Correlation between copy number variations of arm-level result and molecular subtypes
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1N015XH
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1N015XH
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 80 arm-level events and 12 molecular subtypes across 528 patients, 443 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • 1q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 2p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 2q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • 4p gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 4q gain cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 5q gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 6p gain cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

  • 7p gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

  • 8p gain cnv correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • 9p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 9q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 10p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 10q gain cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 11p gain cnv correlated to 'MRNASEQ_CNMF'.

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

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

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

  • 14q gain cnv correlated to 'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 15q gain cnv correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.

  • 16p gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 16q gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 17p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 17q gain cnv correlated to 'MRNA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 18p gain cnv correlated to 'METHLYATION_CNMF'.

  • 18q gain cnv correlated to 'METHLYATION_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 19q gain cnv correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 20p gain 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'.

  • 20q gain 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'.

  • 21q gain cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 22q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CNMF'.

  • xp gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • xq gain cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.

  • 1p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

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

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

  • 4p loss cnv correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 4q loss cnv correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 5p loss cnv correlated to 'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 5q loss cnv correlated to 'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 6p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 6q loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 8q loss cnv correlated to 'METHLYATION_CNMF' and 'RPPA_CNMF'.

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

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

  • 10p loss cnv correlated to 'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 10q loss cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 11p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CHIERARCHICAL'.

  • 11q loss cnv correlated to 'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 12p loss cnv correlated to 'CN_CNMF'.

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

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

  • 15q loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 16p loss cnv correlated to 'RPPA_CHIERARCHICAL' and 'MIRSEQ_CHIERARCHICAL'.

  • 16q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

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

  • 17q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 18p loss 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'.

  • 18q loss 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'.

  • 19p loss cnv correlated to 'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 20p loss cnv correlated to 'MIRSEQ_CNMF'.

