Correlation between copy number variation genes (focal events) and molecular subtypes
Colorectal Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1028QW4
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 72 focal events and 12 molecular subtypes across 616 patients, 433 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1q31.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • amp_2q33.1 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_5p12 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_6p21.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_7p21.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_8p11.23 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • amp_8p11.21 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_8q24.21 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_10q22.3 cnv correlated to 'CN_CNMF'.

  • amp_11p15.5 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_13q12.13 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_13q12.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_13q22.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_16p11.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_17q12 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_17q24.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_19q12 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_20p12.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_20p11.21 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_20q11.21 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_20q12 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_20q13.12 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_1p36.11 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_1p33 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_1p13.2 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_2p12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_2q22.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • del_3p26.3 cnv correlated to 'CN_CNMF'.

  • del_4p16.1 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • del_4q35.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_5q12.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_5q21.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_5q22.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_5q23.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_6q26 cnv correlated to 'RPPA_CNMF'.

  • del_8p23.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_8p22 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_8q11.1 cnv correlated to 'CN_CNMF'.

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

  • del_10p15.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_10q21.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_10q23.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_10q25.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_11q22.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_12p13.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_12q21.33 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_14q11.2 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_14q31.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_15q11.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_15q15.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_15q21.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_15q22.33 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_16p13.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • del_16q23.1 cnv correlated to 'MRNA_CHIERARCHICAL'.

  • del_17p12 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_17q24.3 cnv correlated to 'CN_CNMF'.

  • del_18p11.31 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_18q12.2 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'.

  • del_18q21.2 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'.

  • del_18q22.1 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_19p13.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • del_20p12.1 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_21q11.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_21q21.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 72 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, 433 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
del 14q11 2 212 (34%) 404 4e-05
(0.000179)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.0649
(0.126)
0.0136
(0.0331)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.00035
(0.0012)
1e-05
(5.17e-05)
0.0244
(0.0553)
0.0464
(0.094)
del 14q31 1 220 (36%) 396 0.00035
(0.0012)
5e-05
(0.000216)
1e-05
(5.17e-05)
2e-05
(9.34e-05)
0.0385
(0.0808)
0.0381
(0.0806)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.0262
(0.0586)
1e-05
(5.17e-05)
0.246
(0.37)
0.0234
(0.0534)
amp 13q12 13 402 (65%) 214 3e-05
(0.000136)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.0363
(0.0773)
0.0896
(0.164)
2e-05
(9.34e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
8e-05
(0.000332)
0.127
(0.216)
amp 20q11 21 469 (76%) 147 1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.0338
(0.0728)
0.746
(0.823)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.00123
(0.00381)
0.147
(0.246)
amp 20q12 471 (76%) 145 1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.0452
(0.0922)
0.721
(0.805)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.00014
(0.000547)
0.164
(0.267)
amp 20q13 12 473 (77%) 143 1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.0249
(0.0561)
0.649
(0.742)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.00016
(0.000606)
0.163
(0.267)
del 17p12 370 (60%) 246 1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.141
(0.236)
0.809
(0.862)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.00018
(0.000673)
1e-05
(5.17e-05)
0.0335
(0.0725)
0.0426
(0.0875)
del 18p11 31 370 (60%) 246 1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.41
(0.542)
0.756
(0.829)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
2e-05
(9.34e-05)
0.00056
(0.00183)
del 18q12 2 416 (68%) 200 1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.101
(0.179)
0.279
(0.411)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.00021
(0.000769)
0.00011
(0.000438)
del 18q21 2 432 (70%) 184 1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.0729
(0.139)
0.375
(0.511)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.00019
(0.000705)
9e-05
(0.000372)
del 18q22 1 427 (69%) 189 1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.0951
(0.173)
0.347
(0.481)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.00087
(0.00273)
0.00216
(0.00641)
amp 7p21 3 363 (59%) 253 0.00115
(0.00357)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.00011
(0.000438)
0.161
(0.265)
0.0428
(0.0875)
2e-05
(9.34e-05)
1e-05
(5.17e-05)
0.00085
(0.00269)
1e-05
(5.17e-05)
0.0733
(0.14)
0.256
(0.382)
amp 13q12 2 396 (64%) 220 2e-05
(9.34e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.0708
(0.136)
0.183
(0.293)
2e-05
(9.34e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.00022
(0.000802)
0.0787
(0.148)
amp 13q22 1 397 (64%) 219 2e-05
(9.34e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.248
(0.372)
0.284
(0.416)
3e-05
(0.000136)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.00704
(0.0189)
0.373
(0.511)
amp 16p11 2 173 (28%) 443 0.0423
(0.0872)
0.00023
(0.000831)
1e-05
(5.17e-05)
0.0167
(0.0395)
0.0156
(0.0374)
0.328
(0.464)
3e-05
(0.000136)
2e-05
(9.34e-05)
0.766
(0.836)
0.00389
(0.0109)
0.0201
(0.0466)
0.197
(0.312)
amp 20p11 21 363 (59%) 253 0.00015
(0.000576)
2e-05
(9.34e-05)
1e-05
(5.17e-05)
0.00085
(0.00269)
0.0147
(0.0355)
0.078
(0.147)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.0323
(0.0706)
1e-05
(5.17e-05)
0.094
(0.171)
0.529
(0.654)
del 21q21 1 210 (34%) 406 0.00695
(0.0187)
0.00055
(0.00181)
1e-05
(5.17e-05)
0.00334
(0.00952)
0.633
(0.733)
0.399
(0.534)
0.0001
(0.000406)
0.00066
(0.00213)
0.0172
(0.0406)
0.00868
(0.0226)
0.0765
(0.145)
0.018
(0.042)
amp 17q12 160 (26%) 456 0.0397
(0.0828)
0.0066
(0.0179)
1e-05
(5.17e-05)
0.00855
(0.0224)
0.412
(0.543)
0.0494
(0.0985)
5e-05
(0.000216)
1e-05
(5.17e-05)
0.699
(0.783)
0.0144
(0.0348)
0.072
(0.138)
0.73
(0.811)
del 1p36 11 244 (40%) 372 5e-05
(0.000216)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.00011
(0.000438)
0.0191
(0.0444)
0.219
(0.337)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.378
(0.514)
3e-05
(0.000136)
0.141
(0.236)
0.855
(0.899)
del 15q11 2 249 (40%) 367 0.00042
(0.0014)
0.00014
(0.000547)
1e-05
(5.17e-05)
0.00015
(0.000576)
0.166
(0.27)
0.909
(0.937)
0.00011
(0.000438)
1e-05
(5.17e-05)
0.00166
(0.00503)
0.00084
(0.00268)
0.101
(0.179)
0.104
(0.185)
del 15q15 2 251 (41%) 365 1e-05
(5.17e-05)
5e-05
(0.000216)
1e-05
(5.17e-05)
0.00018
(0.000673)
0.0623
(0.122)
0.577
(0.691)
0.00018
(0.000673)
1e-05
(5.17e-05)
0.00362
(0.0103)
8e-05
(0.000332)
0.0519
(0.103)
0.482
(0.614)
del 15q21 1 248 (40%) 368 0.00031
(0.00108)
0.00049
(0.00162)
1e-05
(5.17e-05)
0.00026
(0.000932)
0.124
(0.213)
0.731
(0.812)
0.0002
(0.000738)
1e-05
(5.17e-05)
0.0111
(0.0276)
0.00187
(0.00563)
0.0801
(0.15)
0.495
(0.625)
del 15q22 33 238 (39%) 378 8e-05
(0.000332)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
3e-05
(0.000136)
0.619
(0.723)
0.476
(0.609)
2e-05
(9.34e-05)
1e-05
(5.17e-05)
0.00253
(0.00734)
8e-05
(0.000332)
0.0834
(0.155)
0.208
(0.323)
del 21q11 2 214 (35%) 402 0.00796
(0.0211)
0.00039
(0.00131)
1e-05
(5.17e-05)
0.00737
(0.0197)
0.336
(0.472)
0.524
(0.652)
0.00013
(0.000513)
0.00033
(0.00115)
0.0179
(0.042)
0.0254
(0.057)
0.177
(0.286)
0.116
(0.201)
del 22q13 32 228 (37%) 388 0.00236
(0.00689)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.0309
(0.0677)
0.105
(0.185)
0.246
(0.37)
0.0266
(0.0593)
1e-05
(5.17e-05)
0.0271
(0.0601)
0.00045
(0.00149)
0.353
(0.487)
0.22
(0.338)
amp 2q33 1 140 (23%) 476 0.0797
(0.15)
0.00131
(0.00403)
1e-05
(5.17e-05)
0.00389
(0.0109)
0.285
(0.416)
0.28
(0.412)
1e-05
(5.17e-05)
8e-05
(0.000332)
0.0414
(0.0857)
0.00424
(0.0118)
0.758
(0.83)
0.923
(0.949)
amp 8q24 21 368 (60%) 248 0.203
(0.317)
0.0214
(0.0494)
1e-05
(5.17e-05)
2e-05
(9.34e-05)
0.353
(0.487)
0.0918
(0.167)
4e-05
(0.000179)
0.00133
(0.00407)
0.106
(0.187)
0.0103
(0.0259)
0.0224
(0.0515)
1
(1.00)
amp 11p15 5 138 (22%) 478 0.00061
(0.00198)
0.0009
(0.00282)
1e-05
(5.17e-05)
0.00224
(0.00661)
0.286
(0.417)
0.673
(0.762)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.953
(0.972)
1e-05
(5.17e-05)
0.585
(0.695)
0.694
(0.779)
amp 17q24 1 144 (23%) 472 0.0306
(0.0672)
0.0123
(0.0302)
1e-05
(5.17e-05)
0.00032
(0.00111)
0.506
(0.633)
0.107
(0.188)
2e-05
(9.34e-05)
1e-05
(5.17e-05)
0.45
(0.581)
0.00577
(0.0158)
0.195
(0.308)
0.45
(0.581)
amp 19q12 139 (23%) 477 0.0158
(0.0379)
0.00253
(0.00734)
1e-05
(5.17e-05)
0.536
(0.658)
0.016
(0.0382)
0.389
(0.523)
0.0404
(0.0838)
0.00933
(0.024)
0.0995
(0.178)
0.0247
(0.0557)
0.154
(0.254)
0.77
(0.839)
amp 20p12 1 278 (45%) 338 0.0166
(0.0395)
0.00262
(0.00755)
1e-05
(5.17e-05)
0.516
(0.643)
0.00201
(0.00601)
0.434
(0.564)
0.166
(0.27)
0.00023
(0.000831)
0.21
(0.325)
1e-05
(5.17e-05)
0.0385
(0.0808)
0.689
(0.775)
del 1p33 176 (29%) 440 0.0385
(0.0808)
0.00229
(0.00673)
1e-05
(5.17e-05)
0.00738
(0.0197)
0.303
(0.437)
0.665
(0.755)
5e-05
(0.000216)
0.00041
(0.00137)
0.0517
(0.103)
0.0268
(0.0595)
0.342
(0.476)
0.749
(0.823)
del 1p13 2 176 (29%) 440 0.38
(0.514)
0.0338
(0.0728)
1e-05
(5.17e-05)
0.0112
(0.0279)
0.592
(0.7)
0.859
(0.902)
0.00021
(0.000769)
0.00028
(0.001)
0.0339
(0.0728)
0.00665
(0.018)
0.537
(0.658)
0.985
(0.996)
del 4q22 1 225 (37%) 391 0.00589
(0.0161)
0.00444
(0.0123)
1e-05
(5.17e-05)
0.0102
(0.0258)
0.545
(0.662)
0.184
(0.293)
0.00487
(0.0134)
1e-05
(5.17e-05)
0.201
(0.315)
0.00039
(0.00131)
0.152
(0.253)
0.285
(0.417)
del 4q35 1 233 (38%) 383 0.00884
(0.0229)
0.00854
(0.0224)
1e-05
(5.17e-05)
0.0105
(0.0264)
0.726
(0.809)
0.257
(0.383)
0.00453
(0.0125)
2e-05
(9.34e-05)
0.0363
(0.0773)
0.1
(0.179)
0.558
(0.675)
0.858
(0.902)
del 5q12 1 159 (26%) 457 0.00031
(0.00108)
2e-05
(9.34e-05)
1e-05
(5.17e-05)
0.00262
(0.00755)
0.116
(0.201)
0.334
(0.47)
0.0307
(0.0673)
1e-05
(5.17e-05)
0.224
(0.342)
0.00016
(0.000606)
0.885
(0.921)
0.54
(0.658)
del 5q23 3 161 (26%) 455 0.00677
(0.0183)
5e-05
(0.000216)
1e-05
(5.17e-05)
0.00303
(0.00867)
0.354
(0.488)
0.641
(0.738)
0.0104
(0.0261)
0.00015
(0.000576)
0.263
(0.39)
6e-05
(0.000257)
0.606
(0.714)
0.96
(0.977)
del 8p23 2 290 (47%) 326 7e-05
(0.000298)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.498
(0.627)
0.891
(0.926)
5e-05
(0.000216)
1e-05
(5.17e-05)
0.0568
(0.112)
0.00092
(0.00287)
0.167
(0.27)
0.439
(0.569)
del 8p22 304 (49%) 312 0.00029
(0.00103)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
2e-05
(9.34e-05)
1
(1.00)
0.899
(0.932)
0.00013
(0.000513)
1e-05
(5.17e-05)
0.0985
(0.177)
0.0001
(0.000406)
0.186
(0.295)
0.378
(0.514)
del 12p13 1 92 (15%) 524 0.00342
(0.00972)
0.00031
(0.00108)
1e-05
(5.17e-05)
0.0528
(0.105)
0.972
(0.986)
0.788
(0.846)
0.0463
(0.0939)
0.00079
(0.00254)
0.0389
(0.0812)
0.156
(0.258)
0.777
(0.842)
0.0437
(0.0893)
del 20p12 1 136 (22%) 480 0.057
(0.112)
0.00231
(0.00677)
1e-05
(5.17e-05)
1e-05
(5.17e-05)
0.181
(0.29)
0.772
(0.84)
0.00015
(0.000576)
1e-05
(5.17e-05)
0.00378
(0.0107)
0.00036
(0.00123)
0.113
(0.197)
0.0989
(0.178)
del 2p12 21 (3%) 595 1
(1.00)
0.781
(0.845)
0.00219
(0.00648)
0.0101
(0.0258)
0.206
(0.32)
0.00179
(0.00541)
0.00937
(0.024)
0.013
(0.0317)
0.00036
(0.00123)
0.0843
(0.156)
1
(1.00)
0.258
(0.383)
del 4p16 1 203 (33%) 413 0.0741
(0.141)
0.00205
(0.00611)
1e-05
(5.17e-05)
0.00508
(0.0139)
0.663
(0.755)
0.498
(0.627)
0.00865
(0.0226)
1e-05
(5.17e-05)
0.423
(0.552)
0.0113
(0.0279)
0.459
(0.591)
0.93
(0.955)
del 5q21 2 187 (30%) 429 0.0289
(0.0637)
0.00082
(0.00262)
1e-05
(5.17e-05)
0.0134
(0.0326)
0.111
(0.194)
0.423
(0.552)
0.255
(0.381)
0.00161
(0.00492)
0.319
(0.454)
0.00087
(0.00273)
0.567
(0.683)
0.987
(0.997)
del 5q22 2 189 (31%) 427 0.00025
(9e-04)
3e-05
(0.000136)
1e-05
(5.17e-05)
0.0415
(0.0859)
0.159
(0.262)
0.395
(0.53)
0.0707
(0.136)
0.0001
(0.000406)
0.246
(0.371)
0.00045
(0.00149)
0.579
(0.691)
0.973
(0.986)
del 10q21 1 139 (23%) 477 0.0117
(0.0288)
0.0381
(0.0806)
1e-05
(5.17e-05)
0.018
(0.042)
0.217
(0.334)
0.808
(0.862)
0.0001
(0.000406)
0.00038
(0.00129)
0.626
(0.727)
0.0807
(0.151)
0.42
(0.552)
0.537
(0.658)
amp 5p12 118 (19%) 498 0.14
(0.236)
0.0281
(0.0622)
1e-05
(5.17e-05)
0.834
(0.885)
0.0101
(0.0257)
0.915
(0.942)
0.00406
(0.0114)
0.00751
(0.02)
0.23
(0.351)
0.703
(0.787)
0.345
(0.48)
0.49
(0.621)
amp 6p21 1 154 (25%) 462 0.0241
(0.0547)
2e-05
(9.34e-05)
1e-05
(5.17e-05)
0.131
(0.224)
0.153
(0.254)
0.294
(0.426)
0.381
(0.515)
0.00029
(0.00103)
0.181
(0.29)
0.025
(0.0561)
0.369
(0.505)
0.098
(0.177)
amp 8p11 23 211 (34%) 405 0.398
(0.533)
0.0866
(0.159)
1e-05
(5.17e-05)
0.0159
(0.0379)
0.219
(0.337)
0.612
(0.719)
0.0235
(0.0536)
0.00892
(0.0231)
0.0225
(0.0516)
0.119
(0.205)
0.555
(0.672)
0.799
(0.854)
amp 8p11 21 256 (42%) 360 0.166
(0.27)
0.0112
(0.0279)
1e-05
(5.17e-05)
0.0167
(0.0395)
0.668
(0.758)
0.312
(0.447)
0.0475
(0.0959)
0.0483
(0.097)
0.124
(0.212)
0.24
(0.364)
0.611
(0.718)
0.614
(0.719)
del 9p21 3 88 (14%) 528 0.506
(0.633)
0.236
(0.359)
0.00016
(0.000606)
0.0346
(0.0742)
0.872
(0.911)
0.298
(0.431)
0.0387
(0.081)
0.0424
(0.0873)
0.184
(0.293)
0.0327
(0.0712)
0.642
(0.739)
0.531
(0.656)
del 10p15 3 115 (19%) 501 0.0769
(0.145)
0.31
(0.446)
1e-05
(5.17e-05)
0.0363
(0.0773)
0.584
(0.695)
0.749
(0.823)
0.00962
(0.0246)
2e-05
(9.34e-05)
0.554
(0.672)
0.194
(0.307)
0.0484
(0.097)
0.0625
(0.122)
del 10q23 31 161 (26%) 455 0.0531
(0.105)
0.588
(0.698)
1e-05
(5.17e-05)
0.0153
(0.0368)
0.785
(0.846)
0.845
(0.894)
0.00477
(0.0132)
6e-05
(0.000257)
0.277
(0.409)
0.0113
(0.0279)
0.177
(0.286)
0.203
(0.317)
del 10q25 2 157 (25%) 459 0.199
(0.314)
0.229
(0.35)
1e-05
(5.17e-05)
0.0186
(0.0432)
0.209
(0.324)
0.932
(0.956)
0.00269
(0.00772)
1e-05
(5.17e-05)
0.327
(0.464)
0.0206
(0.0475)
0.478
(0.61)
0.362
(0.497)
del 12q21 33 90 (15%) 526 0.0242
(0.0548)
0.0115
(0.0282)
1e-05
(5.17e-05)
0.2
(0.314)
0.203
(0.317)
0.0862
(0.159)
0.0636
(0.123)
0.00037
(0.00126)
0.288
(0.418)
0.664
(0.755)
0.665
(0.755)
0.268
(0.396)
del 16p13 3 69 (11%) 547 0.049
(0.0981)
0.0364
(0.0773)
0.00812
(0.0215)
0.727
(0.809)
0.819
(0.871)
0.791
(0.849)
0.272
(0.402)
0.0764
(0.145)
0.526
(0.652)
0.112
(0.196)
0.564
(0.681)
0.962
(0.977)
amp 1q31 1 145 (24%) 471 0.781
(0.845)
0.337
(0.472)
2e-05
(9.34e-05)
0.764
(0.835)
0.104
(0.183)
0.161
(0.265)
0.578
(0.691)
0.427
(0.557)
0.0703
(0.136)
0.331
(0.467)
0.0104
(0.0261)
0.318
(0.453)
del 2q22 1 35 (6%) 581 0.785
(0.846)
0.649
(0.742)
0.0331
(0.0719)
0.498
(0.627)
0.337
(0.472)
0.298
(0.431)
0.169
(0.274)
0.103
(0.182)
0.046
(0.0936)
0.136
(0.23)
0.892
(0.927)
0.52
(0.647)
del 11q22 3 111 (18%) 505 0.31
(0.445)
0.0808
(0.151)
0.00908
(0.0234)
0.405
(0.538)
0.54
(0.658)
0.948
(0.968)
0.685
(0.771)
0.0476
(0.0959)
0.133
(0.226)
0.0826
(0.153)
0.476
(0.609)
0.62
(0.723)
del 19p13 3 97 (16%) 519 0.127
(0.217)
0.206
(0.32)
0.00019
(0.000705)
0.407
(0.541)
0.775
(0.841)
0.854
(0.899)
0.149
(0.248)
0.115
(0.2)
0.896
(0.93)
0.00066
(0.00213)
0.578
(0.691)
0.401
(0.535)
amp 10q22 3 40 (6%) 576 1
(1.00)
0.416
(0.547)
0.00834
(0.022)
0.366
(0.502)
0.0598
(0.117)
0.411
(0.542)
0.647
(0.742)
0.49
(0.621)
0.872
(0.911)
0.937
(0.96)
0.409
(0.541)
0.375
(0.511)
del 3p26 3 93 (15%) 523 0.581
(0.693)
0.634
(0.733)
0.00057
(0.00186)
0.337
(0.472)
0.627
(0.727)
0.124
(0.212)
0.485
(0.616)
0.533
(0.658)
0.946
(0.967)
0.736
(0.817)
0.712
(0.795)
0.471
(0.605)
del 6q26 92 (15%) 524 0.748
(0.823)
0.68
(0.768)
0.257
(0.383)
0.538
(0.658)
0.00188
(0.00564)
0.132
(0.224)
0.0594
(0.116)
0.0856
(0.158)
0.323
(0.459)
0.796
(0.852)
0.149
(0.248)
0.665
(0.755)
del 8q11 1 47 (8%) 569 0.526
(0.652)
0.315
(0.45)
0.00164
(0.00499)
0.334
(0.47)
0.247
(0.371)
0.339
(0.473)
0.284
(0.416)
0.224
(0.342)
0.604
(0.713)
0.745
(0.823)
1
(1.00)
0.648
(0.742)
del 16q23 1 84 (14%) 532 0.0715
(0.137)
0.00131
(0.00403)
0.267
(0.396)
0.481
(0.613)
0.421
(0.552)
0.904
(0.935)
0.621
(0.723)
0.574
(0.688)
0.54
(0.658)
0.0981
(0.177)
0.684
(0.771)
0.403
(0.537)
del 17q24 3 95 (15%) 521 0.905
(0.935)
0.643
(0.739)
1e-05
(5.17e-05)
0.54
(0.658)
0.455
(0.587)
0.438
(0.569)
0.75
(0.824)
0.119
(0.205)
0.154
(0.254)
0.85
(0.897)
0.907
(0.936)
0.46
(0.591)
amp 12p13 33 153 (25%) 463 0.178
(0.287)
0.589
(0.698)
0.301
(0.434)
0.0955
(0.173)
0.962
(0.977)
0.611
(0.718)
0.5
(0.627)
0.0839
(0.155)
0.868
(0.909)
0.109
(0.191)
0.188
(0.299)
0.238
(0.361)
amp 15q26 1 42 (7%) 574 0.745
(0.823)
0.38
(0.514)
0.0558
(0.11)
0.64
(0.738)
0.0991
(0.178)
0.809
(0.862)
0.572
(0.687)
0.829
(0.881)
0.359
(0.493)
0.941
(0.963)
0.959
(0.977)
0.795
(0.852)
del 3p14 2 119 (19%) 497 0.742
(0.822)
0.698
(0.783)
0.117
(0.202)
1
(1.00)
0.349
(0.484)
0.62
(0.723)
0.448
(0.581)
0.845
(0.894)
0.882
(0.919)
0.539
(0.658)
0.134
(0.226)
0.422
(0.552)
del 3q26 31 65 (11%) 551 0.556
(0.672)
0.613
(0.719)
0.0821
(0.153)
0.51
(0.637)
0.787
(0.846)
0.873
(0.911)
0.785
(0.846)
0.199
(0.314)
0.388
(0.523)
0.288
(0.418)
0.0868
(0.159)
0.6
(0.709)
del 6p25 3 80 (13%) 536 0.774
(0.841)
0.339
(0.473)
0.159
(0.262)
0.759
(0.83)
0.624
(0.725)
0.495
(0.625)
0.386
(0.52)
0.401
(0.535)
0.232
(0.352)
0.413
(0.545)
0.314
(0.449)
0.38
(0.514)
del 7q31 1 17 (3%) 599 0.33
(0.467)
0.848
(0.895)
0.567
(0.683)
1
(1.00)
0.48
(0.613)
0.866
(0.908)
0.53
(0.655)
0.991
(1.00)
0.502
(0.629)
0.678
(0.766)
0.634
(0.733)
0.835
(0.886)
'amp_1q31.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S1.  Gene #1: 'amp_1q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
AMP PEAK 1(1Q31.1) MUTATED 27 69 41 8
AMP PEAK 1(1Q31.1) WILD-TYPE 188 178 91 14

