Correlation between copy number variation genes (focal events) and molecular subtypes
Colon 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/C1SQ8ZQG
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 66 focal events and 12 molecular subtypes across 451 patients, 448 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • amp_5p13.2 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

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

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

  • amp_13q12.13 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', and 'MIRSEQ_CHIERARCHICAL'.

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

  • amp_16q12.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_17p11.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_19q13.11 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • amp_20p11.23 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

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

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

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

  • del_1p13.1 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_2q22.1 cnv correlated to 'CN_CNMF'.

  • del_3p26.1 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_3p14.2 cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_3q26.31 cnv correlated to 'CN_CNMF'.

  • del_4p16.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

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

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

  • del_5q21.1 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_5q22.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_6q26 cnv correlated to 'RPPA_CNMF'.

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

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

  • del_8q11.1 cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • del_9p21.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

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

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

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

  • del_12p13.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • del_13q14.13 cnv correlated to 'CN_CNMF'.

  • del_14q31.1 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_15q11.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_15q15.2 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_15q21.1 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_15q22.33 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • del_16q23.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.

  • del_17p12 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_17q24.3 cnv correlated to 'MRNA_CNMF',  'CN_CNMF', and 'MIRSEQ_CNMF'.

  • del_18p11.31 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_18q12.2 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_18q21.2 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_18q22.1 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_19p13.3 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • del_22q13.32 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  '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 66 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, 448 significant findings detected.

Clinical
Features
MRNA
CNMF
MRNA
CHIERARCHICAL
CN
CNMF
METHLYATION
CNMF
RPPA
CNMF
RPPA
CHIERARCHICAL
MRNASEQ
CNMF
MRNASEQ
CHIERARCHICAL
MIRSEQ
CNMF
MIRSEQ
CHIERARCHICAL
MIRSEQ
MATURE
CNMF
MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
amp 20q11 21 323 (72%) 128 1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
0.0107
(0.0236)
0.0001
(0.000352)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
6e-05
(0.000232)
0.0288
(0.0552)
amp 20p11 21 252 (56%) 199 1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
8e-05
(0.000295)
0.00655
(0.0156)
0.0827
(0.133)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
0.00031
(0.000994)
1e-05
(4.86e-05)
0.0309
(0.0587)
0.00867
(0.0197)
amp 20q12 324 (72%) 127 1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
0.0199
(0.0405)
9e-05
(0.000325)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
6e-05
(0.000232)
0.0617
(0.105)
amp 20q13 12 326 (72%) 125 1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
0.0132
(0.0282)
6e-05
(0.000232)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
0.00011
(0.000384)
0.0615
(0.105)
del 18p11 31 248 (55%) 203 1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
0.311
(0.399)
0.00474
(0.0118)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
0.00048
(0.00148)
0.00353
(0.00905)
del 18q12 2 274 (61%) 177 1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
0.368
(0.46)
0.00508
(0.0124)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
0.00022
(0.000723)
0.0255
(0.0497)
del 18q21 2 287 (64%) 164 1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
0.203
(0.283)
0.00703
(0.0164)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
6e-05
(0.000232)
0.0326
(0.0609)
del 18q22 1 286 (63%) 165 1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
0.178
(0.255)
0.0129
(0.0278)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
5e-05
(0.000203)
0.0327
(0.0609)
amp 16p11 2 126 (28%) 325 1e-05
(4.86e-05)
4e-05
(0.000168)
1e-05
(4.86e-05)
0.00789
(0.0182)
0.103
(0.162)
0.0273
(0.0527)
0.00184
(0.00513)
1e-05
(4.86e-05)
0.00055
(0.00165)
0.0012
(0.00342)
0.0245
(0.048)
0.162
(0.235)
del 8p23 2 190 (42%) 261 2e-05
(9.1e-05)
0.00055
(0.00165)
1e-05
(4.86e-05)
0.00028
(0.000905)
0.663
(0.738)
0.0353
(0.0653)
3e-05
(0.000128)
1e-05
(4.86e-05)
0.00024
(0.000782)
0.00051
(0.00157)
0.00299
(0.00792)
0.122
(0.186)
del 8p22 203 (45%) 248 2e-05
(9.1e-05)
0.00012
(0.000417)
1e-05
(4.86e-05)
0.00023
(0.000753)
0.413
(0.509)
0.0168
(0.0348)
3e-05
(0.000128)
1e-05
(4.86e-05)
6e-05
(0.000232)
0.00045
(0.0014)
0.0081
(0.0184)
0.17
(0.245)
del 14q31 1 151 (33%) 300 1e-05
(4.86e-05)
0.0001
(0.000352)
1e-05
(4.86e-05)
0.00018
(0.000609)
0.0206
(0.0414)
0.226
(0.31)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
0.0181
(0.0372)
0.342
(0.431)
del 15q15 2 172 (38%) 279 8e-05
(0.000295)
0.00021
(0.000696)
1e-05
(4.86e-05)
4e-05
(0.000168)
0.0121
(0.0265)
0.159
(0.233)
3e-05
(0.000128)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
0.00094
(0.00275)
0.021
(0.0421)
0.292
(0.382)
del 15q21 1 169 (37%) 282 0.00194
(0.00537)
0.0103
(0.023)
1e-05
(4.86e-05)
9e-05
(0.000325)
0.0459
(0.0817)
0.152
(0.224)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
2e-05
(9.1e-05)
0.00243
(0.00661)
0.0313
(0.0593)
0.26
(0.348)
del 17p12 254 (56%) 197 1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
0.0561
(0.097)
0.00096
(0.0028)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
0.00366
(0.00935)
0.0526
(0.0918)
amp 13q12 13 276 (61%) 175 1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
0.0741
(0.122)
0.0838
(0.135)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
5e-05
(0.000203)
0.0212
(0.0423)
0.169
(0.244)
amp 16q12 1 111 (25%) 340 1e-05
(4.86e-05)
2e-05
(9.1e-05)
1e-05
(4.86e-05)
0.0251
(0.0491)
0.0463
(0.0821)
0.081
(0.132)
0.00298
(0.00792)
1e-05
(4.86e-05)
0.0232
(0.0456)
0.00247
(0.0067)
0.064
(0.108)
0.242
(0.327)
del 1p36 11 168 (37%) 283 3e-05
(0.000128)
0.00317
(0.00828)
1e-05
(4.86e-05)
9e-05
(0.000325)
0.105
(0.165)
0.0305
(0.058)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
0.00054
(0.00163)
1e-05
(4.86e-05)
0.0667
(0.112)
0.635
(0.713)
del 4p16 2 140 (31%) 311 3e-05
(0.000128)
0.00308
(0.0081)
1e-05
(4.86e-05)
0.00665
(0.0158)
0.684
(0.754)
0.00311
(0.00816)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
0.00018
(0.000609)
0.0634
(0.108)
0.04
(0.0725)
0.191
(0.271)
del 4q22 1 152 (34%) 299 0.00017
(0.00058)
0.00554
(0.0134)
1e-05
(4.86e-05)
0.0048
(0.0119)
0.776
(0.835)
0.476
(0.568)
6e-05
(0.000232)
1e-05
(4.86e-05)
0.0001
(0.000352)
0.00609
(0.0146)
0.00703
(0.0164)
0.302
(0.392)
del 5q12 1 106 (24%) 345 6e-05
(0.000232)
0.0155
(0.0326)
1e-05
(4.86e-05)
0.0166
(0.0345)
0.0257
(0.0498)
0.197
(0.276)
0.00013
(0.00045)
7e-05
(0.000262)
0.0006
(0.00179)
0.00631
(0.0151)
0.447
(0.539)
0.308
(0.396)
del 15q11 2 177 (39%) 274 6e-05
(0.000232)
0.0005
(0.00154)
1e-05
(4.86e-05)
9e-05
(0.000325)
0.113
(0.175)
0.351
(0.442)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
0.00336
(0.00867)
0.0166
(0.0345)
0.468
(0.56)
del 15q22 33 161 (36%) 290 1e-05
(4.86e-05)
0.00032
(0.00102)
1e-05
(4.86e-05)
2e-05
(9.1e-05)
0.258
(0.346)
0.22
(0.305)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
0.00053
(0.00161)
0.0366
(0.0674)
0.175
(0.251)
del 20p12 1 87 (19%) 364 0.324
(0.413)
0.0329
(0.0612)
1e-05
(4.86e-05)
0.00019
(0.00064)
0.072
(0.12)
0.0091
(0.0205)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
0.00256
(0.00692)
0.00497
(0.0123)
0.22
(0.305)
0.0486
(0.0859)
del 22q13 32 160 (35%) 291 2e-05
(9.1e-05)
3e-05
(0.000128)
1e-05
(4.86e-05)
0.0314
(0.0593)
0.145
(0.216)
0.0114
(0.025)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
0.00021
(0.000696)
0.0184
(0.0375)
0.325
(0.413)
0.887
(0.912)
amp 11p15 5 93 (21%) 358 2e-05
(9.1e-05)
0.00187
(0.0052)
1e-05
(4.86e-05)
0.00323
(0.00836)
0.179
(0.256)
0.248
(0.335)
3e-05
(0.000128)
1e-05
(4.86e-05)
0.0156
(0.0328)
1e-05
(4.86e-05)
0.246
(0.332)
0.707
(0.773)
amp 13q22 1 277 (61%) 174 1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
0.135
(0.204)
0.143
(0.214)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
7e-05
(0.000262)
0.0738
(0.122)
0.565
(0.656)
amp 17q12 114 (25%) 337 0.00499
(0.0123)
0.0273
(0.0527)
1e-05
(4.86e-05)
0.00447
(0.0112)
0.677
(0.75)
0.0205
(0.0413)
5e-05
(0.000203)
0.00108
(0.0031)
0.279
(0.368)
0.00041
(0.00128)
0.121
(0.184)
0.192
(0.271)
amp 20p11 23 220 (49%) 231 7e-05
(0.000262)
3e-05
(0.000128)
1e-05
(4.86e-05)
0.0521
(0.0915)
0.00945
(0.0211)
0.526
(0.617)
0.00057
(0.0017)
1e-05
(4.86e-05)
0.0123
(0.0269)
5e-05
(0.000203)
0.612
(0.697)
0.264
(0.352)
del 4q35 1 159 (35%) 292 0.0001
(0.000352)
0.00597
(0.0143)
1e-05
(4.86e-05)
0.00037
(0.00116)
0.879
(0.91)
0.304
(0.394)
1e-05
(4.86e-05)
1e-05
(4.86e-05)
0.00035
(0.0011)
0.148
(0.219)
0.0434
(0.0775)
0.964
(0.974)
del 10q23 31 109 (24%) 342 0.00321
(0.00834)
0.0433
(0.0774)
1e-05
(4.86e-05)
0.0148
(0.0314)
0.974
(0.983)
0.13
(0.197)
0.00563
(0.0136)
5e-05
(0.000203)
0.0554
(0.0963)
0.0042
(0.0106)
0.0399
(0.0725)
0.106
(0.166)
del 10q25 2 109 (24%) 342 0.0134
(0.0286)
0.00387
(0.00986)
1e-05
(4.86e-05)
0.00091
(0.00267)
0.118
(0.18)
0.146
(0.218)
3e-05
(0.000128)
1e-05
(4.86e-05)
0.00318
(0.00828)
0.00207
(0.00567)
0.266
(0.353)
0.312
(0.399)
del 12p13 2 60 (13%) 391 0.00053
(0.00161)
0.00805
(0.0184)
1e-05
(4.86e-05)
0.00206
(0.00566)
0.772
(0.833)
0.827
(0.873)
0.00125
(0.00354)
1e-05
(4.86e-05)
0.00426
(0.0107)
0.351
(0.442)
0.0464
(0.0821)
0.0869
(0.139)
amp 2q33 1 92 (20%) 359 0.0148
(0.0314)
0.0982
(0.155)
1e-05
(4.86e-05)
0.0212
(0.0423)
0.233
(0.317)
0.379
(0.471)
5e-05
(0.000203)
0.00201
(0.00555)
0.0177
(0.0364)
0.00103
(0.00297)
0.683
(0.754)
0.319
(0.408)
amp 8q24 21 260 (58%) 191 0.00102
(0.00296)
0.0519
(0.0915)
1e-05
(4.86e-05)
0.00278
(0.00746)
0.18
(0.257)
0.091
(0.145)
0.00052
(0.00159)
6e-05
(0.000232)
0.117
(0.179)
0.0338
(0.0626)
0.0101
(0.0225)
0.158
(0.232)
amp 17q24 1 106 (24%) 345 0.0645
(0.109)
0.0223
(0.044)
1e-05
(4.86e-05)
0.00025
(0.000811)
0.333
(0.421)
0.0586
(0.101)
2e-05
(9.1e-05)
2e-05
(9.1e-05)
0.0331
(0.0614)
0.00792
(0.0182)
0.161
(0.235)
0.73
(0.793)
amp 19q13 11 95 (21%) 356 0.00775
(0.0179)
0.0287
(0.0552)
0.00074
(0.00219)
0.628
(0.712)
0.0173
(0.0357)
0.782
(0.84)
0.191
(0.271)
0.00021
(0.000696)
0.0147
(0.0313)
0.0921
(0.146)
0.0794
(0.13)
0.0067
(0.0158)
amp 20p12 1 195 (43%) 256 1e-05
(4.86e-05)
7e-05
(0.000262)
1e-05
(4.86e-05)
0.168
(0.243)
0.00152
(0.00427)
0.707
(0.773)
0.0524
(0.0917)
1e-05
(4.86e-05)
0.0216
(0.0428)
0.00029
(0.000934)
0.494
(0.585)
0.588
(0.679)
del 1p33 123 (27%) 328 0.0185
(0.0376)
0.376
(0.469)
1e-05
(4.86e-05)
0.00504
(0.0124)
0.374
(0.466)
0.263
(0.351)
0.0001
(0.000352)
2e-05
(9.1e-05)
0.00276
(0.00744)
0.0128
(0.0278)
0.0853
(0.137)
0.631
(0.712)
del 1p13 1 119 (26%) 332 0.0222
(0.0439)
0.238
(0.324)
1e-05
(4.86e-05)
0.00937
(0.021)
0.308
(0.396)
0.289
(0.379)
7e-05
(0.000262)
8e-05
(0.000295)
0.00114
(0.00326)
0.0128
(0.0278)
0.397
(0.492)
0.65
(0.727)
del 5q21 1 127 (28%) 324 0.013
(0.0279)
0.0602
(0.103)
1e-05
(4.86e-05)
0.0371
(0.0679)
0.0429
(0.0768)
0.335
(0.423)
0.00668
(0.0158)
0.0001
(0.000352)
0.00897
(0.0202)
0.0749
(0.123)
0.0783
(0.129)
0.822
(0.869)
del 10q21 1 98 (22%) 353 0.00017
(0.00058)
0.0183
(0.0375)
1e-05
(4.86e-05)
0.0113
(0.0249)
0.633
(0.713)
0.14
(0.21)
3e-05
(0.000128)
3e-05
(0.000128)
0.159
(0.233)
0.0112
(0.0248)
0.191
(0.271)
0.786
(0.842)
del 21q11 2 141 (31%) 310 7e-05
(0.000262)
0.0237
(0.0467)
1e-05
(4.86e-05)
0.00446
(0.0112)
0.893
(0.914)
0.305
(0.395)
1e-05
(4.86e-05)
0.00042
(0.00131)
0.0151
(0.0318)
0.163
(0.236)
0.283
(0.372)
0.858
(0.896)
amp 8p11 21 189 (42%) 262 0.0791
(0.13)
0.0204
(0.0412)
1e-05
(4.86e-05)
0.139
(0.209)
0.604
(0.693)
0.18
(0.256)
0.0292
(0.0558)
0.00158
(0.00442)
0.695
(0.762)
0.0367
(0.0675)
0.0402
(0.0727)
0.172
(0.247)
del 5q22 2 130 (29%) 321 0.0002
(0.000671)
0.00307
(0.0081)
1e-05
(4.86e-05)
0.0545
(0.0948)
0.0624
(0.106)
0.151
(0.224)
0.00035
(0.0011)
7e-05
(0.000262)
0.0028
(0.00749)
0.0649
(0.11)
0.0793
(0.13)
0.69
(0.758)
del 9p21 3 62 (14%) 389 0.00212
(0.00579)
0.0209
(0.0419)
4e-05
(0.000168)
0.266
(0.353)
0.662
(0.738)
0.289
(0.379)
0.0281
(0.0542)
0.00123
(0.00349)
0.0127
(0.0277)
0.127
(0.192)
0.233
(0.317)
0.556
(0.648)
amp 5p13 2 87 (19%) 364 0.00804
(0.0184)
0.205
(0.285)
1e-05
(4.86e-05)
0.816
(0.866)
0.0174
(0.036)
0.873
(0.91)
0.0323
(0.0606)
0.00337
(0.00867)
0.0796
(0.13)
0.953
(0.968)
0.416
(0.512)
0.815
(0.866)
amp 6p21 1 96 (21%) 355 0.0819
(0.133)
0.00017
(0.00058)
1e-05
(4.86e-05)
0.0658
(0.111)
0.402
(0.498)
0.221
(0.305)
0.116
(0.179)
6e-05
(0.000232)
0.00534
(0.013)
0.0316
(0.0596)
0.0937
(0.149)
0.597
(0.687)
amp 17p11 2 44 (10%) 407 0.0325
(0.0608)
0.0118
(0.0258)
0.116
(0.179)
0.202
(0.283)
0.876
(0.91)
0.286
(0.376)
0.166
(0.24)
0.219
(0.304)
0.00285
(0.0076)
0.605
(0.693)
0.0368
(0.0675)
0.0248
(0.0485)
del 10p15 3 80 (18%) 371 0.00678
(0.0159)
0.237
(0.323)
1e-05
(4.86e-05)
0.00489
(0.0121)
0.721
(0.786)
0.232
(0.317)
0.00022
(0.000723)
0.00011
(0.000384)
0.192
(0.271)
0.108
(0.169)
0.0968
(0.153)
0.0525
(0.0917)
del 19p13 3 63 (14%) 388 0.00033
(0.00105)
0.071
(0.118)
0.00067
(0.00199)
0.664
(0.739)
0.576
(0.667)
0.63
(0.712)
0.00725
(0.0168)
0.00087
(0.00256)
0.584
(0.676)
0.00597
(0.0143)
0.52
(0.613)
0.329
(0.417)
del 3p26 1 72 (16%) 379 0.0392
(0.0714)
0.301
(0.391)
1e-05
(4.86e-05)
0.191
(0.271)
0.848
(0.89)
0.776
(0.835)
0.00695
(0.0163)
0.00458
(0.0114)
0.195
(0.275)
0.833
(0.877)
0.154
(0.227)
0.794
(0.847)
del 16q23 1 61 (14%) 390 0.00883
(0.02)
0.0039
(0.0099)
0.14
(0.209)
0.5
(0.592)
0.901
(0.921)
0.553
(0.646)
0.305
(0.395)
0.0158
(0.0331)
0.227
(0.311)
0.251
(0.337)
0.885
(0.911)
0.883
(0.911)
del 17q24 3 69 (15%) 382 0.02
(0.0405)
0.44
(0.535)
3e-05
(0.000128)
0.615
(0.698)
0.411
(0.508)
0.403
(0.499)
0.068
(0.114)
0.126
(0.192)
0.0074
(0.0171)
0.433
(0.53)
0.297
(0.387)
0.447
(0.539)
amp 8p11 23 158 (35%) 293 0.0679
(0.114)
0.119
(0.182)
2e-05
(9.1e-05)
0.223
(0.307)
0.308
(0.396)
0.273
(0.362)
0.126
(0.192)
0.0318
(0.0599)
0.325
(0.413)
0.108
(0.169)
0.0851
(0.137)
0.196
(0.276)
del 3p14 2 88 (20%) 363 0.239
(0.324)
0.598
(0.687)
0.0575
(0.0992)
0.487
(0.579)
0.437
(0.534)
0.637
(0.715)
0.0378
(0.0689)
0.0416
(0.075)
0.711
(0.776)
0.89
(0.912)
0.16
(0.233)
0.812
(0.864)
del 8q11 1 30 (7%) 421 0.0141
(0.0301)
0.0576
(0.0992)
0.00139
(0.00392)
0.953
(0.968)
0.151
(0.224)
0.69
(0.758)
0.732
(0.794)
0.0706
(0.118)
0.425
(0.521)
0.445
(0.539)
0.957
(0.97)
0.728
(0.792)
del 16p13 3 57 (13%) 394 0.873
(0.91)
0.484
(0.576)
0.0427
(0.0767)
0.0954
(0.151)
0.876
(0.91)
0.817
(0.866)
0.0422
(0.076)
0.0816
(0.132)
0.445
(0.539)
0.529
(0.619)
0.331
(0.419)
0.878
(0.91)
del 2q22 1 24 (5%) 427 0.678
(0.75)
0.461
(0.553)
0.0161
(0.0336)
0.599
(0.687)
1
(1.00)
0.425
(0.521)
0.519
(0.612)
0.318
(0.407)
0.0653
(0.11)
0.451
(0.542)
0.087
(0.139)
0.592
(0.683)
del 3q26 31 47 (10%) 404 0.23
(0.315)
0.491
(0.583)
0.00519
(0.0126)
0.417
(0.513)
0.497
(0.588)
0.96
(0.972)
0.137
(0.206)
0.136
(0.204)
0.116
(0.179)
0.674
(0.749)
0.732
(0.794)
0.777
(0.835)
del 6q26 62 (14%) 389 0.36
(0.451)
0.301
(0.391)
0.0736
(0.122)
0.558
(0.649)
0.0296
(0.0565)
0.77
(0.832)
0.354
(0.445)
0.675
(0.749)
0.839
(0.882)
0.821
(0.869)
0.545
(0.638)
0.635
(0.713)
del 13q14 13 19 (4%) 432 0.261
(0.349)
0.659
(0.736)
0.00103
(0.00297)
0.103
(0.162)
0.887
(0.912)
0.801
(0.854)
0.932
(0.949)
0.884
(0.911)
0.65
(0.727)
0.994
(1.00)
0.613
(0.697)
0.111
(0.173)
amp 12p13 33 112 (25%) 339 0.11
(0.172)
0.883
(0.911)
0.161
(0.235)
0.108
(0.169)
0.877
(0.91)
0.569
(0.66)
0.716
(0.782)
0.828
(0.873)
0.451
(0.542)
0.631
(0.712)
0.443
(0.538)
0.998
(1.00)
del 2p21 17 (4%) 434 0.052
(0.0915)
0.201
(0.281)
0.684
(0.754)
0.923
(0.941)
0.524
(0.615)
0.789
(0.843)
0.454
(0.544)
0.274
(0.362)
0.056
(0.097)
0.752
(0.813)
del 6p25 3 56 (12%) 395 0.855
(0.894)
0.555
(0.648)
0.296
(0.386)
0.242
(0.327)
0.44
(0.535)
0.474
(0.566)
0.203
(0.283)
0.911
(0.93)
0.839
(0.882)
0.89
(0.912)
0.0821
(0.133)
0.266
(0.353)
del 7q31 1 13 (3%) 438 0.612
(0.697)
0.612
(0.697)
0.785
(0.841)
0.358
(0.449)
0.421
(0.518)
0.854
(0.894)
0.445
(0.539)
0.61
(0.697)
0.521
(0.613)
0.964
(0.974)
'amp_2q33.1' versus 'MRNA_CNMF'

