Correlation between copy number variations of arm-level result and molecular subtypes
Breast Invasive Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1SJ1J0Q
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1SJ1J0Q
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 80 arm-level events and 12 molecular subtypes across 1007 patients, 555 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

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

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

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

  • 3q 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'.

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

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

  • 5p gain cnv correlated to 'CN_CNMF'.

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

  • 6p 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'.

  • 6q 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'.

  • 7p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

  • 8p gain cnv correlated to 'CN_CNMF'.

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

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

  • 9q gain cnv correlated to 'CN_CNMF'.

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

  • 10q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 11p gain cnv correlated to 'CN_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

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

  • 17p gain cnv correlated to 'CN_CNMF'.

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

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

  • 18q 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'.

  • 19p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  • 7q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 9p 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'.

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

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

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

  • 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 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

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

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

  • 16p loss cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

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

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

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

  • 18q loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 19p 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'.

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

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

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

  • 21q loss cnv correlated to 'CN_CNMF'.

  • 22q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 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, 555 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 Chi-square test Fisher's exact test Chi-square test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
1p gain 191 (19%) 816 3.72e-09
(2.68e-06) 		9.02e-10
(6.64e-07) 		4.68e-17
(4.13e-14) 		2.32e-08
(1.58e-05) 		1.83e-06
(0.00108) 		1.41e-05
(0.0078) 		2.31e-18
(2.07e-15) 		1.26e-15
(1.09e-12) 		4.23e-11
(3.3e-08) 		1.1e-16
(9.6e-14) 		1.05e-09
(7.74e-07) 		4.73e-09
(3.38e-06)
2p gain 113 (11%) 894 9.24e-15
(7.84e-12) 		1.41e-14
(1.19e-11) 		9.97e-18
(8.88e-15) 		2.72e-13
(2.25e-10) 		1.55e-10
(1.18e-07) 		3.16e-10
(2.38e-07) 		2.75e-29
(2.59e-26) 		1.36e-27
(1.27e-24) 		7.91e-23
(7.31e-20) 		1e-22
(9.25e-20) 		3.72e-22
(3.42e-19) 		3.08e-13
(2.54e-10)
2q gain 70 (7%) 937 2.56e-07
(0.00016) 		1.49e-07
(9.48e-05) 		1.63e-09
(1.2e-06) 		7.16e-08
(4.7e-05) 		1.36e-06
(0.000812) 		1.88e-05
(0.0102) 		1.74e-14
(1.46e-11) 		4.97e-14
(4.16e-11) 		1.33e-11
(1.05e-08) 		1.28e-10
(9.81e-08) 		5.16e-13
(4.22e-10) 		3.59e-07
(0.000223)
10p gain 197 (20%) 810 1.8e-09
(1.32e-06) 		5.78e-08
(3.85e-05) 		9.42e-27
(8.8e-24) 		3.63e-15
(3.11e-12) 		2.4e-05
(0.013) 		2.46e-05
(0.0132) 		9.79e-17
(8.57e-14) 		8.79e-17
(7.7e-14) 		2.37e-15
(2.04e-12) 		2.01e-17
(1.77e-14) 		1.25e-12
(1.01e-09) 		2.09e-10
(1.59e-07)
21q gain 184 (18%) 823 5.21e-10
(3.88e-07) 		6.2e-07
(0.00038) 		1.32e-15
(1.14e-12) 		6.71e-09
(4.74e-06) 		0.000202
(0.0929) 		7.86e-05
(0.0393) 		1.99e-16
(1.74e-13) 		2.17e-16
(1.89e-13) 		1.55e-08
(1.06e-05) 		8.44e-13
(6.86e-10) 		1.83e-08
(1.26e-05) 		1.01e-07
(6.57e-05)
3p loss 171 (17%) 836 2.85e-06
(0.00166) 		9e-05
(0.0444) 		9.47e-15
(8.02e-12) 		1.19e-07
(7.67e-05) 		0.000382
(0.164) 		8.85e-05
(0.0439) 		1.61e-10
(1.23e-07) 		7.04e-08
(4.63e-05) 		1.11e-10
(8.49e-08) 		5.66e-08
(3.78e-05) 		4.15e-08
(2.79e-05) 		8.4e-05
(0.0418)
4p loss 330 (33%) 677 2.99e-14
(2.51e-11) 		2.91e-13
(2.41e-10) 		3.95e-37
(3.77e-34) 		5.22e-19
(4.71e-16) 		4.59e-07
(0.000282) 		8.75e-07
(0.000529) 		7.94e-29
(7.46e-26) 		5.35e-27
(5.02e-24) 		1.31e-21
(1.2e-18) 		4.71e-23
(4.36e-20) 		2.02e-20
(1.83e-17) 		8.08e-17
(7.09e-14)
5p loss 132 (13%) 875 6.42e-17
(5.64e-14) 		1.72e-12
(1.38e-09) 		4.32e-35
(4.11e-32) 		9.63e-23
(8.9e-20) 		6.63e-08
(4.37e-05) 		6.96e-10
(5.16e-07) 		2.62e-26
(2.44e-23) 		8.04e-27
(7.52e-24) 		5.43e-25
(5.05e-22) 		1.22e-28
(1.15e-25) 		1.25e-18
(1.12e-15) 		3.62e-18
(3.24e-15)
5q loss 215 (21%) 792 3.8e-26
(3.54e-23) 		1e-20
(9.11e-18) 		1.62e-75
(1.56e-72) 		5.35e-46
(5.11e-43) 		1.2e-13
(9.95e-11) 		1.18e-13
(9.84e-11) 		1.22e-49
(1.16e-46) 		4.74e-52
(4.54e-49) 		4.44e-51
(4.25e-48) 		1.4e-52
(1.34e-49) 		2.22e-34
(2.1e-31) 		1.14e-33
(1.08e-30)
9q loss 269 (27%) 738 6.82e-05
(0.0347) 		3.55e-06
(0.00205) 		3.83e-26
(3.57e-23) 		4.82e-14
(4.04e-11) 		3.37e-06
(0.00196) 		0.000331
(0.145) 		4.44e-13
(3.65e-10) 		3.3e-12
(2.63e-09) 		1.08e-12
(8.73e-10) 		7.74e-15
(6.6e-12) 		3.96e-08
(2.66e-05) 		1.38e-06
(0.000823)
12q loss 124 (12%) 883 5.14e-09
(3.66e-06) 		4.1e-08
(2.76e-05) 		8.11e-15
(6.9e-12) 		1.35e-20
(1.22e-17) 		0.000215
(0.0983) 		1.16e-05
(0.00646) 		1.07e-17
(9.46e-15) 		2.1e-16
(1.83e-13) 		2.78e-14
(2.34e-11) 		3.21e-15
(2.75e-12) 		1.19e-12
(9.65e-10) 		1.14e-10
(8.74e-08)
14q loss 240 (24%) 767 1.2e-14
(1.02e-11) 		5.9e-10
(4.39e-07) 		4.64e-35
(4.4e-32) 		1.67e-20
(1.51e-17) 		5.79e-06
(0.0033) 		4.45e-06
(0.00257) 		1.61e-22
(1.48e-19) 		8.56e-24
(7.94e-21) 		2.3e-21
(2.11e-18) 		1.63e-23
(1.51e-20) 		2.32e-17
(2.05e-14) 		1.04e-15
(8.97e-13)
16q loss 561 (56%) 446 3.87e-09
(2.78e-06) 		2.06e-10
(1.57e-07) 		3.9e-10
(2.91e-07) 		4.28e-12
(3.41e-09) 		0.000111
(0.054) 		1.09e-06
(0.000656) 		3.97e-16
(3.45e-13) 		4.88e-17
(4.3e-14) 		4.5e-13
(3.69e-10) 		7.3e-18
(6.51e-15) 		1.84e-08
(1.26e-05) 		1.95e-07
(0.000124)
17q loss 255 (25%) 752 2.24e-12
(1.79e-09) 		3.34e-10
(2.5e-07) 		5.74e-22
(5.26e-19) 		2.51e-15
(2.15e-12) 		7.36e-10
(5.45e-07) 		2.44e-10
(1.84e-07) 		6.55e-18
(5.85e-15) 		5.78e-17
(5.09e-14) 		5.94e-13
(4.84e-10) 		8.54e-16
(7.4e-13) 		6.07e-09
(4.32e-06) 		2.74e-07
(0.000172)
6p gain 197 (20%) 810 5.32e-07
(0.000326) 		4.84e-06
(0.00277) 		1.21e-33
(1.15e-30) 		1.25e-17
(1.11e-14) 		5.5e-05
(0.0284) 		0.00458
(1.00) 		1.95e-18
(1.75e-15) 		1.57e-19
(1.41e-16) 		4.34e-18
(3.88e-15) 		6.68e-21
(6.07e-18) 		3.04e-15
(2.61e-12) 		1e-10
(7.73e-08)
6q gain 141 (14%) 866 1.58e-07
(1e-04) 		1.45e-05
(0.00797) 		2.21e-32
(2.09e-29) 		2.14e-11
(1.69e-08) 		3.39e-06
(0.00196) 		0.00294
(0.942) 		5.32e-15
(4.55e-12) 		1.01e-13
(8.38e-11) 		6.42e-17
(5.64e-14) 		2.6e-16
(2.26e-13) 		8.99e-14
(7.5e-11) 		1.92e-10
(1.46e-07)
9p gain 130 (13%) 877 8.81e-10
(6.5e-07) 		1.27e-07
(8.17e-05) 		1.03e-17
(9.2e-15) 		4.54e-06
(0.0026) 		0.0085
(1.00) 		3.85e-06
(0.00222) 		2.26e-08
(1.54e-05) 		3.2e-09
(2.32e-06) 		4.46e-06
(0.00257) 		3.31e-08
(2.24e-05) 		0.000536
(0.219) 		0.000248
(0.112)
18p gain 161 (16%) 846 1.1e-06
(0.000656) 		6.37e-08
(4.21e-05) 		8.25e-15
(7.01e-12) 		1.08e-12
(8.76e-10) 		0.00147
(0.531) 		4.82e-05
(0.025) 		8.53e-15
(7.24e-12) 		8.2e-20
(7.4e-17) 		2.16e-11
(1.7e-08) 		7.17e-14
(5.99e-11) 		1.2e-08
(8.35e-06) 		7.29e-10
(5.4e-07)
22q gain 91 (9%) 916 1.66e-05
(0.00912) 		1.76e-06
(0.00104) 		1.28e-11
(1.01e-08) 		5.38e-05
(0.0279) 		8.26e-06
(0.00464) 		0.00376
(1.00) 		6.3e-15
(5.38e-12) 		1.33e-12
(1.07e-09) 		2.11e-09
(1.54e-06) 		3.63e-11
(2.84e-08) 		7.81e-06
(0.00439) 		1.92e-06
(0.00113)
4q loss 294 (29%) 713 1.12e-07
(7.24e-05) 		9.7e-08
(6.32e-05) 		7.72e-29
(7.27e-26) 		3.62e-11
(2.84e-08) 		0.00036
(0.155) 		0.0009
(0.347) 		6.79e-20
(6.14e-17) 		1.05e-17
(9.36e-15) 		1.29e-12
(1.04e-09) 		2.24e-14
(1.89e-11) 		4.43e-13
(3.65e-10) 		1.85e-09
(1.35e-06)
18q gain 140 (14%) 867 7.26e-05
(0.0365) 		0.000119
(0.0573) 		1.39e-12
(1.12e-09) 		7.3e-05
(0.0367) 		0.176
(1.00) 		0.0658
(1.00) 		6.25e-09
(4.43e-06) 		5.18e-10
(3.86e-07) 		8.9e-07
(0.000537) 		1.77e-05
(0.00966) 		0.000462
(0.192) 		0.000233
(0.106)
9p loss 297 (29%) 710 1.92e-05
(0.0104) 		0.000177
(0.0832) 		1.25e-36
(1.19e-33) 		4.02e-15
(3.44e-12) 		0.0017
(0.603) 		0.311
(1.00) 		3.92e-09
(2.81e-06) 		2.29e-10
(1.73e-07) 		4.6e-10
(3.44e-07) 		2.5e-10
(1.88e-07) 		4.13e-07
(0.000255) 		0.000241
(0.109)
13q loss 408 (41%) 599 5.59e-05
(0.0288) 		6.32e-06
(0.00357) 		4.63e-24
(4.31e-21) 		1.96e-08
(1.34e-05) 		0.349
(1.00) 		0.247
(1.00) 		1.92e-08
(1.31e-05) 		3.62e-09
(2.61e-06) 		5.96e-08
(3.96e-05) 		1.39e-07
(8.86e-05) 		2.18e-07
(0.000137) 		0.000194
(0.0903)
15q loss 302 (30%) 705 1.95e-05
(0.0106) 		1.14e-05
(0.00637) 		5.12e-31
(4.84e-28) 		5.11e-13
(4.19e-10) 		0.00426
(1.00) 		0.00195
(0.675) 		1.1e-15
(9.5e-13) 		2.92e-13
(2.41e-10) 		3.14e-14
(2.64e-11) 		5.21e-13
(4.26e-10) 		2.27e-10
(1.72e-07) 		6.46e-09
(4.57e-06)
19p loss 179 (18%) 828 2.62e-05
(0.014) 		2.68e-05
(0.0142) 		1.57e-20
(1.43e-17) 		2.89e-12
(2.3e-09) 		0.0231
(1.00) 		0.0273
(1.00) 		3.19e-08
(2.17e-05) 		5.77e-11
(4.47e-08) 		4.11e-11
(3.22e-08) 		8.21e-12
(6.52e-09) 		6.16e-09
(4.38e-06) 		6.53e-05
(0.0334)
3q gain 202 (20%) 805 0.000917
(0.352) 		3.37e-06
(0.00196) 		1.32e-17
(1.17e-14) 		1.03e-10
(7.91e-08) 		0.0118
(1.00) 		0.106
(1.00) 		8.53e-12
(6.76e-09) 		1.45e-12
(1.17e-09) 		8.42e-13
(6.85e-10) 		3.7e-11
(2.9e-08) 		2e-10
(1.52e-07) 		9.31e-11
(7.2e-08)
8q gain 495 (49%) 512 6.86e-05
(0.0348) 		0.0095
(1.00) 		2.64e-22
(2.43e-19) 		3.88e-13
(3.19e-10) 		0.122
(1.00) 		0.441
(1.00) 		5.01e-07
(0.000307) 		2.87e-09
(2.09e-06) 		4.48e-11
(3.49e-08) 		1.35e-10
(1.03e-07) 		3.33e-11
(2.61e-08) 		1e-07
(6.52e-05)
16p gain 447 (44%) 560 0.000344
(0.149) 		0.000409
(0.175) 		7.97e-10
(5.89e-07) 		1.6e-05
(0.00878) 		0.00236
(0.79) 		0.00216
(0.736) 		2.18e-07
(0.000137) 		1.18e-08
(8.21e-06) 		6.95e-06
(0.00392) 		0.00383
(1.00) 		1.75e-05
(0.00955) 		0.000258
(0.115)
20q gain 422 (42%) 585 7.43e-05
(0.0372) 		0.0074
(1.00) 		2.16e-36
(2.06e-33) 		1.24e-14
(1.05e-11) 		0.0468
(1.00) 		0.424
(1.00) 		8.24e-09
(5.79e-06) 		2.46e-08
(1.67e-05) 		1.37e-06
(0.000816) 		2.12e-06
(0.00125) 		3.44e-05
(0.0181) 		2.81e-05
(0.0149)
17p loss 540 (54%) 467 3.58e-09
(2.58e-06) 		0.0436
(1.00) 		3.99e-22
(3.67e-19) 		1.6e-06
(0.000953) 		8.96e-07
(0.000539) 		0.000628
(0.254) 		6.78e-06
(0.00383) 		0.000454
(0.191) 		5.22e-08
(3.48e-05) 		6.92e-05
(0.0351) 		1.09e-05
(0.00609) 		0.0266
(1.00)
20p gain 389 (39%) 618 3e-05
(0.0158) 		0.00609
(1.00) 		1.6e-31
(1.51e-28) 		3.81e-09
(2.74e-06) 		0.00492
(1.00) 		0.0574
(1.00) 		2.86e-07
(0.000179) 		1.54e-06
(0.000918) 		2.6e-05
(0.0139) 		0.000262
(0.117) 		0.00211
(0.723) 		0.000201
(0.0925)
2p loss 170 (17%) 837 0.012
(1.00) 		6.35e-05
(0.0325) 		7.62e-15
(6.5e-12) 		1.49e-07
(9.48e-05) 		0.00102
(0.388) 		0.0015
(0.541) 		3.63e-08
(2.45e-05) 		1.48e-10
(1.13e-07) 		0.000126
(0.0602) 		0.000314
(0.138) 		0.00161
(0.577) 		0.00033
(0.145)
7p loss 105 (10%) 902 0.0427
(1.00) 		0.00135
(0.491) 		8.19e-10
(6.04e-07) 		7.1e-05
(0.0359) 		0.0891
(1.00) 		0.215
(1.00) 		1.16e-05
(0.00646) 		2.05e-05
(0.0111) 		2.25e-08
(1.54e-05) 		3.51e-08
(2.38e-05) 		0.000122
(0.0586) 		2.9e-05
(0.0154)
8p loss 371 (37%) 636 4.52e-05
(0.0236) 		0.0109
(1.00) 		1.65e-18
(1.48e-15) 		3.86e-07
(0.000239) 		0.0704
(1.00) 		0.219
(1.00) 		2.39e-06
(0.0014) 		3.94e-05
(0.0206) 		6.61e-07
(0.000403) 		1.3e-07
(8.29e-05) 		4.74e-05
(0.0247) 		0.00395
(1.00)
11p loss 259 (26%) 748 0.00536
(1.00) 		0.0672
(1.00) 		3.23e-21
(2.94e-18) 		1.08e-08
(7.51e-06) 		0.00775
(1.00) 		0.00536
(1.00) 		1.63e-07
(0.000103) 		1.17e-07
(7.56e-05) 		5.87e-06
(0.00334) 		3.53e-07
(0.00022) 		2.84e-06
(0.00166) 		0.000293
(0.13)
12p loss 144 (14%) 863 0.00305
(0.969) 		0.00126
(0.461) 		9.43e-08
(6.16e-05) 		6.76e-08
(4.46e-05) 		0.0133
(1.00) 		0.0221
(1.00) 		1.3e-09
(9.55e-07) 		6.3e-07
(0.000385) 		6.28e-08
(4.16e-05) 		1.41e-08
(9.76e-06) 		2.42e-06
(0.00142) 		0.000318
(0.139)
19q loss 152 (15%) 855 0.00372
(1.00) 		0.000338
(0.147) 		2.51e-18
(2.25e-15) 		3.8e-08
(2.56e-05) 		0.108
(1.00) 		0.108
(1.00) 		1.02e-07
(6.59e-05) 		1.8e-12
(1.44e-09) 		1e-08
(6.99e-06) 		3.52e-09
(2.54e-06) 		9.8e-07
(0.000589) 		0.00148
(0.535)
20p loss 88 (9%) 919 0.00352
(1.00) 		0.000956
(0.365) 		1.09e-10
(8.36e-08) 		9.22e-12
(7.3e-09) 		0.189
(1.00) 		0.205
(1.00) 		4.88e-11
(3.79e-08) 		4.75e-11
(3.69e-08) 		2.89e-10
(2.18e-07) 		6.47e-10
(4.81e-07) 		3.23e-08
(2.19e-05) 		8.91e-09
(6.25e-06)
20q loss 51 (5%) 956 0.00774
(1.00) 		0.00962
(1.00) 		1.03e-07
(6.66e-05) 		2.92e-10
(2.2e-07) 		0.177
(1.00) 		0.0389
(1.00) 		5.07e-08
(3.39e-05) 		1.23e-08
(8.54e-06) 		4.39e-07
(0.000271) 		4.88e-08
(3.27e-05) 		8.61e-08
(5.64e-05) 		7.15e-09
(5.04e-06)
11q gain 90 (9%) 917 0.277
(1.00) 		0.88
(1.00) 		4.64e-09
(3.31e-06) 		0.00254
(0.832) 		0.96
(1.00) 		0.566
(1.00) 		0.00015
(0.0709) 		0.000412
(0.176) 		0.000105
(0.0512) 		7.13e-05
(0.0359) 		0.000423
(0.18) 		3.82e-05
(0.02)
12p gain 216 (21%) 791 0.00181
(0.636) 		0.000407
(0.174) 		5.32e-21
(4.84e-18) 		2.83e-09
(2.06e-06) 		0.0768
(1.00) 		0.0112
(1.00) 		1.06e-07
(6.86e-05) 		6.78e-09
(4.78e-06) 		2.41e-05
(0.013) 		7.29e-06
(0.0041) 		0.000743
(0.294) 		0.0153
(1.00)
17q gain 207 (21%) 800 8.87e-09
(6.22e-06) 		5.8e-05
(0.0298) 		5.9e-22
(5.4e-19) 		2.03e-07
(0.000128) 		0.506
(1.00) 		0.0206
(1.00) 		8.59e-07
(0.00052) 		1.21e-08
(8.39e-06) 		0.0579
(1.00) 		2.74e-06
(0.0016) 		0.645
(1.00) 		0.00923
(1.00)
xq gain 131 (13%) 876 0.000972
(0.369) 		8.96e-05
(0.0442) 		9e-09
(6.3e-06) 		0.0024
(0.796) 		0.689
(1.00) 		0.0445
(1.00) 		8.6e-07
(0.000521) 		3.89e-07
(0.00024) 		8.24e-08
(5.41e-05) 		1.57e-05
(0.00863) 		0.00022
(0.1) 		0.016
(1.00)
10q loss 214 (21%) 793 0.00356
(1.00) 		0.00137
(0.499) 		2.32e-13
(1.93e-10) 		4.18e-11
(3.27e-08) 		0.00113
(0.421) 		0.0225
(1.00) 		3.11e-09
(2.26e-06) 		6.04e-08
(4.01e-05) 		0.000115
(0.0555) 		2.02e-07
(0.000127) 		0.000447
(0.188) 		0.00114
(0.422)
3p gain 137 (14%) 870 0.0962
(1.00) 		0.000943
(0.361) 		1.02e-10
(7.86e-08) 		2.65e-05
(0.0141) 		0.364
(1.00) 		0.209
(1.00) 		1.82e-05
(0.00992) 		3.84e-07
(0.000238) 		0.000146
(0.0695) 		0.000168
(0.0794) 		0.00167
(0.596) 		0.00222
(0.751)
1p loss 230 (23%) 777 0.000238
(0.108) 		6.75e-07
(0.000411) 		4.65e-22
(4.27e-19) 		1.25e-07
(8.05e-05) 		0.697
(1.00) 		0.683
(1.00) 		1.04e-07
(6.72e-05) 		9.61e-13
(7.8e-10) 		0.0474
(1.00) 		0.0258
(1.00) 		0.808
(1.00) 		0.15
(1.00)
6q loss 255 (25%) 752 0.00106
(0.401) 		0.00019
(0.0887) 		2.73e-16
(2.37e-13) 		5.57e-05
(0.0288) 		0.281
(1.00) 		0.111
(1.00) 		0.000185
(0.0865) 		0.000125
(0.0601) 		0.0645
(1.00) 		6.05e-06
(0.00343) 		0.022
(1.00) 		0.0109
(1.00)
xq loss 168 (17%) 839 0.139
(1.00) 		0.0319
(1.00) 		4.8e-11
(3.73e-08) 		2.47e-05
(0.0133) 		0.0366
(1.00) 		0.0247
(1.00) 		0.000245
(0.111) 		3.47e-05
(0.0182) 		2.47e-05
(0.0133) 		0.000113
(0.0546) 		0.0273
(1.00) 		0.36
(1.00)
7q gain 247 (25%) 760 0.00175
(0.617) 		0.0145
(1.00) 		7.96e-09
(5.6e-06) 		0.000455
(0.191) 		0.0509
(1.00) 		0.0965
(1.00) 		6.8e-05
(0.0347) 		8.84e-08
(5.78e-05) 		0.00245
(0.806) 		1.25e-05
(0.00697) 		0.0302
(1.00) 		0.00262
(0.85)
10q gain 113 (11%) 894 0.0585
(1.00) 		0.0339
(1.00) 		3.91e-08
(2.64e-05) 		0.00866
(1.00) 		0.0479
(1.00) 		0.0475
(1.00) 		0.000777
(0.304) 		0.000207
(0.0947) 		0.000305
(0.134) 		0.000197
(0.0912) 		8.93e-05
(0.0442) 		0.0199
(1.00)
13q gain 89 (9%) 918 0.302
(1.00) 		0.259
(1.00) 		3.09e-05
(0.0163) 		0.0134
(1.00) 		0.0203
(1.00) 		0.0953
(1.00) 		0.000141
(0.0673) 		8.69e-05
(0.0432) 		0.00028
(0.124) 		0.000489
(0.202) 		0.095
(1.00) 		0.179
(1.00)
19p gain 171 (17%) 836 0.00076
(0.298) 		0.00119
(0.44) 		3.32e-10
(2.49e-07) 		0.0227
(1.00) 		0.0065
(1.00) 		0.0204
(1.00) 		0.000124
(0.0597) 		5.68e-06
(0.00324) 		2.98e-05
(0.0158) 		0.000468
(0.195) 		0.000823
(0.321) 		0.0771
(1.00)
19q gain 202 (20%) 805 0.00334
(1.00) 		0.00311
(0.986) 		6.9e-13
(5.62e-10) 		0.0228
(1.00) 		0.0125
(1.00) 		0.047
(1.00) 		0.000454
(0.191) 		8.08e-05
(0.0403) 		0.000136
(0.0648) 		9.84e-05
(0.0484) 		0.00238
(0.792) 		0.0502
(1.00)
2q loss 192 (19%) 815 0.133
(1.00) 		0.00166
(0.592) 		8.5e-14
(7.1e-11) 		1.78e-06
(0.00105) 		0.000444
(0.188) 		0.000711
(0.284) 		0.000334
(0.146) 		7.96e-07
(0.000483) 		0.00173
(0.613) 		0.00116
(0.427) 		0.00363
(1.00) 		0.00936
(1.00)
3q loss 94 (9%) 913 0.00194
(0.673) 		0.00558
(1.00) 		2.14e-06
(0.00126) 		0.000446
(0.188) 		0.189
(1.00) 		0.0668
(1.00) 		0.000509
(0.21) 		0.000528
(0.217) 		0.000528
(0.217) 		0.00112
(0.417) 		0.00296
(0.944) 		0.39
(1.00)
11q loss 350 (35%) 657 0.000217
(0.0991) 		0.107
(1.00) 		3.11e-30
(2.93e-27) 		1.13e-08
(7.87e-06) 		0.762
(1.00) 		1
(1.00) 		0.000557
(0.226) 		0.00396
(1.00) 		0.337
(1.00) 		4.47e-06
(0.00257) 		0.0774
(1.00) 		0.123
(1.00)
18q loss 303 (30%) 704 0.000199
(0.092) 		0.309
(1.00) 		1.05e-15
(9.04e-13) 		1.48e-08
(1.02e-05) 		0.0267
(1.00) 		0.244
(1.00) 		0.000263
(0.117) 		0.00923
(1.00) 		0.000823
(0.321) 		0.00074
(0.294) 		6.27e-06
(0.00356) 		0.0762
(1.00)
4p gain 73 (7%) 934 0.000105
(0.0513) 		0.00261
(0.85) 		4.75e-13
(3.89e-10) 		0.00055
(0.224) 		0.483
(1.00) 		0.202
(1.00) 		0.0127
(1.00) 		0.000717
(0.285) 		0.252
(1.00) 		0.00035
(0.151) 		0.682
(1.00) 		0.176
(1.00)
5q gain 196 (19%) 811 0.0137
(1.00) 		0.00902
(1.00) 		3.3e-25
(3.07e-22) 		0.000691
(0.277) 		0.000889
(0.344) 		0.000756
(0.298) 		9.87e-05
(0.0485) 		6.76e-07
(0.000411) 		0.000183
(0.0856) 		0.00244
(0.806) 		0.00203
(0.695) 		0.000907
(0.349)
12q gain 179 (18%) 828 0.00262
(0.85) 		0.000961
(0.366) 		2.78e-21
(2.54e-18) 		4.4e-09
(3.15e-06) 		0.223
(1.00) 		0.371
(1.00) 		2.43e-07
(0.000153) 		1.36e-08
(9.43e-06) 		0.0823
(1.00) 		0.019
(1.00) 		0.0837
(1.00) 		0.0581
(1.00)
14q gain 139 (14%) 868 0.00235
(0.787) 		0.0797
(1.00) 		1.64e-09
(1.2e-06) 		0.0118
(1.00) 		0.4
(1.00) 		0.194
(1.00) 		0.000346
(0.149) 		0.000179
(0.0841) 		0.000341
(0.148) 		0.649
(1.00) 		0.0177
(1.00) 		0.147
(1.00)
7q loss 113 (11%) 894 0.0448
(1.00) 		0.0113
(1.00) 		1.31e-05
(0.00722) 		0.189
(1.00) 		0.697
(1.00) 		0.797
(1.00) 		0.00315
(0.991) 		0.000155
(0.0732) 		0.000198
(0.0915) 		7.11e-05
(0.0359) 		0.0019
(0.662) 		0.00245
(0.806)
1q gain 655 (65%) 352 0.000292
(0.129) 		0.892
(1.00) 		4.04e-09
(2.9e-06) 		1.49e-07
(9.48e-05) 		0.727
(1.00) 		0.353
(1.00) 		0.966
(1.00) 		0.84
(1.00) 		0.51
(1.00) 		0.00105
(0.398) 		0.786
(1.00) 		0.564
(1.00)
11p gain 129 (13%) 878 0.71
(1.00) 		0.906
(1.00) 		3.38e-07
(0.000211) 		0.00581
(1.00) 		1
(1.00) 		0.495
(1.00) 		0.00852
(1.00) 		0.00782
(1.00) 		0.000652
(0.262) 		0.00122
(0.449) 		0.000537
(0.219) 		0.000425
(0.18)
6p loss 173 (17%) 834 0.0662
(1.00) 		0.00226
(0.76) 		6.69e-11
(5.18e-08) 		0.000475
(0.197) 		0.636
(1.00) 		0.0619
(1.00) 		0.00131
(0.479) 		0.000101
(0.0495) 		0.196
(1.00) 		0.00113
(0.421) 		0.0512
(1.00) 		0.12
(1.00)
10p loss 162 (16%) 845 0.274
(1.00) 		0.076
(1.00) 		1.28e-05
(0.00712) 		0.000502
(0.207) 		0.258
(1.00) 		0.42
(1.00) 		0.000256
(0.115) 		0.00198
(0.682) 		0.19
(1.00) 		0.00222
(0.751) 		0.144
(1.00) 		0.304
(1.00)
16p loss 156 (15%) 851 0.167
(1.00) 		0.165
(1.00) 		0.000206
(0.0946) 		0.0252
(1.00) 		0.0125
(1.00) 		0.044
(1.00) 		0.0085
(1.00) 		0.00866
(1.00) 		0.000177
(0.0833) 		0.0018
(0.633) 		0.000129
(0.0617) 		0.0193
(1.00)
18p loss 302 (30%) 705 0.000251
(0.112) 		0.402
(1.00) 		2.9e-13
(2.4e-10) 		3.78e-07
(0.000235) 		0.217
(1.00) 		0.777
(1.00) 		0.00348
(1.00) 		0.0235
(1.00) 		0.00311
(0.986) 		0.005
(1.00) 		0.000747
(0.295) 		0.233
(1.00)
22q loss 454 (45%) 553 0.0542
(1.00) 		0.00276
(0.889) 		3.17e-11
(2.49e-08) 		1.29e-05
(0.00715) 		0.0178
(1.00) 		0.00112
(0.417) 		3.65e-05
(0.0191) 		0.000634
(0.256) 		0.0523
(1.00) 		0.0886
(1.00) 		0.434
(1.00) 		0.103
(1.00)
4q gain 68 (7%) 939 2.77e-06
(0.00162) 		0.00182
(0.637) 		2.57e-12
(2.05e-09) 		0.00199
(0.686) 		0.104
(1.00) 		0.0199
(1.00) 		0.0178
(1.00) 		0.00283
(0.908) 		0.3
(1.00) 		0.00109
(0.409) 		0.66
(1.00) 		0.141
(1.00)
7p gain 290 (29%) 717 0.00397
(1.00) 		0.12
(1.00) 		3.18e-09
(2.3e-06) 		0.00809
(1.00) 		0.584
(1.00) 		0.17
(1.00) 		0.0026
(0.848) 		5.79e-05
(0.0297) 		0.125
(1.00) 		0.058
(1.00) 		0.208
(1.00) 		0.535
(1.00)
5p gain 291 (29%) 716 0.0131
(1.00) 		0.855
(1.00) 		7.46e-18
(6.65e-15) 		0.0632
(1.00) 		0.657
(1.00) 		0.16
(1.00) 		0.833
(1.00) 		0.0613
(1.00) 		0.392
(1.00) 		0.672
(1.00) 		0.0402
(1.00) 		0.31
(1.00)
8p gain 270 (27%) 737 0.212
(1.00) 		0.198
(1.00) 		6.11e-08
(4.05e-05) 		0.0043
(1.00) 		0.611
(1.00) 		0.243
(1.00) 		0.039
(1.00) 		0.00192
(0.667) 		0.14
(1.00) 		0.0425
(1.00) 		0.00466
(1.00) 		0.0709
(1.00)
9q gain 112 (11%) 895 0.166
(1.00) 		0.18
(1.00) 		7.99e-12
(6.35e-09) 		0.0997
(1.00) 		0.944
(1.00) 		0.182
(1.00) 		0.0147
(1.00) 		0.0196
(1.00) 		0.124
(1.00) 		0.19
(1.00) 		0.0204
(1.00) 		0.0676
(1.00)
17p gain 104 (10%) 903 0.059
(1.00) 		0.236
(1.00) 		0.000111
(0.054) 		0.00924
(1.00) 		0.671
(1.00) 		0.648
(1.00) 		0.0651
(1.00) 		0.105
(1.00) 		0.323
(1.00) 		0.0104
(1.00) 		0.631
(1.00) 		0.464
(1.00)
21q loss 166 (16%) 841 0.0329
(1.00) 		0.0528
(1.00) 		1.38e-12
(1.11e-09) 		0.000635
(0.256) 		0.772
(1.00) 		0.972
(1.00) 		0.0332
(1.00) 		0.00162
(0.579) 		0.00218
(0.74) 		0.0227
(1.00) 		0.0273
(1.00) 		0.0718
(1.00)
15q gain 85 (8%) 922 0.0863
(1.00) 		0.309
(1.00) 		0.00111
(0.415) 		0.0393
(1.00) 		0.444
(1.00) 		0.238
(1.00) 		0.00536
(1.00) 		0.000759
(0.298) 		0.37
(1.00) 		0.0115
(1.00) 		0.49
(1.00) 		0.454
(1.00)
16q gain 126 (13%) 881 0.571
(1.00) 		0.172
(1.00) 		0.00496
(1.00) 		0.00664
(1.00) 		0.356
(1.00) 		0.564
(1.00) 		0.0698
(1.00) 		0.0359
(1.00) 		0.00332
(1.00) 		0.000872
(0.339) 		0.015
(1.00) 		0.12
(1.00)
1q loss 51 (5%) 956 0.0205
(1.00) 		0.00214
(0.729) 		0.000692
(0.277) 		0.059
(1.00) 		0.262
(1.00) 		0.422
(1.00) 		0.0166
(1.00) 		0.0375
(1.00) 		0.0172
(1.00) 		0.0169
(1.00) 		0.769
(1.00) 		0.727
(1.00)
8q loss 86 (9%) 921 0.0486
(1.00) 		0.19
(1.00) 		0.00241
(0.796) 		0.191
(1.00) 		0.774
(1.00) 		0.401
(1.00) 		0.0072
(1.00) 		0.205
(1.00) 		0.398
(1.00) 		0.657
(1.00) 		0.297
(1.00) 		0.733
(1.00)
'1p gain' versus 'MRNA_CNMF'