Figure S1.  Get High-res Image Gene #1: 'amp_1q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q31.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.026

Table S2.  Gene #1: 'amp_1q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
AMP PEAK 1(1Q31.1) MUTATED 3 15 12 3
AMP PEAK 1(1Q31.1) WILD-TYPE 32 25 26 19

Figure S2.  Get High-res Image Gene #1: 'amp_1q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_2q33.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00131 (Fisher's exact test), Q value = 0.004

Table S3.  Gene #2: 'amp_2q33.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
AMP PEAK 2(2Q33.1) MUTATED 5 27 8
AMP PEAK 2(2Q33.1) WILD-TYPE 45 62 69

Figure S3.  Get High-res Image Gene #2: 'amp_2q33.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_2q33.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S4.  Gene #2: 'amp_2q33.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
AMP PEAK 2(2Q33.1) MUTATED 23 70 33 14
AMP PEAK 2(2Q33.1) WILD-TYPE 192 177 99 8

Figure S4.  Get High-res Image Gene #2: 'amp_2q33.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2q33.1' versus 'METHLYATION_CNMF'

P value = 0.00389 (Fisher's exact test), Q value = 0.011

Table S5.  Gene #2: 'amp_2q33.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
AMP PEAK 2(2Q33.1) MUTATED 22 46 30
AMP PEAK 2(2Q33.1) WILD-TYPE 95 83 114

Figure S5.  Get High-res Image Gene #2: 'amp_2q33.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2q33.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S6.  Gene #2: 'amp_2q33.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
AMP PEAK 2(2Q33.1) MUTATED 56 15 32 36
AMP PEAK 2(2Q33.1) WILD-TYPE 100 113 99 162

Figure S6.  Get High-res Image Gene #2: 'amp_2q33.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2q33.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00033

Table S7.  Gene #2: 'amp_2q33.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
AMP PEAK 2(2Q33.1) MUTATED 27 17 7 13 32 33 10
AMP PEAK 2(2Q33.1) WILD-TYPE 53 69 57 44 58 105 88

Figure S7.  Get High-res Image Gene #2: 'amp_2q33.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_2q33.1' versus 'MIRSEQ_CNMF'

P value = 0.0414 (Fisher's exact test), Q value = 0.086

Table S8.  Gene #2: 'amp_2q33.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
AMP PEAK 2(2Q33.1) MUTATED 40 27 18 33
AMP PEAK 2(2Q33.1) WILD-TYPE 113 68 68 172

Figure S8.  Get High-res Image Gene #2: 'amp_2q33.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_2q33.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00424 (Fisher's exact test), Q value = 0.012

Table S9.  Gene #2: 'amp_2q33.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
AMP PEAK 2(2Q33.1) MUTATED 9 19 5 25 4 15 14 6 21
AMP PEAK 2(2Q33.1) WILD-TYPE 40 55 24 61 73 39 43 26 60

Figure S9.  Get High-res Image Gene #2: 'amp_2q33.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5p12' versus 'MRNA_CHIERARCHICAL'

P value = 0.0281 (Fisher's exact test), Q value = 0.062

Table S10.  Gene #3: 'amp_5p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
AMP PEAK 3(5P12) MUTATED 8 27 11
AMP PEAK 3(5P12) WILD-TYPE 42 62 66

Figure S10.  Get High-res Image Gene #3: 'amp_5p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_5p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S11.  Gene #3: 'amp_5p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
AMP PEAK 3(5P12) MUTATED 17 66 28 7
AMP PEAK 3(5P12) WILD-TYPE 198 181 104 15

Figure S11.  Get High-res Image Gene #3: 'amp_5p12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p12' versus 'RPPA_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.026

Table S12.  Gene #3: 'amp_5p12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 197 177
AMP PEAK 3(5P12) MUTATED 31 32 26
AMP PEAK 3(5P12) WILD-TYPE 77 165 151

Figure S12.  Get High-res Image Gene #3: 'amp_5p12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_5p12' versus 'MRNASEQ_CNMF'

P value = 0.00406 (Fisher's exact test), Q value = 0.011

Table S13.  Gene #3: 'amp_5p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
AMP PEAK 3(5P12) MUTATED 40 12 27 39
AMP PEAK 3(5P12) WILD-TYPE 116 116 104 159

Figure S13.  Get High-res Image Gene #3: 'amp_5p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00751 (Fisher's exact test), Q value = 0.02

Table S14.  Gene #3: 'amp_5p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
AMP PEAK 3(5P12) MUTATED 17 10 6 10 25 36 14
AMP PEAK 3(5P12) WILD-TYPE 63 76 58 47 65 102 84

Figure S14.  Get High-res Image Gene #3: 'amp_5p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MRNA_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.055

Table S15.  Gene #4: 'amp_6p21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
AMP PEAK 4(6P21.1) MUTATED 9 16 22 4
AMP PEAK 4(6P21.1) WILD-TYPE 36 47 43 39

Figure S15.  Get High-res Image Gene #4: 'amp_6p21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_6p21.1' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S16.  Gene #4: 'amp_6p21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
AMP PEAK 4(6P21.1) MUTATED 4 35 12
AMP PEAK 4(6P21.1) WILD-TYPE 46 54 65

Figure S16.  Get High-res Image Gene #4: 'amp_6p21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_6p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S17.  Gene #4: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
AMP PEAK 4(6P21.1) MUTATED 10 93 41 10
AMP PEAK 4(6P21.1) WILD-TYPE 205 154 91 12

Figure S17.  Get High-res Image Gene #4: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.001

Table S18.  Gene #4: 'amp_6p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
AMP PEAK 4(6P21.1) MUTATED 19 20 7 20 31 44 13
AMP PEAK 4(6P21.1) WILD-TYPE 61 66 57 37 59 94 85

Figure S18.  Get High-res Image Gene #4: 'amp_6p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.025 (Fisher's exact test), Q value = 0.056

Table S19.  Gene #4: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
AMP PEAK 4(6P21.1) MUTATED 13 19 6 28 9 12 20 7 28
AMP PEAK 4(6P21.1) WILD-TYPE 36 55 23 58 68 42 37 25 53

Figure S19.  Get High-res Image Gene #4: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7p21.3' versus 'MRNA_CNMF'

P value = 0.00115 (Fisher's exact test), Q value = 0.0036

Table S20.  Gene #5: 'amp_7p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
AMP PEAK 5(7P21.3) MUTATED 16 42 37 15
AMP PEAK 5(7P21.3) WILD-TYPE 29 21 28 28

Figure S20.  Get High-res Image Gene #5: 'amp_7p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_7p21.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S21.  Gene #5: 'amp_7p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
AMP PEAK 5(7P21.3) MUTATED 13 64 33
AMP PEAK 5(7P21.3) WILD-TYPE 37 25 44

Figure S21.  Get High-res Image Gene #5: 'amp_7p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S22.  Gene #5: 'amp_7p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
AMP PEAK 5(7P21.3) MUTATED 60 190 92 21
AMP PEAK 5(7P21.3) WILD-TYPE 155 57 40 1

Figure S22.  Get High-res Image Gene #5: 'amp_7p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7p21.3' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00044

Table S23.  Gene #5: 'amp_7p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
AMP PEAK 5(7P21.3) MUTATED 67 101 79
AMP PEAK 5(7P21.3) WILD-TYPE 50 28 65

Figure S23.  Get High-res Image Gene #5: 'amp_7p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0428 (Fisher's exact test), Q value = 0.088

Table S24.  Gene #5: 'amp_7p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 86
AMP PEAK 5(7P21.3) MUTATED 139 85 56
AMP PEAK 5(7P21.3) WILD-TYPE 89 83 30

Figure S24.  Get High-res Image Gene #5: 'amp_7p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_7p21.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S25.  Gene #5: 'amp_7p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
AMP PEAK 5(7P21.3) MUTATED 118 61 78 104
AMP PEAK 5(7P21.3) WILD-TYPE 38 67 53 94

Figure S25.  Get High-res Image Gene #5: 'amp_7p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S26.  Gene #5: 'amp_7p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
AMP PEAK 5(7P21.3) MUTATED 53 54 14 42 73 91 34
AMP PEAK 5(7P21.3) WILD-TYPE 27 32 50 15 17 47 64

Figure S26.  Get High-res Image Gene #5: 'amp_7p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7p21.3' versus 'MIRSEQ_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.0027

Table S27.  Gene #5: 'amp_7p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
AMP PEAK 5(7P21.3) MUTATED 96 62 62 101
AMP PEAK 5(7P21.3) WILD-TYPE 57 33 24 104

Figure S27.  Get High-res Image Gene #5: 'amp_7p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S28.  Gene #5: 'amp_7p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
AMP PEAK 5(7P21.3) MUTATED 32 49 16 60 22 27 41 16 58
AMP PEAK 5(7P21.3) WILD-TYPE 17 25 13 26 55 27 16 16 23

Figure S28.  Get High-res Image Gene #5: 'amp_7p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S29.  Gene #6: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
AMP PEAK 6(8P11.23) MUTATED 44 88 69 10
AMP PEAK 6(8P11.23) WILD-TYPE 171 159 63 12

Figure S29.  Get High-res Image Gene #6: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.23' versus 'METHLYATION_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.038

Table S30.  Gene #6: 'amp_8p11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
AMP PEAK 6(8P11.23) MUTATED 38 62 48
AMP PEAK 6(8P11.23) WILD-TYPE 79 67 96

Figure S30.  Get High-res Image Gene #6: 'amp_8p11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8p11.23' versus 'MRNASEQ_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 0.054

Table S31.  Gene #6: 'amp_8p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
AMP PEAK 6(8P11.23) MUTATED 66 41 48 54
AMP PEAK 6(8P11.23) WILD-TYPE 90 87 83 144

Figure S31.  Get High-res Image Gene #6: 'amp_8p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00892 (Fisher's exact test), Q value = 0.023

Table S32.  Gene #6: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
AMP PEAK 6(8P11.23) MUTATED 36 28 22 21 39 43 20
AMP PEAK 6(8P11.23) WILD-TYPE 44 58 42 36 51 95 78

Figure S32.  Get High-res Image Gene #6: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.23' versus 'MIRSEQ_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.052

Table S33.  Gene #6: 'amp_8p11.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
AMP PEAK 6(8P11.23) MUTATED 61 32 37 56
AMP PEAK 6(8P11.23) WILD-TYPE 92 63 49 149

Figure S33.  Get High-res Image Gene #6: 'amp_8p11.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8p11.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.028

Table S34.  Gene #7: 'amp_8p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
AMP PEAK 7(8P11.21) MUTATED 13 43 23
AMP PEAK 7(8P11.21) WILD-TYPE 37 46 54

Figure S34.  Get High-res Image Gene #7: 'amp_8p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S35.  Gene #7: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
AMP PEAK 7(8P11.21) MUTATED 47 103 96 10
AMP PEAK 7(8P11.21) WILD-TYPE 168 144 36 12

Figure S35.  Get High-res Image Gene #7: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'METHLYATION_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.04

Table S36.  Gene #7: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
AMP PEAK 7(8P11.21) MUTATED 48 71 56
AMP PEAK 7(8P11.21) WILD-TYPE 69 58 88

Figure S36.  Get High-res Image Gene #7: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CNMF'

P value = 0.0475 (Fisher's exact test), Q value = 0.096

Table S37.  Gene #7: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
AMP PEAK 7(8P11.21) MUTATED 75 46 61 72
AMP PEAK 7(8P11.21) WILD-TYPE 81 82 70 126

Figure S37.  Get High-res Image Gene #7: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0483 (Fisher's exact test), Q value = 0.097

Table S38.  Gene #7: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
AMP PEAK 7(8P11.21) MUTATED 37 35 23 25 48 57 29
AMP PEAK 7(8P11.21) WILD-TYPE 43 51 41 32 42 81 69

Figure S38.  Get High-res Image Gene #7: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.0214 (Fisher's exact test), Q value = 0.049

Table S39.  Gene #8: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
AMP PEAK 8(8Q24.21) MUTATED 23 60 39
AMP PEAK 8(8Q24.21) WILD-TYPE 27 29 38

Figure S39.  Get High-res Image Gene #8: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S40.  Gene #8: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
AMP PEAK 8(8Q24.21) MUTATED 64 158 128 18
AMP PEAK 8(8Q24.21) WILD-TYPE 151 89 4 4

Figure S40.  Get High-res Image Gene #8: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S41.  Gene #8: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
AMP PEAK 8(8Q24.21) MUTATED 67 103 75
AMP PEAK 8(8Q24.21) WILD-TYPE 50 26 69