  • 21q loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 443 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
3q gain 60 (11%) 468 0.0214
(0.0564) 		0.0305
(0.0741) 		0.0103
(0.0316) 		4e-05
(0.00028) 		1e-05
(8.42e-05) 		2e-05
(0.000155) 		4e-05
(0.00028) 		2e-05
(0.000155) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		0.00019
(0.00107) 		0.405
(0.548)
12p gain 121 (23%) 407 0.0219
(0.0572) 		0.0328
(0.0775) 		4e-05
(0.00028) 		0.00016
(0.00092) 		1e-05
(8.42e-05) 		3e-05
(0.000218) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		0.00176
(0.00725) 		0.204
(0.33)
12q gain 122 (23%) 406 0.0211
(0.0563) 		0.0329
(0.0775) 		3e-05
(0.000218) 		0.00014
(0.000815) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		0.00236
(0.00932) 		0.264
(0.397)
3p loss 379 (72%) 149 0.00612
(0.0205) 		0.0103
(0.0316) 		1e-05
(8.42e-05) 		0.00942
(0.0296) 		0.0113
(0.0338) 		0.00016
(0.00092) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		0.0149
(0.0432) 		0.00419
(0.0153) 		0.0236
(0.0606) 		0.77
(0.891)
6p loss 100 (19%) 428 0.0313
(0.0756) 		0.0142
(0.0415) 		1e-05
(8.42e-05) 		0.00315
(0.0121) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		0.173
(0.288) 		0.0304
(0.074)
9p loss 149 (28%) 379 0.00706
(0.023) 		0.0362
(0.0829) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		0.0109
(0.033) 		0.0593
(0.125)
14q loss 216 (41%) 312 1e-05
(8.42e-05) 		6e-05
(0.000392) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		0.0131
(0.0388) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		0.256
(0.39) 		0.0441
(0.0978)
22q loss 39 (7%) 489 0.0215
(0.0565) 		0.0013
(0.00557) 		0.0175
(0.0489) 		0.00998
(0.0311) 		0.00041
(0.00208) 		0.0211
(0.0563) 		1e-05
(8.42e-05) 		2e-05
(0.000155) 		5e-05
(0.000343) 		0.00108
(0.00478) 		0.0384
(0.0867) 		0.253
(0.389)
20p gain 112 (21%) 416 0.243
(0.377) 		0.117
(0.21) 		1e-05
(8.42e-05) 		8e-05
(0.000505) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		4e-05
(0.00028) 		0.0361
(0.0828)
20q gain 115 (22%) 413 0.096
(0.18) 		0.0739
(0.148) 		1e-05
(8.42e-05) 		6e-05
(0.000392) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		3e-05
(0.000218) 		0.0209
(0.0562)
1q loss 37 (7%) 491 0.0381
(0.0863) 		0.0115
(0.0341) 		0.00011
(0.00066) 		0.0108
(0.0327) 		0.0184
(0.0507) 		0.00419
(0.0153) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		0.0322
(0.0767) 		0.0102
(0.0316) 		0.276
(0.412) 		0.62
(0.753)
2p loss 14 (3%) 514 8e-05
(0.000505) 		0.00045
(0.00226) 		0.0336
(0.0786) 		0.0221
(0.0578) 		0.00062
(0.00298) 		0.0002
(0.00111) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		7e-05
(0.000448) 		1e-05
(8.42e-05) 		0.159
(0.268) 		0.376
(0.521)
2q loss 14 (3%) 514 0.0004
(0.00204) 		0.00083
(0.00381) 		0.0102
(0.0316) 		0.0294
(0.0721) 		0.00344
(0.0131) 		0.00017
(0.000966) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		0.0001
(0.000604) 		1e-05
(8.42e-05) 		0.16
(0.27) 		0.378
(0.523)
9q loss 151 (29%) 377 0.0191
(0.052) 		0.0582
