Correlation between copy number variation genes (focal events) and molecular subtypes
Thyroid Adenocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1M61JD3
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1M61JD3
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 98 focal events and 10 molecular subtypes across 501 patients, 424 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1p36.32 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • amp_1q31.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_1q43 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_2p16.1 cnv correlated to 'CN_CNMF'.

  • amp_3p22.3 cnv correlated to 'CN_CNMF'.

  • amp_3p14.1 cnv correlated to 'CN_CNMF'.

  • amp_4p16.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_4q22.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • amp_4q28.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_4q31.21 cnv correlated to 'CN_CNMF'.

  • amp_4q32.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_5p14.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_5q21.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_5q21.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_5q33.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_5q35.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_6p22.3 cnv correlated to 'METHLYATION_CNMF'.

  • amp_6p22.2 cnv correlated to 'METHLYATION_CNMF'.

  • amp_6q27 cnv correlated to 'RPPA_CHIERARCHICAL'.

  • amp_7q11.21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_7q21.11 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_7q31.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_7q34 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_9q22.31 cnv correlated to 'CN_CNMF'.

  • amp_9q31.1 cnv correlated to 'CN_CNMF'.

  • amp_10q24.2 cnv correlated to 'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_10q25.1 cnv correlated to 'CN_CNMF'.

  • amp_11p13 cnv correlated to 'CN_CNMF'.

  • amp_12p11.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_12q21.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_12q23.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_13q14.2 cnv correlated to 'CN_CNMF'.

  • amp_13q34 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.

  • amp_14q12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_14q32.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_18q12.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_18q22.1 cnv correlated to 'CN_CNMF'.

  • amp_18q22.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_19p13.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_20p13 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_20q13.11 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_20q13.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_20q13.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_21q21.3 cnv correlated to 'CN_CNMF'.

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

  • amp_xp22.12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_xp11.4 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_xp11.22 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_xp11.22 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_xp11.21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_xq21.2 cnv correlated to 'CN_CNMF'.

  • amp_xq22.3 cnv correlated to 'CN_CNMF'.

  • amp_xq23 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • amp_xq24 cnv correlated to 'CN_CNMF'.

  • amp_xq24 cnv correlated to 'CN_CNMF'.

  • amp_xq28 cnv correlated to 'CN_CNMF'.

  • del_1q24.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_1q42.13 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • del_2p23.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_2q37.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_4q34.3 cnv correlated to 'CN_CNMF'.

  • del_6q22.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_8p23.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_8p22 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_8p12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_8q24.22 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_9q22.33 cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_10p12.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_10q21.2 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_11p15.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_13q12.13 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_13q22.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_15q25.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_16q23.3 cnv correlated to 'CN_CNMF'.

  • del_17p13.1 cnv correlated to 'CN_CNMF'.

  • del_18q12.3 cnv correlated to 'CN_CNMF'.

  • del_19p13.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_19p13.12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_21q21.1 cnv correlated to 'CN_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_22q12.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_22q13.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_22q13.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_xq23 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_xq22.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 98 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 424 significant findings detected.

Clinical
Features 		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
amp 1q43 29 (6%) 472 1e-05
(0.000153) 		0.0065
(0.0226) 		0.00141
(0.00628) 		0.0383
(0.0929) 		0.00027
(0.0018) 		1e-05
(0.000153) 		0.0195
(0.0536) 		0.0107
(0.0338) 		0.00174
(0.00751) 		0.00259
(0.0105)
amp 1q31 2 29 (6%) 472 1e-05
(0.000153) 		0.0269
(0.0708) 		0.00158
(0.00697) 		0.0219
(0.0594) 		0.00038
(0.00227) 		2e-05
(0.000251) 		0.123
(0.225) 		0.0837
(0.172) 		0.0141
(0.0418) 		0.0307
(0.0777)
amp 5q35 2 20 (4%) 481 1e-05
(0.000153) 		8e-05
(0.000688) 		0.688
(0.84) 		0.0339
(0.0848) 		0.00057
(0.00307) 		4e-05
(0.000413) 		0.00076
(0.0038) 		7e-05
(0.000629) 		0.866
(0.975) 		0.00969
(0.0317)
amp 7q11 21 20 (4%) 481 1e-05
(0.000153) 		7e-05
(0.000629) 		0.534
(0.705) 		0.0166
(0.0479) 		0.00063
(0.0033) 		0.00019
(0.00134) 		0.00282
(0.0113) 		0.00033
(0.00207) 		0.428
(0.594) 		0.0226
(0.061)
amp 7q31 1 22 (4%) 479 1e-05
(0.000153) 		1e-05
(0.000153) 		0.557
(0.719) 		0.0095
(0.0313) 		0.00011
(0.000876) 		4e-05
(0.000413) 		1e-05
(0.000153) 		1e-05
(0.000153) 		0.735
(0.887) 		0.0003
(0.00193)
amp 7q34 22 (4%) 479 1e-05
(0.000153) 		4e-05
(0.000413) 		0.388
(0.552) 		0.0042
(0.0157) 		0.00047
(0.00271) 		0.00029
(0.00189) 		1e-05
(0.000153) 		1e-05
(0.000153) 		0.537
(0.707) 		0.0103
(0.0331)
amp 12q21 31 17 (3%) 484 1e-05
(0.000153) 		1e-05
(0.000153) 		0.865
(0.975) 		0.0391
(0.0946) 		2e-05
(0.000251) 		1e-05
(0.000153) 		1e-05
(0.000153) 		2e-05
(0.000251) 		0.147
(0.259) 		0.00184
(0.00787)
amp 20p13 14 (3%) 487 1e-05
(0.000153) 		3e-05
(0.000342) 		0.633
(0.797) 		0.0155
(0.0456) 		0.00037
(0.00222) 		0.0001
(0.000831) 		0.00048
(0.00275) 		3e-05
(0.000342) 		0.407
(0.57) 		0.0222
(0.0602)
amp 20q13 11 14 (3%) 487 1e-05
(0.000153) 		9e-05
(0.00076) 		0.604
(0.769) 		0.0449
(0.107) 		0.00037
(0.00222) 		9e-05
(0.00076) 		0.00056
(0.00305) 		0.00014
(0.00108) 		0.806
(0.934) 		0.0229
(0.0615)
amp 20q13 2 14 (3%) 487 1e-05
(0.000153) 		0.00065
(0.00335) 		0.54
(0.708) 		0.027
(0.0709) 		0.00339
(0.0132) 		0.00101
(0.00483) 		0.00055
(0.00305) 		0.00091
(0.00437) 		0.671
(0.829) 		0.0439
(0.105)
amp 22q11 21 7 (1%) 494 0.00284
(0.0114) 		0.00444
(0.0164) 		0.00787
(0.0269) 		0.036
(0.0884) 		0.0324
(0.0814) 		0.0299
(0.076) 		0.0278
(0.072) 		0.0108
(0.034)
del 6q22 31 7 (1%) 494 3e-05
(0.000342) 		0.00217
(0.00905) 		0.0125
(0.0374) 		0.577
(0.739) 		0.0272
(0.0712) 		0.0178
(0.0511) 		0.00459
(0.0168) 		0.00081
(0.00397) 		1
(1.00) 		0.0109
(0.0343)
del 8q24 22 7 (1%) 494 0.00065
(0.00335) 		0.0005
(0.00283) 		0.839
(0.959) 		0.17
(0.29) 		0.00162
(0.00709) 		0.00109
(0.00511) 		0.00016
(0.00117) 		7e-05
(0.000629) 		0.00415
(0.0156) 		0.00035
(0.00217)
del 13q22 1 19 (4%) 482 0.00195
(0.00827) 		0.0375
(0.0912) 		0.0549
(0.124) 		0.187
(0.313) 		0.00104
(0.0049) 		0.00081
(0.00397) 		0.003
(0.0119) 		0.00064
(0.00334) 		0.0138
(0.041) 		0.00356
(0.0137)
del 22q12 3 90 (18%) 411 1e-05
(0.000153) 		3e-05
(0.000342) 		0.12
(0.22) 		0.502
(0.672) 		1e-05
(0.000153) 		1e-05
(0.000153) 		0.00049
(0.00279) 		7e-05
(0.000629) 		0.00024
(0.00166) 		0.00037
(0.00222)
del 22q13 1 89 (18%) 412 1e-05
(0.000153) 		1e-05
(0.000153) 		0.12
(0.22) 		0.501
(0.672) 		1e-05
(0.000153) 		1e-05
(0.000153) 		0.0004
(0.00238) 		5e-05
(0.00048) 		0.00016
(0.00117) 		0.00026
(0.00177)
del 22q13 2 89 (18%) 412 1e-05
(0.000153) 		1e-05
(0.000153) 		0.117
(0.218) 		0.501
(0.672) 		1e-05
(0.000153) 		1e-05
(0.000153) 		0.00047
(0.00271) 		4e-05
(0.000413) 		0.00016
(0.00117) 		0.00027
(0.0018)
del 22q13 32 90 (18%) 411 1e-05
(0.000153) 		1e-05
(0.000153) 		0.117
(0.218) 		0.5
(0.672) 		1e-05
(0.000153) 		1e-05
(0.000153) 		0.00015
(0.00114) 		3e-05
(0.000342) 		0.00017
(0.00123) 		0.00019
(0.00134)
amp 4p16 1 7 (1%) 494 0.00057
(0.00307) 		0.0115
(0.0357) 		0.277
(0.416) 		0.424
(0.591) 		0.0282
(0.0726) 		0.0101
(0.0327) 		0.0339
(0.0848) 		0.00623
(0.022) 		0.711
(0.861) 		0.0472
(0.112)
amp 5p14 3 23 (5%) 478 1e-05
(0.000153) 		0.00911
(0.0302) 		0.364
(0.522) 		0.204
(0.331) 		0.00904
(0.03) 		3e-05
(0.000342) 		0.0011
(0.00513) 		0.00011
(0.000876) 		0.302
(0.448) 		0.00222
(0.00914)
amp 5q33 1 21 (4%) 480 1e-05
(0.000153) 		5e-05
(0.00048) 		1
(1.00) 		0.0656
(0.143) 		0.00018
(0.00129) 		4e-05
(0.000413) 		0.00028
(0.00184) 		2e-05
(0.000251) 		0.69
(0.841) 		0.00252
(0.0103)
amp 7q21 11 21 (4%) 480 1e-05
(0.000153) 		0.00026
(0.00177) 		0.804
(0.932) 		0.0532
(0.121) 		0.00211
(0.00887) 		0.00067
(0.00342) 		0.00139
(0.00622) 		0.00014
(0.00108) 		0.45
(0.616) 		0.0027
(0.0109)
amp 12p11 1 16 (3%) 485 1e-05
(0.000153) 		2e-05
(0.000251) 		0.662
(0.82) 		0.281
(0.421) 		8e-05
(0.000688) 		1e-05
(0.000153) 		5e-05
(0.00048) 		1e-05
(0.000153) 		0.606
(0.772) 		0.00234
(0.00959)
amp 12q23 1 17 (3%) 484 1e-05
(0.000153) 		8e-05
(0.000688) 		1
(1.00) 		0.271
(0.413) 		0.00016
(0.00117) 		4e-05
(0.000413) 		0.00011
(0.000876) 		2e-05
(0.000251) 		0.251
(0.391) 		0.00971
(0.0317)
amp 14q12 13 (3%) 488 1e-05
(0.000153) 		0.00219
(0.00906) 		1
(1.00) 		0.16
(0.277) 		0.00343
(0.0133) 		0.00333
(0.013) 		0.0166
(0.0479) 		0.00324
(0.0127) 		0.409
(0.572) 		0.0214
(0.0583)
amp 14q32 31 13 (3%) 488 1e-05
(0.000153) 		0.00013
(0.00102) 		1
(1.00) 		0.158
(0.273) 		0.00061
(0.00321) 		0.00028
(0.00184) 		0.00042
(0.00246) 		4e-05
(0.000413) 		1
(1.00) 		0.00077
(0.00383)
amp xp22 12 10 (2%) 491 1e-05
(0.000153) 		0.0003
(0.00193) 		0.742
(0.894) 		0.299
(0.444) 		0.00645
(0.0225) 		0.00728
(0.025) 		0.0354
(0.0878) 		0.00567
(0.0202) 		0.645
(0.802) 		0.0323
(0.0813)
amp xp11 22 8 (2%) 493 1e-05
(0.000153) 		0.00068
(0.00345) 		0.835
(0.959) 		0.502
(0.672) 		0.0117
(0.0361) 		0.00576
(0.0205) 		0.0133
(0.0398) 		0.00219
(0.00906) 		0.798
(0.93) 		0.0106
(0.0336)
amp xp11 21 9 (2%) 492 1e-05
(0.000153) 		0.00693
(0.0239) 		0.538
(0.707) 		0.683
(0.836) 		0.0296
(0.0754) 		0.0105
(0.0336) 		0.0186
(0.0521) 		0.00384
(0.0147) 		0.826
(0.954) 		0.0189
(0.0525)
del 2p23 1 12 (2%) 489 1e-05
(0.000153) 		2e-05
(0.000251) 		0.774
(0.919) 		0.0913
(0.183) 		3e-05
(0.000342) 		5e-05
(0.00048) 		1e-05
(0.000153) 		1e-05
(0.000153) 		0.254
(0.394) 		0.00012
(0.000948)
del 2q22 1 10 (2%) 491 1e-05
(0.000153) 		2e-05
(0.000251) 		0.772
(0.919) 		0.0909
(0.183) 		7e-05
(0.000629) 		5e-05
(0.00048) 		2e-05
(0.000251) 		1e-05
(0.000153) 		0.233
(0.369) 		0.00054
(0.00302)
del 2q37 3 13 (3%) 488 1e-05
(0.000153) 		1e-05
(0.000153) 		0.632
(0.797) 		0.0955
(0.188) 		2e-05
(0.000251) 		5e-05
(0.00048) 		3e-05
(0.000342) 		1e-05
(0.000153) 		0.0855
(0.175) 		0.00037
(0.00222)
del 8p23 2 4 (1%) 497 0.00018
(0.00129) 		0.0179
(0.0511) 		0.0364
(0.089) 		0.0471
(0.112) 		0.00816
(0.0276) 		0.00437
(0.0162) 		0.11
(0.21) 		0.0184
(0.0521)
del 8p22 4 (1%) 497 0.00011
(0.000876) 		0.0189
(0.0525) 		0.0359
(0.0884) 		0.0475
(0.112) 		0.00827
(0.0279) 		0.00415
(0.0156) 		0.11
(0.21) 		0.0192
(0.0531)
del 8p12 4 (1%) 497 0.0001
(0.000831) 		0.0184
(0.0521) 		0.037
(0.0902) 		0.048
(0.113) 		0.008
(0.0272) 		0.00468
(0.0171) 		0.11
(0.21) 		0.0189
(0.0525)
del 9p21 3 20 (4%) 481 1e-05
(0.000153) 		0.00811
(0.0275) 		0.241
(0.379) 		0.65
(0.807) 		0.0247
(0.0652) 		0.0244
(0.0649) 		0.00042
(0.00246) 		0.00058
(0.00311) 		0.243
(0.381) 		0.00015
(0.00114)
del 10p12 31 7 (1%) 494 1e-05
(0.000153) 		0.0115
(0.0357) 		0.496
(0.671) 		0.266
(0.408) 		0.0192
(0.053) 		0.0151
(0.0445) 		0.00484
(0.0175) 		0.00085
(0.0041) 		0.801
(0.93) 		0.00997
(0.0325)
del 10q23 31 12 (2%) 489 7e-05
(0.000629) 		0.0045
(0.0166) 		0.0528
(0.12) 		0.147
(0.259) 		0.00083
(0.00403) 		0.00471
(0.0172) 		0.00419
(0.0157) 		0.0008
(0.00396) 		0.262
(0.406) 		0.00876
(0.0292)
del 11p15 1 7 (1%) 494 2e-05
(0.000251) 		0.0114
(0.0355) 		0.498
(0.672) 		0.959
(1.00) 		0.00731
(0.025) 		0.0185
(0.0521) 		0.00488
(0.0176) 		0.0007
(0.00354) 		0.799
(0.93) 		0.0102
(0.0328)
del 15q25 3 9 (2%) 492 0.00061
(0.00321) 		0.00111
(0.00513) 		0.241
(0.379) 		0.0615
(0.137) 		0.00404
(0.0154) 		0.00161
(0.00708) 		0.00035
(0.00217) 		8e-05
(0.000688) 		0.45
(0.616) 		0.012
(0.0366)
del 19p13 2 7 (1%) 494 0.00024
(0.00166) 		0.00027
(0.0018) 		0.856
(0.97) 		0.301
(0.447) 		0.00158
(0.00697) 		0.00103
(0.00488) 		0.00021
(0.00147) 		7e-05
(0.000629) 		0.0534
(0.121) 		4e-05
(0.000413)
del 19p13 12 8 (2%) 493 0.00288
(0.0114) 		0.00423
(0.0158) 		0.132
(0.239) 		0.0983
(0.192) 		0.0122
(0.0368) 		0.00528
(0.019) 		0.00121
(0.00554) 		0.00043
(0.00251) 		0.0944
(0.187) 		0.00073
(0.00367)
amp 4q32 3 7 (1%) 494 0.00061
(0.00321) 		0.012
(0.0366) 		0.321
(0.468) 		0.0643
(0.142) 		0.0284
(0.0729) 		0.0174
(0.0499) 		0.0346
(0.0861) 		0.00636
(0.0223) 		0.899
(1.00) 		0.186
(0.311)
amp 5q21 1 23 (5%) 478 1e-05
(0.000153) 		0.00167
(0.00724) 		0.852
(0.968) 		0.079
(0.164) 		0.00633
(0.0222) 		0.0118
(0.0364) 		0.00861
(0.0288) 		0.00586
(0.0207) 		0.875
(0.983) 		0.106
(0.204)
amp 5q21 1 20 (4%) 481 1e-05
(0.000153) 		0.00111
(0.00513) 		1
(1.00) 		0.0813
(0.168) 		0.00305
(0.012) 		0.00056
(0.00305) 		0.00082
(0.004) 		0.00056
(0.00305) 		0.674
(0.83) 		0.0653
(0.143)
amp 19p13 3 8 (2%) 493 1e-05
(0.000153) 		0.00406
(0.0154) 		0.0122
(0.0368) 		0.00533
(0.0191) 		0.00164
(0.00714) 		0.00051
(0.00287) 		0.453
(0.619) 		0.318
(0.464)
amp 20q13 2 13 (3%) 488 1e-05
(0.000153) 		0.00179
(0.00769) 		0.794
(0.93) 		0.0909
(0.183) 		0.00857
(0.0288) 		0.00213
(0.00892) 		0.00969
(0.0317) 		0.00137
(0.00619) 		0.787
(0.929) 		0.107
(0.205)
del 13q12 13 18 (4%) 483 0.00036
(0.00222) 		0.00115
(0.00529) 		0.184
(0.31) 		0.0838
(0.172) 		0.0185
(0.0521) 		0.0364
(0.089) 		0.0744
(0.156) 		0.0207
(0.0567) 		0.432
(0.598) 		0.034
(0.0848)
amp 18q22 3 8 (2%) 493 0.00066
(0.00339) 		0.0241
(0.0645) 		0.0355
(0.0878) 		0.118
(0.218) 		0.0208
(0.0568) 		0.00654
(0.0226) 		0.161
(0.277) 		0.396
(0.558)
del 9q22 33 27 (5%) 474 1e-05
(0.000153) 		0.0928
(0.185) 		0.172
(0.294) 		0.115
(0.214) 		0.157
(0.272) 		0.0274
(0.0715) 		0.00481
(0.0175) 		0.00359
(0.0138) 		0.204
(0.331) 		0.00204
(0.00862)
amp 4q28 2 6 (1%) 495 0.00011
(0.000876) 		0.0285
(0.0729) 		0.0731
(0.154) 		0.0264
(0.0695) 		0.0831
(0.172) 		0.0189
(0.0525) 		0.782
(0.923) 		0.114
(0.214)
del 1q24 2 3 (1%) 498 0.00129
(0.00588) 		0.0491
(0.114) 		0.0984
(0.192) 		0.153
(0.267) 		0.0276
(0.0717) 		0.0166
(0.048) 		1
(1.00) 		0.194
(0.32)
amp 4q22 1 7 (1%) 494 0.00033
(0.00207) 		0.0115
(0.0357) 		1
(1.00) 		0.539
(0.707) 		0.0281
(0.0724) 		0.132
(0.24) 		0.309
(0.454) 		0.136
(0.244) 		0.798
(0.93) 		0.39
(0.552)
amp 10q24 2 3 (1%) 498 0.0502
(0.116) 		0.0482
(0.113) 		0.0988
(0.192) 		0.151
(0.265) 		0.0277
(0.0717) 		0.0165
(0.0479)
amp 13q34 7 (1%) 494 0.00055
(0.00305) 		0.049
(0.114) 		0.145
(0.257) 		0.0358
(0.0883) 		0.0518
(0.118) 		0.169
(0.289) 		0.307
(0.453) 		0.136
(0.244) 		1
(1.00) 		1
(1.00)
amp 18q12 1 7 (1%) 494 4e-05
(0.000413) 		0.0294
(0.075) 		0.0576
(0.129) 		0.118
(0.218) 		0.0989
(0.192) 		0.0311
(0.0787) 		0.269
(0.412) 		0.186
(0.311)
del 1q42 13 5 (1%) 496 0.0165
(0.0479) 		0.169
(0.289) 		0.455
(0.621) 		0.936
(1.00) 		0.0488
(0.114) 		0.156
(0.272) 		0.0415
(0.1) 		0.309
(0.454) 		0.845
(0.963) 		0.193
(0.32)
del 10q21 2 12 (2%) 489 0.00102
(0.00485) 		0.0644
(0.142) 		0.154
(0.269) 		0.674
(0.83) 		0.0185
(0.0521) 		0.0655
(0.143) 		0.135
(0.243) 		0.173
(0.294) 		0.578
(0.739) 		0.0462
(0.11)
del 21q21 1 9 (2%) 492 0.00016
(0.00117) 		0.307
(0.453) 		0.149
(0.262) 		0.325
(0.473) 		0.795
(0.93) 		0.801
(0.93) 		0.0643
(0.142) 		0.0228
(0.0613) 		0.264
(0.407) 		0.0207
(0.0567)
amp 1p36 32 5 (1%) 496 0.00135
(0.00612) 		0.84
(0.959) 		0.442
(0.609) 		0.0393
(0.0949) 		0.631
(0.797) 		0.544
(0.712) 		0.276
(0.416) 		0.835
(0.959)
amp xp11 4 9 (2%) 492 1e-05
(0.000153) 		0.012
(0.0366) 		0.841
(0.959) 		0.504
(0.672) 		0.0974
(0.19) 		0.139
(0.247) 		0.0865
(0.177) 		0.133
(0.241) 		0.797
(0.93) 		0.185
(0.311)
amp xp11 22 8 (2%) 493 1e-05
(0.000153) 		0.012
(0.0366) 		1
(1.00) 		0.282
(0.421) 		0.118
(0.218) 		0.0562
(0.126) 		0.18
(0.305) 		0.0724
(0.154) 		1
(1.00) 		0.184
(0.311)
amp xq23 9 (2%) 492 2e-05
(0.000251) 		0.0563
(0.126) 		1
(1.00) 		0.827
(0.954) 		0.0874
(0.178) 		0.0496
(0.115) 		0.205
(0.331) 		0.134
(0.242) 		1
(1.00) 		0.394
(0.557)
del xq23 4 (1%) 497 0.011
(0.0345) 		0.0462
(0.11) 		0.278
(0.418) 		0.196
(0.323) 		0.0965
(0.19) 		0.246
(0.385) 		0.0751
(0.157) 		0.0906
(0.183) 		0.22
(0.351) 		0.0947
(0.187)
del xq22 3 4 (1%) 497 0.0105
(0.0335) 		0.0445
(0.107) 		0.276
(0.416) 		0.197
(0.324) 		0.0971
(0.19) 		0.246
(0.384) 		0.0756
(0.158) 		0.0906
(0.183) 		0.219
(0.349) 		0.0962
(0.189)
amp 2p16 1 3 (1%) 498 0.0492
(0.114) 		1
(1.00) 		1
(1.00) 		0.875
(0.983) 		1
(1.00) 		1
(1.00) 		0.31
(0.455) 		1
(1.00)
amp 3p22 3 4 (1%) 497 0.011
(0.0345) 		0.184
(0.31) 		1
(1.00) 		0.886
(0.993) 		0.244
(0.382) 		0.317
(0.464) 		0.113
(0.213) 		0.0659
(0.143) 		1
(1.00) 		0.0675
(0.145)
amp 3p14 1 5 (1%) 496 0.0158
(0.0463) 		0.427
(0.594) 		0.781
(0.923) 		0.438
(0.605) 		0.693
(0.842) 		0.439
(0.606) 		0.865
(0.975) 		0.637
(0.798) 		1
(1.00) 		0.639
(0.798)
amp 4q31 21 10 (2%) 491 0.00272
(0.011) 		0.115
(0.214) 		1
(1.00) 		0.577
(0.739) 		0.273
(0.414) 		0.2
(0.328) 		0.522
(0.694) 		0.66
(0.819) 		1
(1.00) 		0.4
(0.563)
amp 6p22 3 3 (1%) 498 0.0511
(0.117) 		0.0485
(0.113) 		0.135
(0.243) 		0.509
(0.678) 		0.303
(0.449) 		0.191
(0.318) 		0.777
(0.921) 		0.191
(0.319)
amp 6p22 2 4 (1%) 497 0.113
(0.213) 		0.046
(0.11) 		0.837
(0.959) 		0.308
(0.453) 		0.0986
(0.192) 		0.247
(0.385) 		0.115
(0.214) 		0.0661
(0.143) 		1
(1.00) 		0.066
(0.143)
amp 6q27 4 (1%) 497 0.112
(0.213) 		0.184
(0.31) 		0.385
(0.55) 		0.0125
(0.0374) 		0.458
(0.624) 		0.395
(0.558) 		0.113
(0.213) 		0.0665
(0.144) 		0.693
(0.842) 		0.0672
(0.145)
amp 9q22 31 6 (1%) 495 0.024
(0.0644) 		0.863
(0.975) 		0.495
(0.671) 		0.852
(0.968) 		0.944
(1.00) 		0.353
(0.509) 		0.779
(0.922) 		1
(1.00) 		0.0649
(0.143) 		0.382
(0.546)
amp 9q31 1 6 (1%) 495 0.0242
(0.0646) 		0.417
(0.582) 		0.279
(0.419) 		0.822
(0.951) 		0.628
(0.797) 		0.438
(0.605) 		1
(1.00) 		0.887
(0.993) 		0.334
(0.485) 		0.774
(0.919)
amp 10q25 1 4 (1%) 497 0.0101
(0.0326) 		0.791
(0.93) 		0.9
(1.00) 		0.877
(0.984) 		0.69
(0.841) 		0.564
(0.727) 		1
(1.00) 		1
(1.00)
amp 11p13 8 (2%) 493 0.00286
(0.0114) 		0.119
(0.219) 		1
(1.00) 		0.112
(0.212) 		0.093
(0.185) 		0.14
(0.248) 		0.157
(0.272) 		0.0833
(0.172) 		0.53
(0.702) 		0.456
(0.622)
amp 13q14 2 6 (1%) 495 8e-05
(0.000688) 		0.0916
(0.183) 		0.383
(0.547) 		0.213
(0.341) 		0.12
(0.22) 		0.264
(0.407) 		0.526
(0.697) 		0.35
(0.505) 		0.747
(0.894) 		0.639
(0.798)
amp 18q22 1 7 (1%) 494 0.00032
(0.00204) 		0.241
(0.379) 		0.496
(0.671) 		0.0888
(0.18) 		0.152
(0.266) 		0.271
(0.413) 		0.268
(0.41) 		0.182
(0.309) 		0.799
(0.93) 		0.636
(0.798)
amp 21q21 3 6 (1%) 495 0.00139
(0.00622) 		0.0711
(0.152) 		0.631
(0.797) 		0.837
(0.959) 		0.525
(0.697) 		0.346
(0.501) 		0.745
(0.894) 		0.641
(0.798)
amp xq21 2 9 (2%) 492 1e-05
(0.000153) 		0.0547
(0.123) 		0.84
(0.959) 		0.504
(0.672) 		0.0877
(0.179) 		0.0733
(0.155) 		0.204
(0.331) 		0.0719
(0.154) 		1
(1.00) 		0.208
(0.332)
amp xq22 3 15 (3%) 486 0.00031
(0.00199) 		0.715
(0.865) 		0.837
(0.959) 		0.503
(0.672) 		0.749
(0.894) 		0.895
(1.00) 		0.948
(1.00) 		0.636
(0.798) 		0.492
(0.669) 		1
(1.00)
amp xq24 9 (2%) 492 2e-05
(0.000251) 		0.0537
(0.122) 		0.539
(0.707) 		0.679
(0.834) 		0.0889
(0.18) 		0.0726
(0.154) 		0.205
(0.331) 		0.0726
(0.154) 		1
(1.00) 		0.207
(0.331)
amp xq24 9 (2%) 492 2e-05
(0.000251) 		0.0552
(0.124) 		0.744
(0.894) 		0.607
(0.772) 		0.202
(0.331) 		0.0739
(0.155) 		0.205
(0.331) 		0.0697
(0.15) 		1
(1.00) 		0.205
(0.331)
amp xq28 10 (2%) 491 5e-05
(0.00048) 		0.129
(0.235) 		0.531
(0.703) 		0.261
(0.405) 		0.274
(0.415) 		0.222
(0.353) 		0.441
(0.608) 		0.23
(0.364) 		0.915
(1.00) 		0.402
(0.564)
del 4q34 3 5 (1%) 496 0.0158
(0.0463) 		0.168
(0.288) 		1
(1.00) 		0.501
(0.672) 		0.387
(0.551) 		0.573
(0.736) 		0.237
(0.375) 		0.0729
(0.154) 		1
(1.00) 		0.0764
(0.159)
del 16q23 3 6 (1%) 495 0.0245
(0.0649) 		0.148
(0.261) 		0.445
(0.61) 		0.444
(0.61) 		0.137
(0.245) 		0.151
(0.264) 		0.225
(0.357) 		0.206
(0.331) 		0.0694
(0.149) 		0.0623
(0.138)
del 17p13 1 8 (2%) 493 0.0137
(0.0408) 		0.413
(0.577) 		1
(1.00) 		0.388
(0.552) 		0.637
(0.798) 		0.596
(0.76) 		0.0919
(0.183) 		0.161
(0.277) 		0.127
(0.231) 		0.206
(0.331)
del 18q12 3 4 (1%) 497 0.00188
(0.00801) 		0.185
(0.311) 		1
(1.00) 		0.389
(0.552) 		0.244
(0.382) 		0.317
(0.464) 		0.0735
(0.155) 		0.0913
(0.183) 		0.532
(0.703) 		0.275
(0.415)
amp 1p32 3 5 (1%) 496 0.14
(0.248) 		0.549
(0.714) 		0.551
(0.714) 		0.697
(0.846) 		0.282
(0.421) 		0.156
(0.272) 		0.553
(0.716) 		0.195
(0.323)
amp 1p31 1 5 (1%) 496 0.0944
(0.187) 		0.551
(0.714) 		0.55
(0.714) 		0.964
(1.00) 		0.863
(0.975) 		0.641
(0.798) 		0.847
(0.964) 		0.684
(0.837)
amp 2q37 2 3 (1%) 498 0.204
(0.331) 		0.548
(0.714) 		0.495
(0.671) 		0.584
(0.746) 		0.203
(0.331) 		0.265
(0.408)
amp 6p21 31 3 (1%) 498 0.0503
(0.116) 		0.548
(0.714) 		0.748
(0.894) 		0.402
(0.564) 		0.205
(0.331) 		0.266
(0.408) 		0.111
(0.211) 		0.274
(0.415)
amp 6p21 2 4 (1%) 497 0.112
(0.212) 		0.793
(0.93) 		0.636
(0.798) 		0.344
(0.499) 		0.669
(0.828) 		0.745
(0.894) 		0.113
(0.213) 		0.567
(0.73) 		0.776
(0.921) 		0.193
(0.32)
amp 6p12 2 3 (1%) 498 0.0503
(0.116) 		0.551
(0.714) 		0.747
(0.894) 		0.72
(0.87) 		0.204
(0.331) 		0.264
(0.407) 		0.109
(0.21) 		0.271
(0.413)
amp 6q12 3 (1%) 498 0.372
(0.534) 		0.121
(0.22) 		0.136
(0.244) 		0.673
(0.83) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
amp 9q34 3 7 (1%) 494 0.0626
(0.139) 		0.294
(0.439) 		0.856
(0.97) 		0.828
(0.954) 		0.63
(0.797) 		0.347
(0.502) 		0.8
(0.93) 		0.628
(0.797) 		0.103
(0.2) 		0.773
(0.919)
del 5p15 2 4 (1%) 497 0.113
(0.213) 		0.363
(0.522) 		0.38
(0.544) 		0.275
(0.415) 		0.557
(0.719) 		0.681
(0.835) 		0.401
(0.564) 		0.566
(0.729)
del 7q34 4 (1%) 497 1
(1.00) 		0.792
(0.93) 		0.748
(0.894) 		0.675
(0.83) 		0.691
(0.841) 		1
(1.00) 		0.333
(0.484) 		1
(1.00)
'amp_1p36.32' versus 'CN_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.0061