Figure S41.  Get High-res Image Gene #8: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00018

Table S42.  Gene #8: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
AMP PEAK 8(8Q24.21) MUTATED 111 57 85 112
AMP PEAK 8(8Q24.21) WILD-TYPE 45 71 46 86

Figure S42.  Get High-res Image Gene #8: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00133 (Fisher's exact test), Q value = 0.0041

Table S43.  Gene #8: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
AMP PEAK 8(8Q24.21) MUTATED 54 44 30 37 66 86 48
AMP PEAK 8(8Q24.21) WILD-TYPE 26 42 34 20 24 52 50

Figure S43.  Get High-res Image Gene #8: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.026

Table S44.  Gene #8: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
AMP PEAK 8(8Q24.21) MUTATED 25 47 21 64 34 32 33 18 50
AMP PEAK 8(8Q24.21) WILD-TYPE 24 27 8 22 43 22 24 14 31

Figure S44.  Get High-res Image Gene #8: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0224 (Fisher's exact test), Q value = 0.051

Table S45.  Gene #8: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
AMP PEAK 8(8Q24.21) MUTATED 20 33 30 12
AMP PEAK 8(8Q24.21) WILD-TYPE 15 7 8 10

Figure S45.  Get High-res Image Gene #8: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_10q22.3' versus 'CN_CNMF'

P value = 0.00834 (Fisher's exact test), Q value = 0.022

Table S46.  Gene #9: 'amp_10q22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
AMP PEAK 9(10Q22.3) MUTATED 6 17 14 3
AMP PEAK 9(10Q22.3) WILD-TYPE 209 230 118 19

Figure S46.  Get High-res Image Gene #9: 'amp_10q22.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11p15.5' versus 'MRNA_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.002

Table S47.  Gene #10: 'amp_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
AMP PEAK 10(11P15.5) MUTATED 4 19 24 5
AMP PEAK 10(11P15.5) WILD-TYPE 41 44 41 38

Figure S47.  Get High-res Image Gene #10: 'amp_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11p15.5' versus 'MRNA_CHIERARCHICAL'

P value = 9e-04 (Fisher's exact test), Q value = 0.0028

Table S48.  Gene #10: 'amp_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
AMP PEAK 10(11P15.5) MUTATED 3 25 24
AMP PEAK 10(11P15.5) WILD-TYPE 47 64 53

Figure S48.  Get High-res Image Gene #10: 'amp_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S49.  Gene #10: 'amp_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
AMP PEAK 10(11P15.5) MUTATED 22 72 35 9
AMP PEAK 10(11P15.5) WILD-TYPE 193 175 97 13

Figure S49.  Get High-res Image Gene #10: 'amp_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11p15.5' versus 'METHLYATION_CNMF'

P value = 0.00224 (Fisher's exact test), Q value = 0.0066

Table S50.  Gene #10: 'amp_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
AMP PEAK 10(11P15.5) MUTATED 25 38 18
AMP PEAK 10(11P15.5) WILD-TYPE 92 91 126

Figure S50.  Get High-res Image Gene #10: 'amp_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11p15.5' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S51.  Gene #10: 'amp_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
AMP PEAK 10(11P15.5) MUTATED 54 11 24 47
AMP PEAK 10(11P15.5) WILD-TYPE 102 117 107 151

Figure S51.  Get High-res Image Gene #10: 'amp_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S52.  Gene #10: 'amp_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
AMP PEAK 10(11P15.5) MUTATED 30 15 2 10 21 43 15
AMP PEAK 10(11P15.5) WILD-TYPE 50 71 62 47 69 95 83

Figure S52.  Get High-res Image Gene #10: 'amp_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S53.  Gene #10: 'amp_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
AMP PEAK 10(11P15.5) MUTATED 5 14 1 26 4 40 14 2 17
AMP PEAK 10(11P15.5) WILD-TYPE 44 60 28 60 73 14 43 30 64

Figure S53.  Get High-res Image Gene #10: 'amp_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_13q12.13' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00014

Table S54.  Gene #12: 'amp_13q12.13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
AMP PEAK 12(13Q12.13) MUTATED 21 49 53 18
AMP PEAK 12(13Q12.13) WILD-TYPE 24 14 12 25

Figure S54.  Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_13q12.13' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S55.  Gene #12: 'amp_13q12.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
AMP PEAK 12(13Q12.13) MUTATED 16 75 50
AMP PEAK 12(13Q12.13) WILD-TYPE 34 14 27

Figure S55.  Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_13q12.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S56.  Gene #12: 'amp_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
AMP PEAK 12(13Q12.13) MUTATED 71 236 82 13
AMP PEAK 12(13Q12.13) WILD-TYPE 144 11 50 9

Figure S56.  Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q12.13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S57.  Gene #12: 'amp_13q12.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
AMP PEAK 12(13Q12.13) MUTATED 68 114 77
AMP PEAK 12(13Q12.13) WILD-TYPE 49 15 67

Figure S57.  Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q12.13' versus 'RPPA_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.077

Table S58.  Gene #12: 'amp_13q12.13' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 197 177
AMP PEAK 12(13Q12.13) MUTATED 74 136 101
AMP PEAK 12(13Q12.13) WILD-TYPE 34 61 76

Figure S58.  Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_13q12.13' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S59.  Gene #12: 'amp_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
AMP PEAK 12(13Q12.13) MUTATED 125 64 80 130
AMP PEAK 12(13Q12.13) WILD-TYPE 31 64 51 68

Figure S59.  Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q12.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S60.  Gene #12: 'amp_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
AMP PEAK 12(13Q12.13) MUTATED 60 55 14 45 75 110 40
AMP PEAK 12(13Q12.13) WILD-TYPE 20 31 50 12 15 28 58

Figure S60.  Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q12.13' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S61.  Gene #12: 'amp_13q12.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
AMP PEAK 12(13Q12.13) MUTATED 99 64 74 116
AMP PEAK 12(13Q12.13) WILD-TYPE 54 31 12 89

Figure S61.  Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q12.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S62.  Gene #12: 'amp_13q12.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
AMP PEAK 12(13Q12.13) MUTATED 31 48 18 64 28 32 47 20 65
AMP PEAK 12(13Q12.13) WILD-TYPE 18 26 11 22 49 22 10 12 16

Figure S62.  Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_13q12.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00033

Table S63.  Gene #12: 'amp_13q12.13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
AMP PEAK 12(13Q12.13) MUTATED 23 33 36 10
AMP PEAK 12(13Q12.13) WILD-TYPE 12 7 2 12

Figure S63.  Get High-res Image Gene #12: 'amp_13q12.13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_13q12.2' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S64.  Gene #13: 'amp_13q12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
AMP PEAK 13(13Q12.2) MUTATED 20 48 51 19
AMP PEAK 13(13Q12.2) WILD-TYPE 25 15 14 24

Figure S64.  Get High-res Image Gene #13: 'amp_13q12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_13q12.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S65.  Gene #13: 'amp_13q12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
AMP PEAK 13(13Q12.2) MUTATED 16 74 48
AMP PEAK 13(13Q12.2) WILD-TYPE 34 15 29

Figure S65.  Get High-res Image Gene #13: 'amp_13q12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_13q12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S66.  Gene #13: 'amp_13q12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
AMP PEAK 13(13Q12.2) MUTATED 68 234 81 13
AMP PEAK 13(13Q12.2) WILD-TYPE 147 13 51 9

Figure S66.  Get High-res Image Gene #13: 'amp_13q12.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q12.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S67.  Gene #13: 'amp_13q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
AMP PEAK 13(13Q12.2) MUTATED 68 114 74
AMP PEAK 13(13Q12.2) WILD-TYPE 49 15 70

Figure S67.  Get High-res Image Gene #13: 'amp_13q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q12.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S68.  Gene #13: 'amp_13q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
AMP PEAK 13(13Q12.2) MUTATED 124 63 79 127
AMP PEAK 13(13Q12.2) WILD-TYPE 32 65 52 71

Figure S68.  Get High-res Image Gene #13: 'amp_13q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S69.  Gene #13: 'amp_13q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
AMP PEAK 13(13Q12.2) MUTATED 59 54 13 45 75 109 38
AMP PEAK 13(13Q12.2) WILD-TYPE 21 32 51 12 15 29 60

Figure S69.  Get High-res Image Gene #13: 'amp_13q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q12.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S70.  Gene #13: 'amp_13q12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
AMP PEAK 13(13Q12.2) MUTATED 96 64 75 112
AMP PEAK 13(13Q12.2) WILD-TYPE 57 31 11 93

Figure S70.  Get High-res Image Gene #13: 'amp_13q12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S71.  Gene #13: 'amp_13q12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
AMP PEAK 13(13Q12.2) MUTATED 31 48 18 60 27 31 47 20 65
AMP PEAK 13(13Q12.2) WILD-TYPE 18 26 11 26 50 23 10 12 16

Figure S71.  Get High-res Image Gene #13: 'amp_13q12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_13q12.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 8e-04

Table S72.  Gene #13: 'amp_13q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
AMP PEAK 13(13Q12.2) MUTATED 22 33 35 10
AMP PEAK 13(13Q12.2) WILD-TYPE 13 7 3 12

Figure S72.  Get High-res Image Gene #13: 'amp_13q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_13q22.1' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S73.  Gene #14: 'amp_13q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
AMP PEAK 14(13Q22.1) MUTATED 19 49 50 19
AMP PEAK 14(13Q22.1) WILD-TYPE 26 14 15 24

Figure S73.  Get High-res Image Gene #14: 'amp_13q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_13q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S74.  Gene #14: 'amp_13q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
AMP PEAK 14(13Q22.1) MUTATED 14 73 50
AMP PEAK 14(13Q22.1) WILD-TYPE 36 16 27

Figure S74.  Get High-res Image Gene #14: 'amp_13q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_13q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S75.  Gene #14: 'amp_13q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
AMP PEAK 14(13Q22.1) MUTATED 73 231 80 13
AMP PEAK 14(13Q22.1) WILD-TYPE 142 16 52 9

Figure S75.  Get High-res Image Gene #14: 'amp_13q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S76.  Gene #14: 'amp_13q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
AMP PEAK 14(13Q22.1) MUTATED 69 109 79
AMP PEAK 14(13Q22.1) WILD-TYPE 48 20 65

Figure S76.  Get High-res Image Gene #14: 'amp_13q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00014

Table S77.  Gene #14: 'amp_13q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
AMP PEAK 14(13Q22.1) MUTATED 122 63 81 128
AMP PEAK 14(13Q22.1) WILD-TYPE 34 65 50 70

Figure S77.  Get High-res Image Gene #14: 'amp_13q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S78.  Gene #14: 'amp_13q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
AMP PEAK 14(13Q22.1) MUTATED 59 52 18 44 73 111 37
AMP PEAK 14(13Q22.1) WILD-TYPE 21 34 46 13 17 27 61

Figure S78.  Get High-res Image Gene #14: 'amp_13q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S79.  Gene #14: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
AMP PEAK 14(13Q22.1) MUTATED 97 65 76 113
AMP PEAK 14(13Q22.1) WILD-TYPE 56 30 10 92

Figure S79.  Get High-res Image Gene #14: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S80.  Gene #14: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
AMP PEAK 14(13Q22.1) MUTATED 31 49 18 59 28 35 48 20 63
AMP PEAK 14(13Q22.1) WILD-TYPE 18 25 11 27 49 19 9 12 18

Figure S80.  Get High-res Image Gene #14: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00704 (Fisher's exact test), Q value = 0.019

Table S81.  Gene #14: 'amp_13q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
AMP PEAK 14(13Q22.1) MUTATED 25 32 34 11
AMP PEAK 14(13Q22.1) WILD-TYPE 10 8 4 11

Figure S81.  Get High-res Image Gene #14: 'amp_13q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_16p11.2' versus 'MRNA_CNMF'

P value = 0.0423 (Fisher's exact test), Q value = 0.087

Table S82.  Gene #16: 'amp_16p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
AMP PEAK 16(16P11.2) MUTATED 10 24 23 7
AMP PEAK 16(16P11.2) WILD-TYPE 35 39 42 36

Figure S82.  Get High-res Image Gene #16: 'amp_16p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_16p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.00083

Table S83.  Gene #16: 'amp_16p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
AMP PEAK 16(16P11.2) MUTATED 8 40 16
AMP PEAK 16(16P11.2) WILD-TYPE 42 49 61

Figure S83.  Get High-res Image Gene #16: 'amp_16p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_16p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S84.  Gene #16: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
AMP PEAK 16(16P11.2) MUTATED 9 116 38 10
AMP PEAK 16(16P11.2) WILD-TYPE 206 131 94 12

Figure S84.  Get High-res Image Gene #16: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_16p11.2' versus 'METHLYATION_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.04

Table S85.  Gene #16: 'amp_16p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
AMP PEAK 16(16P11.2) MUTATED 33 46 29
AMP PEAK 16(16P11.2) WILD-TYPE 84 83 115

Figure S85.  Get High-res Image Gene #16: 'amp_16p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_16p11.2' versus 'RPPA_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.037

Table S86.  Gene #16: 'amp_16p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 197 177
AMP PEAK 16(16P11.2) MUTATED 41 48 41
AMP PEAK 16(16P11.2) WILD-TYPE 67 149 136

Figure S86.  Get High-res Image Gene #16: 'amp_16p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_16p11.2' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00014

Table S87.  Gene #16: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
AMP PEAK 16(16P11.2) MUTATED 60 18 32 62
AMP PEAK 16(16P11.2) WILD-TYPE 96 110 99 136

Figure S87.  Get High-res Image Gene #16: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_16p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S88.  Gene #16: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
AMP PEAK 16(16P11.2) MUTATED 20 24 6 15 35 54 18
AMP PEAK 16(16P11.2) WILD-TYPE 60 62 58 42 55 84 80

Figure S88.  Get High-res Image Gene #16: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00389 (Fisher's exact test), Q value = 0.011

Table S89.  Gene #16: 'amp_16p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
AMP PEAK 16(16P11.2) MUTATED 14 23 5 27 9 13 19 12 33
AMP PEAK 16(16P11.2) WILD-TYPE 35 51 24 59 68 41 38 20 48

Figure S89.  Get High-res Image Gene #16: 'amp_16p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.047

Table S90.  Gene #16: 'amp_16p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
AMP PEAK 16(16P11.2) MUTATED 15 17 11 2
AMP PEAK 16(16P11.2) WILD-TYPE 20 23 27 20

Figure S90.  Get High-res Image Gene #16: 'amp_16p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q12' versus 'MRNA_CNMF'

P value = 0.0397 (Fisher's exact test), Q value = 0.083

Table S91.  Gene #17: 'amp_17q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
AMP PEAK 17(17Q12) MUTATED 8 24 18 7
AMP PEAK 17(17Q12) WILD-TYPE 37 39 47 36

Figure S91.  Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.0066 (Fisher's exact test), Q value = 0.018

Table S92.  Gene #17: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
AMP PEAK 17(17Q12) MUTATED 6 32 19
AMP PEAK 17(17Q12) WILD-TYPE 44 57 58

Figure S92.  Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S93.  Gene #17: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
AMP PEAK 17(17Q12) MUTATED 20 84 49 7
AMP PEAK 17(17Q12) WILD-TYPE 195 163 83 15

Figure S93.  Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 0.00855 (Fisher's exact test), Q value = 0.022

Table S94.  Gene #17: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
AMP PEAK 17(17Q12) MUTATED 28 46 28
AMP PEAK 17(17Q12) WILD-TYPE 89 83 116

Figure S94.  Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.0494 (Fisher's exact test), Q value = 0.099

Table S95.  Gene #17: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 86
AMP PEAK 17(17Q12) MUTATED 59 32 28
AMP PEAK 17(17Q12) WILD-TYPE 169 136 58

Figure S95.  Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00022

Table S96.  Gene #17: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
AMP PEAK 17(17Q12) MUTATED 63 22 24 50
AMP PEAK 17(17Q12) WILD-TYPE 93 106 107 148

Figure S96.  Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S97.  Gene #17: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
AMP PEAK 17(17Q12) MUTATED 30 20 5 13 28 50 13
AMP PEAK 17(17Q12) WILD-TYPE 50 66 59 44 62 88 85

Figure S97.  Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.035

Table S98.  Gene #17: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
AMP PEAK 17(17Q12) MUTATED 15 17 5 32 8 16 15 8 22
AMP PEAK 17(17Q12) WILD-TYPE 34 57 24 54 69 38 42 24 59

Figure S98.  Get High-res Image Gene #17: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q24.1' versus 'MRNA_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 0.067

Table S99.  Gene #18: 'amp_17q24.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
AMP PEAK 18(17Q24.1) MUTATED 5 20 19 7
AMP PEAK 18(17Q24.1) WILD-TYPE 40 43 46 36

Figure S99.  Get High-res Image Gene #18: 'amp_17q24.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q24.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0123 (Fisher's exact test), Q value = 0.03

Table S100.  Gene #18: 'amp_17q24.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
AMP PEAK 18(17Q24.1) MUTATED 5 28 18
AMP PEAK 18(17Q24.1) WILD-TYPE 45 61 59

Figure S100.  Get High-res Image Gene #18: 'amp_17q24.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S101.  Gene #18: 'amp_17q24.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
AMP PEAK 18(17Q24.1) MUTATED 19 81 42 2
AMP PEAK 18(17Q24.1) WILD-TYPE 196 166 90 20

Figure S101.  Get High-res Image Gene #18: 'amp_17q24.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q24.1' versus 'METHLYATION_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0011

Table S102.  Gene #18: 'amp_17q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
AMP PEAK 18(17Q24.1) MUTATED 21 47 25
AMP PEAK 18(17Q24.1) WILD-TYPE 96 82 119

Figure S102.  Get High-res Image Gene #18: 'amp_17q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q24.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S103.  Gene #18: 'amp_17q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
AMP PEAK 18(17Q24.1) MUTATED 59 21 19 44
AMP PEAK 18(17Q24.1) WILD-TYPE 97 107 112 154

Figure S103.  Get High-res Image Gene #18: 'amp_17q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S104.  Gene #18: 'amp_17q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
AMP PEAK 18(17Q24.1) MUTATED 29 20 4 11 24 43 12
AMP PEAK 18(17Q24.1) WILD-TYPE 51 66 60 46 66 95 86

Figure S104.  Get High-res Image Gene #18: 'amp_17q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00577 (Fisher's exact test), Q value = 0.016

Table S105.  Gene #18: 'amp_17q24.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
AMP PEAK 18(17Q24.1) MUTATED 14 13 3 29 7 14 14 6 22
AMP PEAK 18(17Q24.1) WILD-TYPE 35 61 26 57 70 40 43 26 59

Figure S105.  Get High-res Image Gene #18: 'amp_17q24.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MRNA_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.038

Table S106.  Gene #19: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
AMP PEAK 19(19Q12) MUTATED 6 22 9 8
AMP PEAK 19(19Q12) WILD-TYPE 39 41 56 35

