Correlation between copy number variation genes (focal events) and molecular subtypes
Lung Squamous Cell Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C17D2T6R
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C17D2T6R
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 83 focal events and 12 molecular subtypes across 501 patients, 511 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1q21.2 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_2p16.1 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'.

  • amp_2q31.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_3q26.33 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'.

  • amp_4q12 cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_5p15.33 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_5p12 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_6p12.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_6q12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_7p11.2 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_7q21.2 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_8p11.23 cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • amp_8q24.21 cnv correlated to 'CN_CNMF'.

  • amp_9p13.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_11q13.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_12p13.33 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_12q15 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_13q34 cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • amp_14q13.3 cnv correlated to 'MRNA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • amp_14q32.33 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_15q26.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_17q25.1 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_18p11.32 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_18q11.2 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'.

  • amp_19q12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_19q13.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_20p12.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_20q11.21 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_22q11.21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_xq28 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_1p36.11 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'.

  • del_1p13.1 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'.

  • del_2p25.3 cnv correlated to 'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_2q22.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_2q37.1 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'.

  • del_3p25.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_3p13 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3p12.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3p12.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_4p15.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_4q22.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_4q32.3 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'.

  • del_4q35.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_5q12.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_5q31.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_6p25.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_6q22.31 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_6q26 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • del_7q11.22 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_7q36.3 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_8p23.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_9p23 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_9p21.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_9p21.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_9q21.11 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_10p15.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_10q23.31 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'.

  • del_11p15.5 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_11q22.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_11q25 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • del_13q12.11 cnv correlated to 'CN_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_13q14.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_14q11.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_15q11.2 cnv correlated to 'RPPA_CHIERARCHICAL' and 'MIRSEQ_CNMF'.

  • del_15q21.1 cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_16p13.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • del_16q23.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_17p11.2 cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_17q11.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_17q25.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_18q23 cnv correlated to 'CN_CNMF'.

  • del_19p13.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_19q13.32 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • del_21q11.2 cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_21q22.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_22q11.21 cnv correlated to 'MRNA_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_22q13.32 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_xp22.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_xp21.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_xp11.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_xq22.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 83 focal 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, 511 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
amp 3q26 33 452 (90%) 49 0.00044
(0.00198) 		0.00059
(0.00254) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		0.268
(0.375) 		0.0322
(0.0669) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		0.00013
(0.000771) 		1e-05
(8.51e-05) 		0.0186
(0.0425) 		4e-05
(0.000271)
del 1p36 11 228 (46%) 273 3e-05
(0.000209) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		0.0541
(0.104) 		0.00338
(0.0103) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		2e-05
(0.000151) 		1e-05
(8.51e-05)
del 1p13 1 221 (44%) 280 0.00016
(0.000895) 		2e-05
(0.000151) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		0.0231
(0.0508) 		0.204
(0.304) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		0.00042
(0.00192) 		2e-05
(0.000151)
amp 2p16 1 275 (55%) 226 0.0014
(0.00507) 		0.00023
(0.00121) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		0.95
(0.96) 		0.67
(0.75) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		0.00038
(0.00179) 		0.00055
(0.00238) 		0.0312
(0.0651) 		3e-05
(0.000209)
amp 18q11 2 151 (30%) 350 0.00048
(0.00211) 		0.015
(0.0359) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		0.255
(0.364) 		0.748
(0.813) 		1e-05
(8.51e-05) 		5e-05
(0.000332) 		0.0119
(0.0297) 		0.00305
(0.00961) 		0.0498
(0.097) 		4e-05
(0.000271)
del 2q37 1 159 (32%) 342 0.00315
(0.0098) 		0.00071
(0.00298) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		0.386
(0.495) 		0.188
(0.287) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		2e-05
(0.000151) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05)
del 4q32 3 329 (66%) 172 0.00651
(0.0177) 		0.0194
(0.044) 		1e-05
(8.51e-05) 		8e-05
(0.000498) 		0.0682
(0.126) 		0.778
(0.832) 		1e-05
(8.51e-05) 		0.00029
(0.00143) 		0.00073
(0.00303) 		0.00252
(0.00828) 		0.00393
(0.0118) 		1e-05
(8.51e-05)
del 10q23 31 268 (53%) 233 0.00318
(0.00987) 		0.00091
(0.00358) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		0.15
(0.241) 		0.247
(0.357) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		0.00126
(0.00467) 		2e-05
(0.000151) 		0.0222
(0.0492) 		0.00028
(0.00139)
amp 1q21 2 258 (51%) 243 0.0394
(0.0791) 		0.1
(0.176) 		1e-05
(8.51e-05) 		2e-05
(0.000151) 		0.182
(0.279) 		0.0741
(0.136) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		2e-05
(0.000151) 		0.00087
(0.00344) 		0.00412
(0.0121)
amp 2q31 2 172 (34%) 329 0.0196
(0.0442) 		0.0225
(0.0498) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		0.726
(0.796) 		0.636
(0.722) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		0.00273
(0.00877) 		0.255
(0.364) 		0.00333
(0.0102) 		0.00044
(0.00198)
amp 7q21 2 264 (53%) 237 0.102
(0.178) 		0.015
(0.0359) 		1e-05
(8.51e-05) 		2e-05
(0.000151) 		0.0765
(0.139) 		0.559
(0.659) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		0.00017
(0.00093) 		0.00096
(0.00373) 		0.0016
(0.00565) 		0.00079
(0.00319)
amp 9p13 3 136 (27%) 365 0.124
(0.207) 		0.717
(0.79) 		0.00181
(0.00628) 		0.00256
(0.00839) 		0.0688
(0.127) 		0.00302
(0.00955) 		0.00145
(0.00519) 		0.00135
(0.00494) 		0.00665
(0.0179) 		0.00335
(0.0103) 		0.0167
(0.0388) 		0.0126
(0.0311)
amp 15q26 3 179 (36%) 322 0.362
(0.473) 		0.0503
(0.0978) 		1e-05
(8.51e-05) 		0.00033
(0.00159) 		0.459
(0.569) 		0.027
(0.0579) 		3e-05
(0.000209) 		0.00286
(0.00916) 		0.0392
(0.0789) 		0.00638
(0.0175) 		0.00716
(0.0192) 		0.00433
(0.0126)
amp 17q25 1 236 (47%) 265 0.00839
(0.0218) 		0.137
(0.224) 		1e-05
(8.51e-05) 		2e-05
(0.000151) 		0.402
(0.509) 		0.518
(0.623) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		0.00039
(0.00182) 		0.00468
(0.0135) 		0.00122
(0.00453) 		0.00021
(0.00111)
del 3p13 434 (87%) 67 0.253
(0.363) 		0.357
(0.47) 		1e-05
(8.51e-05) 		6e-05
(0.000393) 		0.784
(0.835) 		0.00111
(0.00419) 		0.00076
(0.0031) 		0.00082
(0.00327) 		0.00206
(0.00696) 		1e-05
(8.51e-05) 		0.00075
(0.00309) 		0.00019
(0.00102)
del 3p12 3 427 (85%) 74 0.277
(0.383) 		0.226
(0.331) 		1e-05
(8.51e-05) 		3e-05
(0.000209) 		0.937
(0.949) 		0.00153
(0.00542) 		0.00044
(0.00198) 		0.00493
(0.0141) 		0.0233
(0.0512) 		1e-05
(8.51e-05) 		0.0004
(0.00184) 		0.0011
(0.00417)
del 3p12 3 421 (84%) 80 0.228
(0.333) 		0.394
(0.502) 		1e-05
(8.51e-05) 		0.00012
(0.000716) 		0.969
(0.975) 		0.00653
(0.0177) 		0.00273
(0.00877) 		0.00769
(0.0203) 		0.0257
(0.0557) 		3e-05
(0.000209) 		0.00221
(0.00739) 		0.00301
(0.00955)
del 4p15 2 317 (63%) 184 0.00017
(0.00093) 		3e-05
(0.000209) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		0.775
(0.831) 		0.0642
(0.12) 		0.00014
(0.00082) 		1e-05
(8.51e-05) 		0.00204
(0.00691) 		0.052
(0.101) 		0.00019
(0.00102) 		1e-05
(8.51e-05)
del 4q22 1 285 (57%) 216 0.00297
(0.00945) 		0.00474
(0.0136) 		1e-05
(8.51e-05) 		0.00103
(0.00393) 		0.118
(0.2) 		0.514
(0.619) 		0.00022
(0.00116) 		0.0147
(0.0353) 		0.0164
(0.0383) 		0.00568
(0.0159) 		0.0557
(0.107) 		0.0178
(0.0408)
del 9q21 11 251 (50%) 250 0.00027
(0.00135) 		5e-05
(0.000332) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		0.561
(0.66) 		0.144
(0.234) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		0.051
(0.099) 		0.00963
(0.0247)
del 11p15 5 245 (49%) 256 0.00048
(0.00211) 		0.0118
(0.0295) 		1e-05
(8.51e-05) 		0.00309
(0.00971) 		0.00034
(0.00162) 		0.00026
(0.00132) 		0.00664
(0.0179) 		0.0818
(0.147) 		0.00064
(0.00274) 		0.0868
(0.156) 		0.735
(0.802) 		0.00403
(0.012)
del 17q11 2 132 (26%) 369 0.00012
(0.000716) 		8e-05
(0.000498) 		1e-05
(8.51e-05) 		6e-05
(0.000393) 		0.388
(0.495) 		0.564
(0.661) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		0.00405
(0.012) 		0.00129
(0.00476) 		0.274
(0.381) 		0.00034
(0.00162)
del xq22 3 114 (23%) 387 0.0213
(0.0477) 		0.01
(0.0256) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		0.865
(0.9) 		0.89
(0.916) 		0.00117
(0.00436) 		0.333
(0.447) 		0.00573
(0.0159) 		0.00014
(0.00082) 		0.00854
(0.0221) 		0.00031
(0.00151)
amp 11q13 3 185 (37%) 316 0.0469
(0.0927) 		0.0345
(0.0708) 		1e-05
(8.51e-05) 		0.00073
(0.00303) 		0.26
(0.367) 		0.337
(0.452) 		0.0307
(0.0642) 		0.063
(0.119) 		0.00133
(0.00489) 		0.00517
(0.0147) 		0.191
(0.291) 		0.00273
(0.00877)
amp 12p13 33 255 (51%) 246 0.00792
(0.0207) 		0.0217
(0.0484) 		1e-05
(8.51e-05) 		0.0049
(0.014) 		0.353
(0.469) 		0.635
(0.721) 		1e-05
(8.51e-05) 		0.00162
(0.00568) 		0.134
(0.221) 		0.00273
(0.00877) 		0.251
(0.361) 		0.00602
(0.0167)
amp 18p11 32 179 (36%) 322 0.0436
(0.0867) 		0.0044
(0.0128) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		0.504
(0.612) 		0.979
(0.982) 		0.0409
(0.0819) 		0.00148
(0.00528) 		0.019
(0.0432) 		0.0963
(0.17) 		0.0732
(0.135) 		0.00027
(0.00135)
del 2q22 1 131 (26%) 370 0.32
(0.434) 		0.333
(0.447) 		1e-05
(8.51e-05) 		0.00072
(0.00301) 		0.384
(0.493) 		0.422
(0.532) 		0.00219
(0.00734) 		0.00735
(0.0195) 		0.00016
(0.000895) 		0.00048
(0.00211) 		0.0193
(0.0438) 		0.0242
(0.0528)
del 4q35 2 331 (66%) 170 0.0691
(0.127) 		0.204
(0.305) 		1e-05
(8.51e-05) 		2e-05
(0.000151) 		0.36
(0.472) 		0.861
(0.897) 		3e-05
(0.000209) 		0.00344
(0.0105) 		0.00054
(0.00235) 		0.00743
(0.0197) 		0.0485
(0.095) 		1e-05
(8.51e-05)
del 6q26 134 (27%) 367 0.0416
(0.0829) 		0.00462
(0.0134) 		0.00021
(0.00111) 		8e-05
(0.000498) 		0.921
(0.94) 		0.658
(0.739) 		0.00046
(0.00206) 		0.00607
(0.0167) 		0.0173
(0.04) 		0.0735
(0.135) 		0.0328
(0.068) 		0.103
(0.178)
del 9p23 332 (66%) 169 0.0104
(0.0263) 		0.00184
(0.00636) 		1e-05
(8.51e-05) 		0.0304
(0.0641) 		0.192
(0.291) 		0.169
(0.263) 		0.00017
(0.00093) 		0.00098
(0.0038) 		0.0107
(0.0271) 		0.00015
(0.000864) 		0.623
(0.712) 		0.13
(0.216)
del 10p15 2 219 (44%) 282 0.262
(0.368) 		0.466
(0.576) 		2e-05
(0.000151) 		1e-05
(8.51e-05) 		0.147
(0.239) 		0.142
(0.232) 		1e-05
(8.51e-05) 		0.00012
(0.000716) 		4e-05
(0.000271) 		1e-05
(8.51e-05) 		0.0239
(0.0523) 		0.0102
(0.026)
del 14q11 2 175 (35%) 326 0.0379
(0.0769) 		0.0351
(0.0719) 		0.539
(0.639) 		0.799
(0.846) 		0.261
(0.368) 		0.166
(0.259) 		0.00016
(0.000895) 		0.00016
(0.000895) 		0.0233
(0.0512) 		0.00976
(0.0249) 		0.00076
(0.0031) 		0.0341
(0.0704)
del xp21 1 152 (30%) 349 0.454
(0.565) 		0.481
(0.59) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		0.272
(0.379) 		0.751
(0.814) 		7e-05
(0.000453) 		0.00101
(0.00388) 		0.00605
(0.0167) 		0.00142
(0.00512) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05)
del xp11 3 149 (30%) 352 0.0974
(0.171) 		0.399
(0.507) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		0.107
(0.184) 		0.0634
(0.119) 		0.00012
(0.000716) 		0.00195
(0.00667) 		0.00017
(0.00093) 		0.00047
(0.00209) 		2e-05
(0.000151) 		1e-05
(8.51e-05)
amp 7p11 2 256 (51%) 245 0.115
(0.195) 		0.0307
(0.0642) 		1e-05
(8.51e-05) 		0.0042
(0.0123) 		0.698
(0.778) 		0.595
(0.687) 		0.00196
(0.00669) 		2e-05
(0.000151) 		0.155
(0.247) 		0.0466
(0.0924) 		0.0443
(0.0878) 		0.33
(0.445)
amp 14q32 33 158 (32%) 343 0.0302
(0.0638) 		0.0153
(0.0364) 		0.00186
(0.00641) 		0.00069
(0.00291) 		0.0256
(0.0556) 		0.402
(0.509) 		0.00077
(0.00313) 		0.0004
(0.00184) 		0.519
(0.624) 		0.429
(0.539) 		0.0544
(0.104) 		0.127
(0.212)
del 3p25 3 398 (79%) 103 0.385
(0.494) 		0.199
(0.3) 		0.00172
(0.00599) 		8e-05
(0.000498) 		0.884
(0.913) 		0.228
(0.333) 		0.00287
(0.00916) 		0.00029
(0.00143) 		0.00826
(0.0215) 		0.00015
(0.000864) 		0.016
(0.0375) 		0.0798
(0.144)
del 5q12 1 369 (74%) 132 0.487
(0.596) 		0.433
(0.544) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		0.936
(0.949) 		0.462
(0.572) 		0.00201
(0.00683) 		0.00151
(0.00537) 		0.0114
(0.0286) 		3e-05
(0.000209) 		0.0637
(0.12) 		0.00313
(0.00977)
del 5q31 1 386 (77%) 115 0.159
(0.252) 		0.276
(0.382) 		1e-05
(8.51e-05) 		2e-05
(0.000151) 		0.371
(0.481) 		0.524
(0.626) 		0.0159
(0.0373) 		0.00728
(0.0194) 		0.00386
(0.0117) 		1e-05
(8.51e-05) 		0.0794
(0.144) 		0.00102
(0.00391)
del 17q25 3 102 (20%) 399 0.00479
(0.0137) 		0.012
(0.0298) 		5e-05
(0.000332) 		0.0168
(0.039) 		0.62
(0.709) 		0.994
(0.994) 		0.00137
(0.005) 		0.00143
(0.00514) 		0.644
(0.729) 		0.0134
(0.0328) 		0.773
(0.831) 		0.104
(0.18)
amp 6q12 152 (30%) 349 0.938
(0.95) 		0.731
(0.8) 		3e-05
(0.000209) 		0.0023
(0.00764) 		0.503
(0.611) 		0.602
(0.691) 		0.00094
(0.00367) 		0.00562
(0.0158) 		0.745
(0.81) 		0.0221
(0.0492) 		0.0526
(0.102) 		0.00612
(0.0168)
amp 12q15 178 (36%) 323 0.133
(0.219) 		0.344
(0.46) 		3e-05
(0.000209) 		0.00778
(0.0204) 		0.765
(0.824) 		0.436
(0.546) 		0.00572
(0.0159) 		0.0109
(0.0275) 		0.359
(0.472) 		0.644
(0.729) 		0.0237
(0.0518) 		0.0036
(0.0109)
amp 19q12 224 (45%) 277 0.369
(0.48) 		0.646
(0.73) 		1e-05
(8.51e-05) 		0.0199
(0.0449) 		0.232
(0.337) 		0.357
(0.47) 		0.00263
(0.00859) 		0.0285
(0.0608) 		0.722
(0.794) 		0.566
(0.662) 		0.00755
(0.0199) 		0.00232
(0.00768)
amp 20p12 2 280 (56%) 221 0.00108
(0.00411) 		0.00235
(0.00775) 		1e-05
(8.51e-05) 		0.00039
(0.00182) 		0.903
(0.928) 		0.33
(0.445) 		0.0177
(0.0407) 		0.0155
(0.0368) 		0.0879
(0.157) 		0.647
(0.73) 		0.574
(0.668) 		0.531
(0.633)
amp xq28 124 (25%) 377 0.887
(0.915) 		0.871
(0.904) 		0.0117
(0.0291) 		0.0355
(0.0726) 		0.0369
(0.0751) 		0.0762
(0.139) 		0.0475
(0.0934) 		0.307
(0.419) 		0.203
(0.303) 		0.163
(0.256) 		0.0178
(0.0408) 		0.0324
(0.0672)
del 6p25 3 134 (27%) 367 0.459
(0.569) 		0.283
(0.388) 		0.00027
(0.00135) 		1e-05
(8.51e-05) 		0.202
(0.302) 		0.00673
(0.0181) 		1e-05
(8.51e-05) 		1e-05
(8.51e-05) 		0.136
(0.223) 		0.00082
(0.00327) 		0.115
(0.195) 		0.184
(0.282)
del 6q22 31 122 (24%) 379 0.0388
(0.0782) 		0.00313
(0.00977) 		0.00019
(0.00102) 		0.00074
(0.00306) 		0.477
(0.586) 		0.509
(0.615) 		0.00084
(0.00333) 		0.017
(0.0393) 		0.26
(0.367) 		0.212
(0.314) 		0.197
(0.296) 		0.372
(0.481)
del 7q36 3 104 (21%) 397 0.171
(0.265) 		0.0487
(0.0951) 		0.00407
(0.0121) 		0.275
(0.381) 		0.974
(0.978) 		0.1
(0.176) 		0.00026
(0.00132) 		0.00114
(0.00427) 		0.306
(0.418) 		0.00412
(0.0121) 		0.777
(0.832) 		0.047
(0.0927)
del 11q22 1 162 (32%) 339 0.563
(0.661) 		0.254
(0.364) 		0.00138
(0.00502) 		0.00079
(0.00319) 		0.149
(0.24) 		0.965
(0.973) 		0.014
(0.034) 		0.0384
(0.0776) 		0.00394
(0.0118) 		0.028
(0.0598) 		0.214
(0.316) 		0.148
(0.239)
del 19q13 32 149 (30%) 352 0.827
(0.869) 		0.592
(0.684) 		1e-05
(8.51e-05) 		0.0001
(0.000615) 		0.164
(0.257) 		0.535
(0.636) 		0.0143
(0.0344) 		0.00718
(0.0192) 		0.0376
(0.0764) 		0.507
(0.613) 		0.0137
(0.0334) 		0.153
(0.246)
del 21q22 3 281 (56%) 220 0.774
(0.831) 		0.129
(0.215) 		1e-05
(8.51e-05) 		0.0055
(0.0155) 		0.511
(0.617) 		0.0597
(0.114) 		0.153
(0.246) 		0.0759
(0.139) 		0.0103
(0.0261) 		0.0005
(0.00218) 		0.0144
(0.0346) 		0.0475
(0.0934)
del 22q13 32 128 (26%) 373 0.00024
(0.00124) 		0.0134
(0.0328) 		0.224
(0.329) 		0.027
(0.0579) 		0.401
(0.509) 		0.216
(0.318) 		8e-05
(0.000498) 		1e-05
(8.51e-05) 		0.274
(0.381) 		0.00047
(0.00209) 		0.522
(0.624) 		0.163
(0.256)
del xp22 2 155 (31%) 346 0.714
(0.788) 		0.525
(0.627) 		3e-05
(0.000209) 		2e-05
(0.000151) 		0.356
(0.47) 		0.715
(0.788) 		0.012
(0.0298) 		0.00943
(0.0242) 		0.119
(0.201) 		0.111
(0.19) 		0.00024
(0.00124) 		4e-05
(0.000271)
amp 19q13 2 234 (47%) 267 0.344
(0.46) 		0.257
(0.365) 		1e-05
(8.51e-05) 		0.0267
(0.0575) 		0.371
(0.481) 		0.491
(0.6) 		0.00521
(0.0148) 		0.0803
(0.145) 		0.793
(0.842) 		0.503
(0.611) 		0.0306
(0.0642) 		0.0137
(0.0333)
amp 22q11 21 256 (51%) 245 0.114
(0.195) 		0.159
(0.252) 		0.00015
(0.000864) 		0.00037
(0.00175) 		0.857
(0.894) 		0.616
(0.705) 		8e-05
(0.000498) 		0.00024
(0.00124) 		0.164
(0.257) 		0.0416
(0.0829) 		0.589
(0.682) 		0.276
(0.382)
del 9p21 3 388 (77%) 113 0.196
(0.296) 		0.259
(0.367) 		1e-05
(8.51e-05) 		0.266
(0.373) 		0.81
(0.856) 		0.597
(0.688) 		0.00063
(0.0027) 		0.0158
(0.0372) 		0.452
(0.563) 		0.0115
(0.0289) 		0.378
(0.487) 		0.0228
(0.0503)
del 16q23 1 210 (42%) 291 0.929
(0.945) 		0.114
(0.195) 		0.0142
(0.0344) 		0.294
(0.402) 		0.353
(0.469) 		0.849
(0.888) 		0.0665
(0.124) 		0.0381
(0.0772) 		0.00645
(0.0176) 		0.442
(0.553) 		0.0003
(0.00146) 		0.00038
(0.00179)
del 9p21 1 326 (65%) 175 0.139
(0.227) 		0.284
(0.39) 		1e-05
(8.51e-05) 		0.13
(0.216) 		0.709
(0.784) 		0.63
(0.718) 		0.0003
(0.00146) 		0.00033
(0.00159) 		0.357
(0.47) 		0.00835
(0.0217) 		0.153
(0.246) 		0.357
(0.47)
del 13q14 2 344 (69%) 157 0.119
(0.201) 		0.0992
(0.174) 		0.00331
(0.0102) 		0.0303
(0.064) 		0.705
(0.783) 		0.727
(0.796) 		0.429
(0.539) 		0.574
(0.668) 		0.0738
(0.135) 		0.147
(0.239) 		0.00162
(0.00568) 		0.0195
(0.044)
del 17p11 2 272 (54%) 229 0.244
(0.353) 		0.113
(0.194) 		0.0004
(0.00184) 		0.66
(0.74) 		0.157
(0.25) 		0.00782
(0.0205) 		0.129
(0.214) 		0.0158
(0.0372) 		0.31
(0.421) 		0.0272
(0.0582) 		0.231
(0.336) 		0.154
(0.246)
del 21q11 2 246 (49%) 255 0.564
(0.661) 		0.561
(0.66) 		7e-05
(0.000453) 		0.205
(0.305) 		0.983
(0.984) 		0.726
(0.796) 		0.0855
(0.154) 		0.468
(0.577) 		0.00081
(0.00325) 		0.00021
(0.00111) 		0.185
(0.283) 		0.0147
(0.0352)
amp 4q12 119 (24%) 382 0.877
(0.908) 		0.882
(0.912) 		0.00166
(0.0058) 		0.175
(0.27) 		0.295
(0.404) 		0.135
(0.222) 		0.0621
(0.117) 		0.58
(0.674) 		0.0329
(0.068) 		0.349
(0.466) 		0.394
(0.502) 		0.0365
(0.0745)
amp 5p15 33 387 (77%) 114 0.85
(0.888) 		0.799
(0.846) 		1e-05
(8.51e-05) 		0.00222
(0.00739) 		0.404
(0.511) 		0.372
(0.481) 		0.489
(0.597) 		0.0642
(0.12) 		0.538
(0.638) 		0.00564
(0.0158) 		0.477
(0.586) 		0.281
(0.386)
amp 6p12 1 166 (33%) 335 0.653
(0.735) 		0.498
(0.607) 		1e-05
(8.51e-05) 		0.0527
(0.102) 		0.926
(0.943) 		0.546
(0.645) 		0.00066
(0.00281) 		0.0642
(0.12) 		0.57
(0.665) 		0.118
(0.2) 		0.217
(0.319) 		0.00011
(0.000672)
amp 14q13 3 159 (32%) 342 0.354
(0.469) 		0.0261
(0.0564) 		0.16
(0.253) 		0.302
(0.412) 		0.648
(0.73) 		0.0805
(0.145) 		0.103
(0.178) 		0.00264
(0.00859) 		0.0182
(0.0415) 		0.109
(0.188) 		0.749
(0.813) 		0.839
(0.88)
del 2p25 3 50 (10%) 451 0.122
(0.205) 		0.457
(0.568) 		0.0896
(0.16) 		0.211
(0.313) 		0.258
(0.365) 		0.363
(0.473) 		0.674
(0.755) 		0.605
(0.693) 		0.00876
(0.0226) 		0.36
(0.472) 		0.0476
(0.0934) 		0.0292
(0.0619)
del 7q11 22 48 (10%) 453 0.802
(0.848) 		0.699
(0.778) 		0.00113
(0.00425) 		0.473
(0.583) 		0.847
(0.886) 		0.318
(0.431) 		0.00191
(0.00656) 		0.00101
(0.00388) 		0.644
(0.729) 		0.378
(0.487) 		0.657
(0.738) 		0.906
(0.93)
del 8p23 2 341 (68%) 160 0.586
(0.68) 		0.706
(0.783) 		1e-05
(8.51e-05) 		0.0157
(0.0372) 		0.241
(0.35) 		0.362
(0.473) 		0.112
(0.192) 		0.0927
(0.165) 		0.319
(0.433) 		0.0652
(0.121) 		0.388
(0.495) 		0.0406
(0.0814)
del 11q25 184 (37%) 317 0.799
(0.846) 		0.706
(0.783) 		0.00215
(0.00723) 		0.0602
(0.114) 		0.174
(0.268) 		0.691
(0.772) 		0.0177
(0.0407) 		0.148
(0.239) 		0.0321
(0.0668) 		0.149
(0.24) 		0.382
(0.491) 		0.125
(0.209)
del 13q12 11 331 (66%) 170 0.104
(0.18) 		0.569
(0.665) 		0.00396
(0.0118) 		0.162
(0.256) 		0.909
(0.931) 		0.182
(0.279) 		0.814
(0.857) 		0.971
(0.975) 		0.231
(0.337) 		0.381
(0.49) 		0.00425
(0.0124) 		0.00354
(0.0107)
del 15q21 1 169 (34%) 332 0.452
(0.563) 		0.76
(0.822) 		0.0159
(0.0373) 		0.349
(0.466) 		0.0903
(0.161) 		0.00721
(0.0193) 		0.272
(0.379) 		0.244
(0.353) 		0.00322
(0.00996) 		0.0965
(0.17) 		0.355
(0.47) 		0.168
(0.262)
del 19p13 3 236 (47%) 265 0.446
(0.557) 		0.233
(0.338) 		9e-05
(0.000557) 		0.928
(0.944) 		0.0936
(0.166) 		0.166
(0.259) 		0.0677
(0.126) 		0.0219
(0.0488) 		0.189
(0.289) 		0.00093
(0.00365) 		0.793
(0.842) 		0.0538
(0.104)
amp 5p12 354 (71%) 147 0.96
(0.969) 		0.756
(0.819) 		1e-05
(8.51e-05) 		0.00068
(0.00288) 		0.219
(0.322) 		0.935
(0.949) 		0.363
(0.473) 		0.899
(0.924) 		0.71
(0.784) 		0.0775
(0.141) 		0.0646
(0.12) 		0.71
(0.784)
amp 8p11 23 238 (48%) 263 0.0129
(0.0318) 		0.0921
(0.164) 		0.00016
(0.000895) 		0.0551
(0.105) 		0.19
(0.289) 		0.249
(0.358) 		0.0596
(0.113) 		0.0569
(0.109) 		0.872
(0.904) 		0.175
(0.27) 		0.589
(0.682) 		0.329
(0.445)
amp 13q34 91 (18%) 410 0.981
(0.983) 		0.833
(0.874) 		0.38
(0.49) 		0.775
(0.831) 		0.871
(0.904) 		0.215
(0.318) 		0.744
(0.81) 		0.105
(0.182) 		0.0134
(0.0328) 		0.0343
(0.0706) 		0.967
(0.974) 		0.465
(0.575)
amp 20q11 21 306 (61%) 195 0.811
(0.856) 		0.507
(0.613) 		1e-05
(8.51e-05) 		0.00591
(0.0164) 		0.784
(0.835) 		0.737
(0.803) 		0.634
(0.721) 		0.945
(0.956) 		0.272
(0.379) 		0.372
(0.481) 		0.589
(0.682) 		0.202
(0.303)
del 15q11 2 167 (33%) 334 0.564
(0.661) 		0.521
(0.624) 		0.158
(0.251) 		0.193
(0.292) 		0.0888
(0.159) 		0.0268
(0.0578) 		0.193
(0.292) 		0.0607
(0.115) 		0.0243
(0.053) 		0.54
(0.64) 		0.263
(0.37) 		0.126
(0.211)
del 16p13 3 187 (37%) 314 0.254
(0.364) 		0.449
(0.56) 		0.00425
(0.0124) 		0.123
(0.207) 		0.21
(0.312) 		0.257
(0.365) 		0.514
(0.619) 		0.916
(0.937) 		0.171
(0.266) 		0.634
(0.721) 		0.00926
(0.0238) 		0.101
(0.176)
del 22q11 21 95 (19%) 406 0.0299
(0.0634) 		0.0968
(0.17) 		0.141
(0.23) 		0.0958
(0.17) 		0.13
(0.216) 		0.354
(0.469) 		0.156
(0.249) 		0.00026
(0.00132) 		0.734
(0.802) 		0.405
(0.511) 		0.256
(0.364) 		0.144
(0.234)
amp 8q24 21 352 (70%) 149 0.918
(0.938) 		0.778
(0.832) 		0.0211
(0.0474) 		0.266
(0.373) 		0.825
(0.868) 		0.57
(0.665) 		0.813
(0.857) 		0.548
(0.647) 		0.278
(0.383) 		0.258
(0.365) 		0.844
(0.884) 		0.899
(0.924)
del 18q23 234 (47%) 267 0.598
(0.688) 		0.172
(0.267) 		0.0054
(0.0153) 		0.249
(0.358) 		0.886
(0.914) 		0.19
(0.289) 		0.791
(0.842) 		0.481
(0.59) 		0.502
(0.611) 		0.538
(0.638) 		0.108
(0.186) 		0.644
(0.729)
del 3q11 1 79 (16%) 422 0.763
(0.823) 		0.781
(0.834) 		0.223
(0.328) 		0.87
(0.904) 		0.763
(0.823) 		0.603
(0.692) 		0.77
(0.829) 		0.174
(0.268) 		0.923
(0.941) 		0.52
(0.624) 		0.336
(0.45) 		0.734
(0.802)
del 12q24 31 86 (17%) 415 0.914
(0.936) 		0.597
(0.688) 		0.405
(0.511) 		0.277
(0.383) 		0.198
(0.298) 		0.678
(0.758) 		0.523
(0.625) 		0.694
(0.774) 		0.709
(0.784) 		0.331
(0.447) 		0.394
(0.502) 		0.17
(0.264)
'amp_1q21.2' versus 'MRNA_CNMF'