P value = 3.72e-09 (Chi-square test), Q value = 2.7e-06

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
1P GAIN MUTATED 2 3 17 40 7 18 6 5
1P GAIN WILD-TYPE 19 33 102 56 102 54 14 35

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

'1p gain' versus 'MRNA_CHIERARCHICAL'

P value = 9.02e-10 (Fisher's exact test), Q value = 6.6e-07

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
1P GAIN MUTATED 15 50 33
1P GAIN WILD-TYPE 107 75 233

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

'1p gain' versus 'CN_CNMF'

P value = 4.68e-17 (Chi-square test), Q value = 4.1e-14

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
1P GAIN MUTATED 44 38 9 92 8
1P GAIN WILD-TYPE 327 220 88 144 37

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 2.32e-08 (Chi-square test), Q value = 1.6e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
1P GAIN MUTATED 44 15 16 23 5 29
1P GAIN WILD-TYPE 72 140 92 116 50 83

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

'1p gain' versus 'RPPA_CNMF'

P value = 1.83e-06 (Fisher's exact test), Q value = 0.0011

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
1P GAIN MUTATED 50 19 12
1P GAIN WILD-TYPE 97 114 105

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

'1p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1.41e-05 (Fisher's exact test), Q value = 0.0078

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
1P GAIN MUTATED 31 9 41
1P GAIN WILD-TYPE 130 101 85

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

'1p gain' versus 'MRNASEQ_CNMF'

P value = 2.31e-18 (Fisher's exact test), Q value = 2.1e-15

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
1P GAIN MUTATED 104 21 65
1P GAIN WILD-TYPE 169 165 477

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

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.26e-15 (Fisher's exact test), Q value = 1.1e-12

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
1P GAIN MUTATED 90 61 39
1P GAIN WILD-TYPE 143 378 290

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

'1p gain' versus 'MIRSEQ_CNMF'

P value = 4.23e-11 (Fisher's exact test), Q value = 3.3e-08

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
1P GAIN MUTATED 50 39 95
1P GAIN WILD-TYPE 348 248 197

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

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.1e-16 (Fisher's exact test), Q value = 9.6e-14

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
1P GAIN MUTATED 94 47 43
1P GAIN WILD-TYPE 158 252 383

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

'1p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.05e-09 (Fisher's exact test), Q value = 7.7e-07

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
1P GAIN MUTATED 34 24 68
1P GAIN WILD-TYPE 216 195 130

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

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.73e-09 (Fisher's exact test), Q value = 3.4e-06

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
1P GAIN MUTATED 54 19 53
1P GAIN WILD-TYPE 91 158 292

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

'1q gain' versus 'MRNA_CNMF'

P value = 0.000292 (Chi-square test), Q value = 0.13

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
1Q GAIN MUTATED 14 19 58 66 86 50 12 28
1Q GAIN WILD-TYPE 7 17 61 30 23 22 8 12

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

'1q gain' versus 'CN_CNMF'

P value = 4.04e-09 (Chi-square test), Q value = 2.9e-06

Table S14.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
1Q GAIN MUTATED 218 167 92 151 27
1Q GAIN WILD-TYPE 153 91 5 85 18

Figure S14.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 1.49e-07 (Chi-square test), Q value = 9.5e-05

Table S15.  Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
1Q GAIN MUTATED 76 125 81 73 30 60
1Q GAIN WILD-TYPE 40 30 27 66 25 52