P value = 0.0148 (Fisher's exact test), Q value = 0.031

Table S1.  Gene #1: 'amp_2q33.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
AMP PEAK 1(2Q33.1) MUTATED 1 6 8 3 7
AMP PEAK 1(2Q33.1) WILD-TYPE 30 11 41 24 16

Figure S1.  Get High-res Image Gene #1: 'amp_2q33.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_2q33.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S2.  Gene #1: 'amp_2q33.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
AMP PEAK 1(2Q33.1) MUTATED 18 59 15
AMP PEAK 1(2Q33.1) WILD-TYPE 35 162 162

Figure S2.  Get High-res Image Gene #1: 'amp_2q33.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2q33.1' versus 'METHLYATION_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.042

Table S3.  Gene #1: 'amp_2q33.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
AMP PEAK 1(2Q33.1) MUTATED 18 32 16
AMP PEAK 1(2Q33.1) WILD-TYPE 67 71 90

Figure S3.  Get High-res Image Gene #1: 'amp_2q33.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2q33.1' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 2e-04

Table S4.  Gene #1: 'amp_2q33.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
AMP PEAK 1(2Q33.1) MUTATED 43 10 20 19
AMP PEAK 1(2Q33.1) WILD-TYPE 84 84 77 112

Figure S4.  Get High-res Image Gene #1: 'amp_2q33.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2q33.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00201 (Fisher's exact test), Q value = 0.0055

Table S5.  Gene #1: 'amp_2q33.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
AMP PEAK 1(2Q33.1) MUTATED 19 33 12 26 2
AMP PEAK 1(2Q33.1) WILD-TYPE 60 75 84 103 35

Figure S5.  Get High-res Image Gene #1: 'amp_2q33.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_2q33.1' versus 'MIRSEQ_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.036

Table S6.  Gene #1: 'amp_2q33.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
AMP PEAK 1(2Q33.1) MUTATED 15 16 17 20 10
AMP PEAK 1(2Q33.1) WILD-TYPE 45 72 54 55 94

Figure S6.  Get High-res Image Gene #1: 'amp_2q33.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_2q33.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00103 (Fisher's exact test), Q value = 0.003

Table S7.  Gene #1: '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 79 55 46 17 55 20 26 42 58
AMP PEAK 1(2Q33.1) MUTATED 16 13 13 2 17 1 4 0 12
AMP PEAK 1(2Q33.1) WILD-TYPE 63 42 33 15 38 19 22 42 46

Figure S7.  Get High-res Image Gene #1: 'amp_2q33.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5p13.2' versus 'MRNA_CNMF'

P value = 0.00804 (Fisher's exact test), Q value = 0.018

Table S8.  Gene #2: 'amp_5p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
AMP PEAK 2(5P13.2) MUTATED 2 8 14 3 5
AMP PEAK 2(5P13.2) WILD-TYPE 29 9 35 24 18

Figure S8.  Get High-res Image Gene #2: 'amp_5p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_5p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S9.  Gene #2: 'amp_5p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
AMP PEAK 2(5P13.2) MUTATED 18 55 14
AMP PEAK 2(5P13.2) WILD-TYPE 35 166 163

Figure S9.  Get High-res Image Gene #2: 'amp_5p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p13.2' versus 'RPPA_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.036

Table S10.  Gene #2: 'amp_5p13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 145 125
AMP PEAK 2(5P13.2) MUTATED 25 22 19
AMP PEAK 2(5P13.2) WILD-TYPE 60 123 106

Figure S10.  Get High-res Image Gene #2: 'amp_5p13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_5p13.2' versus 'MRNASEQ_CNMF'

P value = 0.0323 (Fisher's exact test), Q value = 0.061

Table S11.  Gene #2: 'amp_5p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
AMP PEAK 2(5P13.2) MUTATED 31 9 19 28
AMP PEAK 2(5P13.2) WILD-TYPE 96 85 78 103

Figure S11.  Get High-res Image Gene #2: 'amp_5p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00337 (Fisher's exact test), Q value = 0.0087

Table S12.  Gene #2: 'amp_5p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
AMP PEAK 2(5P13.2) MUTATED 24 16 10 32 5
AMP PEAK 2(5P13.2) WILD-TYPE 55 92 86 97 32

Figure S12.  Get High-res Image Gene #2: 'amp_5p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00058

Table S13.  Gene #3: 'amp_6p21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
AMP PEAK 3(6P21.1) MUTATED 2 11 16
AMP PEAK 3(6P21.1) WILD-TYPE 40 57 21

Figure S13.  Get High-res Image Gene #3: '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 = 4.9e-05

Table S14.  Gene #3: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
AMP PEAK 3(6P21.1) MUTATED 16 69 11
AMP PEAK 3(6P21.1) WILD-TYPE 37 152 166

Figure S14.  Get High-res Image Gene #3: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00023

Table S15.  Gene #3: 'amp_6p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
AMP PEAK 3(6P21.1) MUTATED 26 25 9 34 2
AMP PEAK 3(6P21.1) WILD-TYPE 53 83 87 95 35

Figure S15.  Get High-res Image Gene #3: 'amp_6p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_CNMF'

P value = 0.00534 (Fisher's exact test), Q value = 0.013

Table S16.  Gene #3: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
AMP PEAK 3(6P21.1) MUTATED 19 15 18 22 12
AMP PEAK 3(6P21.1) WILD-TYPE 41 73 53 53 92

Figure S16.  Get High-res Image Gene #3: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_6p21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0316 (Fisher's exact test), Q value = 0.06

Table S17.  Gene #3: '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 79 55 46 17 55 20 26 42 58
AMP PEAK 3(6P21.1) MUTATED 19 15 10 2 16 1 3 3 17
AMP PEAK 3(6P21.1) WILD-TYPE 60 40 36 15 39 19 23 39 41

Figure S17.  Get High-res Image Gene #3: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.23' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.1e-05

Table S18.  Gene #4: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
AMP PEAK 4(8P11.23) MUTATED 33 84 41
AMP PEAK 4(8P11.23) WILD-TYPE 20 137 136

Figure S18.  Get High-res Image Gene #4: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0318 (Fisher's exact test), Q value = 0.06

Table S19.  Gene #4: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
AMP PEAK 4(8P11.23) MUTATED 33 45 31 41 6
AMP PEAK 4(8P11.23) WILD-TYPE 46 63 65 88 31

Figure S19.  Get High-res Image Gene #4: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.0204 (Fisher's exact test), Q value = 0.041

Table S20.  Gene #5: 'amp_8p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
AMP PEAK 5(8P11.21) MUTATED 9 26 19
AMP PEAK 5(8P11.21) WILD-TYPE 33 42 18

Figure S20.  Get High-res Image Gene #5: '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 = 4.9e-05

Table S21.  Gene #5: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
AMP PEAK 5(8P11.21) MUTATED 35 108 46
AMP PEAK 5(8P11.21) WILD-TYPE 18 113 131

Figure S21.  Get High-res Image Gene #5: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CNMF'

P value = 0.0292 (Fisher's exact test), Q value = 0.056

Table S22.  Gene #5: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
AMP PEAK 5(8P11.21) MUTATED 59 30 49 49
AMP PEAK 5(8P11.21) WILD-TYPE 68 64 48 82

Figure S22.  Get High-res Image Gene #5: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00158 (Fisher's exact test), Q value = 0.0044

Table S23.  Gene #5: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
AMP PEAK 5(8P11.21) MUTATED 44 49 33 54 7
AMP PEAK 5(8P11.21) WILD-TYPE 35 59 63 75 30

Figure S23.  Get High-res Image Gene #5: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0367 (Fisher's exact test), Q value = 0.067

Table S24.  Gene #5: 'amp_8p11.21' 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 79 55 46 17 55 20 26 42 58
AMP PEAK 5(8P11.21) MUTATED 27 28 19 8 28 12 6 12 28
AMP PEAK 5(8P11.21) WILD-TYPE 52 27 27 9 27 8 20 30 30

Figure S24.  Get High-res Image Gene #5: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0402 (Fisher's exact test), Q value = 0.073

Table S25.  Gene #5: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
AMP PEAK 5(8P11.21) MUTATED 7 13 6 7 2 7
AMP PEAK 5(8P11.21) WILD-TYPE 11 7 10 4 9 2

Figure S25.  Get High-res Image Gene #5: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MRNA_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.003

Table S26.  Gene #6: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
AMP PEAK 6(8Q24.21) MUTATED 8 14 26 14 16
AMP PEAK 6(8Q24.21) WILD-TYPE 23 3 23 13 7

Figure S26.  Get High-res Image Gene #6: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S27.  Gene #6: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
AMP PEAK 6(8Q24.21) MUTATED 41 158 61
AMP PEAK 6(8Q24.21) WILD-TYPE 12 63 116

Figure S27.  Get High-res Image Gene #6: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 0.00278 (Fisher's exact test), Q value = 0.0075

Table S28.  Gene #6: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
AMP PEAK 6(8Q24.21) MUTATED 50 76 54
AMP PEAK 6(8Q24.21) WILD-TYPE 35 27 52

Figure S28.  Get High-res Image Gene #6: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0016

Table S29.  Gene #6: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
AMP PEAK 6(8Q24.21) MUTATED 87 40 62 69
AMP PEAK 6(8Q24.21) WILD-TYPE 40 54 35 62

Figure S29.  Get High-res Image Gene #6: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00023

Table S30.  Gene #6: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
AMP PEAK 6(8Q24.21) MUTATED 56 69 44 78 11
AMP PEAK 6(8Q24.21) WILD-TYPE 23 39 52 51 26

Figure S30.  Get High-res Image Gene #6: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0338 (Fisher's exact test), Q value = 0.063

Table S31.  Gene #6: '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 79 55 46 17 55 20 26 42 58
AMP PEAK 6(8Q24.21) MUTATED 39 35 30 8 40 13 13 17 36
AMP PEAK 6(8Q24.21) WILD-TYPE 40 20 16 9 15 7 13 25 22

Figure S31.  Get High-res Image Gene #6: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.023

Table S32.  Gene #6: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
AMP PEAK 6(8Q24.21) MUTATED 13 17 6 9 4 7
AMP PEAK 6(8Q24.21) WILD-TYPE 5 3 10 2 7 2

Figure S32.  Get High-res Image Gene #6: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_11p15.5' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.1e-05

Table S33.  Gene #7: 'amp_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
AMP PEAK 7(11P15.5) MUTATED 0 4 13 4 13
AMP PEAK 7(11P15.5) WILD-TYPE 31 13 36 23 10

Figure S33.  Get High-res Image Gene #7: 'amp_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11p15.5' versus 'MRNA_CHIERARCHICAL'

P value = 0.00187 (Fisher's exact test), Q value = 0.0052

Table S34.  Gene #7: 'amp_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
AMP PEAK 7(11P15.5) MUTATED 3 16 15
AMP PEAK 7(11P15.5) WILD-TYPE 39 52 22

Figure S34.  Get High-res Image Gene #7: '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 = 4.9e-05

Table S35.  Gene #7: 'amp_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
AMP PEAK 7(11P15.5) MUTATED 15 66 12
AMP PEAK 7(11P15.5) WILD-TYPE 38 155 165

Figure S35.  Get High-res Image Gene #7: 'amp_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11p15.5' versus 'METHLYATION_CNMF'

P value = 0.00323 (Fisher's exact test), Q value = 0.0084

Table S36.  Gene #7: 'amp_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
AMP PEAK 7(11P15.5) MUTATED 17 28 10
AMP PEAK 7(11P15.5) WILD-TYPE 68 75 96

Figure S36.  Get High-res Image Gene #7: 'amp_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11p15.5' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00013

Table S37.  Gene #7: 'amp_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
AMP PEAK 7(11P15.5) MUTATED 41 5 18 28
AMP PEAK 7(11P15.5) WILD-TYPE 86 89 79 103

Figure S37.  Get High-res Image Gene #7: '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 = 4.9e-05

Table S38.  Gene #7: 'amp_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
AMP PEAK 7(11P15.5) MUTATED 21 27 3 40 1
AMP PEAK 7(11P15.5) WILD-TYPE 58 81 93 89 36

Figure S38.  Get High-res Image Gene #7: 'amp_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11p15.5' versus 'MIRSEQ_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.033

Table S39.  Gene #7: 'amp_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
AMP PEAK 7(11P15.5) MUTATED 13 9 16 24 21
AMP PEAK 7(11P15.5) WILD-TYPE 47 79 55 51 83

Figure S39.  Get High-res Image Gene #7: 'amp_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S40.  Gene #7: '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 79 55 46 17 55 20 26 42 58
AMP PEAK 7(11P15.5) MUTATED 7 12 32 0 16 0 2 1 13
AMP PEAK 7(11P15.5) WILD-TYPE 72 43 14 17 39 20 24 41 45

Figure S40.  Get High-res Image Gene #7: 'amp_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_13q12.13' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S41.  Gene #9: 'amp_13q12.13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
AMP PEAK 9(13Q12.13) MUTATED 8 14 42 11 18
AMP PEAK 9(13Q12.13) WILD-TYPE 23 3 7 16 5

Figure S41.  Get High-res Image Gene #9: '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 = 4.9e-05

Table S42.  Gene #9: 'amp_13q12.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
AMP PEAK 9(13Q12.13) MUTATED 13 47 33
AMP PEAK 9(13Q12.13) WILD-TYPE 29 21 4

Figure S42.  Get High-res Image Gene #9: '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 = 4.9e-05

Table S43.  Gene #9: 'amp_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
AMP PEAK 9(13Q12.13) MUTATED 40 197 39
AMP PEAK 9(13Q12.13) WILD-TYPE 13 24 138

Figure S43.  Get High-res Image Gene #9: '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 = 4.9e-05

Table S44.  Gene #9: 'amp_13q12.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
AMP PEAK 9(13Q12.13) MUTATED 42 88 51
AMP PEAK 9(13Q12.13) WILD-TYPE 43 15 55

Figure S44.  Get High-res Image Gene #9: 'amp_13q12.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q12.13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S45.  Gene #9: 'amp_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
AMP PEAK 9(13Q12.13) MUTATED 97 34 58 85
AMP PEAK 9(13Q12.13) WILD-TYPE 30 60 39 46

Figure S45.  Get High-res Image Gene #9: '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 = 4.9e-05

Table S46.  Gene #9: 'amp_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
AMP PEAK 9(13Q12.13) MUTATED 68 76 26 95 9
AMP PEAK 9(13Q12.13) WILD-TYPE 11 32 70 34 28

Figure S46.  Get High-res Image Gene #9: '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 = 4.9e-05

Table S47.  Gene #9: 'amp_13q12.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
AMP PEAK 9(13Q12.13) MUTATED 50 37 46 58 53
AMP PEAK 9(13Q12.13) WILD-TYPE 10 51 25 17 51

Figure S47.  Get High-res Image Gene #9: 'amp_13q12.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q12.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 2e-04

Table S48.  Gene #9: '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 79 55 46 17 55 20 26 42 58
AMP PEAK 9(13Q12.13) MUTATED 50 33 27 5 37 11 16 15 50
AMP PEAK 9(13Q12.13) WILD-TYPE 29 22 19 12 18 9 10 27 8

Figure S48.  Get High-res Image Gene #9: 'amp_13q12.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_13q12.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.042

Table S49.  Gene #9: 'amp_13q12.13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
AMP PEAK 9(13Q12.13) MUTATED 14 13 9 11 4 7
AMP PEAK 9(13Q12.13) WILD-TYPE 4 7 7 0 7 2

Figure S49.  Get High-res Image Gene #9: 'amp_13q12.13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_13q22.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S50.  Gene #10: 'amp_13q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
AMP PEAK 10(13Q22.1) MUTATED 7 15 40 12 17
AMP PEAK 10(13Q22.1) WILD-TYPE 24 2 9 15 6

Figure S50.  Get High-res Image Gene #10: '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 = 4.9e-05

Table S51.  Gene #10: 'amp_13q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
AMP PEAK 10(13Q22.1) MUTATED 12 48 31
AMP PEAK 10(13Q22.1) WILD-TYPE 30 20 6

Figure S51.  Get High-res Image Gene #10: '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 = 4.9e-05

Table S52.  Gene #10: 'amp_13q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
AMP PEAK 10(13Q22.1) MUTATED 39 194 44
AMP PEAK 10(13Q22.1) WILD-TYPE 14 27 133

Figure S52.  Get High-res Image Gene #10: '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 = 4.9e-05

Table S53.  Gene #10: 'amp_13q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
AMP PEAK 10(13Q22.1) MUTATED 43 85 54
AMP PEAK 10(13Q22.1) WILD-TYPE 42 18 52

Figure S53.  Get High-res Image Gene #10: 'amp_13q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S54.  Gene #10: 'amp_13q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
AMP PEAK 10(13Q22.1) MUTATED 96 35 61 83
AMP PEAK 10(13Q22.1) WILD-TYPE 31 59 36 48

Figure S54.  Get High-res Image Gene #10: '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 = 4.9e-05

Table S55.  Gene #10: 'amp_13q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
AMP PEAK 10(13Q22.1) MUTATED 67 76 30 93 9
AMP PEAK 10(13Q22.1) WILD-TYPE 12 32 66 36 28

Figure S55.  Get High-res Image Gene #10: '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 = 4.9e-05