Table S1.  Gene #1: 'amp_1p36.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 1(1P36.32) MUTATED 4 1 0
AMP PEAK 1(1P36.32) WILD-TYPE 52 355 89

Figure S1.  Get High-res Image Gene #1: 'amp_1p36.32' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1p36.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0393 (Fisher's exact test), Q value = 0.095

Table S2.  Gene #1: 'amp_1p36.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 1(1P36.32) MUTATED 4 1 0 0 0
AMP PEAK 1(1P36.32) WILD-TYPE 101 133 86 96 78

Figure S2.  Get High-res Image Gene #1: 'amp_1p36.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S3.  Gene #4: 'amp_1q31.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 4(1Q31.2) MUTATED 19 9 1
AMP PEAK 4(1Q31.2) WILD-TYPE 37 347 88

Figure S3.  Get High-res Image Gene #4: 'amp_1q31.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q31.2' versus 'METHLYATION_CNMF'

P value = 0.0269 (Fisher's exact test), Q value = 0.071

Table S4.  Gene #4: 'amp_1q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 4(1Q31.2) MUTATED 20 3 6
AMP PEAK 4(1Q31.2) WILD-TYPE 257 151 64

Figure S4.  Get High-res Image Gene #4: 'amp_1q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q31.2' versus 'RPPA_CNMF'

P value = 0.00158 (Fisher's exact test), Q value = 0.007

Table S5.  Gene #4: 'amp_1q31.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 79 81
AMP PEAK 4(1Q31.2) MUTATED 0 10 2
AMP PEAK 4(1Q31.2) WILD-TYPE 61 69 79

Figure S5.  Get High-res Image Gene #4: 'amp_1q31.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_1q31.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0219 (Fisher's exact test), Q value = 0.059

Table S6.  Gene #4: 'amp_1q31.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 28 33 29 49 27 9
AMP PEAK 4(1Q31.2) MUTATED 0 1 3 0 3 5 0
AMP PEAK 4(1Q31.2) WILD-TYPE 46 27 30 29 46 22 9

Figure S6.  Get High-res Image Gene #4: 'amp_1q31.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_1q31.2' versus 'MRNASEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0023

Table S7.  Gene #4: 'amp_1q31.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
AMP PEAK 4(1Q31.2) MUTATED 19 3 5 2
AMP PEAK 4(1Q31.2) WILD-TYPE 149 152 54 115

Figure S7.  Get High-res Image Gene #4: 'amp_1q31.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S8.  Gene #4: 'amp_1q31.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 4(1Q31.2) MUTATED 18 3 1 2 5
AMP PEAK 4(1Q31.2) WILD-TYPE 87 131 85 94 73

Figure S8.  Get High-res Image Gene #4: 'amp_1q31.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1q31.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.042

Table S9.  Gene #4: 'amp_1q31.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 164 146
AMP PEAK 4(1Q31.2) MUTATED 15 7 3
AMP PEAK 4(1Q31.2) WILD-TYPE 145 157 143

Figure S9.  Get High-res Image Gene #4: 'amp_1q31.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_1q31.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0307 (Fisher's exact test), Q value = 0.078

Table S10.  Gene #4: 'amp_1q31.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
AMP PEAK 4(1Q31.2) MUTATED 15 3 7
AMP PEAK 4(1Q31.2) WILD-TYPE 150 123 172

Figure S10.  Get High-res Image Gene #4: 'amp_1q31.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q43' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S11.  Gene #5: 'amp_1q43' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 5(1Q43) MUTATED 20 8 1
AMP PEAK 5(1Q43) WILD-TYPE 36 348 88

Figure S11.  Get High-res Image Gene #5: 'amp_1q43' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q43' versus 'METHLYATION_CNMF'

P value = 0.0065 (Fisher's exact test), Q value = 0.023

Table S12.  Gene #5: 'amp_1q43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 5(1Q43) MUTATED 21 2 6
AMP PEAK 5(1Q43) WILD-TYPE 256 152 64

Figure S12.  Get High-res Image Gene #5: 'amp_1q43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q43' versus 'RPPA_CNMF'

P value = 0.00141 (Fisher's exact test), Q value = 0.0063

Table S13.  Gene #5: 'amp_1q43' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 79 81
AMP PEAK 5(1Q43) MUTATED 0 10 2
AMP PEAK 5(1Q43) WILD-TYPE 61 69 79

Figure S13.  Get High-res Image Gene #5: 'amp_1q43' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_1q43' versus 'RPPA_CHIERARCHICAL'

P value = 0.0383 (Fisher's exact test), Q value = 0.093

Table S14.  Gene #5: 'amp_1q43' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 28 33 29 49 27 9
AMP PEAK 5(1Q43) MUTATED 0 1 4 0 3 4 0
AMP PEAK 5(1Q43) WILD-TYPE 46 27 29 29 46 23 9

Figure S14.  Get High-res Image Gene #5: 'amp_1q43' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_1q43' versus 'MRNASEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0018

Table S15.  Gene #5: 'amp_1q43' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
AMP PEAK 5(1Q43) MUTATED 19 2 5 3
AMP PEAK 5(1Q43) WILD-TYPE 149 153 54 114

Figure S15.  Get High-res Image Gene #5: 'amp_1q43' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q43' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S16.  Gene #5: 'amp_1q43' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 5(1Q43) MUTATED 19 2 1 3 4
AMP PEAK 5(1Q43) WILD-TYPE 86 132 85 93 74

Figure S16.  Get High-res Image Gene #5: 'amp_1q43' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1q43' versus 'MIRSEQ_CNMF'

P value = 0.0195 (Fisher's exact test), Q value = 0.054

Table S17.  Gene #5: 'amp_1q43' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
AMP PEAK 5(1Q43) MUTATED 18 5 6
AMP PEAK 5(1Q43) WILD-TYPE 164 146 161

Figure S17.  Get High-res Image Gene #5: 'amp_1q43' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q43' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0107 (Fisher's exact test), Q value = 0.034

Table S18.  Gene #5: 'amp_1q43' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 5(1Q43) MUTATED 18 3 8
AMP PEAK 5(1Q43) WILD-TYPE 161 125 185

Figure S18.  Get High-res Image Gene #5: 'amp_1q43' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q43' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00174 (Fisher's exact test), Q value = 0.0075

Table S19.  Gene #5: 'amp_1q43' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 164 146
AMP PEAK 5(1Q43) MUTATED 17 5 3
AMP PEAK 5(1Q43) WILD-TYPE 143 159 143

Figure S19.  Get High-res Image Gene #5: 'amp_1q43' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_1q43' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00259 (Fisher's exact test), Q value = 0.011

Table S20.  Gene #5: 'amp_1q43' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
AMP PEAK 5(1Q43) MUTATED 17 2 6
AMP PEAK 5(1Q43) WILD-TYPE 148 124 173

Figure S20.  Get High-res Image Gene #5: 'amp_1q43' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_2p16.1' versus 'CN_CNMF'

P value = 0.0492 (Fisher's exact test), Q value = 0.11

Table S21.  Gene #6: 'amp_2p16.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 6(2P16.1) MUTATED 2 1 0
AMP PEAK 6(2P16.1) WILD-TYPE 54 355 89

Figure S21.  Get High-res Image Gene #6: 'amp_2p16.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3p22.3' versus 'CN_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.034

Table S22.  Gene #8: 'amp_3p22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 10(3P22.3) MUTATED 3 1 0
AMP PEAK 10(3P22.3) WILD-TYPE 53 355 89

Figure S22.  Get High-res Image Gene #8: 'amp_3p22.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3p14.1' versus 'CN_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.046

Table S23.  Gene #9: 'amp_3p14.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 11(3P14.1) MUTATED 3 2 0
AMP PEAK 11(3P14.1) WILD-TYPE 53 354 89

Figure S23.  Get High-res Image Gene #9: 'amp_3p14.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4p16.1' versus 'CN_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0031

Table S24.  Gene #10: 'amp_4p16.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 12(4P16.1) MUTATED 5 2 0
AMP PEAK 12(4P16.1) WILD-TYPE 51 354 89

Figure S24.  Get High-res Image Gene #10: 'amp_4p16.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4p16.1' versus 'METHLYATION_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.036