(0.123) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		0.00256
(0.0101) 		0.0959
(0.18)
13q loss 70 (13%) 458 0.00662
(0.0218) 		0.0462
(0.102) 		0.024
(0.0612) 		0.00094
(0.00424) 		1e-05
(8.42e-05) 		2e-05
(0.000155) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		0.19
(0.312) 		0.43
(0.571)
18p loss 93 (18%) 435 0.0915
(0.174) 		0.459
(0.598) 		0.00056
(0.00272) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		0.00084
(0.00384) 		0.00667
(0.0219)
18q loss 95 (18%) 433 0.075
(0.149) 		0.221
(0.351) 		0.00034
(0.00177) 		6e-05
(0.000392) 		1e-05
(8.42e-05) 		2e-05
(0.000155) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		0.00927
(0.0293) 		0.0322
(0.0767)
8q gain 61 (12%) 467 0.334
(0.474) 		0.104
(0.192) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		6e-05
(0.000392) 		2e-05
(0.000155) 		0.775
(0.896)
1p loss 60 (11%) 468 0.00363
(0.0137) 		0.00568
(0.0193) 		0.00569
(0.0193) 		0.433
(0.571) 		0.0135
(0.0397) 		0.0108
(0.0327) 		3e-05
(0.000218) 		6e-05
(0.000392) 		0.00315
(0.0121) 		0.0249
(0.0634) 		0.0663
(0.136) 		0.314
(0.454)
17p loss 46 (9%) 482 0.00021
(0.00115) 		0.00017
(0.000966) 		0.0243
(0.0619) 		0.0552
(0.118) 		0.00056
(0.00272) 		3e-05
(0.000218) 		2e-05
(0.000155) 		1e-05
(8.42e-05) 		2e-05
(0.000155) 		9e-05
(0.000561) 		0.346
(0.486) 		0.17
(0.285)
xq loss 45 (9%) 483 0.0408
(0.0915) 		0.0187
(0.0512) 		0.0002
(0.00111) 		0.00328
(0.0126) 		0.612
(0.744) 		0.033
(0.0776) 		0.0141
(0.041) 		0.0418
(0.0936) 		0.0144
(0.0417) 		0.00163
(0.00677) 		0.292
(0.428) 		0.333
(0.472)
7q gain 173 (33%) 355 0.646
(0.773) 		0.859
(0.97) 		1e-05
(8.42e-05) 		0.0468
(0.103) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		0.0002
(0.00111) 		0.00439
(0.0159) 		0.0165
(0.0466) 		0.026
(0.0657) 		0.13
(0.229) 		0.717
(0.841)
8p gain 31 (6%) 497 0.0724
(0.145) 		0.00109
(0.0048) 		0.00044
(0.00222) 		1e-05
(8.42e-05) 		0.0001
(0.000604) 		3e-05
(0.000218) 		4e-05
(0.00028) 		0.00179
(0.00728) 		0.0172
(0.0481) 		0.289
(0.426)
6q loss 128 (24%) 400 0.108
(0.196) 		0.0521
(0.112) 		1e-05
(8.42e-05) 		0.0842
(0.164) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		6e-05
(0.000392) 		1e-05
(8.42e-05) 		0.00172
(0.00712) 		0.0001
(0.000604) 		0.292
(0.428) 		0.031
(0.075)
21q loss 55 (10%) 473 0.0328
(0.0775) 		0.0894
(0.171) 		0.00069
(0.00326) 		0.0658
(0.135) 		0.0008
(0.00371) 		3e-05
(0.000218) 		0.00081
(0.00374) 		0.00014
(0.000815) 		0.00046
(0.00229) 		0.0049
(0.0174) 		0.774
(0.896) 		0.93
(1.00)
19p gain 51 (10%) 477 0.332
(0.472) 		0.483
(0.619) 		0.00439
(0.0159) 		0.00094
(0.00424) 		0.0013
(0.00557) 		0.0124
(0.0368) 		0.00572
(0.0193) 		0.00073
(0.00344) 		0.00145
(0.00616) 		0.225
(0.356) 		0.875
(0.985) 		0.711
(0.834)
15q loss 35 (7%) 493 0.133
(0.234) 		0.331
(0.471) 		0.005
(0.0176) 		0.155
(0.263) 		0.0292
(0.0719) 		0.016
(0.0457) 		7e-05
(0.000448) 		1e-05
(8.42e-05) 		0.00701
(0.0229) 		0.00654
(0.0216) 		0.0628
(0.131) 		0.0989
(0.185)