P value = 0.0394 (Fisher's exact test), Q value = 0.079

Table S1.  Gene #1: 'amp_1q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
AMP PEAK 1(1Q21.2) MUTATED 18 37 16 16
AMP PEAK 1(1Q21.2) WILD-TYPE 24 15 16 12

Figure S1.  Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S2.  Gene #1: 'amp_1q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
AMP PEAK 1(1Q21.2) MUTATED 73 122 63
AMP PEAK 1(1Q21.2) WILD-TYPE 109 44 90

Figure S2.  Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q21.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S3.  Gene #1: 'amp_1q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
AMP PEAK 1(1Q21.2) MUTATED 57 81 46
AMP PEAK 1(1Q21.2) WILD-TYPE 95 41 47

Figure S3.  Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S4.  Gene #1: 'amp_1q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
AMP PEAK 1(1Q21.2) MUTATED 44 106 80 27
AMP PEAK 1(1Q21.2) WILD-TYPE 69 46 74 52

Figure S4.  Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S5.  Gene #1: 'amp_1q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 1(1Q21.2) MUTATED 63 123 71
AMP PEAK 1(1Q21.2) WILD-TYPE 115 66 60

Figure S5.  Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S6.  Gene #1: 'amp_1q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
AMP PEAK 1(1Q21.2) MUTATED 66 81 41 43 13
AMP PEAK 1(1Q21.2) WILD-TYPE 55 53 80 19 24

Figure S6.  Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S7.  Gene #1: 'amp_1q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 1(1Q21.2) MUTATED 64 67 89 24
AMP PEAK 1(1Q21.2) WILD-TYPE 25 51 110 45

Figure S7.  Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0034

Table S8.  Gene #1: 'amp_1q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
AMP PEAK 1(1Q21.2) MUTATED 30 67 69
AMP PEAK 1(1Q21.2) WILD-TYPE 59 62 47

Figure S8.  Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00412 (Fisher's exact test), Q value = 0.012

Table S9.  Gene #1: 'amp_1q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
AMP PEAK 1(1Q21.2) MUTATED 15 90 61
AMP PEAK 1(1Q21.2) WILD-TYPE 24 61 83

Figure S9.  Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_2p16.1' versus 'MRNA_CNMF'

P value = 0.0014 (Fisher's exact test), Q value = 0.0051

Table S10.  Gene #2: 'amp_2p16.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
AMP PEAK 2(2P16.1) MUTATED 19 40 13 13
AMP PEAK 2(2P16.1) WILD-TYPE 23 12 19 15

Figure S10.  Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_2p16.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.0012

Table S11.  Gene #2: 'amp_2p16.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
AMP PEAK 2(2P16.1) MUTATED 24 42 19
AMP PEAK 2(2P16.1) WILD-TYPE 23 14 32

Figure S11.  Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_2p16.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S12.  Gene #2: 'amp_2p16.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
AMP PEAK 2(2P16.1) MUTATED 67 126 82
AMP PEAK 2(2P16.1) WILD-TYPE 115 40 71

Figure S12.  Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2p16.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S13.  Gene #2: 'amp_2p16.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
AMP PEAK 2(2P16.1) MUTATED 66 90 48
AMP PEAK 2(2P16.1) WILD-TYPE 86 32 45

Figure S13.  Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2p16.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S14.  Gene #2: 'amp_2p16.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
AMP PEAK 2(2P16.1) MUTATED 47 113 87 26
AMP PEAK 2(2P16.1) WILD-TYPE 66 39 67 53

Figure S14.  Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2p16.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S15.  Gene #2: 'amp_2p16.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 2(2P16.1) MUTATED 82 131 60
AMP PEAK 2(2P16.1) WILD-TYPE 96 58 71

Figure S15.  Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_2p16.1' versus 'MIRSEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0018

Table S16.  Gene #2: 'amp_2p16.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
AMP PEAK 2(2P16.1) MUTATED 65 93 50 33 22
AMP PEAK 2(2P16.1) WILD-TYPE 56 41 71 29 15

Figure S16.  Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_2p16.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.0024

Table S17.  Gene #2: 'amp_2p16.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 2(2P16.1) MUTATED 54 64 122 23
AMP PEAK 2(2P16.1) WILD-TYPE 35 54 77 46

Figure S17.  Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_2p16.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0312 (Fisher's exact test), Q value = 0.065

Table S18.  Gene #2: 'amp_2p16.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
AMP PEAK 2(2P16.1) MUTATED 39 76 71
AMP PEAK 2(2P16.1) WILD-TYPE 50 53 45

Figure S18.  Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_2p16.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00021

Table S19.  Gene #2: 'amp_2p16.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
AMP PEAK 2(2P16.1) MUTATED 22 104 60
AMP PEAK 2(2P16.1) WILD-TYPE 17 47 84

Figure S19.  Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_2q31.2' versus 'MRNA_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.044

Table S20.  Gene #3: 'amp_2q31.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
AMP PEAK 3(2Q31.2) MUTATED 10 27 8 10
AMP PEAK 3(2Q31.2) WILD-TYPE 32 25 24 18

Figure S20.  Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_2q31.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0225 (Fisher's exact test), Q value = 0.05

Table S21.  Gene #3: 'amp_2q31.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
AMP PEAK 3(2Q31.2) MUTATED 13 28 14
AMP PEAK 3(2Q31.2) WILD-TYPE 34 28 37

Figure S21.  Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_2q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S22.  Gene #3: 'amp_2q31.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
AMP PEAK 3(2Q31.2) MUTATED 38 80 54
AMP PEAK 3(2Q31.2) WILD-TYPE 144 86 99

Figure S22.  Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2q31.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S23.  Gene #3: 'amp_2q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
AMP PEAK 3(2Q31.2) MUTATED 39 66 26
AMP PEAK 3(2Q31.2) WILD-TYPE 113 56 67

Figure S23.  Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2q31.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S24.  Gene #3: 'amp_2q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
AMP PEAK 3(2Q31.2) MUTATED 28 78 48 17
AMP PEAK 3(2Q31.2) WILD-TYPE 85 74 106 62

Figure S24.  Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S25.  Gene #3: 'amp_2q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 3(2Q31.2) MUTATED 42 91 38
AMP PEAK 3(2Q31.2) WILD-TYPE 136 98 93

Figure S25.  Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_2q31.2' versus 'MIRSEQ_CNMF'

P value = 0.00273 (Fisher's exact test), Q value = 0.0088

Table S26.  Gene #3: 'amp_2q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
AMP PEAK 3(2Q31.2) MUTATED 45 62 29 18 10
AMP PEAK 3(2Q31.2) WILD-TYPE 76 72 92 44 27

Figure S26.  Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_2q31.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00333 (Fisher's exact test), Q value = 0.01

Table S27.  Gene #3: 'amp_2q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
AMP PEAK 3(2Q31.2) MUTATED 18 47 48
AMP PEAK 3(2Q31.2) WILD-TYPE 71 82 68

Figure S27.  Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_2q31.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.002

Table S28.  Gene #3: 'amp_2q31.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
AMP PEAK 3(2Q31.2) MUTATED 9 68 36
AMP PEAK 3(2Q31.2) WILD-TYPE 30 83 108

Figure S28.  Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.33' versus 'MRNA_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.002

Table S29.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
AMP PEAK 4(3Q26.33) MUTATED 40 52 25 23
AMP PEAK 4(3Q26.33) WILD-TYPE 2 0 7 5

Figure S29.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.00059 (Fisher's exact test), Q value = 0.0025

Table S30.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
AMP PEAK 4(3Q26.33) MUTATED 43 56 41
AMP PEAK 4(3Q26.33) WILD-TYPE 4 0 10

Figure S30.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_3q26.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S31.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
AMP PEAK 4(3Q26.33) MUTATED 141 165 146
AMP PEAK 4(3Q26.33) WILD-TYPE 41 1 7

Figure S31.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S32.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
AMP PEAK 4(3Q26.33) MUTATED 121 122 87
AMP PEAK 4(3Q26.33) WILD-TYPE 31 0 6

Figure S32.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.0322 (Fisher's exact test), Q value = 0.067

Table S33.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 41 52 47
AMP PEAK 4(3Q26.33) MUTATED 47 32 50 44
AMP PEAK 4(3Q26.33) WILD-TYPE 7 9 2 3

Figure S33.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_3q26.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S34.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
AMP PEAK 4(3Q26.33) MUTATED 107 152 132 58
AMP PEAK 4(3Q26.33) WILD-TYPE 6 0 22 21

Figure S34.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S35.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 4(3Q26.33) MUTATED 163 188 98
AMP PEAK 4(3Q26.33) WILD-TYPE 15 1 33

Figure S35.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MIRSEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00077

Table S36.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
AMP PEAK 4(3Q26.33) MUTATED 108 130 97 59 35
AMP PEAK 4(3Q26.33) WILD-TYPE 13 4 24 3 2

Figure S36.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S37.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 4(3Q26.33) MUTATED 89 108 189 43
AMP PEAK 4(3Q26.33) WILD-TYPE 0 10 10 26

Figure S37.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.042

Table S38.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
AMP PEAK 4(3Q26.33) MUTATED 73 118 109
AMP PEAK 4(3Q26.33) WILD-TYPE 16 11 7

Figure S38.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00027

Table S39.  Gene #4: 'amp_3q26.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
AMP PEAK 4(3Q26.33) MUTATED 36 146 118
AMP PEAK 4(3Q26.33) WILD-TYPE 3 5 26

Figure S39.  Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q12' versus 'CN_CNMF'

P value = 0.00166 (Fisher's exact test), Q value = 0.0058

Table S40.  Gene #5: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
AMP PEAK 5(4Q12) MUTATED 29 40 50
AMP PEAK 5(4Q12) WILD-TYPE 153 126 103

Figure S40.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_4q12' versus 'MIRSEQ_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 0.068

Table S41.  Gene #5: 'amp_4q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
AMP PEAK 5(4Q12) MUTATED 32 35 20 10 14
AMP PEAK 5(4Q12) WILD-TYPE 89 99 101 52 23

Figure S41.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_4q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0365 (Fisher's exact test), Q value = 0.074

Table S42.  Gene #5: 'amp_4q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
AMP PEAK 5(4Q12) MUTATED 14 33 24
AMP PEAK 5(4Q12) WILD-TYPE 25 118 120