Table S25.  Gene #10: 'amp_4p16.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 12(4P16.1) MUTATED 1 6 0
AMP PEAK 12(4P16.1) WILD-TYPE 276 148 70

Figure S25.  Get High-res Image Gene #10: 'amp_4p16.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_4p16.1' versus 'MRNASEQ_CNMF'

P value = 0.0282 (Fisher's exact test), Q value = 0.073

Table S26.  Gene #10: 'amp_4p16.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
AMP PEAK 12(4P16.1) MUTATED 1 6 0 0
AMP PEAK 12(4P16.1) WILD-TYPE 167 149 59 117

Figure S26.  Get High-res Image Gene #10: 'amp_4p16.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_4p16.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.033

Table S27.  Gene #10: 'amp_4p16.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 12(4P16.1) MUTATED 0 6 0 0 1
AMP PEAK 12(4P16.1) WILD-TYPE 105 128 86 96 77

Figure S27.  Get High-res Image Gene #10: 'amp_4p16.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_4p16.1' versus 'MIRSEQ_CNMF'

P value = 0.0339 (Fisher's exact test), Q value = 0.085

Table S28.  Gene #10: 'amp_4p16.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
AMP PEAK 12(4P16.1) MUTATED 2 5 0
AMP PEAK 12(4P16.1) WILD-TYPE 180 146 167

Figure S28.  Get High-res Image Gene #10: 'amp_4p16.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_4p16.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00623 (Fisher's exact test), Q value = 0.022

Table S29.  Gene #10: 'amp_4p16.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 12(4P16.1) MUTATED 2 5 0
AMP PEAK 12(4P16.1) WILD-TYPE 177 123 193

Figure S29.  Get High-res Image Gene #10: 'amp_4p16.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_4p16.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0472 (Fisher's exact test), Q value = 0.11

Table S30.  Gene #10: 'amp_4p16.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
AMP PEAK 12(4P16.1) MUTATED 3 4 0
AMP PEAK 12(4P16.1) WILD-TYPE 162 122 179

Figure S30.  Get High-res Image Gene #10: 'amp_4p16.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q22.1' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0021

Table S31.  Gene #11: 'amp_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 13(4Q22.1) MUTATED 5 1 1
AMP PEAK 13(4Q22.1) WILD-TYPE 51 355 88

Figure S31.  Get High-res Image Gene #11: 'amp_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4q22.1' versus 'METHLYATION_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.036

Table S32.  Gene #11: 'amp_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 13(4Q22.1) MUTATED 1 6 0
AMP PEAK 13(4Q22.1) WILD-TYPE 276 148 70

Figure S32.  Get High-res Image Gene #11: 'amp_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_4q22.1' versus 'MRNASEQ_CNMF'

P value = 0.0281 (Fisher's exact test), Q value = 0.072

Table S33.  Gene #11: 'amp_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
AMP PEAK 13(4Q22.1) MUTATED 1 6 0 0
AMP PEAK 13(4Q22.1) WILD-TYPE 167 149 59 117

Figure S33.  Get High-res Image Gene #11: 'amp_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_4q28.2' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00088

Table S34.  Gene #12: 'amp_4q28.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 14(4Q28.2) MUTATED 5 1 0
AMP PEAK 14(4Q28.2) WILD-TYPE 51 355 89

Figure S34.  Get High-res Image Gene #12: 'amp_4q28.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4q28.2' versus 'METHLYATION_CNMF'

P value = 0.0285 (Fisher's exact test), Q value = 0.073

Table S35.  Gene #12: 'amp_4q28.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 14(4Q28.2) MUTATED 1 5 0
AMP PEAK 14(4Q28.2) WILD-TYPE 276 149 70

Figure S35.  Get High-res Image Gene #12: 'amp_4q28.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_4q28.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0264 (Fisher's exact test), Q value = 0.07

Table S36.  Gene #12: 'amp_4q28.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 14(4Q28.2) MUTATED 0 5 0 0 1
AMP PEAK 14(4Q28.2) WILD-TYPE 105 129 86 96 77

Figure S36.  Get High-res Image Gene #12: 'amp_4q28.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_4q28.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.053

Table S37.  Gene #12: 'amp_4q28.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 14(4Q28.2) MUTATED 2 4 0
AMP PEAK 14(4Q28.2) WILD-TYPE 177 124 193

Figure S37.  Get High-res Image Gene #12: 'amp_4q28.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_4q31.21' versus 'CN_CNMF'

P value = 0.00272 (Fisher's exact test), Q value = 0.011

Table S38.  Gene #13: 'amp_4q31.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 15(4Q31.21) MUTATED 5 5 0
AMP PEAK 15(4Q31.21) WILD-TYPE 51 351 89

Figure S38.  Get High-res Image Gene #13: 'amp_4q31.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4q32.3' versus 'CN_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0032

Table S39.  Gene #14: 'amp_4q32.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 16(4Q32.3) MUTATED 5 2 0
AMP PEAK 16(4Q32.3) WILD-TYPE 51 354 89

Figure S39.  Get High-res Image Gene #14: 'amp_4q32.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4q32.3' versus 'METHLYATION_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.037

Table S40.  Gene #14: 'amp_4q32.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 16(4Q32.3) MUTATED 1 6 0
AMP PEAK 16(4Q32.3) WILD-TYPE 276 148 70

Figure S40.  Get High-res Image Gene #14: 'amp_4q32.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_4q32.3' versus 'MRNASEQ_CNMF'

P value = 0.0284 (Fisher's exact test), Q value = 0.073

Table S41.  Gene #14: 'amp_4q32.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
AMP PEAK 16(4Q32.3) MUTATED 1 6 0 0
AMP PEAK 16(4Q32.3) WILD-TYPE 167 149 59 117

Figure S41.  Get High-res Image Gene #14: 'amp_4q32.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_4q32.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0174 (Fisher's exact test), Q value = 0.05

Table S42.  Gene #14: 'amp_4q32.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 16(4Q32.3) MUTATED 1 6 0 0 0
AMP PEAK 16(4Q32.3) WILD-TYPE 104 128 86 96 78

Figure S42.  Get High-res Image Gene #14: 'amp_4q32.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_4q32.3' versus 'MIRSEQ_CNMF'

P value = 0.0346 (Fisher's exact test), Q value = 0.086

Table S43.  Gene #14: 'amp_4q32.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
AMP PEAK 16(4Q32.3) MUTATED 2 5 0
AMP PEAK 16(4Q32.3) WILD-TYPE 180 146 167

Figure S43.  Get High-res Image Gene #14: 'amp_4q32.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_4q32.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00636 (Fisher's exact test), Q value = 0.022

Table S44.  Gene #14: 'amp_4q32.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 16(4Q32.3) MUTATED 2 5 0
AMP PEAK 16(4Q32.3) WILD-TYPE 177 123 193

Figure S44.  Get High-res Image Gene #14: 'amp_4q32.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p14.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S45.  Gene #15: 'amp_5p14.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 17(5P14.3) MUTATED 23 0 0
AMP PEAK 17(5P14.3) WILD-TYPE 33 356 89

Figure S45.  Get High-res Image Gene #15: 'amp_5p14.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p14.3' versus 'METHLYATION_CNMF'

P value = 0.00911 (Fisher's exact test), Q value = 0.03

Table S46.  Gene #15: 'amp_5p14.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 17(5P14.3) MUTATED 7 14 2
AMP PEAK 17(5P14.3) WILD-TYPE 270 140 68

Figure S46.  Get High-res Image Gene #15: 'amp_5p14.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p14.3' versus 'MRNASEQ_CNMF'

P value = 0.00904 (Fisher's exact test), Q value = 0.03

Table S47.  Gene #15: 'amp_5p14.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
AMP PEAK 17(5P14.3) MUTATED 7 14 1 1
AMP PEAK 17(5P14.3) WILD-TYPE 161 141 58 116

Figure S47.  Get High-res Image Gene #15: 'amp_5p14.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p14.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00034

Table S48.  Gene #15: 'amp_5p14.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 17(5P14.3) MUTATED 8 14 0 1 0
AMP PEAK 17(5P14.3) WILD-TYPE 97 120 86 95 78

Figure S48.  Get High-res Image Gene #15: 'amp_5p14.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5p14.3' versus 'MIRSEQ_CNMF'

P value = 0.0011 (Fisher's exact test), Q value = 0.0051

Table S49.  Gene #15: 'amp_5p14.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
AMP PEAK 17(5P14.3) MUTATED 9 13 1
AMP PEAK 17(5P14.3) WILD-TYPE 173 138 166

Figure S49.  Get High-res Image Gene #15: 'amp_5p14.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5p14.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00088

Table S50.  Gene #15: 'amp_5p14.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 17(5P14.3) MUTATED 9 13 1
AMP PEAK 17(5P14.3) WILD-TYPE 170 115 192

Figure S50.  Get High-res Image Gene #15: 'amp_5p14.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p14.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00222 (Fisher's exact test), Q value = 0.0091

Table S51.  Gene #15: 'amp_5p14.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
AMP PEAK 17(5P14.3) MUTATED 10 9 1
AMP PEAK 17(5P14.3) WILD-TYPE 155 117 178

Figure S51.  Get High-res Image Gene #15: 'amp_5p14.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S52.  Gene #16: 'amp_5q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 18(5Q21.1) MUTATED 19 3 1
AMP PEAK 18(5Q21.1) WILD-TYPE 37 353 88

Figure S52.  Get High-res Image Gene #16: 'amp_5q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q21.1' versus 'METHLYATION_CNMF'

P value = 0.00167 (Fisher's exact test), Q value = 0.0072

Table S53.  Gene #16: 'amp_5q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 18(5Q21.1) MUTATED 5 14 4
AMP PEAK 18(5Q21.1) WILD-TYPE 272 140 66

Figure S53.  Get High-res Image Gene #16: 'amp_5q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5q21.1' versus 'MRNASEQ_CNMF'

P value = 0.00633 (Fisher's exact test), Q value = 0.022

Table S54.  Gene #16: 'amp_5q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
AMP PEAK 18(5Q21.1) MUTATED 3 15 2 3
AMP PEAK 18(5Q21.1) WILD-TYPE 165 140 57 114

Figure S54.  Get High-res Image Gene #16: 'amp_5q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0118 (Fisher's exact test), Q value = 0.036

Table S55.  Gene #16: 'amp_5q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 18(5Q21.1) MUTATED 2 14 3 3 1
AMP PEAK 18(5Q21.1) WILD-TYPE 103 120 83 93 77

Figure S55.  Get High-res Image Gene #16: 'amp_5q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5q21.1' versus 'MIRSEQ_CNMF'

P value = 0.00861 (Fisher's exact test), Q value = 0.029

Table S56.  Gene #16: 'amp_5q21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
AMP PEAK 18(5Q21.1) MUTATED 5 14 4
AMP PEAK 18(5Q21.1) WILD-TYPE 177 137 163

Figure S56.  Get High-res Image Gene #16: 'amp_5q21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5q21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00586 (Fisher's exact test), Q value = 0.021

Table S57.  Gene #16: 'amp_5q21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 18(5Q21.1) MUTATED 5 13 5
AMP PEAK 18(5Q21.1) WILD-TYPE 174 115 188

Figure S57.  Get High-res Image Gene #16: 'amp_5q21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S58.  Gene #17: 'amp_5q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 19(5Q21.1) MUTATED 18 2 0
AMP PEAK 19(5Q21.1) WILD-TYPE 38 354 89

Figure S58.  Get High-res Image Gene #17: 'amp_5q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q21.1' versus 'METHLYATION_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0051

Table S59.  Gene #17: 'amp_5q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 19(5Q21.1) MUTATED 5 14 1
AMP PEAK 19(5Q21.1) WILD-TYPE 272 140 69

Figure S59.  Get High-res Image Gene #17: 'amp_5q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5q21.1' versus 'MRNASEQ_CNMF'

P value = 0.00305 (Fisher's exact test), Q value = 0.012

Table S60.  Gene #17: 'amp_5q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
AMP PEAK 19(5Q21.1) MUTATED 3 14 0 3
AMP PEAK 19(5Q21.1) WILD-TYPE 165 141 59 114

Figure S60.  Get High-res Image Gene #17: 'amp_5q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.003

Table S61.  Gene #17: 'amp_5q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 19(5Q21.1) MUTATED 2 14 0 3 1
AMP PEAK 19(5Q21.1) WILD-TYPE 103 120 86 93 77

Figure S61.  Get High-res Image Gene #17: 'amp_5q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5q21.1' versus 'MIRSEQ_CNMF'

P value = 0.00082 (Fisher's exact test), Q value = 0.004

Table S62.  Gene #17: 'amp_5q21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
AMP PEAK 19(5Q21.1) MUTATED 3 14 3
AMP PEAK 19(5Q21.1) WILD-TYPE 179 137 164

Figure S62.  Get High-res Image Gene #17: 'amp_5q21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5q21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.003

Table S63.  Gene #17: 'amp_5q21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 19(5Q21.1) MUTATED 3 13 4
AMP PEAK 19(5Q21.1) WILD-TYPE 176 115 189

Figure S63.  Get High-res Image Gene #17: 'amp_5q21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5q33.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S64.  Gene #18: 'amp_5q33.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 20(5Q33.1) MUTATED 18 3 0
AMP PEAK 20(5Q33.1) WILD-TYPE 38 353 89

Figure S64.  Get High-res Image Gene #18: 'amp_5q33.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q33.1' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00048

Table S65.  Gene #18: 'amp_5q33.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 20(5Q33.1) MUTATED 4 16 1
AMP PEAK 20(5Q33.1) WILD-TYPE 273 138 69

Figure S65.  Get High-res Image Gene #18: 'amp_5q33.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5q33.1' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0013

Table S66.  Gene #18: 'amp_5q33.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
AMP PEAK 20(5Q33.1) MUTATED 2 16 0 3
AMP PEAK 20(5Q33.1) WILD-TYPE 166 139 59 114

Figure S66.  Get High-res Image Gene #18: 'amp_5q33.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5q33.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00041

Table S67.  Gene #18: 'amp_5q33.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 20(5Q33.1) MUTATED 2 16 1 2 0
AMP PEAK 20(5Q33.1) WILD-TYPE 103 118 85 94 78

Figure S67.  Get High-res Image Gene #18: 'amp_5q33.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5q33.1' versus 'MIRSEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0018

Table S68.  Gene #18: 'amp_5q33.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
AMP PEAK 20(5Q33.1) MUTATED 4 15 2
AMP PEAK 20(5Q33.1) WILD-TYPE 178 136 165

Figure S68.  Get High-res Image Gene #18: 'amp_5q33.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5q33.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S69.  Gene #18: 'amp_5q33.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 20(5Q33.1) MUTATED 4 15 2
AMP PEAK 20(5Q33.1) WILD-TYPE 175 113 191

Figure S69.  Get High-res Image Gene #18: 'amp_5q33.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5q33.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00252 (Fisher's exact test), Q value = 0.01

Table S70.  Gene #18: 'amp_5q33.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
AMP PEAK 20(5Q33.1) MUTATED 5 11 2
AMP PEAK 20(5Q33.1) WILD-TYPE 160 115 177

Figure S70.  Get High-res Image Gene #18: 'amp_5q33.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5q35.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S71.  Gene #19: 'amp_5q35.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 21(5Q35.2) MUTATED 18 2 0
AMP PEAK 21(5Q35.2) WILD-TYPE 38 354 89

Figure S71.  Get High-res Image Gene #19: 'amp_5q35.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q35.2' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00069

Table S72.  Gene #19: 'amp_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 21(5Q35.2) MUTATED 4 15 1
AMP PEAK 21(5Q35.2) WILD-TYPE 273 139 69

Figure S72.  Get High-res Image Gene #19: 'amp_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5q35.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0339 (Fisher's exact test), Q value = 0.085

Table S73.  Gene #19: 'amp_5q35.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 28 33 29 49 27 9
AMP PEAK 21(5Q35.2) MUTATED 3 1 0 3 0 4 0
AMP PEAK 21(5Q35.2) WILD-TYPE 43 27 33 26 49 23 9

Figure S73.  Get High-res Image Gene #19: 'amp_5q35.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_5q35.2' versus 'MRNASEQ_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0031

Table S74.  Gene #19: 'amp_5q35.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
AMP PEAK 21(5Q35.2) MUTATED 3 15 0 2
AMP PEAK 21(5Q35.2) WILD-TYPE 165 140 59 115

Figure S74.  Get High-res Image Gene #19: 'amp_5q35.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5q35.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00041

Table S75.  Gene #19: 'amp_5q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 21(5Q35.2) MUTATED 3 15 0 2 0
AMP PEAK 21(5Q35.2) WILD-TYPE 102 119 86 94 78

Figure S75.  Get High-res Image Gene #19: 'amp_5q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5q35.2' versus 'MIRSEQ_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0038

Table S76.  Gene #19: 'amp_5q35.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
AMP PEAK 21(5Q35.2) MUTATED 4 14 2
AMP PEAK 21(5Q35.2) WILD-TYPE 178 137 165

Figure S76.  Get High-res Image Gene #19: 'amp_5q35.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5q35.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00063

Table S77.  Gene #19: 'amp_5q35.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 21(5Q35.2) MUTATED 4 14 2
AMP PEAK 21(5Q35.2) WILD-TYPE 175 114 191

Figure S77.  Get High-res Image Gene #19: 'amp_5q35.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5q35.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00969 (Fisher's exact test), Q value = 0.032

Table S78.  Gene #19: 'amp_5q35.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
AMP PEAK 21(5Q35.2) MUTATED 5 10 2
AMP PEAK 21(5Q35.2) WILD-TYPE 160 116 177

Figure S78.  Get High-res Image Gene #19: 'amp_5q35.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6p22.3' versus 'METHLYATION_CNMF'

P value = 0.0485 (Fisher's exact test), Q value = 0.11

Table S79.  Gene #20: 'amp_6p22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 22(6P22.3) MUTATED 0 3 0
AMP PEAK 22(6P22.3) WILD-TYPE 277 151 70

Figure S79.  Get High-res Image Gene #20: 'amp_6p22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p22.2' versus 'METHLYATION_CNMF'

P value = 0.046 (Fisher's exact test), Q value = 0.11

Table S80.  Gene #21: 'amp_6p22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 23(6P22.2) MUTATED 0 3 1
AMP PEAK 23(6P22.2) WILD-TYPE 277 151 69

Figure S80.  Get High-res Image Gene #21: 'amp_6p22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q27' versus 'RPPA_CHIERARCHICAL'

P value = 0.0125 (Fisher's exact test), Q value = 0.037

Table S81.  Gene #26: 'amp_6q27' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 28 33 29 49 27 9
AMP PEAK 28(6Q27) MUTATED 0 0 0 1 0 3 0
AMP PEAK 28(6Q27) WILD-TYPE 46 28 33 28 49 24 9

Figure S81.  Get High-res Image Gene #26: 'amp_6q27' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_7q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S82.  Gene #27: 'amp_7q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 29(7Q11.21) MUTATED 18 2 0
AMP PEAK 29(7Q11.21) WILD-TYPE 38 354 89

Figure S82.  Get High-res Image Gene #27: 'amp_7q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q11.21' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00063

Table S83.  Gene #27: 'amp_7q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 29(7Q11.21) MUTATED 3 15 2
AMP PEAK 29(7Q11.21) WILD-TYPE 274 139 68

Figure S83.  Get High-res Image Gene #27: 'amp_7q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q11.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.048

Table S84.  Gene #27: 'amp_7q11.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 28 33 29 49 27 9
AMP PEAK 29(7Q11.21) MUTATED 3 1 0 2 0 5 0
AMP PEAK 29(7Q11.21) WILD-TYPE 43 27 33 27 49 22 9

Figure S84.  Get High-res Image Gene #27: 'amp_7q11.21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_7q11.21' versus 'MRNASEQ_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.0033

Table S85.  Gene #27: 'amp_7q11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
AMP PEAK 29(7Q11.21) MUTATED 3 15 1 1
AMP PEAK 29(7Q11.21) WILD-TYPE 165 140 58 116

Figure S85.  Get High-res Image Gene #27: 'amp_7q11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.0013

Table S86.  Gene #27: 'amp_7q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 29(7Q11.21) MUTATED 2 15 1 1 1
AMP PEAK 29(7Q11.21) WILD-TYPE 103 119 85 95 77

Figure S86.  Get High-res Image Gene #27: 'amp_7q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q11.21' versus 'MIRSEQ_CNMF'

P value = 0.00282 (Fisher's exact test), Q value = 0.011

Table S87.  Gene #27: 'amp_7q11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
AMP PEAK 29(7Q11.21) MUTATED 5 13 2
AMP PEAK 29(7Q11.21) WILD-TYPE 177 138 165

Figure S87.  Get High-res Image Gene #27: 'amp_7q11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.0021