Figure S15.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'MRNA_CNMF'

P value = 9.24e-15 (Chi-square test), Q value = 7.8e-12

Table S16.  Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
2P GAIN MUTATED 1 1 6 30 1 20 1 0
2P GAIN WILD-TYPE 20 35 113 66 108 52 19 40

Figure S16.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1.41e-14 (Fisher's exact test), Q value = 1.2e-11

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
2P GAIN MUTATED 1 40 19
2P GAIN WILD-TYPE 121 85 247

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

'2p gain' versus 'CN_CNMF'

P value = 9.97e-18 (Chi-square test), Q value = 8.9e-15

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
2P GAIN MUTATED 15 21 8 65 4
2P GAIN WILD-TYPE 356 237 89 171 41

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 2.72e-13 (Chi-square test), Q value = 2.3e-10

Table S19.  Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
2P GAIN MUTATED 36 2 8 13 3 11
2P GAIN WILD-TYPE 80 153 100 126 52 101

Figure S19.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'RPPA_CNMF'

P value = 1.55e-10 (Fisher's exact test), Q value = 1.2e-07

Table S20.  Gene #3: '2p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
2P GAIN MUTATED 39 2 9
2P GAIN WILD-TYPE 108 131 108

Figure S20.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'2p gain' versus 'RPPA_CHIERARCHICAL'

P value = 3.16e-10 (Fisher's exact test), Q value = 2.4e-07

Table S21.  Gene #3: '2p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
2P GAIN MUTATED 9 4 37
2P GAIN WILD-TYPE 152 106 89

Figure S21.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 2.75e-29 (Fisher's exact test), Q value = 2.6e-26

Table S22.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
2P GAIN MUTATED 83 1 28
2P GAIN WILD-TYPE 190 185 514

Figure S22.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.36e-27 (Fisher's exact test), Q value = 1.3e-24

Table S23.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
2P GAIN MUTATED 74 33 5
2P GAIN WILD-TYPE 159 406 324

Figure S23.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 7.91e-23 (Fisher's exact test), Q value = 7.3e-20

Table S24.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
2P GAIN MUTATED 22 7 79
2P GAIN WILD-TYPE 376 280 213

Figure S24.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-22 (Fisher's exact test), Q value = 9.3e-20

Table S25.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
2P GAIN MUTATED 72 24 12
2P GAIN WILD-TYPE 180 275 414

Figure S25.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.72e-22 (Fisher's exact test), Q value = 3.4e-19

Table S26.  Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
2P GAIN MUTATED 10 5 62
2P GAIN WILD-TYPE 240 214 136

Figure S26.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.08e-13 (Fisher's exact test), Q value = 2.5e-10

Table S27.  Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
2P GAIN MUTATED 45 9 23
2P GAIN WILD-TYPE 100 168 322

Figure S27.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'MRNA_CNMF'

P value = 2.56e-07 (Chi-square test), Q value = 0.00016

Table S28.  Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
2Q GAIN MUTATED 1 1 5 17 1 14 0 0
2Q GAIN WILD-TYPE 20 35 114 79 108 58 20 40

Figure S28.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1.49e-07 (Fisher's exact test), Q value = 9.5e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
2Q GAIN MUTATED 1 24 14
2Q GAIN WILD-TYPE 121 101 252

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

'2q gain' versus 'CN_CNMF'

P value = 1.63e-09 (Chi-square test), Q value = 1.2e-06

Table S30.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
2Q GAIN MUTATED 10 13 7 39 1
2Q GAIN WILD-TYPE 361 245 90 197 44

Figure S30.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 7.16e-08 (Chi-square test), Q value = 4.7e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
2Q GAIN MUTATED 21 2 7 5 1 4
2Q GAIN WILD-TYPE 95 153 101 134 54 108

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

'2q gain' versus 'RPPA_CNMF'

P value = 1.36e-06 (Fisher's exact test), Q value = 0.00081

Table S32.  Gene #4: '2q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
2Q GAIN MUTATED 25 2 4
2Q GAIN WILD-TYPE 122 131 113

Figure S32.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'2q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1.88e-05 (Fisher's exact test), Q value = 0.01

Table S33.  Gene #4: '2q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
2Q GAIN MUTATED 6 3 22
2Q GAIN WILD-TYPE 155 107 104

Figure S33.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 1.74e-14 (Fisher's exact test), Q value = 1.5e-11

Table S34.  Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
2Q GAIN MUTATED 48 1 20
2Q GAIN WILD-TYPE 225 185 522

Figure S34.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.97e-14 (Fisher's exact test), Q value = 4.2e-11

Table S35.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
2Q GAIN MUTATED 43 22 4
2Q GAIN WILD-TYPE 190 417 325

Figure S35.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CNMF'

P value = 1.33e-11 (Fisher's exact test), Q value = 1.1e-08

Table S36.  Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
2Q GAIN MUTATED 15 5 46
2Q GAIN WILD-TYPE 383 282 246

Figure S36.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.28e-10 (Fisher's exact test), Q value = 9.8e-08

Table S37.  Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
2Q GAIN MUTATED 41 15 10
2Q GAIN WILD-TYPE 211 284 416

Figure S37.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.16e-13 (Fisher's exact test), Q value = 4.2e-10

Table S38.  Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
2Q GAIN MUTATED 7 4 40
2Q GAIN WILD-TYPE 243 215 158

Figure S38.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.59e-07 (Fisher's exact test), Q value = 0.00022

Table S39.  Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
2Q GAIN MUTATED 28 7 16
2Q GAIN WILD-TYPE 117 170 329

Figure S39.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 1.02e-10 (Chi-square test), Q value = 7.9e-08

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
3P GAIN MUTATED 13 48 21 44 11
3P GAIN WILD-TYPE 358 210 76 192 34

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

'3p gain' versus 'METHLYATION_CNMF'

P value = 2.65e-05 (Chi-square test), Q value = 0.014

Table S41.  Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
3P GAIN MUTATED 28 9 13 18 3 7
3P GAIN WILD-TYPE 88 146 95 121 52 105

Figure S41.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 1.82e-05 (Fisher's exact test), Q value = 0.0099

Table S42.  Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
3P GAIN MUTATED 49 8 79
3P GAIN WILD-TYPE 224 178 463

Figure S42.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.84e-07 (Fisher's exact test), Q value = 0.00024

Table S43.  Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
3P GAIN MUTATED 45 72 19
3P GAIN WILD-TYPE 188 367 310

Figure S43.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CNMF'

P value = 0.000146 (Fisher's exact test), Q value = 0.07

Table S44.  Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
3P GAIN MUTATED 50 23 58
3P GAIN WILD-TYPE 348 264 234

Figure S44.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000168 (Fisher's exact test), Q value = 0.079

Table S45.  Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
3P GAIN MUTATED 51 42 38
3P GAIN WILD-TYPE 201 257 388

Figure S45.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MRNA_CHIERARCHICAL'

P value = 3.37e-06 (Fisher's exact test), Q value = 0.002

Table S46.  Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
3Q GAIN MUTATED 9 39 65
3Q GAIN WILD-TYPE 113 86 201

Figure S46.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 1.32e-17 (Chi-square test), Q value = 1.2e-14

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
3Q GAIN MUTATED 21 63 25 82 11
3Q GAIN WILD-TYPE 350 195 72 154 34

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

'3q gain' versus 'METHLYATION_CNMF'

P value = 1.03e-10 (Chi-square test), Q value = 7.9e-08

Table S48.  Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
3Q GAIN MUTATED 45 10 20 26 7 11
3Q GAIN WILD-TYPE 71 145 88 113 48 101

Figure S48.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 8.53e-12 (Fisher's exact test), Q value = 6.8e-09

Table S49.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
3Q GAIN MUTATED 87 11 103
3Q GAIN WILD-TYPE 186 175 439

Figure S49.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.45e-12 (Fisher's exact test), Q value = 1.2e-09

Table S50.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
3Q GAIN MUTATED 78 94 29
3Q GAIN WILD-TYPE 155 345 300

Figure S50.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 8.42e-13 (Fisher's exact test), Q value = 6.9e-10

Table S51.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
3Q GAIN MUTATED 66 29 100
3Q GAIN WILD-TYPE 332 258 192

Figure S51.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.7e-11 (Fisher's exact test), Q value = 2.9e-08

Table S52.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
3Q GAIN MUTATED 86 59 50
3Q GAIN WILD-TYPE 166 240 376

Figure S52.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-10 (Fisher's exact test), Q value = 1.5e-07

Table S53.  Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
3Q GAIN MUTATED 34 24 70
3Q GAIN WILD-TYPE 216 195 128

Figure S53.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.31e-11 (Fisher's exact test), Q value = 7.2e-08

Table S54.  Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
3Q GAIN MUTATED 58 21 49
3Q GAIN WILD-TYPE 87 156 296

Figure S54.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'MRNA_CNMF'

P value = 0.000105 (Chi-square test), Q value = 0.051

Table S55.  Gene #7: '4p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
4P GAIN MUTATED 1 1 21 3 3 4 0 2
4P GAIN WILD-TYPE 20 35 98 93 106 68 20 38

Figure S55.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p gain' versus 'CN_CNMF'

P value = 4.75e-13 (Chi-square test), Q value = 3.9e-10

Table S56.  Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
4P GAIN MUTATED 6 46 3 14 4
4P GAIN WILD-TYPE 365 212 94 222 41

Figure S56.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.00055 (Chi-square test), Q value = 0.22

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
4P GAIN MUTATED 7 6 9 22 3 3
4P GAIN WILD-TYPE 109 149 99 117 52 109

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

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.15

Table S58.  Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
4P GAIN MUTATED 20 34 16
4P GAIN WILD-TYPE 232 265 410

Figure S58.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'MRNA_CNMF'

P value = 2.77e-06 (Chi-square test), Q value = 0.0016

Table S59.  Gene #8: '4q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
4Q GAIN MUTATED 1 1 22 2 3 2 0 2
4Q GAIN WILD-TYPE 20 35 97 94 106 70 20 38

Figure S59.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q gain' versus 'CN_CNMF'

P value = 2.57e-12 (Chi-square test), Q value = 2.1e-09

Table S60.  Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
4Q GAIN MUTATED 6 42 2 12 6
4Q GAIN WILD-TYPE 365 216 95 224 39

Figure S60.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 7.46e-18 (Chi-square test), Q value = 6.6e-15

Table S61.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
5P GAIN MUTATED 52 107 51 67 14
5P GAIN WILD-TYPE 319 151 46 169 31

Figure S61.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 3.3e-25 (Chi-square test), Q value = 3.1e-22

Table S62.  Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
5Q GAIN MUTATED 42 81 48 15 10
5Q GAIN WILD-TYPE 329 177 49 221 35

Figure S62.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 9.87e-05 (Fisher's exact test), Q value = 0.048

Table S63.  Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
5Q GAIN MUTATED 30 40 124
5Q GAIN WILD-TYPE 243 146 418

Figure S63.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.76e-07 (Fisher's exact test), Q value = 0.00041

Table S64.  Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
5Q GAIN MUTATED 20 109 65
5Q GAIN WILD-TYPE 213 330 264

Figure S64.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CNMF'

P value = 0.000183 (Fisher's exact test), Q value = 0.086

Table S65.  Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
5Q GAIN MUTATED 93 62 34
5Q GAIN WILD-TYPE 305 225 258

Figure S65.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p gain' versus 'MRNA_CNMF'

P value = 5.32e-07 (Chi-square test), Q value = 0.00033

Table S66.  Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S66.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p gain' versus 'MRNA_CHIERARCHICAL'

P value = 4.84e-06 (Fisher's exact test), Q value = 0.0028

Table S67.  Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
6P GAIN MUTATED 10 41 48
6P GAIN WILD-TYPE 112 84 218

Figure S67.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1.21e-33 (Chi-square test), Q value = 1.1e-30

Table S68.  Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
6P GAIN MUTATED 15 41 23 107 11
6P GAIN WILD-TYPE 356 217 74 129 34

Figure S68.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 1.25e-17 (Chi-square test), Q value = 1.1e-14

Table S69.  Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
6P GAIN MUTATED 54 10 25 29 2 11
6P GAIN WILD-TYPE 62 145 83 110 53 101

Figure S69.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p gain' versus 'RPPA_CNMF'

P value = 5.5e-05 (Fisher's exact test), Q value = 0.028

Table S70.  Gene #11: '6p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
6P GAIN MUTATED 46 19 13
6P GAIN WILD-TYPE 101 114 104

Figure S70.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 1.95e-18 (Fisher's exact test), Q value = 1.8e-15

Table S71.  Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
6P GAIN MUTATED 100 9 86
6P GAIN WILD-TYPE 173 177 456

Figure S71.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.57e-19 (Fisher's exact test), Q value = 1.4e-16

Table S72.  Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
6P GAIN MUTATED 90 82 23
6P GAIN WILD-TYPE 143 357 306

Figure S72.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 4.34e-18 (Fisher's exact test), Q value = 3.9e-15

Table S73.  Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
6P GAIN MUTATED 59 22 105
6P GAIN WILD-TYPE 339 265 187

Figure S73.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.68e-21 (Fisher's exact test), Q value = 6.1e-18

Table S74.  Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
6P GAIN MUTATED 98 53 35
6P GAIN WILD-TYPE 154 246 391

Figure S74.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.04e-15 (Fisher's exact test), Q value = 2.6e-12

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
6P GAIN MUTATED 30 19 76
6P GAIN WILD-TYPE 220 200 122

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

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-10 (Fisher's exact test), Q value = 7.7e-08

Table S76.  Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
6P GAIN MUTATED 57 20 48
6P GAIN WILD-TYPE 88 157 297

Figure S76.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'MRNA_CNMF'

P value = 1.58e-07 (Chi-square test), Q value = 1e-04

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

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

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

'6q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1.45e-05 (Fisher's exact test), Q value = 0.008

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
6Q GAIN MUTATED 7 33 32
6Q GAIN WILD-TYPE 115 92 234

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

'6q gain' versus 'CN_CNMF'

P value = 2.21e-32 (Chi-square test), Q value = 2.1e-29

Table S79.  Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
6Q GAIN MUTATED 9 22 16 88 6
6Q GAIN WILD-TYPE 362 236 81 148 39

Figure S79.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 2.14e-11 (Chi-square test), Q value = 1.7e-08

Table S80.  Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
6Q GAIN MUTATED 38 5 16 17 2 11
6Q GAIN WILD-TYPE 78 150 92 122 53 101

Figure S80.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q gain' versus 'RPPA_CNMF'

P value = 3.39e-06 (Fisher's exact test), Q value = 0.002

Table S81.  Gene #12: '6q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
6Q GAIN MUTATED 39 10 9
6Q GAIN WILD-TYPE 108 123 108

Figure S81.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 5.32e-15 (Fisher's exact test), Q value = 4.6e-12

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
6Q GAIN MUTATED 77 7 55
6Q GAIN WILD-TYPE 196 179 487

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

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.01e-13 (Fisher's exact test), Q value = 8.4e-11

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
6Q GAIN MUTATED 67 54 18
6Q GAIN WILD-TYPE 166 385 311

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

'6q gain' versus 'MIRSEQ_CNMF'

P value = 6.42e-17 (Fisher's exact test), Q value = 5.6e-14

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
6Q GAIN MUTATED 36 15 84
6Q GAIN WILD-TYPE 362 272 208

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

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.6e-16 (Fisher's exact test), Q value = 2.3e-13

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
6Q GAIN MUTATED 75 35 25
6Q GAIN WILD-TYPE 177 264 401

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

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.99e-14 (Fisher's exact test), Q value = 7.5e-11

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
6Q GAIN MUTATED 23 12 62
6Q GAIN WILD-TYPE 227 207 136

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

'6q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.92e-10 (Fisher's exact test), Q value = 1.5e-07

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
6Q GAIN MUTATED 48 14 35
6Q GAIN WILD-TYPE 97 163 310

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

'7p gain' versus 'CN_CNMF'

P value = 3.18e-09 (Chi-square test), Q value = 2.3e-06

Table S88.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
7P GAIN MUTATED 70 74 49 84 13
7P GAIN WILD-TYPE 301 184 48 152 32

Figure S88.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.79e-05 (Fisher's exact test), Q value = 0.03

Table S89.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
7P GAIN MUTATED 87 132 68
7P GAIN WILD-TYPE 146 307 261

Figure S89.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 7.96e-09 (Chi-square test), Q value = 5.6e-06

Table S90.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
7Q GAIN MUTATED 59 58 43 76 11
7Q GAIN WILD-TYPE 312 200 54 160 34

Figure S90.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.000455 (Chi-square test), Q value = 0.19

Table S91.  Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
7Q GAIN MUTATED 46 30 27 33 9 19
7Q GAIN WILD-TYPE 70 125 81 106 46 93

Figure S91.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 6.8e-05 (Fisher's exact test), Q value = 0.035

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
7Q GAIN MUTATED 93 34 117
7Q GAIN WILD-TYPE 180 152 425

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

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.84e-08 (Fisher's exact test), Q value = 5.8e-05

Table S93.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
7Q GAIN MUTATED 86 106 52
7Q GAIN WILD-TYPE 147 333 277

Figure S93.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.25e-05 (Fisher's exact test), Q value = 0.007

Table S94.  Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
7Q GAIN MUTATED 86 50 99
7Q GAIN WILD-TYPE 166 249 327

Figure S94.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 6.11e-08 (Chi-square test), Q value = 4e-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 371 258 97 236 45
8P GAIN MUTATED 71 68 39 67 25
8P GAIN WILD-TYPE 300 190 58 169 20

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

'8q gain' versus 'MRNA_CNMF'

P value = 6.86e-05 (Chi-square test), Q value = 0.035

Table S96.  Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
8Q GAIN MUTATED 14 13 73 62 44 35 15 14
8Q GAIN WILD-TYPE 7 23 46 34 65 37 5 26

Figure S96.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 2.64e-22 (Chi-square test), Q value = 2.4e-19

Table S97.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
8Q GAIN MUTATED 112 153 42 150 38
8Q GAIN WILD-TYPE 259 105 55 86 7

Figure S97.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 3.88e-13 (Chi-square test), Q value = 3.2e-10

Table S98.  Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
8Q GAIN MUTATED 80 38 52 83 19 48
8Q GAIN WILD-TYPE 36 117 56 56 36 64

Figure S98.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 5.01e-07 (Fisher's exact test), Q value = 0.00031

Table S99.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
8Q GAIN MUTATED 162 63 266
8Q GAIN WILD-TYPE 111 123 276

Figure S99.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.87e-09 (Fisher's exact test), Q value = 2.1e-06

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
8Q GAIN MUTATED 143 230 118
8Q GAIN WILD-TYPE 90 209 211

Figure S100.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 4.48e-11 (Fisher's exact test), Q value = 3.5e-08

Table S101.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
8Q GAIN MUTATED 196 99 184
8Q GAIN WILD-TYPE 202 188 108

Figure S101.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.35e-10 (Fisher's exact test), Q value = 1e-07

Table S102.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
8Q GAIN MUTATED 163 153 163
8Q GAIN WILD-TYPE 89 146 263

Figure S102.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.33e-11 (Fisher's exact test), Q value = 2.6e-08

Table S103.  Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
8Q GAIN MUTATED 115 70 130
8Q GAIN WILD-TYPE 135 149 68

Figure S103.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-07 (Fisher's exact test), Q value = 6.5e-05

Table S104.  Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
8Q GAIN MUTATED 96 62 157
8Q GAIN WILD-TYPE 49 115 188

Figure S104.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'MRNA_CNMF'

P value = 8.81e-10 (Chi-square test), Q value = 6.5e-07

Table S105.  Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
9P GAIN MUTATED 1 2 3 33 14 9 0 5
9P GAIN WILD-TYPE 20 34 116 63 95 63 20 35

Figure S105.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1.27e-07 (Fisher's exact test), Q value = 8.2e-05