Figure S42.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S43.  Gene #6: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
AMP PEAK 6(5P15.33) MUTATED 126 121 140
AMP PEAK 6(5P15.33) WILD-TYPE 56 45 13

Figure S43.  Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 0.00222 (Fisher's exact test), Q value = 0.0074

Table S44.  Gene #6: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
AMP PEAK 6(5P15.33) MUTATED 114 86 83
AMP PEAK 6(5P15.33) WILD-TYPE 38 36 10

Figure S44.  Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00564 (Fisher's exact test), Q value = 0.016

Table S45.  Gene #6: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 6(5P15.33) MUTATED 66 88 168 45
AMP PEAK 6(5P15.33) WILD-TYPE 23 30 31 24

Figure S45.  Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S46.  Gene #7: 'amp_5p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
AMP PEAK 7(5P12) MUTATED 106 118 130
AMP PEAK 7(5P12) WILD-TYPE 76 48 23

Figure S46.  Get High-res Image Gene #7: 'amp_5p12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p12' versus 'METHLYATION_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.0029

Table S47.  Gene #7: 'amp_5p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
AMP PEAK 7(5P12) MUTATED 98 80 79
AMP PEAK 7(5P12) WILD-TYPE 54 42 14

Figure S47.  Get High-res Image Gene #7: 'amp_5p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S48.  Gene #8: 'amp_6p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
AMP PEAK 8(6P12.1) MUTATED 36 72 58
AMP PEAK 8(6P12.1) WILD-TYPE 146 94 95

Figure S48.  Get High-res Image Gene #8: 'amp_6p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p12.1' versus 'MRNASEQ_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0028

Table S49.  Gene #8: 'amp_6p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
AMP PEAK 8(6P12.1) MUTATED 21 62 57 24
AMP PEAK 8(6P12.1) WILD-TYPE 92 90 97 55

Figure S49.  Get High-res Image Gene #8: 'amp_6p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00067

Table S50.  Gene #8: 'amp_6p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
AMP PEAK 8(6P12.1) MUTATED 13 67 31
AMP PEAK 8(6P12.1) WILD-TYPE 26 84 113

Figure S50.  Get High-res Image Gene #8: 'amp_6p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q12' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00021

Table S51.  Gene #9: 'amp_6q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
AMP PEAK 9(6Q12) MUTATED 33 64 55
AMP PEAK 9(6Q12) WILD-TYPE 149 102 98

Figure S51.  Get High-res Image Gene #9: 'amp_6q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6q12' versus 'METHLYATION_CNMF'

P value = 0.0023 (Fisher's exact test), Q value = 0.0076

Table S52.  Gene #9: 'amp_6q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
AMP PEAK 9(6Q12) MUTATED 34 50 23
AMP PEAK 9(6Q12) WILD-TYPE 118 72 70

Figure S52.  Get High-res Image Gene #9: 'amp_6q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6q12' versus 'MRNASEQ_CNMF'

P value = 0.00094 (Fisher's exact test), Q value = 0.0037

Table S53.  Gene #9: 'amp_6q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
AMP PEAK 9(6Q12) MUTATED 20 58 53 19
AMP PEAK 9(6Q12) WILD-TYPE 93 94 101 60

Figure S53.  Get High-res Image Gene #9: 'amp_6q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00562 (Fisher's exact test), Q value = 0.016

Table S54.  Gene #9: 'amp_6q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 9(6Q12) MUTATED 38 66 46
AMP PEAK 9(6Q12) WILD-TYPE 140 123 85

Figure S54.  Get High-res Image Gene #9: 'amp_6q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0221 (Fisher's exact test), Q value = 0.049

Table S55.  Gene #9: 'amp_6q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 9(6Q12) MUTATED 36 30 66 14
AMP PEAK 9(6Q12) WILD-TYPE 53 88 133 55

Figure S55.  Get High-res Image Gene #9: 'amp_6q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00612 (Fisher's exact test), Q value = 0.017

Table S56.  Gene #9: 'amp_6q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
AMP PEAK 9(6Q12) MUTATED 12 58 31
AMP PEAK 9(6Q12) WILD-TYPE 27 93 113

Figure S56.  Get High-res Image Gene #9: 'amp_6q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0307 (Fisher's exact test), Q value = 0.064

Table S57.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
AMP PEAK 10(7P11.2) MUTATED 23 37 21
AMP PEAK 10(7P11.2) WILD-TYPE 24 19 30

Figure S57.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S58.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
AMP PEAK 10(7P11.2) MUTATED 73 109 74
AMP PEAK 10(7P11.2) WILD-TYPE 109 57 79

Figure S58.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

P value = 0.0042 (Fisher's exact test), Q value = 0.012

Table S59.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
AMP PEAK 10(7P11.2) MUTATED 63 75 48
AMP PEAK 10(7P11.2) WILD-TYPE 89 47 45

Figure S59.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 0.00196 (Fisher's exact test), Q value = 0.0067

Table S60.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
AMP PEAK 10(7P11.2) MUTATED 55 96 72 31
AMP PEAK 10(7P11.2) WILD-TYPE 58 56 82 48

Figure S60.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S61.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 10(7P11.2) MUTATED 78 122 54
AMP PEAK 10(7P11.2) WILD-TYPE 100 67 77

Figure S61.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0466 (Fisher's exact test), Q value = 0.092

Table S62.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 10(7P11.2) MUTATED 58 56 100 33
AMP PEAK 10(7P11.2) WILD-TYPE 31 62 99 36

Figure S62.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0443 (Fisher's exact test), Q value = 0.088

Table S63.  Gene #10: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
AMP PEAK 10(7P11.2) MUTATED 43 58 70
AMP PEAK 10(7P11.2) WILD-TYPE 46 71 46

Figure S63.  Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7q21.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 0.036

Table S64.  Gene #11: 'amp_7q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
AMP PEAK 11(7Q21.2) MUTATED 30 39 22
AMP PEAK 11(7Q21.2) WILD-TYPE 17 17 29

Figure S64.  Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S65.  Gene #11: 'amp_7q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
AMP PEAK 11(7Q21.2) MUTATED 59 122 83
AMP PEAK 11(7Q21.2) WILD-TYPE 123 44 70

Figure S65.  Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q21.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S66.  Gene #11: 'amp_7q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
AMP PEAK 11(7Q21.2) MUTATED 55 83 48
AMP PEAK 11(7Q21.2) WILD-TYPE 97 39 45

Figure S66.  Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7q21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S67.  Gene #11: 'amp_7q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
AMP PEAK 11(7Q21.2) MUTATED 55 108 69 30
AMP PEAK 11(7Q21.2) WILD-TYPE 58 44 85 49

Figure S67.  Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S68.  Gene #11: 'amp_7q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 11(7Q21.2) MUTATED 74 130 58
AMP PEAK 11(7Q21.2) WILD-TYPE 104 59 73

Figure S68.  Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'MIRSEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00093

Table S69.  Gene #11: 'amp_7q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
AMP PEAK 11(7Q21.2) MUTATED 71 86 45 35 17
AMP PEAK 11(7Q21.2) WILD-TYPE 50 48 76 27 20

Figure S69.  Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00096 (Fisher's exact test), Q value = 0.0037

Table S70.  Gene #11: 'amp_7q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 11(7Q21.2) MUTATED 63 63 100 28
AMP PEAK 11(7Q21.2) WILD-TYPE 26 55 99 41

Figure S70.  Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0016 (Fisher's exact test), Q value = 0.0057

Table S71.  Gene #11: 'amp_7q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
AMP PEAK 11(7Q21.2) MUTATED 33 63 72
AMP PEAK 11(7Q21.2) WILD-TYPE 56 66 44

Figure S71.  Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.0032

Table S72.  Gene #11: 'amp_7q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
AMP PEAK 11(7Q21.2) MUTATED 17 93 58
AMP PEAK 11(7Q21.2) WILD-TYPE 22 58 86

Figure S72.  Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p11.23' versus 'MRNA_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.032

Table S73.  Gene #12: 'amp_8p11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
AMP PEAK 12(8P11.23) MUTATED 30 24 12 12
AMP PEAK 12(8P11.23) WILD-TYPE 12 28 20 16

Figure S73.  Get High-res Image Gene #12: 'amp_8p11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8p11.23' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 9e-04

Table S74.  Gene #12: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
AMP PEAK 12(8P11.23) MUTATED 73 71 94
AMP PEAK 12(8P11.23) WILD-TYPE 109 95 59

Figure S74.  Get High-res Image Gene #12: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 0.0211 (Fisher's exact test), Q value = 0.047

Table S75.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
AMP PEAK 13(8Q24.21) MUTATED 118 114 120
AMP PEAK 13(8Q24.21) WILD-TYPE 64 52 33

Figure S75.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_9p13.3' versus 'CN_CNMF'

P value = 0.00181 (Fisher's exact test), Q value = 0.0063

Table S76.  Gene #14: 'amp_9p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
AMP PEAK 14(9P13.3) MUTATED 40 62 34
AMP PEAK 14(9P13.3) WILD-TYPE 142 104 119

Figure S76.  Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_9p13.3' versus 'METHLYATION_CNMF'

P value = 0.00256 (Fisher's exact test), Q value = 0.0084

Table S77.  Gene #14: 'amp_9p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
AMP PEAK 14(9P13.3) MUTATED 33 49 23
AMP PEAK 14(9P13.3) WILD-TYPE 119 73 70

Figure S77.  Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_9p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00302 (Fisher's exact test), Q value = 0.0095

Table S78.  Gene #14: 'amp_9p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 41 52 47
AMP PEAK 14(9P13.3) MUTATED 21 3 11 13
AMP PEAK 14(9P13.3) WILD-TYPE 33 38 41 34

Figure S78.  Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_9p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00145 (Fisher's exact test), Q value = 0.0052

Table S79.  Gene #14: 'amp_9p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
AMP PEAK 14(9P13.3) MUTATED 23 58 41 14
AMP PEAK 14(9P13.3) WILD-TYPE 90 94 113 65

Figure S79.  Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_9p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00135 (Fisher's exact test), Q value = 0.0049

Table S80.  Gene #14: 'amp_9p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 14(9P13.3) MUTATED 34 68 34
AMP PEAK 14(9P13.3) WILD-TYPE 144 121 97

Figure S80.  Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_9p13.3' versus 'MIRSEQ_CNMF'

P value = 0.00665 (Fisher's exact test), Q value = 0.018

Table S81.  Gene #14: 'amp_9p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
AMP PEAK 14(9P13.3) MUTATED 33 40 20 25 13
AMP PEAK 14(9P13.3) WILD-TYPE 88 94 101 37 24

Figure S81.  Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_9p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00335 (Fisher's exact test), Q value = 0.01

Table S82.  Gene #14: 'amp_9p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 14(9P13.3) MUTATED 32 41 48 10
AMP PEAK 14(9P13.3) WILD-TYPE 57 77 151 59

Figure S82.  Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_9p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.039

Table S83.  Gene #14: 'amp_9p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
AMP PEAK 14(9P13.3) MUTATED 15 44 32
AMP PEAK 14(9P13.3) WILD-TYPE 74 85 84

Figure S83.  Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_9p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0126 (Fisher's exact test), Q value = 0.031

Table S84.  Gene #14: 'amp_9p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
AMP PEAK 14(9P13.3) MUTATED 9 53 29
AMP PEAK 14(9P13.3) WILD-TYPE 30 98 115

Figure S84.  Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q13.3' versus 'MRNA_CNMF'

P value = 0.0469 (Fisher's exact test), Q value = 0.093

Table S85.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
AMP PEAK 15(11Q13.3) MUTATED 17 11 11 14
AMP PEAK 15(11Q13.3) WILD-TYPE 25 41 21 14

Figure S85.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11q13.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0345 (Fisher's exact test), Q value = 0.071

Table S86.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
AMP PEAK 15(11Q13.3) MUTATED 19 12 22
AMP PEAK 15(11Q13.3) WILD-TYPE 28 44 29

Figure S86.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S87.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
AMP PEAK 15(11Q13.3) MUTATED 46 62 77
AMP PEAK 15(11Q13.3) WILD-TYPE 136 104 76

Figure S87.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.003

Table S88.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
AMP PEAK 15(11Q13.3) MUTATED 44 45 50
AMP PEAK 15(11Q13.3) WILD-TYPE 108 77 43

Figure S88.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 0.0307 (Fisher's exact test), Q value = 0.064

Table S89.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
AMP PEAK 15(11Q13.3) MUTATED 47 43 67 28
AMP PEAK 15(11Q13.3) WILD-TYPE 66 109 87 51

Figure S89.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

P value = 0.00133 (Fisher's exact test), Q value = 0.0049

Table S90.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
AMP PEAK 15(11Q13.3) MUTATED 46 60 40 12 20
AMP PEAK 15(11Q13.3) WILD-TYPE 75 74 81 50 17

Figure S90.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00517 (Fisher's exact test), Q value = 0.015

Table S91.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 15(11Q13.3) MUTATED 24 47 89 18
AMP PEAK 15(11Q13.3) WILD-TYPE 65 71 110 51

Figure S91.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00273 (Fisher's exact test), Q value = 0.0088

Table S92.  Gene #15: 'amp_11q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
AMP PEAK 15(11Q13.3) MUTATED 21 66 41
AMP PEAK 15(11Q13.3) WILD-TYPE 18 85 103

Figure S92.  Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p13.33' versus 'MRNA_CNMF'

P value = 0.00792 (Fisher's exact test), Q value = 0.021

Table S93.  Gene #16: 'amp_12p13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
AMP PEAK 16(12P13.33) MUTATED 12 33 13 13
AMP PEAK 16(12P13.33) WILD-TYPE 30 19 19 15

Figure S93.  Get High-res Image Gene #16: 'amp_12p13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_12p13.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.0217 (Fisher's exact test), Q value = 0.048

Table S94.  Gene #16: 'amp_12p13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
AMP PEAK 16(12P13.33) MUTATED 17 34 20
AMP PEAK 16(12P13.33) WILD-TYPE 30 22 31

Figure S94.  Get High-res Image Gene #16: 'amp_12p13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_12p13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S95.  Gene #16: 'amp_12p13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
AMP PEAK 16(12P13.33) MUTATED 63 110 82
AMP PEAK 16(12P13.33) WILD-TYPE 119 56 71

Figure S95.  Get High-res Image Gene #16: 'amp_12p13.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p13.33' versus 'METHLYATION_CNMF'

P value = 0.0049 (Fisher's exact test), Q value = 0.014

Table S96.  Gene #16: 'amp_12p13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
AMP PEAK 16(12P13.33) MUTATED 67 76 56
AMP PEAK 16(12P13.33) WILD-TYPE 85 46 37

Figure S96.  Get High-res Image Gene #16: 'amp_12p13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12p13.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S97.  Gene #16: 'amp_12p13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
AMP PEAK 16(12P13.33) MUTATED 37 98 90 28
AMP PEAK 16(12P13.33) WILD-TYPE 76 54 64 51

Figure S97.  Get High-res Image Gene #16: 'amp_12p13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12p13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00162 (Fisher's exact test), Q value = 0.0057

Table S98.  Gene #16: 'amp_12p13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 16(12P13.33) MUTATED 72 111 70
AMP PEAK 16(12P13.33) WILD-TYPE 106 78 61

Figure S98.  Get High-res Image Gene #16: 'amp_12p13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12p13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00273 (Fisher's exact test), Q value = 0.0088

Table S99.  Gene #16: 'amp_12p13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 16(12P13.33) MUTATED 57 58 108 24
AMP PEAK 16(12P13.33) WILD-TYPE 32 60 91 45

Figure S99.  Get High-res Image Gene #16: 'amp_12p13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p13.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00602 (Fisher's exact test), Q value = 0.017

Table S100.  Gene #16: 'amp_12p13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
AMP PEAK 16(12P13.33) MUTATED 20 95 64
AMP PEAK 16(12P13.33) WILD-TYPE 19 56 80

Figure S100.  Get High-res Image Gene #16: 'amp_12p13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00021

Table S101.  Gene #17: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
AMP PEAK 17(12Q15) MUTATED 46 80 52
AMP PEAK 17(12Q15) WILD-TYPE 136 86 101

Figure S101.  Get High-res Image Gene #17: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 0.00778 (Fisher's exact test), Q value = 0.02

Table S102.  Gene #17: 'amp_12q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
AMP PEAK 17(12Q15) MUTATED 42 56 32
AMP PEAK 17(12Q15) WILD-TYPE 110 66 61

Figure S102.  Get High-res Image Gene #17: 'amp_12q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q15' versus 'MRNASEQ_CNMF'

P value = 0.00572 (Fisher's exact test), Q value = 0.016

Table S103.  Gene #17: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
AMP PEAK 17(12Q15) MUTATED 28 69 53 26
AMP PEAK 17(12Q15) WILD-TYPE 85 83 101 53

Figure S103.  Get High-res Image Gene #17: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.027

Table S104.  Gene #17: 'amp_12q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 17(12Q15) MUTATED 48 73 55
AMP PEAK 17(12Q15) WILD-TYPE 130 116 76

Figure S104.  Get High-res Image Gene #17: 'amp_12q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.052

Table S105.  Gene #17: 'amp_12q15' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
AMP PEAK 17(12Q15) MUTATED 22 44 50
AMP PEAK 17(12Q15) WILD-TYPE 67 85 66

Figure S105.  Get High-res Image Gene #17: 'amp_12q15' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12q15' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0036 (Fisher's exact test), Q value = 0.011

Table S106.  Gene #17: 'amp_12q15' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
AMP PEAK 17(12Q15) MUTATED 10 67 39
AMP PEAK 17(12Q15) WILD-TYPE 29 84 105

Figure S106.  Get High-res Image Gene #17: 'amp_12q15' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q34' versus 'MIRSEQ_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.033

Table S107.  Gene #18: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
AMP PEAK 18(13Q34) MUTATED 25 32 21 7 1
AMP PEAK 18(13Q34) WILD-TYPE 96 102 100 55 36

Figure S107.  Get High-res Image Gene #18: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0343 (Fisher's exact test), Q value = 0.071

Table S108.  Gene #18: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 18(13Q34) MUTATED 8 27 41 10
AMP PEAK 18(13Q34) WILD-TYPE 81 91 158 59

Figure S108.  Get High-res Image Gene #18: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_14q13.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0261 (Fisher's exact test), Q value = 0.056

Table S109.  Gene #19: 'amp_14q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
AMP PEAK 19(14Q13.3) MUTATED 23 15 13
AMP PEAK 19(14Q13.3) WILD-TYPE 24 41 38

Figure S109.  Get High-res Image Gene #19: 'amp_14q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_14q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00264 (Fisher's exact test), Q value = 0.0086

Table S110.  Gene #19: 'amp_14q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 19(14Q13.3) MUTATED 73 56 30
AMP PEAK 19(14Q13.3) WILD-TYPE 105 133 101

Figure S110.  Get High-res Image Gene #19: 'amp_14q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_14q13.3' versus 'MIRSEQ_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.042

Table S111.  Gene #19: 'amp_14q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
AMP PEAK 19(14Q13.3) MUTATED 44 45 42 9 14
AMP PEAK 19(14Q13.3) WILD-TYPE 77 89 79 53 23

Figure S111.  Get High-res Image Gene #19: 'amp_14q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_14q32.33' versus 'MRNA_CNMF'

P value = 0.0302 (Fisher's exact test), Q value = 0.064

Table S112.  Gene #20: 'amp_14q32.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
AMP PEAK 20(14Q32.33) MUTATED 20 15 5 9
AMP PEAK 20(14Q32.33) WILD-TYPE 22 37 27 19

Figure S112.  Get High-res Image Gene #20: 'amp_14q32.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_14q32.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.0153 (Fisher's exact test), Q value = 0.036

Table S113.  Gene #20: 'amp_14q32.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
AMP PEAK 20(14Q32.33) MUTATED 22 17 10
AMP PEAK 20(14Q32.33) WILD-TYPE 25 39 41

Figure S113.  Get High-res Image Gene #20: 'amp_14q32.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_14q32.33' versus 'CN_CNMF'

P value = 0.00186 (Fisher's exact test), Q value = 0.0064

Table S114.  Gene #20: 'amp_14q32.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
AMP PEAK 20(14Q32.33) MUTATED 40 62 56
AMP PEAK 20(14Q32.33) WILD-TYPE 142 104 97

Figure S114.  Get High-res Image Gene #20: 'amp_14q32.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_14q32.33' versus 'METHLYATION_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0029

Table S115.  Gene #20: 'amp_14q32.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
AMP PEAK 20(14Q32.33) MUTATED 33 51 35
AMP PEAK 20(14Q32.33) WILD-TYPE 119 71 58

Figure S115.  Get High-res Image Gene #20: 'amp_14q32.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_14q32.33' versus 'RPPA_CNMF'

P value = 0.0256 (Fisher's exact test), Q value = 0.056

Table S116.  Gene #20: 'amp_14q32.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 73 61
AMP PEAK 20(14Q32.33) MUTATED 14 30 13
AMP PEAK 20(14Q32.33) WILD-TYPE 46 43 48

Figure S116.  Get High-res Image Gene #20: 'amp_14q32.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_14q32.33' versus 'MRNASEQ_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.0031

Table S117.  Gene #20: 'amp_14q32.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
AMP PEAK 20(14Q32.33) MUTATED 47 58 36 17
AMP PEAK 20(14Q32.33) WILD-TYPE 66 94 118 62

Figure S117.  Get High-res Image Gene #20: 'amp_14q32.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_14q32.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.0018

Table S118.  Gene #20: 'amp_14q32.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 20(14Q32.33) MUTATED 66 68 24
AMP PEAK 20(14Q32.33) WILD-TYPE 112 121 107