Figure S106.  Get High-res Image Gene #19: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00253 (Fisher's exact test), Q value = 0.0073

Table S107.  Gene #19: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
AMP PEAK 19(19Q12) MUTATED 4 28 13
AMP PEAK 19(19Q12) WILD-TYPE 46 61 64

Figure S107.  Get High-res Image Gene #19: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S108.  Gene #19: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
AMP PEAK 19(19Q12) MUTATED 21 81 29 8
AMP PEAK 19(19Q12) WILD-TYPE 194 166 103 14

Figure S108.  Get High-res Image Gene #19: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q12' versus 'RPPA_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.038

Table S109.  Gene #19: 'amp_19q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 197 177
AMP PEAK 19(19Q12) MUTATED 32 48 28
AMP PEAK 19(19Q12) WILD-TYPE 76 149 149

Figure S109.  Get High-res Image Gene #19: 'amp_19q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 0.0404 (Fisher's exact test), Q value = 0.084

Table S110.  Gene #19: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
AMP PEAK 19(19Q12) MUTATED 48 27 27 36
AMP PEAK 19(19Q12) WILD-TYPE 108 101 104 162

Figure S110.  Get High-res Image Gene #19: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00933 (Fisher's exact test), Q value = 0.024

Table S111.  Gene #19: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
AMP PEAK 19(19Q12) MUTATED 17 24 6 16 27 34 14
AMP PEAK 19(19Q12) WILD-TYPE 63 62 58 41 63 104 84

Figure S111.  Get High-res Image Gene #19: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0247 (Fisher's exact test), Q value = 0.056

Table S112.  Gene #19: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
AMP PEAK 19(19Q12) MUTATED 15 17 6 17 7 11 11 13 20
AMP PEAK 19(19Q12) WILD-TYPE 34 57 23 69 70 43 46 19 61

Figure S112.  Get High-res Image Gene #19: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20p12.1' versus 'MRNA_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.04

Table S113.  Gene #20: 'amp_20p12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
AMP PEAK 20(20P12.1) MUTATED 14 32 39 17
AMP PEAK 20(20P12.1) WILD-TYPE 31 31 26 26

Figure S113.  Get High-res Image Gene #20: 'amp_20p12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20p12.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00262 (Fisher's exact test), Q value = 0.0075

Table S114.  Gene #20: 'amp_20p12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
AMP PEAK 20(20P12.1) MUTATED 13 47 42
AMP PEAK 20(20P12.1) WILD-TYPE 37 42 35

Figure S114.  Get High-res Image Gene #20: 'amp_20p12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S115.  Gene #20: 'amp_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
AMP PEAK 20(20P12.1) MUTATED 70 125 62 21
AMP PEAK 20(20P12.1) WILD-TYPE 145 122 70 1

Figure S115.  Get High-res Image Gene #20: 'amp_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p12.1' versus 'RPPA_CNMF'

P value = 0.00201 (Fisher's exact test), Q value = 0.006

Table S116.  Gene #20: 'amp_20p12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 197 177
AMP PEAK 20(20P12.1) MUTATED 62 82 64
AMP PEAK 20(20P12.1) WILD-TYPE 46 115 113

Figure S116.  Get High-res Image Gene #20: 'amp_20p12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.00083

Table S117.  Gene #20: 'amp_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
AMP PEAK 20(20P12.1) MUTATED 39 38 15 33 40 76 35
AMP PEAK 20(20P12.1) WILD-TYPE 41 48 49 24 50 62 63

Figure S117.  Get High-res Image Gene #20: 'amp_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S118.  Gene #20: 'amp_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
AMP PEAK 20(20P12.1) MUTATED 20 32 13 39 15 28 30 14 52
AMP PEAK 20(20P12.1) WILD-TYPE 29 42 16 47 62 26 27 18 29

Figure S118.  Get High-res Image Gene #20: 'amp_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20p12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0385 (Fisher's exact test), Q value = 0.081

Table S119.  Gene #20: 'amp_20p12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
AMP PEAK 20(20P12.1) MUTATED 18 24 17 5
AMP PEAK 20(20P12.1) WILD-TYPE 17 16 21 17

Figure S119.  Get High-res Image Gene #20: 'amp_20p12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20p11.21' versus 'MRNA_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00058

Table S120.  Gene #21: 'amp_20p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
AMP PEAK 21(20P11.21) MUTATED 16 44 46 19
AMP PEAK 21(20P11.21) WILD-TYPE 29 19 19 24

Figure S120.  Get High-res Image Gene #21: 'amp_20p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20p11.21' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S121.  Gene #21: 'amp_20p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
AMP PEAK 21(20P11.21) MUTATED 14 62 49
AMP PEAK 21(20P11.21) WILD-TYPE 36 27 28

Figure S121.  Get High-res Image Gene #21: 'amp_20p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S122.  Gene #21: 'amp_20p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
AMP PEAK 21(20P11.21) MUTATED 74 185 82 22
AMP PEAK 21(20P11.21) WILD-TYPE 141 62 50 0

Figure S122.  Get High-res Image Gene #21: 'amp_20p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p11.21' versus 'METHLYATION_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.0027

Table S123.  Gene #21: 'amp_20p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
AMP PEAK 21(20P11.21) MUTATED 64 94 75
AMP PEAK 21(20P11.21) WILD-TYPE 53 35 69

Figure S123.  Get High-res Image Gene #21: 'amp_20p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20p11.21' versus 'RPPA_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.036

Table S124.  Gene #21: 'amp_20p11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 197 177
AMP PEAK 21(20P11.21) MUTATED 73 115 89
AMP PEAK 21(20P11.21) WILD-TYPE 35 82 88

Figure S124.  Get High-res Image Gene #21: 'amp_20p11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20p11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S125.  Gene #21: 'amp_20p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
AMP PEAK 21(20P11.21) MUTATED 121 56 70 113
AMP PEAK 21(20P11.21) WILD-TYPE 35 72 61 85

Figure S125.  Get High-res Image Gene #21: 'amp_20p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S126.  Gene #21: 'amp_20p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
AMP PEAK 21(20P11.21) MUTATED 56 51 17 40 61 99 36
AMP PEAK 21(20P11.21) WILD-TYPE 24 35 47 17 29 39 62

Figure S126.  Get High-res Image Gene #21: 'amp_20p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20p11.21' versus 'MIRSEQ_CNMF'

P value = 0.0323 (Fisher's exact test), Q value = 0.071

Table S127.  Gene #21: 'amp_20p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
AMP PEAK 21(20P11.21) MUTATED 93 61 57 104
AMP PEAK 21(20P11.21) WILD-TYPE 60 34 29 101

Figure S127.  Get High-res Image Gene #21: 'amp_20p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S128.  Gene #21: 'amp_20p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
AMP PEAK 21(20P11.21) MUTATED 28 41 19 58 18 38 38 15 60
AMP PEAK 21(20P11.21) WILD-TYPE 21 33 10 28 59 16 19 17 21

Figure S128.  Get High-res Image Gene #21: 'amp_20p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S129.  Gene #22: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
AMP PEAK 22(20Q11.21) MUTATED 19 61 59 25
AMP PEAK 22(20Q11.21) WILD-TYPE 26 2 6 18

Figure S129.  Get High-res Image Gene #22: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q11.21' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S130.  Gene #22: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
AMP PEAK 22(20Q11.21) MUTATED 15 86 63
AMP PEAK 22(20Q11.21) WILD-TYPE 35 3 14

Figure S130.  Get High-res Image Gene #22: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S131.  Gene #22: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
AMP PEAK 22(20Q11.21) MUTATED 92 245 110 22
AMP PEAK 22(20Q11.21) WILD-TYPE 123 2 22 0

Figure S131.  Get High-res Image Gene #22: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S132.  Gene #22: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
AMP PEAK 22(20Q11.21) MUTATED 83 128 88
AMP PEAK 22(20Q11.21) WILD-TYPE 34 1 56

Figure S132.  Get High-res Image Gene #22: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'RPPA_CNMF'

P value = 0.0338 (Fisher's exact test), Q value = 0.073

Table S133.  Gene #22: 'amp_20q11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 197 177
AMP PEAK 22(20Q11.21) MUTATED 86 157 122
AMP PEAK 22(20Q11.21) WILD-TYPE 22 40 55

Figure S133.  Get High-res Image Gene #22: 'amp_20q11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S134.  Gene #22: 'amp_20q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
AMP PEAK 22(20Q11.21) MUTATED 152 74 93 147
AMP PEAK 22(20Q11.21) WILD-TYPE 4 54 38 51

Figure S134.  Get High-res Image Gene #22: 'amp_20q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S135.  Gene #22: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
AMP PEAK 22(20Q11.21) MUTATED 74 63 17 50 84 132 46
AMP PEAK 22(20Q11.21) WILD-TYPE 6 23 47 7 6 6 52

Figure S135.  Get High-res Image Gene #22: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S136.  Gene #22: 'amp_20q11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
AMP PEAK 22(20Q11.21) MUTATED 111 78 83 137
AMP PEAK 22(20Q11.21) WILD-TYPE 42 17 3 68

Figure S136.  Get High-res Image Gene #22: 'amp_20q11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S137.  Gene #22: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
AMP PEAK 22(20Q11.21) MUTATED 36 56 20 74 28 48 51 20 76
AMP PEAK 22(20Q11.21) WILD-TYPE 13 18 9 12 49 6 6 12 5

Figure S137.  Get High-res Image Gene #22: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00123 (Fisher's exact test), Q value = 0.0038

Table S138.  Gene #22: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
AMP PEAK 22(20Q11.21) MUTATED 28 37 35 12
AMP PEAK 22(20Q11.21) WILD-TYPE 7 3 3 10

Figure S138.  Get High-res Image Gene #22: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S139.  Gene #23: 'amp_20q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
AMP PEAK 23(20Q12) MUTATED 18 61 59 24
AMP PEAK 23(20Q12) WILD-TYPE 27 2 6 19

Figure S139.  Get High-res Image Gene #23: 'amp_20q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S140.  Gene #23: 'amp_20q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
AMP PEAK 23(20Q12) MUTATED 14 86 62
AMP PEAK 23(20Q12) WILD-TYPE 36 3 15

Figure S140.  Get High-res Image Gene #23: 'amp_20q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S141.  Gene #23: 'amp_20q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
AMP PEAK 23(20Q12) MUTATED 91 245 113 22
AMP PEAK 23(20Q12) WILD-TYPE 124 2 19 0

Figure S141.  Get High-res Image Gene #23: 'amp_20q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S142.  Gene #23: 'amp_20q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
AMP PEAK 23(20Q12) MUTATED 84 128 91
AMP PEAK 23(20Q12) WILD-TYPE 33 1 53

Figure S142.  Get High-res Image Gene #23: 'amp_20q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q12' versus 'RPPA_CNMF'

P value = 0.0452 (Fisher's exact test), Q value = 0.092

Table S143.  Gene #23: 'amp_20q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 197 177
AMP PEAK 23(20Q12) MUTATED 85 158 123
AMP PEAK 23(20Q12) WILD-TYPE 23 39 54

Figure S143.  Get High-res Image Gene #23: 'amp_20q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S144.  Gene #23: 'amp_20q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
AMP PEAK 23(20Q12) MUTATED 152 75 95 146
AMP PEAK 23(20Q12) WILD-TYPE 4 53 36 52

Figure S144.  Get High-res Image Gene #23: 'amp_20q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S145.  Gene #23: 'amp_20q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
AMP PEAK 23(20Q12) MUTATED 74 64 19 50 85 132 44
AMP PEAK 23(20Q12) WILD-TYPE 6 22 45 7 5 6 54

Figure S145.  Get High-res Image Gene #23: 'amp_20q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S146.  Gene #23: 'amp_20q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
AMP PEAK 23(20Q12) MUTATED 113 79 83 136
AMP PEAK 23(20Q12) WILD-TYPE 40 16 3 69

Figure S146.  Get High-res Image Gene #23: 'amp_20q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S147.  Gene #23: 'amp_20q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
AMP PEAK 23(20Q12) MUTATED 36 57 20 75 28 48 51 20 76
AMP PEAK 23(20Q12) WILD-TYPE 13 17 9 11 49 6 6 12 5

Figure S147.  Get High-res Image Gene #23: 'amp_20q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00055

Table S148.  Gene #23: 'amp_20q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
AMP PEAK 23(20Q12) MUTATED 29 38 36 12
AMP PEAK 23(20Q12) WILD-TYPE 6 2 2 10

Figure S148.  Get High-res Image Gene #23: 'amp_20q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S149.  Gene #24: 'amp_20q13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
AMP PEAK 24(20Q13.12) MUTATED 19 61 59 25
AMP PEAK 24(20Q13.12) WILD-TYPE 26 2 6 18

Figure S149.  Get High-res Image Gene #24: 'amp_20q13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q13.12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S150.  Gene #24: 'amp_20q13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
AMP PEAK 24(20Q13.12) MUTATED 15 86 63
AMP PEAK 24(20Q13.12) WILD-TYPE 35 3 14

Figure S150.  Get High-res Image Gene #24: 'amp_20q13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q13.12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S151.  Gene #24: 'amp_20q13.12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
AMP PEAK 24(20Q13.12) MUTATED 93 245 113 22
AMP PEAK 24(20Q13.12) WILD-TYPE 122 2 19 0

Figure S151.  Get High-res Image Gene #24: 'amp_20q13.12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S152.  Gene #24: 'amp_20q13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
AMP PEAK 24(20Q13.12) MUTATED 84 128 91
AMP PEAK 24(20Q13.12) WILD-TYPE 33 1 53

Figure S152.  Get High-res Image Gene #24: 'amp_20q13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.12' versus 'RPPA_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 0.056

Table S153.  Gene #24: 'amp_20q13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 197 177
AMP PEAK 24(20Q13.12) MUTATED 85 160 123
AMP PEAK 24(20Q13.12) WILD-TYPE 23 37 54

Figure S153.  Get High-res Image Gene #24: 'amp_20q13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q13.12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S154.  Gene #24: 'amp_20q13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
AMP PEAK 24(20Q13.12) MUTATED 152 75 95 148
AMP PEAK 24(20Q13.12) WILD-TYPE 4 53 36 50

Figure S154.  Get High-res Image Gene #24: 'amp_20q13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q13.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S155.  Gene #24: 'amp_20q13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
AMP PEAK 24(20Q13.12) MUTATED 74 64 19 50 85 132 46
AMP PEAK 24(20Q13.12) WILD-TYPE 6 22 45 7 5 6 52

Figure S155.  Get High-res Image Gene #24: 'amp_20q13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S156.  Gene #24: 'amp_20q13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
AMP PEAK 24(20Q13.12) MUTATED 114 79 83 138
AMP PEAK 24(20Q13.12) WILD-TYPE 39 16 3 67

Figure S156.  Get High-res Image Gene #24: 'amp_20q13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q13.12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S157.  Gene #24: 'amp_20q13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
AMP PEAK 24(20Q13.12) MUTATED 36 57 21 75 30 48 51 20 76
AMP PEAK 24(20Q13.12) WILD-TYPE 13 17 8 11 47 6 6 12 5

Figure S157.  Get High-res Image Gene #24: 'amp_20q13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00061

Table S158.  Gene #24: 'amp_20q13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
AMP PEAK 24(20Q13.12) MUTATED 29 38 36 12
AMP PEAK 24(20Q13.12) WILD-TYPE 6 2 2 10

Figure S158.  Get High-res Image Gene #24: 'amp_20q13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00022

Table S159.  Gene #25: 'del_1p36.11' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
DEL PEAK 1(1P36.11) MUTATED 14 37 34 8
DEL PEAK 1(1P36.11) WILD-TYPE 31 26 31 35

Figure S159.  Get High-res Image Gene #25: '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 = 5.2e-05

Table S160.  Gene #25: 'del_1p36.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 1(1P36.11) MUTATED 12 54 27
DEL PEAK 1(1P36.11) WILD-TYPE 38 35 50

Figure S160.  Get High-res Image Gene #25: '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 = 5.2e-05

Table S161.  Gene #25: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 1(1P36.11) MUTATED 34 131 63 16
DEL PEAK 1(1P36.11) WILD-TYPE 181 116 69 6

Figure S161.  Get High-res Image Gene #25: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00044

Table S162.  Gene #25: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 1(1P36.11) MUTATED 42 68 40
DEL PEAK 1(1P36.11) WILD-TYPE 75 61 104

Figure S162.  Get High-res Image Gene #25: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.11' versus 'RPPA_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.044

Table S163.  Gene #25: 'del_1p36.11' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 197 177
DEL PEAK 1(1P36.11) MUTATED 42 89 55
DEL PEAK 1(1P36.11) WILD-TYPE 66 108 122

Figure S163.  Get High-res Image Gene #25: 'del_1p36.11' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S164.  Gene #25: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 1(1P36.11) MUTATED 81 28 54 80
DEL PEAK 1(1P36.11) WILD-TYPE 75 100 77 118

Figure S164.  Get High-res Image Gene #25: '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 = 5.2e-05

Table S165.  Gene #25: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 1(1P36.11) MUTATED 36 30 6 22 48 72 29
DEL PEAK 1(1P36.11) WILD-TYPE 44 56 58 35 42 66 69

Figure S165.  Get High-res Image Gene #25: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00014

Table S166.  Gene #25: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 1(1P36.11) MUTATED 20 28 8 38 12 32 23 12 41
DEL PEAK 1(1P36.11) WILD-TYPE 29 46 21 48 65 22 34 20 40

Figure S166.  Get High-res Image Gene #25: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p33' versus 'MRNA_CNMF'

P value = 0.0385 (Fisher's exact test), Q value = 0.081

Table S167.  Gene #26: 'del_1p33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
DEL PEAK 2(1P33) MUTATED 12 21 22 5
DEL PEAK 2(1P33) WILD-TYPE 33 42 43 38

Figure S167.  Get High-res Image Gene #26: 'del_1p33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p33' versus 'MRNA_CHIERARCHICAL'

P value = 0.00229 (Fisher's exact test), Q value = 0.0067

Table S168.  Gene #26: 'del_1p33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 2(1P33) MUTATED 10 36 14
DEL PEAK 2(1P33) WILD-TYPE 40 53 63

Figure S168.  Get High-res Image Gene #26: 'del_1p33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S169.  Gene #26: 'del_1p33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 2(1P33) MUTATED 21 103 38 14
DEL PEAK 2(1P33) WILD-TYPE 194 144 94 8

Figure S169.  Get High-res Image Gene #26: 'del_1p33' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p33' versus 'METHLYATION_CNMF'

P value = 0.00738 (Fisher's exact test), Q value = 0.02

Table S170.  Gene #26: 'del_1p33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 2(1P33) MUTATED 36 49 30
DEL PEAK 2(1P33) WILD-TYPE 81 80 114

Figure S170.  Get High-res Image Gene #26: 'del_1p33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p33' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00022

