21Q LOSS WILD-TYPE 198 57 136 87

Figure S587.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00364 (Fisher's exact test), Q value = 0.0074

Table S588.  Gene #79: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
21Q LOSS MUTATED 30 9 7
21Q LOSS WILD-TYPE 142 87 123

Figure S588.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.6e-05

Table S589.  Gene #79: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
21Q LOSS MUTATED 28 1 17
21Q LOSS WILD-TYPE 116 114 122

Figure S589.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'MRNA_CNMF'

P value = 0.00196 (Fisher's exact test), Q value = 0.0042

Table S590.  Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
22Q LOSS MUTATED 0 6 0 0
22Q LOSS WILD-TYPE 14 11 12 10

Figure S590.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00759 (Fisher's exact test), Q value = 0.014

Table S591.  Gene #80: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
22Q LOSS MUTATED 2 4 0 0 0
22Q LOSS WILD-TYPE 12 5 7 7 16

Figure S591.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S592.  Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
22Q LOSS MUTATED 96 3 4 3 3
22Q LOSS WILD-TYPE 73 302 15 6 34

Figure S592.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S593.  Gene #80: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
22Q LOSS MUTATED 67 20 13
22Q LOSS WILD-TYPE 98 69 158

Figure S593.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CNMF'

P value = 0.0388 (Fisher's exact test), Q value = 0.064

Table S594.  Gene #80: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
22Q LOSS MUTATED 4 8 2 1 1 5
22Q LOSS WILD-TYPE 37 29 37 11 40 19

Figure S594.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S595.  Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
22Q LOSS MUTATED 85 6 17
22Q LOSS WILD-TYPE 149 147 133

Figure S595.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S596.  Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
22Q LOSS MUTATED 62 1 7 1 22 13 2
22Q LOSS WILD-TYPE 61 52 40 64 86 53 73

Figure S596.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S597.  Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
22Q LOSS MUTATED 79 11 17
22Q LOSS WILD-TYPE 144 139 140

Figure S597.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S598.  Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
22Q LOSS MUTATED 43 0 13 51
22Q LOSS WILD-TYPE 176 58 124 65

Figure S598.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00382 (Fisher's exact test), Q value = 0.0077

Table S599.  Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
22Q LOSS MUTATED 51 25 18
22Q LOSS WILD-TYPE 121 71 112

Figure S599.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00033

Table S600.  Gene #80: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
22Q LOSS MUTATED 50 15 29
22Q LOSS WILD-TYPE 94 100 110

Figure S600.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'MRNA_CNMF'

P value = 0.00164 (Fisher's exact test), Q value = 0.0035

Table S601.  Gene #81: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
XP LOSS MUTATED 0 6 0 0
XP LOSS WILD-TYPE 14 11 12 10

Figure S601.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp loss' versus 'MRNA_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.00095

Table S602.  Gene #81: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
XP LOSS MUTATED 1 5 0 0 0
XP LOSS WILD-TYPE 13 4 7 7 16

Figure S602.  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 = 3e-05

Table S603.  Gene #81: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
XP LOSS MUTATED 76 1 3 2 3
XP LOSS WILD-TYPE 93 304 16 7 34

Figure S603.  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 = 3e-05

Table S604.  Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
XP LOSS MUTATED 46 16 8
XP LOSS WILD-TYPE 119 73 163

Figure S604.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp loss' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.6e-05

Table S605.  Gene #81: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
XP LOSS MUTATED 2 14 2 1 1 2
XP LOSS WILD-TYPE 39 23 37 11 40 22

Figure S605.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S606.  Gene #81: 'xp loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
XP LOSS MUTATED 73 5 6
XP LOSS WILD-TYPE 161 148 144

Figure S606.  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 = 3e-05

Table S607.  Gene #81: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
XP LOSS MUTATED 52 2 6 1 19 4 0
XP LOSS WILD-TYPE 71 51 41 64 89 62 75

Figure S607.  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 = 3e-05

Table S608.  Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
XP LOSS MUTATED 61 12 9
XP LOSS WILD-TYPE 162 138 148

Figure S608.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S609.  Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
XP LOSS MUTATED 34 0 4 44
XP LOSS WILD-TYPE 185 58 133 72

Figure S609.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0015

Table S610.  Gene #81: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
XP LOSS MUTATED 44 13 12
XP LOSS WILD-TYPE 128 83 118

Figure S610.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S611.  Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
XP LOSS MUTATED 43 6 20
XP LOSS WILD-TYPE 101 109 119

Figure S611.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'MRNA_CNMF'

P value = 0.00831 (Fisher's exact test), Q value = 0.016

Table S612.  Gene #82: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
XQ LOSS MUTATED 0 5 0 0
XQ LOSS WILD-TYPE 14 12 12 10

Figure S612.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xq loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0047 (Fisher's exact test), Q value = 0.0092

Table S613.  Gene #82: 'xq loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
XQ LOSS MUTATED 1 4 0 0 0
XQ LOSS WILD-TYPE 13 5 7 7 16

Figure S613.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S614.  Gene #82: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 169 305 19 9 37
XQ LOSS MUTATED 64 1 3 2 1
XQ LOSS WILD-TYPE 105 304 16 7 36

Figure S614.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S615.  Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 89 171
XQ LOSS MUTATED 42 12 6
XQ LOSS WILD-TYPE 123 77 165

Figure S615.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 5e-04

Table S616.  Gene #82: 'xq loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
XQ LOSS MUTATED 3 13 2 1 1 1
XQ LOSS WILD-TYPE 38 24 37 11 40 23

Figure S616.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S617.  Gene #82: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 153 150
XQ LOSS MUTATED 61 4 5
XQ LOSS WILD-TYPE 173 149 145

Figure S617.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S618.  Gene #82: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 123 53 47 65 108 66 75
XQ LOSS MUTATED 40 2 8 1 15 4 0
XQ LOSS WILD-TYPE 83 51 39 64 93 62 75

Figure S618.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S619.  Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 223 150 157
XQ LOSS MUTATED 51 9 8
XQ LOSS WILD-TYPE 172 141 149

Figure S619.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S620.  Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 219 58 137 116
XQ LOSS MUTATED 26 0 4 38
XQ LOSS WILD-TYPE 193 58 133 78

Figure S620.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00576 (Fisher's exact test), Q value = 0.011

Table S621.  Gene #82: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 96 130
XQ LOSS MUTATED 37 9 13
XQ LOSS WILD-TYPE 135 87 117

Figure S621.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S622.  Gene #82: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 144 115 139
XQ LOSS MUTATED 41 4 14
XQ LOSS WILD-TYPE 103 111 125

Figure S622.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UCEC-TP/15106276/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UCEC-TP/15120652/UCEC-TP.transferedmergedcluster.txt

  • Number of patients = 539

  • Number of significantly arm-level cnvs = 82

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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