Table S88.  Gene #27: 'amp_7q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 29(7Q11.21) MUTATED 5 13 2
AMP PEAK 29(7Q11.21) WILD-TYPE 174 115 191

Figure S88.  Get High-res Image Gene #27: 'amp_7q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0226 (Fisher's exact test), Q value = 0.061

Table S89.  Gene #27: 'amp_7q11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
AMP PEAK 29(7Q11.21) MUTATED 6 9 2
AMP PEAK 29(7Q11.21) WILD-TYPE 159 117 177

Figure S89.  Get High-res Image Gene #27: 'amp_7q11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q21.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S90.  Gene #28: 'amp_7q21.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 30(7Q21.11) MUTATED 20 1 0
AMP PEAK 30(7Q21.11) WILD-TYPE 36 355 89

Figure S90.  Get High-res Image Gene #28: 'amp_7q21.11' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q21.11' versus 'METHLYATION_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0018

Table S91.  Gene #28: 'amp_7q21.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 30(7Q21.11) MUTATED 4 15 2
AMP PEAK 30(7Q21.11) WILD-TYPE 273 139 68

Figure S91.  Get High-res Image Gene #28: 'amp_7q21.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q21.11' versus 'MRNASEQ_CNMF'

P value = 0.00211 (Fisher's exact test), Q value = 0.0089

Table S92.  Gene #28: 'amp_7q21.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
AMP PEAK 30(7Q21.11) MUTATED 3 15 1 2
AMP PEAK 30(7Q21.11) WILD-TYPE 165 140 58 115

Figure S92.  Get High-res Image Gene #28: 'amp_7q21.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7q21.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00067 (Fisher's exact test), Q value = 0.0034

Table S93.  Gene #28: 'amp_7q21.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 30(7Q21.11) MUTATED 2 15 1 2 1
AMP PEAK 30(7Q21.11) WILD-TYPE 103 119 85 94 77

Figure S93.  Get High-res Image Gene #28: 'amp_7q21.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q21.11' versus 'MIRSEQ_CNMF'

P value = 0.00139 (Fisher's exact test), Q value = 0.0062

Table S94.  Gene #28: 'amp_7q21.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
AMP PEAK 30(7Q21.11) MUTATED 5 14 2
AMP PEAK 30(7Q21.11) WILD-TYPE 177 137 165

Figure S94.  Get High-res Image Gene #28: 'amp_7q21.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7q21.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.0011

Table S95.  Gene #28: 'amp_7q21.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 30(7Q21.11) MUTATED 5 14 2
AMP PEAK 30(7Q21.11) WILD-TYPE 174 114 191

Figure S95.  Get High-res Image Gene #28: 'amp_7q21.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q21.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0027 (Fisher's exact test), Q value = 0.011

Table S96.  Gene #28: 'amp_7q21.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
AMP PEAK 30(7Q21.11) MUTATED 5 11 2
AMP PEAK 30(7Q21.11) WILD-TYPE 160 115 177

Figure S96.  Get High-res Image Gene #28: 'amp_7q21.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S97.  Gene #29: 'amp_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 31(7Q31.1) MUTATED 19 2 1
AMP PEAK 31(7Q31.1) WILD-TYPE 37 354 88

Figure S97.  Get High-res Image Gene #29: 'amp_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q31.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S98.  Gene #29: 'amp_7q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 31(7Q31.1) MUTATED 2 18 2
AMP PEAK 31(7Q31.1) WILD-TYPE 275 136 68

Figure S98.  Get High-res Image Gene #29: 'amp_7q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q31.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0095 (Fisher's exact test), Q value = 0.031

Table S99.  Gene #29: 'amp_7q31.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 28 33 29 49 27 9
AMP PEAK 31(7Q31.1) MUTATED 5 1 0 2 0 5 0
AMP PEAK 31(7Q31.1) WILD-TYPE 41 27 33 27 49 22 9

Figure S99.  Get High-res Image Gene #29: 'amp_7q31.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_7q31.1' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00088

Table S100.  Gene #29: 'amp_7q31.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
AMP PEAK 31(7Q31.1) MUTATED 3 17 1 1
AMP PEAK 31(7Q31.1) WILD-TYPE 165 138 58 116

Figure S100.  Get High-res Image Gene #29: 'amp_7q31.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00041

Table S101.  Gene #29: 'amp_7q31.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 31(7Q31.1) MUTATED 2 17 1 1 1
AMP PEAK 31(7Q31.1) WILD-TYPE 103 117 85 95 77

Figure S101.  Get High-res Image Gene #29: 'amp_7q31.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S102.  Gene #29: 'amp_7q31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
AMP PEAK 31(7Q31.1) MUTATED 5 16 1
AMP PEAK 31(7Q31.1) WILD-TYPE 177 135 166

Figure S102.  Get High-res Image Gene #29: 'amp_7q31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S103.  Gene #29: 'amp_7q31.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 31(7Q31.1) MUTATED 5 16 1
AMP PEAK 31(7Q31.1) WILD-TYPE 174 112 192

Figure S103.  Get High-res Image Gene #29: 'amp_7q31.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0019

Table S104.  Gene #29: 'amp_7q31.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
AMP PEAK 31(7Q31.1) MUTATED 6 12 1
AMP PEAK 31(7Q31.1) WILD-TYPE 159 114 178

Figure S104.  Get High-res Image Gene #29: 'amp_7q31.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S105.  Gene #30: 'amp_7q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 32(7Q34) MUTATED 19 2 1
AMP PEAK 32(7Q34) WILD-TYPE 37 354 88

Figure S105.  Get High-res Image Gene #30: 'amp_7q34' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q34' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00041

Table S106.  Gene #30: 'amp_7q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 32(7Q34) MUTATED 3 16 3
AMP PEAK 32(7Q34) WILD-TYPE 274 138 67

Figure S106.  Get High-res Image Gene #30: 'amp_7q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q34' versus 'RPPA_CHIERARCHICAL'

P value = 0.0042 (Fisher's exact test), Q value = 0.016

Table S107.  Gene #30: 'amp_7q34' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 28 33 29 49 27 9
AMP PEAK 32(7Q34) MUTATED 4 1 0 2 0 6 0
AMP PEAK 32(7Q34) WILD-TYPE 42 27 33 27 49 21 9

Figure S107.  Get High-res Image Gene #30: 'amp_7q34' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_7q34' versus 'MRNASEQ_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0027

Table S108.  Gene #30: 'amp_7q34' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
AMP PEAK 32(7Q34) MUTATED 3 16 2 1
AMP PEAK 32(7Q34) WILD-TYPE 165 139 57 116

Figure S108.  Get High-res Image Gene #30: 'amp_7q34' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.0019

Table S109.  Gene #30: 'amp_7q34' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 32(7Q34) MUTATED 2 16 2 1 1
AMP PEAK 32(7Q34) WILD-TYPE 103 118 84 95 77

Figure S109.  Get High-res Image Gene #30: 'amp_7q34' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q34' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S110.  Gene #30: 'amp_7q34' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
AMP PEAK 32(7Q34) MUTATED 4 17 1
AMP PEAK 32(7Q34) WILD-TYPE 178 134 166

Figure S110.  Get High-res Image Gene #30: 'amp_7q34' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S111.  Gene #30: 'amp_7q34' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 32(7Q34) MUTATED 4 17 1
AMP PEAK 32(7Q34) WILD-TYPE 175 111 192

Figure S111.  Get High-res Image Gene #30: 'amp_7q34' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q34' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.033

Table S112.  Gene #30: 'amp_7q34' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
AMP PEAK 32(7Q34) MUTATED 5 11 3
AMP PEAK 32(7Q34) WILD-TYPE 160 115 176

Figure S112.  Get High-res Image Gene #30: 'amp_7q34' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9q22.31' versus 'CN_CNMF'

P value = 0.024 (Fisher's exact test), Q value = 0.064

Table S113.  Gene #31: 'amp_9q22.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 33(9Q22.31) MUTATED 3 2 1
AMP PEAK 33(9Q22.31) WILD-TYPE 53 354 88

Figure S113.  Get High-res Image Gene #31: 'amp_9q22.31' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9q31.1' versus 'CN_CNMF'

P value = 0.0242 (Fisher's exact test), Q value = 0.065

Table S114.  Gene #32: 'amp_9q31.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 34(9Q31.1) MUTATED 3 2 1
AMP PEAK 34(9Q31.1) WILD-TYPE 53 354 88

Figure S114.  Get High-res Image Gene #32: 'amp_9q31.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10q24.2' versus 'METHLYATION_CNMF'

P value = 0.0482 (Fisher's exact test), Q value = 0.11

Table S115.  Gene #34: 'amp_10q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 36(10Q24.2) MUTATED 0 3 0
AMP PEAK 36(10Q24.2) WILD-TYPE 277 151 70

Figure S115.  Get High-res Image Gene #34: 'amp_10q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_10q24.2' versus 'MIRSEQ_CNMF'

P value = 0.0277 (Fisher's exact test), Q value = 0.072

Table S116.  Gene #34: 'amp_10q24.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
AMP PEAK 36(10Q24.2) MUTATED 0 3 0
AMP PEAK 36(10Q24.2) WILD-TYPE 182 148 167

Figure S116.  Get High-res Image Gene #34: 'amp_10q24.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_10q24.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0165 (Fisher's exact test), Q value = 0.048

Table S117.  Gene #34: 'amp_10q24.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 36(10Q24.2) MUTATED 0 3 0
AMP PEAK 36(10Q24.2) WILD-TYPE 179 125 193

Figure S117.  Get High-res Image Gene #34: 'amp_10q24.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_10q25.1' versus 'CN_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.033

Table S118.  Gene #35: 'amp_10q25.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 37(10Q25.1) MUTATED 3 1 0
AMP PEAK 37(10Q25.1) WILD-TYPE 53 355 89

Figure S118.  Get High-res Image Gene #35: 'amp_10q25.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11p13' versus 'CN_CNMF'

P value = 0.00286 (Fisher's exact test), Q value = 0.011

Table S119.  Gene #36: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 38(11P13) MUTATED 4 2 2
AMP PEAK 38(11P13) WILD-TYPE 52 354 87

Figure S119.  Get High-res Image Gene #36: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p11.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S120.  Gene #37: 'amp_12p11.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 39(12P11.1) MUTATED 15 1 0
AMP PEAK 39(12P11.1) WILD-TYPE 41 355 89

Figure S120.  Get High-res Image Gene #37: 'amp_12p11.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p11.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S121.  Gene #37: 'amp_12p11.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 39(12P11.1) MUTATED 2 14 0
AMP PEAK 39(12P11.1) WILD-TYPE 275 140 70

Figure S121.  Get High-res Image Gene #37: 'amp_12p11.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12p11.1' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00069

Table S122.  Gene #37: 'amp_12p11.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
AMP PEAK 39(12P11.1) MUTATED 1 14 0 1
AMP PEAK 39(12P11.1) WILD-TYPE 167 141 59 116

Figure S122.  Get High-res Image Gene #37: 'amp_12p11.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12p11.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S123.  Gene #37: 'amp_12p11.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 39(12P11.1) MUTATED 1 14 0 1 0
AMP PEAK 39(12P11.1) WILD-TYPE 104 120 86 95 78

Figure S123.  Get High-res Image Gene #37: 'amp_12p11.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_12p11.1' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00048

Table S124.  Gene #37: 'amp_12p11.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
AMP PEAK 39(12P11.1) MUTATED 2 13 1
AMP PEAK 39(12P11.1) WILD-TYPE 180 138 166

Figure S124.  Get High-res Image Gene #37: 'amp_12p11.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_12p11.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S125.  Gene #37: 'amp_12p11.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 39(12P11.1) MUTATED 2 13 1
AMP PEAK 39(12P11.1) WILD-TYPE 177 115 192

Figure S125.  Get High-res Image Gene #37: 'amp_12p11.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_12p11.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00234 (Fisher's exact test), Q value = 0.0096

Table S126.  Gene #37: 'amp_12p11.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
AMP PEAK 39(12P11.1) MUTATED 3 9 1
AMP PEAK 39(12P11.1) WILD-TYPE 162 117 178

Figure S126.  Get High-res Image Gene #37: 'amp_12p11.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q21.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S127.  Gene #38: 'amp_12q21.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 40(12Q21.31) MUTATED 14 1 2
AMP PEAK 40(12Q21.31) WILD-TYPE 42 355 87

Figure S127.  Get High-res Image Gene #38: 'amp_12q21.31' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q21.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S128.  Gene #38: 'amp_12q21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 40(12Q21.31) MUTATED 2 15 0
AMP PEAK 40(12Q21.31) WILD-TYPE 275 139 70

Figure S128.  Get High-res Image Gene #38: 'amp_12q21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12q21.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0391 (Fisher's exact test), Q value = 0.095

Table S129.  Gene #38: 'amp_12q21.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 28 33 29 49 27 9
AMP PEAK 40(12Q21.31) MUTATED 3 1 0 4 0 3 0
AMP PEAK 40(12Q21.31) WILD-TYPE 43 27 33 25 49 24 9

Figure S129.  Get High-res Image Gene #38: 'amp_12q21.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_12q21.31' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S130.  Gene #38: 'amp_12q21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
AMP PEAK 40(12Q21.31) MUTATED 0 15 0 2
AMP PEAK 40(12Q21.31) WILD-TYPE 168 140 59 115

Figure S130.  Get High-res Image Gene #38: 'amp_12q21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12q21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S131.  Gene #38: 'amp_12q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 40(12Q21.31) MUTATED 0 15 1 1 0
AMP PEAK 40(12Q21.31) WILD-TYPE 105 119 85 95 78

Figure S131.  Get High-res Image Gene #38: 'amp_12q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_12q21.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S132.  Gene #38: 'amp_12q21.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
AMP PEAK 40(12Q21.31) MUTATED 1 14 2
AMP PEAK 40(12Q21.31) WILD-TYPE 181 137 165

Figure S132.  Get High-res Image Gene #38: 'amp_12q21.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_12q21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S133.  Gene #38: 'amp_12q21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 40(12Q21.31) MUTATED 1 14 2
AMP PEAK 40(12Q21.31) WILD-TYPE 178 114 191

Figure S133.  Get High-res Image Gene #38: 'amp_12q21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_12q21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00184 (Fisher's exact test), Q value = 0.0079

Table S134.  Gene #38: 'amp_12q21.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
AMP PEAK 40(12Q21.31) MUTATED 2 10 2
AMP PEAK 40(12Q21.31) WILD-TYPE 163 116 177

Figure S134.  Get High-res Image Gene #38: 'amp_12q21.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S135.  Gene #39: 'amp_12q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 41(12Q23.1) MUTATED 14 2 1
AMP PEAK 41(12Q23.1) WILD-TYPE 42 354 88

Figure S135.  Get High-res Image Gene #39: 'amp_12q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q23.1' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00069

Table S136.  Gene #39: 'amp_12q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 41(12Q23.1) MUTATED 3 14 0
AMP PEAK 41(12Q23.1) WILD-TYPE 274 140 70

Figure S136.  Get High-res Image Gene #39: 'amp_12q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12q23.1' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0012

Table S137.  Gene #39: 'amp_12q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
AMP PEAK 41(12Q23.1) MUTATED 1 14 0 2
AMP PEAK 41(12Q23.1) WILD-TYPE 167 141 59 115

Figure S137.  Get High-res Image Gene #39: 'amp_12q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00041

Table S138.  Gene #39: 'amp_12q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 41(12Q23.1) MUTATED 0 14 0 2 1
AMP PEAK 41(12Q23.1) WILD-TYPE 105 120 86 94 77

Figure S138.  Get High-res Image Gene #39: 'amp_12q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_12q23.1' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00088

Table S139.  Gene #39: 'amp_12q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
AMP PEAK 41(12Q23.1) MUTATED 3 13 1
AMP PEAK 41(12Q23.1) WILD-TYPE 179 138 166

Figure S139.  Get High-res Image Gene #39: 'amp_12q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_12q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S140.  Gene #39: 'amp_12q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 41(12Q23.1) MUTATED 2 13 2
AMP PEAK 41(12Q23.1) WILD-TYPE 177 115 191

Figure S140.  Get High-res Image Gene #39: 'amp_12q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_12q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00971 (Fisher's exact test), Q value = 0.032

Table S141.  Gene #39: 'amp_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
AMP PEAK 41(12Q23.1) MUTATED 3 9 2
AMP PEAK 41(12Q23.1) WILD-TYPE 162 117 177

Figure S141.  Get High-res Image Gene #39: 'amp_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q14.2' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00069

Table S142.  Gene #40: 'amp_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 42(13Q14.2) MUTATED 5 1 0
AMP PEAK 42(13Q14.2) WILD-TYPE 51 355 89

Figure S142.  Get High-res Image Gene #40: 'amp_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q34' versus 'CN_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.003

Table S143.  Gene #41: 'amp_13q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 43(13Q34) MUTATED 5 2 0
AMP PEAK 43(13Q34) WILD-TYPE 51 354 89

Figure S143.  Get High-res Image Gene #41: 'amp_13q34' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q34' versus 'METHLYATION_CNMF'

P value = 0.049 (Fisher's exact test), Q value = 0.11

Table S144.  Gene #41: 'amp_13q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 43(13Q34) MUTATED 1 4 2
AMP PEAK 43(13Q34) WILD-TYPE 276 150 68

Figure S144.  Get High-res Image Gene #41: 'amp_13q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q34' versus 'RPPA_CHIERARCHICAL'

P value = 0.0358 (Fisher's exact test), Q value = 0.088

Table S145.  Gene #41: 'amp_13q34' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 28 33 29 49 27 9
AMP PEAK 43(13Q34) MUTATED 1 0 0 0 0 3 0
AMP PEAK 43(13Q34) WILD-TYPE 45 28 33 29 49 24 9

Figure S145.  Get High-res Image Gene #41: 'amp_13q34' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_14q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S146.  Gene #42: 'amp_14q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 44(14Q12) MUTATED 10 2 1
AMP PEAK 44(14Q12) WILD-TYPE 46 354 88

Figure S146.  Get High-res Image Gene #42: 'amp_14q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_14q12' versus 'METHLYATION_CNMF'

P value = 0.00219 (Fisher's exact test), Q value = 0.0091

Table S147.  Gene #42: 'amp_14q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 44(14Q12) MUTATED 3 10 0
AMP PEAK 44(14Q12) WILD-TYPE 274 144 70

Figure S147.  Get High-res Image Gene #42: 'amp_14q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_14q12' versus 'MRNASEQ_CNMF'

P value = 0.00343 (Fisher's exact test), Q value = 0.013

Table S148.  Gene #42: 'amp_14q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
AMP PEAK 44(14Q12) MUTATED 3 10 0 0
AMP PEAK 44(14Q12) WILD-TYPE 165 145 59 117

Figure S148.  Get High-res Image Gene #42: 'amp_14q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_14q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00333 (Fisher's exact test), Q value = 0.013

Table S149.  Gene #42: 'amp_14q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 44(14Q12) MUTATED 1 10 1 0 1
AMP PEAK 44(14Q12) WILD-TYPE 104 124 85 96 77

Figure S149.  Get High-res Image Gene #42: 'amp_14q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_14q12' versus 'MIRSEQ_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.048

Table S150.  Gene #42: 'amp_14q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
AMP PEAK 44(14Q12) MUTATED 2 9 2
AMP PEAK 44(14Q12) WILD-TYPE 180 142 165

Figure S150.  Get High-res Image Gene #42: 'amp_14q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_14q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00324 (Fisher's exact test), Q value = 0.013

Table S151.  Gene #42: 'amp_14q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 44(14Q12) MUTATED 2 9 2
AMP PEAK 44(14Q12) WILD-TYPE 177 119 191

Figure S151.  Get High-res Image Gene #42: 'amp_14q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_14q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0214 (Fisher's exact test), Q value = 0.058

Table S152.  Gene #42: 'amp_14q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
AMP PEAK 44(14Q12) MUTATED 4 7 1
AMP PEAK 44(14Q12) WILD-TYPE 161 119 178

Figure S152.  Get High-res Image Gene #42: 'amp_14q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_14q32.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S153.  Gene #43: 'amp_14q32.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 45(14Q32.31) MUTATED 10 2 1
AMP PEAK 45(14Q32.31) WILD-TYPE 46 354 88

Figure S153.  Get High-res Image Gene #43: 'amp_14q32.31' versus Molecular Subtype #1: 'CN_CNMF'

'amp_14q32.31' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.001

Table S154.  Gene #43: 'amp_14q32.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 45(14Q32.31) MUTATED 1 11 1
AMP PEAK 45(14Q32.31) WILD-TYPE 276 143 69

Figure S154.  Get High-res Image Gene #43: 'amp_14q32.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_14q32.31' versus 'MRNASEQ_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0032