Table S171.  Gene #26: 'del_1p33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 2(1P33) MUTATED 64 21 39 51
DEL PEAK 2(1P33) WILD-TYPE 92 107 92 147

Figure S171.  Get High-res Image Gene #26: 'del_1p33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0014

Table S172.  Gene #26: 'del_1p33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 2(1P33) MUTATED 29 21 7 18 34 47 19
DEL PEAK 2(1P33) WILD-TYPE 51 65 57 39 56 91 79

Figure S172.  Get High-res Image Gene #26: 'del_1p33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 0.059

Table S173.  Gene #26: 'del_1p33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 2(1P33) MUTATED 15 20 5 25 11 24 18 9 25
DEL PEAK 2(1P33) WILD-TYPE 34 54 24 61 66 30 39 23 56

Figure S173.  Get High-res Image Gene #26: 'del_1p33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p13.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0338 (Fisher's exact test), Q value = 0.073

Table S174.  Gene #27: 'del_1p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 3(1P13.2) MUTATED 10 32 15
DEL PEAK 3(1P13.2) WILD-TYPE 40 57 62

Figure S174.  Get High-res Image Gene #27: 'del_1p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S175.  Gene #27: 'del_1p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 3(1P13.2) MUTATED 25 103 35 13
DEL PEAK 3(1P13.2) WILD-TYPE 190 144 97 9

Figure S175.  Get High-res Image Gene #27: 'del_1p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p13.2' versus 'METHLYATION_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.028

Table S176.  Gene #27: 'del_1p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 3(1P13.2) MUTATED 33 51 33
DEL PEAK 3(1P13.2) WILD-TYPE 84 78 111

Figure S176.  Get High-res Image Gene #27: 'del_1p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p13.2' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00077

Table S177.  Gene #27: 'del_1p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 3(1P13.2) MUTATED 59 20 43 53
DEL PEAK 3(1P13.2) WILD-TYPE 97 108 88 145

Figure S177.  Get High-res Image Gene #27: 'del_1p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.001

Table S178.  Gene #27: 'del_1p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 3(1P13.2) MUTATED 30 20 8 15 37 46 19
DEL PEAK 3(1P13.2) WILD-TYPE 50 66 56 42 53 92 79

Figure S178.  Get High-res Image Gene #27: 'del_1p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.2' versus 'MIRSEQ_CNMF'

P value = 0.0339 (Fisher's exact test), Q value = 0.073

Table S179.  Gene #27: 'del_1p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
DEL PEAK 3(1P13.2) MUTATED 39 35 29 46
DEL PEAK 3(1P13.2) WILD-TYPE 114 60 57 159

Figure S179.  Get High-res Image Gene #27: 'del_1p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p13.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S180.  Gene #27: 'del_1p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 3(1P13.2) MUTATED 15 18 6 26 8 22 19 9 26
DEL PEAK 3(1P13.2) WILD-TYPE 34 56 23 60 69 32 38 23 55

Figure S180.  Get High-res Image Gene #27: 'del_1p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2p12' versus 'CN_CNMF'

P value = 0.00219 (Fisher's exact test), Q value = 0.0065

Table S181.  Gene #28: 'del_2p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 4(2P12) MUTATED 1 10 10 0
DEL PEAK 4(2P12) WILD-TYPE 214 237 122 22

Figure S181.  Get High-res Image Gene #28: 'del_2p12' versus Molecular Subtype #3: 'CN_CNMF'

'del_2p12' versus 'METHLYATION_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.026

Table S182.  Gene #28: 'del_2p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 4(2P12) MUTATED 0 6 1
DEL PEAK 4(2P12) WILD-TYPE 117 123 143

Figure S182.  Get High-res Image Gene #28: 'del_2p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2p12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00179 (Fisher's exact test), Q value = 0.0054

Table S183.  Gene #28: 'del_2p12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 86
DEL PEAK 4(2P12) MUTATED 6 2 9
DEL PEAK 4(2P12) WILD-TYPE 222 166 77

Figure S183.  Get High-res Image Gene #28: 'del_2p12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_2p12' versus 'MRNASEQ_CNMF'

P value = 0.00937 (Fisher's exact test), Q value = 0.024

Table S184.  Gene #28: 'del_2p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 4(2P12) MUTATED 4 1 2 14
DEL PEAK 4(2P12) WILD-TYPE 152 127 129 184

Figure S184.  Get High-res Image Gene #28: 'del_2p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.013 (Fisher's exact test), Q value = 0.032

Table S185.  Gene #28: 'del_2p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 4(2P12) MUTATED 0 1 0 2 2 8 8
DEL PEAK 4(2P12) WILD-TYPE 80 85 64 55 88 130 90

Figure S185.  Get High-res Image Gene #28: 'del_2p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2p12' versus 'MIRSEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0012

Table S186.  Gene #28: 'del_2p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
DEL PEAK 4(2P12) MUTATED 1 0 8 11
DEL PEAK 4(2P12) WILD-TYPE 152 95 78 194

Figure S186.  Get High-res Image Gene #28: 'del_2p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'CN_CNMF'

P value = 0.0331 (Fisher's exact test), Q value = 0.072

Table S187.  Gene #29: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 5(2Q22.1) MUTATED 5 19 9 2
DEL PEAK 5(2Q22.1) WILD-TYPE 210 228 123 20

Figure S187.  Get High-res Image Gene #29: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q22.1' versus 'MIRSEQ_CNMF'

P value = 0.046 (Fisher's exact test), Q value = 0.094

Table S188.  Gene #29: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
DEL PEAK 5(2Q22.1) MUTATED 4 3 9 14
DEL PEAK 5(2Q22.1) WILD-TYPE 149 92 77 191

Figure S188.  Get High-res Image Gene #29: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p26.3' versus 'CN_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0019

Table S189.  Gene #30: 'del_3p26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 6(3P26.3) MUTATED 18 51 18 6
DEL PEAK 6(3P26.3) WILD-TYPE 197 196 114 16

Figure S189.  Get High-res Image Gene #30: 'del_3p26.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00205 (Fisher's exact test), Q value = 0.0061

Table S190.  Gene #33: 'del_4p16.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 9(4P16.1) MUTATED 11 43 21
DEL PEAK 9(4P16.1) WILD-TYPE 39 46 56

Figure S190.  Get High-res Image Gene #33: 'del_4p16.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4p16.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S191.  Gene #33: 'del_4p16.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 9(4P16.1) MUTATED 23 111 52 17
DEL PEAK 9(4P16.1) WILD-TYPE 192 136 80 5

Figure S191.  Get High-res Image Gene #33: 'del_4p16.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.1' versus 'METHLYATION_CNMF'

P value = 0.00508 (Fisher's exact test), Q value = 0.014

Table S192.  Gene #33: 'del_4p16.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 9(4P16.1) MUTATED 36 55 35
DEL PEAK 9(4P16.1) WILD-TYPE 81 74 109

Figure S192.  Get High-res Image Gene #33: 'del_4p16.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p16.1' versus 'MRNASEQ_CNMF'

P value = 0.00865 (Fisher's exact test), Q value = 0.023

Table S193.  Gene #33: 'del_4p16.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 9(4P16.1) MUTATED 60 27 48 67
DEL PEAK 9(4P16.1) WILD-TYPE 96 101 83 131

Figure S193.  Get High-res Image Gene #33: 'del_4p16.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p16.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S194.  Gene #33: 'del_4p16.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 9(4P16.1) MUTATED 29 25 5 19 41 58 25
DEL PEAK 9(4P16.1) WILD-TYPE 51 61 59 38 49 80 73

Figure S194.  Get High-res Image Gene #33: 'del_4p16.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.028

Table S195.  Gene #33: 'del_4p16.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 9(4P16.1) MUTATED 17 18 9 33 14 14 21 12 37
DEL PEAK 9(4P16.1) WILD-TYPE 32 56 20 53 63 40 36 20 44

Figure S195.  Get High-res Image Gene #33: 'del_4p16.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MRNA_CNMF'

P value = 0.00589 (Fisher's exact test), Q value = 0.016

Table S196.  Gene #34: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
DEL PEAK 10(4Q22.1) MUTATED 14 27 30 7
DEL PEAK 10(4Q22.1) WILD-TYPE 31 36 35 36

Figure S196.  Get High-res Image Gene #34: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00444 (Fisher's exact test), Q value = 0.012

Table S197.  Gene #34: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 10(4Q22.1) MUTATED 11 43 24
DEL PEAK 10(4Q22.1) WILD-TYPE 39 46 53

Figure S197.  Get High-res Image Gene #34: '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 = 5.2e-05

Table S198.  Gene #34: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 10(4Q22.1) MUTATED 28 126 55 16
DEL PEAK 10(4Q22.1) WILD-TYPE 187 121 77 6

Figure S198.  Get High-res Image Gene #34: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.026

Table S199.  Gene #34: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 10(4Q22.1) MUTATED 47 59 41
DEL PEAK 10(4Q22.1) WILD-TYPE 70 70 103

Figure S199.  Get High-res Image Gene #34: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00487 (Fisher's exact test), Q value = 0.013

Table S200.  Gene #34: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 10(4Q22.1) MUTATED 69 31 49 75
DEL PEAK 10(4Q22.1) WILD-TYPE 87 97 82 123

Figure S200.  Get High-res Image Gene #34: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S201.  Gene #34: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 10(4Q22.1) MUTATED 36 25 8 27 40 61 27
DEL PEAK 10(4Q22.1) WILD-TYPE 44 61 56 30 50 77 71

Figure S201.  Get High-res Image Gene #34: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0013

Table S202.  Gene #34: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 10(4Q22.1) MUTATED 18 18 9 39 15 19 25 10 42
DEL PEAK 10(4Q22.1) WILD-TYPE 31 56 20 47 62 35 32 22 39

Figure S202.  Get High-res Image Gene #34: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MRNA_CNMF'

P value = 0.00884 (Fisher's exact test), Q value = 0.023

Table S203.  Gene #35: 'del_4q35.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
DEL PEAK 11(4Q35.1) MUTATED 13 29 29 8
DEL PEAK 11(4Q35.1) WILD-TYPE 32 34 36 35

Figure S203.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q35.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00854 (Fisher's exact test), Q value = 0.022

Table S204.  Gene #35: 'del_4q35.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 11(4Q35.1) MUTATED 12 43 24
DEL PEAK 11(4Q35.1) WILD-TYPE 38 46 53

Figure S204.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q35.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S205.  Gene #35: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 11(4Q35.1) MUTATED 26 129 61 17
DEL PEAK 11(4Q35.1) WILD-TYPE 189 118 71 5

Figure S205.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q35.1' versus 'METHLYATION_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.026

Table S206.  Gene #35: 'del_4q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 11(4Q35.1) MUTATED 48 60 42
DEL PEAK 11(4Q35.1) WILD-TYPE 69 69 102

Figure S206.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q35.1' versus 'MRNASEQ_CNMF'

P value = 0.00453 (Fisher's exact test), Q value = 0.013

Table S207.  Gene #35: 'del_4q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 11(4Q35.1) MUTATED 69 32 55 76
DEL PEAK 11(4Q35.1) WILD-TYPE 87 96 76 122

Figure S207.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S208.  Gene #35: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 11(4Q35.1) MUTATED 38 26 8 26 44 61 29
DEL PEAK 11(4Q35.1) WILD-TYPE 42 60 56 31 46 77 69

Figure S208.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MIRSEQ_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.077

Table S209.  Gene #35: 'del_4q35.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
DEL PEAK 11(4Q35.1) MUTATED 55 34 44 68
DEL PEAK 11(4Q35.1) WILD-TYPE 98 61 42 137

Figure S209.  Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q12.1' versus 'MRNA_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0011

Table S210.  Gene #36: 'del_5q12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
DEL PEAK 12(5Q12.1) MUTATED 10 21 19 1
DEL PEAK 12(5Q12.1) WILD-TYPE 35 42 46 42

Figure S210.  Get High-res Image Gene #36: 'del_5q12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q12.1' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S211.  Gene #36: 'del_5q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 12(5Q12.1) MUTATED 9 36 6
DEL PEAK 12(5Q12.1) WILD-TYPE 41 53 71

Figure S211.  Get High-res Image Gene #36: 'del_5q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S212.  Gene #36: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 12(5Q12.1) MUTATED 11 74 61 13
DEL PEAK 12(5Q12.1) WILD-TYPE 204 173 71 9

Figure S212.  Get High-res Image Gene #36: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 0.00262 (Fisher's exact test), Q value = 0.0075

Table S213.  Gene #36: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 12(5Q12.1) MUTATED 30 50 29
DEL PEAK 12(5Q12.1) WILD-TYPE 87 79 115

Figure S213.  Get High-res Image Gene #36: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q12.1' versus 'MRNASEQ_CNMF'

P value = 0.0307 (Fisher's exact test), Q value = 0.067

Table S214.  Gene #36: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 12(5Q12.1) MUTATED 49 22 39 49
DEL PEAK 12(5Q12.1) WILD-TYPE 107 106 92 149

Figure S214.  Get High-res Image Gene #36: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S215.  Gene #36: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 12(5Q12.1) MUTATED 25 19 4 21 32 43 15
DEL PEAK 12(5Q12.1) WILD-TYPE 55 67 60 36 58 95 83

Figure S215.  Get High-res Image Gene #36: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00061

Table S216.  Gene #36: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 12(5Q12.1) MUTATED 12 17 12 31 8 5 16 9 27
DEL PEAK 12(5Q12.1) WILD-TYPE 37 57 17 55 69 49 41 23 54

Figure S216.  Get High-res Image Gene #36: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q21.2' versus 'MRNA_CNMF'

P value = 0.0289 (Fisher's exact test), Q value = 0.064

Table S217.  Gene #37: 'del_5q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
DEL PEAK 13(5Q21.2) MUTATED 10 23 23 6
DEL PEAK 13(5Q21.2) WILD-TYPE 35 40 42 37

Figure S217.  Get High-res Image Gene #37: 'del_5q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q21.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00082 (Fisher's exact test), Q value = 0.0026

Table S218.  Gene #37: 'del_5q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 13(5Q21.2) MUTATED 10 38 14
DEL PEAK 13(5Q21.2) WILD-TYPE 40 51 63

Figure S218.  Get High-res Image Gene #37: 'del_5q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S219.  Gene #37: 'del_5q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 13(5Q21.2) MUTATED 17 84 72 14
DEL PEAK 13(5Q21.2) WILD-TYPE 198 163 60 8

Figure S219.  Get High-res Image Gene #37: 'del_5q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q21.2' versus 'METHLYATION_CNMF'

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

Table S220.  Gene #37: 'del_5q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 13(5Q21.2) MUTATED 34 54 37
DEL PEAK 13(5Q21.2) WILD-TYPE 83 75 107

Figure S220.  Get High-res Image Gene #37: 'del_5q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00161 (Fisher's exact test), Q value = 0.0049

Table S221.  Gene #37: 'del_5q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 13(5Q21.2) MUTATED 28 24 8 20 34 51 21
DEL PEAK 13(5Q21.2) WILD-TYPE 52 62 56 37 56 87 77

Figure S221.  Get High-res Image Gene #37: 'del_5q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00087 (Fisher's exact test), Q value = 0.0027

Table S222.  Gene #37: 'del_5q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 13(5Q21.2) MUTATED 15 18 13 34 10 11 21 13 29
DEL PEAK 13(5Q21.2) WILD-TYPE 34 56 16 52 67 43 36 19 52

Figure S222.  Get High-res Image Gene #37: 'del_5q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q22.2' versus 'MRNA_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 9e-04

Table S223.  Gene #38: 'del_5q22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
DEL PEAK 14(5Q22.2) MUTATED 9 24 25 3
DEL PEAK 14(5Q22.2) WILD-TYPE 36 39 40 40

Figure S223.  Get High-res Image Gene #38: 'del_5q22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q22.2' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00014

Table S224.  Gene #38: 'del_5q22.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 14(5Q22.2) MUTATED 9 40 12
DEL PEAK 14(5Q22.2) WILD-TYPE 41 49 65

Figure S224.  Get High-res Image Gene #38: 'del_5q22.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S225.  Gene #38: 'del_5q22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 14(5Q22.2) MUTATED 22 85 68 14
DEL PEAK 14(5Q22.2) WILD-TYPE 193 162 64 8

Figure S225.  Get High-res Image Gene #38: 'del_5q22.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q22.2' versus 'METHLYATION_CNMF'

P value = 0.0415 (Fisher's exact test), Q value = 0.086

Table S226.  Gene #38: 'del_5q22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 14(5Q22.2) MUTATED 36 53 39
DEL PEAK 14(5Q22.2) WILD-TYPE 81 76 105

Figure S226.  Get High-res Image Gene #38: 'del_5q22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00041

Table S227.  Gene #38: 'del_5q22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 14(5Q22.2) MUTATED 32 25 8 22 30 53 18
DEL PEAK 14(5Q22.2) WILD-TYPE 48 61 56 35 60 85 80

Figure S227.  Get High-res Image Gene #38: 'del_5q22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0015

Table S228.  Gene #38: 'del_5q22.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 14(5Q22.2) MUTATED 16 16 13 37 10 13 21 13 28
DEL PEAK 14(5Q22.2) WILD-TYPE 33 58 16 49 67 41 36 19 53

Figure S228.  Get High-res Image Gene #38: 'del_5q22.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q23.3' versus 'MRNA_CNMF'

P value = 0.00677 (Fisher's exact test), Q value = 0.018

Table S229.  Gene #39: 'del_5q23.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
DEL PEAK 15(5Q23.3) MUTATED 9 21 19 3
DEL PEAK 15(5Q23.3) WILD-TYPE 36 42 46 40

Figure S229.  Get High-res Image Gene #39: 'del_5q23.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q23.3' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00022

Table S230.  Gene #39: 'del_5q23.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 15(5Q23.3) MUTATED 9 35 8
DEL PEAK 15(5Q23.3) WILD-TYPE 41 54 69

Figure S230.  Get High-res Image Gene #39: 'del_5q23.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S231.  Gene #39: 'del_5q23.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 15(5Q23.3) MUTATED 10 72 67 12
DEL PEAK 15(5Q23.3) WILD-TYPE 205 175 65 10

Figure S231.  Get High-res Image Gene #39: 'del_5q23.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q23.3' versus 'METHLYATION_CNMF'

P value = 0.00303 (Fisher's exact test), Q value = 0.0087

Table S232.  Gene #39: 'del_5q23.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 15(5Q23.3) MUTATED 33 49 28
DEL PEAK 15(5Q23.3) WILD-TYPE 84 80 116

Figure S232.  Get High-res Image Gene #39: 'del_5q23.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q23.3' versus 'MRNASEQ_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.026

Table S233.  Gene #39: 'del_5q23.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 15(5Q23.3) MUTATED 54 22 35 50
DEL PEAK 15(5Q23.3) WILD-TYPE 102 106 96 148

Figure S233.  Get High-res Image Gene #39: 'del_5q23.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00058