Figure S118.  Get High-res Image Gene #20: 'amp_14q32.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S119.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
AMP PEAK 21(15Q26.3) MUTATED 41 82 56
AMP PEAK 21(15Q26.3) WILD-TYPE 141 84 97

Figure S119.  Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_15q26.3' versus 'METHLYATION_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0016

Table S120.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
AMP PEAK 21(15Q26.3) MUTATED 36 56 36
AMP PEAK 21(15Q26.3) WILD-TYPE 116 66 57

Figure S120.  Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_15q26.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.027 (Fisher's exact test), Q value = 0.058

Table S121.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 41 52 47
AMP PEAK 21(15Q26.3) MUTATED 12 15 19 24
AMP PEAK 21(15Q26.3) WILD-TYPE 42 26 33 23

Figure S121.  Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_15q26.3' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00021

Table S122.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
AMP PEAK 21(15Q26.3) MUTATED 28 76 49 23
AMP PEAK 21(15Q26.3) WILD-TYPE 85 76 105 56

Figure S122.  Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00286 (Fisher's exact test), Q value = 0.0092

Table S123.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 21(15Q26.3) MUTATED 57 84 35
AMP PEAK 21(15Q26.3) WILD-TYPE 121 105 96

Figure S123.  Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'MIRSEQ_CNMF'

P value = 0.0392 (Fisher's exact test), Q value = 0.079

Table S124.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
AMP PEAK 21(15Q26.3) MUTATED 40 57 33 29 14
AMP PEAK 21(15Q26.3) WILD-TYPE 81 77 88 33 23

Figure S124.  Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_15q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00638 (Fisher's exact test), Q value = 0.017

Table S125.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 21(15Q26.3) MUTATED 44 39 74 16
AMP PEAK 21(15Q26.3) WILD-TYPE 45 79 125 53

Figure S125.  Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00716 (Fisher's exact test), Q value = 0.019

Table S126.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
AMP PEAK 21(15Q26.3) MUTATED 19 48 48
AMP PEAK 21(15Q26.3) WILD-TYPE 70 81 68

Figure S126.  Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_15q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00433 (Fisher's exact test), Q value = 0.013

Table S127.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
AMP PEAK 21(15Q26.3) MUTATED 12 66 37
AMP PEAK 21(15Q26.3) WILD-TYPE 27 85 107

Figure S127.  Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q25.1' versus 'MRNA_CNMF'

P value = 0.00839 (Fisher's exact test), Q value = 0.022

Table S128.  Gene #22: 'amp_17q25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
AMP PEAK 22(17Q25.1) MUTATED 20 31 9 19
AMP PEAK 22(17Q25.1) WILD-TYPE 22 21 23 9

Figure S128.  Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q25.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S129.  Gene #22: 'amp_17q25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
AMP PEAK 22(17Q25.1) MUTATED 54 112 70
AMP PEAK 22(17Q25.1) WILD-TYPE 128 54 83

Figure S129.  Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q25.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S130.  Gene #22: 'amp_17q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
AMP PEAK 22(17Q25.1) MUTATED 47 76 44
AMP PEAK 22(17Q25.1) WILD-TYPE 105 46 49

Figure S130.  Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q25.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S131.  Gene #22: 'amp_17q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
AMP PEAK 22(17Q25.1) MUTATED 41 97 70 26
AMP PEAK 22(17Q25.1) WILD-TYPE 72 55 84 53

Figure S131.  Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S132.  Gene #22: 'amp_17q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 22(17Q25.1) MUTATED 67 115 52
AMP PEAK 22(17Q25.1) WILD-TYPE 111 74 79

Figure S132.  Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q25.1' versus 'MIRSEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0018

Table S133.  Gene #22: 'amp_17q25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
AMP PEAK 22(17Q25.1) MUTATED 62 78 38 26 19
AMP PEAK 22(17Q25.1) WILD-TYPE 59 56 83 36 18

Figure S133.  Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00468 (Fisher's exact test), Q value = 0.014

Table S134.  Gene #22: 'amp_17q25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 22(17Q25.1) MUTATED 53 51 97 22
AMP PEAK 22(17Q25.1) WILD-TYPE 36 67 102 47

Figure S134.  Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q25.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00122 (Fisher's exact test), Q value = 0.0045

Table S135.  Gene #22: 'amp_17q25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
AMP PEAK 22(17Q25.1) MUTATED 27 63 64
AMP PEAK 22(17Q25.1) WILD-TYPE 62 66 52

Figure S135.  Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q25.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.0011

Table S136.  Gene #22: 'amp_17q25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
AMP PEAK 22(17Q25.1) MUTATED 14 88 52
AMP PEAK 22(17Q25.1) WILD-TYPE 25 63 92

Figure S136.  Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18p11.32' versus 'MRNA_CNMF'

P value = 0.0436 (Fisher's exact test), Q value = 0.087

Table S137.  Gene #23: 'amp_18p11.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
AMP PEAK 23(18P11.32) MUTATED 13 27 8 8
AMP PEAK 23(18P11.32) WILD-TYPE 29 25 24 20

Figure S137.  Get High-res Image Gene #23: 'amp_18p11.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_18p11.32' versus 'MRNA_CHIERARCHICAL'

P value = 0.0044 (Fisher's exact test), Q value = 0.013

Table S138.  Gene #23: 'amp_18p11.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
AMP PEAK 23(18P11.32) MUTATED 13 30 13
AMP PEAK 23(18P11.32) WILD-TYPE 34 26 38

Figure S138.  Get High-res Image Gene #23: 'amp_18p11.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_18p11.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S139.  Gene #23: 'amp_18p11.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
AMP PEAK 23(18P11.32) MUTATED 38 81 60
AMP PEAK 23(18P11.32) WILD-TYPE 144 85 93

Figure S139.  Get High-res Image Gene #23: 'amp_18p11.32' versus Molecular Subtype #3: 'CN_CNMF'

'amp_18p11.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S140.  Gene #23: 'amp_18p11.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
AMP PEAK 23(18P11.32) MUTATED 33 55 44
AMP PEAK 23(18P11.32) WILD-TYPE 119 67 49

Figure S140.  Get High-res Image Gene #23: 'amp_18p11.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_18p11.32' versus 'MRNASEQ_CNMF'

P value = 0.0409 (Fisher's exact test), Q value = 0.082

Table S141.  Gene #23: 'amp_18p11.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
AMP PEAK 23(18P11.32) MUTATED 37 68 51 22
AMP PEAK 23(18P11.32) WILD-TYPE 76 84 103 57

Figure S141.  Get High-res Image Gene #23: 'amp_18p11.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_18p11.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00148 (Fisher's exact test), Q value = 0.0053

Table S142.  Gene #23: 'amp_18p11.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 23(18P11.32) MUTATED 50 86 42
AMP PEAK 23(18P11.32) WILD-TYPE 128 103 89

Figure S142.  Get High-res Image Gene #23: 'amp_18p11.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_18p11.32' versus 'MIRSEQ_CNMF'

P value = 0.019 (Fisher's exact test), Q value = 0.043

Table S143.  Gene #23: 'amp_18p11.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
AMP PEAK 23(18P11.32) MUTATED 42 58 30 24 17
AMP PEAK 23(18P11.32) WILD-TYPE 79 76 91 38 20

Figure S143.  Get High-res Image Gene #23: 'amp_18p11.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_18p11.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.0014

Table S144.  Gene #23: 'amp_18p11.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
AMP PEAK 23(18P11.32) MUTATED 11 71 36
AMP PEAK 23(18P11.32) WILD-TYPE 28 80 108

Figure S144.  Get High-res Image Gene #23: 'amp_18p11.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18q11.2' versus 'MRNA_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.0021

Table S145.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
AMP PEAK 24(18Q11.2) MUTATED 8 25 5 15
AMP PEAK 24(18Q11.2) WILD-TYPE 34 27 27 13

Figure S145.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_18q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 0.036

Table S146.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
AMP PEAK 24(18Q11.2) MUTATED 10 27 16
AMP PEAK 24(18Q11.2) WILD-TYPE 37 29 35

Figure S146.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_18q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S147.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
AMP PEAK 24(18Q11.2) MUTATED 30 76 45
AMP PEAK 24(18Q11.2) WILD-TYPE 152 90 108

Figure S147.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S148.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
AMP PEAK 24(18Q11.2) MUTATED 26 52 29
AMP PEAK 24(18Q11.2) WILD-TYPE 126 70 64

Figure S148.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S149.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
AMP PEAK 24(18Q11.2) MUTATED 26 64 51 9
AMP PEAK 24(18Q11.2) WILD-TYPE 87 88 103 70

Figure S149.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00033

Table S150.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 24(18Q11.2) MUTATED 35 77 38
AMP PEAK 24(18Q11.2) WILD-TYPE 143 112 93

Figure S150.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.03

Table S151.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
AMP PEAK 24(18Q11.2) MUTATED 38 47 22 24 12
AMP PEAK 24(18Q11.2) WILD-TYPE 83 87 99 38 25

Figure S151.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00305 (Fisher's exact test), Q value = 0.0096

Table S152.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 24(18Q11.2) MUTATED 38 32 62 11
AMP PEAK 24(18Q11.2) WILD-TYPE 51 86 137 58

Figure S152.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0498 (Fisher's exact test), Q value = 0.097

Table S153.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
AMP PEAK 24(18Q11.2) MUTATED 17 37 40
AMP PEAK 24(18Q11.2) WILD-TYPE 72 92 76

Figure S153.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00027

Table S154.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
AMP PEAK 24(18Q11.2) MUTATED 7 61 26
AMP PEAK 24(18Q11.2) WILD-TYPE 32 90 118

Figure S154.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S155.  Gene #25: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
AMP PEAK 25(19Q12) MUTATED 56 106 62
AMP PEAK 25(19Q12) WILD-TYPE 126 60 91

Figure S155.  Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.045

Table S156.  Gene #25: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
AMP PEAK 25(19Q12) MUTATED 61 69 40
AMP PEAK 25(19Q12) WILD-TYPE 91 53 53

Figure S156.  Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 0.00263 (Fisher's exact test), Q value = 0.0086

Table S157.  Gene #25: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
AMP PEAK 25(19Q12) MUTATED 37 83 72 30
AMP PEAK 25(19Q12) WILD-TYPE 76 69 82 49

Figure S157.  Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0285 (Fisher's exact test), Q value = 0.061

Table S158.  Gene #25: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 25(19Q12) MUTATED 66 96 60
AMP PEAK 25(19Q12) WILD-TYPE 112 93 71

Figure S158.  Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00755 (Fisher's exact test), Q value = 0.02

Table S159.  Gene #25: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
AMP PEAK 25(19Q12) MUTATED 35 50 66
AMP PEAK 25(19Q12) WILD-TYPE 54 79 50

Figure S159.  Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00232 (Fisher's exact test), Q value = 0.0077

Table S160.  Gene #25: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
AMP PEAK 25(19Q12) MUTATED 18 83 50
AMP PEAK 25(19Q12) WILD-TYPE 21 68 94

Figure S160.  Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S161.  Gene #26: 'amp_19q13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
AMP PEAK 26(19Q13.2) MUTATED 60 107 67
AMP PEAK 26(19Q13.2) WILD-TYPE 122 59 86

Figure S161.  Get High-res Image Gene #26: 'amp_19q13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q13.2' versus 'METHLYATION_CNMF'

P value = 0.0267 (Fisher's exact test), Q value = 0.057

Table S162.  Gene #26: 'amp_19q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
AMP PEAK 26(19Q13.2) MUTATED 64 70 40
AMP PEAK 26(19Q13.2) WILD-TYPE 88 52 53

Figure S162.  Get High-res Image Gene #26: 'amp_19q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19q13.2' versus 'MRNASEQ_CNMF'

P value = 0.00521 (Fisher's exact test), Q value = 0.015

Table S163.  Gene #26: 'amp_19q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
AMP PEAK 26(19Q13.2) MUTATED 39 85 74 33
AMP PEAK 26(19Q13.2) WILD-TYPE 74 67 80 46

Figure S163.  Get High-res Image Gene #26: 'amp_19q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 0.064

Table S164.  Gene #26: 'amp_19q13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
AMP PEAK 26(19Q13.2) MUTATED 40 52 66
AMP PEAK 26(19Q13.2) WILD-TYPE 49 77 50

Figure S164.  Get High-res Image Gene #26: 'amp_19q13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 0.033

Table S165.  Gene #26: 'amp_19q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
AMP PEAK 26(19Q13.2) MUTATED 20 83 55
AMP PEAK 26(19Q13.2) WILD-TYPE 19 68 89

Figure S165.  Get High-res Image Gene #26: 'amp_19q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20p12.2' versus 'MRNA_CNMF'

P value = 0.00108 (Fisher's exact test), Q value = 0.0041

Table S166.  Gene #27: 'amp_20p12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
AMP PEAK 27(20P12.2) MUTATED 23 37 9 12
AMP PEAK 27(20P12.2) WILD-TYPE 19 15 23 16

Figure S166.  Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20p12.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00235 (Fisher's exact test), Q value = 0.0078

Table S167.  Gene #27: 'amp_20p12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
AMP PEAK 27(20P12.2) MUTATED 27 37 17
AMP PEAK 27(20P12.2) WILD-TYPE 20 19 34

Figure S167.  Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20p12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S168.  Gene #27: 'amp_20p12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
AMP PEAK 27(20P12.2) MUTATED 70 119 91
AMP PEAK 27(20P12.2) WILD-TYPE 112 47 62

Figure S168.  Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p12.2' versus 'METHLYATION_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0018

Table S169.  Gene #27: 'amp_20p12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
AMP PEAK 27(20P12.2) MUTATED 74 87 49
AMP PEAK 27(20P12.2) WILD-TYPE 78 35 44

Figure S169.  Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20p12.2' versus 'MRNASEQ_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.041

Table S170.  Gene #27: 'amp_20p12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
AMP PEAK 27(20P12.2) MUTATED 56 101 82 40
AMP PEAK 27(20P12.2) WILD-TYPE 57 51 72 39

Figure S170.  Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20p12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0155 (Fisher's exact test), Q value = 0.037

Table S171.  Gene #27: 'amp_20p12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 27(20P12.2) MUTATED 94 121 64
AMP PEAK 27(20P12.2) WILD-TYPE 84 68 67

Figure S171.  Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S172.  Gene #28: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
AMP PEAK 28(20Q11.21) MUTATED 82 114 110
AMP PEAK 28(20Q11.21) WILD-TYPE 100 52 43

Figure S172.  Get High-res Image Gene #28: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q11.21' versus 'METHLYATION_CNMF'

P value = 0.00591 (Fisher's exact test), Q value = 0.016

Table S173.  Gene #28: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
AMP PEAK 28(20Q11.21) MUTATED 80 87 58
AMP PEAK 28(20Q11.21) WILD-TYPE 72 35 35

Figure S173.  Get High-res Image Gene #28: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_22q11.21' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00086

Table S174.  Gene #29: 'amp_22q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
AMP PEAK 29(22Q11.21) MUTATED 71 100 85
AMP PEAK 29(22Q11.21) WILD-TYPE 111 66 68

Figure S174.  Get High-res Image Gene #29: 'amp_22q11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_22q11.21' versus 'METHLYATION_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0018

Table S175.  Gene #29: 'amp_22q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
AMP PEAK 29(22Q11.21) MUTATED 62 79 51
AMP PEAK 29(22Q11.21) WILD-TYPE 90 43 42

Figure S175.  Get High-res Image Gene #29: 'amp_22q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_22q11.21' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 5e-04

Table S176.  Gene #29: 'amp_22q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
AMP PEAK 29(22Q11.21) MUTATED 55 100 68 31
AMP PEAK 29(22Q11.21) WILD-TYPE 58 52 86 48

Figure S176.  Get High-res Image Gene #29: 'amp_22q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_22q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0012

Table S177.  Gene #29: 'amp_22q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
AMP PEAK 29(22Q11.21) MUTATED 97 110 47
AMP PEAK 29(22Q11.21) WILD-TYPE 81 79 84

Figure S177.  Get High-res Image Gene #29: 'amp_22q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_22q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0416 (Fisher's exact test), Q value = 0.083

Table S178.  Gene #29: 'amp_22q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
AMP PEAK 29(22Q11.21) MUTATED 48 55 114 27
AMP PEAK 29(22Q11.21) WILD-TYPE 41 63 85 42

Figure S178.  Get High-res Image Gene #29: 'amp_22q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_xq28' versus 'CN_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.029

Table S179.  Gene #30: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
AMP PEAK 30(XQ28) MUTATED 34 54 36
AMP PEAK 30(XQ28) WILD-TYPE 148 112 117

Figure S179.  Get High-res Image Gene #30: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xq28' versus 'METHLYATION_CNMF'

P value = 0.0355 (Fisher's exact test), Q value = 0.073

Table S180.  Gene #30: 'amp_xq28' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
AMP PEAK 30(XQ28) MUTATED 28 39 23
AMP PEAK 30(XQ28) WILD-TYPE 124 83 70

Figure S180.  Get High-res Image Gene #30: 'amp_xq28' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xq28' versus 'RPPA_CNMF'

P value = 0.0369 (Fisher's exact test), Q value = 0.075

Table S181.  Gene #30: 'amp_xq28' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 73 61
AMP PEAK 30(XQ28) MUTATED 14 26 10
AMP PEAK 30(XQ28) WILD-TYPE 46 47 51

Figure S181.  Get High-res Image Gene #30: 'amp_xq28' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_xq28' versus 'MRNASEQ_CNMF'

P value = 0.0475 (Fisher's exact test), Q value = 0.093

Table S182.  Gene #30: 'amp_xq28' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
AMP PEAK 30(XQ28) MUTATED 19 48 36 18
AMP PEAK 30(XQ28) WILD-TYPE 94 104 118 61

Figure S182.  Get High-res Image Gene #30: 'amp_xq28' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xq28' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0178 (Fisher's exact test), Q value = 0.041

Table S183.  Gene #30: 'amp_xq28' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
AMP PEAK 30(XQ28) MUTATED 17 25 39
AMP PEAK 30(XQ28) WILD-TYPE 72 104 77

Figure S183.  Get High-res Image Gene #30: 'amp_xq28' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_xq28' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0324 (Fisher's exact test), Q value = 0.067

Table S184.  Gene #30: 'amp_xq28' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
AMP PEAK 30(XQ28) MUTATED 12 44 25
AMP PEAK 30(XQ28) WILD-TYPE 27 107 119

Figure S184.  Get High-res Image Gene #30: 'amp_xq28' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.11' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00021

Table S185.  Gene #31: 'del_1p36.11' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
DEL PEAK 1(1P36.11) MUTATED 12 39 13 10
DEL PEAK 1(1P36.11) WILD-TYPE 30 13 19 18

Figure S185.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.11' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S186.  Gene #31: 'del_1p36.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 1(1P36.11) MUTATED 14 43 17
DEL PEAK 1(1P36.11) WILD-TYPE 33 13 34

Figure S186.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S187.  Gene #31: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 1(1P36.11) MUTATED 45 138 45
DEL PEAK 1(1P36.11) WILD-TYPE 137 28 108

Figure S187.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S188.  Gene #31: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 1(1P36.11) MUTATED 30 96 35
DEL PEAK 1(1P36.11) WILD-TYPE 122 26 58

Figure S188.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.11' versus 'RPPA_CHIERARCHICAL'

P value = 0.00338 (Fisher's exact test), Q value = 0.01

Table S189.  Gene #31: 'del_1p36.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 41 52 47
DEL PEAK 1(1P36.11) MUTATED 26 15 15 30
DEL PEAK 1(1P36.11) WILD-TYPE 28 26 37 17

Figure S189.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S190.  Gene #31: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 1(1P36.11) MUTATED 32 120 52 23
DEL PEAK 1(1P36.11) WILD-TYPE 81 32 102 56

Figure S190.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S191.  Gene #31: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 1(1P36.11) MUTATED 46 140 41
DEL PEAK 1(1P36.11) WILD-TYPE 132 49 90

Figure S191.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S192.  Gene #31: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 1(1P36.11) MUTATED 57 74 31 43 11
DEL PEAK 1(1P36.11) WILD-TYPE 64 60 90 19 26

Figure S192.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S193.  Gene #31: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 1(1P36.11) MUTATED 66 52 83 15
DEL PEAK 1(1P36.11) WILD-TYPE 23 66 116 54

Figure S193.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S194.  Gene #31: 'del_1p36.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
DEL PEAK 1(1P36.11) MUTATED 21 56 67
DEL PEAK 1(1P36.11) WILD-TYPE 68 73 49

Figure S194.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S195.  Gene #31: 'del_1p36.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 1(1P36.11) MUTATED 9 90 45
DEL PEAK 1(1P36.11) WILD-TYPE 30 61 99

Figure S195.  Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p13.1' versus 'MRNA_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 9e-04

Table S196.  Gene #32: 'del_1p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
DEL PEAK 2(1P13.1) MUTATED 17 37 9 9
DEL PEAK 2(1P13.1) WILD-TYPE 25 15 23 19

Figure S196.  Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p13.1' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S197.  Gene #32: 'del_1p13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 2(1P13.1) MUTATED 19 39 14
DEL PEAK 2(1P13.1) WILD-TYPE 28 17 37

Figure S197.  Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S198.  Gene #32: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 2(1P13.1) MUTATED 47 124 50
DEL PEAK 2(1P13.1) WILD-TYPE 135 42 103