Table S56.  Gene #10: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
AMP PEAK 10(13Q22.1) MUTATED 50 38 46 61 51
AMP PEAK 10(13Q22.1) WILD-TYPE 10 50 25 14 53

Figure S56.  Get High-res Image Gene #10: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00026

Table S57.  Gene #10: '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 79 55 46 17 55 20 26 42 58
AMP PEAK 10(13Q22.1) MUTATED 51 34 30 5 36 12 16 14 48
AMP PEAK 10(13Q22.1) WILD-TYPE 28 21 16 12 19 8 10 28 10

Figure S57.  Get High-res Image Gene #10: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S58.  Gene #11: 'amp_16p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
AMP PEAK 11(16P11.2) MUTATED 1 9 18 3 14
AMP PEAK 11(16P11.2) WILD-TYPE 30 8 31 24 9

Figure S58.  Get High-res Image Gene #11: 'amp_16p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_16p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00017

Table S59.  Gene #11: 'amp_16p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
AMP PEAK 11(16P11.2) MUTATED 5 18 22
AMP PEAK 11(16P11.2) WILD-TYPE 37 50 15

Figure S59.  Get High-res Image Gene #11: '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 = 4.9e-05

Table S60.  Gene #11: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
AMP PEAK 11(16P11.2) MUTATED 15 101 10
AMP PEAK 11(16P11.2) WILD-TYPE 38 120 167

Figure S60.  Get High-res Image Gene #11: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_16p11.2' versus 'METHLYATION_CNMF'

P value = 0.00789 (Fisher's exact test), Q value = 0.018

Table S61.  Gene #11: 'amp_16p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
AMP PEAK 11(16P11.2) MUTATED 26 36 18
AMP PEAK 11(16P11.2) WILD-TYPE 59 67 88

Figure S61.  Get High-res Image Gene #11: 'amp_16p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_16p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0273 (Fisher's exact test), Q value = 0.053

Table S62.  Gene #11: 'amp_16p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 43 86 22 20 26
AMP PEAK 11(16P11.2) MUTATED 20 3 14 12 12 22 2 6 6
AMP PEAK 11(16P11.2) WILD-TYPE 31 30 21 27 31 64 20 14 20

Figure S62.  Get High-res Image Gene #11: 'amp_16p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_16p11.2' versus 'MRNASEQ_CNMF'

P value = 0.00184 (Fisher's exact test), Q value = 0.0051

Table S63.  Gene #11: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
AMP PEAK 11(16P11.2) MUTATED 45 14 23 44
AMP PEAK 11(16P11.2) WILD-TYPE 82 80 74 87

Figure S63.  Get High-res Image Gene #11: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_16p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S64.  Gene #11: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
AMP PEAK 11(16P11.2) MUTATED 30 30 12 53 1
AMP PEAK 11(16P11.2) WILD-TYPE 49 78 84 76 36

Figure S64.  Get High-res Image Gene #11: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'MIRSEQ_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0016

Table S65.  Gene #11: 'amp_16p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
AMP PEAK 11(16P11.2) MUTATED 21 16 25 32 20
AMP PEAK 11(16P11.2) WILD-TYPE 39 72 46 43 84

Figure S65.  Get High-res Image Gene #11: 'amp_16p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_16p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0012 (Fisher's exact test), Q value = 0.0034

Table S66.  Gene #11: '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 79 55 46 17 55 20 26 42 58
AMP PEAK 11(16P11.2) MUTATED 21 17 12 0 19 4 10 5 26
AMP PEAK 11(16P11.2) WILD-TYPE 58 38 34 17 36 16 16 37 32

Figure S66.  Get High-res Image Gene #11: 'amp_16p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0245 (Fisher's exact test), Q value = 0.048

Table S67.  Gene #11: 'amp_16p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
AMP PEAK 11(16P11.2) MUTATED 8 7 4 5 0 6
AMP PEAK 11(16P11.2) WILD-TYPE 10 13 12 6 11 3

Figure S67.  Get High-res Image Gene #11: 'amp_16p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_16q12.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S68.  Gene #12: 'amp_16q12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
AMP PEAK 12(16Q12.1) MUTATED 0 6 17 3 14
AMP PEAK 12(16Q12.1) WILD-TYPE 31 11 32 24 9

Figure S68.  Get High-res Image Gene #12: 'amp_16q12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_16q12.1' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9.1e-05

Table S69.  Gene #12: 'amp_16q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
AMP PEAK 12(16Q12.1) MUTATED 2 18 20
AMP PEAK 12(16Q12.1) WILD-TYPE 40 50 17

Figure S69.  Get High-res Image Gene #12: 'amp_16q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_16q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S70.  Gene #12: 'amp_16q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
AMP PEAK 12(16Q12.1) MUTATED 13 92 6
AMP PEAK 12(16Q12.1) WILD-TYPE 40 129 171

Figure S70.  Get High-res Image Gene #12: 'amp_16q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_16q12.1' versus 'METHLYATION_CNMF'

P value = 0.0251 (Fisher's exact test), Q value = 0.049

Table S71.  Gene #12: 'amp_16q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
AMP PEAK 12(16Q12.1) MUTATED 24 30 16
AMP PEAK 12(16Q12.1) WILD-TYPE 61 73 90

Figure S71.  Get High-res Image Gene #12: 'amp_16q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_16q12.1' versus 'RPPA_CNMF'

P value = 0.0463 (Fisher's exact test), Q value = 0.082

Table S72.  Gene #12: 'amp_16q12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 145 125
AMP PEAK 12(16Q12.1) MUTATED 29 29 27
AMP PEAK 12(16Q12.1) WILD-TYPE 56 116 98

Figure S72.  Get High-res Image Gene #12: 'amp_16q12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_16q12.1' versus 'MRNASEQ_CNMF'

P value = 0.00298 (Fisher's exact test), Q value = 0.0079

Table S73.  Gene #12: 'amp_16q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
AMP PEAK 12(16Q12.1) MUTATED 41 12 20 38
AMP PEAK 12(16Q12.1) WILD-TYPE 86 82 77 93

Figure S73.  Get High-res Image Gene #12: 'amp_16q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_16q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S74.  Gene #12: 'amp_16q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
AMP PEAK 12(16Q12.1) MUTATED 29 25 10 47 0
AMP PEAK 12(16Q12.1) WILD-TYPE 50 83 86 82 37

Figure S74.  Get High-res Image Gene #12: 'amp_16q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_16q12.1' versus 'MIRSEQ_CNMF'

P value = 0.0232 (Fisher's exact test), Q value = 0.046

Table S75.  Gene #12: 'amp_16q12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
AMP PEAK 12(16Q12.1) MUTATED 18 15 24 24 19
AMP PEAK 12(16Q12.1) WILD-TYPE 42 73 47 51 85

Figure S75.  Get High-res Image Gene #12: 'amp_16q12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_16q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00247 (Fisher's exact test), Q value = 0.0067

Table S76.  Gene #12: 'amp_16q12.1' 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 79 55 46 17 55 20 26 42 58
AMP PEAK 12(16Q12.1) MUTATED 17 16 12 0 16 3 8 4 24
AMP PEAK 12(16Q12.1) WILD-TYPE 62 39 34 17 39 17 18 38 34

Figure S76.  Get High-res Image Gene #12: 'amp_16q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17p11.2' versus 'MRNA_CNMF'

P value = 0.0325 (Fisher's exact test), Q value = 0.061

Table S77.  Gene #13: 'amp_17p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
AMP PEAK 13(17P11.2) MUTATED 2 4 3 0 4
AMP PEAK 13(17P11.2) WILD-TYPE 29 13 46 27 19

Figure S77.  Get High-res Image Gene #13: 'amp_17p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0118 (Fisher's exact test), Q value = 0.026

Table S78.  Gene #13: 'amp_17p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
AMP PEAK 13(17P11.2) MUTATED 2 3 8
AMP PEAK 13(17P11.2) WILD-TYPE 40 65 29

Figure S78.  Get High-res Image Gene #13: 'amp_17p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17p11.2' versus 'MIRSEQ_CNMF'

P value = 0.00285 (Fisher's exact test), Q value = 0.0076

Table S79.  Gene #13: 'amp_17p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
AMP PEAK 13(17P11.2) MUTATED 6 6 9 15 3
AMP PEAK 13(17P11.2) WILD-TYPE 54 82 62 60 101

Figure S79.  Get High-res Image Gene #13: 'amp_17p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0368 (Fisher's exact test), Q value = 0.067

Table S80.  Gene #13: 'amp_17p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
AMP PEAK 13(17P11.2) MUTATED 0 5 1 3 0 2
AMP PEAK 13(17P11.2) WILD-TYPE 18 15 15 8 11 7

Figure S80.  Get High-res Image Gene #13: 'amp_17p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0248 (Fisher's exact test), Q value = 0.049

Table S81.  Gene #13: 'amp_17p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 12 9 8 12 9 7 13 9 6
AMP PEAK 13(17P11.2) MUTATED 0 1 2 0 1 4 2 1 0
AMP PEAK 13(17P11.2) WILD-TYPE 12 8 6 12 8 3 11 8 6

Figure S81.  Get High-res Image Gene #13: 'amp_17p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q12' versus 'MRNA_CNMF'

P value = 0.00499 (Fisher's exact test), Q value = 0.012

Table S82.  Gene #14: 'amp_17q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
AMP PEAK 14(17Q12) MUTATED 2 7 16 3 8
AMP PEAK 14(17Q12) WILD-TYPE 29 10 33 24 15

Figure S82.  Get High-res Image Gene #14: 'amp_17q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.0273 (Fisher's exact test), Q value = 0.053

Table S83.  Gene #14: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
AMP PEAK 14(17Q12) MUTATED 5 17 14
AMP PEAK 14(17Q12) WILD-TYPE 37 51 23

Figure S83.  Get High-res Image Gene #14: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S84.  Gene #14: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
AMP PEAK 14(17Q12) MUTATED 16 81 17
AMP PEAK 14(17Q12) WILD-TYPE 37 140 160

Figure S84.  Get High-res Image Gene #14: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 0.00447 (Fisher's exact test), Q value = 0.011

Table S85.  Gene #14: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
AMP PEAK 14(17Q12) MUTATED 18 39 20
AMP PEAK 14(17Q12) WILD-TYPE 67 64 86

Figure S85.  Get High-res Image Gene #14: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.0205 (Fisher's exact test), Q value = 0.041

Table S86.  Gene #14: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 43 86 22 20 26
AMP PEAK 14(17Q12) MUTATED 17 5 6 8 13 19 0 5 10
AMP PEAK 14(17Q12) WILD-TYPE 34 28 29 31 30 67 22 15 16

Figure S86.  Get High-res Image Gene #14: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 2e-04

Table S87.  Gene #14: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
AMP PEAK 14(17Q12) MUTATED 52 15 17 29
AMP PEAK 14(17Q12) WILD-TYPE 75 79 80 102

Figure S87.  Get High-res Image Gene #14: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00108 (Fisher's exact test), Q value = 0.0031

Table S88.  Gene #14: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
AMP PEAK 14(17Q12) MUTATED 21 38 12 37 5
AMP PEAK 14(17Q12) WILD-TYPE 58 70 84 92 32

Figure S88.  Get High-res Image Gene #14: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0013

Table S89.  Gene #14: '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 79 55 46 17 55 20 26 42 58
AMP PEAK 14(17Q12) MUTATED 22 13 16 0 22 3 7 2 16
AMP PEAK 14(17Q12) WILD-TYPE 57 42 30 17 33 17 19 40 42

Figure S89.  Get High-res Image Gene #14: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q24.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0223 (Fisher's exact test), Q value = 0.044

Table S90.  Gene #15: 'amp_17q24.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
AMP PEAK 15(17Q24.1) MUTATED 4 15 13
AMP PEAK 15(17Q24.1) WILD-TYPE 38 53 24

Figure S90.  Get High-res Image Gene #15: '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 = 4.9e-05

Table S91.  Gene #15: 'amp_17q24.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
AMP PEAK 15(17Q24.1) MUTATED 13 78 15
AMP PEAK 15(17Q24.1) WILD-TYPE 40 143 162

Figure S91.  Get High-res Image Gene #15: 'amp_17q24.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q24.1' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.00081

Table S92.  Gene #15: 'amp_17q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
AMP PEAK 15(17Q24.1) MUTATED 14 40 19
AMP PEAK 15(17Q24.1) WILD-TYPE 71 63 87

Figure S92.  Get High-res Image Gene #15: '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 = 9.1e-05

Table S93.  Gene #15: 'amp_17q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
AMP PEAK 15(17Q24.1) MUTATED 51 15 15 25
AMP PEAK 15(17Q24.1) WILD-TYPE 76 79 82 106

Figure S93.  Get High-res Image Gene #15: 'amp_17q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9.1e-05

Table S94.  Gene #15: 'amp_17q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
AMP PEAK 15(17Q24.1) MUTATED 21 39 8 34 4
AMP PEAK 15(17Q24.1) WILD-TYPE 58 69 88 95 33

Figure S94.  Get High-res Image Gene #15: 'amp_17q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q24.1' versus 'MIRSEQ_CNMF'

P value = 0.0331 (Fisher's exact test), Q value = 0.061

Table S95.  Gene #15: 'amp_17q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
AMP PEAK 15(17Q24.1) MUTATED 19 17 14 25 17
AMP PEAK 15(17Q24.1) WILD-TYPE 41 71 57 50 87

Figure S95.  Get High-res Image Gene #15: 'amp_17q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00792 (Fisher's exact test), Q value = 0.018

Table S96.  Gene #15: '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 79 55 46 17 55 20 26 42 58
AMP PEAK 15(17Q24.1) MUTATED 23 10 14 0 19 2 6 4 14
AMP PEAK 15(17Q24.1) WILD-TYPE 56 45 32 17 36 18 20 38 44

Figure S96.  Get High-res Image Gene #15: 'amp_17q24.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19q13.11' versus 'MRNA_CNMF'

P value = 0.00775 (Fisher's exact test), Q value = 0.018

Table S97.  Gene #16: 'amp_19q13.11' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
AMP PEAK 16(19Q13.11) MUTATED 0 6 9 6 4
AMP PEAK 16(19Q13.11) WILD-TYPE 31 11 40 21 19

Figure S97.  Get High-res Image Gene #16: 'amp_19q13.11' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q13.11' versus 'MRNA_CHIERARCHICAL'

P value = 0.0287 (Fisher's exact test), Q value = 0.055

Table S98.  Gene #16: 'amp_19q13.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
AMP PEAK 16(19Q13.11) MUTATED 2 16 7
AMP PEAK 16(19Q13.11) WILD-TYPE 40 52 30

Figure S98.  Get High-res Image Gene #16: 'amp_19q13.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q13.11' versus 'CN_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.0022

Table S99.  Gene #16: 'amp_19q13.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
AMP PEAK 16(19Q13.11) MUTATED 17 56 22
AMP PEAK 16(19Q13.11) WILD-TYPE 36 165 155

Figure S99.  Get High-res Image Gene #16: 'amp_19q13.11' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q13.11' versus 'RPPA_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 0.036

Table S100.  Gene #16: 'amp_19q13.11' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 145 125
AMP PEAK 16(19Q13.11) MUTATED 25 33 17
AMP PEAK 16(19Q13.11) WILD-TYPE 60 112 108

Figure S100.  Get High-res Image Gene #16: 'amp_19q13.11' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19q13.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 7e-04

Table S101.  Gene #16: 'amp_19q13.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
AMP PEAK 16(19Q13.11) MUTATED 28 24 13 29 1
AMP PEAK 16(19Q13.11) WILD-TYPE 51 84 83 100 36

Figure S101.  Get High-res Image Gene #16: 'amp_19q13.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q13.11' versus 'MIRSEQ_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.031

Table S102.  Gene #16: 'amp_19q13.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
AMP PEAK 16(19Q13.11) MUTATED 19 14 21 14 14
AMP PEAK 16(19Q13.11) WILD-TYPE 41 74 50 61 90

Figure S102.  Get High-res Image Gene #16: 'amp_19q13.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19q13.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0067 (Fisher's exact test), Q value = 0.016

Table S103.  Gene #16: 'amp_19q13.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 12 9 8 12 9 7 13 9 6
AMP PEAK 16(19Q13.11) MUTATED 4 4 5 1 1 1 0 1 0
AMP PEAK 16(19Q13.11) WILD-TYPE 8 5 3 11 8 6 13 8 6

Figure S103.  Get High-res Image Gene #16: 'amp_19q13.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20p12.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S104.  Gene #17: 'amp_20p12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
AMP PEAK 17(20P12.1) MUTATED 3 10 27 13 17
AMP PEAK 17(20P12.1) WILD-TYPE 28 7 22 14 6

Figure S104.  Get High-res Image Gene #17: 'amp_20p12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20p12.1' versus 'MRNA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00026

Table S105.  Gene #17: 'amp_20p12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
AMP PEAK 17(20P12.1) MUTATED 9 43 18
AMP PEAK 17(20P12.1) WILD-TYPE 33 25 19

Figure S105.  Get High-res Image Gene #17: '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 = 4.9e-05

Table S106.  Gene #17: 'amp_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
AMP PEAK 17(20P12.1) MUTATED 52 104 39
AMP PEAK 17(20P12.1) WILD-TYPE 1 117 138

Figure S106.  Get High-res Image Gene #17: 'amp_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p12.1' versus 'RPPA_CNMF'

P value = 0.00152 (Fisher's exact test), Q value = 0.0043

Table S107.  Gene #17: 'amp_20p12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 145 125
AMP PEAK 17(20P12.1) MUTATED 47 59 38
AMP PEAK 17(20P12.1) WILD-TYPE 38 86 87

Figure S107.  Get High-res Image Gene #17: 'amp_20p12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S108.  Gene #17: 'amp_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
AMP PEAK 17(20P12.1) MUTATED 34 52 28 74 5
AMP PEAK 17(20P12.1) WILD-TYPE 45 56 68 55 32

Figure S108.  Get High-res Image Gene #17: 'amp_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20p12.1' versus 'MIRSEQ_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 0.043

Table S109.  Gene #17: 'amp_20p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
AMP PEAK 17(20P12.1) MUTATED 31 27 34 39 40
AMP PEAK 17(20P12.1) WILD-TYPE 29 61 37 36 64

Figure S109.  Get High-res Image Gene #17: 'amp_20p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.00093

Table S110.  Gene #17: '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 79 55 46 17 55 20 26 42 58
AMP PEAK 17(20P12.1) MUTATED 32 21 21 4 27 9 12 7 38
AMP PEAK 17(20P12.1) WILD-TYPE 47 34 25 13 28 11 14 35 20

Figure S110.  Get High-res Image Gene #17: 'amp_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20p11.23' versus 'MRNA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00026

Table S111.  Gene #18: 'amp_20p11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
AMP PEAK 18(20P11.23) MUTATED 4 9 29 14 17
AMP PEAK 18(20P11.23) WILD-TYPE 27 8 20 13 6

Figure S111.  Get High-res Image Gene #18: 'amp_20p11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20p11.23' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00013

Table S112.  Gene #18: 'amp_20p11.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
AMP PEAK 18(20P11.23) MUTATED 10 46 17
AMP PEAK 18(20P11.23) WILD-TYPE 32 22 20

Figure S112.  Get High-res Image Gene #18: 'amp_20p11.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S113.  Gene #18: 'amp_20p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
AMP PEAK 18(20P11.23) MUTATED 53 124 43
AMP PEAK 18(20P11.23) WILD-TYPE 0 97 134

Figure S113.  Get High-res Image Gene #18: 'amp_20p11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p11.23' versus 'RPPA_CNMF'

P value = 0.00945 (Fisher's exact test), Q value = 0.021

Table S114.  Gene #18: 'amp_20p11.23' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 145 125
AMP PEAK 18(20P11.23) MUTATED 48 71 45
AMP PEAK 18(20P11.23) WILD-TYPE 37 74 80

Figure S114.  Get High-res Image Gene #18: 'amp_20p11.23' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20p11.23' versus 'MRNASEQ_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0017

Table S115.  Gene #18: 'amp_20p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
AMP PEAK 18(20P11.23) MUTATED 79 33 42 64
AMP PEAK 18(20P11.23) WILD-TYPE 48 61 55 67