Table S155.  Gene #43: 'amp_14q32.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
AMP PEAK 45(14Q32.31) MUTATED 2 11 0 0
AMP PEAK 45(14Q32.31) WILD-TYPE 166 144 59 117

Figure S155.  Get High-res Image Gene #43: 'amp_14q32.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_14q32.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.0018

Table S156.  Gene #43: 'amp_14q32.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 45(14Q32.31) MUTATED 1 11 0 0 1
AMP PEAK 45(14Q32.31) WILD-TYPE 104 123 86 96 77

Figure S156.  Get High-res Image Gene #43: 'amp_14q32.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_14q32.31' versus 'MIRSEQ_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0025

Table S157.  Gene #43: 'amp_14q32.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
AMP PEAK 45(14Q32.31) MUTATED 3 10 0
AMP PEAK 45(14Q32.31) WILD-TYPE 179 141 167

Figure S157.  Get High-res Image Gene #43: 'amp_14q32.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_14q32.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00041

Table S158.  Gene #43: 'amp_14q32.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 45(14Q32.31) MUTATED 3 10 0
AMP PEAK 45(14Q32.31) WILD-TYPE 176 118 193

Figure S158.  Get High-res Image Gene #43: 'amp_14q32.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_14q32.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00077 (Fisher's exact test), Q value = 0.0038

Table S159.  Gene #43: 'amp_14q32.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
AMP PEAK 45(14Q32.31) MUTATED 4 8 0
AMP PEAK 45(14Q32.31) WILD-TYPE 161 118 179

Figure S159.  Get High-res Image Gene #43: 'amp_14q32.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18q12.1' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00041

Table S160.  Gene #44: 'amp_18q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 48(18Q12.1) MUTATED 5 0 2
AMP PEAK 48(18Q12.1) WILD-TYPE 51 356 87

Figure S160.  Get High-res Image Gene #44: 'amp_18q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18q12.1' versus 'METHLYATION_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 0.075

Table S161.  Gene #44: 'amp_18q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 48(18Q12.1) MUTATED 1 5 1
AMP PEAK 48(18Q12.1) WILD-TYPE 276 149 69

Figure S161.  Get High-res Image Gene #44: 'amp_18q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_18q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0311 (Fisher's exact test), Q value = 0.079

Table S162.  Gene #44: 'amp_18q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 48(18Q12.1) MUTATED 1 5 1
AMP PEAK 48(18Q12.1) WILD-TYPE 178 123 192

Figure S162.  Get High-res Image Gene #44: 'amp_18q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_18q22.1' versus 'CN_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.002

Table S163.  Gene #45: 'amp_18q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 49(18Q22.1) MUTATED 5 1 1
AMP PEAK 49(18Q22.1) WILD-TYPE 51 355 88

Figure S163.  Get High-res Image Gene #45: 'amp_18q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18q22.3' versus 'CN_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0034

Table S164.  Gene #46: 'amp_18q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 50(18Q22.3) MUTATED 5 2 1
AMP PEAK 50(18Q22.3) WILD-TYPE 51 354 88

Figure S164.  Get High-res Image Gene #46: 'amp_18q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18q22.3' versus 'METHLYATION_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.064

Table S165.  Gene #46: 'amp_18q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 50(18Q22.3) MUTATED 1 5 2
AMP PEAK 50(18Q22.3) WILD-TYPE 276 149 68

Figure S165.  Get High-res Image Gene #46: 'amp_18q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_18q22.3' versus 'MRNASEQ_CNMF'

P value = 0.0355 (Fisher's exact test), Q value = 0.088

Table S166.  Gene #46: 'amp_18q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
AMP PEAK 50(18Q22.3) MUTATED 0 5 2 1
AMP PEAK 50(18Q22.3) WILD-TYPE 168 150 57 116

Figure S166.  Get High-res Image Gene #46: 'amp_18q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_18q22.3' versus 'MIRSEQ_CNMF'

P value = 0.0208 (Fisher's exact test), Q value = 0.057

Table S167.  Gene #46: 'amp_18q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
AMP PEAK 50(18Q22.3) MUTATED 1 6 1
AMP PEAK 50(18Q22.3) WILD-TYPE 181 145 166

Figure S167.  Get High-res Image Gene #46: 'amp_18q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_18q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00654 (Fisher's exact test), Q value = 0.023

Table S168.  Gene #46: 'amp_18q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 50(18Q22.3) MUTATED 1 6 1
AMP PEAK 50(18Q22.3) WILD-TYPE 178 122 192

Figure S168.  Get High-res Image Gene #46: 'amp_18q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S169.  Gene #47: 'amp_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 51(19P13.3) MUTATED 7 1 0
AMP PEAK 51(19P13.3) WILD-TYPE 49 355 89

Figure S169.  Get High-res Image Gene #47: 'amp_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19p13.3' versus 'METHLYATION_CNMF'

P value = 0.00406 (Fisher's exact test), Q value = 0.015

Table S170.  Gene #47: 'amp_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 51(19P13.3) MUTATED 1 7 0
AMP PEAK 51(19P13.3) WILD-TYPE 276 147 70

Figure S170.  Get High-res Image Gene #47: 'amp_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19p13.3' versus 'MRNASEQ_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.037

Table S171.  Gene #47: 'amp_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
AMP PEAK 51(19P13.3) MUTATED 1 7 0 0
AMP PEAK 51(19P13.3) WILD-TYPE 167 148 59 117

Figure S171.  Get High-res Image Gene #47: 'amp_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00533 (Fisher's exact test), Q value = 0.019

Table S172.  Gene #47: 'amp_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 51(19P13.3) MUTATED 1 7 0 0 0
AMP PEAK 51(19P13.3) WILD-TYPE 104 127 86 96 78

Figure S172.  Get High-res Image Gene #47: 'amp_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.3' versus 'MIRSEQ_CNMF'

P value = 0.00164 (Fisher's exact test), Q value = 0.0071

Table S173.  Gene #47: 'amp_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
AMP PEAK 51(19P13.3) MUTATED 1 7 0
AMP PEAK 51(19P13.3) WILD-TYPE 181 144 167

Figure S173.  Get High-res Image Gene #47: 'amp_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.0029

Table S174.  Gene #47: 'amp_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 51(19P13.3) MUTATED 0 7 1
AMP PEAK 51(19P13.3) WILD-TYPE 179 121 192

Figure S174.  Get High-res Image Gene #47: 'amp_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S175.  Gene #48: 'amp_20p13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 52(20P13) MUTATED 13 0 1
AMP PEAK 52(20P13) WILD-TYPE 43 356 88

Figure S175.  Get High-res Image Gene #48: 'amp_20p13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20p13' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00034

Table S176.  Gene #48: 'amp_20p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 52(20P13) MUTATED 1 12 1
AMP PEAK 52(20P13) WILD-TYPE 276 142 69

Figure S176.  Get High-res Image Gene #48: 'amp_20p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20p13' versus 'RPPA_CHIERARCHICAL'

P value = 0.0155 (Fisher's exact test), Q value = 0.046

Table S177.  Gene #48: 'amp_20p13' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 28 33 29 49 27 9
AMP PEAK 52(20P13) MUTATED 1 1 0 3 0 4 0
AMP PEAK 52(20P13) WILD-TYPE 45 27 33 26 49 23 9

Figure S177.  Get High-res Image Gene #48: 'amp_20p13' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_20p13' versus 'MRNASEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0022

Table S178.  Gene #48: 'amp_20p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
AMP PEAK 52(20P13) MUTATED 1 12 0 1
AMP PEAK 52(20P13) WILD-TYPE 167 143 59 116

Figure S178.  Get High-res Image Gene #48: 'amp_20p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_20p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00083

Table S179.  Gene #48: 'amp_20p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 52(20P13) MUTATED 1 12 0 1 0
AMP PEAK 52(20P13) WILD-TYPE 104 122 86 95 78

Figure S179.  Get High-res Image Gene #48: 'amp_20p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20p13' versus 'MIRSEQ_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.0028

Table S180.  Gene #48: 'amp_20p13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
AMP PEAK 52(20P13) MUTATED 2 11 1
AMP PEAK 52(20P13) WILD-TYPE 180 140 166

Figure S180.  Get High-res Image Gene #48: 'amp_20p13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_20p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00034

Table S181.  Gene #48: 'amp_20p13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 52(20P13) MUTATED 2 11 1
AMP PEAK 52(20P13) WILD-TYPE 177 117 192

Figure S181.  Get High-res Image Gene #48: 'amp_20p13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0222 (Fisher's exact test), Q value = 0.06

Table S182.  Gene #48: 'amp_20p13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
AMP PEAK 52(20P13) MUTATED 3 7 1
AMP PEAK 52(20P13) WILD-TYPE 162 119 178

Figure S182.  Get High-res Image Gene #48: 'amp_20p13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S183.  Gene #49: 'amp_20q13.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 53(20Q13.11) MUTATED 12 0 2
AMP PEAK 53(20Q13.11) WILD-TYPE 44 356 87

Figure S183.  Get High-res Image Gene #49: 'amp_20q13.11' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.11' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00076

Table S184.  Gene #49: 'amp_20q13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 53(20Q13.11) MUTATED 1 12 1
AMP PEAK 53(20Q13.11) WILD-TYPE 276 142 69

Figure S184.  Get High-res Image Gene #49: 'amp_20q13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q13.11' versus 'RPPA_CHIERARCHICAL'

P value = 0.0449 (Fisher's exact test), Q value = 0.11

Table S185.  Gene #49: 'amp_20q13.11' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 28 33 29 49 27 9
AMP PEAK 53(20Q13.11) MUTATED 1 1 0 3 0 3 0
AMP PEAK 53(20Q13.11) WILD-TYPE 45 27 33 26 49 24 9

Figure S185.  Get High-res Image Gene #49: 'amp_20q13.11' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_20q13.11' versus 'MRNASEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0022

Table S186.  Gene #49: 'amp_20q13.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
AMP PEAK 53(20Q13.11) MUTATED 1 12 0 1
AMP PEAK 53(20Q13.11) WILD-TYPE 167 143 59 116

Figure S186.  Get High-res Image Gene #49: 'amp_20q13.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_20q13.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00076

Table S187.  Gene #49: 'amp_20q13.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 53(20Q13.11) MUTATED 1 12 0 1 0
AMP PEAK 53(20Q13.11) WILD-TYPE 104 122 86 95 78

Figure S187.  Get High-res Image Gene #49: 'amp_20q13.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.11' versus 'MIRSEQ_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.003

Table S188.  Gene #49: 'amp_20q13.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
AMP PEAK 53(20Q13.11) MUTATED 2 11 1
AMP PEAK 53(20Q13.11) WILD-TYPE 180 140 166

Figure S188.  Get High-res Image Gene #49: 'amp_20q13.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_20q13.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.0011

Table S189.  Gene #49: 'amp_20q13.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 53(20Q13.11) MUTATED 2 11 1
AMP PEAK 53(20Q13.11) WILD-TYPE 177 117 192

Figure S189.  Get High-res Image Gene #49: 'amp_20q13.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0229 (Fisher's exact test), Q value = 0.062

Table S190.  Gene #49: 'amp_20q13.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
AMP PEAK 53(20Q13.11) MUTATED 3 7 1
AMP PEAK 53(20Q13.11) WILD-TYPE 162 119 178

Figure S190.  Get High-res Image Gene #49: 'amp_20q13.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S191.  Gene #50: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 54(20Q13.2) MUTATED 13 0 1
AMP PEAK 54(20Q13.2) WILD-TYPE 43 356 88

Figure S191.  Get High-res Image Gene #50: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.2' versus 'METHLYATION_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.0034

Table S192.  Gene #50: 'amp_20q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 54(20Q13.2) MUTATED 2 11 1
AMP PEAK 54(20Q13.2) WILD-TYPE 275 143 69

Figure S192.  Get High-res Image Gene #50: 'amp_20q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.027 (Fisher's exact test), Q value = 0.071

Table S193.  Gene #50: 'amp_20q13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 28 33 29 49 27 9
AMP PEAK 54(20Q13.2) MUTATED 1 1 0 2 0 4 0
AMP PEAK 54(20Q13.2) WILD-TYPE 45 27 33 27 49 23 9

Figure S193.  Get High-res Image Gene #50: 'amp_20q13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_20q13.2' versus 'MRNASEQ_CNMF'

P value = 0.00339 (Fisher's exact test), Q value = 0.013

Table S194.  Gene #50: 'amp_20q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
AMP PEAK 54(20Q13.2) MUTATED 2 11 0 1
AMP PEAK 54(20Q13.2) WILD-TYPE 166 144 59 116

Figure S194.  Get High-res Image Gene #50: 'amp_20q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_20q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00101 (Fisher's exact test), Q value = 0.0048

Table S195.  Gene #50: 'amp_20q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 54(20Q13.2) MUTATED 1 11 0 1 1
AMP PEAK 54(20Q13.2) WILD-TYPE 104 123 86 95 77

Figure S195.  Get High-res Image Gene #50: 'amp_20q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.003

Table S196.  Gene #50: 'amp_20q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
AMP PEAK 54(20Q13.2) MUTATED 2 11 1
AMP PEAK 54(20Q13.2) WILD-TYPE 180 140 166

Figure S196.  Get High-res Image Gene #50: 'amp_20q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_20q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00091 (Fisher's exact test), Q value = 0.0044

Table S197.  Gene #50: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 54(20Q13.2) MUTATED 2 10 2
AMP PEAK 54(20Q13.2) WILD-TYPE 177 118 191

Figure S197.  Get High-res Image Gene #50: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0439 (Fisher's exact test), Q value = 0.11

Table S198.  Gene #50: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
AMP PEAK 54(20Q13.2) MUTATED 3 6 1
AMP PEAK 54(20Q13.2) WILD-TYPE 162 120 178

Figure S198.  Get High-res Image Gene #50: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S199.  Gene #51: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 55(20Q13.2) MUTATED 13 0 0
AMP PEAK 55(20Q13.2) WILD-TYPE 43 356 89

Figure S199.  Get High-res Image Gene #51: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.2' versus 'METHLYATION_CNMF'

P value = 0.00179 (Fisher's exact test), Q value = 0.0077

Table S200.  Gene #51: 'amp_20q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 55(20Q13.2) MUTATED 2 10 1
AMP PEAK 55(20Q13.2) WILD-TYPE 275 144 69

Figure S200.  Get High-res Image Gene #51: 'amp_20q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q13.2' versus 'MRNASEQ_CNMF'

P value = 0.00857 (Fisher's exact test), Q value = 0.029

Table S201.  Gene #51: 'amp_20q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
AMP PEAK 55(20Q13.2) MUTATED 2 10 0 1
AMP PEAK 55(20Q13.2) WILD-TYPE 166 145 59 116

Figure S201.  Get High-res Image Gene #51: 'amp_20q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_20q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00213 (Fisher's exact test), Q value = 0.0089

Table S202.  Gene #51: 'amp_20q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 55(20Q13.2) MUTATED 2 10 0 1 0
AMP PEAK 55(20Q13.2) WILD-TYPE 103 124 86 95 78

Figure S202.  Get High-res Image Gene #51: 'amp_20q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_CNMF'

P value = 0.00969 (Fisher's exact test), Q value = 0.032

Table S203.  Gene #51: 'amp_20q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
AMP PEAK 55(20Q13.2) MUTATED 3 9 1
AMP PEAK 55(20Q13.2) WILD-TYPE 179 142 166

Figure S203.  Get High-res Image Gene #51: 'amp_20q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_20q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00137 (Fisher's exact test), Q value = 0.0062

Table S204.  Gene #51: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 55(20Q13.2) MUTATED 3 9 1
AMP PEAK 55(20Q13.2) WILD-TYPE 176 119 192

Figure S204.  Get High-res Image Gene #51: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_21q21.3' versus 'CN_CNMF'

P value = 0.00139 (Fisher's exact test), Q value = 0.0062

Table S205.  Gene #52: 'amp_21q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 56(21Q21.3) MUTATED 4 1 1
AMP PEAK 56(21Q21.3) WILD-TYPE 52 355 88

Figure S205.  Get High-res Image Gene #52: 'amp_21q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_22q11.21' versus 'CN_CNMF'

P value = 0.00284 (Fisher's exact test), Q value = 0.011

Table S206.  Gene #53: 'amp_22q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 57(22Q11.21) MUTATED 2 1 4
AMP PEAK 57(22Q11.21) WILD-TYPE 54 355 85

Figure S206.  Get High-res Image Gene #53: 'amp_22q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_22q11.21' versus 'METHLYATION_CNMF'

P value = 0.00444 (Fisher's exact test), Q value = 0.016

Table S207.  Gene #53: 'amp_22q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 57(22Q11.21) MUTATED 0 5 2
AMP PEAK 57(22Q11.21) WILD-TYPE 277 149 68

Figure S207.  Get High-res Image Gene #53: 'amp_22q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_22q11.21' versus 'MRNASEQ_CNMF'

P value = 0.00787 (Fisher's exact test), Q value = 0.027

Table S208.  Gene #53: 'amp_22q11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
AMP PEAK 57(22Q11.21) MUTATED 0 5 2 0
AMP PEAK 57(22Q11.21) WILD-TYPE 168 150 57 117

Figure S208.  Get High-res Image Gene #53: 'amp_22q11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_22q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.036 (Fisher's exact test), Q value = 0.088

Table S209.  Gene #53: 'amp_22q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 57(22Q11.21) MUTATED 0 5 2 0 0
AMP PEAK 57(22Q11.21) WILD-TYPE 105 129 84 96 78

Figure S209.  Get High-res Image Gene #53: 'amp_22q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_22q11.21' versus 'MIRSEQ_CNMF'

P value = 0.0324 (Fisher's exact test), Q value = 0.081

Table S210.  Gene #53: 'amp_22q11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
AMP PEAK 57(22Q11.21) MUTATED 2 5 0
AMP PEAK 57(22Q11.21) WILD-TYPE 180 146 167

Figure S210.  Get High-res Image Gene #53: 'amp_22q11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_22q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0299 (Fisher's exact test), Q value = 0.076

Table S211.  Gene #53: 'amp_22q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 57(22Q11.21) MUTATED 1 5 1
AMP PEAK 57(22Q11.21) WILD-TYPE 178 123 192

Figure S211.  Get High-res Image Gene #53: 'amp_22q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_22q11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0278 (Fisher's exact test), Q value = 0.072

Table S212.  Gene #53: 'amp_22q11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 164 146
AMP PEAK 57(22Q11.21) MUTATED 2 0 5
AMP PEAK 57(22Q11.21) WILD-TYPE 158 164 141

Figure S212.  Get High-res Image Gene #53: 'amp_22q11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_22q11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.034

Table S213.  Gene #53: 'amp_22q11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
AMP PEAK 57(22Q11.21) MUTATED 2 5 0
AMP PEAK 57(22Q11.21) WILD-TYPE 163 121 179

Figure S213.  Get High-res Image Gene #53: 'amp_22q11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xp22.12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S214.  Gene #54: 'amp_xp22.12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 58(XP22.12) MUTATED 8 1 1
AMP PEAK 58(XP22.12) WILD-TYPE 48 355 88

Figure S214.  Get High-res Image Gene #54: 'amp_xp22.12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp22.12' versus 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0019

Table S215.  Gene #54: 'amp_xp22.12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 58(XP22.12) MUTATED 0 8 2
AMP PEAK 58(XP22.12) WILD-TYPE 277 146 68

Figure S215.  Get High-res Image Gene #54: 'amp_xp22.12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xp22.12' versus 'MRNASEQ_CNMF'

P value = 0.00645 (Fisher's exact test), Q value = 0.022

Table S216.  Gene #54: 'amp_xp22.12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
AMP PEAK 58(XP22.12) MUTATED 1 8 1 0
AMP PEAK 58(XP22.12) WILD-TYPE 167 147 58 117

Figure S216.  Get High-res Image Gene #54: 'amp_xp22.12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_xp22.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00728 (Fisher's exact test), Q value = 0.025

Table S217.  Gene #54: 'amp_xp22.12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 58(XP22.12) MUTATED 1 8 1 0 0
AMP PEAK 58(XP22.12) WILD-TYPE 104 126 85 96 78

Figure S217.  Get High-res Image Gene #54: 'amp_xp22.12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_xp22.12' versus 'MIRSEQ_CNMF'

P value = 0.0354 (Fisher's exact test), Q value = 0.088

Table S218.  Gene #54: 'amp_xp22.12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
AMP PEAK 58(XP22.12) MUTATED 2 7 1
AMP PEAK 58(XP22.12) WILD-TYPE 180 144 166

Figure S218.  Get High-res Image Gene #54: 'amp_xp22.12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_xp22.12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00567 (Fisher's exact test), Q value = 0.02

Table S219.  Gene #54: 'amp_xp22.12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 58(XP22.12) MUTATED 2 7 1
AMP PEAK 58(XP22.12) WILD-TYPE 177 121 192