Table S234.  Gene #39: 'del_5q23.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 15(5Q23.3) MUTATED 28 16 6 22 28 43 18
DEL PEAK 15(5Q23.3) WILD-TYPE 52 70 58 35 62 95 80

Figure S234.  Get High-res Image Gene #39: 'del_5q23.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00026

Table S235.  Gene #39: 'del_5q23.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 15(5Q23.3) MUTATED 13 16 11 36 8 6 18 10 23
DEL PEAK 15(5Q23.3) WILD-TYPE 36 58 18 50 69 48 39 22 58

Figure S235.  Get High-res Image Gene #39: 'del_5q23.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'RPPA_CNMF'

P value = 0.00188 (Fisher's exact test), Q value = 0.0056

Table S236.  Gene #41: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 197 177
DEL PEAK 17(6Q26) MUTATED 27 26 17
DEL PEAK 17(6Q26) WILD-TYPE 81 171 160

Figure S236.  Get High-res Image Gene #41: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_8p23.2' versus 'MRNA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 3e-04

Table S237.  Gene #43: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
DEL PEAK 19(8P23.2) MUTATED 17 42 37 11
DEL PEAK 19(8P23.2) WILD-TYPE 28 21 28 32

Figure S237.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p23.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S238.  Gene #43: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 19(8P23.2) MUTATED 14 59 34
DEL PEAK 19(8P23.2) WILD-TYPE 36 30 43

Figure S238.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S239.  Gene #43: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 19(8P23.2) MUTATED 23 152 105 10
DEL PEAK 19(8P23.2) WILD-TYPE 192 95 27 12

Figure S239.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S240.  Gene #43: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 19(8P23.2) MUTATED 48 83 51
DEL PEAK 19(8P23.2) WILD-TYPE 69 46 93

Figure S240.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00022

Table S241.  Gene #43: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 19(8P23.2) MUTATED 87 37 66 99
DEL PEAK 19(8P23.2) WILD-TYPE 69 91 65 99

Figure S241.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S242.  Gene #43: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 19(8P23.2) MUTATED 38 33 10 31 59 83 35
DEL PEAK 19(8P23.2) WILD-TYPE 42 53 54 26 31 55 63

Figure S242.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00092 (Fisher's exact test), Q value = 0.0029

Table S243.  Gene #43: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 19(8P23.2) MUTATED 20 33 11 52 21 27 32 13 46
DEL PEAK 19(8P23.2) WILD-TYPE 29 41 18 34 56 27 25 19 35

Figure S243.  Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p22' versus 'MRNA_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.001

Table S244.  Gene #44: 'del_8p22' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
DEL PEAK 20(8P22) MUTATED 16 40 40 13
DEL PEAK 20(8P22) WILD-TYPE 29 23 25 30

Figure S244.  Get High-res Image Gene #44: 'del_8p22' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p22' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S245.  Gene #44: 'del_8p22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 20(8P22) MUTATED 13 59 37
DEL PEAK 20(8P22) WILD-TYPE 37 30 40

Figure S245.  Get High-res Image Gene #44: 'del_8p22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S246.  Gene #44: 'del_8p22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 20(8P22) MUTATED 25 157 111 11
DEL PEAK 20(8P22) WILD-TYPE 190 90 21 11

Figure S246.  Get High-res Image Gene #44: 'del_8p22' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p22' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S247.  Gene #44: 'del_8p22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 20(8P22) MUTATED 51 87 56
DEL PEAK 20(8P22) WILD-TYPE 66 42 88

Figure S247.  Get High-res Image Gene #44: 'del_8p22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p22' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00051

Table S248.  Gene #44: 'del_8p22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 20(8P22) MUTATED 92 42 69 100
DEL PEAK 20(8P22) WILD-TYPE 64 86 62 98

Figure S248.  Get High-res Image Gene #44: 'del_8p22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S249.  Gene #44: 'del_8p22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 20(8P22) MUTATED 39 39 10 32 62 85 36
DEL PEAK 20(8P22) WILD-TYPE 41 47 54 25 28 53 62

Figure S249.  Get High-res Image Gene #44: 'del_8p22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00041

Table S250.  Gene #44: 'del_8p22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 20(8P22) MUTATED 20 36 15 55 20 28 33 13 48
DEL PEAK 20(8P22) WILD-TYPE 29 38 14 31 57 26 24 19 33

Figure S250.  Get High-res Image Gene #44: 'del_8p22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8q11.1' versus 'CN_CNMF'

P value = 0.00164 (Fisher's exact test), Q value = 0.005

Table S251.  Gene #45: 'del_8q11.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 21(8Q11.1) MUTATED 8 30 6 3
DEL PEAK 21(8Q11.1) WILD-TYPE 207 217 126 19

Figure S251.  Get High-res Image Gene #45: 'del_8q11.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00061

Table S252.  Gene #46: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 22(9P21.3) MUTATED 14 49 21 4
DEL PEAK 22(9P21.3) WILD-TYPE 201 198 111 18

Figure S252.  Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 0.0346 (Fisher's exact test), Q value = 0.074

Table S253.  Gene #46: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 22(9P21.3) MUTATED 18 27 14
DEL PEAK 22(9P21.3) WILD-TYPE 99 102 130

Figure S253.  Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 0.0387 (Fisher's exact test), Q value = 0.081

Table S254.  Gene #46: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 22(9P21.3) MUTATED 32 14 21 21
DEL PEAK 22(9P21.3) WILD-TYPE 124 114 110 177

Figure S254.  Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0424 (Fisher's exact test), Q value = 0.087

Table S255.  Gene #46: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 22(9P21.3) MUTATED 11 12 4 14 16 23 8
DEL PEAK 22(9P21.3) WILD-TYPE 69 74 60 43 74 115 90

Figure S255.  Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0327 (Fisher's exact test), Q value = 0.071

Table S256.  Gene #46: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 22(9P21.3) MUTATED 8 10 3 18 2 9 11 4 13
DEL PEAK 22(9P21.3) WILD-TYPE 41 64 26 68 75 45 46 28 68

Figure S256.  Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S257.  Gene #47: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 23(10P15.3) MUTATED 14 52 40 9
DEL PEAK 23(10P15.3) WILD-TYPE 201 195 92 13

Figure S257.  Get High-res Image Gene #47: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.077

Table S258.  Gene #47: 'del_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 23(10P15.3) MUTATED 23 34 20
DEL PEAK 23(10P15.3) WILD-TYPE 94 95 124

Figure S258.  Get High-res Image Gene #47: 'del_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 0.00962 (Fisher's exact test), Q value = 0.025

Table S259.  Gene #47: 'del_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 23(10P15.3) MUTATED 41 14 25 34
DEL PEAK 23(10P15.3) WILD-TYPE 115 114 106 164

Figure S259.  Get High-res Image Gene #47: 'del_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S260.  Gene #47: 'del_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 23(10P15.3) MUTATED 14 12 3 11 33 29 12
DEL PEAK 23(10P15.3) WILD-TYPE 66 74 61 46 57 109 86

Figure S260.  Get High-res Image Gene #47: 'del_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0484 (Fisher's exact test), Q value = 0.097

Table S261.  Gene #47: 'del_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
DEL PEAK 23(10P15.3) MUTATED 8 14 9 1
DEL PEAK 23(10P15.3) WILD-TYPE 27 26 29 21

Figure S261.  Get High-res Image Gene #47: 'del_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q21.1' versus 'MRNA_CNMF'

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

Table S262.  Gene #48: 'del_10q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
DEL PEAK 24(10Q21.1) MUTATED 6 14 23 5
DEL PEAK 24(10Q21.1) WILD-TYPE 39 49 42 38

Figure S262.  Get High-res Image Gene #48: 'del_10q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q21.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0381 (Fisher's exact test), Q value = 0.081

Table S263.  Gene #48: 'del_10q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 24(10Q21.1) MUTATED 6 27 15
DEL PEAK 24(10Q21.1) WILD-TYPE 44 62 62

Figure S263.  Get High-res Image Gene #48: 'del_10q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S264.  Gene #48: 'del_10q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 24(10Q21.1) MUTATED 15 70 45 9
DEL PEAK 24(10Q21.1) WILD-TYPE 200 177 87 13

Figure S264.  Get High-res Image Gene #48: 'del_10q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q21.1' versus 'METHLYATION_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.042

Table S265.  Gene #48: 'del_10q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 24(10Q21.1) MUTATED 21 41 28
DEL PEAK 24(10Q21.1) WILD-TYPE 96 88 116

Figure S265.  Get High-res Image Gene #48: 'del_10q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q21.1' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00041

Table S266.  Gene #48: 'del_10q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 24(10Q21.1) MUTATED 54 16 25 43
DEL PEAK 24(10Q21.1) WILD-TYPE 102 112 106 155

Figure S266.  Get High-res Image Gene #48: 'del_10q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.0013

Table S267.  Gene #48: 'del_10q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 24(10Q21.1) MUTATED 20 18 3 13 30 38 16
DEL PEAK 24(10Q21.1) WILD-TYPE 60 68 61 44 60 100 82

Figure S267.  Get High-res Image Gene #48: 'del_10q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S268.  Gene #49: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 25(10Q23.31) MUTATED 20 74 57 10
DEL PEAK 25(10Q23.31) WILD-TYPE 195 173 75 12

Figure S268.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.037

Table S269.  Gene #49: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 25(10Q23.31) MUTATED 25 48 36
DEL PEAK 25(10Q23.31) WILD-TYPE 92 81 108

Figure S269.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 0.00477 (Fisher's exact test), Q value = 0.013

Table S270.  Gene #49: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 25(10Q23.31) MUTATED 57 25 33 44
DEL PEAK 25(10Q23.31) WILD-TYPE 99 103 98 154

Figure S270.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00026

Table S271.  Gene #49: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 25(10Q23.31) MUTATED 27 21 4 13 38 33 23
DEL PEAK 25(10Q23.31) WILD-TYPE 53 65 60 44 52 105 75

Figure S271.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.028

Table S272.  Gene #49: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 25(10Q23.31) MUTATED 11 24 6 33 9 12 15 6 24
DEL PEAK 25(10Q23.31) WILD-TYPE 38 50 23 53 68 42 42 26 57

Figure S272.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S273.  Gene #50: 'del_10q25.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 26(10Q25.2) MUTATED 20 73 52 12
DEL PEAK 26(10Q25.2) WILD-TYPE 195 174 80 10

Figure S273.  Get High-res Image Gene #50: 'del_10q25.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q25.2' versus 'METHLYATION_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.043

Table S274.  Gene #50: 'del_10q25.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 26(10Q25.2) MUTATED 23 45 34
DEL PEAK 26(10Q25.2) WILD-TYPE 94 84 110

Figure S274.  Get High-res Image Gene #50: 'del_10q25.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q25.2' versus 'MRNASEQ_CNMF'

P value = 0.00269 (Fisher's exact test), Q value = 0.0077

Table S275.  Gene #50: 'del_10q25.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 26(10Q25.2) MUTATED 53 19 33 50
DEL PEAK 26(10Q25.2) WILD-TYPE 103 109 98 148

Figure S275.  Get High-res Image Gene #50: 'del_10q25.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S276.  Gene #50: 'del_10q25.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 26(10Q25.2) MUTATED 26 15 2 11 39 35 27
DEL PEAK 26(10Q25.2) WILD-TYPE 54 71 62 46 51 103 71

Figure S276.  Get High-res Image Gene #50: 'del_10q25.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q25.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0206 (Fisher's exact test), Q value = 0.048

Table S277.  Gene #50: 'del_10q25.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 26(10Q25.2) MUTATED 9 21 6 32 10 10 14 8 26
DEL PEAK 26(10Q25.2) WILD-TYPE 40 53 23 54 67 44 43 24 55

Figure S277.  Get High-res Image Gene #50: 'del_10q25.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11q22.3' versus 'CN_CNMF'

P value = 0.00908 (Fisher's exact test), Q value = 0.023

Table S278.  Gene #51: 'del_11q22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 27(11Q22.3) MUTATED 25 58 24 4
DEL PEAK 27(11Q22.3) WILD-TYPE 190 189 108 18

Figure S278.  Get High-res Image Gene #51: 'del_11q22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0476 (Fisher's exact test), Q value = 0.096

Table S279.  Gene #51: 'del_11q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 27(11Q22.3) MUTATED 15 17 3 13 13 29 20
DEL PEAK 27(11Q22.3) WILD-TYPE 65 69 61 44 77 109 78

Figure S279.  Get High-res Image Gene #51: 'del_11q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MRNA_CNMF'

P value = 0.00342 (Fisher's exact test), Q value = 0.0097

Table S280.  Gene #52: 'del_12p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
DEL PEAK 28(12P13.1) MUTATED 2 14 11 1
DEL PEAK 28(12P13.1) WILD-TYPE 43 49 54 42

Figure S280.  Get High-res Image Gene #52: 'del_12p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12p13.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.0011

Table S281.  Gene #52: 'del_12p13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 28(12P13.1) MUTATED 0 19 9
DEL PEAK 28(12P13.1) WILD-TYPE 50 70 68

Figure S281.  Get High-res Image Gene #52: 'del_12p13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S282.  Gene #52: 'del_12p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 28(12P13.1) MUTATED 6 62 21 3
DEL PEAK 28(12P13.1) WILD-TYPE 209 185 111 19

Figure S282.  Get High-res Image Gene #52: 'del_12p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_12p13.1' versus 'MRNASEQ_CNMF'

P value = 0.0463 (Fisher's exact test), Q value = 0.094

Table S283.  Gene #52: 'del_12p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 28(12P13.1) MUTATED 34 13 18 27
DEL PEAK 28(12P13.1) WILD-TYPE 122 115 113 171

Figure S283.  Get High-res Image Gene #52: 'del_12p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.0025

Table S284.  Gene #52: 'del_12p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 28(12P13.1) MUTATED 18 12 1 12 16 25 8
DEL PEAK 28(12P13.1) WILD-TYPE 62 74 63 45 74 113 90

Figure S284.  Get High-res Image Gene #52: 'del_12p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_CNMF'

P value = 0.0389 (Fisher's exact test), Q value = 0.081

Table S285.  Gene #52: 'del_12p13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
DEL PEAK 28(12P13.1) MUTATED 18 21 18 25
DEL PEAK 28(12P13.1) WILD-TYPE 135 74 68 180

Figure S285.  Get High-res Image Gene #52: 'del_12p13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_12p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0437 (Fisher's exact test), Q value = 0.089

Table S286.  Gene #52: 'del_12p13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 16 34 22
DEL PEAK 28(12P13.1) MUTATED 8 5 3 7
DEL PEAK 28(12P13.1) WILD-TYPE 55 11 31 15

Figure S286.  Get High-res Image Gene #52: 'del_12p13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q21.33' versus 'MRNA_CNMF'

P value = 0.0242 (Fisher's exact test), Q value = 0.055

Table S287.  Gene #53: 'del_12q21.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
DEL PEAK 29(12Q21.33) MUTATED 4 15 12 2
DEL PEAK 29(12Q21.33) WILD-TYPE 41 48 53 41

Figure S287.  Get High-res Image Gene #53: 'del_12q21.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12q21.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.0115 (Fisher's exact test), Q value = 0.028

Table S288.  Gene #53: 'del_12q21.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 29(12Q21.33) MUTATED 3 21 9
DEL PEAK 29(12Q21.33) WILD-TYPE 47 68 68

Figure S288.  Get High-res Image Gene #53: 'del_12q21.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12q21.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S289.  Gene #53: 'del_12q21.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 29(12Q21.33) MUTATED 6 61 18 5
DEL PEAK 29(12Q21.33) WILD-TYPE 209 186 114 17

Figure S289.  Get High-res Image Gene #53: 'del_12q21.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q21.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.0013

Table S290.  Gene #53: 'del_12q21.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 29(12Q21.33) MUTATED 16 4 3 10 21 26 10
DEL PEAK 29(12Q21.33) WILD-TYPE 64 82 61 47 69 112 88

Figure S290.  Get High-res Image Gene #53: 'del_12q21.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q11.2' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00018

Table S291.  Gene #54: 'del_14q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
DEL PEAK 30(14Q11.2) MUTATED 8 32 32 7
DEL PEAK 30(14Q11.2) WILD-TYPE 37 31 33 36

Figure S291.  Get High-res Image Gene #54: 'del_14q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S292.  Gene #54: 'del_14q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 30(14Q11.2) MUTATED 5 47 27
DEL PEAK 30(14Q11.2) WILD-TYPE 45 42 50

Figure S292.  Get High-res Image Gene #54: 'del_14q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S293.  Gene #54: 'del_14q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 30(14Q11.2) MUTATED 21 158 25 8
DEL PEAK 30(14Q11.2) WILD-TYPE 194 89 107 14

Figure S293.  Get High-res Image Gene #54: 'del_14q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S294.  Gene #54: 'del_14q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 30(14Q11.2) MUTATED 35 65 32
DEL PEAK 30(14Q11.2) WILD-TYPE 82 64 112

Figure S294.  Get High-res Image Gene #54: 'del_14q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.033

Table S295.  Gene #54: 'del_14q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 86
DEL PEAK 30(14Q11.2) MUTATED 72 54 42
DEL PEAK 30(14Q11.2) WILD-TYPE 156 114 44

Figure S295.  Get High-res Image Gene #54: 'del_14q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_14q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S296.  Gene #54: 'del_14q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 30(14Q11.2) MUTATED 83 25 30 73
DEL PEAK 30(14Q11.2) WILD-TYPE 73 103 101 125

Figure S296.  Get High-res Image Gene #54: 'del_14q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S297.  Gene #54: 'del_14q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 30(14Q11.2) MUTATED 37 25 3 23 38 67 18
DEL PEAK 30(14Q11.2) WILD-TYPE 43 61 61 34 52 71 80

Figure S297.  Get High-res Image Gene #54: 'del_14q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0012

Table S298.  Gene #54: 'del_14q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
DEL PEAK 30(14Q11.2) MUTATED 43 34 46 59
DEL PEAK 30(14Q11.2) WILD-TYPE 110 61 40 146

Figure S298.  Get High-res Image Gene #54: 'del_14q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_14q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S299.  Gene #54: 'del_14q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 30(14Q11.2) MUTATED 14 20 9 28 9 29 29 10 34
DEL PEAK 30(14Q11.2) WILD-TYPE 35 54 20 58 68 25 28 22 47

Figure S299.  Get High-res Image Gene #54: 'del_14q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 0.055

Table S300.  Gene #54: 'del_14q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
DEL PEAK 30(14Q11.2) MUTATED 15 14 23 5
DEL PEAK 30(14Q11.2) WILD-TYPE 20 26 15 17

Figure S300.  Get High-res Image Gene #54: 'del_14q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_14q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0464 (Fisher's exact test), Q value = 0.094

Table S301.  Gene #54: 'del_14q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 16 34 22
DEL PEAK 30(14Q11.2) MUTATED 20 6 17 14
DEL PEAK 30(14Q11.2) WILD-TYPE 43 10 17 8