Figure S115.  Get High-res Image Gene #18: 'amp_20p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20p11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S116.  Gene #18: 'amp_20p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
AMP PEAK 18(20P11.23) MUTATED 42 62 30 78 6
AMP PEAK 18(20P11.23) WILD-TYPE 37 46 66 51 31

Figure S116.  Get High-res Image Gene #18: 'amp_20p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20p11.23' versus 'MIRSEQ_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.027

Table S117.  Gene #18: 'amp_20p11.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
AMP PEAK 18(20P11.23) MUTATED 34 33 40 44 43
AMP PEAK 18(20P11.23) WILD-TYPE 26 55 31 31 61

Figure S117.  Get High-res Image Gene #18: 'amp_20p11.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20p11.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 2e-04

Table S118.  Gene #18: 'amp_20p11.23' 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 79 55 46 17 55 20 26 42 58
AMP PEAK 18(20P11.23) MUTATED 35 26 26 4 35 9 12 8 39
AMP PEAK 18(20P11.23) WILD-TYPE 44 29 20 13 20 11 14 34 19

Figure S118.  Get High-res Image Gene #18: 'amp_20p11.23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20p11.21' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S119.  Gene #19: 'amp_20p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
AMP PEAK 19(20P11.21) MUTATED 4 9 36 14 19
AMP PEAK 19(20P11.21) WILD-TYPE 27 8 13 13 4

Figure S119.  Get High-res Image Gene #19: 'amp_20p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20p11.21' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S120.  Gene #19: 'amp_20p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
AMP PEAK 19(20P11.21) MUTATED 10 47 25
AMP PEAK 19(20P11.21) WILD-TYPE 32 21 12

Figure S120.  Get High-res Image Gene #19: '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 = 4.9e-05

Table S121.  Gene #19: 'amp_20p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
AMP PEAK 19(20P11.21) MUTATED 53 154 45
AMP PEAK 19(20P11.21) WILD-TYPE 0 67 132

Figure S121.  Get High-res Image Gene #19: 'amp_20p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p11.21' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00029

Table S122.  Gene #19: 'amp_20p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
AMP PEAK 19(20P11.21) MUTATED 39 76 51
AMP PEAK 19(20P11.21) WILD-TYPE 46 27 55

Figure S122.  Get High-res Image Gene #19: 'amp_20p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20p11.21' versus 'RPPA_CNMF'

P value = 0.00655 (Fisher's exact test), Q value = 0.016

Table S123.  Gene #19: 'amp_20p11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 145 125
AMP PEAK 19(20P11.21) MUTATED 56 81 55
AMP PEAK 19(20P11.21) WILD-TYPE 29 64 70

Figure S123.  Get High-res Image Gene #19: '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 = 4.9e-05

Table S124.  Gene #19: 'amp_20p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
AMP PEAK 19(20P11.21) MUTATED 96 34 49 71
AMP PEAK 19(20P11.21) WILD-TYPE 31 60 48 60

Figure S124.  Get High-res Image Gene #19: '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 = 4.9e-05

Table S125.  Gene #19: 'amp_20p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
AMP PEAK 19(20P11.21) MUTATED 51 75 31 87 6
AMP PEAK 19(20P11.21) WILD-TYPE 28 33 65 42 31

Figure S125.  Get High-res Image Gene #19: 'amp_20p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20p11.21' versus 'MIRSEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.00099

Table S126.  Gene #19: 'amp_20p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
AMP PEAK 19(20P11.21) MUTATED 43 39 44 50 46
AMP PEAK 19(20P11.21) WILD-TYPE 17 49 27 25 58

Figure S126.  Get High-res Image Gene #19: '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 = 4.9e-05

Table S127.  Gene #19: '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 79 55 46 17 55 20 26 42 58
AMP PEAK 19(20P11.21) MUTATED 45 29 31 4 37 11 13 8 44
AMP PEAK 19(20P11.21) WILD-TYPE 34 26 15 13 18 9 13 34 14

Figure S127.  Get High-res Image Gene #19: 'amp_20p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0309 (Fisher's exact test), Q value = 0.059

Table S128.  Gene #19: 'amp_20p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
AMP PEAK 19(20P11.21) MUTATED 16 13 7 7 4 7
AMP PEAK 19(20P11.21) WILD-TYPE 2 7 9 4 7 2

Figure S128.  Get High-res Image Gene #19: 'amp_20p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00867 (Fisher's exact test), Q value = 0.02

Table S129.  Gene #19: 'amp_20p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 12 9 8 12 9 7 13 9 6
AMP PEAK 19(20P11.21) MUTATED 11 2 7 8 5 5 6 4 6
AMP PEAK 19(20P11.21) WILD-TYPE 1 7 1 4 4 2 7 5 0

Figure S129.  Get High-res Image Gene #19: 'amp_20p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S130.  Gene #20: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
AMP PEAK 20(20Q11.21) MUTATED 5 14 48 17 21
AMP PEAK 20(20Q11.21) WILD-TYPE 26 3 1 10 2

Figure S130.  Get High-res Image Gene #20: '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 = 4.9e-05

Table S131.  Gene #20: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
AMP PEAK 20(20Q11.21) MUTATED 11 59 35
AMP PEAK 20(20Q11.21) WILD-TYPE 31 9 2

Figure S131.  Get High-res Image Gene #20: '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 = 4.9e-05

Table S132.  Gene #20: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
AMP PEAK 20(20Q11.21) MUTATED 53 213 57
AMP PEAK 20(20Q11.21) WILD-TYPE 0 8 120

Figure S132.  Get High-res Image Gene #20: '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 = 4.9e-05

Table S133.  Gene #20: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
AMP PEAK 20(20Q11.21) MUTATED 52 100 60
AMP PEAK 20(20Q11.21) WILD-TYPE 33 3 46

Figure S133.  Get High-res Image Gene #20: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'RPPA_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.024

Table S134.  Gene #20: 'amp_20q11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 145 125
AMP PEAK 20(20Q11.21) MUTATED 67 107 76
AMP PEAK 20(20Q11.21) WILD-TYPE 18 38 49

Figure S134.  Get High-res Image Gene #20: 'amp_20q11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q11.21' versus 'RPPA_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00035

Table S135.  Gene #20: 'amp_20q11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 43 86 22 20 26
AMP PEAK 20(20Q11.21) MUTATED 46 20 29 25 31 49 11 16 23
AMP PEAK 20(20Q11.21) WILD-TYPE 5 13 6 14 12 37 11 4 3

Figure S135.  Get High-res Image Gene #20: 'amp_20q11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S136.  Gene #20: 'amp_20q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
AMP PEAK 20(20Q11.21) MUTATED 123 41 67 90
AMP PEAK 20(20Q11.21) WILD-TYPE 4 53 30 41

Figure S136.  Get High-res Image Gene #20: '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 = 4.9e-05

Table S137.  Gene #20: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
AMP PEAK 20(20Q11.21) MUTATED 73 96 34 111 7
AMP PEAK 20(20Q11.21) WILD-TYPE 6 12 62 18 30

Figure S137.  Get High-res Image Gene #20: '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 = 4.9e-05

Table S138.  Gene #20: 'amp_20q11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
AMP PEAK 20(20Q11.21) MUTATED 55 45 57 68 59
AMP PEAK 20(20Q11.21) WILD-TYPE 5 43 14 7 45

Figure S138.  Get High-res Image Gene #20: '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 = 4.9e-05

Table S139.  Gene #20: '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 79 55 46 17 55 20 26 42 58
AMP PEAK 20(20Q11.21) MUTATED 59 40 42 4 44 13 16 13 53
AMP PEAK 20(20Q11.21) WILD-TYPE 20 15 4 13 11 7 10 29 5

Figure S139.  Get High-res Image Gene #20: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00023

Table S140.  Gene #20: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
AMP PEAK 20(20Q11.21) MUTATED 17 17 8 11 4 9
AMP PEAK 20(20Q11.21) WILD-TYPE 1 3 8 0 7 0

Figure S140.  Get High-res Image Gene #20: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0288 (Fisher's exact test), Q value = 0.055

Table S141.  Gene #20: 'amp_20q11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 12 9 8 12 9 7 13 9 6
AMP PEAK 20(20Q11.21) MUTATED 12 6 8 9 5 5 7 8 6
AMP PEAK 20(20Q11.21) WILD-TYPE 0 3 0 3 4 2 6 1 0

Figure S141.  Get High-res Image Gene #20: 'amp_20q11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S142.  Gene #21: 'amp_20q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
AMP PEAK 21(20Q12) MUTATED 5 13 48 16 21
AMP PEAK 21(20Q12) WILD-TYPE 26 4 1 11 2

Figure S142.  Get High-res Image Gene #21: 'amp_20q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S143.  Gene #21: 'amp_20q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
AMP PEAK 21(20Q12) MUTATED 10 58 35
AMP PEAK 21(20Q12) WILD-TYPE 32 10 2

Figure S143.  Get High-res Image Gene #21: 'amp_20q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S144.  Gene #21: 'amp_20q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
AMP PEAK 21(20Q12) MUTATED 53 213 58
AMP PEAK 21(20Q12) WILD-TYPE 0 8 119

Figure S144.  Get High-res Image Gene #21: 'amp_20q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S145.  Gene #21: 'amp_20q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
AMP PEAK 21(20Q12) MUTATED 53 100 62
AMP PEAK 21(20Q12) WILD-TYPE 32 3 44

Figure S145.  Get High-res Image Gene #21: 'amp_20q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q12' versus 'RPPA_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.04

Table S146.  Gene #21: 'amp_20q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 145 125
AMP PEAK 21(20Q12) MUTATED 66 108 77
AMP PEAK 21(20Q12) WILD-TYPE 19 37 48

Figure S146.  Get High-res Image Gene #21: 'amp_20q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q12' versus 'RPPA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00033

Table S147.  Gene #21: 'amp_20q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 43 86 22 20 26
AMP PEAK 21(20Q12) MUTATED 46 19 29 27 31 49 11 16 23
AMP PEAK 21(20Q12) WILD-TYPE 5 14 6 12 12 37 11 4 3

Figure S147.  Get High-res Image Gene #21: 'amp_20q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S148.  Gene #21: 'amp_20q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
AMP PEAK 21(20Q12) MUTATED 123 42 69 88
AMP PEAK 21(20Q12) WILD-TYPE 4 52 28 43

Figure S148.  Get High-res Image Gene #21: 'amp_20q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S149.  Gene #21: 'amp_20q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
AMP PEAK 21(20Q12) MUTATED 74 96 36 110 6
AMP PEAK 21(20Q12) WILD-TYPE 5 12 60 19 31

Figure S149.  Get High-res Image Gene #21: 'amp_20q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S150.  Gene #21: 'amp_20q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
AMP PEAK 21(20Q12) MUTATED 55 45 58 69 58
AMP PEAK 21(20Q12) WILD-TYPE 5 43 13 6 46

Figure S150.  Get High-res Image Gene #21: 'amp_20q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S151.  Gene #21: '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 79 55 46 17 55 20 26 42 58
AMP PEAK 21(20Q12) MUTATED 59 41 42 4 45 13 16 12 53
AMP PEAK 21(20Q12) WILD-TYPE 20 14 4 13 10 7 10 30 5

Figure S151.  Get High-res Image Gene #21: 'amp_20q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00023

Table S152.  Gene #21: 'amp_20q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
AMP PEAK 21(20Q12) MUTATED 17 18 9 11 4 9
AMP PEAK 21(20Q12) WILD-TYPE 1 2 7 0 7 0

Figure S152.  Get High-res Image Gene #21: '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 = 4.9e-05

Table S153.  Gene #22: 'amp_20q13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
AMP PEAK 22(20Q13.12) MUTATED 5 14 48 17 21
AMP PEAK 22(20Q13.12) WILD-TYPE 26 3 1 10 2

Figure S153.  Get High-res Image Gene #22: '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 = 4.9e-05

Table S154.  Gene #22: 'amp_20q13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
AMP PEAK 22(20Q13.12) MUTATED 11 59 35
AMP PEAK 22(20Q13.12) WILD-TYPE 31 9 2

Figure S154.  Get High-res Image Gene #22: '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 = 4.9e-05

Table S155.  Gene #22: 'amp_20q13.12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
AMP PEAK 22(20Q13.12) MUTATED 53 214 59
AMP PEAK 22(20Q13.12) WILD-TYPE 0 7 118

Figure S155.  Get High-res Image Gene #22: '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 = 4.9e-05

Table S156.  Gene #22: 'amp_20q13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
AMP PEAK 22(20Q13.12) MUTATED 53 100 62
AMP PEAK 22(20Q13.12) WILD-TYPE 32 3 44

Figure S156.  Get High-res Image Gene #22: 'amp_20q13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.12' versus 'RPPA_CNMF'

P value = 0.0132 (Fisher's exact test), Q value = 0.028

Table S157.  Gene #22: 'amp_20q13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 145 125
AMP PEAK 22(20Q13.12) MUTATED 66 110 77
AMP PEAK 22(20Q13.12) WILD-TYPE 19 35 48

Figure S157.  Get High-res Image Gene #22: 'amp_20q13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q13.12' versus 'RPPA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00023

Table S158.  Gene #22: 'amp_20q13.12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 43 86 22 20 26
AMP PEAK 22(20Q13.12) MUTATED 46 19 29 28 32 49 11 16 23
AMP PEAK 22(20Q13.12) WILD-TYPE 5 14 6 11 11 37 11 4 3

Figure S158.  Get High-res Image Gene #22: 'amp_20q13.12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20q13.12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S159.  Gene #22: 'amp_20q13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
AMP PEAK 22(20Q13.12) MUTATED 123 42 69 90
AMP PEAK 22(20Q13.12) WILD-TYPE 4 52 28 41

Figure S159.  Get High-res Image Gene #22: '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 = 4.9e-05

Table S160.  Gene #22: 'amp_20q13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
AMP PEAK 22(20Q13.12) MUTATED 74 96 36 111 7
AMP PEAK 22(20Q13.12) WILD-TYPE 5 12 60 18 30

Figure S160.  Get High-res Image Gene #22: '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 = 4.9e-05

Table S161.  Gene #22: 'amp_20q13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
AMP PEAK 22(20Q13.12) MUTATED 56 45 58 69 60
AMP PEAK 22(20Q13.12) WILD-TYPE 4 43 13 6 44

Figure S161.  Get High-res Image Gene #22: '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 = 4.9e-05

Table S162.  Gene #22: '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 79 55 46 17 55 20 26 42 58
AMP PEAK 22(20Q13.12) MUTATED 59 41 42 4 45 14 16 14 53
AMP PEAK 22(20Q13.12) WILD-TYPE 20 14 4 13 10 6 10 28 5

Figure S162.  Get High-res Image Gene #22: 'amp_20q13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00038

Table S163.  Gene #22: 'amp_20q13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
AMP PEAK 22(20Q13.12) MUTATED 17 18 9 11 4 9
AMP PEAK 22(20Q13.12) WILD-TYPE 1 2 7 0 7 0

Figure S163.  Get High-res Image Gene #22: 'amp_20q13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00013

Table S164.  Gene #23: 'del_1p36.11' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 1(1P36.11) MUTATED 3 10 29 5 12
DEL PEAK 1(1P36.11) WILD-TYPE 28 7 20 22 11

Figure S164.  Get High-res Image Gene #23: 'del_1p36.11' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.11' versus 'MRNA_CHIERARCHICAL'

P value = 0.00317 (Fisher's exact test), Q value = 0.0083

Table S165.  Gene #23: 'del_1p36.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
DEL PEAK 1(1P36.11) MUTATED 8 32 19
DEL PEAK 1(1P36.11) WILD-TYPE 34 36 18

Figure S165.  Get High-res Image Gene #23: '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 = 4.9e-05

Table S166.  Gene #23: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 1(1P36.11) MUTATED 28 120 20
DEL PEAK 1(1P36.11) WILD-TYPE 25 101 157

Figure S166.  Get High-res Image Gene #23: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00033

Table S167.  Gene #23: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
DEL PEAK 1(1P36.11) MUTATED 26 54 27
DEL PEAK 1(1P36.11) WILD-TYPE 59 49 79

Figure S167.  Get High-res Image Gene #23: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.11' versus 'RPPA_CHIERARCHICAL'

P value = 0.0305 (Fisher's exact test), Q value = 0.058

Table S168.  Gene #23: 'del_1p36.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 43 86 22 20 26
DEL PEAK 1(1P36.11) MUTATED 22 12 15 15 19 17 8 10 12
DEL PEAK 1(1P36.11) WILD-TYPE 29 21 20 24 24 69 14 10 14

Figure S168.  Get High-res Image Gene #23: 'del_1p36.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S169.  Gene #23: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 1(1P36.11) MUTATED 68 14 38 47
DEL PEAK 1(1P36.11) WILD-TYPE 59 80 59 84

Figure S169.  Get High-res Image Gene #23: '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 = 4.9e-05

Table S170.  Gene #23: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 1(1P36.11) MUTATED 42 48 12 61 4
DEL PEAK 1(1P36.11) WILD-TYPE 37 60 84 68 33

Figure S170.  Get High-res Image Gene #23: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.0016

Table S171.  Gene #23: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
DEL PEAK 1(1P36.11) MUTATED 30 25 28 39 27
DEL PEAK 1(1P36.11) WILD-TYPE 30 63 43 36 77

Figure S171.  Get High-res Image Gene #23: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S172.  Gene #23: '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 79 55 46 17 55 20 26 42 58
DEL PEAK 1(1P36.11) MUTATED 32 20 29 0 20 4 6 9 29
DEL PEAK 1(1P36.11) WILD-TYPE 47 35 17 17 35 16 20 33 29

Figure S172.  Get High-res Image Gene #23: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p33' versus 'MRNA_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.038

Table S173.  Gene #24: 'del_1p33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 2(1P33) MUTATED 6 8 17 2 7
DEL PEAK 2(1P33) WILD-TYPE 25 9 32 25 16

Figure S173.  Get High-res Image Gene #24: 'del_1p33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S174.  Gene #24: 'del_1p33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 2(1P33) MUTATED 22 89 12
DEL PEAK 2(1P33) WILD-TYPE 31 132 165

Figure S174.  Get High-res Image Gene #24: 'del_1p33' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p33' versus 'METHLYATION_CNMF'

P value = 0.00504 (Fisher's exact test), Q value = 0.012

Table S175.  Gene #24: 'del_1p33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
DEL PEAK 2(1P33) MUTATED 21 40 20
DEL PEAK 2(1P33) WILD-TYPE 64 63 86

Figure S175.  Get High-res Image Gene #24: 'del_1p33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p33' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00035

Table S176.  Gene #24: 'del_1p33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 2(1P33) MUTATED 49 11 28 34
DEL PEAK 2(1P33) WILD-TYPE 78 83 69 97

Figure S176.  Get High-res Image Gene #24: 'del_1p33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 9.1e-05

Table S177.  Gene #24: 'del_1p33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 2(1P33) MUTATED 34 33 10 39 6
DEL PEAK 2(1P33) WILD-TYPE 45 75 86 90 31

Figure S177.  Get High-res Image Gene #24: 'del_1p33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p33' versus 'MIRSEQ_CNMF'

P value = 0.00276 (Fisher's exact test), Q value = 0.0074

Table S178.  Gene #24: 'del_1p33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
DEL PEAK 2(1P33) MUTATED 22 16 24 27 18
DEL PEAK 2(1P33) WILD-TYPE 38 72 47 48 86

Figure S178.  Get High-res Image Gene #24: 'del_1p33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0128 (Fisher's exact test), Q value = 0.028

Table S179.  Gene #24: '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 79 55 46 17 55 20 26 42 58
DEL PEAK 2(1P33) MUTATED 25 14 20 0 16 2 6 8 16
DEL PEAK 2(1P33) WILD-TYPE 54 41 26 17 39 18 20 34 42

Figure S179.  Get High-res Image Gene #24: 'del_1p33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p13.1' versus 'MRNA_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 0.044

Table S180.  Gene #25: 'del_1p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 3(1P13.1) MUTATED 5 9 15 3 5
DEL PEAK 3(1P13.1) WILD-TYPE 26 8 34 24 18

Figure S180.  Get High-res Image Gene #25: 'del_1p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S181.  Gene #25: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 3(1P13.1) MUTATED 21 84 14
DEL PEAK 3(1P13.1) WILD-TYPE 32 137 163

Figure S181.  Get High-res Image Gene #25: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p13.1' versus 'METHLYATION_CNMF'