Table S106.  Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
9P GAIN MUTATED 11 36 20
9P GAIN WILD-TYPE 111 89 246

Figure S106.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 1.03e-17 (Chi-square test), Q value = 9.2e-15

Table S107.  Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
9P GAIN MUTATED 22 13 30 57 8
9P GAIN WILD-TYPE 349 245 67 179 37

Figure S107.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 4.54e-06 (Chi-square test), Q value = 0.0026

Table S108.  Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
9P GAIN MUTATED 32 17 10 12 2 11
9P GAIN WILD-TYPE 84 138 98 127 53 101

Figure S108.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p gain' versus 'RPPA_CHIERARCHICAL'

P value = 3.85e-06 (Fisher's exact test), Q value = 0.0022

Table S109.  Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
9P GAIN MUTATED 10 10 33
9P GAIN WILD-TYPE 151 100 93

Figure S109.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 2.26e-08 (Fisher's exact test), Q value = 1.5e-05

Table S110.  Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
9P GAIN MUTATED 65 16 49
9P GAIN WILD-TYPE 208 170 493

Figure S110.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.2e-09 (Fisher's exact test), Q value = 2.3e-06

Table S111.  Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
9P GAIN MUTATED 60 43 27
9P GAIN WILD-TYPE 173 396 302

Figure S111.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_CNMF'

P value = 4.46e-06 (Fisher's exact test), Q value = 0.0026

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
9P GAIN MUTATED 37 26 62
9P GAIN WILD-TYPE 361 261 230

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

'9p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.31e-08 (Fisher's exact test), Q value = 2.2e-05

Table S113.  Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
9P GAIN MUTATED 59 20 46
9P GAIN WILD-TYPE 193 279 380

Figure S113.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000536 (Fisher's exact test), Q value = 0.22

Table S114.  Gene #17: '9p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
9P GAIN MUTATED 31 17 41
9P GAIN WILD-TYPE 219 202 157

Figure S114.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000248 (Fisher's exact test), Q value = 0.11

Table S115.  Gene #17: '9p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
9P GAIN MUTATED 34 14 41
9P GAIN WILD-TYPE 111 163 304

Figure S115.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 7.99e-12 (Chi-square test), Q value = 6.4e-09

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
9Q GAIN MUTATED 23 17 30 37 5
9Q GAIN WILD-TYPE 348 241 67 199 40

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

'10p gain' versus 'MRNA_CNMF'

P value = 1.8e-09 (Chi-square test), Q value = 1.3e-06

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
10P GAIN MUTATED 2 4 17 41 11 26 6 4
10P GAIN WILD-TYPE 19 32 102 55 98 46 14 36

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

'10p gain' versus 'MRNA_CHIERARCHICAL'

P value = 5.78e-08 (Fisher's exact test), Q value = 3.8e-05

Table S118.  Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
10P GAIN MUTATED 16 51 44
10P GAIN WILD-TYPE 106 74 222

Figure S118.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 9.42e-27 (Chi-square test), Q value = 8.8e-24

Table S119.  Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
10P GAIN MUTATED 22 47 18 102 8
10P GAIN WILD-TYPE 349 211 79 134 37

Figure S119.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 3.63e-15 (Chi-square test), Q value = 3.1e-12

Table S120.  Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
10P GAIN MUTATED 52 9 19 25 3 18
10P GAIN WILD-TYPE 64 146 89 114 52 94

Figure S120.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p gain' versus 'RPPA_CNMF'

P value = 2.4e-05 (Fisher's exact test), Q value = 0.013

Table S121.  Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
10P GAIN MUTATED 51 17 20
10P GAIN WILD-TYPE 96 116 97

Figure S121.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p gain' versus 'RPPA_CHIERARCHICAL'

P value = 2.46e-05 (Fisher's exact test), Q value = 0.013

Table S122.  Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
10P GAIN MUTATED 23 19 46
10P GAIN WILD-TYPE 138 91 80

Figure S122.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 9.79e-17 (Fisher's exact test), Q value = 8.6e-14

Table S123.  Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
10P GAIN MUTATED 102 15 80
10P GAIN WILD-TYPE 171 171 462

Figure S123.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.79e-17 (Fisher's exact test), Q value = 7.7e-14

Table S124.  Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
10P GAIN MUTATED 92 72 33
10P GAIN WILD-TYPE 141 367 296

Figure S124.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CNMF'

P value = 2.37e-15 (Fisher's exact test), Q value = 2e-12

Table S125.  Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
10P GAIN MUTATED 59 28 104
10P GAIN WILD-TYPE 339 259 188

Figure S125.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.01e-17 (Fisher's exact test), Q value = 1.8e-14

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
10P GAIN MUTATED 98 47 46
10P GAIN WILD-TYPE 154 252 380

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

'10p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.25e-12 (Fisher's exact test), Q value = 1e-09

Table S127.  Gene #19: '10p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
10P GAIN MUTATED 33 20 72
10P GAIN WILD-TYPE 217 199 126

Figure S127.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.09e-10 (Fisher's exact test), Q value = 1.6e-07

Table S128.  Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
10P GAIN MUTATED 56 18 51
10P GAIN WILD-TYPE 89 159 294

Figure S128.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 3.91e-08 (Chi-square test), Q value = 2.6e-05

Table S129.  Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
10Q GAIN MUTATED 16 28 16 48 5
10Q GAIN WILD-TYPE 355 230 81 188 40

Figure S129.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000207 (Fisher's exact test), Q value = 0.095

Table S130.  Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
10Q GAIN MUTATED 39 54 20
10Q GAIN WILD-TYPE 194 385 309

Figure S130.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_CNMF'

P value = 0.000305 (Fisher's exact test), Q value = 0.13

Table S131.  Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
10Q GAIN MUTATED 41 19 50
10Q GAIN WILD-TYPE 357 268 242

Figure S131.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000197 (Fisher's exact test), Q value = 0.091

Table S132.  Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
10Q GAIN MUTATED 47 27 36
10Q GAIN WILD-TYPE 205 272 390

Figure S132.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.93e-05 (Fisher's exact test), Q value = 0.044

Table S133.  Gene #20: '10q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
10Q GAIN MUTATED 24 12 37
10Q GAIN WILD-TYPE 226 207 161

Figure S133.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 3.38e-07 (Chi-square test), Q value = 0.00021

Table S134.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
11P GAIN MUTATED 18 43 14 47 7
11P GAIN WILD-TYPE 353 215 83 189 38

Figure S134.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000537 (Fisher's exact test), Q value = 0.22

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
11P GAIN MUTATED 40 13 32
11P GAIN WILD-TYPE 210 206 166

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

'11p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000425 (Fisher's exact test), Q value = 0.18

Table S136.  Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
11P GAIN MUTATED 26 9 50
11P GAIN WILD-TYPE 119 168 295

Figure S136.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 4.64e-09 (Chi-square test), Q value = 3.3e-06

Table S137.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
11Q GAIN MUTATED 11 19 10 43 7
11Q GAIN WILD-TYPE 360 239 87 193 38

Figure S137.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.071

Table S138.  Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
11Q GAIN MUTATED 42 10 38
11Q GAIN WILD-TYPE 231 176 504

Figure S138.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000412 (Fisher's exact test), Q value = 0.18

Table S139.  Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
11Q GAIN MUTATED 35 38 17
11Q GAIN WILD-TYPE 198 401 312

Figure S139.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CNMF'

P value = 0.000105 (Fisher's exact test), Q value = 0.051

Table S140.  Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
11Q GAIN MUTATED 29 14 43
11Q GAIN WILD-TYPE 369 273 249

Figure S140.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.13e-05 (Fisher's exact test), Q value = 0.036

Table S141.  Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
11Q GAIN MUTATED 40 20 26
11Q GAIN WILD-TYPE 212 279 400

Figure S141.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000423 (Fisher's exact test), Q value = 0.18

Table S142.  Gene #22: '11q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
11Q GAIN MUTATED 21 9 30
11Q GAIN WILD-TYPE 229 210 168

Figure S142.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.82e-05 (Fisher's exact test), Q value = 0.02

Table S143.  Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
11Q GAIN MUTATED 25 5 30
11Q GAIN WILD-TYPE 120 172 315

Figure S143.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.000407 (Fisher's exact test), Q value = 0.17

Table S144.  Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
12P GAIN MUTATED 13 38 63
12P GAIN WILD-TYPE 109 87 203

Figure S144.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 5.32e-21 (Chi-square test), Q value = 4.8e-18

Table S145.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
12P GAIN MUTATED 17 82 28 78 11
12P GAIN WILD-TYPE 354 176 69 158 34

Figure S145.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 2.83e-09 (Chi-square test), Q value = 2.1e-06

Table S146.  Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
12P GAIN MUTATED 37 15 22 49 6 12
12P GAIN WILD-TYPE 79 140 86 90 49 100

Figure S146.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1.06e-07 (Fisher's exact test), Q value = 6.9e-05

Table S147.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
12P GAIN MUTATED 78 15 123
12P GAIN WILD-TYPE 195 171 419

Figure S147.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.78e-09 (Fisher's exact test), Q value = 4.8e-06

Table S148.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
12P GAIN MUTATED 70 110 36
12P GAIN WILD-TYPE 163 329 293

Figure S148.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 2.41e-05 (Fisher's exact test), Q value = 0.013

Table S149.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
12P GAIN MUTATED 75 43 88
12P GAIN WILD-TYPE 323 244 204

Figure S149.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.29e-06 (Fisher's exact test), Q value = 0.0041

Table S150.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
12P GAIN MUTATED 78 64 64
12P GAIN WILD-TYPE 174 235 362

Figure S150.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 2.78e-21 (Chi-square test), Q value = 2.5e-18

Table S151.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
12Q GAIN MUTATED 16 88 28 37 10
12Q GAIN WILD-TYPE 355 170 69 199 35

Figure S151.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 4.4e-09 (Chi-square test), Q value = 3.1e-06

Table S152.  Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
12Q GAIN MUTATED 15 19 21 49 6 7
12Q GAIN WILD-TYPE 101 136 87 90 49 105

Figure S152.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 2.43e-07 (Fisher's exact test), Q value = 0.00015

Table S153.  Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
12Q GAIN MUTATED 39 13 126
12Q GAIN WILD-TYPE 234 173 416

Figure S153.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.36e-08 (Fisher's exact test), Q value = 9.4e-06

Table S154.  Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
12Q GAIN MUTATED 30 114 34
12Q GAIN WILD-TYPE 203 325 295

Figure S154.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 3.09e-05 (Chi-square test), Q value = 0.016

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
13Q GAIN MUTATED 14 26 8 37 4
13Q GAIN WILD-TYPE 357 232 89 199 41

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

'13q gain' versus 'MRNASEQ_CNMF'

P value = 0.000141 (Fisher's exact test), Q value = 0.067

Table S156.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
13Q GAIN MUTATED 37 5 47
13Q GAIN WILD-TYPE 236 181 495

Figure S156.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.69e-05 (Fisher's exact test), Q value = 0.043

Table S157.  Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
13Q GAIN MUTATED 32 44 13
13Q GAIN WILD-TYPE 201 395 316

Figure S157.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.12

Table S158.  Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
13Q GAIN MUTATED 25 17 42
13Q GAIN WILD-TYPE 373 270 250

Figure S158.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000489 (Fisher's exact test), Q value = 0.2

Table S159.  Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
13Q GAIN MUTATED 35 27 22
13Q GAIN WILD-TYPE 217 272 404

Figure S159.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 1.64e-09 (Chi-square test), Q value = 1.2e-06

Table S160.  Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
14Q GAIN MUTATED 25 61 22 23 8
14Q GAIN WILD-TYPE 346 197 75 213 37

Figure S160.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.000346 (Fisher's exact test), Q value = 0.15

Table S161.  Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
14Q GAIN MUTATED 30 13 95
14Q GAIN WILD-TYPE 243 173 447

Figure S161.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000179 (Fisher's exact test), Q value = 0.084

Table S162.  Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
14Q GAIN MUTATED 25 83 30
14Q GAIN WILD-TYPE 208 356 299

Figure S162.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 0.000341 (Fisher's exact test), Q value = 0.15

Table S163.  Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
14Q GAIN MUTATED 76 26 33
14Q GAIN WILD-TYPE 322 261 259

Figure S163.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p gain' versus 'MRNA_CNMF'

P value = 0.000344 (Chi-square test), Q value = 0.15

Table S164.  Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
16P GAIN MUTATED 11 14 54 33 72 34 12 14
16P GAIN WILD-TYPE 10 22 65 63 37 38 8 26

Figure S164.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.000409 (Fisher's exact test), Q value = 0.17

Table S165.  Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
16P GAIN MUTATED 54 43 147
16P GAIN WILD-TYPE 68 82 119

Figure S165.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 7.97e-10 (Chi-square test), Q value = 5.9e-07

Table S166.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
16P GAIN MUTATED 144 128 71 83 21
16P GAIN WILD-TYPE 227 130 26 153 24

Figure S166.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 1.6e-05 (Chi-square test), Q value = 0.0088

Table S167.  Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
16P GAIN MUTATED 39 83 55 59 14 32
16P GAIN WILD-TYPE 77 72 53 80 41 80

Figure S167.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 2.18e-07 (Fisher's exact test), Q value = 0.00014

Table S168.  Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
16P GAIN MUTATED 86 79 280
16P GAIN WILD-TYPE 187 107 262

Figure S168.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.18e-08 (Fisher's exact test), Q value = 8.2e-06

Table S169.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
16P GAIN MUTATED 67 232 146
16P GAIN WILD-TYPE 166 207 183

Figure S169.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 6.95e-06 (Fisher's exact test), Q value = 0.0039

Table S170.  Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
16P GAIN MUTATED 204 131 96
16P GAIN WILD-TYPE 194 156 196

Figure S170.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.75e-05 (Fisher's exact test), Q value = 0.0096

Table S171.  Gene #28: '16p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
16P GAIN MUTATED 124 104 58
16P GAIN WILD-TYPE 126 115 140

Figure S171.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000258 (Fisher's exact test), Q value = 0.12

Table S172.  Gene #28: '16p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
16P GAIN MUTATED 41 83 162
16P GAIN WILD-TYPE 104 94 183

Figure S172.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 0.000111 (Chi-square test), Q value = 0.054

Table S173.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
17P GAIN MUTATED 21 44 11 21 7
17P GAIN WILD-TYPE 350 214 86 215 38

Figure S173.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'MRNA_CNMF'

P value = 8.87e-09 (Chi-square test), Q value = 6.2e-06

Table S174.  Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
17Q GAIN MUTATED 3 8 47 8 9 11 5 5
17Q GAIN WILD-TYPE 18 28 72 88 100 61 15 35

Figure S174.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q gain' versus 'MRNA_CHIERARCHICAL'

P value = 5.8e-05 (Fisher's exact test), Q value = 0.03

Table S175.  Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
17Q GAIN MUTATED 15 12 69
17Q GAIN WILD-TYPE 107 113 197

Figure S175.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 5.9e-22 (Chi-square test), Q value = 5.4e-19

Table S176.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
17Q GAIN MUTATED 36 107 17 33 14
17Q GAIN WILD-TYPE 335 151 80 203 31

Figure S176.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 2.03e-07 (Chi-square test), Q value = 0.00013

Table S177.  Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
17Q GAIN MUTATED 13 26 29 54 8 18
17Q GAIN WILD-TYPE 103 129 79 85 47 94

Figure S177.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 8.59e-07 (Fisher's exact test), Q value = 0.00052

Table S178.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
17Q GAIN MUTATED 37 24 145
17Q GAIN WILD-TYPE 236 162 397

Figure S178.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.21e-08 (Fisher's exact test), Q value = 8.4e-06

Table S179.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
17Q GAIN MUTATED 27 128 51
17Q GAIN WILD-TYPE 206 311 278

Figure S179.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.74e-06 (Fisher's exact test), Q value = 0.0016

Table S180.  Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
17Q GAIN MUTATED 39 91 69
17Q GAIN WILD-TYPE 213 208 357

Figure S180.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MRNA_CNMF'

P value = 1.1e-06 (Chi-square test), Q value = 0.00066

Table S181.  Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
18P GAIN MUTATED 1 1 19 35 16 10 4 1
18P GAIN WILD-TYPE 20 35 100 61 93 62 16 39

Figure S181.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p gain' versus 'MRNA_CHIERARCHICAL'

P value = 6.37e-08 (Fisher's exact test), Q value = 4.2e-05

Table S182.  Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
18P GAIN MUTATED 7 41 39
18P GAIN WILD-TYPE 115 84 227

Figure S182.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 8.25e-15 (Chi-square test), Q value = 7e-12

Table S183.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
18P GAIN MUTATED 20 40 18 73 10
18P GAIN WILD-TYPE 351 218 79 163 35

Figure S183.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 1.08e-12 (Chi-square test), Q value = 8.8e-10

Table S184.  Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
18P GAIN MUTATED 43 13 11 16 1 12
18P GAIN WILD-TYPE 73 142 97 123 54 100

Figure S184.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'RPPA_CHIERARCHICAL'

P value = 4.82e-05 (Fisher's exact test), Q value = 0.025

Table S185.  Gene #32: '18p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
18P GAIN MUTATED 22 10 38
18P GAIN WILD-TYPE 139 100 88

Figure S185.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 8.53e-15 (Fisher's exact test), Q value = 7.2e-12

Table S186.  Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
18P GAIN MUTATED 79 5 76
18P GAIN WILD-TYPE 194 181 466

Figure S186.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.2e-20 (Fisher's exact test), Q value = 7.4e-17

Table S187.  Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
18P GAIN MUTATED 78 68 14
18P GAIN WILD-TYPE 155 371 315

Figure S187.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 2.16e-11 (Fisher's exact test), Q value = 1.7e-08

Table S188.  Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
18P GAIN MUTATED 44 24 82
18P GAIN WILD-TYPE 354 263 210

Figure S188.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.17e-14 (Fisher's exact test), Q value = 6e-11

Table S189.  Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
18P GAIN MUTATED 79 33 38
18P GAIN WILD-TYPE 173 266 388

Figure S189.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.2e-08 (Fisher's exact test), Q value = 8.3e-06

Table S190.  Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
18P GAIN MUTATED 30 17 57
18P GAIN WILD-TYPE 220 202 141

Figure S190.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.29e-10 (Fisher's exact test), Q value = 5.4e-07

Table S191.  Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
18P GAIN MUTATED 48 12 44
18P GAIN WILD-TYPE 97 165 301

Figure S191.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'MRNA_CNMF'

P value = 7.26e-05 (Chi-square test), Q value = 0.036

Table S192.  Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
18Q GAIN MUTATED 2 1 21 29 17 5 4 1
18Q GAIN WILD-TYPE 19 35 98 67 92 67 16 39

Figure S192.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.000119 (Fisher's exact test), Q value = 0.057

Table S193.  Gene #33: '18q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
18Q GAIN MUTATED 7 31 42
18Q GAIN WILD-TYPE 115 94 224

Figure S193.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 1.39e-12 (Chi-square test), Q value = 1.1e-09

Table S194.  Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
18Q GAIN MUTATED 15 36 19 60 10
18Q GAIN WILD-TYPE 356 222 78 176 35

Figure S194.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 7.3e-05 (Chi-square test), Q value = 0.037

Table S195.  Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
18Q GAIN MUTATED 29 13 11 17 2 9
18Q GAIN WILD-TYPE 87 142 97 122 53 103

Figure S195.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 6.25e-09 (Fisher's exact test), Q value = 4.4e-06

Table S196.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
18Q GAIN MUTATED 58 5 76
18Q GAIN WILD-TYPE 215 181 466

Figure S196.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.18e-10 (Fisher's exact test), Q value = 3.9e-07

Table S197.  Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
18Q GAIN MUTATED 55 67 17
18Q GAIN WILD-TYPE 178 372 312

Figure S197.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 8.9e-07 (Fisher's exact test), Q value = 0.00054

Table S198.  Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
18Q GAIN MUTATED 45 21 64
18Q GAIN WILD-TYPE 353 266 228