Figure S301.  Get High-res Image Gene #54: 'del_14q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q31.1' versus 'MRNA_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0012

Table S302.  Gene #55: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
DEL PEAK 31(14Q31.1) MUTATED 11 32 32 8
DEL PEAK 31(14Q31.1) WILD-TYPE 34 31 33 35

Figure S302.  Get High-res Image Gene #55: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q31.1' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00022

Table S303.  Gene #55: 'del_14q31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 31(14Q31.1) MUTATED 8 48 27
DEL PEAK 31(14Q31.1) WILD-TYPE 42 41 50

Figure S303.  Get High-res Image Gene #55: 'del_14q31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S304.  Gene #55: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 31(14Q31.1) MUTATED 22 159 29 10
DEL PEAK 31(14Q31.1) WILD-TYPE 193 88 103 12

Figure S304.  Get High-res Image Gene #55: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q31.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S305.  Gene #55: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 31(14Q31.1) MUTATED 34 67 35
DEL PEAK 31(14Q31.1) WILD-TYPE 83 62 109

Figure S305.  Get High-res Image Gene #55: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q31.1' versus 'RPPA_CNMF'

P value = 0.0385 (Fisher's exact test), Q value = 0.081

Table S306.  Gene #55: 'del_14q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 197 177
DEL PEAK 31(14Q31.1) MUTATED 43 80 51
DEL PEAK 31(14Q31.1) WILD-TYPE 65 117 126

Figure S306.  Get High-res Image Gene #55: 'del_14q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_14q31.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0381 (Fisher's exact test), Q value = 0.081

Table S307.  Gene #55: 'del_14q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 86
DEL PEAK 31(14Q31.1) MUTATED 73 60 41
DEL PEAK 31(14Q31.1) WILD-TYPE 155 108 45

Figure S307.  Get High-res Image Gene #55: 'del_14q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_14q31.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S308.  Gene #55: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 31(14Q31.1) MUTATED 83 27 32 77
DEL PEAK 31(14Q31.1) WILD-TYPE 73 101 99 121

Figure S308.  Get High-res Image Gene #55: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S309.  Gene #55: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 31(14Q31.1) MUTATED 35 27 6 25 36 69 21
DEL PEAK 31(14Q31.1) WILD-TYPE 45 59 58 32 54 69 77

Figure S309.  Get High-res Image Gene #55: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MIRSEQ_CNMF'

P value = 0.0262 (Fisher's exact test), Q value = 0.059

Table S310.  Gene #55: 'del_14q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
DEL PEAK 31(14Q31.1) MUTATED 47 36 42 66
DEL PEAK 31(14Q31.1) WILD-TYPE 106 59 44 139

Figure S310.  Get High-res Image Gene #55: 'del_14q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_14q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S311.  Gene #55: 'del_14q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 31(14Q31.1) MUTATED 15 21 9 31 9 29 27 12 38
DEL PEAK 31(14Q31.1) WILD-TYPE 34 53 20 55 68 25 30 20 43

Figure S311.  Get High-res Image Gene #55: 'del_14q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0234 (Fisher's exact test), Q value = 0.053

Table S312.  Gene #55: 'del_14q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 16 34 22
DEL PEAK 31(14Q31.1) MUTATED 21 6 18 15
DEL PEAK 31(14Q31.1) WILD-TYPE 42 10 16 7

Figure S312.  Get High-res Image Gene #55: 'del_14q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q11.2' versus 'MRNA_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0014

Table S313.  Gene #56: 'del_15q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
DEL PEAK 32(15Q11.2) MUTATED 12 33 36 10
DEL PEAK 32(15Q11.2) WILD-TYPE 33 30 29 33

Figure S313.  Get High-res Image Gene #56: 'del_15q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00055

Table S314.  Gene #56: 'del_15q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 32(15Q11.2) MUTATED 12 52 27
DEL PEAK 32(15Q11.2) WILD-TYPE 38 37 50

Figure S314.  Get High-res Image Gene #56: 'del_15q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S315.  Gene #56: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 32(15Q11.2) MUTATED 23 150 61 15
DEL PEAK 32(15Q11.2) WILD-TYPE 192 97 71 7

Figure S315.  Get High-res Image Gene #56: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q11.2' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00058

Table S316.  Gene #56: 'del_15q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 32(15Q11.2) MUTATED 39 71 47
DEL PEAK 32(15Q11.2) WILD-TYPE 78 58 97

Figure S316.  Get High-res Image Gene #56: 'del_15q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00044

Table S317.  Gene #56: 'del_15q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 32(15Q11.2) MUTATED 82 33 52 81
DEL PEAK 32(15Q11.2) WILD-TYPE 74 95 79 117

Figure S317.  Get High-res Image Gene #56: 'del_15q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S318.  Gene #56: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 32(15Q11.2) MUTATED 38 32 3 23 52 65 35
DEL PEAK 32(15Q11.2) WILD-TYPE 42 54 61 34 38 73 63

Figure S318.  Get High-res Image Gene #56: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00166 (Fisher's exact test), Q value = 0.005

Table S319.  Gene #56: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
DEL PEAK 32(15Q11.2) MUTATED 52 46 47 71
DEL PEAK 32(15Q11.2) WILD-TYPE 101 49 39 134

Figure S319.  Get High-res Image Gene #56: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00084 (Fisher's exact test), Q value = 0.0027

Table S320.  Gene #56: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 32(15Q11.2) MUTATED 16 34 8 44 16 18 29 13 38
DEL PEAK 32(15Q11.2) WILD-TYPE 33 40 21 42 61 36 28 19 43

Figure S320.  Get High-res Image Gene #56: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_15q15.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S321.  Gene #57: 'del_15q15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
DEL PEAK 33(15Q15.2) MUTATED 11 34 38 9
DEL PEAK 33(15Q15.2) WILD-TYPE 34 29 27 34

Figure S321.  Get High-res Image Gene #57: 'del_15q15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q15.2' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00022

Table S322.  Gene #57: 'del_15q15.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 33(15Q15.2) MUTATED 11 53 28
DEL PEAK 33(15Q15.2) WILD-TYPE 39 36 49

Figure S322.  Get High-res Image Gene #57: 'del_15q15.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q15.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S323.  Gene #57: 'del_15q15.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 33(15Q15.2) MUTATED 25 146 64 16
DEL PEAK 33(15Q15.2) WILD-TYPE 190 101 68 6

Figure S323.  Get High-res Image Gene #57: 'del_15q15.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q15.2' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00067

Table S324.  Gene #57: 'del_15q15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 33(15Q15.2) MUTATED 42 71 45
DEL PEAK 33(15Q15.2) WILD-TYPE 75 58 99

Figure S324.  Get High-res Image Gene #57: 'del_15q15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q15.2' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00067

Table S325.  Gene #57: 'del_15q15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 33(15Q15.2) MUTATED 84 36 49 81
DEL PEAK 33(15Q15.2) WILD-TYPE 72 92 82 117

Figure S325.  Get High-res Image Gene #57: 'del_15q15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q15.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S326.  Gene #57: 'del_15q15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 33(15Q15.2) MUTATED 41 32 5 23 47 66 36
DEL PEAK 33(15Q15.2) WILD-TYPE 39 54 59 34 43 72 62

Figure S326.  Get High-res Image Gene #57: 'del_15q15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q15.2' versus 'MIRSEQ_CNMF'

P value = 0.00362 (Fisher's exact test), Q value = 0.01

Table S327.  Gene #57: 'del_15q15.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
DEL PEAK 33(15Q15.2) MUTATED 51 44 47 73
DEL PEAK 33(15Q15.2) WILD-TYPE 102 51 39 132

Figure S327.  Get High-res Image Gene #57: 'del_15q15.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q15.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00033

Table S328.  Gene #57: 'del_15q15.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 33(15Q15.2) MUTATED 17 30 9 43 13 19 30 14 40
DEL PEAK 33(15Q15.2) WILD-TYPE 32 44 20 43 64 35 27 18 41

Figure S328.  Get High-res Image Gene #57: 'del_15q15.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_15q21.1' versus 'MRNA_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0011

Table S329.  Gene #58: 'del_15q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
DEL PEAK 34(15Q21.1) MUTATED 14 33 37 9
DEL PEAK 34(15Q21.1) WILD-TYPE 31 30 28 34

Figure S329.  Get High-res Image Gene #58: 'del_15q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q21.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.0016

Table S330.  Gene #58: 'del_15q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 34(15Q21.1) MUTATED 14 52 27
DEL PEAK 34(15Q21.1) WILD-TYPE 36 37 50

Figure S330.  Get High-res Image Gene #58: 'del_15q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S331.  Gene #58: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 34(15Q21.1) MUTATED 26 142 64 16
DEL PEAK 34(15Q21.1) WILD-TYPE 189 105 68 6

Figure S331.  Get High-res Image Gene #58: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q21.1' versus 'METHLYATION_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.00093

Table S332.  Gene #58: 'del_15q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 34(15Q21.1) MUTATED 41 69 44
DEL PEAK 34(15Q21.1) WILD-TYPE 76 60 100

Figure S332.  Get High-res Image Gene #58: 'del_15q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q21.1' versus 'MRNASEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.00074

Table S333.  Gene #58: 'del_15q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 34(15Q21.1) MUTATED 82 35 48 82
DEL PEAK 34(15Q21.1) WILD-TYPE 74 93 83 116

Figure S333.  Get High-res Image Gene #58: 'del_15q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S334.  Gene #58: 'del_15q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 34(15Q21.1) MUTATED 39 31 5 23 46 65 38
DEL PEAK 34(15Q21.1) WILD-TYPE 41 55 59 34 44 73 60

Figure S334.  Get High-res Image Gene #58: 'del_15q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q21.1' versus 'MIRSEQ_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.028

Table S335.  Gene #58: 'del_15q21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
DEL PEAK 34(15Q21.1) MUTATED 51 44 45 74
DEL PEAK 34(15Q21.1) WILD-TYPE 102 51 41 131

Figure S335.  Get High-res Image Gene #58: 'del_15q21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00187 (Fisher's exact test), Q value = 0.0056

Table S336.  Gene #58: 'del_15q21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 34(15Q21.1) MUTATED 17 30 9 42 15 19 29 14 39
DEL PEAK 34(15Q21.1) WILD-TYPE 32 44 20 44 62 35 28 18 42

Figure S336.  Get High-res Image Gene #58: 'del_15q21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_15q22.33' versus 'MRNA_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00033

Table S337.  Gene #59: 'del_15q22.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
DEL PEAK 35(15Q22.33) MUTATED 12 31 35 7
DEL PEAK 35(15Q22.33) WILD-TYPE 33 32 30 36

Figure S337.  Get High-res Image Gene #59: 'del_15q22.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q22.33' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S338.  Gene #59: 'del_15q22.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 35(15Q22.33) MUTATED 11 52 22
DEL PEAK 35(15Q22.33) WILD-TYPE 39 37 55

Figure S338.  Get High-res Image Gene #59: 'del_15q22.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q22.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S339.  Gene #59: 'del_15q22.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 35(15Q22.33) MUTATED 18 140 63 17
DEL PEAK 35(15Q22.33) WILD-TYPE 197 107 69 5

Figure S339.  Get High-res Image Gene #59: 'del_15q22.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q22.33' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00014

Table S340.  Gene #59: 'del_15q22.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 35(15Q22.33) MUTATED 41 70 41
DEL PEAK 35(15Q22.33) WILD-TYPE 76 59 103

Figure S340.  Get High-res Image Gene #59: 'del_15q22.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q22.33' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S341.  Gene #59: 'del_15q22.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 35(15Q22.33) MUTATED 80 29 50 78
DEL PEAK 35(15Q22.33) WILD-TYPE 76 99 81 120

Figure S341.  Get High-res Image Gene #59: 'del_15q22.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q22.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S342.  Gene #59: 'del_15q22.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 35(15Q22.33) MUTATED 37 29 3 23 50 64 31
DEL PEAK 35(15Q22.33) WILD-TYPE 43 57 61 34 40 74 67

Figure S342.  Get High-res Image Gene #59: 'del_15q22.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q22.33' versus 'MIRSEQ_CNMF'

P value = 0.00253 (Fisher's exact test), Q value = 0.0073

Table S343.  Gene #59: 'del_15q22.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
DEL PEAK 35(15Q22.33) MUTATED 50 45 44 66
DEL PEAK 35(15Q22.33) WILD-TYPE 103 50 42 139

Figure S343.  Get High-res Image Gene #59: 'del_15q22.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q22.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00033

Table S344.  Gene #59: 'del_15q22.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 35(15Q22.33) MUTATED 17 31 8 37 11 18 29 14 40
DEL PEAK 35(15Q22.33) WILD-TYPE 32 43 21 49 66 36 28 18 41

Figure S344.  Get High-res Image Gene #59: 'del_15q22.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MRNA_CNMF'

P value = 0.049 (Fisher's exact test), Q value = 0.098

Table S345.  Gene #60: 'del_16p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
DEL PEAK 36(16P13.3) MUTATED 6 12 6 1
DEL PEAK 36(16P13.3) WILD-TYPE 39 51 59 42

Figure S345.  Get High-res Image Gene #60: 'del_16p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_16p13.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0364 (Fisher's exact test), Q value = 0.077

Table S346.  Gene #60: 'del_16p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 36(16P13.3) MUTATED 5 16 4
DEL PEAK 36(16P13.3) WILD-TYPE 45 73 73

Figure S346.  Get High-res Image Gene #60: 'del_16p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_16p13.3' versus 'CN_CNMF'

P value = 0.00812 (Fisher's exact test), Q value = 0.021

Table S347.  Gene #60: 'del_16p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 36(16P13.3) MUTATED 14 28 24 3
DEL PEAK 36(16P13.3) WILD-TYPE 201 219 108 19

Figure S347.  Get High-res Image Gene #60: 'del_16p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q23.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00131 (Fisher's exact test), Q value = 0.004

Table S348.  Gene #61: 'del_16q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 37(16Q23.1) MUTATED 15 10 5
DEL PEAK 37(16Q23.1) WILD-TYPE 35 79 72

Figure S348.  Get High-res Image Gene #61: 'del_16q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S349.  Gene #62: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
DEL PEAK 38(17P12) MUTATED 17 51 50 15
DEL PEAK 38(17P12) WILD-TYPE 28 12 15 28

Figure S349.  Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S350.  Gene #62: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 38(17P12) MUTATED 14 70 49
DEL PEAK 38(17P12) WILD-TYPE 36 19 28

Figure S350.  Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S351.  Gene #62: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 38(17P12) MUTATED 46 204 105 15
DEL PEAK 38(17P12) WILD-TYPE 169 43 27 7

Figure S351.  Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S352.  Gene #62: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 38(17P12) MUTATED 57 106 71
DEL PEAK 38(17P12) WILD-TYPE 60 23 73

Figure S352.  Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S353.  Gene #62: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 38(17P12) MUTATED 122 53 72 121
DEL PEAK 38(17P12) WILD-TYPE 34 75 59 77

Figure S353.  Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S354.  Gene #62: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 38(17P12) MUTATED 58 49 8 39 68 106 40
DEL PEAK 38(17P12) WILD-TYPE 22 37 56 18 22 32 58

Figure S354.  Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00067

Table S355.  Gene #62: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
DEL PEAK 38(17P12) MUTATED 86 57 69 111
DEL PEAK 38(17P12) WILD-TYPE 67 38 17 94

Figure S355.  Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S356.  Gene #62: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 38(17P12) MUTATED 26 43 18 60 20 38 41 17 60
DEL PEAK 38(17P12) WILD-TYPE 23 31 11 26 57 16 16 15 21

Figure S356.  Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0335 (Fisher's exact test), Q value = 0.072

Table S357.  Gene #62: 'del_17p12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
DEL PEAK 38(17P12) MUTATED 20 28 29 9
DEL PEAK 38(17P12) WILD-TYPE 15 12 9 13

Figure S357.  Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0426 (Fisher's exact test), Q value = 0.088

Table S358.  Gene #62: 'del_17p12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 16 34 22
DEL PEAK 38(17P12) MUTATED 35 12 20 19
DEL PEAK 38(17P12) WILD-TYPE 28 4 14 3

Figure S358.  Get High-res Image Gene #62: 'del_17p12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S359.  Gene #63: 'del_17q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 39(17Q24.3) MUTATED 15 43 27 10
DEL PEAK 39(17Q24.3) WILD-TYPE 200 204 105 12

Figure S359.  Get High-res Image Gene #63: 'del_17q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_18p11.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S360.  Gene #64: 'del_18p11.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
DEL PEAK 40(18P11.31) MUTATED 11 52 50 14
DEL PEAK 40(18P11.31) WILD-TYPE 34 11 15 29

Figure S360.  Get High-res Image Gene #64: 'del_18p11.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18p11.31' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S361.  Gene #64: 'del_18p11.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 40(18P11.31) MUTATED 9 75 43
DEL PEAK 40(18P11.31) WILD-TYPE 41 14 34

Figure S361.  Get High-res Image Gene #64: 'del_18p11.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18p11.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S362.  Gene #64: 'del_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 40(18P11.31) MUTATED 45 221 87 17
DEL PEAK 40(18P11.31) WILD-TYPE 170 26 45 5

Figure S362.  Get High-res Image Gene #64: 'del_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_18p11.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S363.  Gene #64: 'del_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 40(18P11.31) MUTATED 62 120 59
DEL PEAK 40(18P11.31) WILD-TYPE 55 9 85

Figure S363.  Get High-res Image Gene #64: 'del_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18p11.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S364.  Gene #64: 'del_18p11.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 40(18P11.31) MUTATED 141 41 72 114
DEL PEAK 40(18P11.31) WILD-TYPE 15 87 59 84

Figure S364.  Get High-res Image Gene #64: 'del_18p11.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18p11.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S365.  Gene #64: 'del_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 40(18P11.31) MUTATED 66 46 6 40 70 106 34
DEL PEAK 40(18P11.31) WILD-TYPE 14 40 58 17 20 32 64

Figure S365.  Get High-res Image Gene #64: 'del_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18p11.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S366.  Gene #64: 'del_18p11.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
DEL PEAK 40(18P11.31) MUTATED 84 60 74 101
DEL PEAK 40(18P11.31) WILD-TYPE 69 35 12 104

Figure S366.  Get High-res Image Gene #64: 'del_18p11.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18p11.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S367.  Gene #64: 'del_18p11.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 40(18P11.31) MUTATED 26 41 17 57 15 41 42 16 64
DEL PEAK 40(18P11.31) WILD-TYPE 23 33 12 29 62 13 15 16 17

Figure S367.  Get High-res Image Gene #64: 'del_18p11.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18p11.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.3e-05

Table S368.  Gene #64: 'del_18p11.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
DEL PEAK 40(18P11.31) MUTATED 24 28 34 6
DEL PEAK 40(18P11.31) WILD-TYPE 11 12 4 16