P value = 0.00937 (Fisher's exact test), Q value = 0.021

Table S182.  Gene #25: 'del_1p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
DEL PEAK 3(1P13.1) MUTATED 18 39 22
DEL PEAK 3(1P13.1) WILD-TYPE 67 64 84

Figure S182.  Get High-res Image Gene #25: 'del_1p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p13.1' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00026

Table S183.  Gene #25: 'del_1p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 3(1P13.1) MUTATED 46 9 28 35
DEL PEAK 3(1P13.1) WILD-TYPE 81 85 69 96

Figure S183.  Get High-res Image Gene #25: 'del_1p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00029

Table S184.  Gene #25: 'del_1p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 3(1P13.1) MUTATED 31 31 12 40 4
DEL PEAK 3(1P13.1) WILD-TYPE 48 77 84 89 33

Figure S184.  Get High-res Image Gene #25: 'del_1p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.1' versus 'MIRSEQ_CNMF'

P value = 0.00114 (Fisher's exact test), Q value = 0.0033

Table S185.  Gene #25: 'del_1p13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
DEL PEAK 3(1P13.1) MUTATED 21 17 23 26 14
DEL PEAK 3(1P13.1) WILD-TYPE 39 71 48 49 90

Figure S185.  Get High-res Image Gene #25: 'del_1p13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0128 (Fisher's exact test), Q value = 0.028

Table S186.  Gene #25: 'del_1p13.1' 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 79 55 46 17 55 20 26 42 58
DEL PEAK 3(1P13.1) MUTATED 23 11 19 0 15 3 6 6 18
DEL PEAK 3(1P13.1) WILD-TYPE 56 44 27 17 40 17 20 36 40

Figure S186.  Get High-res Image Gene #25: 'del_1p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q22.1' versus 'CN_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.034

Table S187.  Gene #27: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 5(2Q22.1) MUTATED 6 14 4
DEL PEAK 5(2Q22.1) WILD-TYPE 47 207 173

Figure S187.  Get High-res Image Gene #27: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p26.1' versus 'MRNA_CNMF'

P value = 0.0392 (Fisher's exact test), Q value = 0.071

Table S188.  Gene #28: 'del_3p26.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 6(3P26.1) MUTATED 3 5 13 1 3
DEL PEAK 6(3P26.1) WILD-TYPE 28 12 36 26 20

Figure S188.  Get High-res Image Gene #28: 'del_3p26.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p26.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S189.  Gene #28: 'del_3p26.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 6(3P26.1) MUTATED 13 50 9
DEL PEAK 6(3P26.1) WILD-TYPE 40 171 168

Figure S189.  Get High-res Image Gene #28: 'del_3p26.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p26.1' versus 'MRNASEQ_CNMF'

P value = 0.00695 (Fisher's exact test), Q value = 0.016

Table S190.  Gene #28: 'del_3p26.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 6(3P26.1) MUTATED 25 5 18 24
DEL PEAK 6(3P26.1) WILD-TYPE 102 89 79 107

Figure S190.  Get High-res Image Gene #28: 'del_3p26.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p26.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00458 (Fisher's exact test), Q value = 0.011

Table S191.  Gene #28: 'del_3p26.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 6(3P26.1) MUTATED 18 17 7 28 2
DEL PEAK 6(3P26.1) WILD-TYPE 61 91 89 101 35

Figure S191.  Get High-res Image Gene #28: 'del_3p26.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MRNASEQ_CNMF'

P value = 0.0378 (Fisher's exact test), Q value = 0.069

Table S192.  Gene #29: 'del_3p14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 7(3P14.2) MUTATED 29 9 22 28
DEL PEAK 7(3P14.2) WILD-TYPE 98 85 75 103

Figure S192.  Get High-res Image Gene #29: 'del_3p14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0416 (Fisher's exact test), Q value = 0.075

Table S193.  Gene #29: 'del_3p14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 7(3P14.2) MUTATED 19 25 9 29 6
DEL PEAK 7(3P14.2) WILD-TYPE 60 83 87 100 31

Figure S193.  Get High-res Image Gene #29: 'del_3p14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3q26.31' versus 'CN_CNMF'

P value = 0.00519 (Fisher's exact test), Q value = 0.013

Table S194.  Gene #30: 'del_3q26.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 8(3Q26.31) MUTATED 9 29 9
DEL PEAK 8(3Q26.31) WILD-TYPE 44 192 168

Figure S194.  Get High-res Image Gene #30: 'del_3q26.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.2' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00013

Table S195.  Gene #31: 'del_4p16.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 9(4P16.2) MUTATED 2 9 22 4 12
DEL PEAK 9(4P16.2) WILD-TYPE 29 8 27 23 11

Figure S195.  Get High-res Image Gene #31: 'del_4p16.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4p16.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00308 (Fisher's exact test), Q value = 0.0081

Table S196.  Gene #31: 'del_4p16.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
DEL PEAK 9(4P16.2) MUTATED 6 25 18
DEL PEAK 9(4P16.2) WILD-TYPE 36 43 19

Figure S196.  Get High-res Image Gene #31: 'del_4p16.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4p16.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S197.  Gene #31: 'del_4p16.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 9(4P16.2) MUTATED 31 97 12
DEL PEAK 9(4P16.2) WILD-TYPE 22 124 165

Figure S197.  Get High-res Image Gene #31: 'del_4p16.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.2' versus 'METHLYATION_CNMF'

P value = 0.00665 (Fisher's exact test), Q value = 0.016

Table S198.  Gene #31: 'del_4p16.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
DEL PEAK 9(4P16.2) MUTATED 22 43 24
DEL PEAK 9(4P16.2) WILD-TYPE 63 60 82

Figure S198.  Get High-res Image Gene #31: 'del_4p16.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p16.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00311 (Fisher's exact test), Q value = 0.0082

Table S199.  Gene #31: 'del_4p16.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 43 86 22 20 26
DEL PEAK 9(4P16.2) MUTATED 18 7 12 12 20 14 7 1 9
DEL PEAK 9(4P16.2) WILD-TYPE 33 26 23 27 23 72 15 19 17

Figure S199.  Get High-res Image Gene #31: 'del_4p16.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4p16.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S200.  Gene #31: 'del_4p16.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 9(4P16.2) MUTATED 54 10 32 43
DEL PEAK 9(4P16.2) WILD-TYPE 73 84 65 88

Figure S200.  Get High-res Image Gene #31: 'del_4p16.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p16.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S201.  Gene #31: 'del_4p16.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 9(4P16.2) MUTATED 36 38 8 53 4
DEL PEAK 9(4P16.2) WILD-TYPE 43 70 88 76 33

Figure S201.  Get High-res Image Gene #31: 'del_4p16.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.2' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00061

Table S202.  Gene #31: 'del_4p16.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
DEL PEAK 9(4P16.2) MUTATED 25 16 23 33 21
DEL PEAK 9(4P16.2) WILD-TYPE 35 72 48 42 83

Figure S202.  Get High-res Image Gene #31: 'del_4p16.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4p16.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.04 (Fisher's exact test), Q value = 0.072

Table S203.  Gene #31: 'del_4p16.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
DEL PEAK 9(4P16.2) MUTATED 7 8 3 2 0 5
DEL PEAK 9(4P16.2) WILD-TYPE 11 12 13 9 11 4

Figure S203.  Get High-res Image Gene #31: 'del_4p16.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q22.1' versus 'MRNA_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00058

Table S204.  Gene #32: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 10(4Q22.1) MUTATED 4 7 21 3 14
DEL PEAK 10(4Q22.1) WILD-TYPE 27 10 28 24 9

Figure S204.  Get High-res Image Gene #32: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00554 (Fisher's exact test), Q value = 0.013

Table S205.  Gene #32: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
DEL PEAK 10(4Q22.1) MUTATED 6 27 16
DEL PEAK 10(4Q22.1) WILD-TYPE 36 41 21

Figure S205.  Get High-res Image Gene #32: '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 = 4.9e-05

Table S206.  Gene #32: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 10(4Q22.1) MUTATED 29 105 18
DEL PEAK 10(4Q22.1) WILD-TYPE 24 116 159

Figure S206.  Get High-res Image Gene #32: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 0.0048 (Fisher's exact test), Q value = 0.012

Table S207.  Gene #32: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
DEL PEAK 10(4Q22.1) MUTATED 27 48 27
DEL PEAK 10(4Q22.1) WILD-TYPE 58 55 79

Figure S207.  Get High-res Image Gene #32: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00023

Table S208.  Gene #32: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 10(4Q22.1) MUTATED 58 15 31 47
DEL PEAK 10(4Q22.1) WILD-TYPE 69 79 66 84

Figure S208.  Get High-res Image Gene #32: '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 = 4.9e-05

Table S209.  Gene #32: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 10(4Q22.1) MUTATED 39 45 10 53 4
DEL PEAK 10(4Q22.1) WILD-TYPE 40 63 86 76 33

Figure S209.  Get High-res Image Gene #32: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00035

Table S210.  Gene #32: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
DEL PEAK 10(4Q22.1) MUTATED 29 17 22 35 25
DEL PEAK 10(4Q22.1) WILD-TYPE 31 71 49 40 79

Figure S210.  Get High-res Image Gene #32: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00609 (Fisher's exact test), Q value = 0.015

Table S211.  Gene #32: '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 79 55 46 17 55 20 26 42 58
DEL PEAK 10(4Q22.1) MUTATED 24 14 18 1 22 5 6 9 29
DEL PEAK 10(4Q22.1) WILD-TYPE 55 41 28 16 33 15 20 33 29

Figure S211.  Get High-res Image Gene #32: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00703 (Fisher's exact test), Q value = 0.016

Table S212.  Gene #32: 'del_4q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
DEL PEAK 10(4Q22.1) MUTATED 12 9 4 4 0 4
DEL PEAK 10(4Q22.1) WILD-TYPE 6 11 12 7 11 5

Figure S212.  Get High-res Image Gene #32: 'del_4q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q35.1' versus 'MRNA_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00035

Table S213.  Gene #33: 'del_4q35.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 11(4Q35.1) MUTATED 3 7 24 5 14
DEL PEAK 11(4Q35.1) WILD-TYPE 28 10 25 22 9

Figure S213.  Get High-res Image Gene #33: 'del_4q35.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q35.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00597 (Fisher's exact test), Q value = 0.014

Table S214.  Gene #33: 'del_4q35.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
DEL PEAK 11(4Q35.1) MUTATED 7 29 17
DEL PEAK 11(4Q35.1) WILD-TYPE 35 39 20

Figure S214.  Get High-res Image Gene #33: '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 = 4.9e-05

Table S215.  Gene #33: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 11(4Q35.1) MUTATED 27 115 17
DEL PEAK 11(4Q35.1) WILD-TYPE 26 106 160

Figure S215.  Get High-res Image Gene #33: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q35.1' versus 'METHLYATION_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0012

Table S216.  Gene #33: 'del_4q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
DEL PEAK 11(4Q35.1) MUTATED 28 50 24
DEL PEAK 11(4Q35.1) WILD-TYPE 57 53 82

Figure S216.  Get High-res Image Gene #33: 'del_4q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q35.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S217.  Gene #33: 'del_4q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 11(4Q35.1) MUTATED 63 15 32 48
DEL PEAK 11(4Q35.1) WILD-TYPE 64 79 65 83

Figure S217.  Get High-res Image Gene #33: 'del_4q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S218.  Gene #33: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 11(4Q35.1) MUTATED 40 44 12 56 6
DEL PEAK 11(4Q35.1) WILD-TYPE 39 64 84 73 31

Figure S218.  Get High-res Image Gene #33: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MIRSEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0011

Table S219.  Gene #33: 'del_4q35.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
DEL PEAK 11(4Q35.1) MUTATED 28 18 25 36 27
DEL PEAK 11(4Q35.1) WILD-TYPE 32 70 46 39 77

Figure S219.  Get High-res Image Gene #33: 'del_4q35.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q35.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0434 (Fisher's exact test), Q value = 0.078

Table S220.  Gene #33: 'del_4q35.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
DEL PEAK 11(4Q35.1) MUTATED 11 7 3 5 2 6
DEL PEAK 11(4Q35.1) WILD-TYPE 7 13 13 6 9 3

Figure S220.  Get High-res Image Gene #33: 'del_4q35.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q12.1' versus 'MRNA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00023

Table S221.  Gene #34: 'del_5q12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 12(5Q12.1) MUTATED 3 9 14 0 8
DEL PEAK 12(5Q12.1) WILD-TYPE 28 8 35 27 15

Figure S221.  Get High-res Image Gene #34: 'del_5q12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q12.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0155 (Fisher's exact test), Q value = 0.033

Table S222.  Gene #34: 'del_5q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
DEL PEAK 12(5Q12.1) MUTATED 6 13 15
DEL PEAK 12(5Q12.1) WILD-TYPE 36 55 22

Figure S222.  Get High-res Image Gene #34: '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 = 4.9e-05

Table S223.  Gene #34: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 12(5Q12.1) MUTATED 17 78 11
DEL PEAK 12(5Q12.1) WILD-TYPE 36 143 166

Figure S223.  Get High-res Image Gene #34: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.035

Table S224.  Gene #34: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
DEL PEAK 12(5Q12.1) MUTATED 21 34 17
DEL PEAK 12(5Q12.1) WILD-TYPE 64 69 89

Figure S224.  Get High-res Image Gene #34: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q12.1' versus 'RPPA_CNMF'

P value = 0.0257 (Fisher's exact test), Q value = 0.05

Table S225.  Gene #34: 'del_5q12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 145 125
DEL PEAK 12(5Q12.1) MUTATED 28 27 23
DEL PEAK 12(5Q12.1) WILD-TYPE 57 118 102

Figure S225.  Get High-res Image Gene #34: 'del_5q12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_5q12.1' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00045

Table S226.  Gene #34: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 12(5Q12.1) MUTATED 44 8 24 30
DEL PEAK 12(5Q12.1) WILD-TYPE 83 86 73 101

Figure S226.  Get High-res Image Gene #34: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00026

Table S227.  Gene #34: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 12(5Q12.1) MUTATED 29 29 9 35 4
DEL PEAK 12(5Q12.1) WILD-TYPE 50 79 87 94 33

Figure S227.  Get High-res Image Gene #34: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0018

Table S228.  Gene #34: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
DEL PEAK 12(5Q12.1) MUTATED 22 10 20 22 16
DEL PEAK 12(5Q12.1) WILD-TYPE 38 78 51 53 88

Figure S228.  Get High-res Image Gene #34: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00631 (Fisher's exact test), Q value = 0.015

Table S229.  Gene #34: '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 79 55 46 17 55 20 26 42 58
DEL PEAK 12(5Q12.1) MUTATED 14 16 6 0 18 6 6 5 19
DEL PEAK 12(5Q12.1) WILD-TYPE 65 39 40 17 37 14 20 37 39

Figure S229.  Get High-res Image Gene #34: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q21.1' versus 'MRNA_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.028

Table S230.  Gene #35: 'del_5q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 13(5Q21.1) MUTATED 3 8 19 5 7
DEL PEAK 13(5Q21.1) WILD-TYPE 28 9 30 22 16

Figure S230.  Get High-res Image Gene #35: 'del_5q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S231.  Gene #35: 'del_5q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 13(5Q21.1) MUTATED 18 89 20
DEL PEAK 13(5Q21.1) WILD-TYPE 35 132 157

Figure S231.  Get High-res Image Gene #35: 'del_5q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q21.1' versus 'METHLYATION_CNMF'

P value = 0.0371 (Fisher's exact test), Q value = 0.068

Table S232.  Gene #35: 'del_5q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
DEL PEAK 13(5Q21.1) MUTATED 25 38 22
DEL PEAK 13(5Q21.1) WILD-TYPE 60 65 84

Figure S232.  Get High-res Image Gene #35: 'del_5q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q21.1' versus 'RPPA_CNMF'

P value = 0.0429 (Fisher's exact test), Q value = 0.077

Table S233.  Gene #35: 'del_5q21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 145 125
DEL PEAK 13(5Q21.1) MUTATED 31 33 28
DEL PEAK 13(5Q21.1) WILD-TYPE 54 112 97

Figure S233.  Get High-res Image Gene #35: 'del_5q21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_5q21.1' versus 'MRNASEQ_CNMF'

P value = 0.00668 (Fisher's exact test), Q value = 0.016

Table S234.  Gene #35: 'del_5q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 13(5Q21.1) MUTATED 50 18 23 36
DEL PEAK 13(5Q21.1) WILD-TYPE 77 76 74 95

Figure S234.  Get High-res Image Gene #35: 'del_5q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00035

Table S235.  Gene #35: 'del_5q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 13(5Q21.1) MUTATED 29 36 12 44 6
DEL PEAK 13(5Q21.1) WILD-TYPE 50 72 84 85 31

Figure S235.  Get High-res Image Gene #35: 'del_5q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q21.1' versus 'MIRSEQ_CNMF'

P value = 0.00897 (Fisher's exact test), Q value = 0.02

Table S236.  Gene #35: 'del_5q21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
DEL PEAK 13(5Q21.1) MUTATED 23 17 24 26 20
DEL PEAK 13(5Q21.1) WILD-TYPE 37 71 47 49 84

Figure S236.  Get High-res Image Gene #35: 'del_5q21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q22.2' versus 'MRNA_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.00067

Table S237.  Gene #36: 'del_5q22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 14(5Q22.2) MUTATED 2 8 19 2 8
DEL PEAK 14(5Q22.2) WILD-TYPE 29 9 30 25 15

Figure S237.  Get High-res Image Gene #36: 'del_5q22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q22.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00307 (Fisher's exact test), Q value = 0.0081

Table S238.  Gene #36: 'del_5q22.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
DEL PEAK 14(5Q22.2) MUTATED 5 17 17
DEL PEAK 14(5Q22.2) WILD-TYPE 37 51 20

Figure S238.  Get High-res Image Gene #36: '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 = 4.9e-05

Table S239.  Gene #36: 'del_5q22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 14(5Q22.2) MUTATED 18 90 22
DEL PEAK 14(5Q22.2) WILD-TYPE 35 131 155

Figure S239.  Get High-res Image Gene #36: 'del_5q22.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q22.2' versus 'MRNASEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0011

Table S240.  Gene #36: 'del_5q22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 14(5Q22.2) MUTATED 54 16 25 34
DEL PEAK 14(5Q22.2) WILD-TYPE 73 78 72 97

Figure S240.  Get High-res Image Gene #36: 'del_5q22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00026

Table S241.  Gene #36: 'del_5q22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 14(5Q22.2) MUTATED 29 38 15 44 3
DEL PEAK 14(5Q22.2) WILD-TYPE 50 70 81 85 34

Figure S241.  Get High-res Image Gene #36: 'del_5q22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q22.2' versus 'MIRSEQ_CNMF'

P value = 0.0028 (Fisher's exact test), Q value = 0.0075

Table S242.  Gene #36: 'del_5q22.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
DEL PEAK 14(5Q22.2) MUTATED 26 18 24 26 20
DEL PEAK 14(5Q22.2) WILD-TYPE 34 70 47 49 84

Figure S242.  Get High-res Image Gene #36: 'del_5q22.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q26' versus 'RPPA_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 0.057

Table S243.  Gene #38: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 145 125
DEL PEAK 16(6Q26) MUTATED 16 22 9
DEL PEAK 16(6Q26) WILD-TYPE 69 123 116

Figure S243.  Get High-res Image Gene #38: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_8p23.2' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.1e-05

Table S244.  Gene #40: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 18(8P23.2) MUTATED 3 12 26 7 14
DEL PEAK 18(8P23.2) WILD-TYPE 28 5 23 20 9

Figure S244.  Get High-res Image Gene #40: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p23.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.0016

Table S245.  Gene #40: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
DEL PEAK 18(8P23.2) MUTATED 8 32 22
DEL PEAK 18(8P23.2) WILD-TYPE 34 36 15

Figure S245.  Get High-res Image Gene #40: '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 = 4.9e-05

Table S246.  Gene #40: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 18(8P23.2) MUTATED 12 157 21
DEL PEAK 18(8P23.2) WILD-TYPE 41 64 156

Figure S246.  Get High-res Image Gene #40: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.00091

Table S247.  Gene #40: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
DEL PEAK 18(8P23.2) MUTATED 33 60 33
DEL PEAK 18(8P23.2) WILD-TYPE 52 43 73