Figure S198.  Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S199.  Gene #32: 'del_1p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 2(1P13.1) MUTATED 40 83 34
DEL PEAK 2(1P13.1) WILD-TYPE 112 39 59

Figure S199.  Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p13.1' versus 'RPPA_CNMF'

P value = 0.0231 (Fisher's exact test), Q value = 0.051

Table S200.  Gene #32: 'del_1p13.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 73 61
DEL PEAK 2(1P13.1) MUTATED 35 26 24
DEL PEAK 2(1P13.1) WILD-TYPE 25 47 37

Figure S200.  Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S201.  Gene #32: 'del_1p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 2(1P13.1) MUTATED 34 107 55 24
DEL PEAK 2(1P13.1) WILD-TYPE 79 45 99 55

Figure S201.  Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S202.  Gene #32: 'del_1p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 2(1P13.1) MUTATED 48 125 47
DEL PEAK 2(1P13.1) WILD-TYPE 130 64 84

Figure S202.  Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S203.  Gene #32: 'del_1p13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 2(1P13.1) MUTATED 51 70 28 44 17
DEL PEAK 2(1P13.1) WILD-TYPE 70 64 93 18 20

Figure S203.  Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S204.  Gene #32: 'del_1p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 2(1P13.1) MUTATED 62 53 79 16
DEL PEAK 2(1P13.1) WILD-TYPE 27 65 120 53

Figure S204.  Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0019

Table S205.  Gene #32: 'del_1p13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
DEL PEAK 2(1P13.1) MUTATED 23 57 62
DEL PEAK 2(1P13.1) WILD-TYPE 66 72 54

Figure S205.  Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S206.  Gene #32: 'del_1p13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 2(1P13.1) MUTATED 10 88 44
DEL PEAK 2(1P13.1) WILD-TYPE 29 63 100

Figure S206.  Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2p25.3' versus 'MIRSEQ_CNMF'

P value = 0.00876 (Fisher's exact test), Q value = 0.023

Table S207.  Gene #33: 'del_2p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 3(2P25.3) MUTATED 18 19 4 4 3
DEL PEAK 3(2P25.3) WILD-TYPE 103 115 117 58 34

Figure S207.  Get High-res Image Gene #33: 'del_2p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2p25.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0476 (Fisher's exact test), Q value = 0.093

Table S208.  Gene #33: 'del_2p25.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
DEL PEAK 3(2P25.3) MUTATED 3 11 15
DEL PEAK 3(2P25.3) WILD-TYPE 86 118 101

Figure S208.  Get High-res Image Gene #33: 'del_2p25.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_2p25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0292 (Fisher's exact test), Q value = 0.062

Table S209.  Gene #33: 'del_2p25.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 3(2P25.3) MUTATED 2 20 7
DEL PEAK 3(2P25.3) WILD-TYPE 37 131 137

Figure S209.  Get High-res Image Gene #33: 'del_2p25.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S210.  Gene #34: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 4(2Q22.1) MUTATED 26 64 41
DEL PEAK 4(2Q22.1) WILD-TYPE 156 102 112

Figure S210.  Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.003

Table S211.  Gene #34: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 4(2Q22.1) MUTATED 23 42 27
DEL PEAK 4(2Q22.1) WILD-TYPE 129 80 66

Figure S211.  Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00219 (Fisher's exact test), Q value = 0.0073

Table S212.  Gene #34: 'del_2q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 4(2Q22.1) MUTATED 24 50 47 10
DEL PEAK 4(2Q22.1) WILD-TYPE 89 102 107 69

Figure S212.  Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00735 (Fisher's exact test), Q value = 0.02

Table S213.  Gene #34: 'del_2q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 4(2Q22.1) MUTATED 33 62 36
DEL PEAK 4(2Q22.1) WILD-TYPE 145 127 95

Figure S213.  Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 9e-04

Table S214.  Gene #34: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 4(2Q22.1) MUTATED 37 48 16 20 6
DEL PEAK 4(2Q22.1) WILD-TYPE 84 86 105 42 31

Figure S214.  Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00048 (Fisher's exact test), Q value = 0.0021

Table S215.  Gene #34: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 4(2Q22.1) MUTATED 35 38 45 9
DEL PEAK 4(2Q22.1) WILD-TYPE 54 80 154 60

Figure S215.  Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0193 (Fisher's exact test), Q value = 0.044

Table S216.  Gene #34: 'del_2q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
DEL PEAK 4(2Q22.1) MUTATED 13 39 33
DEL PEAK 4(2Q22.1) WILD-TYPE 76 90 83

Figure S216.  Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_2q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0242 (Fisher's exact test), Q value = 0.053

Table S217.  Gene #34: 'del_2q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 4(2Q22.1) MUTATED 9 49 27
DEL PEAK 4(2Q22.1) WILD-TYPE 30 102 117

Figure S217.  Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q37.1' versus 'MRNA_CNMF'

P value = 0.00315 (Fisher's exact test), Q value = 0.0098

Table S218.  Gene #35: 'del_2q37.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
DEL PEAK 5(2Q37.1) MUTATED 7 26 7 10
DEL PEAK 5(2Q37.1) WILD-TYPE 35 26 25 18

Figure S218.  Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_2q37.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00071 (Fisher's exact test), Q value = 0.003

Table S219.  Gene #35: 'del_2q37.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 5(2Q37.1) MUTATED 11 29 10
DEL PEAK 5(2Q37.1) WILD-TYPE 36 27 41

Figure S219.  Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_2q37.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S220.  Gene #35: 'del_2q37.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 5(2Q37.1) MUTATED 33 85 41
DEL PEAK 5(2Q37.1) WILD-TYPE 149 81 112

Figure S220.  Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q37.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S221.  Gene #35: 'del_2q37.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 5(2Q37.1) MUTATED 27 60 33
DEL PEAK 5(2Q37.1) WILD-TYPE 125 62 60

Figure S221.  Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q37.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S222.  Gene #35: 'del_2q37.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 5(2Q37.1) MUTATED 33 72 43 10
DEL PEAK 5(2Q37.1) WILD-TYPE 80 80 111 69

Figure S222.  Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q37.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S223.  Gene #35: 'del_2q37.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 5(2Q37.1) MUTATED 38 88 32
DEL PEAK 5(2Q37.1) WILD-TYPE 140 101 99

Figure S223.  Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S224.  Gene #35: 'del_2q37.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 5(2Q37.1) MUTATED 38 70 17 21 7
DEL PEAK 5(2Q37.1) WILD-TYPE 83 64 104 41 30

Figure S224.  Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q37.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S225.  Gene #35: 'del_2q37.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 5(2Q37.1) MUTATED 34 54 56 9
DEL PEAK 5(2Q37.1) WILD-TYPE 55 64 143 60

Figure S225.  Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S226.  Gene #35: 'del_2q37.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
DEL PEAK 5(2Q37.1) MUTATED 11 45 50
DEL PEAK 5(2Q37.1) WILD-TYPE 78 84 66

Figure S226.  Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_2q37.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S227.  Gene #35: 'del_2q37.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 5(2Q37.1) MUTATED 4 69 33
DEL PEAK 5(2Q37.1) WILD-TYPE 35 82 111

Figure S227.  Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p25.3' versus 'CN_CNMF'

P value = 0.00172 (Fisher's exact test), Q value = 0.006

Table S228.  Gene #36: 'del_3p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 6(3P25.3) MUTATED 133 146 119
DEL PEAK 6(3P25.3) WILD-TYPE 49 20 34

Figure S228.  Get High-res Image Gene #36: 'del_3p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p25.3' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 5e-04

Table S229.  Gene #36: 'del_3p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 6(3P25.3) MUTATED 105 109 78
DEL PEAK 6(3P25.3) WILD-TYPE 47 13 15

Figure S229.  Get High-res Image Gene #36: 'del_3p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p25.3' versus 'MRNASEQ_CNMF'

P value = 0.00287 (Fisher's exact test), Q value = 0.0092

Table S230.  Gene #36: 'del_3p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 6(3P25.3) MUTATED 87 133 123 53
DEL PEAK 6(3P25.3) WILD-TYPE 26 19 31 26

Figure S230.  Get High-res Image Gene #36: 'del_3p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.0014

Table S231.  Gene #36: 'del_3p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 6(3P25.3) MUTATED 141 165 90
DEL PEAK 6(3P25.3) WILD-TYPE 37 24 41

Figure S231.  Get High-res Image Gene #36: 'del_3p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p25.3' versus 'MIRSEQ_CNMF'

P value = 0.00826 (Fisher's exact test), Q value = 0.022

Table S232.  Gene #36: 'del_3p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 6(3P25.3) MUTATED 94 116 83 52 31
DEL PEAK 6(3P25.3) WILD-TYPE 27 18 38 10 6

Figure S232.  Get High-res Image Gene #36: 'del_3p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00086

Table S233.  Gene #36: 'del_3p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 6(3P25.3) MUTATED 76 94 166 40
DEL PEAK 6(3P25.3) WILD-TYPE 13 24 33 29

Figure S233.  Get High-res Image Gene #36: 'del_3p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p25.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.037

Table S234.  Gene #36: 'del_3p25.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
DEL PEAK 6(3P25.3) MUTATED 62 103 100
DEL PEAK 6(3P25.3) WILD-TYPE 27 26 16

Figure S234.  Get High-res Image Gene #36: 'del_3p25.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S235.  Gene #37: 'del_3p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 7(3P13) MUTATED 136 157 141
DEL PEAK 7(3P13) WILD-TYPE 46 9 12

Figure S235.  Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p13' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00039

Table S236.  Gene #37: 'del_3p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 7(3P13) MUTATED 117 116 85
DEL PEAK 7(3P13) WILD-TYPE 35 6 8

Figure S236.  Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p13' versus 'RPPA_CHIERARCHICAL'

P value = 0.00111 (Fisher's exact test), Q value = 0.0042

Table S237.  Gene #37: 'del_3p13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 41 52 47
DEL PEAK 7(3P13) MUTATED 48 27 49 43
DEL PEAK 7(3P13) WILD-TYPE 6 14 3 4

Figure S237.  Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p13' versus 'MRNASEQ_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0031

Table S238.  Gene #37: 'del_3p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 7(3P13) MUTATED 101 140 133 57
DEL PEAK 7(3P13) WILD-TYPE 12 12 21 22

Figure S238.  Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00082 (Fisher's exact test), Q value = 0.0033

Table S239.  Gene #37: 'del_3p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 7(3P13) MUTATED 154 175 102
DEL PEAK 7(3P13) WILD-TYPE 24 14 29

Figure S239.  Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p13' versus 'MIRSEQ_CNMF'

P value = 0.00206 (Fisher's exact test), Q value = 0.007

Table S240.  Gene #37: 'del_3p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 7(3P13) MUTATED 105 125 92 56 33
DEL PEAK 7(3P13) WILD-TYPE 16 9 29 6 4

Figure S240.  Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S241.  Gene #37: 'del_3p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 7(3P13) MUTATED 79 104 185 43
DEL PEAK 7(3P13) WILD-TYPE 10 14 14 26

Figure S241.  Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00075 (Fisher's exact test), Q value = 0.0031

Table S242.  Gene #37: 'del_3p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
DEL PEAK 7(3P13) MUTATED 67 116 108
DEL PEAK 7(3P13) WILD-TYPE 22 13 8

Figure S242.  Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.001

Table S243.  Gene #37: 'del_3p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 7(3P13) MUTATED 34 143 114
DEL PEAK 7(3P13) WILD-TYPE 5 8 30

Figure S243.  Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p12.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S244.  Gene #38: 'del_3p12.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 8(3P12.3) MUTATED 134 156 137
DEL PEAK 8(3P12.3) WILD-TYPE 48 10 16

Figure S244.  Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p12.3' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00021

Table S245.  Gene #38: 'del_3p12.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 8(3P12.3) MUTATED 114 115 83
DEL PEAK 8(3P12.3) WILD-TYPE 38 7 10

Figure S245.  Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p12.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00153 (Fisher's exact test), Q value = 0.0054

Table S246.  Gene #38: 'del_3p12.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 41 52 47
DEL PEAK 8(3P12.3) MUTATED 46 27 49 43
DEL PEAK 8(3P12.3) WILD-TYPE 8 14 3 4

Figure S246.  Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p12.3' versus 'MRNASEQ_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.002

Table S247.  Gene #38: 'del_3p12.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 8(3P12.3) MUTATED 99 138 132 55
DEL PEAK 8(3P12.3) WILD-TYPE 14 14 22 24

Figure S247.  Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p12.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00493 (Fisher's exact test), Q value = 0.014

Table S248.  Gene #38: 'del_3p12.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 8(3P12.3) MUTATED 152 171 101
DEL PEAK 8(3P12.3) WILD-TYPE 26 18 30

Figure S248.  Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p12.3' versus 'MIRSEQ_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 0.051

Table S249.  Gene #38: 'del_3p12.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 8(3P12.3) MUTATED 103 121 92 56 32
DEL PEAK 8(3P12.3) WILD-TYPE 18 13 29 6 5

Figure S249.  Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p12.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S250.  Gene #38: 'del_3p12.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 8(3P12.3) MUTATED 79 103 180 42
DEL PEAK 8(3P12.3) WILD-TYPE 10 15 19 27

Figure S250.  Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p12.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0018

Table S251.  Gene #38: 'del_3p12.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
DEL PEAK 8(3P12.3) MUTATED 65 114 107
DEL PEAK 8(3P12.3) WILD-TYPE 24 15 9

Figure S251.  Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p12.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0011 (Fisher's exact test), Q value = 0.0042

Table S252.  Gene #38: 'del_3p12.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 8(3P12.3) MUTATED 34 140 112
DEL PEAK 8(3P12.3) WILD-TYPE 5 11 32

Figure S252.  Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p12.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S253.  Gene #39: 'del_3p12.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 9(3P12.3) MUTATED 133 153 135
DEL PEAK 9(3P12.3) WILD-TYPE 49 13 18

Figure S253.  Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p12.3' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00072

Table S254.  Gene #39: 'del_3p12.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 9(3P12.3) MUTATED 113 114 81
DEL PEAK 9(3P12.3) WILD-TYPE 39 8 12

Figure S254.  Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p12.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00653 (Fisher's exact test), Q value = 0.018

Table S255.  Gene #39: 'del_3p12.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 41 52 47
DEL PEAK 9(3P12.3) MUTATED 45 27 48 42
DEL PEAK 9(3P12.3) WILD-TYPE 9 14 4 5

Figure S255.  Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p12.3' versus 'MRNASEQ_CNMF'

P value = 0.00273 (Fisher's exact test), Q value = 0.0088

Table S256.  Gene #39: 'del_3p12.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 9(3P12.3) MUTATED 96 136 131 55
DEL PEAK 9(3P12.3) WILD-TYPE 17 16 23 24

Figure S256.  Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p12.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00769 (Fisher's exact test), Q value = 0.02

Table S257.  Gene #39: 'del_3p12.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 9(3P12.3) MUTATED 149 169 100
DEL PEAK 9(3P12.3) WILD-TYPE 29 20 31

Figure S257.  Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p12.3' versus 'MIRSEQ_CNMF'

P value = 0.0257 (Fisher's exact test), Q value = 0.056

Table S258.  Gene #39: 'del_3p12.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 9(3P12.3) MUTATED 102 118 90 56 32
DEL PEAK 9(3P12.3) WILD-TYPE 19 16 31 6 5

Figure S258.  Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p12.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00021

Table S259.  Gene #39: 'del_3p12.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 9(3P12.3) MUTATED 79 101 176 42
DEL PEAK 9(3P12.3) WILD-TYPE 10 17 23 27

Figure S259.  Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p12.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00221 (Fisher's exact test), Q value = 0.0074

Table S260.  Gene #39: 'del_3p12.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
DEL PEAK 9(3P12.3) MUTATED 65 113 105
DEL PEAK 9(3P12.3) WILD-TYPE 24 16 11

Figure S260.  Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p12.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00301 (Fisher's exact test), Q value = 0.0095

Table S261.  Gene #39: 'del_3p12.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 9(3P12.3) MUTATED 34 138 111
DEL PEAK 9(3P12.3) WILD-TYPE 5 13 33

Figure S261.  Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p15.2' versus 'MRNA_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00093

Table S262.  Gene #41: 'del_4p15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
DEL PEAK 11(4P15.2) MUTATED 31 41 12 13
DEL PEAK 11(4P15.2) WILD-TYPE 11 11 20 15

Figure S262.  Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4p15.2' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00021

Table S263.  Gene #41: 'del_4p15.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 11(4P15.2) MUTATED 34 44 19
DEL PEAK 11(4P15.2) WILD-TYPE 13 12 32

Figure S263.  Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4p15.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S264.  Gene #41: 'del_4p15.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 11(4P15.2) MUTATED 88 136 93
DEL PEAK 11(4P15.2) WILD-TYPE 94 30 60

Figure S264.  Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p15.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S265.  Gene #41: 'del_4p15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 11(4P15.2) MUTATED 73 95 64
DEL PEAK 11(4P15.2) WILD-TYPE 79 27 29

Figure S265.  Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p15.2' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00082

Table S266.  Gene #41: 'del_4p15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 11(4P15.2) MUTATED 74 116 83 43
DEL PEAK 11(4P15.2) WILD-TYPE 39 36 71 36

Figure S266.  Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p15.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S267.  Gene #41: 'del_4p15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 11(4P15.2) MUTATED 106 147 63
DEL PEAK 11(4P15.2) WILD-TYPE 72 42 68

Figure S267.  Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p15.2' versus 'MIRSEQ_CNMF'

P value = 0.00204 (Fisher's exact test), Q value = 0.0069

Table S268.  Gene #41: 'del_4p15.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 11(4P15.2) MUTATED 81 101 63 38 21
DEL PEAK 11(4P15.2) WILD-TYPE 40 33 58 24 16

Figure S268.  Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4p15.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.001

Table S269.  Gene #41: 'del_4p15.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
DEL PEAK 11(4P15.2) MUTATED 43 80 89
DEL PEAK 11(4P15.2) WILD-TYPE 46 49 27

Figure S269.  Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4p15.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S270.  Gene #41: 'del_4p15.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 11(4P15.2) MUTATED 19 116 77
DEL PEAK 11(4P15.2) WILD-TYPE 20 35 67

Figure S270.  Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.1' versus 'MRNA_CNMF'

P value = 0.00297 (Fisher's exact test), Q value = 0.0095

Table S271.  Gene #42: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
DEL PEAK 12(4Q22.1) MUTATED 29 38 11 16
DEL PEAK 12(4Q22.1) WILD-TYPE 13 14 21 12

Figure S271.  Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00474 (Fisher's exact test), Q value = 0.014

Table S272.  Gene #42: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 12(4Q22.1) MUTATED 31 41 22
DEL PEAK 12(4Q22.1) WILD-TYPE 16 15 29

Figure S272.  Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S273.  Gene #42: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 12(4Q22.1) MUTATED 82 123 80
DEL PEAK 12(4Q22.1) WILD-TYPE 100 43 73

Figure S273.  Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.0039

Table S274.  Gene #42: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 12(4Q22.1) MUTATED 68 82 52
DEL PEAK 12(4Q22.1) WILD-TYPE 84 40 41

Figure S274.  Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0012

Table S275.  Gene #42: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 12(4Q22.1) MUTATED 61 107 82 33
DEL PEAK 12(4Q22.1) WILD-TYPE 52 45 72 46

Figure S275.  Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0147 (Fisher's exact test), Q value = 0.035

Table S276.  Gene #42: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 12(4Q22.1) MUTATED 97 122 64
DEL PEAK 12(4Q22.1) WILD-TYPE 81 67 67

Figure S276.  Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.038

Table S277.  Gene #42: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 12(4Q22.1) MUTATED 79 77 54 39 23
DEL PEAK 12(4Q22.1) WILD-TYPE 42 57 67 23 14

Figure S277.  Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00568 (Fisher's exact test), Q value = 0.016

Table S278.  Gene #42: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 12(4Q22.1) MUTATED 61 67 116 28
DEL PEAK 12(4Q22.1) WILD-TYPE 28 51 83 41

Figure S278.  Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0178 (Fisher's exact test), Q value = 0.041

Table S279.  Gene #42: 'del_4q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 12(4Q22.1) MUTATED 22 95 67
DEL PEAK 12(4Q22.1) WILD-TYPE 17 56 77

Figure S279.  Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q32.3' versus 'MRNA_CNMF'

P value = 0.00651 (Fisher's exact test), Q value = 0.018

Table S280.  Gene #43: 'del_4q32.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
DEL PEAK 13(4Q32.3) MUTATED 29 42 14 20
DEL PEAK 13(4Q32.3) WILD-TYPE 13 10 18 8

Figure S280.  Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q32.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0194 (Fisher's exact test), Q value = 0.044

Table S281.  Gene #43: 'del_4q32.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 13(4Q32.3) MUTATED 32 45 28
DEL PEAK 13(4Q32.3) WILD-TYPE 15 11 23

Figure S281.  Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q32.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S282.  Gene #43: 'del_4q32.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 13(4Q32.3) MUTATED 95 141 93
DEL PEAK 13(4Q32.3) WILD-TYPE 87 25 60

Figure S282.  Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q32.3' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 5e-04

Table S283.  Gene #43: 'del_4q32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 13(4Q32.3) MUTATED 80 94 65
DEL PEAK 13(4Q32.3) WILD-TYPE 72 28 28

Figure S283.  Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q32.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S284.  Gene #43: 'del_4q32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 13(4Q32.3) MUTATED 72 122 94 39
DEL PEAK 13(4Q32.3) WILD-TYPE 41 30 60 40

Figure S284.  Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q32.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.0014