Figure S368.  Get High-res Image Gene #64: 'del_18p11.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18p11.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0018

Table S369.  Gene #64: 'del_18p11.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 16 34 22
DEL PEAK 40(18P11.31) MUTATED 34 14 23 21
DEL PEAK 40(18P11.31) WILD-TYPE 29 2 11 1

Figure S369.  Get High-res Image Gene #64: 'del_18p11.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q12.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S370.  Gene #65: 'del_18q12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
DEL PEAK 41(18Q12.2) MUTATED 17 55 54 18
DEL PEAK 41(18Q12.2) WILD-TYPE 28 8 11 25

Figure S370.  Get High-res Image Gene #65: 'del_18q12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q12.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S371.  Gene #65: 'del_18q12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 41(18Q12.2) MUTATED 14 79 51
DEL PEAK 41(18Q12.2) WILD-TYPE 36 10 26

Figure S371.  Get High-res Image Gene #65: 'del_18q12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18q12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S372.  Gene #65: 'del_18q12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 41(18Q12.2) MUTATED 53 232 114 17
DEL PEAK 41(18Q12.2) WILD-TYPE 162 15 18 5

Figure S372.  Get High-res Image Gene #65: 'del_18q12.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q12.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S373.  Gene #65: 'del_18q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 41(18Q12.2) MUTATED 71 123 74
DEL PEAK 41(18Q12.2) WILD-TYPE 46 6 70

Figure S373.  Get High-res Image Gene #65: 'del_18q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q12.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S374.  Gene #65: 'del_18q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 41(18Q12.2) MUTATED 143 56 83 132
DEL PEAK 41(18Q12.2) WILD-TYPE 13 72 48 66

Figure S374.  Get High-res Image Gene #65: 'del_18q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S375.  Gene #65: 'del_18q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 41(18Q12.2) MUTATED 67 58 8 45 77 114 45
DEL PEAK 41(18Q12.2) WILD-TYPE 13 28 56 12 13 24 53

Figure S375.  Get High-res Image Gene #65: 'del_18q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q12.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S376.  Gene #65: 'del_18q12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
DEL PEAK 41(18Q12.2) MUTATED 93 67 81 121
DEL PEAK 41(18Q12.2) WILD-TYPE 60 28 5 84

Figure S376.  Get High-res Image Gene #65: 'del_18q12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18q12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S377.  Gene #65: 'del_18q12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 41(18Q12.2) MUTATED 31 47 18 65 21 43 50 19 68
DEL PEAK 41(18Q12.2) WILD-TYPE 18 27 11 21 56 11 7 13 13

Figure S377.  Get High-res Image Gene #65: 'del_18q12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q12.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00077

Table S378.  Gene #65: 'del_18q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
DEL PEAK 41(18Q12.2) MUTATED 26 32 36 10
DEL PEAK 41(18Q12.2) WILD-TYPE 9 8 2 12

Figure S378.  Get High-res Image Gene #65: 'del_18q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00044

Table S379.  Gene #65: 'del_18q12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 16 34 22
DEL PEAK 41(18Q12.2) MUTATED 40 16 26 22
DEL PEAK 41(18Q12.2) WILD-TYPE 23 0 8 0

Figure S379.  Get High-res Image Gene #65: 'del_18q12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q21.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S380.  Gene #66: 'del_18q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
DEL PEAK 42(18Q21.2) MUTATED 17 56 55 19
DEL PEAK 42(18Q21.2) WILD-TYPE 28 7 10 24

Figure S380.  Get High-res Image Gene #66: 'del_18q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q21.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S381.  Gene #66: 'del_18q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 42(18Q21.2) MUTATED 14 79 54
DEL PEAK 42(18Q21.2) WILD-TYPE 36 10 23

Figure S381.  Get High-res Image Gene #66: 'del_18q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S382.  Gene #66: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 42(18Q21.2) MUTATED 62 235 117 18
DEL PEAK 42(18Q21.2) WILD-TYPE 153 12 15 4

Figure S382.  Get High-res Image Gene #66: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S383.  Gene #66: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 42(18Q21.2) MUTATED 71 124 86
DEL PEAK 42(18Q21.2) WILD-TYPE 46 5 58

Figure S383.  Get High-res Image Gene #66: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S384.  Gene #66: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 42(18Q21.2) MUTATED 144 63 88 135
DEL PEAK 42(18Q21.2) WILD-TYPE 12 65 43 63

Figure S384.  Get High-res Image Gene #66: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S385.  Gene #66: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 42(18Q21.2) MUTATED 68 62 13 45 80 116 46
DEL PEAK 42(18Q21.2) WILD-TYPE 12 24 51 12 10 22 52

Figure S385.  Get High-res Image Gene #66: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S386.  Gene #66: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
DEL PEAK 42(18Q21.2) MUTATED 103 68 81 126
DEL PEAK 42(18Q21.2) WILD-TYPE 50 27 5 79

Figure S386.  Get High-res Image Gene #66: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S387.  Gene #66: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 42(18Q21.2) MUTATED 32 50 22 65 25 44 51 19 70
DEL PEAK 42(18Q21.2) WILD-TYPE 17 24 7 21 52 10 6 13 11

Figure S387.  Get High-res Image Gene #66: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 7e-04

Table S388.  Gene #66: 'del_18q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
DEL PEAK 42(18Q21.2) MUTATED 27 33 37 11
DEL PEAK 42(18Q21.2) WILD-TYPE 8 7 1 11

Figure S388.  Get High-res Image Gene #66: 'del_18q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00037

Table S389.  Gene #66: 'del_18q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 16 34 22
DEL PEAK 42(18Q21.2) MUTATED 41 16 29 22
DEL PEAK 42(18Q21.2) WILD-TYPE 22 0 5 0

Figure S389.  Get High-res Image Gene #66: 'del_18q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q22.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S390.  Gene #67: 'del_18q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
DEL PEAK 43(18Q22.1) MUTATED 17 56 54 20
DEL PEAK 43(18Q22.1) WILD-TYPE 28 7 11 23

Figure S390.  Get High-res Image Gene #67: 'del_18q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S391.  Gene #67: 'del_18q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 43(18Q22.1) MUTATED 15 79 53
DEL PEAK 43(18Q22.1) WILD-TYPE 35 10 24

Figure S391.  Get High-res Image Gene #67: 'del_18q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S392.  Gene #67: 'del_18q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 43(18Q22.1) MUTATED 60 235 114 18
DEL PEAK 43(18Q22.1) WILD-TYPE 155 12 18 4

Figure S392.  Get High-res Image Gene #67: 'del_18q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S393.  Gene #67: 'del_18q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 43(18Q22.1) MUTATED 68 124 84
DEL PEAK 43(18Q22.1) WILD-TYPE 49 5 60

Figure S393.  Get High-res Image Gene #67: 'del_18q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S394.  Gene #67: 'del_18q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 43(18Q22.1) MUTATED 143 62 85 135
DEL PEAK 43(18Q22.1) WILD-TYPE 13 66 46 63

Figure S394.  Get High-res Image Gene #67: 'del_18q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S395.  Gene #67: 'del_18q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 43(18Q22.1) MUTATED 67 61 13 43 79 115 47
DEL PEAK 43(18Q22.1) WILD-TYPE 13 25 51 14 11 23 51

Figure S395.  Get High-res Image Gene #67: 'del_18q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q22.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S396.  Gene #67: 'del_18q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
DEL PEAK 43(18Q22.1) MUTATED 101 66 80 126
DEL PEAK 43(18Q22.1) WILD-TYPE 52 29 6 79

Figure S396.  Get High-res Image Gene #67: 'del_18q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S397.  Gene #67: 'del_18q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 43(18Q22.1) MUTATED 32 49 21 63 26 43 51 19 69
DEL PEAK 43(18Q22.1) WILD-TYPE 17 25 8 23 51 11 6 13 12

Figure S397.  Get High-res Image Gene #67: 'del_18q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0027

Table S398.  Gene #67: 'del_18q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 40 38 22
DEL PEAK 43(18Q22.1) MUTATED 27 32 36 11
DEL PEAK 43(18Q22.1) WILD-TYPE 8 8 2 11

Figure S398.  Get High-res Image Gene #67: 'del_18q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00216 (Fisher's exact test), Q value = 0.0064

Table S399.  Gene #67: 'del_18q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 16 34 22
DEL PEAK 43(18Q22.1) MUTATED 41 16 29 20
DEL PEAK 43(18Q22.1) WILD-TYPE 22 0 5 2

Figure S399.  Get High-res Image Gene #67: 'del_18q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 7e-04

Table S400.  Gene #68: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 44(19P13.3) MUTATED 16 47 29 5
DEL PEAK 44(19P13.3) WILD-TYPE 199 200 103 17

Figure S400.  Get High-res Image Gene #68: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.0021

Table S401.  Gene #68: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 44(19P13.3) MUTATED 9 7 5 29 5 6 7 6 14
DEL PEAK 44(19P13.3) WILD-TYPE 40 67 24 57 72 48 50 26 67

Figure S401.  Get High-res Image Gene #68: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00231 (Fisher's exact test), Q value = 0.0068

Table S402.  Gene #69: 'del_20p12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 45(20P12.1) MUTATED 4 28 12
DEL PEAK 45(20P12.1) WILD-TYPE 46 61 65

Figure S402.  Get High-res Image Gene #69: 'del_20p12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_20p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S403.  Gene #69: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 45(20P12.1) MUTATED 16 83 37 0
DEL PEAK 45(20P12.1) WILD-TYPE 199 164 95 22

Figure S403.  Get High-res Image Gene #69: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_20p12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S404.  Gene #69: 'del_20p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 45(20P12.1) MUTATED 23 50 19
DEL PEAK 45(20P12.1) WILD-TYPE 94 79 125

Figure S404.  Get High-res Image Gene #69: 'del_20p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_20p12.1' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00058

Table S405.  Gene #69: 'del_20p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 45(20P12.1) MUTATED 55 21 26 33
DEL PEAK 45(20P12.1) WILD-TYPE 101 107 105 165

Figure S405.  Get High-res Image Gene #69: 'del_20p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S406.  Gene #69: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 45(20P12.1) MUTATED 25 21 0 14 29 36 10
DEL PEAK 45(20P12.1) WILD-TYPE 55 65 64 43 61 102 88

Figure S406.  Get High-res Image Gene #69: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_CNMF'

P value = 0.00378 (Fisher's exact test), Q value = 0.011

Table S407.  Gene #69: 'del_20p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
DEL PEAK 45(20P12.1) MUTATED 33 17 31 34
DEL PEAK 45(20P12.1) WILD-TYPE 120 78 55 171

Figure S407.  Get High-res Image Gene #69: 'del_20p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_20p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.0012

Table S408.  Gene #69: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 45(20P12.1) MUTATED 9 16 6 30 6 11 16 1 20
DEL PEAK 45(20P12.1) WILD-TYPE 40 58 23 56 71 43 41 31 61

Figure S408.  Get High-res Image Gene #69: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MRNA_CNMF'

P value = 0.00796 (Fisher's exact test), Q value = 0.021

Table S409.  Gene #70: 'del_21q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
DEL PEAK 46(21Q11.2) MUTATED 11 30 24 8
DEL PEAK 46(21Q11.2) WILD-TYPE 34 33 41 35

Figure S409.  Get High-res Image Gene #70: 'del_21q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_21q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0013

Table S410.  Gene #70: 'del_21q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 46(21Q11.2) MUTATED 11 44 18
DEL PEAK 46(21Q11.2) WILD-TYPE 39 45 59

Figure S410.  Get High-res Image Gene #70: 'del_21q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_21q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S411.  Gene #70: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 46(21Q11.2) MUTATED 37 117 46 14
DEL PEAK 46(21Q11.2) WILD-TYPE 178 130 86 8

Figure S411.  Get High-res Image Gene #70: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 0.00737 (Fisher's exact test), Q value = 0.02

Table S412.  Gene #70: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 46(21Q11.2) MUTATED 37 60 42
DEL PEAK 46(21Q11.2) WILD-TYPE 80 69 102

Figure S412.  Get High-res Image Gene #70: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00051

Table S413.  Gene #70: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 46(21Q11.2) MUTATED 77 32 40 63
DEL PEAK 46(21Q11.2) WILD-TYPE 79 96 91 135

Figure S413.  Get High-res Image Gene #70: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_21q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.0011

Table S414.  Gene #70: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 46(21Q11.2) MUTATED 35 27 9 23 38 55 25
DEL PEAK 46(21Q11.2) WILD-TYPE 45 59 55 34 52 83 73

Figure S414.  Get High-res Image Gene #70: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.042

Table S415.  Gene #70: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
DEL PEAK 46(21Q11.2) MUTATED 48 32 43 65
DEL PEAK 46(21Q11.2) WILD-TYPE 105 63 43 140

Figure S415.  Get High-res Image Gene #70: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_21q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0254 (Fisher's exact test), Q value = 0.057

Table S416.  Gene #70: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 46(21Q11.2) MUTATED 17 20 8 31 17 25 28 10 32
DEL PEAK 46(21Q11.2) WILD-TYPE 32 54 21 55 60 29 29 22 49

Figure S416.  Get High-res Image Gene #70: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_21q21.1' versus 'MRNA_CNMF'

P value = 0.00695 (Fisher's exact test), Q value = 0.019

Table S417.  Gene #71: 'del_21q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
DEL PEAK 47(21Q21.1) MUTATED 11 29 23 7
DEL PEAK 47(21Q21.1) WILD-TYPE 34 34 42 36

Figure S417.  Get High-res Image Gene #71: 'del_21q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_21q21.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.0018

Table S418.  Gene #71: 'del_21q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 47(21Q21.1) MUTATED 10 42 18
DEL PEAK 47(21Q21.1) WILD-TYPE 40 47 59

Figure S418.  Get High-res Image Gene #71: 'del_21q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_21q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S419.  Gene #71: 'del_21q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 47(21Q21.1) MUTATED 37 114 45 14
DEL PEAK 47(21Q21.1) WILD-TYPE 178 133 87 8

Figure S419.  Get High-res Image Gene #71: 'del_21q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q21.1' versus 'METHLYATION_CNMF'

P value = 0.00334 (Fisher's exact test), Q value = 0.0095

Table S420.  Gene #71: 'del_21q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 47(21Q21.1) MUTATED 37 61 41
DEL PEAK 47(21Q21.1) WILD-TYPE 80 68 103

Figure S420.  Get High-res Image Gene #71: 'del_21q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_21q21.1' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00041

Table S421.  Gene #71: 'del_21q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 47(21Q21.1) MUTATED 76 31 39 62
DEL PEAK 47(21Q21.1) WILD-TYPE 80 97 92 136

Figure S421.  Get High-res Image Gene #71: 'del_21q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_21q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.0021

Table S422.  Gene #71: 'del_21q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 47(21Q21.1) MUTATED 32 27 10 21 40 55 23
DEL PEAK 47(21Q21.1) WILD-TYPE 48 59 54 36 50 83 75

Figure S422.  Get High-res Image Gene #71: 'del_21q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_21q21.1' versus 'MIRSEQ_CNMF'

P value = 0.0172 (Fisher's exact test), Q value = 0.041

Table S423.  Gene #71: 'del_21q21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
DEL PEAK 47(21Q21.1) MUTATED 46 33 42 63
DEL PEAK 47(21Q21.1) WILD-TYPE 107 62 44 142

Figure S423.  Get High-res Image Gene #71: 'del_21q21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_21q21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00868 (Fisher's exact test), Q value = 0.023

Table S424.  Gene #71: 'del_21q21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 47(21Q21.1) MUTATED 17 21 7 32 15 23 28 8 33
DEL PEAK 47(21Q21.1) WILD-TYPE 32 53 22 54 62 31 29 24 48

Figure S424.  Get High-res Image Gene #71: 'del_21q21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_21q21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.018 (Fisher's exact test), Q value = 0.042

Table S425.  Gene #71: 'del_21q21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 16 34 22
DEL PEAK 47(21Q21.1) MUTATED 19 9 20 12
DEL PEAK 47(21Q21.1) WILD-TYPE 44 7 14 10

Figure S425.  Get High-res Image Gene #71: 'del_21q21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.32' versus 'MRNA_CNMF'

P value = 0.00236 (Fisher's exact test), Q value = 0.0069

Table S426.  Gene #72: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 63 65 43
DEL PEAK 48(22Q13.32) MUTATED 13 31 33 9
DEL PEAK 48(22Q13.32) WILD-TYPE 32 32 32 34

Figure S426.  Get High-res Image Gene #72: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_22q13.32' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S427.  Gene #72: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 77
DEL PEAK 48(22Q13.32) MUTATED 7 47 32
DEL PEAK 48(22Q13.32) WILD-TYPE 43 42 45

Figure S427.  Get High-res Image Gene #72: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.2e-05

Table S428.  Gene #72: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 215 247 132 22
DEL PEAK 48(22Q13.32) MUTATED 29 130 55 14
DEL PEAK 48(22Q13.32) WILD-TYPE 186 117 77 8

Figure S428.  Get High-res Image Gene #72: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 0.0309 (Fisher's exact test), Q value = 0.068

Table S429.  Gene #72: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 129 144
DEL PEAK 48(22Q13.32) MUTATED 44 55 40
DEL PEAK 48(22Q13.32) WILD-TYPE 73 74 104

Figure S429.  Get High-res Image Gene #72: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 0.0266 (Fisher's exact test), Q value = 0.059

Table S430.  Gene #72: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 128 131 198
DEL PEAK 48(22Q13.32) MUTATED 69 35 46 77
DEL PEAK 48(22Q13.32) WILD-TYPE 87 93 85 121

Figure S430.  Get High-res Image Gene #72: '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 = 5.2e-05

Table S431.  Gene #72: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 98
DEL PEAK 48(22Q13.32) MUTATED 34 29 8 24 38 67 27
DEL PEAK 48(22Q13.32) WILD-TYPE 46 57 56 33 52 71 71

Figure S431.  Get High-res Image Gene #72: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CNMF'

P value = 0.0271 (Fisher's exact test), Q value = 0.06

Table S432.  Gene #72: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 95 86 205
DEL PEAK 48(22Q13.32) MUTATED 47 37 43 72
DEL PEAK 48(22Q13.32) WILD-TYPE 106 58 43 133

Figure S432.  Get High-res Image Gene #72: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_22q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0015

Table S433.  Gene #72: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 49 74 29 86 77 54 57 32 81
DEL PEAK 48(22Q13.32) MUTATED 16 26 3 34 17 23 29 12 39
DEL PEAK 48(22Q13.32) WILD-TYPE 33 48 26 52 60 31 28 20 42

Figure S433.  Get High-res Image Gene #72: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_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/COADREAD-TP/22524544/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/COADREAD-TP/22555066/COADREAD-TP.transferedmergedcluster.txt

  • Number of patients = 616

  • Number of significantly focal cnvs = 72

  • 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)