Figure S247.  Get High-res Image Gene #40: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0353 (Fisher's exact test), Q value = 0.065

Table S248.  Gene #40: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 43 86 22 20 26
DEL PEAK 18(8P23.2) MUTATED 30 9 17 14 16 29 5 7 13
DEL PEAK 18(8P23.2) WILD-TYPE 21 24 18 25 27 57 17 13 13

Figure S248.  Get High-res Image Gene #40: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00013

Table S249.  Gene #40: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 18(8P23.2) MUTATED 70 20 45 55
DEL PEAK 18(8P23.2) WILD-TYPE 57 74 52 76

Figure S249.  Get High-res Image Gene #40: '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 = 4.9e-05

Table S250.  Gene #40: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 18(8P23.2) MUTATED 49 49 19 68 5
DEL PEAK 18(8P23.2) WILD-TYPE 30 59 77 61 32

Figure S250.  Get High-res Image Gene #40: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00078

Table S251.  Gene #40: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
DEL PEAK 18(8P23.2) MUTATED 34 22 32 41 39
DEL PEAK 18(8P23.2) WILD-TYPE 26 66 39 34 65

Figure S251.  Get High-res Image Gene #40: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.0016

Table S252.  Gene #40: '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 79 55 46 17 55 20 26 42 58
DEL PEAK 18(8P23.2) MUTATED 35 24 23 1 30 6 8 10 31
DEL PEAK 18(8P23.2) WILD-TYPE 44 31 23 16 25 14 18 32 27

Figure S252.  Get High-res Image Gene #40: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00299 (Fisher's exact test), Q value = 0.0079

Table S253.  Gene #40: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
DEL PEAK 18(8P23.2) MUTATED 12 11 5 5 1 8
DEL PEAK 18(8P23.2) WILD-TYPE 6 9 11 6 10 1

Figure S253.  Get High-res Image Gene #40: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p22' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.1e-05

Table S254.  Gene #41: 'del_8p22' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 19(8P22) MUTATED 2 11 27 9 14
DEL PEAK 19(8P22) WILD-TYPE 29 6 22 18 9

Figure S254.  Get High-res Image Gene #41: 'del_8p22' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p22' versus 'MRNA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00042

Table S255.  Gene #41: 'del_8p22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
DEL PEAK 19(8P22) MUTATED 7 34 22
DEL PEAK 19(8P22) WILD-TYPE 35 34 15

Figure S255.  Get High-res Image Gene #41: 'del_8p22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S256.  Gene #41: 'del_8p22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 19(8P22) MUTATED 13 165 25
DEL PEAK 19(8P22) WILD-TYPE 40 56 152

Figure S256.  Get High-res Image Gene #41: 'del_8p22' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p22' versus 'METHLYATION_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00075

Table S257.  Gene #41: 'del_8p22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
DEL PEAK 19(8P22) MUTATED 36 65 37
DEL PEAK 19(8P22) WILD-TYPE 49 38 69

Figure S257.  Get High-res Image Gene #41: 'del_8p22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p22' versus 'RPPA_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.035

Table S258.  Gene #41: 'del_8p22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 43 86 22 20 26
DEL PEAK 19(8P22) MUTATED 33 12 16 15 17 31 5 9 15
DEL PEAK 19(8P22) WILD-TYPE 18 21 19 24 26 55 17 11 11

Figure S258.  Get High-res Image Gene #41: 'del_8p22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_8p22' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00013

Table S259.  Gene #41: 'del_8p22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 19(8P22) MUTATED 76 25 47 55
DEL PEAK 19(8P22) WILD-TYPE 51 69 50 76

Figure S259.  Get High-res Image Gene #41: 'del_8p22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S260.  Gene #41: 'del_8p22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 19(8P22) MUTATED 52 54 23 69 5
DEL PEAK 19(8P22) WILD-TYPE 27 54 73 60 32

Figure S260.  Get High-res Image Gene #41: 'del_8p22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p22' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00023

Table S261.  Gene #41: 'del_8p22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
DEL PEAK 19(8P22) MUTATED 37 24 36 42 41
DEL PEAK 19(8P22) WILD-TYPE 23 64 35 33 63

Figure S261.  Get High-res Image Gene #41: 'del_8p22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0014

Table S262.  Gene #41: '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 79 55 46 17 55 20 26 42 58
DEL PEAK 19(8P22) MUTATED 35 30 24 1 32 9 8 11 30
DEL PEAK 19(8P22) WILD-TYPE 44 25 22 16 23 11 18 31 28

Figure S262.  Get High-res Image Gene #41: 'del_8p22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0081 (Fisher's exact test), Q value = 0.018

Table S263.  Gene #41: 'del_8p22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
DEL PEAK 19(8P22) MUTATED 12 12 5 6 1 7
DEL PEAK 19(8P22) WILD-TYPE 6 8 11 5 10 2

Figure S263.  Get High-res Image Gene #41: 'del_8p22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8q11.1' versus 'MRNA_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.03

Table S264.  Gene #42: 'del_8q11.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 20(8Q11.1) MUTATED 0 4 7 3 0
DEL PEAK 20(8Q11.1) WILD-TYPE 31 13 42 24 23

Figure S264.  Get High-res Image Gene #42: 'del_8q11.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8q11.1' versus 'CN_CNMF'

P value = 0.00139 (Fisher's exact test), Q value = 0.0039

Table S265.  Gene #42: 'del_8q11.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 20(8Q11.1) MUTATED 2 24 4
DEL PEAK 20(8Q11.1) WILD-TYPE 51 197 173

Figure S265.  Get High-res Image Gene #42: 'del_8q11.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'MRNA_CNMF'

P value = 0.00212 (Fisher's exact test), Q value = 0.0058

Table S266.  Gene #43: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 21(9P21.3) MUTATED 0 6 8 1 4
DEL PEAK 21(9P21.3) WILD-TYPE 31 11 41 26 19

Figure S266.  Get High-res Image Gene #43: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p21.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0209 (Fisher's exact test), Q value = 0.042

Table S267.  Gene #43: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
DEL PEAK 21(9P21.3) MUTATED 1 10 8
DEL PEAK 21(9P21.3) WILD-TYPE 41 58 29

Figure S267.  Get High-res Image Gene #43: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00017

Table S268.  Gene #43: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 21(9P21.3) MUTATED 10 43 9
DEL PEAK 21(9P21.3) WILD-TYPE 43 178 168

Figure S268.  Get High-res Image Gene #43: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 0.0281 (Fisher's exact test), Q value = 0.054

Table S269.  Gene #43: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 21(9P21.3) MUTATED 26 7 15 14
DEL PEAK 21(9P21.3) WILD-TYPE 101 87 82 117

Figure S269.  Get High-res Image Gene #43: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00123 (Fisher's exact test), Q value = 0.0035

Table S270.  Gene #43: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 21(9P21.3) MUTATED 16 19 6 21 0
DEL PEAK 21(9P21.3) WILD-TYPE 63 89 90 108 37

Figure S270.  Get High-res Image Gene #43: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.028

Table S271.  Gene #43: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
DEL PEAK 21(9P21.3) MUTATED 8 8 11 19 8
DEL PEAK 21(9P21.3) WILD-TYPE 52 80 60 56 96

Figure S271.  Get High-res Image Gene #43: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10p15.3' versus 'MRNA_CNMF'

P value = 0.00678 (Fisher's exact test), Q value = 0.016

Table S272.  Gene #44: 'del_10p15.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 22(10P15.3) MUTATED 1 5 8 1 7
DEL PEAK 22(10P15.3) WILD-TYPE 30 12 41 26 16

Figure S272.  Get High-res Image Gene #44: 'del_10p15.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S273.  Gene #44: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 22(10P15.3) MUTATED 15 56 9
DEL PEAK 22(10P15.3) WILD-TYPE 38 165 168

Figure S273.  Get High-res Image Gene #44: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 0.00489 (Fisher's exact test), Q value = 0.012

Table S274.  Gene #44: 'del_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
DEL PEAK 22(10P15.3) MUTATED 15 30 12
DEL PEAK 22(10P15.3) WILD-TYPE 70 73 94

Figure S274.  Get High-res Image Gene #44: 'del_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00072

Table S275.  Gene #44: 'del_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 22(10P15.3) MUTATED 34 5 19 21
DEL PEAK 22(10P15.3) WILD-TYPE 93 89 78 110

Figure S275.  Get High-res Image Gene #44: 'del_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00038

Table S276.  Gene #44: 'del_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 22(10P15.3) MUTATED 27 19 7 23 3
DEL PEAK 22(10P15.3) WILD-TYPE 52 89 89 106 34

Figure S276.  Get High-res Image Gene #44: 'del_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q21.1' versus 'MRNA_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00058

Table S277.  Gene #45: 'del_10q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 23(10Q21.1) MUTATED 1 6 13 0 7
DEL PEAK 23(10Q21.1) WILD-TYPE 30 11 36 27 16

Figure S277.  Get High-res Image Gene #45: 'del_10q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q21.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0183 (Fisher's exact test), Q value = 0.037

Table S278.  Gene #45: 'del_10q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
DEL PEAK 23(10Q21.1) MUTATED 2 16 9
DEL PEAK 23(10Q21.1) WILD-TYPE 40 52 28

Figure S278.  Get High-res Image Gene #45: '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 = 4.9e-05

Table S279.  Gene #45: 'del_10q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 23(10Q21.1) MUTATED 16 71 11
DEL PEAK 23(10Q21.1) WILD-TYPE 37 150 166

Figure S279.  Get High-res Image Gene #45: 'del_10q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q21.1' versus 'METHLYATION_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.025

Table S280.  Gene #45: 'del_10q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
DEL PEAK 23(10Q21.1) MUTATED 17 35 18
DEL PEAK 23(10Q21.1) WILD-TYPE 68 68 88

Figure S280.  Get High-res Image Gene #45: 'del_10q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q21.1' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00013

Table S281.  Gene #45: 'del_10q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 23(10Q21.1) MUTATED 45 7 20 25
DEL PEAK 23(10Q21.1) WILD-TYPE 82 87 77 106

Figure S281.  Get High-res Image Gene #45: 'del_10q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00013

Table S282.  Gene #45: 'del_10q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 23(10Q21.1) MUTATED 28 27 9 32 1
DEL PEAK 23(10Q21.1) WILD-TYPE 51 81 87 97 36

Figure S282.  Get High-res Image Gene #45: 'del_10q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.025

Table S283.  Gene #45: 'del_10q21.1' 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 79 55 46 17 55 20 26 42 58
DEL PEAK 23(10Q21.1) MUTATED 17 16 10 0 17 1 3 4 15
DEL PEAK 23(10Q21.1) WILD-TYPE 62 39 36 17 38 19 23 38 43

Figure S283.  Get High-res Image Gene #45: 'del_10q21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MRNA_CNMF'

P value = 0.00321 (Fisher's exact test), Q value = 0.0083

Table S284.  Gene #46: 'del_10q23.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 24(10Q23.31) MUTATED 0 5 11 5 8
DEL PEAK 24(10Q23.31) WILD-TYPE 31 12 38 22 15

Figure S284.  Get High-res Image Gene #46: 'del_10q23.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q23.31' versus 'MRNA_CHIERARCHICAL'

P value = 0.0433 (Fisher's exact test), Q value = 0.077

Table S285.  Gene #46: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
DEL PEAK 24(10Q23.31) MUTATED 3 17 9
DEL PEAK 24(10Q23.31) WILD-TYPE 39 51 28

Figure S285.  Get High-res Image Gene #46: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S286.  Gene #46: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 24(10Q23.31) MUTATED 21 75 13
DEL PEAK 24(10Q23.31) WILD-TYPE 32 146 164

Figure S286.  Get High-res Image Gene #46: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 0.0148 (Fisher's exact test), Q value = 0.031

Table S287.  Gene #46: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
DEL PEAK 24(10Q23.31) MUTATED 18 38 22
DEL PEAK 24(10Q23.31) WILD-TYPE 67 65 84

Figure S287.  Get High-res Image Gene #46: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 0.00563 (Fisher's exact test), Q value = 0.014

Table S288.  Gene #46: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 24(10Q23.31) MUTATED 45 16 21 26
DEL PEAK 24(10Q23.31) WILD-TYPE 82 78 76 105

Figure S288.  Get High-res Image Gene #46: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 2e-04

Table S289.  Gene #46: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 24(10Q23.31) MUTATED 29 32 12 33 2
DEL PEAK 24(10Q23.31) WILD-TYPE 50 76 84 96 35

Figure S289.  Get High-res Image Gene #46: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0042 (Fisher's exact test), Q value = 0.011

Table S290.  Gene #46: '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 79 55 46 17 55 20 26 42 58
DEL PEAK 24(10Q23.31) MUTATED 19 20 9 0 20 2 4 5 15
DEL PEAK 24(10Q23.31) WILD-TYPE 60 35 37 17 35 18 22 37 43

Figure S290.  Get High-res Image Gene #46: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0399 (Fisher's exact test), Q value = 0.072

Table S291.  Gene #46: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
DEL PEAK 24(10Q23.31) MUTATED 4 7 2 4 0 5
DEL PEAK 24(10Q23.31) WILD-TYPE 14 13 14 7 11 4

Figure S291.  Get High-res Image Gene #46: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q25.2' versus 'MRNA_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.029

Table S292.  Gene #47: 'del_10q25.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 25(10Q25.2) MUTATED 1 5 10 6 9
DEL PEAK 25(10Q25.2) WILD-TYPE 30 12 39 21 14

Figure S292.  Get High-res Image Gene #47: 'del_10q25.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q25.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00387 (Fisher's exact test), Q value = 0.0099

Table S293.  Gene #47: 'del_10q25.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
DEL PEAK 25(10Q25.2) MUTATED 2 20 9
DEL PEAK 25(10Q25.2) WILD-TYPE 40 48 28

Figure S293.  Get High-res Image Gene #47: 'del_10q25.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S294.  Gene #47: 'del_10q25.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 25(10Q25.2) MUTATED 22 78 9
DEL PEAK 25(10Q25.2) WILD-TYPE 31 143 168

Figure S294.  Get High-res Image Gene #47: 'del_10q25.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q25.2' versus 'METHLYATION_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.0027

Table S295.  Gene #47: 'del_10q25.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
DEL PEAK 25(10Q25.2) MUTATED 16 40 19
DEL PEAK 25(10Q25.2) WILD-TYPE 69 63 87

Figure S295.  Get High-res Image Gene #47: 'del_10q25.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q25.2' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00013

Table S296.  Gene #47: 'del_10q25.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 25(10Q25.2) MUTATED 48 9 21 30
DEL PEAK 25(10Q25.2) WILD-TYPE 79 85 76 101

Figure S296.  Get High-res Image Gene #47: '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 = 4.9e-05

Table S297.  Gene #47: 'del_10q25.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 25(10Q25.2) MUTATED 32 29 7 39 1
DEL PEAK 25(10Q25.2) WILD-TYPE 47 79 89 90 36

Figure S297.  Get High-res Image Gene #47: 'del_10q25.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q25.2' versus 'MIRSEQ_CNMF'

P value = 0.00318 (Fisher's exact test), Q value = 0.0083

Table S298.  Gene #47: 'del_10q25.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
DEL PEAK 25(10Q25.2) MUTATED 20 10 22 22 20
DEL PEAK 25(10Q25.2) WILD-TYPE 40 78 49 53 84

Figure S298.  Get High-res Image Gene #47: 'del_10q25.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q25.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00207 (Fisher's exact test), Q value = 0.0057

Table S299.  Gene #47: '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 79 55 46 17 55 20 26 42 58
DEL PEAK 25(10Q25.2) MUTATED 17 17 9 0 22 2 4 5 18
DEL PEAK 25(10Q25.2) WILD-TYPE 62 38 37 17 33 18 22 37 40

Figure S299.  Get High-res Image Gene #47: 'del_10q25.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12p13.2' versus 'MRNA_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.0016

Table S300.  Gene #48: 'del_12p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 26(12P13.2) MUTATED 0 6 8 0 3
DEL PEAK 26(12P13.2) WILD-TYPE 31 11 41 27 20

Figure S300.  Get High-res Image Gene #48: 'del_12p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12p13.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00805 (Fisher's exact test), Q value = 0.018

Table S301.  Gene #48: 'del_12p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
DEL PEAK 26(12P13.2) MUTATED 0 11 6
DEL PEAK 26(12P13.2) WILD-TYPE 42 57 31

Figure S301.  Get High-res Image Gene #48: 'del_12p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S302.  Gene #48: 'del_12p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 26(12P13.2) MUTATED 5 53 2
DEL PEAK 26(12P13.2) WILD-TYPE 48 168 175

Figure S302.  Get High-res Image Gene #48: 'del_12p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_12p13.2' versus 'METHLYATION_CNMF'

P value = 0.00206 (Fisher's exact test), Q value = 0.0057

Table S303.  Gene #48: 'del_12p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
DEL PEAK 26(12P13.2) MUTATED 8 26 10
DEL PEAK 26(12P13.2) WILD-TYPE 77 77 96

Figure S303.  Get High-res Image Gene #48: 'del_12p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12p13.2' versus 'MRNASEQ_CNMF'

P value = 0.00125 (Fisher's exact test), Q value = 0.0035

Table S304.  Gene #48: 'del_12p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 26(12P13.2) MUTATED 28 4 12 16
DEL PEAK 26(12P13.2) WILD-TYPE 99 90 85 115

Figure S304.  Get High-res Image Gene #48: 'del_12p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S305.  Gene #48: 'del_12p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 26(12P13.2) MUTATED 16 21 2 21 0
DEL PEAK 26(12P13.2) WILD-TYPE 63 87 94 108 37

Figure S305.  Get High-res Image Gene #48: 'del_12p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.2' versus 'MIRSEQ_CNMF'

P value = 0.00426 (Fisher's exact test), Q value = 0.011

Table S306.  Gene #48: 'del_12p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
DEL PEAK 26(12P13.2) MUTATED 12 5 13 14 7
DEL PEAK 26(12P13.2) WILD-TYPE 48 83 58 61 97

Figure S306.  Get High-res Image Gene #48: 'del_12p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_12p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0464 (Fisher's exact test), Q value = 0.082

Table S307.  Gene #48: 'del_12p13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
DEL PEAK 26(12P13.2) MUTATED 2 1 1 2 0 4
DEL PEAK 26(12P13.2) WILD-TYPE 16 19 15 9 11 5

Figure S307.  Get High-res Image Gene #48: 'del_12p13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_13q14.13' versus 'CN_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.003

Table S308.  Gene #49: 'del_13q14.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 27(13Q14.13) MUTATED 8 5 6
DEL PEAK 27(13Q14.13) WILD-TYPE 45 216 171

Figure S308.  Get High-res Image Gene #49: 'del_13q14.13' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q31.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S309.  Gene #50: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 28(14Q31.1) MUTATED 2 9 31 4 9
DEL PEAK 28(14Q31.1) WILD-TYPE 29 8 18 23 14

Figure S309.  Get High-res Image Gene #50: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q31.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00035

Table S310.  Gene #50: 'del_14q31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
DEL PEAK 28(14Q31.1) MUTATED 5 29 21
DEL PEAK 28(14Q31.1) WILD-TYPE 37 39 16

Figure S310.  Get High-res Image Gene #50: '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 = 4.9e-05

Table S311.  Gene #50: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 28(14Q31.1) MUTATED 16 123 12
DEL PEAK 28(14Q31.1) WILD-TYPE 37 98 165

Figure S311.  Get High-res Image Gene #50: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q31.1' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00061

Table S312.  Gene #50: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
DEL PEAK 28(14Q31.1) MUTATED 20 49 25
DEL PEAK 28(14Q31.1) WILD-TYPE 65 54 81

Figure S312.  Get High-res Image Gene #50: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q31.1' versus 'RPPA_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.041

Table S313.  Gene #50: 'del_14q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 145 125
DEL PEAK 28(14Q31.1) MUTATED 31 57 30
DEL PEAK 28(14Q31.1) WILD-TYPE 54 88 95

Figure S313.  Get High-res Image Gene #50: 'del_14q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_14q31.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S314.  Gene #50: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 28(14Q31.1) MUTATED 66 13 24 48
DEL PEAK 28(14Q31.1) WILD-TYPE 61 81 73 83

Figure S314.  Get High-res Image Gene #50: '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 = 4.9e-05