Figure S198.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.77e-05 (Fisher's exact test), Q value = 0.0097

Table S199.  Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
18Q GAIN MUTATED 55 37 38
18Q GAIN WILD-TYPE 197 262 388

Figure S199.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000462 (Fisher's exact test), Q value = 0.19

Table S200.  Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
18Q GAIN MUTATED 26 17 40
18Q GAIN WILD-TYPE 224 202 158

Figure S200.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000233 (Fisher's exact test), Q value = 0.11

Table S201.  Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
18Q GAIN MUTATED 30 10 43
18Q GAIN WILD-TYPE 115 167 302

Figure S201.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 3.32e-10 (Chi-square test), Q value = 2.5e-07

Table S202.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
19P GAIN MUTATED 31 39 27 67 7
19P GAIN WILD-TYPE 340 219 70 169 38

Figure S202.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.000124 (Fisher's exact test), Q value = 0.06

Table S203.  Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
19P GAIN MUTATED 69 23 77
19P GAIN WILD-TYPE 204 163 465

Figure S203.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.68e-06 (Fisher's exact test), Q value = 0.0032

Table S204.  Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
19P GAIN MUTATED 65 61 43
19P GAIN WILD-TYPE 168 378 286

Figure S204.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 2.98e-05 (Fisher's exact test), Q value = 0.016

Table S205.  Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
19P GAIN MUTATED 50 40 74
19P GAIN WILD-TYPE 348 247 218

Figure S205.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000468 (Fisher's exact test), Q value = 0.19

Table S206.  Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
19P GAIN MUTATED 63 42 59
19P GAIN WILD-TYPE 189 257 367

Figure S206.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 6.9e-13 (Chi-square test), Q value = 5.6e-10

Table S207.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
19Q GAIN MUTATED 33 49 31 78 11
19Q GAIN WILD-TYPE 338 209 66 158 34

Figure S207.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.000454 (Fisher's exact test), Q value = 0.19

Table S208.  Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
19Q GAIN MUTATED 77 29 94
19Q GAIN WILD-TYPE 196 157 448

Figure S208.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.08e-05 (Fisher's exact test), Q value = 0.04

Table S209.  Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
19Q GAIN MUTATED 70 79 51
19Q GAIN WILD-TYPE 163 360 278

Figure S209.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 0.000136 (Fisher's exact test), Q value = 0.065

Table S210.  Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
19Q GAIN MUTATED 64 48 83
19Q GAIN WILD-TYPE 334 239 209

Figure S210.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.84e-05 (Fisher's exact test), Q value = 0.048

Table S211.  Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
19Q GAIN MUTATED 74 54 67
19Q GAIN WILD-TYPE 178 245 359

Figure S211.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MRNA_CNMF'

P value = 3e-05 (Chi-square test), Q value = 0.016

Table S212.  Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
20P GAIN MUTATED 8 13 49 42 34 42 15 7
20P GAIN WILD-TYPE 13 23 70 54 75 30 5 33

Figure S212.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1.6e-31 (Chi-square test), Q value = 1.5e-28

Table S213.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
20P GAIN MUTATED 53 142 56 118 20
20P GAIN WILD-TYPE 318 116 41 118 25

Figure S213.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 3.81e-09 (Chi-square test), Q value = 2.7e-06

Table S214.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
20P GAIN MUTATED 47 35 49 79 13 33
20P GAIN WILD-TYPE 69 120 59 60 42 79

Figure S214.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 2.86e-07 (Fisher's exact test), Q value = 0.00018

Table S215.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
20P GAIN MUTATED 118 40 229
20P GAIN WILD-TYPE 155 146 313

Figure S215.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.54e-06 (Fisher's exact test), Q value = 0.00092

Table S216.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
20P GAIN MUTATED 96 200 91
20P GAIN WILD-TYPE 137 239 238

Figure S216.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 2.6e-05 (Fisher's exact test), Q value = 0.014

Table S217.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
20P GAIN MUTATED 165 80 132
20P GAIN WILD-TYPE 233 207 160

Figure S217.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000262 (Fisher's exact test), Q value = 0.12

Table S218.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
20P GAIN MUTATED 117 125 135
20P GAIN WILD-TYPE 135 174 291

Figure S218.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000201 (Fisher's exact test), Q value = 0.093

Table S219.  Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
20P GAIN MUTATED 60 45 149
20P GAIN WILD-TYPE 85 132 196

Figure S219.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 7.43e-05 (Chi-square test), Q value = 0.037

Table S220.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
20Q GAIN MUTATED 7 13 61 40 35 42 15 10
20Q GAIN WILD-TYPE 14 23 58 56 74 30 5 30

Figure S220.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 2.16e-36 (Chi-square test), Q value = 2.1e-33

Table S221.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
20Q GAIN MUTATED 59 165 56 120 22
20Q GAIN WILD-TYPE 312 93 41 116 23

Figure S221.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1.24e-14 (Chi-square test), Q value = 1e-11

Table S222.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
20Q GAIN MUTATED 52 36 55 91 12 33
20Q GAIN WILD-TYPE 64 119 53 48 43 79

Figure S222.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 8.24e-09 (Fisher's exact test), Q value = 5.8e-06

Table S223.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
20Q GAIN MUTATED 122 42 255
20Q GAIN WILD-TYPE 151 144 287

Figure S223.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.46e-08 (Fisher's exact test), Q value = 1.7e-05

Table S224.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
20Q GAIN MUTATED 100 222 97
20Q GAIN WILD-TYPE 133 217 232

Figure S224.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 1.37e-06 (Fisher's exact test), Q value = 0.00082

Table S225.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
20Q GAIN MUTATED 186 85 141
20Q GAIN WILD-TYPE 212 202 151

Figure S225.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.12e-06 (Fisher's exact test), Q value = 0.0012

Table S226.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
20Q GAIN MUTATED 120 151 141
20Q GAIN WILD-TYPE 132 148 285

Figure S226.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.44e-05 (Fisher's exact test), Q value = 0.018

Table S227.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
20Q GAIN MUTATED 121 66 96
20Q GAIN WILD-TYPE 129 153 102

Figure S227.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.81e-05 (Fisher's exact test), Q value = 0.015

Table S228.  Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
20Q GAIN MUTATED 65 50 168
20Q GAIN WILD-TYPE 80 127 177

Figure S228.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'MRNA_CNMF'

P value = 5.21e-10 (Chi-square test), Q value = 3.9e-07

Table S229.  Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
21Q GAIN MUTATED 2 2 16 31 11 31 8 3
21Q GAIN WILD-TYPE 19 34 103 65 98 41 12 37

Figure S229.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q gain' versus 'MRNA_CHIERARCHICAL'

P value = 6.2e-07 (Fisher's exact test), Q value = 0.00038

Table S230.  Gene #38: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
21Q GAIN MUTATED 11 45 48
21Q GAIN WILD-TYPE 111 80 218

Figure S230.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1.32e-15 (Chi-square test), Q value = 1.1e-12

Table S231.  Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
21Q GAIN MUTATED 31 36 23 83 11
21Q GAIN WILD-TYPE 340 222 74 153 34

Figure S231.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 6.71e-09 (Chi-square test), Q value = 4.7e-06

Table S232.  Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
21Q GAIN MUTATED 43 14 21 18 5 14
21Q GAIN WILD-TYPE 73 141 87 121 50 98

Figure S232.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q gain' versus 'RPPA_CNMF'

P value = 0.000202 (Fisher's exact test), Q value = 0.093

Table S233.  Gene #38: '21q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
21Q GAIN MUTATED 47 16 22
21Q GAIN WILD-TYPE 100 117 95

Figure S233.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'21q gain' versus 'RPPA_CHIERARCHICAL'

P value = 7.86e-05 (Fisher's exact test), Q value = 0.039

Table S234.  Gene #38: '21q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
21Q GAIN MUTATED 24 17 44
21Q GAIN WILD-TYPE 137 93 82

Figure S234.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 1.99e-16 (Fisher's exact test), Q value = 1.7e-13

Table S235.  Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
21Q GAIN MUTATED 95 11 77
21Q GAIN WILD-TYPE 178 175 465

Figure S235.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.17e-16 (Fisher's exact test), Q value = 1.9e-13

Table S236.  Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
21Q GAIN MUTATED 83 76 24
21Q GAIN WILD-TYPE 150 363 305

Figure S236.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 1.55e-08 (Fisher's exact test), Q value = 1.1e-05

Table S237.  Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
21Q GAIN MUTATED 61 31 86
21Q GAIN WILD-TYPE 337 256 206

Figure S237.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.44e-13 (Fisher's exact test), Q value = 6.9e-10

Table S238.  Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
21Q GAIN MUTATED 87 41 50
21Q GAIN WILD-TYPE 165 258 376

Figure S238.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.83e-08 (Fisher's exact test), Q value = 1.3e-05

Table S239.  Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
21Q GAIN MUTATED 35 23 64
21Q GAIN WILD-TYPE 215 196 134

Figure S239.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.01e-07 (Fisher's exact test), Q value = 6.6e-05

Table S240.  Gene #38: '21q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
21Q GAIN MUTATED 51 21 50
21Q GAIN WILD-TYPE 94 156 295

Figure S240.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q gain' versus 'MRNA_CNMF'

P value = 1.66e-05 (Chi-square test), Q value = 0.0091

Table S241.  Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
22Q GAIN MUTATED 3 0 12 18 2 15 2 0
22Q GAIN WILD-TYPE 18 36 107 78 107 57 18 40

Figure S241.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1.76e-06 (Fisher's exact test), Q value = 0.001

Table S242.  Gene #39: '22q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
22Q GAIN MUTATED 1 24 27
22Q GAIN WILD-TYPE 121 101 239

Figure S242.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 1.28e-11 (Chi-square test), Q value = 1e-08

Table S243.  Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
22Q GAIN MUTATED 10 27 3 47 4
22Q GAIN WILD-TYPE 361 231 94 189 41

Figure S243.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 5.38e-05 (Chi-square test), Q value = 0.028

Table S244.  Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
22Q GAIN MUTATED 20 3 14 12 1 7
22Q GAIN WILD-TYPE 96 152 94 127 54 105

Figure S244.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'RPPA_CNMF'

P value = 8.26e-06 (Fisher's exact test), Q value = 0.0046

Table S245.  Gene #39: '22q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
22Q GAIN MUTATED 31 5 8
22Q GAIN WILD-TYPE 116 128 109

Figure S245.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 6.3e-15 (Fisher's exact test), Q value = 5.4e-12

Table S246.  Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
22Q GAIN MUTATED 54 0 36
22Q GAIN WILD-TYPE 219 186 506

Figure S246.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.33e-12 (Fisher's exact test), Q value = 1.1e-09

Table S247.  Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
22Q GAIN MUTATED 44 41 5
22Q GAIN WILD-TYPE 189 398 324

Figure S247.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 2.11e-09 (Fisher's exact test), Q value = 1.5e-06

Table S248.  Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
22Q GAIN MUTATED 31 7 50
22Q GAIN WILD-TYPE 367 280 242

Figure S248.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.63e-11 (Fisher's exact test), Q value = 2.8e-08

Table S249.  Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
22Q GAIN MUTATED 49 25 14
22Q GAIN WILD-TYPE 203 274 412

Figure S249.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.81e-06 (Fisher's exact test), Q value = 0.0044

Table S250.  Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
22Q GAIN MUTATED 19 7 33
22Q GAIN WILD-TYPE 231 212 165

Figure S250.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.92e-06 (Fisher's exact test), Q value = 0.0011

Table S251.  Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
22Q GAIN MUTATED 27 4 28
22Q GAIN WILD-TYPE 118 173 317

Figure S251.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'MRNA_CHIERARCHICAL'

P value = 8.96e-05 (Fisher's exact test), Q value = 0.044

Table S252.  Gene #40: 'xq gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
XQ GAIN MUTATED 8 33 40
XQ GAIN WILD-TYPE 114 92 226

Figure S252.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 9e-09 (Chi-square test), Q value = 6.3e-06

Table S253.  Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
XQ GAIN MUTATED 16 39 18 50 8
XQ GAIN WILD-TYPE 355 219 79 186 37

Figure S253.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 8.6e-07 (Fisher's exact test), Q value = 0.00052

Table S254.  Gene #40: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
XQ GAIN MUTATED 54 7 69
XQ GAIN WILD-TYPE 219 179 473

Figure S254.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.89e-07 (Fisher's exact test), Q value = 0.00024

Table S255.  Gene #40: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
XQ GAIN MUTATED 48 63 19
XQ GAIN WILD-TYPE 185 376 310

Figure S255.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CNMF'

P value = 8.24e-08 (Fisher's exact test), Q value = 5.4e-05

Table S256.  Gene #40: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
XQ GAIN MUTATED 50 14 59
XQ GAIN WILD-TYPE 348 273 233

Figure S256.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.57e-05 (Fisher's exact test), Q value = 0.0086

Table S257.  Gene #40: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
XQ GAIN MUTATED 52 37 34
XQ GAIN WILD-TYPE 200 262 392

Figure S257.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.1

Table S258.  Gene #40: 'xq gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
XQ GAIN MUTATED 27 12 36
XQ GAIN WILD-TYPE 223 207 162

Figure S258.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MRNA_CNMF'

P value = 0.000238 (Chi-square test), Q value = 0.11

Table S259.  Gene #41: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
1P LOSS MUTATED 3 6 34 10 28 30 3 7
1P LOSS WILD-TYPE 18 30 85 86 81 42 17 33

Figure S259.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 6.75e-07 (Fisher's exact test), Q value = 0.00041

Table S260.  Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
1P LOSS MUTATED 18 15 88
1P LOSS WILD-TYPE 104 110 178

Figure S260.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 4.65e-22 (Chi-square test), Q value = 4.3e-19

Table S261.  Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
1P LOSS MUTATED 35 93 48 42 12
1P LOSS WILD-TYPE 336 165 49 194 33

Figure S261.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1.25e-07 (Chi-square test), Q value = 8.1e-05

Table S262.  Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
1P LOSS MUTATED 16 26 40 45 7 13
1P LOSS WILD-TYPE 100 129 68 94 48 99

Figure S262.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1.04e-07 (Fisher's exact test), Q value = 6.7e-05

Table S263.  Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
1P LOSS MUTATED 43 25 161
1P LOSS WILD-TYPE 230 161 381

Figure S263.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.61e-13 (Fisher's exact test), Q value = 7.8e-10

Table S264.  Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
1P LOSS MUTATED 28 149 52
1P LOSS WILD-TYPE 205 290 277

Figure S264.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MRNA_CHIERARCHICAL'

P value = 6.35e-05 (Fisher's exact test), Q value = 0.033

Table S265.  Gene #43: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
2P LOSS MUTATED 15 11 67
2P LOSS WILD-TYPE 107 114 199

Figure S265.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 7.62e-15 (Chi-square test), Q value = 6.5e-12

Table S266.  Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
2P LOSS MUTATED 26 77 29 29 9
2P LOSS WILD-TYPE 345 181 68 207 36

Figure S266.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 1.49e-07 (Chi-square test), Q value = 9.5e-05

Table S267.  Gene #43: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
2P LOSS MUTATED 9 23 22 41 3 7
2P LOSS WILD-TYPE 107 132 86 98 52 105

Figure S267.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 3.63e-08 (Fisher's exact test), Q value = 2.5e-05

Table S268.  Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
2P LOSS MUTATED 25 18 125
2P LOSS WILD-TYPE 248 168 417

Figure S268.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.48e-10 (Fisher's exact test), Q value = 1.1e-07

Table S269.  Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
2P LOSS MUTATED 17 112 39
2P LOSS WILD-TYPE 216 327 290

Figure S269.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 0.000126 (Fisher's exact test), Q value = 0.06

Table S270.  Gene #43: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
2P LOSS MUTATED 91 35 37
2P LOSS WILD-TYPE 307 252 255

Figure S270.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000314 (Fisher's exact test), Q value = 0.14

Table S271.  Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
2P LOSS MUTATED 29 71 63
2P LOSS WILD-TYPE 223 228 363

Figure S271.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.14

Table S272.  Gene #43: '2p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
2P LOSS MUTATED 13 19 73
2P LOSS WILD-TYPE 132 158 272

Figure S272.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 8.5e-14 (Chi-square test), Q value = 7.1e-11

Table S273.  Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
2Q LOSS MUTATED 28 80 31 42 11
2Q LOSS WILD-TYPE 343 178 66 194 34

Figure S273.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 1.78e-06 (Chi-square test), Q value = 0.0011

Table S274.  Gene #44: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
2Q LOSS MUTATED 18 22 20 46 4 10
2Q LOSS WILD-TYPE 98 133 88 93 51 102

Figure S274.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q loss' versus 'RPPA_CNMF'

P value = 0.000444 (Fisher's exact test), Q value = 0.19

Table S275.  Gene #44: '2q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
2Q LOSS MUTATED 32 36 10
2Q LOSS WILD-TYPE 115 97 107

Figure S275.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 0.000334 (Fisher's exact test), Q value = 0.15

Table S276.  Gene #44: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
2Q LOSS MUTATED 47 19 124
2Q LOSS WILD-TYPE 226 167 418

Figure S276.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.96e-07 (Fisher's exact test), Q value = 0.00048

Table S277.  Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
2Q LOSS MUTATED 33 116 41
2Q LOSS WILD-TYPE 200 323 288

Figure S277.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MRNA_CNMF'

P value = 2.85e-06 (Chi-square test), Q value = 0.0017

Table S278.  Gene #45: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
3P LOSS MUTATED 0 7 19 29 4 19 6 4
3P LOSS WILD-TYPE 21 29 100 67 105 53 14 36

Figure S278.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p loss' versus 'MRNA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.044

Table S279.  Gene #45: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
3P LOSS MUTATED 15 38 35
3P LOSS WILD-TYPE 107 87 231

Figure S279.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 9.47e-15 (Chi-square test), Q value = 8e-12

Table S280.  Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
3P LOSS MUTATED 25 52 15 76 3
3P LOSS WILD-TYPE 346 206 82 160 42

Figure S280.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1.19e-07 (Chi-square test), Q value = 7.7e-05

Table S281.  Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
3P LOSS MUTATED 35 8 26 27 5 12
3P LOSS WILD-TYPE 81 147 82 112 50 100

Figure S281.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CNMF'

P value = 0.000382 (Fisher's exact test), Q value = 0.16

Table S282.  Gene #45: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
3P LOSS MUTATED 43 18 14
3P LOSS WILD-TYPE 104 115 103

Figure S282.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 8.85e-05 (Fisher's exact test), Q value = 0.044

Table S283.  Gene #45: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
3P LOSS MUTATED 21 14 40
3P LOSS WILD-TYPE 140 96 86

Figure S283.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1.61e-10 (Fisher's exact test), Q value = 1.2e-07

Table S284.  Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
3P LOSS MUTATED 82 16 71
3P LOSS WILD-TYPE 191 170 471

Figure S284.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.04e-08 (Fisher's exact test), Q value = 4.6e-05

Table S285.  Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
3P LOSS MUTATED 68 66 35
3P LOSS WILD-TYPE 165 373 294

Figure S285.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 1.11e-10 (Fisher's exact test), Q value = 8.5e-08

Table S286.  Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
3P LOSS MUTATED 48 29 86
3P LOSS WILD-TYPE 350 258 206

Figure S286.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.66e-08 (Fisher's exact test), Q value = 3.8e-05

Table S287.  Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
3P LOSS MUTATED 70 49 44
3P LOSS WILD-TYPE 182 250 382

Figure S287.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.15e-08 (Fisher's exact test), Q value = 2.8e-05

Table S288.  Gene #45: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
3P LOSS MUTATED 32 20 59
3P LOSS WILD-TYPE 218 199 139

Figure S288.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.4e-05 (Fisher's exact test), Q value = 0.042

Table S289.  Gene #45: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
3P LOSS MUTATED 42 21 48
3P LOSS WILD-TYPE 103 156 297