Table S285.  Gene #43: 'del_4q32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 13(4Q32.3) MUTATED 110 144 73
DEL PEAK 13(4Q32.3) WILD-TYPE 68 45 58

Figure S285.  Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q32.3' versus 'MIRSEQ_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.003

Table S286.  Gene #43: 'del_4q32.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 13(4Q32.3) MUTATED 85 95 60 46 28
DEL PEAK 13(4Q32.3) WILD-TYPE 36 39 61 16 9

Figure S286.  Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q32.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00252 (Fisher's exact test), Q value = 0.0083

Table S287.  Gene #43: 'del_4q32.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 13(4Q32.3) MUTATED 66 75 140 33
DEL PEAK 13(4Q32.3) WILD-TYPE 23 43 59 36

Figure S287.  Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q32.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00393 (Fisher's exact test), Q value = 0.012

Table S288.  Gene #43: 'del_4q32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
DEL PEAK 13(4Q32.3) MUTATED 48 82 88
DEL PEAK 13(4Q32.3) WILD-TYPE 41 47 28

Figure S288.  Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q32.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S289.  Gene #43: 'del_4q32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 13(4Q32.3) MUTATED 27 120 71
DEL PEAK 13(4Q32.3) WILD-TYPE 12 31 73

Figure S289.  Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q35.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S290.  Gene #44: 'del_4q35.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 14(4Q35.2) MUTATED 98 140 93
DEL PEAK 14(4Q35.2) WILD-TYPE 84 26 60

Figure S290.  Get High-res Image Gene #44: 'del_4q35.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q35.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S291.  Gene #44: 'del_4q35.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 14(4Q35.2) MUTATED 79 96 64
DEL PEAK 14(4Q35.2) WILD-TYPE 73 26 29

Figure S291.  Get High-res Image Gene #44: 'del_4q35.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q35.2' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00021

Table S292.  Gene #44: 'del_4q35.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 14(4Q35.2) MUTATED 70 122 98 39
DEL PEAK 14(4Q35.2) WILD-TYPE 43 30 56 40

Figure S292.  Get High-res Image Gene #44: 'del_4q35.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q35.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00344 (Fisher's exact test), Q value = 0.01

Table S293.  Gene #44: 'del_4q35.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 14(4Q35.2) MUTATED 113 141 75
DEL PEAK 14(4Q35.2) WILD-TYPE 65 48 56

Figure S293.  Get High-res Image Gene #44: 'del_4q35.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.2' versus 'MIRSEQ_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.0023

Table S294.  Gene #44: 'del_4q35.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 14(4Q35.2) MUTATED 85 91 61 49 28
DEL PEAK 14(4Q35.2) WILD-TYPE 36 43 60 13 9

Figure S294.  Get High-res Image Gene #44: 'del_4q35.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q35.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00743 (Fisher's exact test), Q value = 0.02

Table S295.  Gene #44: 'del_4q35.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 14(4Q35.2) MUTATED 67 74 138 35
DEL PEAK 14(4Q35.2) WILD-TYPE 22 44 61 34

Figure S295.  Get High-res Image Gene #44: 'del_4q35.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q35.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0485 (Fisher's exact test), Q value = 0.095

Table S296.  Gene #44: 'del_4q35.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
DEL PEAK 14(4Q35.2) MUTATED 51 82 85
DEL PEAK 14(4Q35.2) WILD-TYPE 38 47 31

Figure S296.  Get High-res Image Gene #44: 'del_4q35.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q35.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S297.  Gene #44: 'del_4q35.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 14(4Q35.2) MUTATED 28 117 73
DEL PEAK 14(4Q35.2) WILD-TYPE 11 34 71

Figure S297.  Get High-res Image Gene #44: 'del_4q35.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S298.  Gene #45: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 15(5Q12.1) MUTATED 99 136 134
DEL PEAK 15(5Q12.1) WILD-TYPE 83 30 19

Figure S298.  Get High-res Image Gene #45: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S299.  Gene #45: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 15(5Q12.1) MUTATED 91 100 77
DEL PEAK 15(5Q12.1) WILD-TYPE 61 22 16

Figure S299.  Get High-res Image Gene #45: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q12.1' versus 'MRNASEQ_CNMF'

P value = 0.00201 (Fisher's exact test), Q value = 0.0068

Table S300.  Gene #45: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 15(5Q12.1) MUTATED 78 126 114 48
DEL PEAK 15(5Q12.1) WILD-TYPE 35 26 40 31

Figure S300.  Get High-res Image Gene #45: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00151 (Fisher's exact test), Q value = 0.0054

Table S301.  Gene #45: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 15(5Q12.1) MUTATED 131 153 82
DEL PEAK 15(5Q12.1) WILD-TYPE 47 36 49

Figure S301.  Get High-res Image Gene #45: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.029

Table S302.  Gene #45: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 15(5Q12.1) MUTATED 92 99 81 46 35
DEL PEAK 15(5Q12.1) WILD-TYPE 29 35 40 16 2

Figure S302.  Get High-res Image Gene #45: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00021

Table S303.  Gene #45: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 15(5Q12.1) MUTATED 66 82 167 38
DEL PEAK 15(5Q12.1) WILD-TYPE 23 36 32 31

Figure S303.  Get High-res Image Gene #45: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00313 (Fisher's exact test), Q value = 0.0098

Table S304.  Gene #45: 'del_5q12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 15(5Q12.1) MUTATED 31 122 92
DEL PEAK 15(5Q12.1) WILD-TYPE 8 29 52

Figure S304.  Get High-res Image Gene #45: 'del_5q12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S305.  Gene #46: 'del_5q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 16(5Q31.1) MUTATED 110 138 138
DEL PEAK 16(5Q31.1) WILD-TYPE 72 28 15

Figure S305.  Get High-res Image Gene #46: 'del_5q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q31.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S306.  Gene #46: 'del_5q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 16(5Q31.1) MUTATED 98 102 84
DEL PEAK 16(5Q31.1) WILD-TYPE 54 20 9

Figure S306.  Get High-res Image Gene #46: 'del_5q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q31.1' versus 'MRNASEQ_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.037

Table S307.  Gene #46: 'del_5q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 16(5Q31.1) MUTATED 85 129 116 53
DEL PEAK 16(5Q31.1) WILD-TYPE 28 23 38 26

Figure S307.  Get High-res Image Gene #46: 'del_5q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00728 (Fisher's exact test), Q value = 0.019

Table S308.  Gene #46: 'del_5q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 16(5Q31.1) MUTATED 137 157 89
DEL PEAK 16(5Q31.1) WILD-TYPE 41 32 42

Figure S308.  Get High-res Image Gene #46: 'del_5q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q31.1' versus 'MIRSEQ_CNMF'

P value = 0.00386 (Fisher's exact test), Q value = 0.012

Table S309.  Gene #46: 'del_5q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 16(5Q31.1) MUTATED 93 108 85 46 36
DEL PEAK 16(5Q31.1) WILD-TYPE 28 26 36 16 1

Figure S309.  Get High-res Image Gene #46: 'del_5q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S310.  Gene #46: 'del_5q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 16(5Q31.1) MUTATED 69 90 171 38
DEL PEAK 16(5Q31.1) WILD-TYPE 20 28 28 31

Figure S310.  Get High-res Image Gene #46: 'del_5q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00102 (Fisher's exact test), Q value = 0.0039

Table S311.  Gene #46: 'del_5q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 16(5Q31.1) MUTATED 33 128 97
DEL PEAK 16(5Q31.1) WILD-TYPE 6 23 47

Figure S311.  Get High-res Image Gene #46: 'del_5q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0014

Table S312.  Gene #47: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 17(6P25.3) MUTATED 42 63 29
DEL PEAK 17(6P25.3) WILD-TYPE 140 103 124

Figure S312.  Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S313.  Gene #47: 'del_6p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 17(6P25.3) MUTATED 29 55 20
DEL PEAK 17(6P25.3) WILD-TYPE 123 67 73

Figure S313.  Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6p25.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00673 (Fisher's exact test), Q value = 0.018

Table S314.  Gene #47: 'del_6p25.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 41 52 47
DEL PEAK 17(6P25.3) MUTATED 14 14 18 4
DEL PEAK 17(6P25.3) WILD-TYPE 40 27 34 43

Figure S314.  Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S315.  Gene #47: 'del_6p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 17(6P25.3) MUTATED 30 63 23 17
DEL PEAK 17(6P25.3) WILD-TYPE 83 89 131 62

Figure S315.  Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S316.  Gene #47: 'del_6p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 17(6P25.3) MUTATED 37 78 18
DEL PEAK 17(6P25.3) WILD-TYPE 141 111 113

Figure S316.  Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00082 (Fisher's exact test), Q value = 0.0033

Table S317.  Gene #47: 'del_6p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 17(6P25.3) MUTATED 39 32 45 12
DEL PEAK 17(6P25.3) WILD-TYPE 50 86 154 57

Figure S317.  Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q22.31' versus 'MRNA_CNMF'

P value = 0.0388 (Fisher's exact test), Q value = 0.078

Table S318.  Gene #48: 'del_6q22.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
DEL PEAK 18(6Q22.31) MUTATED 8 20 4 6
DEL PEAK 18(6Q22.31) WILD-TYPE 34 32 28 22

Figure S318.  Get High-res Image Gene #48: 'del_6q22.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_6q22.31' versus 'MRNA_CHIERARCHICAL'

P value = 0.00313 (Fisher's exact test), Q value = 0.0098

Table S319.  Gene #48: 'del_6q22.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 18(6Q22.31) MUTATED 10 22 6
DEL PEAK 18(6Q22.31) WILD-TYPE 37 34 45

Figure S319.  Get High-res Image Gene #48: 'del_6q22.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_6q22.31' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.001

Table S320.  Gene #48: 'del_6q22.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 18(6Q22.31) MUTATED 32 59 31
DEL PEAK 18(6Q22.31) WILD-TYPE 150 107 122

Figure S320.  Get High-res Image Gene #48: 'del_6q22.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q22.31' versus 'METHLYATION_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.0031

Table S321.  Gene #48: 'del_6q22.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 18(6Q22.31) MUTATED 29 46 17
DEL PEAK 18(6Q22.31) WILD-TYPE 123 76 76

Figure S321.  Get High-res Image Gene #48: 'del_6q22.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q22.31' versus 'MRNASEQ_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.0033

Table S322.  Gene #48: 'del_6q22.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 18(6Q22.31) MUTATED 20 55 29 17
DEL PEAK 18(6Q22.31) WILD-TYPE 93 97 125 62

Figure S322.  Get High-res Image Gene #48: 'del_6q22.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q22.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.017 (Fisher's exact test), Q value = 0.039

Table S323.  Gene #48: 'del_6q22.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 18(6Q22.31) MUTATED 38 59 24
DEL PEAK 18(6Q22.31) WILD-TYPE 140 130 107

Figure S323.  Get High-res Image Gene #48: 'del_6q22.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MRNA_CNMF'

P value = 0.0416 (Fisher's exact test), Q value = 0.083

Table S324.  Gene #49: 'del_6q26' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
DEL PEAK 19(6Q26) MUTATED 8 21 5 6
DEL PEAK 19(6Q26) WILD-TYPE 34 31 27 22

Figure S324.  Get High-res Image Gene #49: 'del_6q26' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_6q26' versus 'MRNA_CHIERARCHICAL'

P value = 0.00462 (Fisher's exact test), Q value = 0.013

Table S325.  Gene #49: 'del_6q26' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 19(6Q26) MUTATED 10 23 7
DEL PEAK 19(6Q26) WILD-TYPE 37 33 44

Figure S325.  Get High-res Image Gene #49: 'del_6q26' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0011

Table S326.  Gene #49: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 19(6Q26) MUTATED 35 64 35
DEL PEAK 19(6Q26) WILD-TYPE 147 102 118

Figure S326.  Get High-res Image Gene #49: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 5e-04

Table S327.  Gene #49: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 19(6Q26) MUTATED 29 52 21
DEL PEAK 19(6Q26) WILD-TYPE 123 70 72

Figure S327.  Get High-res Image Gene #49: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0021

Table S328.  Gene #49: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 19(6Q26) MUTATED 23 60 34 16
DEL PEAK 19(6Q26) WILD-TYPE 90 92 120 63

Figure S328.  Get High-res Image Gene #49: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00607 (Fisher's exact test), Q value = 0.017

Table S329.  Gene #49: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 19(6Q26) MUTATED 38 66 29
DEL PEAK 19(6Q26) WILD-TYPE 140 123 102

Figure S329.  Get High-res Image Gene #49: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 0.04

Table S330.  Gene #49: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 19(6Q26) MUTATED 38 41 20 21 7
DEL PEAK 19(6Q26) WILD-TYPE 83 93 101 41 30

Figure S330.  Get High-res Image Gene #49: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0328 (Fisher's exact test), Q value = 0.068

Table S331.  Gene #49: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
DEL PEAK 19(6Q26) MUTATED 15 35 38
DEL PEAK 19(6Q26) WILD-TYPE 74 94 78

Figure S331.  Get High-res Image Gene #49: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7q11.22' versus 'CN_CNMF'

P value = 0.00113 (Fisher's exact test), Q value = 0.0042

Table S332.  Gene #50: 'del_7q11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 20(7Q11.22) MUTATED 13 9 26
DEL PEAK 20(7Q11.22) WILD-TYPE 169 157 127

Figure S332.  Get High-res Image Gene #50: 'del_7q11.22' versus Molecular Subtype #3: 'CN_CNMF'

'del_7q11.22' versus 'MRNASEQ_CNMF'

P value = 0.00191 (Fisher's exact test), Q value = 0.0066

Table S333.  Gene #50: 'del_7q11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 20(7Q11.22) MUTATED 7 8 27 6
DEL PEAK 20(7Q11.22) WILD-TYPE 106 144 127 73

Figure S333.  Get High-res Image Gene #50: 'del_7q11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7q11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00101 (Fisher's exact test), Q value = 0.0039

Table S334.  Gene #50: 'del_7q11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 20(7Q11.22) MUTATED 12 12 24
DEL PEAK 20(7Q11.22) WILD-TYPE 166 177 107

Figure S334.  Get High-res Image Gene #50: 'del_7q11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7q36.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0487 (Fisher's exact test), Q value = 0.095

Table S335.  Gene #51: 'del_7q36.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 21(7Q36.3) MUTATED 14 6 11
DEL PEAK 21(7Q36.3) WILD-TYPE 33 50 40

Figure S335.  Get High-res Image Gene #51: 'del_7q36.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_7q36.3' versus 'CN_CNMF'

P value = 0.00407 (Fisher's exact test), Q value = 0.012

Table S336.  Gene #51: 'del_7q36.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 21(7Q36.3) MUTATED 39 22 43
DEL PEAK 21(7Q36.3) WILD-TYPE 143 144 110

Figure S336.  Get High-res Image Gene #51: 'del_7q36.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_7q36.3' versus 'MRNASEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0013

Table S337.  Gene #51: 'del_7q36.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 21(7Q36.3) MUTATED 28 18 47 11
DEL PEAK 21(7Q36.3) WILD-TYPE 85 134 107 68

Figure S337.  Get High-res Image Gene #51: 'del_7q36.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7q36.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00114 (Fisher's exact test), Q value = 0.0043

Table S338.  Gene #51: 'del_7q36.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 21(7Q36.3) MUTATED 44 24 36
DEL PEAK 21(7Q36.3) WILD-TYPE 134 165 95

Figure S338.  Get High-res Image Gene #51: 'del_7q36.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7q36.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00412 (Fisher's exact test), Q value = 0.012

Table S339.  Gene #51: 'del_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 21(7Q36.3) MUTATED 14 29 49 5
DEL PEAK 21(7Q36.3) WILD-TYPE 75 89 150 64

Figure S339.  Get High-res Image Gene #51: 'del_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7q36.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.047 (Fisher's exact test), Q value = 0.093

Table S340.  Gene #51: 'del_7q36.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 21(7Q36.3) MUTATED 14 31 25
DEL PEAK 21(7Q36.3) WILD-TYPE 25 120 119

Figure S340.  Get High-res Image Gene #51: 'del_7q36.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S341.  Gene #52: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 22(8P23.2) MUTATED 101 120 120
DEL PEAK 22(8P23.2) WILD-TYPE 81 46 33

Figure S341.  Get High-res Image Gene #52: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.037

Table S342.  Gene #52: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 22(8P23.2) MUTATED 90 91 67
DEL PEAK 22(8P23.2) WILD-TYPE 62 31 26

Figure S342.  Get High-res Image Gene #52: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0406 (Fisher's exact test), Q value = 0.081

Table S343.  Gene #52: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 22(8P23.2) MUTATED 30 108 86
DEL PEAK 22(8P23.2) WILD-TYPE 9 43 58

Figure S343.  Get High-res Image Gene #52: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'MRNA_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.026

Table S344.  Gene #53: 'del_9p23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
DEL PEAK 23(9P23) MUTATED 36 30 19 16
DEL PEAK 23(9P23) WILD-TYPE 6 22 13 12

Figure S344.  Get High-res Image Gene #53: 'del_9p23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p23' versus 'MRNA_CHIERARCHICAL'

P value = 0.00184 (Fisher's exact test), Q value = 0.0064

Table S345.  Gene #53: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 23(9P23) MUTATED 40 30 31
DEL PEAK 23(9P23) WILD-TYPE 7 26 20

Figure S345.  Get High-res Image Gene #53: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S346.  Gene #53: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 23(9P23) MUTATED 102 101 129
DEL PEAK 23(9P23) WILD-TYPE 80 65 24

Figure S346.  Get High-res Image Gene #53: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 0.0304 (Fisher's exact test), Q value = 0.064

Table S347.  Gene #53: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 23(9P23) MUTATED 94 78 72
DEL PEAK 23(9P23) WILD-TYPE 58 44 21

Figure S347.  Get High-res Image Gene #53: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00093

Table S348.  Gene #53: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 23(9P23) MUTATED 89 87 110 43
DEL PEAK 23(9P23) WILD-TYPE 24 65 44 36

Figure S348.  Get High-res Image Gene #53: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00098 (Fisher's exact test), Q value = 0.0038

Table S349.  Gene #53: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 23(9P23) MUTATED 136 112 81
DEL PEAK 23(9P23) WILD-TYPE 42 77 50

Figure S349.  Get High-res Image Gene #53: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.027

Table S350.  Gene #53: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 23(9P23) MUTATED 78 97 74 36 32
DEL PEAK 23(9P23) WILD-TYPE 43 37 47 26 5

Figure S350.  Get High-res Image Gene #53: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00086

Table S351.  Gene #53: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 23(9P23) MUTATED 50 81 151 35
DEL PEAK 23(9P23) WILD-TYPE 39 37 48 34

Figure S351.  Get High-res Image Gene #53: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S352.  Gene #54: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 24(9P21.3) MUTATED 121 130 137
DEL PEAK 24(9P21.3) WILD-TYPE 61 36 16

Figure S352.  Get High-res Image Gene #54: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.0027

Table S353.  Gene #54: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 24(9P21.3) MUTATED 100 112 122 51
DEL PEAK 24(9P21.3) WILD-TYPE 13 40 32 28

Figure S353.  Get High-res Image Gene #54: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0158 (Fisher's exact test), Q value = 0.037

Table S354.  Gene #54: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 24(9P21.3) MUTATED 150 141 94
DEL PEAK 24(9P21.3) WILD-TYPE 28 48 37

Figure S354.  Get High-res Image Gene #54: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0115 (Fisher's exact test), Q value = 0.029

Table S355.  Gene #54: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 24(9P21.3) MUTATED 68 95 165 44
DEL PEAK 24(9P21.3) WILD-TYPE 21 23 34 25

Figure S355.  Get High-res Image Gene #54: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0228 (Fisher's exact test), Q value = 0.05

Table S356.  Gene #54: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 24(9P21.3) MUTATED 36 121 105
DEL PEAK 24(9P21.3) WILD-TYPE 3 30 39

Figure S356.  Get High-res Image Gene #54: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S357.  Gene #55: 'del_9p21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 25(9P21.1) MUTATED 106 97 123
DEL PEAK 25(9P21.1) WILD-TYPE 76 69 30

Figure S357.  Get High-res Image Gene #55: 'del_9p21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.1' versus 'MRNASEQ_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0015

Table S358.  Gene #55: 'del_9p21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 25(9P21.1) MUTATED 88 85 107 43
DEL PEAK 25(9P21.1) WILD-TYPE 25 67 47 36

Figure S358.  Get High-res Image Gene #55: 'del_9p21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.0016

Table S359.  Gene #55: 'del_9p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 25(9P21.1) MUTATED 135 106 82
DEL PEAK 25(9P21.1) WILD-TYPE 43 83 49

Figure S359.  Get High-res Image Gene #55: 'del_9p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00835 (Fisher's exact test), Q value = 0.022

Table S360.  Gene #55: 'del_9p21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 25(9P21.1) MUTATED 51 84 140 36
DEL PEAK 25(9P21.1) WILD-TYPE 38 34 59 33

Figure S360.  Get High-res Image Gene #55: 'del_9p21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MRNA_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0014

Table S361.  Gene #56: 'del_9q21.11' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
DEL PEAK 26(9Q21.11) MUTATED 28 13 19 15
DEL PEAK 26(9Q21.11) WILD-TYPE 14 39 13 13

Figure S361.  Get High-res Image Gene #56: 'del_9q21.11' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9q21.11' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00033

Table S362.  Gene #56: 'del_9q21.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 26(9Q21.11) MUTATED 31 14 30
DEL PEAK 26(9Q21.11) WILD-TYPE 16 42 21