Table S315.  Gene #50: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 28(14Q31.1) MUTATED 33 46 10 60 2
DEL PEAK 28(14Q31.1) WILD-TYPE 46 62 86 69 35

Figure S315.  Get High-res Image Gene #50: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S316.  Gene #50: 'del_14q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
DEL PEAK 28(14Q31.1) MUTATED 25 16 26 43 21
DEL PEAK 28(14Q31.1) WILD-TYPE 35 72 45 32 83

Figure S316.  Get High-res Image Gene #50: '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 = 4.9e-05

Table S317.  Gene #50: '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 79 55 46 17 55 20 26 42 58
DEL PEAK 28(14Q31.1) MUTATED 31 12 25 1 15 5 7 5 30
DEL PEAK 28(14Q31.1) WILD-TYPE 48 43 21 16 40 15 19 37 28

Figure S317.  Get High-res Image Gene #50: 'del_14q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.037

Table S318.  Gene #50: 'del_14q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
DEL PEAK 28(14Q31.1) MUTATED 10 4 6 6 1 6
DEL PEAK 28(14Q31.1) WILD-TYPE 8 16 10 5 10 3

Figure S318.  Get High-res Image Gene #50: 'del_14q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q11.2' versus 'MRNA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00023

Table S319.  Gene #51: 'del_15q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 29(15Q11.2) MUTATED 3 10 27 7 13
DEL PEAK 29(15Q11.2) WILD-TYPE 28 7 22 20 10

Figure S319.  Get High-res Image Gene #51: 'del_15q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.0015

Table S320.  Gene #51: 'del_15q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
DEL PEAK 29(15Q11.2) MUTATED 7 33 20
DEL PEAK 29(15Q11.2) WILD-TYPE 35 35 17

Figure S320.  Get High-res Image Gene #51: '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 = 4.9e-05

Table S321.  Gene #51: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 29(15Q11.2) MUTATED 30 129 18
DEL PEAK 29(15Q11.2) WILD-TYPE 23 92 159

Figure S321.  Get High-res Image Gene #51: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q11.2' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00033

Table S322.  Gene #51: 'del_15q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
DEL PEAK 29(15Q11.2) MUTATED 24 58 33
DEL PEAK 29(15Q11.2) WILD-TYPE 61 45 73

Figure S322.  Get High-res Image Gene #51: 'del_15q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S323.  Gene #51: 'del_15q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 29(15Q11.2) MUTATED 66 18 37 55
DEL PEAK 29(15Q11.2) WILD-TYPE 61 76 60 76

Figure S323.  Get High-res Image Gene #51: '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 = 4.9e-05

Table S324.  Gene #51: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 29(15Q11.2) MUTATED 44 52 11 63 6
DEL PEAK 29(15Q11.2) WILD-TYPE 35 56 85 66 31

Figure S324.  Get High-res Image Gene #51: 'del_15q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S325.  Gene #51: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
DEL PEAK 29(15Q11.2) MUTATED 29 20 38 38 30
DEL PEAK 29(15Q11.2) WILD-TYPE 31 68 33 37 74

Figure S325.  Get High-res Image Gene #51: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00336 (Fisher's exact test), Q value = 0.0087

Table S326.  Gene #51: '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 79 55 46 17 55 20 26 42 58
DEL PEAK 29(15Q11.2) MUTATED 35 23 16 1 26 5 7 11 31
DEL PEAK 29(15Q11.2) WILD-TYPE 44 32 30 16 29 15 19 31 27

Figure S326.  Get High-res Image Gene #51: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.035

Table S327.  Gene #51: 'del_15q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
DEL PEAK 29(15Q11.2) MUTATED 12 9 7 7 1 7
DEL PEAK 29(15Q11.2) WILD-TYPE 6 11 9 4 10 2

Figure S327.  Get High-res Image Gene #51: 'del_15q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q15.2' versus 'MRNA_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00029

Table S328.  Gene #52: 'del_15q15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 30(15Q15.2) MUTATED 2 10 25 8 13
DEL PEAK 30(15Q15.2) WILD-TYPE 29 7 24 19 10

Figure S328.  Get High-res Image Gene #52: 'del_15q15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q15.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 7e-04

Table S329.  Gene #52: 'del_15q15.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
DEL PEAK 30(15Q15.2) MUTATED 6 33 19
DEL PEAK 30(15Q15.2) WILD-TYPE 36 35 18

Figure S329.  Get High-res Image Gene #52: '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 = 4.9e-05

Table S330.  Gene #52: 'del_15q15.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 30(15Q15.2) MUTATED 29 124 19
DEL PEAK 30(15Q15.2) WILD-TYPE 24 97 158

Figure S330.  Get High-res Image Gene #52: 'del_15q15.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q15.2' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00017

Table S331.  Gene #52: 'del_15q15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
DEL PEAK 30(15Q15.2) MUTATED 25 57 30
DEL PEAK 30(15Q15.2) WILD-TYPE 60 46 76

Figure S331.  Get High-res Image Gene #52: 'del_15q15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q15.2' versus 'RPPA_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.026

Table S332.  Gene #52: 'del_15q15.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 145 125
DEL PEAK 30(15Q15.2) MUTATED 42 47 38
DEL PEAK 30(15Q15.2) WILD-TYPE 43 98 87

Figure S332.  Get High-res Image Gene #52: 'del_15q15.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_15q15.2' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00013

Table S333.  Gene #52: 'del_15q15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 30(15Q15.2) MUTATED 65 19 34 53
DEL PEAK 30(15Q15.2) WILD-TYPE 62 75 63 78

Figure S333.  Get High-res Image Gene #52: '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 = 4.9e-05

Table S334.  Gene #52: 'del_15q15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 30(15Q15.2) MUTATED 41 50 12 63 5
DEL PEAK 30(15Q15.2) WILD-TYPE 38 58 84 66 32

Figure S334.  Get High-res Image Gene #52: 'del_15q15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q15.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S335.  Gene #52: 'del_15q15.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
DEL PEAK 30(15Q15.2) MUTATED 29 17 36 36 30
DEL PEAK 30(15Q15.2) WILD-TYPE 31 71 35 39 74

Figure S335.  Get High-res Image Gene #52: 'del_15q15.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q15.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.0027

Table S336.  Gene #52: '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 79 55 46 17 55 20 26 42 58
DEL PEAK 30(15Q15.2) MUTATED 34 19 16 0 27 5 8 10 29
DEL PEAK 30(15Q15.2) WILD-TYPE 45 36 30 17 28 15 18 32 29

Figure S336.  Get High-res Image Gene #52: 'del_15q15.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_15q15.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.021 (Fisher's exact test), Q value = 0.042

Table S337.  Gene #52: 'del_15q15.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
DEL PEAK 30(15Q15.2) MUTATED 11 8 7 7 1 7
DEL PEAK 30(15Q15.2) WILD-TYPE 7 12 9 4 10 2

Figure S337.  Get High-res Image Gene #52: 'del_15q15.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q21.1' versus 'MRNA_CNMF'

P value = 0.00194 (Fisher's exact test), Q value = 0.0054

Table S338.  Gene #53: 'del_15q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 31(15Q21.1) MUTATED 5 10 24 7 13
DEL PEAK 31(15Q21.1) WILD-TYPE 26 7 25 20 10

Figure S338.  Get High-res Image Gene #53: 'del_15q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q21.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.023

Table S339.  Gene #53: 'del_15q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
DEL PEAK 31(15Q21.1) MUTATED 9 31 19
DEL PEAK 31(15Q21.1) WILD-TYPE 33 37 18

Figure S339.  Get High-res Image Gene #53: '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 = 4.9e-05

Table S340.  Gene #53: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 31(15Q21.1) MUTATED 28 120 21
DEL PEAK 31(15Q21.1) WILD-TYPE 25 101 156

Figure S340.  Get High-res Image Gene #53: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q21.1' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00033

Table S341.  Gene #53: 'del_15q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
DEL PEAK 31(15Q21.1) MUTATED 24 55 29
DEL PEAK 31(15Q21.1) WILD-TYPE 61 48 77

Figure S341.  Get High-res Image Gene #53: 'del_15q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q21.1' versus 'RPPA_CNMF'

P value = 0.0459 (Fisher's exact test), Q value = 0.082

Table S342.  Gene #53: 'del_15q21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 145 125
DEL PEAK 31(15Q21.1) MUTATED 40 48 39
DEL PEAK 31(15Q21.1) WILD-TYPE 45 97 86

Figure S342.  Get High-res Image Gene #53: 'del_15q21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_15q21.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S343.  Gene #53: 'del_15q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 31(15Q21.1) MUTATED 63 18 33 54
DEL PEAK 31(15Q21.1) WILD-TYPE 64 76 64 77

Figure S343.  Get High-res Image Gene #53: '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 = 4.9e-05

Table S344.  Gene #53: 'del_15q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 31(15Q21.1) MUTATED 39 49 11 61 8
DEL PEAK 31(15Q21.1) WILD-TYPE 40 59 85 68 29

Figure S344.  Get High-res Image Gene #53: 'del_15q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q21.1' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.1e-05

Table S345.  Gene #53: 'del_15q21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
DEL PEAK 31(15Q21.1) MUTATED 28 17 36 35 31
DEL PEAK 31(15Q21.1) WILD-TYPE 32 71 35 40 73

Figure S345.  Get High-res Image Gene #53: 'del_15q21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00243 (Fisher's exact test), Q value = 0.0066

Table S346.  Gene #53: '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 79 55 46 17 55 20 26 42 58
DEL PEAK 31(15Q21.1) MUTATED 33 19 16 0 26 5 8 11 29
DEL PEAK 31(15Q21.1) WILD-TYPE 46 36 30 17 29 15 18 31 29

Figure S346.  Get High-res Image Gene #53: 'del_15q21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_15q21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.059

Table S347.  Gene #53: 'del_15q21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
DEL PEAK 31(15Q21.1) MUTATED 10 8 7 7 1 7
DEL PEAK 31(15Q21.1) WILD-TYPE 8 12 9 4 10 2

Figure S347.  Get High-res Image Gene #53: 'del_15q21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q22.33' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S348.  Gene #54: 'del_15q22.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 32(15Q22.33) MUTATED 2 10 23 4 13
DEL PEAK 32(15Q22.33) WILD-TYPE 29 7 26 23 10

Figure S348.  Get High-res Image Gene #54: 'del_15q22.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q22.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.001

Table S349.  Gene #54: 'del_15q22.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
DEL PEAK 32(15Q22.33) MUTATED 5 29 18
DEL PEAK 32(15Q22.33) WILD-TYPE 37 39 19

Figure S349.  Get High-res Image Gene #54: '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 = 4.9e-05

Table S350.  Gene #54: 'del_15q22.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 32(15Q22.33) MUTATED 29 119 13
DEL PEAK 32(15Q22.33) WILD-TYPE 24 102 164

Figure S350.  Get High-res Image Gene #54: 'del_15q22.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q22.33' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.1e-05

Table S351.  Gene #54: 'del_15q22.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
DEL PEAK 32(15Q22.33) MUTATED 25 56 27
DEL PEAK 32(15Q22.33) WILD-TYPE 60 47 79

Figure S351.  Get High-res Image Gene #54: 'del_15q22.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q22.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S352.  Gene #54: 'del_15q22.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 32(15Q22.33) MUTATED 63 15 33 49
DEL PEAK 32(15Q22.33) WILD-TYPE 64 79 64 82

Figure S352.  Get High-res Image Gene #54: '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 = 4.9e-05

Table S353.  Gene #54: 'del_15q22.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 32(15Q22.33) MUTATED 41 47 11 58 3
DEL PEAK 32(15Q22.33) WILD-TYPE 38 61 85 71 34

Figure S353.  Get High-res Image Gene #54: 'del_15q22.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q22.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S354.  Gene #54: 'del_15q22.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
DEL PEAK 32(15Q22.33) MUTATED 27 16 37 34 25
DEL PEAK 32(15Q22.33) WILD-TYPE 33 72 34 41 79

Figure S354.  Get High-res Image Gene #54: 'del_15q22.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q22.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.0016

Table S355.  Gene #54: '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 79 55 46 17 55 20 26 42 58
DEL PEAK 32(15Q22.33) MUTATED 34 20 16 0 22 4 8 7 28
DEL PEAK 32(15Q22.33) WILD-TYPE 45 35 30 17 33 16 18 35 30

Figure S355.  Get High-res Image Gene #54: 'del_15q22.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_15q22.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0366 (Fisher's exact test), Q value = 0.067

Table S356.  Gene #54: 'del_15q22.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
DEL PEAK 32(15Q22.33) MUTATED 9 8 7 7 1 7
DEL PEAK 32(15Q22.33) WILD-TYPE 9 12 9 4 10 2

Figure S356.  Get High-res Image Gene #54: 'del_15q22.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16p13.3' versus 'CN_CNMF'

P value = 0.0427 (Fisher's exact test), Q value = 0.077

Table S357.  Gene #55: 'del_16p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 33(16P13.3) MUTATED 9 34 14
DEL PEAK 33(16P13.3) WILD-TYPE 44 187 163

Figure S357.  Get High-res Image Gene #55: 'del_16p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_16p13.3' versus 'MRNASEQ_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.076

Table S358.  Gene #55: 'del_16p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 33(16P13.3) MUTATED 23 6 9 19
DEL PEAK 33(16P13.3) WILD-TYPE 104 88 88 112

Figure S358.  Get High-res Image Gene #55: 'del_16p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNA_CNMF'

P value = 0.00883 (Fisher's exact test), Q value = 0.02

Table S359.  Gene #56: 'del_16q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 34(16Q23.1) MUTATED 11 0 5 4 2
DEL PEAK 34(16Q23.1) WILD-TYPE 20 17 44 23 21

Figure S359.  Get High-res Image Gene #56: 'del_16q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_16q23.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0039 (Fisher's exact test), Q value = 0.0099

Table S360.  Gene #56: 'del_16q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
DEL PEAK 34(16Q23.1) MUTATED 13 5 4
DEL PEAK 34(16Q23.1) WILD-TYPE 29 63 33

Figure S360.  Get High-res Image Gene #56: 'del_16q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0158 (Fisher's exact test), Q value = 0.033

Table S361.  Gene #56: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 34(16Q23.1) MUTATED 9 13 15 12 12
DEL PEAK 34(16Q23.1) WILD-TYPE 70 95 81 117 25

Figure S361.  Get High-res Image Gene #56: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S362.  Gene #57: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 35(17P12) MUTATED 3 13 40 10 16
DEL PEAK 35(17P12) WILD-TYPE 28 4 9 17 7

Figure S362.  Get High-res Image Gene #57: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S363.  Gene #57: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
DEL PEAK 35(17P12) MUTATED 8 46 28
DEL PEAK 35(17P12) WILD-TYPE 34 22 9

Figure S363.  Get High-res Image Gene #57: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S364.  Gene #57: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 35(17P12) MUTATED 30 195 29
DEL PEAK 35(17P12) WILD-TYPE 23 26 148

Figure S364.  Get High-res Image Gene #57: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S365.  Gene #57: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
DEL PEAK 35(17P12) MUTATED 37 88 43
DEL PEAK 35(17P12) WILD-TYPE 48 15 63

Figure S365.  Get High-res Image Gene #57: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00096 (Fisher's exact test), Q value = 0.0028

Table S366.  Gene #57: 'del_17p12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 43 86 22 20 26
DEL PEAK 35(17P12) MUTATED 35 14 26 22 23 37 8 10 21
DEL PEAK 35(17P12) WILD-TYPE 16 19 9 17 20 49 14 10 5

Figure S366.  Get High-res Image Gene #57: 'del_17p12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S367.  Gene #57: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 35(17P12) MUTATED 104 27 48 74
DEL PEAK 35(17P12) WILD-TYPE 23 67 49 57

Figure S367.  Get High-res Image Gene #57: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S368.  Gene #57: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 35(17P12) MUTATED 55 83 20 91 4
DEL PEAK 35(17P12) WILD-TYPE 24 25 76 38 33

Figure S368.  Get High-res Image Gene #57: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S369.  Gene #57: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
DEL PEAK 35(17P12) MUTATED 49 32 41 60 42
DEL PEAK 35(17P12) WILD-TYPE 11 56 30 15 62

Figure S369.  Get High-res Image Gene #57: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S370.  Gene #57: '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 79 55 46 17 55 20 26 42 58
DEL PEAK 35(17P12) MUTATED 49 28 34 0 35 11 12 11 44
DEL PEAK 35(17P12) WILD-TYPE 30 27 12 17 20 9 14 31 14

Figure S370.  Get High-res Image Gene #57: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00366 (Fisher's exact test), Q value = 0.0094

Table S371.  Gene #57: 'del_17p12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
DEL PEAK 35(17P12) MUTATED 16 14 8 7 2 7
DEL PEAK 35(17P12) WILD-TYPE 2 6 8 4 9 2

Figure S371.  Get High-res Image Gene #57: 'del_17p12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17q24.3' versus 'MRNA_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.04

Table S372.  Gene #58: 'del_17q24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 36(17Q24.3) MUTATED 1 4 12 1 4
DEL PEAK 36(17Q24.3) WILD-TYPE 30 13 37 26 19

Figure S372.  Get High-res Image Gene #58: 'del_17q24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17q24.3' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00013

Table S373.  Gene #58: 'del_17q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 36(17Q24.3) MUTATED 14 44 11
DEL PEAK 36(17Q24.3) WILD-TYPE 39 177 166

Figure S373.  Get High-res Image Gene #58: 'del_17q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_17q24.3' versus 'MIRSEQ_CNMF'

P value = 0.0074 (Fisher's exact test), Q value = 0.017

Table S374.  Gene #58: 'del_17q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
DEL PEAK 36(17Q24.3) MUTATED 16 8 13 15 9
DEL PEAK 36(17Q24.3) WILD-TYPE 44 80 58 60 95

Figure S374.  Get High-res Image Gene #58: 'del_17q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18p11.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S375.  Gene #59: 'del_18p11.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 37(18P11.31) MUTATED 1 11 43 8 17
DEL PEAK 37(18P11.31) WILD-TYPE 30 6 6 19 6

Figure S375.  Get High-res Image Gene #59: '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 = 4.9e-05

Table S376.  Gene #59: 'del_18p11.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
DEL PEAK 37(18P11.31) MUTATED 5 46 29
DEL PEAK 37(18P11.31) WILD-TYPE 37 22 8

Figure S376.  Get High-res Image Gene #59: '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 = 4.9e-05

Table S377.  Gene #59: 'del_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 37(18P11.31) MUTATED 37 188 23
DEL PEAK 37(18P11.31) WILD-TYPE 16 33 154

Figure S377.  Get High-res Image Gene #59: '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 = 4.9e-05

Table S378.  Gene #59: 'del_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
DEL PEAK 37(18P11.31) MUTATED 38 93 35
DEL PEAK 37(18P11.31) WILD-TYPE 47 10 71

Figure S378.  Get High-res Image Gene #59: 'del_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18p11.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00474 (Fisher's exact test), Q value = 0.012

Table S379.  Gene #59: 'del_18p11.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 43 86 22 20 26
DEL PEAK 37(18P11.31) MUTATED 29 18 24 17 24 36 9 11 22
DEL PEAK 37(18P11.31) WILD-TYPE 22 15 11 22 19 50 13 9 4

Figure S379.  Get High-res Image Gene #59: 'del_18p11.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_18p11.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S380.  Gene #59: 'del_18p11.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 37(18P11.31) MUTATED 110 19 50 68
DEL PEAK 37(18P11.31) WILD-TYPE 17 75 47 63

Figure S380.  Get High-res Image Gene #59: '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 = 4.9e-05

Table S381.  Gene #59: 'del_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 37(18P11.31) MUTATED 61 83 10 91 2
DEL PEAK 37(18P11.31) WILD-TYPE 18 25 86 38 35

Figure S381.  Get High-res Image Gene #59: '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 = 4.9e-05

Table S382.  Gene #59: 'del_18p11.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
DEL PEAK 37(18P11.31) MUTATED 50 25 42 57 40
DEL PEAK 37(18P11.31) WILD-TYPE 10 63 29 18 64

Figure S382.  Get High-res Image Gene #59: '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 = 4.9e-05

Table S383.  Gene #59: '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 79 55 46 17 55 20 26 42 58
DEL PEAK 37(18P11.31) MUTATED 44 26 35 0 31 10 14 9 45
DEL PEAK 37(18P11.31) WILD-TYPE 35 29 11 17 24 10 12 33 13