Figure S289.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 2.14e-06 (Chi-square test), Q value = 0.0013

Table S290.  Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
3Q LOSS MUTATED 12 31 10 38 3
3Q LOSS WILD-TYPE 359 227 87 198 42

Figure S290.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 0.000446 (Chi-square test), Q value = 0.19

Table S291.  Gene #46: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
3Q LOSS MUTATED 20 7 14 17 2 4
3Q LOSS WILD-TYPE 96 148 94 122 53 108

Figure S291.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 0.000509 (Fisher's exact test), Q value = 0.21

Table S292.  Gene #46: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
3Q LOSS MUTATED 40 8 45
3Q LOSS WILD-TYPE 233 178 497

Figure S292.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000528 (Fisher's exact test), Q value = 0.22

Table S293.  Gene #46: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
3Q LOSS MUTATED 33 44 16
3Q LOSS WILD-TYPE 200 395 313

Figure S293.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 0.000528 (Fisher's exact test), Q value = 0.22

Table S294.  Gene #46: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
3Q LOSS MUTATED 29 17 43
3Q LOSS WILD-TYPE 369 270 249

Figure S294.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MRNA_CNMF'

P value = 2.99e-14 (Chi-square test), Q value = 2.5e-11

Table S295.  Gene #47: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
4P LOSS MUTATED 4 8 24 59 22 41 8 7
4P LOSS WILD-TYPE 17 28 95 37 87 31 12 33

Figure S295.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 2.91e-13 (Fisher's exact test), Q value = 2.4e-10

Table S296.  Gene #47: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
4P LOSS MUTATED 21 76 76
4P LOSS WILD-TYPE 101 49 190

Figure S296.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 3.95e-37 (Chi-square test), Q value = 3.8e-34

Table S297.  Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
4P LOSS MUTATED 52 68 45 151 14
4P LOSS WILD-TYPE 319 190 52 85 31

Figure S297.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 5.22e-19 (Chi-square test), Q value = 4.7e-16

Table S298.  Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
4P LOSS MUTATED 79 31 36 33 8 28
4P LOSS WILD-TYPE 37 124 72 106 47 84

Figure S298.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CNMF'

P value = 4.59e-07 (Fisher's exact test), Q value = 0.00028

Table S299.  Gene #47: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
4P LOSS MUTATED 76 39 25
4P LOSS WILD-TYPE 71 94 92

Figure S299.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p loss' versus 'RPPA_CHIERARCHICAL'

P value = 8.75e-07 (Fisher's exact test), Q value = 0.00053

Table S300.  Gene #47: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
4P LOSS MUTATED 45 27 68
4P LOSS WILD-TYPE 116 83 58

Figure S300.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 7.94e-29 (Fisher's exact test), Q value = 7.5e-26

Table S301.  Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
4P LOSS MUTATED 162 25 140
4P LOSS WILD-TYPE 111 161 402

Figure S301.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.35e-27 (Fisher's exact test), Q value = 5e-24

Table S302.  Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
4P LOSS MUTATED 143 126 58
4P LOSS WILD-TYPE 90 313 271

Figure S302.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 1.31e-21 (Fisher's exact test), Q value = 1.2e-18

Table S303.  Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
4P LOSS MUTATED 111 48 157
4P LOSS WILD-TYPE 287 239 135

Figure S303.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.71e-23 (Fisher's exact test), Q value = 4.4e-20

Table S304.  Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
4P LOSS MUTATED 147 79 90
4P LOSS WILD-TYPE 105 220 336

Figure S304.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.02e-20 (Fisher's exact test), Q value = 1.8e-17

Table S305.  Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
4P LOSS MUTATED 67 34 115
4P LOSS WILD-TYPE 183 185 83

Figure S305.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.08e-17 (Fisher's exact test), Q value = 7.1e-14

Table S306.  Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
4P LOSS MUTATED 89 31 96
4P LOSS WILD-TYPE 56 146 249

Figure S306.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'MRNA_CNMF'

P value = 1.12e-07 (Chi-square test), Q value = 7.2e-05

Table S307.  Gene #48: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
4Q LOSS MUTATED 4 8 24 46 21 36 7 7
4Q LOSS WILD-TYPE 17 28 95 50 88 36 13 33

Figure S307.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q loss' versus 'MRNA_CHIERARCHICAL'

P value = 9.7e-08 (Fisher's exact test), Q value = 6.3e-05

Table S308.  Gene #48: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
4Q LOSS MUTATED 20 61 72
4Q LOSS WILD-TYPE 102 64 194

Figure S308.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 7.72e-29 (Chi-square test), Q value = 7.3e-26

Table S309.  Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
4Q LOSS MUTATED 47 62 45 128 12
4Q LOSS WILD-TYPE 324 196 52 108 33

Figure S309.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 3.62e-11 (Chi-square test), Q value = 2.8e-08

Table S310.  Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
4Q LOSS MUTATED 65 32 32 30 8 27
4Q LOSS WILD-TYPE 51 123 76 109 47 85

Figure S310.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'RPPA_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.15

Table S311.  Gene #48: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
4Q LOSS MUTATED 64 35 26
4Q LOSS WILD-TYPE 83 98 91

Figure S311.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 6.79e-20 (Fisher's exact test), Q value = 6.1e-17

Table S312.  Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
4Q LOSS MUTATED 135 21 135
4Q LOSS WILD-TYPE 138 165 407

Figure S312.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.05e-17 (Fisher's exact test), Q value = 9.4e-15

Table S313.  Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
4Q LOSS MUTATED 118 120 53
4Q LOSS WILD-TYPE 115 319 276

Figure S313.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 1.29e-12 (Fisher's exact test), Q value = 1e-09

Table S314.  Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
4Q LOSS MUTATED 106 46 127
4Q LOSS WILD-TYPE 292 241 165

Figure S314.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.24e-14 (Fisher's exact test), Q value = 1.9e-11

Table S315.  Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
4Q LOSS MUTATED 122 70 87
4Q LOSS WILD-TYPE 130 229 339

Figure S315.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.43e-13 (Fisher's exact test), Q value = 3.6e-10

Table S316.  Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
4Q LOSS MUTATED 62 31 93
4Q LOSS WILD-TYPE 188 188 105

Figure S316.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.85e-09 (Fisher's exact test), Q value = 1.4e-06

Table S317.  Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
4Q LOSS MUTATED 69 28 89
4Q LOSS WILD-TYPE 76 149 256

Figure S317.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'MRNA_CNMF'

P value = 6.42e-17 (Chi-square test), Q value = 5.6e-14

Table S318.  Gene #49: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
5P LOSS MUTATED 1 2 8 42 5 11 1 2
5P LOSS WILD-TYPE 20 34 111 54 104 61 19 38

Figure S318.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.72e-12 (Fisher's exact test), Q value = 1.4e-09

Table S319.  Gene #49: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
5P LOSS MUTATED 6 44 22
5P LOSS WILD-TYPE 116 81 244

Figure S319.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 4.32e-35 (Chi-square test), Q value = 4.1e-32

Table S320.  Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
5P LOSS MUTATED 16 17 4 89 6
5P LOSS WILD-TYPE 355 241 93 147 39

Figure S320.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 9.63e-23 (Chi-square test), Q value = 8.9e-20

Table S321.  Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
5P LOSS MUTATED 48 3 8 12 1 15
5P LOSS WILD-TYPE 68 152 100 127 54 97

Figure S321.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'RPPA_CNMF'

P value = 6.63e-08 (Fisher's exact test), Q value = 4.4e-05

Table S322.  Gene #49: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
5P LOSS MUTATED 43 9 9
5P LOSS WILD-TYPE 104 124 108

Figure S322.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5p loss' versus 'RPPA_CHIERARCHICAL'

P value = 6.96e-10 (Fisher's exact test), Q value = 5.2e-07

Table S323.  Gene #49: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
5P LOSS MUTATED 11 8 42
5P LOSS WILD-TYPE 150 102 84

Figure S323.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 2.62e-26 (Fisher's exact test), Q value = 2.4e-23

Table S324.  Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
5P LOSS MUTATED 90 5 37
5P LOSS WILD-TYPE 183 181 505

Figure S324.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.04e-27 (Fisher's exact test), Q value = 7.5e-24

Table S325.  Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
5P LOSS MUTATED 83 37 12
5P LOSS WILD-TYPE 150 402 317

Figure S325.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 5.43e-25 (Fisher's exact test), Q value = 5e-22

Table S326.  Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
5P LOSS MUTATED 25 12 92
5P LOSS WILD-TYPE 373 275 200

Figure S326.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.22e-28 (Fisher's exact test), Q value = 1.1e-25

Table S327.  Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
5P LOSS MUTATED 87 28 14
5P LOSS WILD-TYPE 165 271 412

Figure S327.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.25e-18 (Fisher's exact test), Q value = 1.1e-15

Table S328.  Gene #49: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
5P LOSS MUTATED 15 8 63
5P LOSS WILD-TYPE 235 211 135

Figure S328.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.62e-18 (Fisher's exact test), Q value = 3.2e-15

Table S329.  Gene #49: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
5P LOSS MUTATED 53 6 27
5P LOSS WILD-TYPE 92 171 318

Figure S329.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'MRNA_CNMF'

P value = 3.8e-26 (Chi-square test), Q value = 3.5e-23

Table S330.  Gene #50: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
5Q LOSS MUTATED 2 4 14 61 4 20 5 3
5Q LOSS WILD-TYPE 19 32 105 35 105 52 15 37

Figure S330.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-20 (Fisher's exact test), Q value = 9.1e-18

Table S331.  Gene #50: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
5Q LOSS MUTATED 10 68 35
5Q LOSS WILD-TYPE 112 57 231

Figure S331.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1.62e-75 (Chi-square test), Q value = 1.6e-72

Table S332.  Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
5Q LOSS MUTATED 21 26 5 153 10
5Q LOSS WILD-TYPE 350 232 92 83 35

Figure S332.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 5.35e-46 (Chi-square test), Q value = 5.1e-43

Table S333.  Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
5Q LOSS MUTATED 82 3 11 21 4 24
5Q LOSS WILD-TYPE 34 152 97 118 51 88

Figure S333.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'RPPA_CNMF'

P value = 1.2e-13 (Fisher's exact test), Q value = 1e-10

Table S334.  Gene #50: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
5Q LOSS MUTATED 67 11 18
5Q LOSS WILD-TYPE 80 122 99

Figure S334.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1.18e-13 (Fisher's exact test), Q value = 9.8e-11

Table S335.  Gene #50: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
5Q LOSS MUTATED 21 13 62
5Q LOSS WILD-TYPE 140 97 64

Figure S335.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 1.22e-49 (Fisher's exact test), Q value = 1.2e-46

Table S336.  Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
5Q LOSS MUTATED 148 8 59
5Q LOSS WILD-TYPE 125 178 483

Figure S336.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.74e-52 (Fisher's exact test), Q value = 4.5e-49

Table S337.  Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
5Q LOSS MUTATED 138 57 20
5Q LOSS WILD-TYPE 95 382 309

Figure S337.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 4.44e-51 (Fisher's exact test), Q value = 4.2e-48

Table S338.  Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
5Q LOSS MUTATED 37 17 154
5Q LOSS WILD-TYPE 361 270 138

Figure S338.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.4e-52 (Fisher's exact test), Q value = 1.3e-49

Table S339.  Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
5Q LOSS MUTATED 142 42 24
5Q LOSS WILD-TYPE 110 257 402

Figure S339.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.22e-34 (Fisher's exact test), Q value = 2.1e-31

Table S340.  Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
5Q LOSS MUTATED 25 13 104
5Q LOSS WILD-TYPE 225 206 94

Figure S340.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.14e-33 (Fisher's exact test), Q value = 1.1e-30

Table S341.  Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
5Q LOSS MUTATED 88 13 41
5Q LOSS WILD-TYPE 57 164 304

Figure S341.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 6.69e-11 (Chi-square test), Q value = 5.2e-08

Table S342.  Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
6P LOSS MUTATED 39 79 17 26 12
6P LOSS WILD-TYPE 332 179 80 210 33

Figure S342.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.000475 (Chi-square test), Q value = 0.2

Table S343.  Gene #51: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
6P LOSS MUTATED 13 18 18 39 4 20
6P LOSS WILD-TYPE 103 137 90 100 51 92

Figure S343.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000101 (Fisher's exact test), Q value = 0.05

Table S344.  Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
6P LOSS MUTATED 25 100 47
6P LOSS WILD-TYPE 208 339 282

Figure S344.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.089

Table S345.  Gene #52: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
6Q LOSS MUTATED 35 15 80
6Q LOSS WILD-TYPE 87 110 186

Figure S345.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 2.73e-16 (Chi-square test), Q value = 2.4e-13

Table S346.  Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
6Q LOSS MUTATED 67 111 25 32 20
6Q LOSS WILD-TYPE 304 147 72 204 25

Figure S346.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 5.57e-05 (Chi-square test), Q value = 0.029

Table S347.  Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
6Q LOSS MUTATED 21 41 27 57 7 23
6Q LOSS WILD-TYPE 95 114 81 82 48 89

Figure S347.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.000185 (Fisher's exact test), Q value = 0.086

Table S348.  Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
6Q LOSS MUTATED 45 49 160
6Q LOSS WILD-TYPE 228 137 382

Figure S348.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000125 (Fisher's exact test), Q value = 0.06

Table S349.  Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
6Q LOSS MUTATED 37 134 83
6Q LOSS WILD-TYPE 196 305 246

Figure S349.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.05e-06 (Fisher's exact test), Q value = 0.0034

Table S350.  Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
6Q LOSS MUTATED 38 98 113
6Q LOSS WILD-TYPE 214 201 313

Figure S350.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

P value = 8.19e-10 (Chi-square test), Q value = 6e-07

Table S351.  Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
7P LOSS MUTATED 11 37 7 46 4
7P LOSS WILD-TYPE 360 221 90 190 41

Figure S351.  Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 7.1e-05 (Chi-square test), Q value = 0.036

Table S352.  Gene #53: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
7P LOSS MUTATED 23 7 11 18 1 6
7P LOSS WILD-TYPE 93 148 97 121 54 106

Figure S352.  Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 1.16e-05 (Fisher's exact test), Q value = 0.0065

Table S353.  Gene #53: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
7P LOSS MUTATED 45 6 53
7P LOSS WILD-TYPE 228 180 489

Figure S353.  Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.05e-05 (Fisher's exact test), Q value = 0.011

Table S354.  Gene #53: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
7P LOSS MUTATED 36 53 15
7P LOSS WILD-TYPE 197 386 314

Figure S354.  Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_CNMF'

P value = 2.25e-08 (Fisher's exact test), Q value = 1.5e-05

Table S355.  Gene #53: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
7P LOSS MUTATED 37 10 53
7P LOSS WILD-TYPE 361 277 239

Figure S355.  Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.51e-08 (Fisher's exact test), Q value = 2.4e-05

Table S356.  Gene #53: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
7P LOSS MUTATED 43 39 18
7P LOSS WILD-TYPE 209 260 408

Figure S356.  Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000122 (Fisher's exact test), Q value = 0.059

Table S357.  Gene #53: '7p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
7P LOSS MUTATED 17 9 31
7P LOSS WILD-TYPE 233 210 167

Figure S357.  Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.9e-05 (Fisher's exact test), Q value = 0.015

Table S358.  Gene #53: '7p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
7P LOSS MUTATED 25 5 27
7P LOSS WILD-TYPE 120 172 318

Figure S358.  Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 1.31e-05 (Chi-square test), Q value = 0.0072

Table S359.  Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
7Q LOSS MUTATED 19 45 11 35 3
7Q LOSS WILD-TYPE 352 213 86 201 42

Figure S359.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

'7q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000155 (Fisher's exact test), Q value = 0.073

Table S360.  Gene #54: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
7Q LOSS MUTATED 22 69 21
7Q LOSS WILD-TYPE 211 370 308

Figure S360.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 0.000198 (Fisher's exact test), Q value = 0.092

Table S361.  Gene #54: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
7Q LOSS MUTATED 50 15 44
7Q LOSS WILD-TYPE 348 272 248

Figure S361.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.11e-05 (Fisher's exact test), Q value = 0.036

Table S362.  Gene #54: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
7Q LOSS MUTATED 35 47 27
7Q LOSS WILD-TYPE 217 252 399

Figure S362.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MRNA_CNMF'

P value = 4.52e-05 (Chi-square test), Q value = 0.024

Table S363.  Gene #55: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
8P LOSS MUTATED 5 11 56 45 22 37 11 17
8P LOSS WILD-TYPE 16 25 63 51 87 35 9 23

Figure S363.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1.65e-18 (Chi-square test), Q value = 1.5e-15

Table S364.  Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
8P LOSS MUTATED 83 126 19 126 17
8P LOSS WILD-TYPE 288 132 78 110 28

Figure S364.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 3.86e-07 (Chi-square test), Q value = 0.00024

Table S365.  Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
8P LOSS MUTATED 52 33 40 69 10 37
8P LOSS WILD-TYPE 64 122 68 70 45 75

Figure S365.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 2.39e-06 (Fisher's exact test), Q value = 0.0014

Table S366.  Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
8P LOSS MUTATED 126 43 200
8P LOSS WILD-TYPE 147 143 342

Figure S366.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.94e-05 (Fisher's exact test), Q value = 0.021

Table S367.  Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
8P LOSS MUTATED 107 170 92
8P LOSS WILD-TYPE 126 269 237

Figure S367.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 6.61e-07 (Fisher's exact test), Q value = 4e-04

Table S368.  Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
8P LOSS MUTATED 152 74 137
8P LOSS WILD-TYPE 246 213 155

Figure S368.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.3e-07 (Fisher's exact test), Q value = 8.3e-05

Table S369.  Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
8P LOSS MUTATED 121 124 118
8P LOSS WILD-TYPE 131 175 308

Figure S369.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.74e-05 (Fisher's exact test), Q value = 0.025

Table S370.  Gene #55: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
8P LOSS MUTATED 96 55 90
8P LOSS WILD-TYPE 154 164 108

Figure S370.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MRNA_CNMF'

P value = 1.92e-05 (Chi-square test), Q value = 0.01

Table S371.  Gene #57: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
9P LOSS MUTATED 7 10 53 31 18 33 9 6
9P LOSS WILD-TYPE 14 26 66 65 91 39 11 34

Figure S371.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000177 (Fisher's exact test), Q value = 0.083

Table S372.  Gene #57: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
9P LOSS MUTATED 22 42 103
9P LOSS WILD-TYPE 100 83 163

Figure S372.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1.25e-36 (Chi-square test), Q value = 1.2e-33

Table S373.  Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
9P LOSS MUTATED 36 143 16 93 9
9P LOSS WILD-TYPE 335 115 81 143 36

Figure S373.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 4.02e-15 (Chi-square test), Q value = 3.4e-12

Table S374.  Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
9P LOSS MUTATED 42 16 39 69 10 16
9P LOSS WILD-TYPE 74 139 69 70 45 96

Figure S374.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 3.92e-09 (Fisher's exact test), Q value = 2.8e-06

Table S375.  Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
9P LOSS MUTATED 91 22 182
9P LOSS WILD-TYPE 182 164 360

Figure S375.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.29e-10 (Fisher's exact test), Q value = 1.7e-07

Table S376.  Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
9P LOSS MUTATED 76 165 54
9P LOSS WILD-TYPE 157 274 275

Figure S376.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 4.6e-10 (Fisher's exact test), Q value = 3.4e-07

Table S377.  Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
9P LOSS MUTATED 133 44 110
9P LOSS WILD-TYPE 265 243 182

Figure S377.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.5e-10 (Fisher's exact test), Q value = 1.9e-07

Table S378.  Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
9P LOSS MUTATED 97 111 79
9P LOSS WILD-TYPE 155 188 347

Figure S378.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.13e-07 (Fisher's exact test), Q value = 0.00025

Table S379.  Gene #57: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
9P LOSS MUTATED 72 35 78
9P LOSS WILD-TYPE 178 184 120