Figure S219.  Get High-res Image Gene #54: 'amp_xp22.12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_xp22.12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0323 (Fisher's exact test), Q value = 0.081

Table S220.  Gene #54: 'amp_xp22.12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
AMP PEAK 58(XP22.12) MUTATED 2 6 1
AMP PEAK 58(XP22.12) WILD-TYPE 163 120 178

Figure S220.  Get High-res Image Gene #54: 'amp_xp22.12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xp11.4' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S221.  Gene #55: 'amp_xp11.4' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 59(XP11.4) MUTATED 9 0 0
AMP PEAK 59(XP11.4) WILD-TYPE 47 356 89

Figure S221.  Get High-res Image Gene #55: 'amp_xp11.4' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp11.4' versus 'METHLYATION_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.037

Table S222.  Gene #55: 'amp_xp11.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 59(XP11.4) MUTATED 1 6 2
AMP PEAK 59(XP11.4) WILD-TYPE 276 148 68

Figure S222.  Get High-res Image Gene #55: 'amp_xp11.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xp11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S223.  Gene #56: 'amp_xp11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 60(XP11.22) MUTATED 7 1 0
AMP PEAK 60(XP11.22) WILD-TYPE 49 355 89

Figure S223.  Get High-res Image Gene #56: 'amp_xp11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp11.22' versus 'METHLYATION_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.037

Table S224.  Gene #56: 'amp_xp11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 60(XP11.22) MUTATED 1 6 1
AMP PEAK 60(XP11.22) WILD-TYPE 276 148 69

Figure S224.  Get High-res Image Gene #56: 'amp_xp11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xp11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S225.  Gene #57: 'amp_xp11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 61(XP11.22) MUTATED 8 0 0
AMP PEAK 61(XP11.22) WILD-TYPE 48 356 89

Figure S225.  Get High-res Image Gene #57: 'amp_xp11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp11.22' versus 'METHLYATION_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.0035

Table S226.  Gene #57: 'amp_xp11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 61(XP11.22) MUTATED 0 7 1
AMP PEAK 61(XP11.22) WILD-TYPE 277 147 69

Figure S226.  Get High-res Image Gene #57: 'amp_xp11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xp11.22' versus 'MRNASEQ_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.036

Table S227.  Gene #57: 'amp_xp11.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
AMP PEAK 61(XP11.22) MUTATED 1 7 0 0
AMP PEAK 61(XP11.22) WILD-TYPE 167 148 59 117

Figure S227.  Get High-res Image Gene #57: 'amp_xp11.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_xp11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00576 (Fisher's exact test), Q value = 0.02

Table S228.  Gene #57: 'amp_xp11.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 61(XP11.22) MUTATED 1 7 0 0 0
AMP PEAK 61(XP11.22) WILD-TYPE 104 127 86 96 78

Figure S228.  Get High-res Image Gene #57: 'amp_xp11.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.22' versus 'MIRSEQ_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.04

Table S229.  Gene #57: 'amp_xp11.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
AMP PEAK 61(XP11.22) MUTATED 2 6 0
AMP PEAK 61(XP11.22) WILD-TYPE 180 145 167

Figure S229.  Get High-res Image Gene #57: 'amp_xp11.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_xp11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00219 (Fisher's exact test), Q value = 0.0091

Table S230.  Gene #57: 'amp_xp11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 61(XP11.22) MUTATED 2 6 0
AMP PEAK 61(XP11.22) WILD-TYPE 177 122 193

Figure S230.  Get High-res Image Gene #57: 'amp_xp11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_xp11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0106 (Fisher's exact test), Q value = 0.034

Table S231.  Gene #57: 'amp_xp11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
AMP PEAK 61(XP11.22) MUTATED 2 5 0
AMP PEAK 61(XP11.22) WILD-TYPE 163 121 179

Figure S231.  Get High-res Image Gene #57: 'amp_xp11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xp11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S232.  Gene #58: 'amp_xp11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 62(XP11.21) MUTATED 8 1 0
AMP PEAK 62(XP11.21) WILD-TYPE 48 355 89

Figure S232.  Get High-res Image Gene #58: 'amp_xp11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp11.21' versus 'METHLYATION_CNMF'

P value = 0.00693 (Fisher's exact test), Q value = 0.024

Table S233.  Gene #58: 'amp_xp11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
AMP PEAK 62(XP11.21) MUTATED 1 7 1
AMP PEAK 62(XP11.21) WILD-TYPE 276 147 69

Figure S233.  Get High-res Image Gene #58: 'amp_xp11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xp11.21' versus 'MRNASEQ_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 0.075

Table S234.  Gene #58: 'amp_xp11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
AMP PEAK 62(XP11.21) MUTATED 2 7 0 0
AMP PEAK 62(XP11.21) WILD-TYPE 166 148 59 117

Figure S234.  Get High-res Image Gene #58: 'amp_xp11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_xp11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.034

Table S235.  Gene #58: 'amp_xp11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 62(XP11.21) MUTATED 2 7 0 0 0
AMP PEAK 62(XP11.21) WILD-TYPE 103 127 86 96 78

Figure S235.  Get High-res Image Gene #58: 'amp_xp11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.21' versus 'MIRSEQ_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.052

Table S236.  Gene #58: 'amp_xp11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
AMP PEAK 62(XP11.21) MUTATED 3 6 0
AMP PEAK 62(XP11.21) WILD-TYPE 179 145 167

Figure S236.  Get High-res Image Gene #58: 'amp_xp11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_xp11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00384 (Fisher's exact test), Q value = 0.015

Table S237.  Gene #58: 'amp_xp11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
AMP PEAK 62(XP11.21) MUTATED 3 6 0
AMP PEAK 62(XP11.21) WILD-TYPE 176 122 193

Figure S237.  Get High-res Image Gene #58: 'amp_xp11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_xp11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.053

Table S238.  Gene #58: 'amp_xp11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
AMP PEAK 62(XP11.21) MUTATED 3 5 0
AMP PEAK 62(XP11.21) WILD-TYPE 162 121 179

Figure S238.  Get High-res Image Gene #58: 'amp_xp11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xq21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S239.  Gene #59: 'amp_xq21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 63(XQ21.2) MUTATED 8 1 0
AMP PEAK 63(XQ21.2) WILD-TYPE 48 355 89

Figure S239.  Get High-res Image Gene #59: 'amp_xq21.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq22.3' versus 'CN_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.002

Table S240.  Gene #60: 'amp_xq22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 64(XQ22.3) MUTATED 7 8 0
AMP PEAK 64(XQ22.3) WILD-TYPE 49 348 89

Figure S240.  Get High-res Image Gene #60: 'amp_xq22.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq23' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S241.  Gene #61: 'amp_xq23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 65(XQ23) MUTATED 7 2 0
AMP PEAK 65(XQ23) WILD-TYPE 49 354 89

Figure S241.  Get High-res Image Gene #61: 'amp_xq23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0496 (Fisher's exact test), Q value = 0.11

Table S242.  Gene #61: 'amp_xq23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
AMP PEAK 65(XQ23) MUTATED 1 6 0 0 2
AMP PEAK 65(XQ23) WILD-TYPE 104 128 86 96 76

Figure S242.  Get High-res Image Gene #61: 'amp_xq23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_xq24' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S243.  Gene #62: 'amp_xq24' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 66(XQ24) MUTATED 7 2 0
AMP PEAK 66(XQ24) WILD-TYPE 49 354 89

Figure S243.  Get High-res Image Gene #62: 'amp_xq24' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq24' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S244.  Gene #63: 'amp_xq24' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 67(XQ24) MUTATED 7 2 0
AMP PEAK 67(XQ24) WILD-TYPE 49 354 89

Figure S244.  Get High-res Image Gene #63: 'amp_xq24' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq28' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00048

Table S245.  Gene #64: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
AMP PEAK 68(XQ28) MUTATED 7 3 0
AMP PEAK 68(XQ28) WILD-TYPE 49 353 89

Figure S245.  Get High-res Image Gene #64: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q24.2' versus 'CN_CNMF'

P value = 0.00129 (Fisher's exact test), Q value = 0.0059

Table S246.  Gene #65: 'del_1q24.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 1(1Q24.2) MUTATED 3 0 0
DEL PEAK 1(1Q24.2) WILD-TYPE 53 356 89

Figure S246.  Get High-res Image Gene #65: 'del_1q24.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q24.2' versus 'METHLYATION_CNMF'

P value = 0.0491 (Fisher's exact test), Q value = 0.11

Table S247.  Gene #65: 'del_1q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
DEL PEAK 1(1Q24.2) MUTATED 0 3 0
DEL PEAK 1(1Q24.2) WILD-TYPE 277 151 70

Figure S247.  Get High-res Image Gene #65: 'del_1q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1q24.2' versus 'MIRSEQ_CNMF'

P value = 0.0276 (Fisher's exact test), Q value = 0.072

Table S248.  Gene #65: 'del_1q24.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
DEL PEAK 1(1Q24.2) MUTATED 0 3 0
DEL PEAK 1(1Q24.2) WILD-TYPE 182 148 167

Figure S248.  Get High-res Image Gene #65: 'del_1q24.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1q24.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.048

Table S249.  Gene #65: 'del_1q24.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
DEL PEAK 1(1Q24.2) MUTATED 0 3 0
DEL PEAK 1(1Q24.2) WILD-TYPE 179 125 193

Figure S249.  Get High-res Image Gene #65: 'del_1q24.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1q42.13' versus 'CN_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.048

Table S250.  Gene #66: 'del_1q42.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 2(1Q42.13) MUTATED 3 2 0
DEL PEAK 2(1Q42.13) WILD-TYPE 53 354 89

Figure S250.  Get High-res Image Gene #66: 'del_1q42.13' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q42.13' versus 'MRNASEQ_CNMF'

P value = 0.0488 (Fisher's exact test), Q value = 0.11

Table S251.  Gene #66: 'del_1q42.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
DEL PEAK 2(1Q42.13) MUTATED 0 4 1 0
DEL PEAK 2(1Q42.13) WILD-TYPE 168 151 58 117

Figure S251.  Get High-res Image Gene #66: 'del_1q42.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1q42.13' versus 'MIRSEQ_CNMF'

P value = 0.0415 (Fisher's exact test), Q value = 0.1

Table S252.  Gene #66: 'del_1q42.13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
DEL PEAK 2(1Q42.13) MUTATED 1 4 0
DEL PEAK 2(1Q42.13) WILD-TYPE 181 147 167

Figure S252.  Get High-res Image Gene #66: 'del_1q42.13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2p23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S253.  Gene #67: 'del_2p23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 3(2P23.1) MUTATED 9 1 2
DEL PEAK 3(2P23.1) WILD-TYPE 47 355 87

Figure S253.  Get High-res Image Gene #67: 'del_2p23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2p23.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S254.  Gene #67: 'del_2p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
DEL PEAK 3(2P23.1) MUTATED 0 11 1
DEL PEAK 3(2P23.1) WILD-TYPE 277 143 69

Figure S254.  Get High-res Image Gene #67: 'del_2p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2p23.1' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00034

Table S255.  Gene #67: 'del_2p23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
DEL PEAK 3(2P23.1) MUTATED 0 12 0 0
DEL PEAK 3(2P23.1) WILD-TYPE 168 143 59 117

Figure S255.  Get High-res Image Gene #67: 'del_2p23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2p23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00048

Table S256.  Gene #67: 'del_2p23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
DEL PEAK 3(2P23.1) MUTATED 0 11 1 0 0
DEL PEAK 3(2P23.1) WILD-TYPE 105 123 85 96 78

Figure S256.  Get High-res Image Gene #67: 'del_2p23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2p23.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S257.  Gene #67: 'del_2p23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
DEL PEAK 3(2P23.1) MUTATED 0 12 0
DEL PEAK 3(2P23.1) WILD-TYPE 182 139 167

Figure S257.  Get High-res Image Gene #67: 'del_2p23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2p23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S258.  Gene #67: 'del_2p23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
DEL PEAK 3(2P23.1) MUTATED 0 11 1
DEL PEAK 3(2P23.1) WILD-TYPE 179 117 192

Figure S258.  Get High-res Image Gene #67: 'del_2p23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2p23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00095

Table S259.  Gene #67: 'del_2p23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
DEL PEAK 3(2P23.1) MUTATED 1 8 0
DEL PEAK 3(2P23.1) WILD-TYPE 164 118 179

Figure S259.  Get High-res Image Gene #67: 'del_2p23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S260.  Gene #68: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 4(2Q22.1) MUTATED 10 0 0
DEL PEAK 4(2Q22.1) WILD-TYPE 46 356 89

Figure S260.  Get High-res Image Gene #68: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S261.  Gene #68: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
DEL PEAK 4(2Q22.1) MUTATED 0 10 0
DEL PEAK 4(2Q22.1) WILD-TYPE 277 144 70

Figure S261.  Get High-res Image Gene #68: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00063

Table S262.  Gene #68: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
DEL PEAK 4(2Q22.1) MUTATED 0 10 0 0
DEL PEAK 4(2Q22.1) WILD-TYPE 168 145 59 117

Figure S262.  Get High-res Image Gene #68: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00048

Table S263.  Gene #68: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
DEL PEAK 4(2Q22.1) MUTATED 0 10 0 0 0
DEL PEAK 4(2Q22.1) WILD-TYPE 105 124 86 96 78

Figure S263.  Get High-res Image Gene #68: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S264.  Gene #68: 'del_2q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
DEL PEAK 4(2Q22.1) MUTATED 0 10 0
DEL PEAK 4(2Q22.1) WILD-TYPE 182 141 167

Figure S264.  Get High-res Image Gene #68: 'del_2q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S265.  Gene #68: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
DEL PEAK 4(2Q22.1) MUTATED 0 10 0
DEL PEAK 4(2Q22.1) WILD-TYPE 179 118 193

Figure S265.  Get High-res Image Gene #68: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.003

Table S266.  Gene #68: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
DEL PEAK 4(2Q22.1) MUTATED 1 7 0
DEL PEAK 4(2Q22.1) WILD-TYPE 164 119 179

Figure S266.  Get High-res Image Gene #68: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S267.  Gene #69: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 5(2Q37.3) MUTATED 11 2 0
DEL PEAK 5(2Q37.3) WILD-TYPE 45 354 89

Figure S267.  Get High-res Image Gene #69: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S268.  Gene #69: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
DEL PEAK 5(2Q37.3) MUTATED 0 12 1
DEL PEAK 5(2Q37.3) WILD-TYPE 277 142 69

Figure S268.  Get High-res Image Gene #69: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S269.  Gene #69: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
DEL PEAK 5(2Q37.3) MUTATED 0 12 0 1
DEL PEAK 5(2Q37.3) WILD-TYPE 168 143 59 116

Figure S269.  Get High-res Image Gene #69: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00048

Table S270.  Gene #69: 'del_2q37.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
DEL PEAK 5(2Q37.3) MUTATED 0 12 1 0 0
DEL PEAK 5(2Q37.3) WILD-TYPE 105 122 85 96 78

Figure S270.  Get High-res Image Gene #69: 'del_2q37.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00034

Table S271.  Gene #69: 'del_2q37.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
DEL PEAK 5(2Q37.3) MUTATED 1 12 0
DEL PEAK 5(2Q37.3) WILD-TYPE 181 139 167

Figure S271.  Get High-res Image Gene #69: 'del_2q37.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S272.  Gene #69: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
DEL PEAK 5(2Q37.3) MUTATED 0 12 1
DEL PEAK 5(2Q37.3) WILD-TYPE 179 116 192

Figure S272.  Get High-res Image Gene #69: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.0022

Table S273.  Gene #69: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
DEL PEAK 5(2Q37.3) MUTATED 1 9 1
DEL PEAK 5(2Q37.3) WILD-TYPE 164 117 178

Figure S273.  Get High-res Image Gene #69: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.046

Table S274.  Gene #70: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 7(4Q34.3) MUTATED 3 2 0
DEL PEAK 7(4Q34.3) WILD-TYPE 53 354 89

Figure S274.  Get High-res Image Gene #70: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q22.31' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00034

Table S275.  Gene #72: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 11(6Q22.31) MUTATED 6 1 0
DEL PEAK 11(6Q22.31) WILD-TYPE 50 355 89

Figure S275.  Get High-res Image Gene #72: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q22.31' versus 'METHLYATION_CNMF'

P value = 0.00217 (Fisher's exact test), Q value = 0.009

Table S276.  Gene #72: 'del_6q22.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
DEL PEAK 11(6Q22.31) MUTATED 0 6 1
DEL PEAK 11(6Q22.31) WILD-TYPE 277 148 69

Figure S276.  Get High-res Image Gene #72: 'del_6q22.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q22.31' versus 'RPPA_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.037

Table S277.  Gene #72: 'del_6q22.31' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 79 81
DEL PEAK 11(6Q22.31) MUTATED 0 0 5
DEL PEAK 11(6Q22.31) WILD-TYPE 61 79 76

Figure S277.  Get High-res Image Gene #72: 'del_6q22.31' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_6q22.31' versus 'MRNASEQ_CNMF'

P value = 0.0272 (Fisher's exact test), Q value = 0.071

Table S278.  Gene #72: 'del_6q22.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
DEL PEAK 11(6Q22.31) MUTATED 1 6 0 0
DEL PEAK 11(6Q22.31) WILD-TYPE 167 149 59 117

Figure S278.  Get High-res Image Gene #72: 'del_6q22.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q22.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0178 (Fisher's exact test), Q value = 0.051

Table S279.  Gene #72: 'del_6q22.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
DEL PEAK 11(6Q22.31) MUTATED 1 6 0 0 0
DEL PEAK 11(6Q22.31) WILD-TYPE 104 128 86 96 78

Figure S279.  Get High-res Image Gene #72: 'del_6q22.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q22.31' versus 'MIRSEQ_CNMF'

P value = 0.00459 (Fisher's exact test), Q value = 0.017

Table S280.  Gene #72: 'del_6q22.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
DEL PEAK 11(6Q22.31) MUTATED 1 6 0
DEL PEAK 11(6Q22.31) WILD-TYPE 181 145 167

Figure S280.  Get High-res Image Gene #72: 'del_6q22.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6q22.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00081 (Fisher's exact test), Q value = 0.004

Table S281.  Gene #72: 'del_6q22.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
DEL PEAK 11(6Q22.31) MUTATED 1 6 0
DEL PEAK 11(6Q22.31) WILD-TYPE 178 122 193

Figure S281.  Get High-res Image Gene #72: 'del_6q22.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q22.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.034

Table S282.  Gene #72: 'del_6q22.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
DEL PEAK 11(6Q22.31) MUTATED 2 5 0
DEL PEAK 11(6Q22.31) WILD-TYPE 163 121 179

Figure S282.  Get High-res Image Gene #72: 'del_6q22.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0013

Table S283.  Gene #74: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 14(8P23.2) MUTATED 4 0 0
DEL PEAK 14(8P23.2) WILD-TYPE 52 356 89

Figure S283.  Get High-res Image Gene #74: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.051

Table S284.  Gene #74: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
DEL PEAK 14(8P23.2) MUTATED 0 4 0
DEL PEAK 14(8P23.2) WILD-TYPE 277 150 70

Figure S284.  Get High-res Image Gene #74: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 0.0364 (Fisher's exact test), Q value = 0.089

Table S285.  Gene #74: 'del_8p23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
DEL PEAK 14(8P23.2) MUTATED 0 4 0 0
DEL PEAK 14(8P23.2) WILD-TYPE 168 151 59 117

Figure S285.  Get High-res Image Gene #74: 'del_8p23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0471 (Fisher's exact test), Q value = 0.11

Table S286.  Gene #74: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
DEL PEAK 14(8P23.2) MUTATED 0 4 0 0 0
DEL PEAK 14(8P23.2) WILD-TYPE 105 130 86 96 78

Figure S286.  Get High-res Image Gene #74: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 0.00816 (Fisher's exact test), Q value = 0.028

Table S287.  Gene #74: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
DEL PEAK 14(8P23.2) MUTATED 0 4 0
DEL PEAK 14(8P23.2) WILD-TYPE 182 147 167

Figure S287.  Get High-res Image Gene #74: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00437 (Fisher's exact test), Q value = 0.016

Table S288.  Gene #74: 'del_8p23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
DEL PEAK 14(8P23.2) MUTATED 0 4 0
DEL PEAK 14(8P23.2) WILD-TYPE 179 124 193

Figure S288.  Get High-res Image Gene #74: 'del_8p23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0184 (Fisher's exact test), Q value = 0.052

Table S289.  Gene #74: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
DEL PEAK 14(8P23.2) MUTATED 0 3 0
DEL PEAK 14(8P23.2) WILD-TYPE 165 123 179

Figure S289.  Get High-res Image Gene #74: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p22' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00088

Table S290.  Gene #75: 'del_8p22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 15(8P22) MUTATED 4 0 0
DEL PEAK 15(8P22) WILD-TYPE 52 356 89