Figure S383.  Get High-res Image Gene #59: 'del_18p11.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18p11.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.0015

Table S384.  Gene #59: 'del_18p11.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
DEL PEAK 37(18P11.31) MUTATED 16 12 7 7 1 7
DEL PEAK 37(18P11.31) WILD-TYPE 2 8 9 4 10 2

Figure S384.  Get High-res Image Gene #59: 'del_18p11.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18p11.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00353 (Fisher's exact test), Q value = 0.009

Table S385.  Gene #59: 'del_18p11.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 12 9 8 12 9 7 13 9 6
DEL PEAK 37(18P11.31) MUTATED 10 6 6 5 3 2 4 8 6
DEL PEAK 37(18P11.31) WILD-TYPE 2 3 2 7 6 5 9 1 0

Figure S385.  Get High-res Image Gene #59: '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 = 4.9e-05

Table S386.  Gene #60: 'del_18q12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 38(18Q12.2) MUTATED 1 14 44 11 16
DEL PEAK 38(18Q12.2) WILD-TYPE 30 3 5 16 7

Figure S386.  Get High-res Image Gene #60: '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 = 4.9e-05

Table S387.  Gene #60: 'del_18q12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
DEL PEAK 38(18Q12.2) MUTATED 6 51 29
DEL PEAK 38(18Q12.2) WILD-TYPE 36 17 8

Figure S387.  Get High-res Image Gene #60: '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 = 4.9e-05

Table S388.  Gene #60: 'del_18q12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 38(18Q12.2) MUTATED 39 204 31
DEL PEAK 38(18Q12.2) WILD-TYPE 14 17 146

Figure S388.  Get High-res Image Gene #60: '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 = 4.9e-05

Table S389.  Gene #60: 'del_18q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
DEL PEAK 38(18Q12.2) MUTATED 43 97 43
DEL PEAK 38(18Q12.2) WILD-TYPE 42 6 63

Figure S389.  Get High-res Image Gene #60: 'del_18q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q12.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00508 (Fisher's exact test), Q value = 0.012

Table S390.  Gene #60: 'del_18q12.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 43 86 22 20 26
DEL PEAK 38(18Q12.2) MUTATED 36 17 25 23 26 38 9 13 21
DEL PEAK 38(18Q12.2) WILD-TYPE 15 16 10 16 17 48 13 7 5

Figure S390.  Get High-res Image Gene #60: 'del_18q12.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_18q12.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S391.  Gene #60: 'del_18q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 38(18Q12.2) MUTATED 114 26 57 76
DEL PEAK 38(18Q12.2) WILD-TYPE 13 68 40 55

Figure S391.  Get High-res Image Gene #60: '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 = 4.9e-05

Table S392.  Gene #60: 'del_18q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 38(18Q12.2) MUTATED 67 87 19 97 3
DEL PEAK 38(18Q12.2) WILD-TYPE 12 21 77 32 34

Figure S392.  Get High-res Image Gene #60: '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 = 4.9e-05

Table S393.  Gene #60: 'del_18q12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
DEL PEAK 38(18Q12.2) MUTATED 51 31 47 62 48
DEL PEAK 38(18Q12.2) WILD-TYPE 9 57 24 13 56

Figure S393.  Get High-res Image Gene #60: '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 = 4.9e-05

Table S394.  Gene #60: '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 79 55 46 17 55 20 26 42 58
DEL PEAK 38(18Q12.2) MUTATED 54 32 37 1 34 10 13 10 48
DEL PEAK 38(18Q12.2) WILD-TYPE 25 23 9 16 21 10 13 32 10

Figure S394.  Get High-res Image Gene #60: 'del_18q12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q12.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00072

Table S395.  Gene #60: 'del_18q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
DEL PEAK 38(18Q12.2) MUTATED 16 14 10 9 1 8
DEL PEAK 38(18Q12.2) WILD-TYPE 2 6 6 2 10 1

Figure S395.  Get High-res Image Gene #60: 'del_18q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0255 (Fisher's exact test), Q value = 0.05

Table S396.  Gene #60: 'del_18q12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 12 9 8 12 9 7 13 9 6
DEL PEAK 38(18Q12.2) MUTATED 10 7 7 7 5 2 6 9 5
DEL PEAK 38(18Q12.2) WILD-TYPE 2 2 1 5 4 5 7 0 1

Figure S396.  Get High-res Image Gene #60: '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 = 4.9e-05

Table S397.  Gene #61: 'del_18q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 39(18Q21.2) MUTATED 1 14 44 12 16
DEL PEAK 39(18Q21.2) WILD-TYPE 30 3 5 15 7

Figure S397.  Get High-res Image Gene #61: '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 = 4.9e-05

Table S398.  Gene #61: 'del_18q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
DEL PEAK 39(18Q21.2) MUTATED 6 52 29
DEL PEAK 39(18Q21.2) WILD-TYPE 36 16 8

Figure S398.  Get High-res Image Gene #61: '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 = 4.9e-05

Table S399.  Gene #61: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 39(18Q21.2) MUTATED 40 208 39
DEL PEAK 39(18Q21.2) WILD-TYPE 13 13 138

Figure S399.  Get High-res Image Gene #61: '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 = 4.9e-05

Table S400.  Gene #61: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
DEL PEAK 39(18Q21.2) MUTATED 43 99 53
DEL PEAK 39(18Q21.2) WILD-TYPE 42 4 53

Figure S400.  Get High-res Image Gene #61: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q21.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00703 (Fisher's exact test), Q value = 0.016

Table S401.  Gene #61: 'del_18q21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 43 86 22 20 26
DEL PEAK 39(18Q21.2) MUTATED 38 18 25 26 27 41 10 15 21
DEL PEAK 39(18Q21.2) WILD-TYPE 13 15 10 13 16 45 12 5 5

Figure S401.  Get High-res Image Gene #61: 'del_18q21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S402.  Gene #61: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 39(18Q21.2) MUTATED 115 33 61 77
DEL PEAK 39(18Q21.2) WILD-TYPE 12 61 36 54

Figure S402.  Get High-res Image Gene #61: '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 = 4.9e-05

Table S403.  Gene #61: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 39(18Q21.2) MUTATED 69 89 27 97 4
DEL PEAK 39(18Q21.2) WILD-TYPE 10 19 69 32 33

Figure S403.  Get High-res Image Gene #61: '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 = 4.9e-05

Table S404.  Gene #61: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
DEL PEAK 39(18Q21.2) MUTATED 53 37 48 64 50
DEL PEAK 39(18Q21.2) WILD-TYPE 7 51 23 11 54

Figure S404.  Get High-res Image Gene #61: '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 = 4.9e-05

Table S405.  Gene #61: '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 79 55 46 17 55 20 26 42 58
DEL PEAK 39(18Q21.2) MUTATED 56 34 38 2 35 14 13 12 48
DEL PEAK 39(18Q21.2) WILD-TYPE 23 21 8 15 20 6 13 30 10

Figure S405.  Get High-res Image Gene #61: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00023

Table S406.  Gene #61: 'del_18q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
DEL PEAK 39(18Q21.2) MUTATED 18 15 10 9 2 8
DEL PEAK 39(18Q21.2) WILD-TYPE 0 5 6 2 9 1

Figure S406.  Get High-res Image Gene #61: 'del_18q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0326 (Fisher's exact test), Q value = 0.061

Table S407.  Gene #61: 'del_18q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 12 9 8 12 9 7 13 9 6
DEL PEAK 39(18Q21.2) MUTATED 10 7 7 9 5 3 6 9 6
DEL PEAK 39(18Q21.2) WILD-TYPE 2 2 1 3 4 4 7 0 0

Figure S407.  Get High-res Image Gene #61: '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 = 4.9e-05

Table S408.  Gene #62: 'del_18q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 40(18Q22.1) MUTATED 1 14 45 12 16
DEL PEAK 40(18Q22.1) WILD-TYPE 30 3 4 15 7

Figure S408.  Get High-res Image Gene #62: '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 = 4.9e-05

Table S409.  Gene #62: 'del_18q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
DEL PEAK 40(18Q22.1) MUTATED 7 52 29
DEL PEAK 40(18Q22.1) WILD-TYPE 35 16 8

Figure S409.  Get High-res Image Gene #62: '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 = 4.9e-05

Table S410.  Gene #62: 'del_18q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 40(18Q22.1) MUTATED 41 208 37
DEL PEAK 40(18Q22.1) WILD-TYPE 12 13 140

Figure S410.  Get High-res Image Gene #62: '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 = 4.9e-05

Table S411.  Gene #62: 'del_18q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
DEL PEAK 40(18Q22.1) MUTATED 42 99 52
DEL PEAK 40(18Q22.1) WILD-TYPE 43 4 54

Figure S411.  Get High-res Image Gene #62: 'del_18q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q22.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0129 (Fisher's exact test), Q value = 0.028

Table S412.  Gene #62: 'del_18q22.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 43 86 22 20 26
DEL PEAK 40(18Q22.1) MUTATED 37 19 26 26 28 41 10 13 21
DEL PEAK 40(18Q22.1) WILD-TYPE 14 14 9 13 15 45 12 7 5

Figure S412.  Get High-res Image Gene #62: 'del_18q22.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_18q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S413.  Gene #62: 'del_18q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 40(18Q22.1) MUTATED 114 32 61 78
DEL PEAK 40(18Q22.1) WILD-TYPE 13 62 36 53

Figure S413.  Get High-res Image Gene #62: '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 = 4.9e-05

Table S414.  Gene #62: 'del_18q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 40(18Q22.1) MUTATED 69 88 26 97 5
DEL PEAK 40(18Q22.1) WILD-TYPE 10 20 70 32 32

Figure S414.  Get High-res Image Gene #62: '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 = 4.9e-05

Table S415.  Gene #62: 'del_18q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
DEL PEAK 40(18Q22.1) MUTATED 53 35 48 64 51
DEL PEAK 40(18Q22.1) WILD-TYPE 7 53 23 11 53

Figure S415.  Get High-res Image Gene #62: '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 = 4.9e-05

Table S416.  Gene #62: '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 79 55 46 17 55 20 26 42 58
DEL PEAK 40(18Q22.1) MUTATED 56 34 38 2 34 13 13 13 48
DEL PEAK 40(18Q22.1) WILD-TYPE 23 21 8 15 21 7 13 29 10

Figure S416.  Get High-res Image Gene #62: 'del_18q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 2e-04

Table S417.  Gene #62: 'del_18q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 20 16 11 11 9
DEL PEAK 40(18Q22.1) MUTATED 18 15 10 9 2 8
DEL PEAK 40(18Q22.1) WILD-TYPE 0 5 6 2 9 1

Figure S417.  Get High-res Image Gene #62: 'del_18q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0327 (Fisher's exact test), Q value = 0.061

Table S418.  Gene #62: 'del_18q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 12 9 8 12 9 7 13 9 6
DEL PEAK 40(18Q22.1) MUTATED 10 7 7 9 5 3 6 9 6
DEL PEAK 40(18Q22.1) WILD-TYPE 2 2 1 3 4 4 7 0 0

Figure S418.  Get High-res Image Gene #62: 'del_18q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'MRNA_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.001

Table S419.  Gene #63: 'del_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 41(19P13.3) MUTATED 0 8 12 3 4
DEL PEAK 41(19P13.3) WILD-TYPE 31 9 37 24 19

Figure S419.  Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19p13.3' versus 'CN_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.002

Table S420.  Gene #63: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 41(19P13.3) MUTATED 7 44 12
DEL PEAK 41(19P13.3) WILD-TYPE 46 177 165

Figure S420.  Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00725 (Fisher's exact test), Q value = 0.017

Table S421.  Gene #63: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 41(19P13.3) MUTATED 24 4 14 21
DEL PEAK 41(19P13.3) WILD-TYPE 103 90 83 110

Figure S421.  Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00087 (Fisher's exact test), Q value = 0.0026

Table S422.  Gene #63: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 41(19P13.3) MUTATED 10 20 5 27 1
DEL PEAK 41(19P13.3) WILD-TYPE 69 88 91 102 36

Figure S422.  Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00597 (Fisher's exact test), Q value = 0.014

Table S423.  Gene #63: '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 79 55 46 17 55 20 26 42 58
DEL PEAK 41(19P13.3) MUTATED 10 3 6 0 15 4 3 2 13
DEL PEAK 41(19P13.3) WILD-TYPE 69 52 40 17 40 16 23 40 45

Figure S423.  Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0329 (Fisher's exact test), Q value = 0.061

Table S424.  Gene #64: 'del_20p12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
DEL PEAK 42(20P12.1) MUTATED 3 11 11
DEL PEAK 42(20P12.1) WILD-TYPE 39 57 26

Figure S424.  Get High-res Image Gene #64: '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 = 4.9e-05

Table S425.  Gene #64: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 42(20P12.1) MUTATED 1 78 8
DEL PEAK 42(20P12.1) WILD-TYPE 52 143 169

Figure S425.  Get High-res Image Gene #64: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_20p12.1' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00064

Table S426.  Gene #64: 'del_20p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
DEL PEAK 42(20P12.1) MUTATED 14 35 12
DEL PEAK 42(20P12.1) WILD-TYPE 71 68 94

Figure S426.  Get High-res Image Gene #64: 'del_20p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_20p12.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0091 (Fisher's exact test), Q value = 0.02

Table S427.  Gene #64: 'del_20p12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 43 86 22 20 26
DEL PEAK 42(20P12.1) MUTATED 12 1 12 11 6 14 2 6 8
DEL PEAK 42(20P12.1) WILD-TYPE 39 32 23 28 37 72 20 14 18

Figure S427.  Get High-res Image Gene #64: 'del_20p12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_20p12.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S428.  Gene #64: 'del_20p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 42(20P12.1) MUTATED 46 7 15 19
DEL PEAK 42(20P12.1) WILD-TYPE 81 87 82 112

Figure S428.  Get High-res Image Gene #64: '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 = 4.9e-05

Table S429.  Gene #64: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 42(20P12.1) MUTATED 24 31 5 23 4
DEL PEAK 42(20P12.1) WILD-TYPE 55 77 91 106 33

Figure S429.  Get High-res Image Gene #64: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_CNMF'

P value = 0.00256 (Fisher's exact test), Q value = 0.0069

Table S430.  Gene #64: 'del_20p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
DEL PEAK 42(20P12.1) MUTATED 21 13 11 19 12
DEL PEAK 42(20P12.1) WILD-TYPE 39 75 60 56 92

Figure S430.  Get High-res Image Gene #64: 'del_20p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_20p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00497 (Fisher's exact test), Q value = 0.012

Table S431.  Gene #64: '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 79 55 46 17 55 20 26 42 58
DEL PEAK 42(20P12.1) MUTATED 16 13 15 0 14 5 1 3 9
DEL PEAK 42(20P12.1) WILD-TYPE 63 42 31 17 41 15 25 39 49

Figure S431.  Get High-res Image Gene #64: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0486 (Fisher's exact test), Q value = 0.086

Table S432.  Gene #64: 'del_20p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 12 9 8 12 9 7 13 9 6
DEL PEAK 42(20P12.1) MUTATED 2 3 2 4 0 1 0 4 3
DEL PEAK 42(20P12.1) WILD-TYPE 10 6 6 8 9 6 13 5 3

Figure S432.  Get High-res Image Gene #64: 'del_20p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q11.2' versus 'MRNA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00026

Table S433.  Gene #65: 'del_21q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 43(21Q11.2) MUTATED 2 8 26 7 5
DEL PEAK 43(21Q11.2) WILD-TYPE 29 9 23 20 18

Figure S433.  Get High-res Image Gene #65: 'del_21q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_21q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0237 (Fisher's exact test), Q value = 0.047

Table S434.  Gene #65: 'del_21q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
DEL PEAK 43(21Q11.2) MUTATED 7 28 13
DEL PEAK 43(21Q11.2) WILD-TYPE 35 40 24

Figure S434.  Get High-res Image Gene #65: '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 = 4.9e-05

Table S435.  Gene #65: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 43(21Q11.2) MUTATED 29 92 20
DEL PEAK 43(21Q11.2) WILD-TYPE 24 129 157

Figure S435.  Get High-res Image Gene #65: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 0.00446 (Fisher's exact test), Q value = 0.011

Table S436.  Gene #65: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
DEL PEAK 43(21Q11.2) MUTATED 22 44 24
DEL PEAK 43(21Q11.2) WILD-TYPE 63 59 82

Figure S436.  Get High-res Image Gene #65: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S437.  Gene #65: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 43(21Q11.2) MUTATED 61 14 28 37
DEL PEAK 43(21Q11.2) WILD-TYPE 66 80 69 94

Figure S437.  Get High-res Image Gene #65: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_21q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.0013

Table S438.  Gene #65: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 43(21Q11.2) MUTATED 35 35 18 47 5
DEL PEAK 43(21Q11.2) WILD-TYPE 44 73 78 82 32

Figure S438.  Get High-res Image Gene #65: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_CNMF'

P value = 0.0151 (Fisher's exact test), Q value = 0.032

Table S439.  Gene #65: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
DEL PEAK 43(21Q11.2) MUTATED 25 17 25 28 27
DEL PEAK 43(21Q11.2) WILD-TYPE 35 71 46 47 77

Figure S439.  Get High-res Image Gene #65: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_22q13.32' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 9.1e-05

Table S440.  Gene #66: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 17 49 27 23
DEL PEAK 44(22Q13.32) MUTATED 3 11 26 6 11
DEL PEAK 44(22Q13.32) WILD-TYPE 28 6 23 21 12

Figure S440.  Get High-res Image Gene #66: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_22q13.32' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00013

Table S441.  Gene #66: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 68 37
DEL PEAK 44(22Q13.32) MUTATED 5 36 16
DEL PEAK 44(22Q13.32) WILD-TYPE 37 32 21

Figure S441.  Get High-res Image Gene #66: '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 = 4.9e-05

Table S442.  Gene #66: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 221 177
DEL PEAK 44(22Q13.32) MUTATED 28 116 16
DEL PEAK 44(22Q13.32) WILD-TYPE 25 105 161

Figure S442.  Get High-res Image Gene #66: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 0.0314 (Fisher's exact test), Q value = 0.059

Table S443.  Gene #66: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 103 106
DEL PEAK 44(22Q13.32) MUTATED 28 44 27
DEL PEAK 44(22Q13.32) WILD-TYPE 57 59 79

Figure S443.  Get High-res Image Gene #66: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q13.32' versus 'RPPA_CHIERARCHICAL'

P value = 0.0114 (Fisher's exact test), Q value = 0.025

Table S444.  Gene #66: 'del_22q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 43 86 22 20 26
DEL PEAK 44(22Q13.32) MUTATED 17 7 23 10 14 25 7 7 10
DEL PEAK 44(22Q13.32) WILD-TYPE 34 26 12 29 29 61 15 13 16

Figure S444.  Get High-res Image Gene #66: 'del_22q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.9e-05

Table S445.  Gene #66: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 94 97 131
DEL PEAK 44(22Q13.32) MUTATED 58 15 36 50
DEL PEAK 44(22Q13.32) WILD-TYPE 69 79 61 81

Figure S445.  Get High-res Image Gene #66: '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 = 4.9e-05

Table S446.  Gene #66: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 37
DEL PEAK 44(22Q13.32) MUTATED 37 45 13 61 3
DEL PEAK 44(22Q13.32) WILD-TYPE 42 63 83 68 34

Figure S446.  Get High-res Image Gene #66: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 7e-04

Table S447.  Gene #66: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 88 71 75 104
DEL PEAK 44(22Q13.32) MUTATED 26 17 28 37 28
DEL PEAK 44(22Q13.32) WILD-TYPE 34 71 43 38 76

Figure S447.  Get High-res Image Gene #66: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_22q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0184 (Fisher's exact test), Q value = 0.037

Table S448.  Gene #66: '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 79 55 46 17 55 20 26 42 58
DEL PEAK 44(22Q13.32) MUTATED 32 17 20 1 18 3 9 10 26
DEL PEAK 44(22Q13.32) WILD-TYPE 47 38 26 16 37 17 17 32 32

Figure S448.  Get High-res Image Gene #66: '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/COAD-TP/22508739/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/COAD-TP/22541003/COAD-TP.transferedmergedcluster.txt

  • Number of patients = 451

  • Number of significantly focal cnvs = 66

  • 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)