Figure S379.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000241 (Fisher's exact test), Q value = 0.11

Table S380.  Gene #57: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
9P LOSS MUTATED 48 29 108
9P LOSS WILD-TYPE 97 148 237

Figure S380.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'MRNA_CNMF'

P value = 6.82e-05 (Chi-square test), Q value = 0.035

Table S381.  Gene #58: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
9Q LOSS MUTATED 7 5 42 41 19 23 8 4
9Q LOSS WILD-TYPE 14 31 77 55 90 49 12 36

Figure S381.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 3.55e-06 (Fisher's exact test), Q value = 0.002

Table S382.  Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
9Q LOSS MUTATED 15 47 87
9Q LOSS WILD-TYPE 107 78 179

Figure S382.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 3.83e-26 (Chi-square test), Q value = 3.6e-23

Table S383.  Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
9Q LOSS MUTATED 33 111 16 97 12
9Q LOSS WILD-TYPE 338 147 81 139 33

Figure S383.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 4.82e-14 (Chi-square test), Q value = 4e-11

Table S384.  Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
9Q LOSS MUTATED 50 15 30 58 5 18
9Q LOSS WILD-TYPE 66 140 78 81 50 94

Figure S384.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CNMF'

P value = 3.37e-06 (Fisher's exact test), Q value = 0.002

Table S385.  Gene #58: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
9Q LOSS MUTATED 66 29 23
9Q LOSS WILD-TYPE 81 104 94

Figure S385.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.000331 (Fisher's exact test), Q value = 0.14

Table S386.  Gene #58: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
9Q LOSS MUTATED 42 22 54
9Q LOSS WILD-TYPE 119 88 72

Figure S386.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 4.44e-13 (Fisher's exact test), Q value = 3.6e-10

Table S387.  Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
9Q LOSS MUTATED 103 15 149
9Q LOSS WILD-TYPE 170 171 393

Figure S387.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.3e-12 (Fisher's exact test), Q value = 2.6e-09

Table S388.  Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
9Q LOSS MUTATED 87 137 43
9Q LOSS WILD-TYPE 146 302 286

Figure S388.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 1.08e-12 (Fisher's exact test), Q value = 8.7e-10

Table S389.  Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
9Q LOSS MUTATED 101 38 117
9Q LOSS WILD-TYPE 297 249 175

Figure S389.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.74e-15 (Fisher's exact test), Q value = 6.6e-12

Table S390.  Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
9Q LOSS MUTATED 106 88 62
9Q LOSS WILD-TYPE 146 211 364

Figure S390.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.96e-08 (Fisher's exact test), Q value = 2.7e-05

Table S391.  Gene #58: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
9Q LOSS MUTATED 54 33 78
9Q LOSS WILD-TYPE 196 186 120

Figure S391.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.38e-06 (Fisher's exact test), Q value = 0.00082

Table S392.  Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
9Q LOSS MUTATED 56 24 85
9Q LOSS WILD-TYPE 89 153 260

Figure S392.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1.28e-05 (Chi-square test), Q value = 0.0071

Table S393.  Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
10P LOSS MUTATED 30 53 20 49 10
10P LOSS WILD-TYPE 341 205 77 187 35

Figure S393.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.000502 (Chi-square test), Q value = 0.21

Table S394.  Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
10P LOSS MUTATED 31 19 20 30 8 7
10P LOSS WILD-TYPE 85 136 88 109 47 105

Figure S394.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.000256 (Fisher's exact test), Q value = 0.11

Table S395.  Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
10P LOSS MUTATED 54 13 93
10P LOSS WILD-TYPE 219 173 449

Figure S395.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 2.32e-13 (Chi-square test), Q value = 1.9e-10

Table S396.  Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
10Q LOSS MUTATED 31 69 21 79 14
10Q LOSS WILD-TYPE 340 189 76 157 31

Figure S396.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 4.18e-11 (Chi-square test), Q value = 3.3e-08

Table S397.  Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
10Q LOSS MUTATED 49 18 28 42 8 9
10Q LOSS WILD-TYPE 67 137 80 97 47 103

Figure S397.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 3.11e-09 (Fisher's exact test), Q value = 2.3e-06

Table S398.  Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
10Q LOSS MUTATED 84 14 114
10Q LOSS WILD-TYPE 189 172 428

Figure S398.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.04e-08 (Fisher's exact test), Q value = 4e-05

Table S399.  Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
10Q LOSS MUTATED 71 103 38
10Q LOSS WILD-TYPE 162 336 291

Figure S399.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.000115 (Fisher's exact test), Q value = 0.055

Table S400.  Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
10Q LOSS MUTATED 77 44 86
10Q LOSS WILD-TYPE 321 243 206

Figure S400.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.02e-07 (Fisher's exact test), Q value = 0.00013

Table S401.  Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
10Q LOSS MUTATED 80 68 59
10Q LOSS WILD-TYPE 172 231 367

Figure S401.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000447 (Fisher's exact test), Q value = 0.19

Table S402.  Gene #60: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
10Q LOSS MUTATED 50 33 61
10Q LOSS WILD-TYPE 200 186 137

Figure S402.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 3.23e-21 (Chi-square test), Q value = 2.9e-18

Table S403.  Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
11P LOSS MUTATED 32 102 28 89 8
11P LOSS WILD-TYPE 339 156 69 147 37

Figure S403.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 1.08e-08 (Chi-square test), Q value = 7.5e-06

Table S404.  Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
11P LOSS MUTATED 43 17 35 50 10 16
11P LOSS WILD-TYPE 73 138 73 89 45 96

Figure S404.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 1.63e-07 (Fisher's exact test), Q value = 1e-04

Table S405.  Gene #61: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
11P LOSS MUTATED 93 22 144
11P LOSS WILD-TYPE 180 164 398

Figure S405.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.17e-07 (Fisher's exact test), Q value = 7.6e-05

Table S406.  Gene #61: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
11P LOSS MUTATED 78 131 50
11P LOSS WILD-TYPE 155 308 279

Figure S406.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 5.87e-06 (Fisher's exact test), Q value = 0.0033

Table S407.  Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
11P LOSS MUTATED 94 50 102
11P LOSS WILD-TYPE 304 237 190

Figure S407.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.53e-07 (Fisher's exact test), Q value = 0.00022

Table S408.  Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
11P LOSS MUTATED 86 88 72
11P LOSS WILD-TYPE 166 211 354

Figure S408.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.84e-06 (Fisher's exact test), Q value = 0.0017

Table S409.  Gene #61: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
11P LOSS MUTATED 60 32 71
11P LOSS WILD-TYPE 190 187 127

Figure S409.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000293 (Fisher's exact test), Q value = 0.13

Table S410.  Gene #61: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
11P LOSS MUTATED 50 27 86
11P LOSS WILD-TYPE 95 150 259

Figure S410.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'MRNA_CNMF'

P value = 0.000217 (Chi-square test), Q value = 0.099

Table S411.  Gene #62: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
11Q LOSS MUTATED 5 16 64 28 26 28 6 15
11Q LOSS WILD-TYPE 16 20 55 68 83 44 14 25

Figure S411.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 3.11e-30 (Chi-square test), Q value = 2.9e-27

Table S412.  Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
11Q LOSS MUTATED 60 160 36 84 10
11Q LOSS WILD-TYPE 311 98 61 152 35

Figure S412.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 1.13e-08 (Chi-square test), Q value = 7.9e-06

Table S413.  Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
11Q LOSS MUTATED 39 38 49 73 14 22
11Q LOSS WILD-TYPE 77 117 59 66 41 90

Figure S413.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.000557 (Fisher's exact test), Q value = 0.23

Table S414.  Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
11Q LOSS MUTATED 86 47 216
11Q LOSS WILD-TYPE 187 139 326

Figure S414.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.47e-06 (Fisher's exact test), Q value = 0.0026

Table S415.  Gene #62: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
11Q LOSS MUTATED 83 136 118
11Q LOSS WILD-TYPE 169 163 308

Figure S415.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 9.43e-08 (Chi-square test), Q value = 6.2e-05

Table S416.  Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
12P LOSS MUTATED 33 38 12 60 1
12P LOSS WILD-TYPE 338 220 85 176 44

Figure S416.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 6.76e-08 (Chi-square test), Q value = 4.5e-05

Table S417.  Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
12P LOSS MUTATED 38 12 13 17 7 10
12P LOSS WILD-TYPE 78 143 95 122 48 102

Figure S417.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 1.3e-09 (Fisher's exact test), Q value = 9.6e-07

Table S418.  Gene #63: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
12P LOSS MUTATED 72 16 55
12P LOSS WILD-TYPE 201 170 487

Figure S418.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.3e-07 (Fisher's exact test), Q value = 0.00039

Table S419.  Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
12P LOSS MUTATED 59 53 31
12P LOSS WILD-TYPE 174 386 298

Figure S419.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CNMF'

P value = 6.28e-08 (Fisher's exact test), Q value = 4.2e-05

Table S420.  Gene #63: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
12P LOSS MUTATED 47 22 70
12P LOSS WILD-TYPE 351 265 222

Figure S420.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.41e-08 (Fisher's exact test), Q value = 9.8e-06

Table S421.  Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
12P LOSS MUTATED 63 42 34
12P LOSS WILD-TYPE 189 257 392

Figure S421.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.42e-06 (Fisher's exact test), Q value = 0.0014

Table S422.  Gene #63: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
12P LOSS MUTATED 28 17 49
12P LOSS WILD-TYPE 222 202 149

Figure S422.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000318 (Fisher's exact test), Q value = 0.14

Table S423.  Gene #63: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
12P LOSS MUTATED 35 15 44
12P LOSS WILD-TYPE 110 162 301

Figure S423.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'MRNA_CNMF'

P value = 5.14e-09 (Chi-square test), Q value = 3.7e-06

Table S424.  Gene #64: '12q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
12Q LOSS MUTATED 2 4 7 32 5 7 2 3
12Q LOSS WILD-TYPE 19 32 112 64 104 65 18 37

Figure S424.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'12q loss' versus 'MRNA_CHIERARCHICAL'

P value = 4.1e-08 (Fisher's exact test), Q value = 2.8e-05

Table S425.  Gene #64: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
12Q LOSS MUTATED 8 35 19
12Q LOSS WILD-TYPE 114 90 247

Figure S425.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 8.11e-15 (Chi-square test), Q value = 6.9e-12

Table S426.  Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
12Q LOSS MUTATED 24 21 11 66 2
12Q LOSS WILD-TYPE 347 237 86 170 43

Figure S426.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 1.35e-20 (Chi-square test), Q value = 1.2e-17

Table S427.  Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
12Q LOSS MUTATED 47 5 13 12 2 8
12Q LOSS WILD-TYPE 69 150 95 127 53 104

Figure S427.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q loss' versus 'RPPA_CNMF'

P value = 0.000215 (Fisher's exact test), Q value = 0.098

Table S428.  Gene #64: '12q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
12Q LOSS MUTATED 32 9 9
12Q LOSS WILD-TYPE 115 124 108

Figure S428.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'12q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1.16e-05 (Fisher's exact test), Q value = 0.0065

Table S429.  Gene #64: '12q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
12Q LOSS MUTATED 13 6 31
12Q LOSS WILD-TYPE 148 104 95

Figure S429.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 1.07e-17 (Fisher's exact test), Q value = 9.5e-15

Table S430.  Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
12Q LOSS MUTATED 77 12 34
12Q LOSS WILD-TYPE 196 174 508

Figure S430.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.1e-16 (Fisher's exact test), Q value = 1.8e-13

Table S431.  Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
12Q LOSS MUTATED 69 32 22
12Q LOSS WILD-TYPE 164 407 307

Figure S431.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 2.78e-14 (Fisher's exact test), Q value = 2.3e-11

Table S432.  Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
12Q LOSS MUTATED 26 18 74
12Q LOSS WILD-TYPE 372 269 218

Figure S432.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.21e-15 (Fisher's exact test), Q value = 2.8e-12

Table S433.  Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
12Q LOSS MUTATED 69 24 25
12Q LOSS WILD-TYPE 183 275 401

Figure S433.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.19e-12 (Fisher's exact test), Q value = 9.6e-10

Table S434.  Gene #64: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
12Q LOSS MUTATED 19 13 58
12Q LOSS WILD-TYPE 231 206 140

Figure S434.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.14e-10 (Fisher's exact test), Q value = 8.7e-08

Table S435.  Gene #64: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
12Q LOSS MUTATED 46 12 32
12Q LOSS WILD-TYPE 99 165 313

Figure S435.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'MRNA_CNMF'

P value = 5.59e-05 (Chi-square test), Q value = 0.029

Table S436.  Gene #65: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
13Q LOSS MUTATED 7 14 62 51 30 38 9 8
13Q LOSS WILD-TYPE 14 22 57 45 79 34 11 32

Figure S436.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q loss' versus 'MRNA_CHIERARCHICAL'

P value = 6.32e-06 (Fisher's exact test), Q value = 0.0036

Table S437.  Gene #65: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
13Q LOSS MUTATED 31 69 119
13Q LOSS WILD-TYPE 91 56 147

Figure S437.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 4.63e-24 (Chi-square test), Q value = 4.3e-21

Table S438.  Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
13Q LOSS MUTATED 70 141 52 119 26
13Q LOSS WILD-TYPE 301 117 45 117 19

Figure S438.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 1.96e-08 (Chi-square test), Q value = 1.3e-05

Table S439.  Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
13Q LOSS MUTATED 68 43 52 64 11 35
13Q LOSS WILD-TYPE 48 112 56 75 44 77

Figure S439.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1.92e-08 (Fisher's exact test), Q value = 1.3e-05

Table S440.  Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
13Q LOSS MUTATED 141 45 219
13Q LOSS WILD-TYPE 132 141 323

Figure S440.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.62e-09 (Fisher's exact test), Q value = 2.6e-06

Table S441.  Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
13Q LOSS MUTATED 124 189 92
13Q LOSS WILD-TYPE 109 250 237

Figure S441.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 5.96e-08 (Fisher's exact test), Q value = 4e-05

Table S442.  Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
13Q LOSS MUTATED 169 81 150
13Q LOSS WILD-TYPE 229 206 142

Figure S442.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.39e-07 (Fisher's exact test), Q value = 8.9e-05

Table S443.  Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
13Q LOSS MUTATED 135 129 136
13Q LOSS WILD-TYPE 117 170 290

Figure S443.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.18e-07 (Fisher's exact test), Q value = 0.00014

Table S444.  Gene #65: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
13Q LOSS MUTATED 89 63 108
13Q LOSS WILD-TYPE 161 156 90

Figure S444.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000194 (Fisher's exact test), Q value = 0.09

Table S445.  Gene #65: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
13Q LOSS MUTATED 77 55 128
13Q LOSS WILD-TYPE 68 122 217

Figure S445.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

P value = 1.2e-14 (Chi-square test), Q value = 1e-11

Table S446.  Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
14Q LOSS MUTATED 3 1 30 50 7 14 9 5
14Q LOSS WILD-TYPE 18 35 89 46 102 58 11 35

Figure S446.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 5.9e-10 (Fisher's exact test), Q value = 4.4e-07

Table S447.  Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
14Q LOSS MUTATED 14 56 49
14Q LOSS WILD-TYPE 108 69 217

Figure S447.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 4.64e-35 (Chi-square test), Q value = 4.4e-32

Table S448.  Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
14Q LOSS MUTATED 32 53 19 127 9
14Q LOSS WILD-TYPE 339 205 78 109 36

Figure S448.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1.67e-20 (Chi-square test), Q value = 1.5e-17

Table S449.  Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
14Q LOSS MUTATED 68 13 28 31 7 20
14Q LOSS WILD-TYPE 48 142 80 108 48 92

Figure S449.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 5.79e-06 (Fisher's exact test), Q value = 0.0033

Table S450.  Gene #66: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
14Q LOSS MUTATED 54 16 25
14Q LOSS WILD-TYPE 93 117 92

Figure S450.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 4.45e-06 (Fisher's exact test), Q value = 0.0026

Table S451.  Gene #66: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
14Q LOSS MUTATED 24 21 50
14Q LOSS WILD-TYPE 137 89 76

Figure S451.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1.61e-22 (Fisher's exact test), Q value = 1.5e-19

Table S452.  Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
14Q LOSS MUTATED 125 17 97
14Q LOSS WILD-TYPE 148 169 445

Figure S452.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.56e-24 (Fisher's exact test), Q value = 7.9e-21

Table S453.  Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
14Q LOSS MUTATED 115 85 39
14Q LOSS WILD-TYPE 118 354 290

Figure S453.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 2.3e-21 (Fisher's exact test), Q value = 2.1e-18

Table S454.  Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
14Q LOSS MUTATED 63 38 130
14Q LOSS WILD-TYPE 335 249 162

Figure S454.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.63e-23 (Fisher's exact test), Q value = 1.5e-20

Table S455.  Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
14Q LOSS MUTATED 121 53 57
14Q LOSS WILD-TYPE 131 246 369

Figure S455.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.32e-17 (Fisher's exact test), Q value = 2.1e-14

Table S456.  Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
14Q LOSS MUTATED 44 29 96
14Q LOSS WILD-TYPE 206 190 102

Figure S456.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.04e-15 (Fisher's exact test), Q value = 9e-13

Table S457.  Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
14Q LOSS MUTATED 77 28 64
14Q LOSS WILD-TYPE 68 149 281

Figure S457.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'MRNA_CNMF'

P value = 1.95e-05 (Chi-square test), Q value = 0.011

Table S458.  Gene #67: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
15Q LOSS MUTATED 4 9 31 45 22 33 8 6
15Q LOSS WILD-TYPE 17 27 88 51 87 39 12 34

Figure S458.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1.14e-05 (Fisher's exact test), Q value = 0.0064

Table S459.  Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
15Q LOSS MUTATED 20 55 83
15Q LOSS WILD-TYPE 102 70 183

Figure S459.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 5.12e-31 (Chi-square test), Q value = 4.8e-28

Table S460.  Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
15Q LOSS MUTATED 37 78 47 126 14
15Q LOSS WILD-TYPE 334 180 50 110 31

Figure S460.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 5.11e-13 (Chi-square test), Q value = 4.2e-10

Table S461.  Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
15Q LOSS MUTATED 66 24 35 48 10 22
15Q LOSS WILD-TYPE 50 131 73 91 45 90

Figure S461.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1.1e-15 (Fisher's exact test), Q value = 9.5e-13

Table S462.  Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
15Q LOSS MUTATED 126 21 153
15Q LOSS WILD-TYPE 147 165 389

Figure S462.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.92e-13 (Fisher's exact test), Q value = 2.4e-10

Table S463.  Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
15Q LOSS MUTATED 106 140 54
15Q LOSS WILD-TYPE 127 299 275

Figure S463.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 3.14e-14 (Fisher's exact test), Q value = 2.6e-11

Table S464.  Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
15Q LOSS MUTATED 109 46 133
15Q LOSS WILD-TYPE 289 241 159

Figure S464.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.21e-13 (Fisher's exact test), Q value = 4.3e-10

Table S465.  Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
15Q LOSS MUTATED 121 79 88
15Q LOSS WILD-TYPE 131 220 338

Figure S465.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.27e-10 (Fisher's exact test), Q value = 1.7e-07

Table S466.  Gene #67: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
15Q LOSS MUTATED 72 33 88
15Q LOSS WILD-TYPE 178 186 110

Figure S466.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.46e-09 (Fisher's exact test), Q value = 4.6e-06

Table S467.  Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
15Q LOSS MUTATED 69 29 95
15Q LOSS WILD-TYPE 76 148 250

Figure S467.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 0.000206 (Chi-square test), Q value = 0.095

Table S468.  Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
16P LOSS MUTATED 44 36 11 59 6
16P LOSS WILD-TYPE 327 222 86 177 39

Figure S468.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 0.000177 (Fisher's exact test), Q value = 0.083

Table S469.  Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
16P LOSS MUTATED 47 39 68
16P LOSS WILD-TYPE 351 248 224