17q loss 28 (5%) 500 0.00151
(0.0063) 		0.00052
(0.00256) 		0.0537
(0.115) 		0.0744
(0.148) 		0.155
(0.263) 		0.00273
(0.0107) 		0.0001
(0.000604) 		1e-05
(8.42e-05) 		0.00031
(0.00164) 		0.00496
(0.0175) 		0.532
(0.672) 		0.424
(0.567)
xp loss 45 (9%) 483 0.0261
(0.0657) 		0.0192
(0.0521) 		0.00021
(0.00115) 		0.0228
(0.0589) 		0.551
(0.687) 		0.189
(0.311) 		0.00447
(0.0161) 		0.0214
(0.0564) 		0.129
(0.228) 		0.00101
(0.00453) 		0.0788
(0.155) 		0.243
(0.377)
1p gain 22 (4%) 506 1
(1.00) 		0.726
(0.85) 		0.00125
(0.00541) 		0.004
(0.0147) 		0.0958
(0.18) 		0.521
(0.66) 		0.0326
(0.0775) 		0.00514
(0.0179) 		5e-05
(0.000343) 		0.0154
(0.0444) 		0.753
(0.878) 		0.315
(0.454)
4p gain 13 (2%) 515 0.0481
(0.105) 		0.16
(0.27) 		0.038
(0.0863) 		3e-05
(0.000218) 		0.00377
(0.014) 		0.00057
(0.00275) 		0.00552
(0.019) 		0.0979
(0.184)
7p gain 173 (33%) 355 0.645
(0.772) 		0.858
(0.97) 		1e-05
(8.42e-05) 		0.0643
(0.133) 		1e-05
(8.42e-05) 		1e-05
(8.42e-05) 		0.00029
(0.00155) 		0.00802
(0.0256) 		0.0381
(0.0863) 		0.105
(0.192) 		0.198
(0.323) 		0.846
(0.959)
14q gain 16 (3%) 512 0.79
(0.906) 		0.573
(0.704) 		0.0861
(0.166) 		0.205
(0.332) 		0.00179
(0.00728) 		0.034
(0.0793) 		0.0392
(0.0884) 		0.00024
(0.00129) 		0.028
(0.0692) 		0.0473
(0.104)
19q gain 57 (11%) 471 0.151
(0.257) 		0.222
(0.352) 		0.0558
(0.119) 		0.00014
(0.000815) 		1e-05
(8.42e-05) 		0.00079
(0.00368) 		0.00091
(0.00414) 		0.00012
(0.000711) 		7e-05
(0.000448) 		0.0782
(0.154) 		0.673
(0.798) 		0.361
(0.503)
xp gain 32 (6%) 496 1
(1.00) 		0.525
(0.664) 		0.0421
(0.0939) 		0.256
(0.39) 		9e-05
(0.000561) 		0.00111
(0.00487) 		0.0355
(0.0817) 		0.00077
(0.00361) 		0.0472
(0.104) 		0.0939
(0.177) 		0.263
(0.396) 		0.916
(1.00)
4q loss 65 (12%) 463 0.431
(0.571) 		0.782
(0.9) 		0.203
(0.329) 		0.00387
(0.0143) 		0.00033
(0.00174) 		0.0162
(0.0459) 		0.00377
(0.014) 		5e-05
(0.000343) 		0.236
(0.369) 		0.0715
(0.145) 		0.46
(0.598) 		0.0262
(0.0657)
1q gain 51 (10%) 477 0.468
(0.604) 		0.899
(1.00) 		1e-05
(8.42e-05) 		0.0336
(0.0786) 		0.149
(0.256) 		0.208
(0.335) 		0.00036
(0.00187) 		0.00185
(0.00746) 		2e-05
(0.000155) 		0.15
(0.257) 		0.506
(0.645) 		1
(1.00)
3p gain 20 (4%) 508 0.0656
(0.135) 		0.434
(0.572) 		0.1
(0.187) 		0.118
(0.212) 		0.107
(0.195) 		0.00012
(0.000711) 		0.00177
(0.00726) 		0.00069
(0.00326) 		0.0001
(0.000604) 		0.00372
(0.0139) 		0.538
(0.676) 		0.655
(0.782)
4q gain 13 (2%) 515 0.0356
(0.0817) 		0.0846
(0.164) 		0.269
(0.401) 		0.0015
(0.00629) 		0.00372
(0.0139) 		0.00441
(0.0159) 		0.00574
(0.0193) 		0.185
(0.305)
5p gain 191 (36%) 337 0.78
(0.899) 		0.923
(1.00) 		1e-05
(8.42e-05) 		0.617
(0.75) 		0.0265
(0.0663) 		0.967
(1.00) 		0.0171
(0.0481) 		0.0188
(0.0515) 		0.885
(0.993) 		0.323
(0.464) 		0.0209
(0.0562) 		0.892
(0.998)
10p gain 16 (3%) 512 0.045
(0.0994) 		0.591
(0.721) 		0.0657
(0.135) 		0.115
(0.209) 		0.00131
(0.00559) 		0.00049
(0.00242) 		0.0342
(0.0794) 		0.0394
(0.0887)
16p gain 107 (20%) 421 0.341
(0.483) 		0.38