Figure S290.  Get High-res Image Gene #75: 'del_8p22' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p22' versus 'METHLYATION_CNMF'

P value = 0.0189 (Fisher's exact test), Q value = 0.053

Table S291.  Gene #75: 'del_8p22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
DEL PEAK 15(8P22) MUTATED 0 4 0
DEL PEAK 15(8P22) WILD-TYPE 277 150 70

Figure S291.  Get High-res Image Gene #75: 'del_8p22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p22' versus 'MRNASEQ_CNMF'

P value = 0.0359 (Fisher's exact test), Q value = 0.088

Table S292.  Gene #75: 'del_8p22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
DEL PEAK 15(8P22) MUTATED 0 4 0 0
DEL PEAK 15(8P22) WILD-TYPE 168 151 59 117

Figure S292.  Get High-res Image Gene #75: 'del_8p22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0475 (Fisher's exact test), Q value = 0.11

Table S293.  Gene #75: 'del_8p22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
DEL PEAK 15(8P22) MUTATED 0 4 0 0 0
DEL PEAK 15(8P22) WILD-TYPE 105 130 86 96 78

Figure S293.  Get High-res Image Gene #75: 'del_8p22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p22' versus 'MIRSEQ_CNMF'

P value = 0.00827 (Fisher's exact test), Q value = 0.028

Table S294.  Gene #75: 'del_8p22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
DEL PEAK 15(8P22) MUTATED 0 4 0
DEL PEAK 15(8P22) WILD-TYPE 182 147 167

Figure S294.  Get High-res Image Gene #75: 'del_8p22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00415 (Fisher's exact test), Q value = 0.016

Table S295.  Gene #75: 'del_8p22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
DEL PEAK 15(8P22) MUTATED 0 4 0
DEL PEAK 15(8P22) WILD-TYPE 179 124 193

Figure S295.  Get High-res Image Gene #75: 'del_8p22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0192 (Fisher's exact test), Q value = 0.053

Table S296.  Gene #75: 'del_8p22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
DEL PEAK 15(8P22) MUTATED 0 3 0
DEL PEAK 15(8P22) WILD-TYPE 165 123 179

Figure S296.  Get High-res Image Gene #75: 'del_8p22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p12' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00083

Table S297.  Gene #76: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 16(8P12) MUTATED 4 0 0
DEL PEAK 16(8P12) WILD-TYPE 52 356 89

Figure S297.  Get High-res Image Gene #76: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p12' versus 'METHLYATION_CNMF'

P value = 0.0184 (Fisher's exact test), Q value = 0.052

Table S298.  Gene #76: 'del_8p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
DEL PEAK 16(8P12) MUTATED 0 4 0
DEL PEAK 16(8P12) WILD-TYPE 277 150 70

Figure S298.  Get High-res Image Gene #76: 'del_8p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p12' versus 'MRNASEQ_CNMF'

P value = 0.037 (Fisher's exact test), Q value = 0.09

Table S299.  Gene #76: 'del_8p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
DEL PEAK 16(8P12) MUTATED 0 4 0 0
DEL PEAK 16(8P12) WILD-TYPE 168 151 59 117

Figure S299.  Get High-res Image Gene #76: 'del_8p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.048 (Fisher's exact test), Q value = 0.11

Table S300.  Gene #76: 'del_8p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
DEL PEAK 16(8P12) MUTATED 0 4 0 0 0
DEL PEAK 16(8P12) WILD-TYPE 105 130 86 96 78

Figure S300.  Get High-res Image Gene #76: 'del_8p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p12' versus 'MIRSEQ_CNMF'

P value = 0.008 (Fisher's exact test), Q value = 0.027

Table S301.  Gene #76: 'del_8p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
DEL PEAK 16(8P12) MUTATED 0 4 0
DEL PEAK 16(8P12) WILD-TYPE 182 147 167

Figure S301.  Get High-res Image Gene #76: 'del_8p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00468 (Fisher's exact test), Q value = 0.017

Table S302.  Gene #76: 'del_8p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
DEL PEAK 16(8P12) MUTATED 0 4 0
DEL PEAK 16(8P12) WILD-TYPE 179 124 193

Figure S302.  Get High-res Image Gene #76: 'del_8p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.053

Table S303.  Gene #76: 'del_8p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
DEL PEAK 16(8P12) MUTATED 0 3 0
DEL PEAK 16(8P12) WILD-TYPE 165 123 179

Figure S303.  Get High-res Image Gene #76: 'del_8p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8q24.22' versus 'CN_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.0034

Table S304.  Gene #77: 'del_8q24.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 17(8Q24.22) MUTATED 5 2 0
DEL PEAK 17(8Q24.22) WILD-TYPE 51 354 89

Figure S304.  Get High-res Image Gene #77: 'del_8q24.22' versus Molecular Subtype #1: 'CN_CNMF'

'del_8q24.22' versus 'METHLYATION_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0028

Table S305.  Gene #77: 'del_8q24.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
DEL PEAK 17(8Q24.22) MUTATED 0 7 0
DEL PEAK 17(8Q24.22) WILD-TYPE 277 147 70

Figure S305.  Get High-res Image Gene #77: 'del_8q24.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8q24.22' versus 'MRNASEQ_CNMF'

P value = 0.00162 (Fisher's exact test), Q value = 0.0071

Table S306.  Gene #77: 'del_8q24.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
DEL PEAK 17(8Q24.22) MUTATED 0 7 0 0
DEL PEAK 17(8Q24.22) WILD-TYPE 168 148 59 117

Figure S306.  Get High-res Image Gene #77: 'del_8q24.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8q24.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00109 (Fisher's exact test), Q value = 0.0051

Table S307.  Gene #77: 'del_8q24.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
DEL PEAK 17(8Q24.22) MUTATED 0 7 0 0 0
DEL PEAK 17(8Q24.22) WILD-TYPE 105 127 86 96 78

Figure S307.  Get High-res Image Gene #77: 'del_8q24.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8q24.22' versus 'MIRSEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0012

Table S308.  Gene #77: 'del_8q24.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
DEL PEAK 17(8Q24.22) MUTATED 0 7 0
DEL PEAK 17(8Q24.22) WILD-TYPE 182 144 167

Figure S308.  Get High-res Image Gene #77: 'del_8q24.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8q24.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00063

Table S309.  Gene #77: 'del_8q24.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
DEL PEAK 17(8Q24.22) MUTATED 0 7 0
DEL PEAK 17(8Q24.22) WILD-TYPE 179 121 193

Figure S309.  Get High-res Image Gene #77: 'del_8q24.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8q24.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00415 (Fisher's exact test), Q value = 0.016

Table S310.  Gene #77: 'del_8q24.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 164 146
DEL PEAK 17(8Q24.22) MUTATED 0 6 0
DEL PEAK 17(8Q24.22) WILD-TYPE 160 158 146

Figure S310.  Get High-res Image Gene #77: 'del_8q24.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8q24.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.0022

Table S311.  Gene #77: 'del_8q24.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
DEL PEAK 17(8Q24.22) MUTATED 0 6 0
DEL PEAK 17(8Q24.22) WILD-TYPE 165 120 179

Figure S311.  Get High-res Image Gene #77: 'del_8q24.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S312.  Gene #78: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 18(9P21.3) MUTATED 16 2 2
DEL PEAK 18(9P21.3) WILD-TYPE 40 354 87

Figure S312.  Get High-res Image Gene #78: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 0.00811 (Fisher's exact test), Q value = 0.028

Table S313.  Gene #78: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
DEL PEAK 18(9P21.3) MUTATED 5 12 3
DEL PEAK 18(9P21.3) WILD-TYPE 272 142 67

Figure S313.  Get High-res Image Gene #78: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.065

Table S314.  Gene #78: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
DEL PEAK 18(9P21.3) MUTATED 3 12 3 2
DEL PEAK 18(9P21.3) WILD-TYPE 165 143 56 115

Figure S314.  Get High-res Image Gene #78: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0244 (Fisher's exact test), Q value = 0.065

Table S315.  Gene #78: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
DEL PEAK 18(9P21.3) MUTATED 4 12 1 2 1
DEL PEAK 18(9P21.3) WILD-TYPE 101 122 85 94 77

Figure S315.  Get High-res Image Gene #78: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0025

Table S316.  Gene #78: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
DEL PEAK 18(9P21.3) MUTATED 9 11 0
DEL PEAK 18(9P21.3) WILD-TYPE 173 140 167

Figure S316.  Get High-res Image Gene #78: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.0031

Table S317.  Gene #78: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
DEL PEAK 18(9P21.3) MUTATED 8 11 1
DEL PEAK 18(9P21.3) WILD-TYPE 171 117 192

Figure S317.  Get High-res Image Gene #78: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.0011

Table S318.  Gene #78: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
DEL PEAK 18(9P21.3) MUTATED 8 10 0
DEL PEAK 18(9P21.3) WILD-TYPE 157 116 179

Figure S318.  Get High-res Image Gene #78: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q22.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S319.  Gene #79: 'del_9q22.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 19(9Q22.33) MUTATED 21 2 4
DEL PEAK 19(9Q22.33) WILD-TYPE 35 354 85

Figure S319.  Get High-res Image Gene #79: 'del_9q22.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q22.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0274 (Fisher's exact test), Q value = 0.071

Table S320.  Gene #79: 'del_9q22.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
DEL PEAK 19(9Q22.33) MUTATED 8 13 1 3 2
DEL PEAK 19(9Q22.33) WILD-TYPE 97 121 85 93 76

Figure S320.  Get High-res Image Gene #79: 'del_9q22.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9q22.33' versus 'MIRSEQ_CNMF'

P value = 0.00481 (Fisher's exact test), Q value = 0.017

Table S321.  Gene #79: 'del_9q22.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
DEL PEAK 19(9Q22.33) MUTATED 13 12 2
DEL PEAK 19(9Q22.33) WILD-TYPE 169 139 165

Figure S321.  Get High-res Image Gene #79: 'del_9q22.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9q22.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00359 (Fisher's exact test), Q value = 0.014

Table S322.  Gene #79: 'del_9q22.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
DEL PEAK 19(9Q22.33) MUTATED 12 12 3
DEL PEAK 19(9Q22.33) WILD-TYPE 167 116 190

Figure S322.  Get High-res Image Gene #79: 'del_9q22.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9q22.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00204 (Fisher's exact test), Q value = 0.0086

Table S323.  Gene #79: 'del_9q22.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
DEL PEAK 19(9Q22.33) MUTATED 12 11 2
DEL PEAK 19(9Q22.33) WILD-TYPE 153 115 177

Figure S323.  Get High-res Image Gene #79: 'del_9q22.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p12.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S324.  Gene #80: 'del_10p12.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 20(10P12.31) MUTATED 6 0 1
DEL PEAK 20(10P12.31) WILD-TYPE 50 356 88

Figure S324.  Get High-res Image Gene #80: 'del_10p12.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p12.31' versus 'METHLYATION_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.036

Table S325.  Gene #80: 'del_10p12.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
DEL PEAK 20(10P12.31) MUTATED 1 6 0
DEL PEAK 20(10P12.31) WILD-TYPE 276 148 70

Figure S325.  Get High-res Image Gene #80: 'del_10p12.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p12.31' versus 'MRNASEQ_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.053

Table S326.  Gene #80: 'del_10p12.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
DEL PEAK 20(10P12.31) MUTATED 0 6 0 1
DEL PEAK 20(10P12.31) WILD-TYPE 168 149 59 116

Figure S326.  Get High-res Image Gene #80: 'del_10p12.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p12.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0151 (Fisher's exact test), Q value = 0.045

Table S327.  Gene #80: 'del_10p12.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
DEL PEAK 20(10P12.31) MUTATED 0 6 0 1 0
DEL PEAK 20(10P12.31) WILD-TYPE 105 128 86 95 78

Figure S327.  Get High-res Image Gene #80: 'del_10p12.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10p12.31' versus 'MIRSEQ_CNMF'

P value = 0.00484 (Fisher's exact test), Q value = 0.018

Table S328.  Gene #80: 'del_10p12.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
DEL PEAK 20(10P12.31) MUTATED 1 6 0
DEL PEAK 20(10P12.31) WILD-TYPE 181 145 167

Figure S328.  Get High-res Image Gene #80: 'del_10p12.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10p12.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00085 (Fisher's exact test), Q value = 0.0041

Table S329.  Gene #80: 'del_10p12.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
DEL PEAK 20(10P12.31) MUTATED 1 6 0
DEL PEAK 20(10P12.31) WILD-TYPE 178 122 193

Figure S329.  Get High-res Image Gene #80: 'del_10p12.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10p12.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00997 (Fisher's exact test), Q value = 0.032

Table S330.  Gene #80: 'del_10p12.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
DEL PEAK 20(10P12.31) MUTATED 2 5 0
DEL PEAK 20(10P12.31) WILD-TYPE 163 121 179

Figure S330.  Get High-res Image Gene #80: 'del_10p12.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q21.2' versus 'CN_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.0049

Table S331.  Gene #81: 'del_10q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 21(10Q21.2) MUTATED 6 4 2
DEL PEAK 21(10Q21.2) WILD-TYPE 50 352 87

Figure S331.  Get High-res Image Gene #81: 'del_10q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q21.2' versus 'MRNASEQ_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.052

Table S332.  Gene #81: 'del_10q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
DEL PEAK 21(10Q21.2) MUTATED 0 7 2 3
DEL PEAK 21(10Q21.2) WILD-TYPE 168 148 57 114

Figure S332.  Get High-res Image Gene #81: 'del_10q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0462 (Fisher's exact test), Q value = 0.11

Table S333.  Gene #81: 'del_10q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
DEL PEAK 21(10Q21.2) MUTATED 5 6 1
DEL PEAK 21(10Q21.2) WILD-TYPE 160 120 178

Figure S333.  Get High-res Image Gene #81: 'del_10q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00063

Table S334.  Gene #82: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 22(10Q23.31) MUTATED 7 3 2
DEL PEAK 22(10Q23.31) WILD-TYPE 49 353 87

Figure S334.  Get High-res Image Gene #82: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 0.0045 (Fisher's exact test), Q value = 0.017

Table S335.  Gene #82: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
DEL PEAK 22(10Q23.31) MUTATED 2 9 1
DEL PEAK 22(10Q23.31) WILD-TYPE 275 145 69

Figure S335.  Get High-res Image Gene #82: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.004

Table S336.  Gene #82: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
DEL PEAK 22(10Q23.31) MUTATED 0 10 0 2
DEL PEAK 22(10Q23.31) WILD-TYPE 168 145 59 115

Figure S336.  Get High-res Image Gene #82: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00471 (Fisher's exact test), Q value = 0.017

Table S337.  Gene #82: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
DEL PEAK 22(10Q23.31) MUTATED 0 9 1 2 0
DEL PEAK 22(10Q23.31) WILD-TYPE 105 125 85 94 78

Figure S337.  Get High-res Image Gene #82: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 0.00419 (Fisher's exact test), Q value = 0.016

Table S338.  Gene #82: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
DEL PEAK 22(10Q23.31) MUTATED 2 9 1
DEL PEAK 22(10Q23.31) WILD-TYPE 180 142 166

Figure S338.  Get High-res Image Gene #82: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-04 (Fisher's exact test), Q value = 0.004

Table S339.  Gene #82: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
DEL PEAK 22(10Q23.31) MUTATED 2 9 1
DEL PEAK 22(10Q23.31) WILD-TYPE 177 119 192

Figure S339.  Get High-res Image Gene #82: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00876 (Fisher's exact test), Q value = 0.029

Table S340.  Gene #82: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
DEL PEAK 22(10Q23.31) MUTATED 3 8 1
DEL PEAK 22(10Q23.31) WILD-TYPE 162 118 178

Figure S340.  Get High-res Image Gene #82: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S341.  Gene #83: 'del_11p15.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 23(11P15.1) MUTATED 6 0 1
DEL PEAK 23(11P15.1) WILD-TYPE 50 356 88

Figure S341.  Get High-res Image Gene #83: 'del_11p15.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.1' versus 'METHLYATION_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.035

Table S342.  Gene #83: 'del_11p15.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
DEL PEAK 23(11P15.1) MUTATED 1 6 0
DEL PEAK 23(11P15.1) WILD-TYPE 276 148 70

Figure S342.  Get High-res Image Gene #83: 'del_11p15.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.1' versus 'MRNASEQ_CNMF'

P value = 0.00731 (Fisher's exact test), Q value = 0.025

Table S343.  Gene #83: 'del_11p15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
DEL PEAK 23(11P15.1) MUTATED 0 6 1 0
DEL PEAK 23(11P15.1) WILD-TYPE 168 149 58 117

Figure S343.  Get High-res Image Gene #83: 'del_11p15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11p15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0185 (Fisher's exact test), Q value = 0.052

Table S344.  Gene #83: 'del_11p15.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
DEL PEAK 23(11P15.1) MUTATED 1 6 0 0 0
DEL PEAK 23(11P15.1) WILD-TYPE 104 128 86 96 78

Figure S344.  Get High-res Image Gene #83: 'del_11p15.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.1' versus 'MIRSEQ_CNMF'

P value = 0.00488 (Fisher's exact test), Q value = 0.018

Table S345.  Gene #83: 'del_11p15.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
DEL PEAK 23(11P15.1) MUTATED 1 6 0
DEL PEAK 23(11P15.1) WILD-TYPE 181 145 167

Figure S345.  Get High-res Image Gene #83: 'del_11p15.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11p15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.0035

Table S346.  Gene #83: 'del_11p15.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
DEL PEAK 23(11P15.1) MUTATED 1 6 0
DEL PEAK 23(11P15.1) WILD-TYPE 178 122 193

Figure S346.  Get High-res Image Gene #83: 'del_11p15.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.033

Table S347.  Gene #83: 'del_11p15.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
DEL PEAK 23(11P15.1) MUTATED 2 5 0
DEL PEAK 23(11P15.1) WILD-TYPE 163 121 179

Figure S347.  Get High-res Image Gene #83: 'del_11p15.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q12.13' versus 'CN_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0022

Table S348.  Gene #84: 'del_13q12.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 24(13Q12.13) MUTATED 8 7 3
DEL PEAK 24(13Q12.13) WILD-TYPE 48 349 86

Figure S348.  Get High-res Image Gene #84: 'del_13q12.13' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q12.13' versus 'METHLYATION_CNMF'

P value = 0.00115 (Fisher's exact test), Q value = 0.0053

Table S349.  Gene #84: 'del_13q12.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
DEL PEAK 24(13Q12.13) MUTATED 3 12 3
DEL PEAK 24(13Q12.13) WILD-TYPE 274 142 67

Figure S349.  Get High-res Image Gene #84: 'del_13q12.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q12.13' versus 'MRNASEQ_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.052

Table S350.  Gene #84: 'del_13q12.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
DEL PEAK 24(13Q12.13) MUTATED 2 11 3 2
DEL PEAK 24(13Q12.13) WILD-TYPE 166 144 56 115

Figure S350.  Get High-res Image Gene #84: 'del_13q12.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q12.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0364 (Fisher's exact test), Q value = 0.089

Table S351.  Gene #84: 'del_13q12.13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
DEL PEAK 24(13Q12.13) MUTATED 2 10 4 2 0
DEL PEAK 24(13Q12.13) WILD-TYPE 103 124 82 94 78

Figure S351.  Get High-res Image Gene #84: 'del_13q12.13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q12.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0207 (Fisher's exact test), Q value = 0.057

Table S352.  Gene #84: 'del_13q12.13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
DEL PEAK 24(13Q12.13) MUTATED 4 10 4
DEL PEAK 24(13Q12.13) WILD-TYPE 175 118 189

Figure S352.  Get High-res Image Gene #84: 'del_13q12.13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q12.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.034 (Fisher's exact test), Q value = 0.085

Table S353.  Gene #84: 'del_13q12.13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
DEL PEAK 24(13Q12.13) MUTATED 4 10 4
DEL PEAK 24(13Q12.13) WILD-TYPE 161 116 175

Figure S353.  Get High-res Image Gene #84: 'del_13q12.13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q22.1' versus 'CN_CNMF'

P value = 0.00195 (Fisher's exact test), Q value = 0.0083

Table S354.  Gene #85: 'del_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 25(13Q22.1) MUTATED 7 8 4
DEL PEAK 25(13Q22.1) WILD-TYPE 49 348 85

Figure S354.  Get High-res Image Gene #85: 'del_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q22.1' versus 'METHLYATION_CNMF'

P value = 0.0375 (Fisher's exact test), Q value = 0.091

Table S355.  Gene #85: 'del_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
DEL PEAK 25(13Q22.1) MUTATED 6 11 2
DEL PEAK 25(13Q22.1) WILD-TYPE 271 143 68

Figure S355.  Get High-res Image Gene #85: 'del_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.0049