Figure S469.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000129 (Fisher's exact test), Q value = 0.062

Table S470.  Gene #68: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
16P LOSS MUTATED 27 32 51
16P LOSS WILD-TYPE 223 187 147

Figure S470.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MRNA_CNMF'

P value = 3.87e-09 (Chi-square test), Q value = 2.8e-06

Table S471.  Gene #69: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
16Q LOSS MUTATED 12 21 62 28 82 40 12 31
16Q LOSS WILD-TYPE 9 15 57 68 27 32 8 9

Figure S471.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2.06e-10 (Fisher's exact test), Q value = 1.6e-07

Table S472.  Gene #69: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
16Q LOSS MUTATED 79 38 171
16Q LOSS WILD-TYPE 43 87 95

Figure S472.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 3.9e-10 (Chi-square test), Q value = 2.9e-07

Table S473.  Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
16Q LOSS MUTATED 224 140 76 93 28
16Q LOSS WILD-TYPE 147 118 21 143 17

Figure S473.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 4.28e-12 (Chi-square test), Q value = 3.4e-09

Table S474.  Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
16Q LOSS MUTATED 42 119 74 64 26 54
16Q LOSS WILD-TYPE 74 36 34 75 29 58

Figure S474.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'RPPA_CNMF'

P value = 0.000111 (Fisher's exact test), Q value = 0.054

Table S475.  Gene #69: '16q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
16Q LOSS MUTATED 59 86 68
16Q LOSS WILD-TYPE 88 47 49

Figure S475.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'16q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1.09e-06 (Fisher's exact test), Q value = 0.00066

Table S476.  Gene #69: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
16Q LOSS MUTATED 105 64 44
16Q LOSS WILD-TYPE 56 46 82

Figure S476.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 3.97e-16 (Fisher's exact test), Q value = 3.4e-13

Table S477.  Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
16Q LOSS MUTATED 94 126 338
16Q LOSS WILD-TYPE 179 60 204

Figure S477.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.88e-17 (Fisher's exact test), Q value = 4.3e-14

Table S478.  Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
16Q LOSS MUTATED 75 259 224
16Q LOSS WILD-TYPE 158 180 105

Figure S478.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 4.5e-13 (Fisher's exact test), Q value = 3.7e-10

Table S479.  Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
16Q LOSS MUTATED 245 190 110
16Q LOSS WILD-TYPE 153 97 182

Figure S479.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.3e-18 (Fisher's exact test), Q value = 6.5e-15

Table S480.  Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
16Q LOSS MUTATED 95 148 302
16Q LOSS WILD-TYPE 157 151 124

Figure S480.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.84e-08 (Fisher's exact test), Q value = 1.3e-05

Table S481.  Gene #69: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
16Q LOSS MUTATED 144 148 77
16Q LOSS WILD-TYPE 106 71 121

Figure S481.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.95e-07 (Fisher's exact test), Q value = 0.00012

Table S482.  Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
16Q LOSS MUTATED 52 116 201
16Q LOSS WILD-TYPE 93 61 144

Figure S482.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 3.58e-09 (Chi-square test), Q value = 2.6e-06

Table S483.  Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
17P LOSS MUTATED 13 23 68 61 30 56 11 21
17P LOSS WILD-TYPE 8 13 51 35 79 16 9 19

Figure S483.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 3.99e-22 (Chi-square test), Q value = 3.7e-19

Table S484.  Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
17P LOSS MUTATED 129 168 47 174 22
17P LOSS WILD-TYPE 242 90 50 62 23

Figure S484.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1.6e-06 (Chi-square test), Q value = 0.00095

Table S485.  Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
17P LOSS MUTATED 73 62 62 89 26 41
17P LOSS WILD-TYPE 43 93 46 50 29 71

Figure S485.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'RPPA_CNMF'

P value = 8.96e-07 (Fisher's exact test), Q value = 0.00054

Table S486.  Gene #70: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
17P LOSS MUTATED 106 56 59
17P LOSS WILD-TYPE 41 77 58

Figure S486.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 6.78e-06 (Fisher's exact test), Q value = 0.0038

Table S487.  Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
17P LOSS MUTATED 179 83 275
17P LOSS WILD-TYPE 94 103 267

Figure S487.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000454 (Fisher's exact test), Q value = 0.19

Table S488.  Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
17P LOSS MUTATED 148 235 154
17P LOSS WILD-TYPE 85 204 175

Figure S488.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 5.22e-08 (Fisher's exact test), Q value = 3.5e-05

Table S489.  Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
17P LOSS MUTATED 201 127 196
17P LOSS WILD-TYPE 197 160 96

Figure S489.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.92e-05 (Fisher's exact test), Q value = 0.035

Table S490.  Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
17P LOSS MUTATED 163 159 202
17P LOSS WILD-TYPE 89 140 224

Figure S490.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.09e-05 (Fisher's exact test), Q value = 0.0061

Table S491.  Gene #70: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
17P LOSS MUTATED 129 93 130
17P LOSS WILD-TYPE 121 126 68

Figure S491.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q loss' versus 'MRNA_CNMF'

P value = 2.24e-12 (Chi-square test), Q value = 1.8e-09

Table S492.  Gene #71: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
17Q LOSS MUTATED 4 4 22 51 13 34 4 12
17Q LOSS WILD-TYPE 17 32 97 45 96 38 16 28

Figure S492.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q loss' versus 'MRNA_CHIERARCHICAL'

P value = 3.34e-10 (Fisher's exact test), Q value = 2.5e-07

Table S493.  Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
17Q LOSS MUTATED 24 65 55
17Q LOSS WILD-TYPE 98 60 211

Figure S493.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 5.74e-22 (Chi-square test), Q value = 5.3e-19

Table S494.  Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
17Q LOSS MUTATED 50 57 25 117 6
17Q LOSS WILD-TYPE 321 201 72 119 39

Figure S494.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 2.51e-15 (Chi-square test), Q value = 2.2e-12

Table S495.  Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
17Q LOSS MUTATED 58 13 17 31 5 27
17Q LOSS WILD-TYPE 58 142 91 108 50 85

Figure S495.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'RPPA_CNMF'

P value = 7.36e-10 (Fisher's exact test), Q value = 5.4e-07

Table S496.  Gene #71: '17q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
17Q LOSS MUTATED 70 17 32
17Q LOSS WILD-TYPE 77 116 85

Figure S496.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'17q loss' versus 'RPPA_CHIERARCHICAL'

P value = 2.44e-10 (Fisher's exact test), Q value = 1.8e-07

Table S497.  Gene #71: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
17Q LOSS MUTATED 27 26 66
17Q LOSS WILD-TYPE 134 84 60

Figure S497.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 6.55e-18 (Fisher's exact test), Q value = 5.8e-15

Table S498.  Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
17Q LOSS MUTATED 125 31 96
17Q LOSS WILD-TYPE 148 155 446

Figure S498.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.78e-17 (Fisher's exact test), Q value = 5.1e-14

Table S499.  Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
17Q LOSS MUTATED 111 82 59
17Q LOSS WILD-TYPE 122 357 270

Figure S499.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 5.94e-13 (Fisher's exact test), Q value = 4.8e-10

Table S500.  Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
17Q LOSS MUTATED 76 50 122
17Q LOSS WILD-TYPE 322 237 170

Figure S500.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.54e-16 (Fisher's exact test), Q value = 7.4e-13

Table S501.  Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
17Q LOSS MUTATED 114 65 69
17Q LOSS WILD-TYPE 138 234 357

Figure S501.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.07e-09 (Fisher's exact test), Q value = 4.3e-06

Table S502.  Gene #71: '17q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
17Q LOSS MUTATED 50 35 81
17Q LOSS WILD-TYPE 200 184 117

Figure S502.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.74e-07 (Fisher's exact test), Q value = 0.00017

Table S503.  Gene #71: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
17Q LOSS MUTATED 61 28 77
17Q LOSS WILD-TYPE 84 149 268

Figure S503.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'MRNA_CNMF'

P value = 0.000251 (Chi-square test), Q value = 0.11

Table S504.  Gene #72: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
18P LOSS MUTATED 6 11 36 27 19 38 9 13
18P LOSS WILD-TYPE 15 25 83 69 90 34 11 27

Figure S504.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 2.9e-13 (Chi-square test), Q value = 2.4e-10

Table S505.  Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
18P LOSS MUTATED 58 105 41 88 10
18P LOSS WILD-TYPE 313 153 56 148 35

Figure S505.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 3.78e-07 (Chi-square test), Q value = 0.00023

Table S506.  Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
18P LOSS MUTATED 33 25 48 58 12 27
18P LOSS WILD-TYPE 83 130 60 81 43 85

Figure S506.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNA_CNMF'

P value = 0.000199 (Chi-square test), Q value = 0.092

Table S507.  Gene #73: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
18Q LOSS MUTATED 5 11 34 27 19 38 7 9
18Q LOSS WILD-TYPE 16 25 85 69 90 34 13 31

Figure S507.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 1.05e-15 (Chi-square test), Q value = 9e-13

Table S508.  Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
18Q LOSS MUTATED 54 105 42 93 9
18Q LOSS WILD-TYPE 317 153 55 143 36

Figure S508.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1.48e-08 (Chi-square test), Q value = 1e-05

Table S509.  Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
18Q LOSS MUTATED 40 25 49 60 11 24
18Q LOSS WILD-TYPE 76 130 59 79 44 88

Figure S509.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 0.000263 (Fisher's exact test), Q value = 0.12

Table S510.  Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
18Q LOSS MUTATED 98 35 167
18Q LOSS WILD-TYPE 175 151 375

Figure S510.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.27e-06 (Fisher's exact test), Q value = 0.0036

Table S511.  Gene #73: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
18Q LOSS MUTATED 78 42 81
18Q LOSS WILD-TYPE 172 177 117

Figure S511.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MRNA_CNMF'

P value = 2.62e-05 (Chi-square test), Q value = 0.014

Table S512.  Gene #74: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
19P LOSS MUTATED 3 6 30 20 8 25 1 2
19P LOSS WILD-TYPE 18 30 89 76 101 47 19 38

Figure S512.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p loss' versus 'MRNA_CHIERARCHICAL'

P value = 2.68e-05 (Fisher's exact test), Q value = 0.014

Table S513.  Gene #74: '19p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
19P LOSS MUTATED 7 25 63
19P LOSS WILD-TYPE 115 100 203

Figure S513.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1.57e-20 (Chi-square test), Q value = 1.4e-17

Table S514.  Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
19P LOSS MUTATED 17 85 9 60 8
19P LOSS WILD-TYPE 354 173 88 176 37

Figure S514.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 2.89e-12 (Chi-square test), Q value = 2.3e-09

Table S515.  Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
19P LOSS MUTATED 31 5 16 47 4 13
19P LOSS WILD-TYPE 85 150 92 92 51 99

Figure S515.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 3.19e-08 (Fisher's exact test), Q value = 2.2e-05

Table S516.  Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
19P LOSS MUTATED 69 10 99
19P LOSS WILD-TYPE 204 176 443

Figure S516.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.77e-11 (Fisher's exact test), Q value = 4.5e-08

Table S517.  Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
19P LOSS MUTATED 52 104 22
19P LOSS WILD-TYPE 181 335 307

Figure S517.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 4.11e-11 (Fisher's exact test), Q value = 3.2e-08

Table S518.  Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
19P LOSS MUTATED 71 19 81
19P LOSS WILD-TYPE 327 268 211

Figure S518.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.21e-12 (Fisher's exact test), Q value = 6.5e-09

Table S519.  Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
19P LOSS MUTATED 62 75 34
19P LOSS WILD-TYPE 190 224 392

Figure S519.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.16e-09 (Fisher's exact test), Q value = 4.4e-06

Table S520.  Gene #74: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
19P LOSS MUTATED 41 15 58
19P LOSS WILD-TYPE 209 204 140

Figure S520.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.53e-05 (Fisher's exact test), Q value = 0.033

Table S521.  Gene #74: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
19P LOSS MUTATED 40 16 58
19P LOSS WILD-TYPE 105 161 287

Figure S521.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000338 (Fisher's exact test), Q value = 0.15

Table S522.  Gene #75: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
19Q LOSS MUTATED 6 19 52
19Q LOSS WILD-TYPE 116 106 214

Figure S522.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 2.51e-18 (Chi-square test), Q value = 2.2e-15

Table S523.  Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
19Q LOSS MUTATED 16 77 5 45 9
19Q LOSS WILD-TYPE 355 181 92 191 36

Figure S523.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 3.8e-08 (Chi-square test), Q value = 2.6e-05

Table S524.  Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
19Q LOSS MUTATED 24 4 17 37 2 16
19Q LOSS WILD-TYPE 92 151 91 102 53 96

Figure S524.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1.02e-07 (Fisher's exact test), Q value = 6.6e-05

Table S525.  Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
19Q LOSS MUTATED 58 7 87
19Q LOSS WILD-TYPE 215 179 455

Figure S525.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.8e-12 (Fisher's exact test), Q value = 1.4e-09

Table S526.  Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
19Q LOSS MUTATED 46 92 14
19Q LOSS WILD-TYPE 187 347 315

Figure S526.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1e-08 (Fisher's exact test), Q value = 7e-06

Table S527.  Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
19Q LOSS MUTATED 62 17 68
19Q LOSS WILD-TYPE 336 270 224

Figure S527.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.52e-09 (Fisher's exact test), Q value = 2.5e-06

Table S528.  Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
19Q LOSS MUTATED 49 67 31
19Q LOSS WILD-TYPE 203 232 395

Figure S528.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.8e-07 (Fisher's exact test), Q value = 0.00059

Table S529.  Gene #75: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
19Q LOSS MUTATED 36 13 47
19Q LOSS WILD-TYPE 214 206 151

Figure S529.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p loss' versus 'CN_CNMF'

P value = 1.09e-10 (Chi-square test), Q value = 8.4e-08

Table S530.  Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
20P LOSS MUTATED 9 26 5 45 3
20P LOSS WILD-TYPE 362 232 92 191 42

Figure S530.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 9.22e-12 (Chi-square test), Q value = 7.3e-09

Table S531.  Gene #76: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
20P LOSS MUTATED 32 5 9 11 3 3
20P LOSS WILD-TYPE 84 150 99 128 52 109

Figure S531.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 4.88e-11 (Fisher's exact test), Q value = 3.8e-08

Table S532.  Gene #76: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
20P LOSS MUTATED 51 3 34
20P LOSS WILD-TYPE 222 183 508

Figure S532.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.75e-11 (Fisher's exact test), Q value = 3.7e-08

Table S533.  Gene #76: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
20P LOSS MUTATED 45 35 8
20P LOSS WILD-TYPE 188 404 321

Figure S533.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_CNMF'

P value = 2.89e-10 (Fisher's exact test), Q value = 2.2e-07

Table S534.  Gene #76: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
20P LOSS MUTATED 20 10 52
20P LOSS WILD-TYPE 378 277 240

Figure S534.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.47e-10 (Fisher's exact test), Q value = 4.8e-07

Table S535.  Gene #76: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
20P LOSS MUTATED 43 27 12
20P LOSS WILD-TYPE 209 272 414

Figure S535.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.23e-08 (Fisher's exact test), Q value = 2.2e-05

Table S536.  Gene #76: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
20P LOSS MUTATED 10 9 37
20P LOSS WILD-TYPE 240 210 161

Figure S536.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.91e-09 (Fisher's exact test), Q value = 6.2e-06

Table S537.  Gene #76: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
20P LOSS MUTATED 32 8 16
20P LOSS WILD-TYPE 113 169 329

Figure S537.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q loss' versus 'CN_CNMF'

P value = 1.03e-07 (Chi-square test), Q value = 6.7e-05

Table S538.  Gene #77: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
20Q LOSS MUTATED 4 12 4 29 2
20Q LOSS WILD-TYPE 367 246 93 207 43

Figure S538.  Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

'20q loss' versus 'METHLYATION_CNMF'

P value = 2.92e-10 (Chi-square test), Q value = 2.2e-07

Table S539.  Gene #77: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
20Q LOSS MUTATED 22 3 2 5 1 3
20Q LOSS WILD-TYPE 94 152 106 134 54 109

Figure S539.  Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q loss' versus 'MRNASEQ_CNMF'

P value = 5.07e-08 (Fisher's exact test), Q value = 3.4e-05

Table S540.  Gene #77: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
20Q LOSS MUTATED 33 3 15
20Q LOSS WILD-TYPE 240 183 527

Figure S540.  Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.23e-08 (Fisher's exact test), Q value = 8.5e-06

Table S541.  Gene #77: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
20Q LOSS MUTATED 31 14 6
20Q LOSS WILD-TYPE 202 425 323

Figure S541.  Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_CNMF'

P value = 4.39e-07 (Fisher's exact test), Q value = 0.00027

Table S542.  Gene #77: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
20Q LOSS MUTATED 8 8 32
20Q LOSS WILD-TYPE 390 279 260

Figure S542.  Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.88e-08 (Fisher's exact test), Q value = 3.3e-05

Table S543.  Gene #77: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
20Q LOSS MUTATED 31 7 10
20Q LOSS WILD-TYPE 221 292 416

Figure S543.  Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.61e-08 (Fisher's exact test), Q value = 5.6e-05

Table S544.  Gene #77: '20q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
20Q LOSS MUTATED 2 7 25
20Q LOSS WILD-TYPE 248 212 173

Figure S544.  Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.15e-09 (Fisher's exact test), Q value = 5e-06

Table S545.  Gene #77: '20q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
20Q LOSS MUTATED 23 6 5
20Q LOSS WILD-TYPE 122 171 340

Figure S545.  Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 1.38e-12 (Chi-square test), Q value = 1.1e-09

Table S546.  Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
21Q LOSS MUTATED 19 71 18 48 10
21Q LOSS WILD-TYPE 352 187 79 188 35

Figure S546.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 3.17e-11 (Chi-square test), Q value = 2.5e-08

Table S547.  Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
22Q LOSS MUTATED 121 141 66 102 24
22Q LOSS WILD-TYPE 250 117 31 134 21

Figure S547.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1.29e-05 (Chi-square test), Q value = 0.0071

Table S548.  Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
22Q LOSS MUTATED 51 60 52 87 17 38
22Q LOSS WILD-TYPE 65 95 56 52 38 74

Figure S548.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 3.65e-05 (Fisher's exact test), Q value = 0.019

Table S549.  Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
22Q LOSS MUTATED 97 76 279
22Q LOSS WILD-TYPE 176 110 263

Figure S549.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 4.8e-11 (Chi-square test), Q value = 3.7e-08

Table S550.  Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
XQ LOSS MUTATED 24 62 14 62 6
XQ LOSS WILD-TYPE 347 196 83 174 39

Figure S550.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 2.47e-05 (Chi-square test), Q value = 0.013

Table S551.  Gene #80: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
XQ LOSS MUTATED 26 15 24 34 6 6
XQ LOSS WILD-TYPE 90 140 84 105 49 106

Figure S551.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.000245 (Fisher's exact test), Q value = 0.11

Table S552.  Gene #80: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
XQ LOSS MUTATED 56 14 98
XQ LOSS WILD-TYPE 217 172 444

Figure S552.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.47e-05 (Fisher's exact test), Q value = 0.018

Table S553.  Gene #80: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
XQ LOSS MUTATED 47 90 31
XQ LOSS WILD-TYPE 186 349 298

Figure S553.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 2.47e-05 (Fisher's exact test), Q value = 0.013

Table S554.  Gene #80: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
XQ LOSS MUTATED 77 25 62
XQ LOSS WILD-TYPE 321 262 230

Figure S554.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000113 (Fisher's exact test), Q value = 0.055

Table S555.  Gene #80: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
XQ LOSS MUTATED 45 70 49
XQ LOSS WILD-TYPE 207 229 377

Figure S555.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Molecular subtypes file = BRCA-TP.transferedmergedcluster.txt

  • Number of patients = 1007

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have mutations, K = 3

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[2] 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)
[3] 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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