Figure S362.  Get High-res Image Gene #56: 'del_9q21.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9q21.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S363.  Gene #56: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 26(9Q21.11) MUTATED 88 53 110
DEL PEAK 26(9Q21.11) WILD-TYPE 94 113 43

Figure S363.  Get High-res Image Gene #56: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q21.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S364.  Gene #56: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 26(9Q21.11) MUTATED 89 33 62
DEL PEAK 26(9Q21.11) WILD-TYPE 63 89 31

Figure S364.  Get High-res Image Gene #56: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q21.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S365.  Gene #56: 'del_9q21.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 26(9Q21.11) MUTATED 73 36 100 40
DEL PEAK 26(9Q21.11) WILD-TYPE 40 116 54 39

Figure S365.  Get High-res Image Gene #56: 'del_9q21.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9q21.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S366.  Gene #56: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 26(9Q21.11) MUTATED 125 46 78
DEL PEAK 26(9Q21.11) WILD-TYPE 53 143 53

Figure S366.  Get High-res Image Gene #56: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S367.  Gene #56: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 26(9Q21.11) MUTATED 58 62 71 17 29
DEL PEAK 26(9Q21.11) WILD-TYPE 63 72 50 45 8

Figure S367.  Get High-res Image Gene #56: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9q21.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S368.  Gene #56: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 26(9Q21.11) MUTATED 23 54 129 31
DEL PEAK 26(9Q21.11) WILD-TYPE 66 64 70 38

Figure S368.  Get High-res Image Gene #56: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00963 (Fisher's exact test), Q value = 0.025

Table S369.  Gene #56: 'del_9q21.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 26(9Q21.11) MUTATED 29 72 72
DEL PEAK 26(9Q21.11) WILD-TYPE 10 79 72

Figure S369.  Get High-res Image Gene #56: 'del_9q21.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p15.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S370.  Gene #57: 'del_10p15.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 27(10P15.2) MUTATED 58 94 67
DEL PEAK 27(10P15.2) WILD-TYPE 124 72 86

Figure S370.  Get High-res Image Gene #57: 'del_10p15.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_10p15.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S371.  Gene #57: 'del_10p15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 27(10P15.2) MUTATED 47 88 29
DEL PEAK 27(10P15.2) WILD-TYPE 105 34 64

Figure S371.  Get High-res Image Gene #57: 'del_10p15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10p15.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S372.  Gene #57: 'del_10p15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 27(10P15.2) MUTATED 39 94 60 25
DEL PEAK 27(10P15.2) WILD-TYPE 74 58 94 54

Figure S372.  Get High-res Image Gene #57: 'del_10p15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10p15.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00072

Table S373.  Gene #57: 'del_10p15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 27(10P15.2) MUTATED 66 106 46
DEL PEAK 27(10P15.2) WILD-TYPE 112 83 85

Figure S373.  Get High-res Image Gene #57: 'del_10p15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.2' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00027

Table S374.  Gene #57: 'del_10p15.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 27(10P15.2) MUTATED 53 64 35 40 20
DEL PEAK 27(10P15.2) WILD-TYPE 68 70 86 22 17

Figure S374.  Get High-res Image Gene #57: 'del_10p15.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10p15.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S375.  Gene #57: 'del_10p15.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 27(10P15.2) MUTATED 63 42 91 16
DEL PEAK 27(10P15.2) WILD-TYPE 26 76 108 53

Figure S375.  Get High-res Image Gene #57: 'del_10p15.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0239 (Fisher's exact test), Q value = 0.052

Table S376.  Gene #57: 'del_10p15.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
DEL PEAK 27(10P15.2) MUTATED 30 54 61
DEL PEAK 27(10P15.2) WILD-TYPE 59 75 55

Figure S376.  Get High-res Image Gene #57: 'del_10p15.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10p15.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.026

Table S377.  Gene #57: 'del_10p15.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 27(10P15.2) MUTATED 19 77 49
DEL PEAK 27(10P15.2) WILD-TYPE 20 74 95

Figure S377.  Get High-res Image Gene #57: 'del_10p15.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'MRNA_CNMF'

P value = 0.00318 (Fisher's exact test), Q value = 0.0099

Table S378.  Gene #58: 'del_10q23.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
DEL PEAK 28(10Q23.31) MUTATED 17 38 13 13
DEL PEAK 28(10Q23.31) WILD-TYPE 25 14 19 15

Figure S378.  Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q23.31' versus 'MRNA_CHIERARCHICAL'

P value = 0.00091 (Fisher's exact test), Q value = 0.0036

Table S379.  Gene #58: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 28(10Q23.31) MUTATED 17 40 24
DEL PEAK 28(10Q23.31) WILD-TYPE 30 16 27

Figure S379.  Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S380.  Gene #58: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 28(10Q23.31) MUTATED 74 119 75
DEL PEAK 28(10Q23.31) WILD-TYPE 108 47 78

Figure S380.  Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S381.  Gene #58: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 28(10Q23.31) MUTATED 57 92 49
DEL PEAK 28(10Q23.31) WILD-TYPE 95 30 44

Figure S381.  Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S382.  Gene #58: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 28(10Q23.31) MUTATED 49 114 69 35
DEL PEAK 28(10Q23.31) WILD-TYPE 64 38 85 44

Figure S382.  Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S383.  Gene #58: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 28(10Q23.31) MUTATED 78 135 54
DEL PEAK 28(10Q23.31) WILD-TYPE 100 54 77

Figure S383.  Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 0.00126 (Fisher's exact test), Q value = 0.0047

Table S384.  Gene #58: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 28(10Q23.31) MUTATED 60 83 49 42 20
DEL PEAK 28(10Q23.31) WILD-TYPE 61 51 72 20 17

Figure S384.  Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S385.  Gene #58: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 28(10Q23.31) MUTATED 64 51 112 27
DEL PEAK 28(10Q23.31) WILD-TYPE 25 67 87 42

Figure S385.  Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 0.049

Table S386.  Gene #58: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
DEL PEAK 28(10Q23.31) MUTATED 38 69 72
DEL PEAK 28(10Q23.31) WILD-TYPE 51 60 44

Figure S386.  Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.0014

Table S387.  Gene #58: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 28(10Q23.31) MUTATED 20 99 60
DEL PEAK 28(10Q23.31) WILD-TYPE 19 52 84

Figure S387.  Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'MRNA_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.0021

Table S388.  Gene #59: 'del_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
DEL PEAK 29(11P15.5) MUTATED 30 21 9 18
DEL PEAK 29(11P15.5) WILD-TYPE 12 31 23 10

Figure S388.  Get High-res Image Gene #59: 'del_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11p15.5' versus 'MRNA_CHIERARCHICAL'

P value = 0.0118 (Fisher's exact test), Q value = 0.029

Table S389.  Gene #59: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 29(11P15.5) MUTATED 32 22 24
DEL PEAK 29(11P15.5) WILD-TYPE 15 34 27

Figure S389.  Get High-res Image Gene #59: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S390.  Gene #59: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 29(11P15.5) MUTATED 63 80 102
DEL PEAK 29(11P15.5) WILD-TYPE 119 86 51

Figure S390.  Get High-res Image Gene #59: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 0.00309 (Fisher's exact test), Q value = 0.0097

Table S391.  Gene #59: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 29(11P15.5) MUTATED 61 57 58
DEL PEAK 29(11P15.5) WILD-TYPE 91 65 35

Figure S391.  Get High-res Image Gene #59: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11p15.5' versus 'RPPA_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0016

Table S392.  Gene #59: 'del_11p15.5' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 73 61
DEL PEAK 29(11P15.5) MUTATED 33 46 18
DEL PEAK 29(11P15.5) WILD-TYPE 27 27 43

Figure S392.  Get High-res Image Gene #59: 'del_11p15.5' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_11p15.5' versus 'RPPA_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.0013

Table S393.  Gene #59: 'del_11p15.5' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 41 52 47
DEL PEAK 29(11P15.5) MUTATED 28 15 38 16
DEL PEAK 29(11P15.5) WILD-TYPE 26 26 14 31

Figure S393.  Get High-res Image Gene #59: 'del_11p15.5' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 0.00664 (Fisher's exact test), Q value = 0.018

Table S394.  Gene #59: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 29(11P15.5) MUTATED 63 67 86 28
DEL PEAK 29(11P15.5) WILD-TYPE 50 85 68 51

Figure S394.  Get High-res Image Gene #59: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.0027

Table S395.  Gene #59: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 29(11P15.5) MUTATED 68 78 55 17 18
DEL PEAK 29(11P15.5) WILD-TYPE 53 56 66 45 19

Figure S395.  Get High-res Image Gene #59: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00403 (Fisher's exact test), Q value = 0.012

Table S396.  Gene #59: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 29(11P15.5) MUTATED 24 84 56
DEL PEAK 29(11P15.5) WILD-TYPE 15 67 88

Figure S396.  Get High-res Image Gene #59: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q22.1' versus 'CN_CNMF'

P value = 0.00138 (Fisher's exact test), Q value = 0.005

Table S397.  Gene #60: 'del_11q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 30(11Q22.1) MUTATED 42 68 52
DEL PEAK 30(11Q22.1) WILD-TYPE 140 98 101

Figure S397.  Get High-res Image Gene #60: 'del_11q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q22.1' versus 'METHLYATION_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.0032

Table S398.  Gene #60: 'del_11q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 30(11Q22.1) MUTATED 36 50 41
DEL PEAK 30(11Q22.1) WILD-TYPE 116 72 52

Figure S398.  Get High-res Image Gene #60: 'del_11q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q22.1' versus 'MRNASEQ_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.034

Table S399.  Gene #60: 'del_11q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 30(11Q22.1) MUTATED 34 62 49 16
DEL PEAK 30(11Q22.1) WILD-TYPE 79 90 105 63

Figure S399.  Get High-res Image Gene #60: 'del_11q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0384 (Fisher's exact test), Q value = 0.078

Table S400.  Gene #60: 'del_11q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 30(11Q22.1) MUTATED 49 74 38
DEL PEAK 30(11Q22.1) WILD-TYPE 129 115 93

Figure S400.  Get High-res Image Gene #60: 'del_11q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q22.1' versus 'MIRSEQ_CNMF'

P value = 0.00394 (Fisher's exact test), Q value = 0.012

Table S401.  Gene #60: 'del_11q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 30(11Q22.1) MUTATED 30 60 31 22 13
DEL PEAK 30(11Q22.1) WILD-TYPE 91 74 90 40 24

Figure S401.  Get High-res Image Gene #60: 'del_11q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.028 (Fisher's exact test), Q value = 0.06

Table S402.  Gene #60: 'del_11q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 30(11Q22.1) MUTATED 38 40 64 14
DEL PEAK 30(11Q22.1) WILD-TYPE 51 78 135 55

Figure S402.  Get High-res Image Gene #60: 'del_11q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11q25' versus 'CN_CNMF'

P value = 0.00215 (Fisher's exact test), Q value = 0.0072

Table S403.  Gene #61: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 31(11Q25) MUTATED 51 77 56
DEL PEAK 31(11Q25) WILD-TYPE 131 89 97

Figure S403.  Get High-res Image Gene #61: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q25' versus 'MRNASEQ_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.041

Table S404.  Gene #61: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 31(11Q25) MUTATED 37 67 60 19
DEL PEAK 31(11Q25) WILD-TYPE 76 85 94 60

Figure S404.  Get High-res Image Gene #61: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q25' versus 'MIRSEQ_CNMF'

P value = 0.0321 (Fisher's exact test), Q value = 0.067

Table S405.  Gene #61: 'del_11q25' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 31(11Q25) MUTATED 37 63 36 23 13
DEL PEAK 31(11Q25) WILD-TYPE 84 71 85 39 24

Figure S405.  Get High-res Image Gene #61: 'del_11q25' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q12.11' versus 'CN_CNMF'

P value = 0.00396 (Fisher's exact test), Q value = 0.012

Table S406.  Gene #63: 'del_13q12.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 33(13Q12.11) MUTATED 107 108 116
DEL PEAK 33(13Q12.11) WILD-TYPE 75 58 37

Figure S406.  Get High-res Image Gene #63: 'del_13q12.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q12.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00425 (Fisher's exact test), Q value = 0.012

Table S407.  Gene #63: 'del_13q12.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
DEL PEAK 33(13Q12.11) MUTATED 47 90 86
DEL PEAK 33(13Q12.11) WILD-TYPE 42 39 30

Figure S407.  Get High-res Image Gene #63: 'del_13q12.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_13q12.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00354 (Fisher's exact test), Q value = 0.011

Table S408.  Gene #63: 'del_13q12.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 33(13Q12.11) MUTATED 23 115 85
DEL PEAK 33(13Q12.11) WILD-TYPE 16 36 59

Figure S408.  Get High-res Image Gene #63: 'del_13q12.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 0.00331 (Fisher's exact test), Q value = 0.01

Table S409.  Gene #64: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 34(13Q14.2) MUTATED 112 112 120
DEL PEAK 34(13Q14.2) WILD-TYPE 70 54 33

Figure S409.  Get High-res Image Gene #64: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 0.0303 (Fisher's exact test), Q value = 0.064

Table S410.  Gene #64: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 34(13Q14.2) MUTATED 91 88 69
DEL PEAK 34(13Q14.2) WILD-TYPE 61 34 24

Figure S410.  Get High-res Image Gene #64: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00162 (Fisher's exact test), Q value = 0.0057

Table S411.  Gene #64: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
DEL PEAK 34(13Q14.2) MUTATED 48 95 88
DEL PEAK 34(13Q14.2) WILD-TYPE 41 34 28

Figure S411.  Get High-res Image Gene #64: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0195 (Fisher's exact test), Q value = 0.044

Table S412.  Gene #64: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 34(13Q14.2) MUTATED 24 116 91
DEL PEAK 34(13Q14.2) WILD-TYPE 15 35 53

Figure S412.  Get High-res Image Gene #64: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q11.2' versus 'MRNA_CNMF'

P value = 0.0379 (Fisher's exact test), Q value = 0.077

Table S413.  Gene #65: 'del_14q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
DEL PEAK 35(14Q11.2) MUTATED 7 21 14 10
DEL PEAK 35(14Q11.2) WILD-TYPE 35 31 18 18

Figure S413.  Get High-res Image Gene #65: 'del_14q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0351 (Fisher's exact test), Q value = 0.072

Table S414.  Gene #65: 'del_14q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 35(14Q11.2) MUTATED 9 22 21
DEL PEAK 35(14Q11.2) WILD-TYPE 38 34 30

Figure S414.  Get High-res Image Gene #65: 'del_14q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 9e-04

Table S415.  Gene #65: 'del_14q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 35(14Q11.2) MUTATED 25 57 71 20
DEL PEAK 35(14Q11.2) WILD-TYPE 88 95 83 59

Figure S415.  Get High-res Image Gene #65: 'del_14q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 9e-04

Table S416.  Gene #65: 'del_14q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 35(14Q11.2) MUTATED 43 69 61
DEL PEAK 35(14Q11.2) WILD-TYPE 135 120 70

Figure S416.  Get High-res Image Gene #65: 'del_14q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q11.2' versus 'MIRSEQ_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 0.051

Table S417.  Gene #65: 'del_14q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 35(14Q11.2) MUTATED 42 47 32 32 13
DEL PEAK 35(14Q11.2) WILD-TYPE 79 87 89 30 24

Figure S417.  Get High-res Image Gene #65: 'del_14q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_14q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00976 (Fisher's exact test), Q value = 0.025

Table S418.  Gene #65: 'del_14q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 35(14Q11.2) MUTATED 42 42 67 15
DEL PEAK 35(14Q11.2) WILD-TYPE 47 76 132 54

Figure S418.  Get High-res Image Gene #65: 'del_14q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0031

Table S419.  Gene #65: 'del_14q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
DEL PEAK 35(14Q11.2) MUTATED 18 57 45
DEL PEAK 35(14Q11.2) WILD-TYPE 71 72 71

Figure S419.  Get High-res Image Gene #65: 'del_14q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_14q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0341 (Fisher's exact test), Q value = 0.07

Table S420.  Gene #65: 'del_14q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 35(14Q11.2) MUTATED 7 60 53
DEL PEAK 35(14Q11.2) WILD-TYPE 32 91 91

Figure S420.  Get High-res Image Gene #65: 'del_14q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 0.058

Table S421.  Gene #66: 'del_15q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 41 52 47
DEL PEAK 36(15Q11.2) MUTATED 22 6 20 17
DEL PEAK 36(15Q11.2) WILD-TYPE 32 35 32 30

Figure S421.  Get High-res Image Gene #66: 'del_15q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_CNMF'

P value = 0.0243 (Fisher's exact test), Q value = 0.053

Table S422.  Gene #66: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 36(15Q11.2) MUTATED 50 50 30 15 14
DEL PEAK 36(15Q11.2) WILD-TYPE 71 84 91 47 23

Figure S422.  Get High-res Image Gene #66: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q21.1' versus 'CN_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.037

Table S423.  Gene #67: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 37(15Q21.1) MUTATED 47 62 60
DEL PEAK 37(15Q21.1) WILD-TYPE 135 104 93

Figure S423.  Get High-res Image Gene #67: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q21.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00721 (Fisher's exact test), Q value = 0.019

Table S424.  Gene #67: 'del_15q21.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 41 52 47
DEL PEAK 37(15Q21.1) MUTATED 23 5 20 17
DEL PEAK 37(15Q21.1) WILD-TYPE 31 36 32 30

Figure S424.  Get High-res Image Gene #67: 'del_15q21.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_15q21.1' versus 'MIRSEQ_CNMF'

P value = 0.00322 (Fisher's exact test), Q value = 0.01

Table S425.  Gene #67: 'del_15q21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 37(15Q21.1) MUTATED 46 53 27 16 18
DEL PEAK 37(15Q21.1) WILD-TYPE 75 81 94 46 19

Figure S425.  Get High-res Image Gene #67: 'del_15q21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16p13.3' versus 'CN_CNMF'

P value = 0.00425 (Fisher's exact test), Q value = 0.012

Table S426.  Gene #68: 'del_16p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 38(16P13.3) MUTATED 51 69 67
DEL PEAK 38(16P13.3) WILD-TYPE 131 97 86

Figure S426.  Get High-res Image Gene #68: 'del_16p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00926 (Fisher's exact test), Q value = 0.024

Table S427.  Gene #68: 'del_16p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
DEL PEAK 38(16P13.3) MUTATED 25 45 56
DEL PEAK 38(16P13.3) WILD-TYPE 64 84 60

Figure S427.  Get High-res Image Gene #68: 'del_16p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.034

Table S428.  Gene #69: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 39(16Q23.1) MUTATED 62 82 66
DEL PEAK 39(16Q23.1) WILD-TYPE 120 84 87

Figure S428.  Get High-res Image Gene #69: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0381 (Fisher's exact test), Q value = 0.077

Table S429.  Gene #69: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 39(16Q23.1) MUTATED 61 88 59
DEL PEAK 39(16Q23.1) WILD-TYPE 117 101 72

Figure S429.  Get High-res Image Gene #69: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 0.00645 (Fisher's exact test), Q value = 0.018

Table S430.  Gene #69: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 39(16Q23.1) MUTATED 46 62 40 29 24
DEL PEAK 39(16Q23.1) WILD-TYPE 75 72 81 33 13

Figure S430.  Get High-res Image Gene #69: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0015

Table S431.  Gene #69: 'del_16q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
DEL PEAK 39(16Q23.1) MUTATED 22 60 59
DEL PEAK 39(16Q23.1) WILD-TYPE 67 69 57

Figure S431.  Get High-res Image Gene #69: 'del_16q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.0018

Table S432.  Gene #69: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 39(16Q23.1) MUTATED 10 81 50
DEL PEAK 39(16Q23.1) WILD-TYPE 29 70 94

Figure S432.  Get High-res Image Gene #69: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p11.2' versus 'CN_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0018

Table S433.  Gene #70: 'del_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 40(17P11.2) MUTATED 83 87 102
DEL PEAK 40(17P11.2) WILD-TYPE 99 79 51

Figure S433.  Get High-res Image Gene #70: 'del_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00782 (Fisher's exact test), Q value = 0.02

Table S434.  Gene #70: 'del_17p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 41 52 47
DEL PEAK 40(17P11.2) MUTATED 35 14 28 18
DEL PEAK 40(17P11.2) WILD-TYPE 19 27 24 29

Figure S434.  Get High-res Image Gene #70: 'del_17p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_17p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0158 (Fisher's exact test), Q value = 0.037

Table S435.  Gene #70: 'del_17p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 40(17P11.2) MUTATED 112 92 67
DEL PEAK 40(17P11.2) WILD-TYPE 66 97 64

Figure S435.  Get High-res Image Gene #70: 'del_17p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0272 (Fisher's exact test), Q value = 0.058

Table S436.  Gene #70: 'del_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 40(17P11.2) MUTATED 42 67 122 30
DEL PEAK 40(17P11.2) WILD-TYPE 47 51 77 39

Figure S436.  Get High-res Image Gene #70: 'del_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17q11.2' versus 'MRNA_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00072

Table S437.  Gene #71: 'del_17q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
DEL PEAK 41(17Q11.2) MUTATED 21 5 11 6
DEL PEAK 41(17Q11.2) WILD-TYPE 21 47 21 22

Figure S437.  Get High-res Image Gene #71: 'del_17q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 5e-04

Table S438.  Gene #71: 'del_17q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 41(17Q11.2) MUTATED 21 5 17
DEL PEAK 41(17Q11.2) WILD-TYPE 26 51 34