Table S356.  Gene #85: 'del_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
DEL PEAK 25(13Q22.1) MUTATED 0 11 2 6
DEL PEAK 25(13Q22.1) WILD-TYPE 168 144 57 111

Figure S356.  Get High-res Image Gene #85: 'del_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00081 (Fisher's exact test), Q value = 0.004

Table S357.  Gene #85: 'del_13q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
DEL PEAK 25(13Q22.1) MUTATED 0 11 2 6 0
DEL PEAK 25(13Q22.1) WILD-TYPE 105 123 84 90 78

Figure S357.  Get High-res Image Gene #85: 'del_13q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q22.1' versus 'MIRSEQ_CNMF'

P value = 0.003 (Fisher's exact test), Q value = 0.012

Table S358.  Gene #85: 'del_13q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
DEL PEAK 25(13Q22.1) MUTATED 1 11 7
DEL PEAK 25(13Q22.1) WILD-TYPE 181 140 160

Figure S358.  Get High-res Image Gene #85: 'del_13q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_13q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00064 (Fisher's exact test), Q value = 0.0033

Table S359.  Gene #85: 'del_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
DEL PEAK 25(13Q22.1) MUTATED 1 11 7
DEL PEAK 25(13Q22.1) WILD-TYPE 178 117 186

Figure S359.  Get High-res Image Gene #85: 'del_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0138 (Fisher's exact test), Q value = 0.041

Table S360.  Gene #85: 'del_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 164 146
DEL PEAK 25(13Q22.1) MUTATED 1 8 9
DEL PEAK 25(13Q22.1) WILD-TYPE 159 156 137

Figure S360.  Get High-res Image Gene #85: 'del_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_13q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00356 (Fisher's exact test), Q value = 0.014

Table S361.  Gene #85: 'del_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
DEL PEAK 25(13Q22.1) MUTATED 1 10 7
DEL PEAK 25(13Q22.1) WILD-TYPE 164 116 172

Figure S361.  Get High-res Image Gene #85: 'del_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q25.3' versus 'CN_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0032

Table S362.  Gene #86: 'del_15q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 27(15Q25.3) MUTATED 5 2 2
DEL PEAK 27(15Q25.3) WILD-TYPE 51 354 87

Figure S362.  Get High-res Image Gene #86: 'del_15q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q25.3' versus 'METHLYATION_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0051

Table S363.  Gene #86: 'del_15q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
DEL PEAK 27(15Q25.3) MUTATED 1 8 0
DEL PEAK 27(15Q25.3) WILD-TYPE 276 146 70

Figure S363.  Get High-res Image Gene #86: 'del_15q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q25.3' versus 'MRNASEQ_CNMF'

P value = 0.00404 (Fisher's exact test), Q value = 0.015

Table S364.  Gene #86: 'del_15q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
DEL PEAK 27(15Q25.3) MUTATED 1 8 0 0
DEL PEAK 27(15Q25.3) WILD-TYPE 167 147 59 117

Figure S364.  Get High-res Image Gene #86: 'del_15q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00161 (Fisher's exact test), Q value = 0.0071

Table S365.  Gene #86: 'del_15q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
DEL PEAK 27(15Q25.3) MUTATED 1 8 0 0 0
DEL PEAK 27(15Q25.3) WILD-TYPE 104 126 86 96 78

Figure S365.  Get High-res Image Gene #86: 'del_15q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q25.3' versus 'MIRSEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0022

Table S366.  Gene #86: 'del_15q25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
DEL PEAK 27(15Q25.3) MUTATED 0 8 1
DEL PEAK 27(15Q25.3) WILD-TYPE 182 143 166

Figure S366.  Get High-res Image Gene #86: 'del_15q25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_15q25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00069

Table S367.  Gene #86: 'del_15q25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
DEL PEAK 27(15Q25.3) MUTATED 0 8 1
DEL PEAK 27(15Q25.3) WILD-TYPE 179 120 192

Figure S367.  Get High-res Image Gene #86: 'del_15q25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.037

Table S368.  Gene #86: 'del_15q25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
DEL PEAK 27(15Q25.3) MUTATED 1 6 1
DEL PEAK 27(15Q25.3) WILD-TYPE 164 120 178

Figure S368.  Get High-res Image Gene #86: 'del_15q25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.3' versus 'CN_CNMF'

P value = 0.0245 (Fisher's exact test), Q value = 0.065

Table S369.  Gene #87: 'del_16q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 29(16Q23.3) MUTATED 3 2 1
DEL PEAK 29(16Q23.3) WILD-TYPE 53 354 88

Figure S369.  Get High-res Image Gene #87: 'del_16q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.1' versus 'CN_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.041

Table S370.  Gene #88: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 30(17P13.1) MUTATED 4 3 1
DEL PEAK 30(17P13.1) WILD-TYPE 52 353 88

Figure S370.  Get High-res Image Gene #88: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q12.3' versus 'CN_CNMF'

P value = 0.00188 (Fisher's exact test), Q value = 0.008

Table S371.  Gene #89: 'del_18q12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 31(18Q12.3) MUTATED 3 0 1
DEL PEAK 31(18Q12.3) WILD-TYPE 53 356 88

Figure S371.  Get High-res Image Gene #89: 'del_18q12.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.2' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0017

Table S372.  Gene #90: 'del_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 32(19P13.2) MUTATED 5 1 1
DEL PEAK 32(19P13.2) WILD-TYPE 51 355 88

Figure S372.  Get High-res Image Gene #90: 'del_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.2' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0018

Table S373.  Gene #90: 'del_19p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
DEL PEAK 32(19P13.2) MUTATED 0 7 0
DEL PEAK 32(19P13.2) WILD-TYPE 277 147 70

Figure S373.  Get High-res Image Gene #90: 'del_19p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.2' versus 'MRNASEQ_CNMF'

P value = 0.00158 (Fisher's exact test), Q value = 0.007

Table S374.  Gene #90: 'del_19p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
DEL PEAK 32(19P13.2) MUTATED 0 7 0 0
DEL PEAK 32(19P13.2) WILD-TYPE 168 148 59 117

Figure S374.  Get High-res Image Gene #90: 'del_19p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00103 (Fisher's exact test), Q value = 0.0049

Table S375.  Gene #90: 'del_19p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
DEL PEAK 32(19P13.2) MUTATED 0 7 0 0 0
DEL PEAK 32(19P13.2) WILD-TYPE 105 127 86 96 78

Figure S375.  Get High-res Image Gene #90: 'del_19p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.2' versus 'MIRSEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0015

Table S376.  Gene #90: 'del_19p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
DEL PEAK 32(19P13.2) MUTATED 0 7 0
DEL PEAK 32(19P13.2) WILD-TYPE 182 144 167

Figure S376.  Get High-res Image Gene #90: 'del_19p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00063

Table S377.  Gene #90: 'del_19p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
DEL PEAK 32(19P13.2) MUTATED 0 7 0
DEL PEAK 32(19P13.2) WILD-TYPE 179 121 193

Figure S377.  Get High-res Image Gene #90: 'del_19p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00041

Table S378.  Gene #90: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
DEL PEAK 32(19P13.2) MUTATED 0 7 0
DEL PEAK 32(19P13.2) WILD-TYPE 165 119 179

Figure S378.  Get High-res Image Gene #90: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.12' versus 'CN_CNMF'

P value = 0.00288 (Fisher's exact test), Q value = 0.011

Table S379.  Gene #91: 'del_19p13.12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 33(19P13.12) MUTATED 4 2 2
DEL PEAK 33(19P13.12) WILD-TYPE 52 354 87

Figure S379.  Get High-res Image Gene #91: 'del_19p13.12' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.12' versus 'METHLYATION_CNMF'

P value = 0.00423 (Fisher's exact test), Q value = 0.016

Table S380.  Gene #91: 'del_19p13.12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
DEL PEAK 33(19P13.12) MUTATED 1 7 0
DEL PEAK 33(19P13.12) WILD-TYPE 276 147 70

Figure S380.  Get High-res Image Gene #91: 'del_19p13.12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.12' versus 'MRNASEQ_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.037

Table S381.  Gene #91: 'del_19p13.12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
DEL PEAK 33(19P13.12) MUTATED 1 7 0 0
DEL PEAK 33(19P13.12) WILD-TYPE 167 148 59 117

Figure S381.  Get High-res Image Gene #91: 'del_19p13.12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00528 (Fisher's exact test), Q value = 0.019

Table S382.  Gene #91: 'del_19p13.12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
DEL PEAK 33(19P13.12) MUTATED 1 7 0 0 0
DEL PEAK 33(19P13.12) WILD-TYPE 104 127 86 96 78

Figure S382.  Get High-res Image Gene #91: 'del_19p13.12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.12' versus 'MIRSEQ_CNMF'

P value = 0.00121 (Fisher's exact test), Q value = 0.0055

Table S383.  Gene #91: 'del_19p13.12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
DEL PEAK 33(19P13.12) MUTATED 0 7 1
DEL PEAK 33(19P13.12) WILD-TYPE 182 144 166

Figure S383.  Get High-res Image Gene #91: 'del_19p13.12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19p13.12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.0025

Table S384.  Gene #91: 'del_19p13.12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
DEL PEAK 33(19P13.12) MUTATED 0 7 1
DEL PEAK 33(19P13.12) WILD-TYPE 179 121 192

Figure S384.  Get High-res Image Gene #91: 'del_19p13.12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.0037

Table S385.  Gene #91: 'del_19p13.12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
DEL PEAK 33(19P13.12) MUTATED 0 7 1
DEL PEAK 33(19P13.12) WILD-TYPE 165 119 178

Figure S385.  Get High-res Image Gene #91: 'del_19p13.12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q21.1' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0012

Table S386.  Gene #92: 'del_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 36(21Q21.1) MUTATED 6 2 1
DEL PEAK 36(21Q21.1) WILD-TYPE 50 354 88

Figure S386.  Get High-res Image Gene #92: 'del_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0228 (Fisher's exact test), Q value = 0.061

Table S387.  Gene #92: 'del_21q21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
DEL PEAK 36(21Q21.1) MUTATED 5 4 0
DEL PEAK 36(21Q21.1) WILD-TYPE 174 124 193

Figure S387.  Get High-res Image Gene #92: 'del_21q21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_21q21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0207 (Fisher's exact test), Q value = 0.057

Table S388.  Gene #92: 'del_21q21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
DEL PEAK 36(21Q21.1) MUTATED 6 2 0
DEL PEAK 36(21Q21.1) WILD-TYPE 159 124 179

Figure S388.  Get High-res Image Gene #92: 'del_21q21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q12.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S389.  Gene #93: 'del_22q12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 37(22Q12.3) MUTATED 13 0 77
DEL PEAK 37(22Q12.3) WILD-TYPE 43 356 12

Figure S389.  Get High-res Image Gene #93: 'del_22q12.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q12.3' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00034

Table S390.  Gene #93: 'del_22q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
DEL PEAK 37(22Q12.3) MUTATED 37 47 6
DEL PEAK 37(22Q12.3) WILD-TYPE 240 107 64

Figure S390.  Get High-res Image Gene #93: 'del_22q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q12.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S391.  Gene #93: 'del_22q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
DEL PEAK 37(22Q12.3) MUTATED 8 47 8 27
DEL PEAK 37(22Q12.3) WILD-TYPE 160 108 51 90

Figure S391.  Get High-res Image Gene #93: 'del_22q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q12.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S392.  Gene #93: 'del_22q12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
DEL PEAK 37(22Q12.3) MUTATED 9 42 13 24 2
DEL PEAK 37(22Q12.3) WILD-TYPE 96 92 73 72 76

Figure S392.  Get High-res Image Gene #93: 'del_22q12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q12.3' versus 'MIRSEQ_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0028

Table S393.  Gene #93: 'del_22q12.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
DEL PEAK 37(22Q12.3) MUTATED 24 43 23
DEL PEAK 37(22Q12.3) WILD-TYPE 158 108 144

Figure S393.  Get High-res Image Gene #93: 'del_22q12.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q12.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00063

Table S394.  Gene #93: 'del_22q12.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
DEL PEAK 37(22Q12.3) MUTATED 22 40 28
DEL PEAK 37(22Q12.3) WILD-TYPE 157 88 165

Figure S394.  Get High-res Image Gene #93: 'del_22q12.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q12.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0017

Table S395.  Gene #93: 'del_22q12.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 164 146
DEL PEAK 37(22Q12.3) MUTATED 17 24 41
DEL PEAK 37(22Q12.3) WILD-TYPE 143 140 105

Figure S395.  Get High-res Image Gene #93: 'del_22q12.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q12.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.0022

Table S396.  Gene #93: 'del_22q12.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
DEL PEAK 37(22Q12.3) MUTATED 22 37 23
DEL PEAK 37(22Q12.3) WILD-TYPE 143 89 156

Figure S396.  Get High-res Image Gene #93: 'del_22q12.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S397.  Gene #94: 'del_22q13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 38(22Q13.1) MUTATED 13 0 76
DEL PEAK 38(22Q13.1) WILD-TYPE 43 356 13

Figure S397.  Get High-res Image Gene #94: 'del_22q13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S398.  Gene #94: 'del_22q13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
DEL PEAK 38(22Q13.1) MUTATED 36 47 6
DEL PEAK 38(22Q13.1) WILD-TYPE 241 107 64

Figure S398.  Get High-res Image Gene #94: 'del_22q13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S399.  Gene #94: 'del_22q13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
DEL PEAK 38(22Q13.1) MUTATED 8 47 8 26
DEL PEAK 38(22Q13.1) WILD-TYPE 160 108 51 91

Figure S399.  Get High-res Image Gene #94: 'del_22q13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S400.  Gene #94: 'del_22q13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
DEL PEAK 38(22Q13.1) MUTATED 9 42 13 23 2
DEL PEAK 38(22Q13.1) WILD-TYPE 96 92 73 73 76

Figure S400.  Get High-res Image Gene #94: 'del_22q13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.1' versus 'MIRSEQ_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0024

Table S401.  Gene #94: 'del_22q13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
DEL PEAK 38(22Q13.1) MUTATED 23 43 23
DEL PEAK 38(22Q13.1) WILD-TYPE 159 108 144

Figure S401.  Get High-res Image Gene #94: 'del_22q13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00048

Table S402.  Gene #94: 'del_22q13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
DEL PEAK 38(22Q13.1) MUTATED 21 40 28
DEL PEAK 38(22Q13.1) WILD-TYPE 158 88 165

Figure S402.  Get High-res Image Gene #94: 'del_22q13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0012

Table S403.  Gene #94: 'del_22q13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 164 146
DEL PEAK 38(22Q13.1) MUTATED 17 23 41
DEL PEAK 38(22Q13.1) WILD-TYPE 143 141 105

Figure S403.  Get High-res Image Gene #94: 'del_22q13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.0018

Table S404.  Gene #94: 'del_22q13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
DEL PEAK 38(22Q13.1) MUTATED 22 37 22
DEL PEAK 38(22Q13.1) WILD-TYPE 143 89 157

Figure S404.  Get High-res Image Gene #94: 'del_22q13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S405.  Gene #95: 'del_22q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 39(22Q13.2) MUTATED 13 0 76
DEL PEAK 39(22Q13.2) WILD-TYPE 43 356 13

Figure S405.  Get High-res Image Gene #95: 'del_22q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S406.  Gene #95: 'del_22q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
DEL PEAK 39(22Q13.2) MUTATED 36 47 6
DEL PEAK 39(22Q13.2) WILD-TYPE 241 107 64

Figure S406.  Get High-res Image Gene #95: 'del_22q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S407.  Gene #95: 'del_22q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
DEL PEAK 39(22Q13.2) MUTATED 8 47 8 26
DEL PEAK 39(22Q13.2) WILD-TYPE 160 108 51 91

Figure S407.  Get High-res Image Gene #95: 'del_22q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S408.  Gene #95: 'del_22q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
DEL PEAK 39(22Q13.2) MUTATED 9 42 13 23 2
DEL PEAK 39(22Q13.2) WILD-TYPE 96 92 73 73 76

Figure S408.  Get High-res Image Gene #95: 'del_22q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.2' versus 'MIRSEQ_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0027

Table S409.  Gene #95: 'del_22q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
DEL PEAK 39(22Q13.2) MUTATED 23 43 23
DEL PEAK 39(22Q13.2) WILD-TYPE 159 108 144

Figure S409.  Get High-res Image Gene #95: 'del_22q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00041

Table S410.  Gene #95: 'del_22q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
DEL PEAK 39(22Q13.2) MUTATED 21 40 28
DEL PEAK 39(22Q13.2) WILD-TYPE 158 88 165

Figure S410.  Get High-res Image Gene #95: 'del_22q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0012

Table S411.  Gene #95: 'del_22q13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 164 146
DEL PEAK 39(22Q13.2) MUTATED 17 23 41
DEL PEAK 39(22Q13.2) WILD-TYPE 143 141 105

Figure S411.  Get High-res Image Gene #95: 'del_22q13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.0018

Table S412.  Gene #95: 'del_22q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
DEL PEAK 39(22Q13.2) MUTATED 22 37 22
DEL PEAK 39(22Q13.2) WILD-TYPE 143 89 157

Figure S412.  Get High-res Image Gene #95: 'del_22q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S413.  Gene #96: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 40(22Q13.32) MUTATED 13 1 76
DEL PEAK 40(22Q13.32) WILD-TYPE 43 355 13

Figure S413.  Get High-res Image Gene #96: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S414.  Gene #96: 'del_22q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
DEL PEAK 40(22Q13.32) MUTATED 36 48 6
DEL PEAK 40(22Q13.32) WILD-TYPE 241 106 64

Figure S414.  Get High-res Image Gene #96: 'del_22q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S415.  Gene #96: 'del_22q13.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 168 155 59 117
DEL PEAK 40(22Q13.32) MUTATED 8 48 8 26
DEL PEAK 40(22Q13.32) WILD-TYPE 160 107 51 91

Figure S415.  Get High-res Image Gene #96: 'del_22q13.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S416.  Gene #96: 'del_22q13.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 105 134 86 96 78
DEL PEAK 40(22Q13.32) MUTATED 9 43 13 23 2
DEL PEAK 40(22Q13.32) WILD-TYPE 96 91 73 73 76

Figure S416.  Get High-res Image Gene #96: 'del_22q13.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0011

Table S417.  Gene #96: 'del_22q13.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 151 167
DEL PEAK 40(22Q13.32) MUTATED 23 44 23
DEL PEAK 40(22Q13.32) WILD-TYPE 159 107 144

Figure S417.  Get High-res Image Gene #96: 'del_22q13.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00034

Table S418.  Gene #96: 'del_22q13.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 128 193
DEL PEAK 40(22Q13.32) MUTATED 21 41 28
DEL PEAK 40(22Q13.32) WILD-TYPE 158 87 165

Figure S418.  Get High-res Image Gene #96: 'del_22q13.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0012

Table S419.  Gene #96: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 164 146
DEL PEAK 40(22Q13.32) MUTATED 17 24 41
DEL PEAK 40(22Q13.32) WILD-TYPE 143 140 105

Figure S419.  Get High-res Image Gene #96: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.0013

Table S420.  Gene #96: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 126 179
DEL PEAK 40(22Q13.32) MUTATED 22 38 22
DEL PEAK 40(22Q13.32) WILD-TYPE 143 88 157

Figure S420.  Get High-res Image Gene #96: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xq23' versus 'CN_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.035

Table S421.  Gene #97: 'del_xq23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 41(XQ23) MUTATED 3 1 0
DEL PEAK 41(XQ23) WILD-TYPE 53 355 89

Figure S421.  Get High-res Image Gene #97: 'del_xq23' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq23' versus 'METHLYATION_CNMF'

P value = 0.0462 (Fisher's exact test), Q value = 0.11

Table S422.  Gene #97: 'del_xq23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
DEL PEAK 41(XQ23) MUTATED 0 3 1
DEL PEAK 41(XQ23) WILD-TYPE 277 151 69

Figure S422.  Get High-res Image Gene #97: 'del_xq23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq22.3' versus 'CN_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.034

Table S423.  Gene #98: 'del_xq22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 356 89
DEL PEAK 42(XQ22.3) MUTATED 3 1 0
DEL PEAK 42(XQ22.3) WILD-TYPE 53 355 89

Figure S423.  Get High-res Image Gene #98: 'del_xq22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq22.3' versus 'METHLYATION_CNMF'

P value = 0.0445 (Fisher's exact test), Q value = 0.11

Table S424.  Gene #98: 'del_xq22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 277 154 70
DEL PEAK 42(XQ22.3) MUTATED 0 3 1
DEL PEAK 42(XQ22.3) WILD-TYPE 277 151 69

Figure S424.  Get High-res Image Gene #98: 'del_xq22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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/THCA-TP/15101913/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/THCA-TP/15125146/THCA-TP.transferedmergedcluster.txt

  • Number of patients = 501

  • Number of significantly focal cnvs = 98

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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