Figure S438.  Get High-res Image Gene #71: 'del_17q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S439.  Gene #71: 'del_17q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 41(17Q11.2) MUTATED 50 17 65
DEL PEAK 41(17Q11.2) WILD-TYPE 132 149 88

Figure S439.  Get High-res Image Gene #71: 'del_17q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_17q11.2' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00039

Table S440.  Gene #71: 'del_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 41(17Q11.2) MUTATED 49 14 29
DEL PEAK 41(17Q11.2) WILD-TYPE 103 108 64

Figure S440.  Get High-res Image Gene #71: 'del_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S441.  Gene #71: 'del_17q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 41(17Q11.2) MUTATED 43 13 50 25
DEL PEAK 41(17Q11.2) WILD-TYPE 70 139 104 54

Figure S441.  Get High-res Image Gene #71: 'del_17q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S442.  Gene #71: 'del_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 41(17Q11.2) MUTATED 74 19 38
DEL PEAK 41(17Q11.2) WILD-TYPE 104 170 93

Figure S442.  Get High-res Image Gene #71: 'del_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00405 (Fisher's exact test), Q value = 0.012

Table S443.  Gene #71: 'del_17q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 41(17Q11.2) MUTATED 37 26 39 10 16
DEL PEAK 41(17Q11.2) WILD-TYPE 84 108 82 52 21

Figure S443.  Get High-res Image Gene #71: 'del_17q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00129 (Fisher's exact test), Q value = 0.0048

Table S444.  Gene #71: 'del_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 41(17Q11.2) MUTATED 12 27 64 25
DEL PEAK 41(17Q11.2) WILD-TYPE 77 91 135 44

Figure S444.  Get High-res Image Gene #71: 'del_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.0016

Table S445.  Gene #71: 'del_17q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 41(17Q11.2) MUTATED 17 25 46
DEL PEAK 41(17Q11.2) WILD-TYPE 22 126 98

Figure S445.  Get High-res Image Gene #71: 'del_17q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q25.3' versus 'MRNA_CNMF'

P value = 0.00479 (Fisher's exact test), Q value = 0.014

Table S446.  Gene #72: 'del_17q25.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
DEL PEAK 42(17Q25.3) MUTATED 16 5 7 3
DEL PEAK 42(17Q25.3) WILD-TYPE 26 47 25 25

Figure S446.  Get High-res Image Gene #72: 'del_17q25.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17q25.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.03

Table S447.  Gene #72: 'del_17q25.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 42(17Q25.3) MUTATED 15 5 11
DEL PEAK 42(17Q25.3) WILD-TYPE 32 51 40

Figure S447.  Get High-res Image Gene #72: 'del_17q25.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17q25.3' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00033

Table S448.  Gene #72: 'del_17q25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 42(17Q25.3) MUTATED 37 18 47
DEL PEAK 42(17Q25.3) WILD-TYPE 145 148 106

Figure S448.  Get High-res Image Gene #72: 'del_17q25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_17q25.3' versus 'METHLYATION_CNMF'

P value = 0.0168 (Fisher's exact test), Q value = 0.039

Table S449.  Gene #72: 'del_17q25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 42(17Q25.3) MUTATED 34 15 25
DEL PEAK 42(17Q25.3) WILD-TYPE 118 107 68

Figure S449.  Get High-res Image Gene #72: 'del_17q25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17q25.3' versus 'MRNASEQ_CNMF'

P value = 0.00137 (Fisher's exact test), Q value = 0.005

Table S450.  Gene #72: 'del_17q25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 42(17Q25.3) MUTATED 35 18 35 14
DEL PEAK 42(17Q25.3) WILD-TYPE 78 134 119 65

Figure S450.  Get High-res Image Gene #72: 'del_17q25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17q25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00143 (Fisher's exact test), Q value = 0.0051

Table S451.  Gene #72: 'del_17q25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 42(17Q25.3) MUTATED 51 25 26
DEL PEAK 42(17Q25.3) WILD-TYPE 127 164 105

Figure S451.  Get High-res Image Gene #72: 'del_17q25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17q25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.033

Table S452.  Gene #72: 'del_17q25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 42(17Q25.3) MUTATED 8 28 48 15
DEL PEAK 42(17Q25.3) WILD-TYPE 81 90 151 54

Figure S452.  Get High-res Image Gene #72: 'del_17q25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q23' versus 'CN_CNMF'

P value = 0.0054 (Fisher's exact test), Q value = 0.015

Table S453.  Gene #73: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 43(18Q23) MUTATED 68 84 82
DEL PEAK 43(18Q23) WILD-TYPE 114 82 71

Figure S453.  Get High-res Image Gene #73: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.3' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00056

Table S454.  Gene #74: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 44(19P13.3) MUTATED 67 76 93
DEL PEAK 44(19P13.3) WILD-TYPE 115 90 60

Figure S454.  Get High-res Image Gene #74: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0219 (Fisher's exact test), Q value = 0.049

Table S455.  Gene #74: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 44(19P13.3) MUTATED 86 76 73
DEL PEAK 44(19P13.3) WILD-TYPE 92 113 58

Figure S455.  Get High-res Image Gene #74: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00093 (Fisher's exact test), Q value = 0.0036

Table S456.  Gene #74: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 44(19P13.3) MUTATED 30 57 112 25
DEL PEAK 44(19P13.3) WILD-TYPE 59 61 87 44

Figure S456.  Get High-res Image Gene #74: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S457.  Gene #75: 'del_19q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 45(19Q13.32) MUTATED 32 73 44
DEL PEAK 45(19Q13.32) WILD-TYPE 150 93 109

Figure S457.  Get High-res Image Gene #75: 'del_19q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.32' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00061

Table S458.  Gene #75: 'del_19q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 45(19Q13.32) MUTATED 26 46 35
DEL PEAK 45(19Q13.32) WILD-TYPE 126 76 58

Figure S458.  Get High-res Image Gene #75: 'del_19q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.32' versus 'MRNASEQ_CNMF'

P value = 0.0143 (Fisher's exact test), Q value = 0.034

Table S459.  Gene #75: 'del_19q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 45(19Q13.32) MUTATED 28 61 39 21
DEL PEAK 45(19Q13.32) WILD-TYPE 85 91 115 58

Figure S459.  Get High-res Image Gene #75: 'del_19q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00718 (Fisher's exact test), Q value = 0.019

Table S460.  Gene #75: 'del_19q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 45(19Q13.32) MUTATED 42 72 35
DEL PEAK 45(19Q13.32) WILD-TYPE 136 117 96

Figure S460.  Get High-res Image Gene #75: 'del_19q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.32' versus 'MIRSEQ_CNMF'

P value = 0.0376 (Fisher's exact test), Q value = 0.076

Table S461.  Gene #75: 'del_19q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 45(19Q13.32) MUTATED 35 50 24 21 11
DEL PEAK 45(19Q13.32) WILD-TYPE 86 84 97 41 26

Figure S461.  Get High-res Image Gene #75: 'del_19q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.033

Table S462.  Gene #75: 'del_19q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
DEL PEAK 45(19Q13.32) MUTATED 16 42 41
DEL PEAK 45(19Q13.32) WILD-TYPE 73 87 75

Figure S462.  Get High-res Image Gene #75: 'del_19q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_21q11.2' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00045

Table S463.  Gene #76: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 46(21Q11.2) MUTATED 66 92 88
DEL PEAK 46(21Q11.2) WILD-TYPE 116 74 65

Figure S463.  Get High-res Image Gene #76: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0033

Table S464.  Gene #76: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 46(21Q11.2) MUTATED 61 79 47 23 25
DEL PEAK 46(21Q11.2) WILD-TYPE 60 55 74 39 12

Figure S464.  Get High-res Image Gene #76: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_21q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.0011

Table S465.  Gene #76: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 46(21Q11.2) MUTATED 42 66 109 18
DEL PEAK 46(21Q11.2) WILD-TYPE 47 52 90 51

Figure S465.  Get High-res Image Gene #76: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0147 (Fisher's exact test), Q value = 0.035

Table S466.  Gene #76: 'del_21q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 46(21Q11.2) MUTATED 22 85 58
DEL PEAK 46(21Q11.2) WILD-TYPE 17 66 86

Figure S466.  Get High-res Image Gene #76: 'del_21q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S467.  Gene #77: 'del_21q22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 47(21Q22.3) MUTATED 71 110 100
DEL PEAK 47(21Q22.3) WILD-TYPE 111 56 53

Figure S467.  Get High-res Image Gene #77: 'del_21q22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q22.3' versus 'METHLYATION_CNMF'

P value = 0.0055 (Fisher's exact test), Q value = 0.016

Table S468.  Gene #77: 'del_21q22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 47(21Q22.3) MUTATED 68 78 53
DEL PEAK 47(21Q22.3) WILD-TYPE 84 44 40

Figure S468.  Get High-res Image Gene #77: 'del_21q22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_21q22.3' versus 'MIRSEQ_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.026

Table S469.  Gene #77: 'del_21q22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 47(21Q22.3) MUTATED 78 79 53 34 25
DEL PEAK 47(21Q22.3) WILD-TYPE 43 55 68 28 12

Figure S469.  Get High-res Image Gene #77: 'del_21q22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_21q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.0022

Table S470.  Gene #77: 'del_21q22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 47(21Q22.3) MUTATED 55 70 121 23
DEL PEAK 47(21Q22.3) WILD-TYPE 34 48 78 46

Figure S470.  Get High-res Image Gene #77: 'del_21q22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_21q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.035

Table S471.  Gene #77: 'del_21q22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
DEL PEAK 47(21Q22.3) MUTATED 38 67 73
DEL PEAK 47(21Q22.3) WILD-TYPE 51 62 43

Figure S471.  Get High-res Image Gene #77: 'del_21q22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_21q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0475 (Fisher's exact test), Q value = 0.093

Table S472.  Gene #77: 'del_21q22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 47(21Q22.3) MUTATED 21 91 66
DEL PEAK 47(21Q22.3) WILD-TYPE 18 60 78

Figure S472.  Get High-res Image Gene #77: 'del_21q22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q11.21' versus 'MRNA_CNMF'

P value = 0.0299 (Fisher's exact test), Q value = 0.063

Table S473.  Gene #78: 'del_22q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
DEL PEAK 48(22Q11.21) MUTATED 4 11 8 11
DEL PEAK 48(22Q11.21) WILD-TYPE 38 41 24 17

Figure S473.  Get High-res Image Gene #78: 'del_22q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_22q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.0013

Table S474.  Gene #78: 'del_22q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 48(22Q11.21) MUTATED 23 31 41
DEL PEAK 48(22Q11.21) WILD-TYPE 155 158 90

Figure S474.  Get High-res Image Gene #78: 'del_22q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MRNA_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0012

Table S475.  Gene #79: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
DEL PEAK 49(22Q13.32) MUTATED 8 8 8 17
DEL PEAK 49(22Q13.32) WILD-TYPE 34 44 24 11

Figure S475.  Get High-res Image Gene #79: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_22q13.32' versus 'MRNA_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.033

Table S476.  Gene #79: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 49(22Q13.32) MUTATED 11 9 21
DEL PEAK 49(22Q13.32) WILD-TYPE 36 47 30

Figure S476.  Get High-res Image Gene #79: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 0.027 (Fisher's exact test), Q value = 0.058

Table S477.  Gene #79: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 49(22Q13.32) MUTATED 47 21 26
DEL PEAK 49(22Q13.32) WILD-TYPE 105 101 67

Figure S477.  Get High-res Image Gene #79: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 5e-04

Table S478.  Gene #79: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 49(22Q13.32) MUTATED 29 23 59 17
DEL PEAK 49(22Q13.32) WILD-TYPE 84 129 95 62

Figure S478.  Get High-res Image Gene #79: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S479.  Gene #79: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 49(22Q13.32) MUTATED 39 30 59
DEL PEAK 49(22Q13.32) WILD-TYPE 139 159 72

Figure S479.  Get High-res Image Gene #79: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.0021

Table S480.  Gene #79: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 49(22Q13.32) MUTATED 11 38 59 10
DEL PEAK 49(22Q13.32) WILD-TYPE 78 80 140 59

Figure S480.  Get High-res Image Gene #79: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_xp22.2' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00021

Table S481.  Gene #80: 'del_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 50(XP22.2) MUTATED 35 69 51
DEL PEAK 50(XP22.2) WILD-TYPE 147 97 102

Figure S481.  Get High-res Image Gene #80: 'del_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_xp22.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S482.  Gene #80: 'del_xp22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 50(XP22.2) MUTATED 26 49 38
DEL PEAK 50(XP22.2) WILD-TYPE 126 73 55

Figure S482.  Get High-res Image Gene #80: 'del_xp22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xp22.2' versus 'MRNASEQ_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.03

Table S483.  Gene #80: 'del_xp22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 50(XP22.2) MUTATED 34 60 44 15
DEL PEAK 50(XP22.2) WILD-TYPE 79 92 110 64

Figure S483.  Get High-res Image Gene #80: 'del_xp22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_xp22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00943 (Fisher's exact test), Q value = 0.024

Table S484.  Gene #80: 'del_xp22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 50(XP22.2) MUTATED 49 73 31
DEL PEAK 50(XP22.2) WILD-TYPE 129 116 100

Figure S484.  Get High-res Image Gene #80: 'del_xp22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_xp22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0012

Table S485.  Gene #80: 'del_xp22.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
DEL PEAK 50(XP22.2) MUTATED 15 39 50
DEL PEAK 50(XP22.2) WILD-TYPE 74 90 66

Figure S485.  Get High-res Image Gene #80: 'del_xp22.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_xp22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00027

Table S486.  Gene #80: 'del_xp22.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 50(XP22.2) MUTATED 8 66 30
DEL PEAK 50(XP22.2) WILD-TYPE 31 85 114

Figure S486.  Get High-res Image Gene #80: 'del_xp22.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S487.  Gene #81: 'del_xp21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 51(XP21.1) MUTATED 30 73 49
DEL PEAK 51(XP21.1) WILD-TYPE 152 93 104

Figure S487.  Get High-res Image Gene #81: 'del_xp21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S488.  Gene #81: 'del_xp21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 51(XP21.1) MUTATED 21 51 38
DEL PEAK 51(XP21.1) WILD-TYPE 131 71 55

Figure S488.  Get High-res Image Gene #81: 'del_xp21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xp21.1' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00045

Table S489.  Gene #81: 'del_xp21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 51(XP21.1) MUTATED 35 66 34 15
DEL PEAK 51(XP21.1) WILD-TYPE 78 86 120 64

Figure S489.  Get High-res Image Gene #81: 'del_xp21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_xp21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00101 (Fisher's exact test), Q value = 0.0039

Table S490.  Gene #81: 'del_xp21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 51(XP21.1) MUTATED 47 75 28
DEL PEAK 51(XP21.1) WILD-TYPE 131 114 103

Figure S490.  Get High-res Image Gene #81: 'del_xp21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_CNMF'

P value = 0.00605 (Fisher's exact test), Q value = 0.017

Table S491.  Gene #81: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 51(XP21.1) MUTATED 40 48 22 25 12
DEL PEAK 51(XP21.1) WILD-TYPE 81 86 99 37 25

Figure S491.  Get High-res Image Gene #81: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_xp21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00142 (Fisher's exact test), Q value = 0.0051

Table S492.  Gene #81: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 51(XP21.1) MUTATED 38 40 59 10
DEL PEAK 51(XP21.1) WILD-TYPE 51 78 140 59

Figure S492.  Get High-res Image Gene #81: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S493.  Gene #81: 'del_xp21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
DEL PEAK 51(XP21.1) MUTATED 10 43 47
DEL PEAK 51(XP21.1) WILD-TYPE 79 86 69

Figure S493.  Get High-res Image Gene #81: 'del_xp21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_xp21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S494.  Gene #81: 'del_xp21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 51(XP21.1) MUTATED 6 67 27
DEL PEAK 51(XP21.1) WILD-TYPE 33 84 117

Figure S494.  Get High-res Image Gene #81: 'del_xp21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp11.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S495.  Gene #82: 'del_xp11.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 52(XP11.3) MUTATED 30 73 46
DEL PEAK 52(XP11.3) WILD-TYPE 152 93 107

Figure S495.  Get High-res Image Gene #82: 'del_xp11.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_xp11.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S496.  Gene #82: 'del_xp11.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 52(XP11.3) MUTATED 20 53 35
DEL PEAK 52(XP11.3) WILD-TYPE 132 69 58

Figure S496.  Get High-res Image Gene #82: 'del_xp11.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xp11.3' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00072

Table S497.  Gene #82: 'del_xp11.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 52(XP11.3) MUTATED 31 65 39 13
DEL PEAK 52(XP11.3) WILD-TYPE 82 87 115 66

Figure S497.  Get High-res Image Gene #82: 'del_xp11.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_xp11.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00195 (Fisher's exact test), Q value = 0.0067

Table S498.  Gene #82: 'del_xp11.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
DEL PEAK 52(XP11.3) MUTATED 47 73 28
DEL PEAK 52(XP11.3) WILD-TYPE 131 116 103

Figure S498.  Get High-res Image Gene #82: 'del_xp11.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_xp11.3' versus 'MIRSEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00093

Table S499.  Gene #82: 'del_xp11.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 52(XP11.3) MUTATED 36 50 18 26 13
DEL PEAK 52(XP11.3) WILD-TYPE 85 84 103 36 24

Figure S499.  Get High-res Image Gene #82: 'del_xp11.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_xp11.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.0021

Table S500.  Gene #82: 'del_xp11.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 52(XP11.3) MUTATED 38 38 58 9
DEL PEAK 52(XP11.3) WILD-TYPE 51 80 141 60

Figure S500.  Get High-res Image Gene #82: 'del_xp11.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_xp11.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S501.  Gene #82: 'del_xp11.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
DEL PEAK 52(XP11.3) MUTATED 10 40 47
DEL PEAK 52(XP11.3) WILD-TYPE 79 89 69

Figure S501.  Get High-res Image Gene #82: 'del_xp11.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_xp11.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S502.  Gene #82: 'del_xp11.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 52(XP11.3) MUTATED 7 64 26
DEL PEAK 52(XP11.3) WILD-TYPE 32 87 118

Figure S502.  Get High-res Image Gene #82: 'del_xp11.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xq22.3' versus 'MRNA_CNMF'

P value = 0.0213 (Fisher's exact test), Q value = 0.048

Table S503.  Gene #83: 'del_xq22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
DEL PEAK 53(XQ22.3) MUTATED 15 7 5 10
DEL PEAK 53(XQ22.3) WILD-TYPE 27 45 27 18

Figure S503.  Get High-res Image Gene #83: 'del_xq22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_xq22.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.01 (Fisher's exact test), Q value = 0.026

Table S504.  Gene #83: 'del_xq22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
DEL PEAK 53(XQ22.3) MUTATED 18 7 12
DEL PEAK 53(XQ22.3) WILD-TYPE 29 49 39

Figure S504.  Get High-res Image Gene #83: 'del_xq22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_xq22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S505.  Gene #83: 'del_xq22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
DEL PEAK 53(XQ22.3) MUTATED 19 37 58
DEL PEAK 53(XQ22.3) WILD-TYPE 163 129 95

Figure S505.  Get High-res Image Gene #83: 'del_xq22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_xq22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.5e-05

Table S506.  Gene #83: 'del_xq22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
DEL PEAK 53(XQ22.3) MUTATED 14 30 35
DEL PEAK 53(XQ22.3) WILD-TYPE 138 92 58

Figure S506.  Get High-res Image Gene #83: 'del_xq22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xq22.3' versus 'MRNASEQ_CNMF'

P value = 0.00117 (Fisher's exact test), Q value = 0.0044

Table S507.  Gene #83: 'del_xq22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
DEL PEAK 53(XQ22.3) MUTATED 36 31 39 7
DEL PEAK 53(XQ22.3) WILD-TYPE 77 121 115 72

Figure S507.  Get High-res Image Gene #83: 'del_xq22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_xq22.3' versus 'MIRSEQ_CNMF'

P value = 0.00573 (Fisher's exact test), Q value = 0.016

Table S508.  Gene #83: 'del_xq22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
DEL PEAK 53(XQ22.3) MUTATED 32 39 15 12 12
DEL PEAK 53(XQ22.3) WILD-TYPE 89 95 106 50 25

Figure S508.  Get High-res Image Gene #83: 'del_xq22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_xq22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00082

Table S509.  Gene #83: 'del_xq22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
DEL PEAK 53(XQ22.3) MUTATED 20 33 54 3
DEL PEAK 53(XQ22.3) WILD-TYPE 69 85 145 66

Figure S509.  Get High-res Image Gene #83: 'del_xq22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_xq22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00854 (Fisher's exact test), Q value = 0.022

Table S510.  Gene #83: 'del_xq22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
DEL PEAK 53(XQ22.3) MUTATED 11 27 35
DEL PEAK 53(XQ22.3) WILD-TYPE 78 102 81

Figure S510.  Get High-res Image Gene #83: 'del_xq22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_xq22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.0015

Table S511.  Gene #83: 'del_xq22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
DEL PEAK 53(XQ22.3) MUTATED 10 46 17
DEL PEAK 53(XQ22.3) WILD-TYPE 29 105 127

Figure S511.  Get High-res Image Gene #83: 'del_xq22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = all_lesions.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUSC-TP/15093660/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LUSC-TP/15114194/LUSC-TP.transferedmergedcluster.txt

  • Number of patients = 501

  • Number of significantly focal cnvs = 83

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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