(0.525) 		1e-05
(8.42e-05) 		0.376
(0.521) 		0.0203
(0.0546) 		0.178
(0.294) 		0.00034
(0.00177) 		0.00459
(0.0164) 		0.0509
(0.11) 		0.00905
(0.0287) 		0.257
(0.391) 		0.407
(0.549)
16q gain 99 (19%) 429 0.346
(0.486) 		0.348
(0.487) 		2e-05
(0.000155) 		0.14
(0.243) 		0.00559
(0.0192) 		0.0918
(0.174) 		0.00067
(0.0032) 		0.0162
(0.0459) 		0.0072
(0.0234) 		0.0804
(0.158) 		0.431
(0.571) 		0.457
(0.596)
17q gain 33 (6%) 495 0.101
(0.189) 		0.0262
(0.0657) 		0.257
(0.39) 		0.756
(0.88) 		0.117
(0.211) 		0.228
(0.358) 		6e-05
(0.000392) 		0.0015
(0.00629) 		0.0184
(0.0506) 		0.281
(0.417) 		0.00393
(0.0145) 		0.694
(0.816)
5p loss 8 (2%) 520 0.673
(0.798) 		0.255
(0.39) 		0.00223
(0.00885) 		0.026
(0.0657) 		0.104
(0.192) 		0.0052
(0.0181) 		0.0236
(0.0606) 		0.0274
(0.0681) 		0.482
(0.619) 		0.875
(0.985)
10q loss 89 (17%) 439 0.412
(0.554) 		0.402
(0.548) 		0.0293
(0.072) 		0.0844
(0.164) 		0.816
(0.929) 		0.0213
(0.0564) 		0.269
(0.401) 		0.00193
(0.00769) 		0.00261
(0.0102) 		0.00572
(0.0193) 		0.93
(1.00) 		0.516
(0.656)
11q loss 23 (4%) 505 0.217
(0.347) 		0.376
(0.521) 		0.0684
(0.139) 		0.143
(0.248) 		0.164
(0.275) 		0.0102
(0.0316) 		0.00624
(0.0208) 		0.00037
(0.00191) 		0.0164
(0.0464) 		0.00976
(0.0306) 		0.381
(0.525) 		0.57
(0.702)
19p loss 11 (2%) 517 0.674
(0.798) 		0.0642
(0.133) 		0.00022
(0.00119) 		0.00193
(0.00769) 		0.135
(0.236) 		0.0113
(0.0338) 		0.027
(0.0672) 		0.00537
(0.0185) 		0.0573
(0.121) 		0.104
(0.192)
13q gain 22 (4%) 506 0.0108
(0.0327) 		0.0367
(0.0837) 		0.227
(0.357) 		0.431
(0.571) 		0.0488
(0.106) 		0.122
(0.218) 		0.0279
(0.0691) 		0.536
(0.675) 		0.198
(0.323) 		0.343
(0.484)
17p gain 26 (5%) 502 0.023
(0.0595) 		0.00535
(0.0185) 		0.57
(0.702) 		0.888
(0.995) 		0.132
(0.232) 		0.102
(0.189) 		0.00102
(0.00455) 		0.00507
(0.0178) 		0.149
(0.256) 		0.411
(0.554) 		0.063
(0.131) 		0.807
(0.921)
21q gain 50 (9%) 478 0.286
(0.422) 		0.207
(0.334) 		0.147
(0.255) 		0.00337
(0.0129) 		0.162
(0.272) 		0.0624
(0.131) 		0.00105
(0.00467) 		0.00314
(0.0121) 		0.00802
(0.0256) 		0.119
(0.212) 		0.292
(0.428) 		0.226
(0.356)
4p loss 72 (14%) 456 0.39
(0.536) 		0.817
(0.929) 		0.397
(0.543) 		0.00457
(0.0164) 		0.0004
(0.00204) 		0.0587
(0.123) 		0.0565
(0.12) 		0.00146
(0.00617) 		0.282
(0.418) 		0.102
(0.189) 		0.0722
(0.145) 		0.044
(0.0978)
5q loss 7 (1%) 521 0.4
(0.547) 		0.435
(0.573) 		0.0103
(0.0316) 		0.0763
(0.151) 		0.155
(0.263) 		0.00632
(0.021) 		0.049
(0.107) 		0.0317
(0.0761) 		0.484
(0.62) 		0.874
(0.985)
8p loss 137 (26%) 391 0.15
(0.256) 		0.165
(0.276) 		0.0491
(0.107) 		0.477
(0.614) 		0.0724
(0.145) 		0.978
(1.00) 		0.032
(0.0767) 		0.00125
(0.00541) 		0.113
(0.204) 		0.0179
(0.0497) 		0.253
(0.389) 		0.342
(0.483)
10p loss 68 (13%) 460 0.263
(0.396) 		0.402
(0.548) 		0.183
(0.303) 		0.364
(0.507) 		0.394
(0.541) 		0.0177
(0.0491) 		0.0683
(0.139) 		0.00055
(0.00269) 		0.00739
(0.0238) 		0.0309
(0.0749) 		0.903
(1.00) 		0.418
(0.562)
2p gain 78 (15%) 450 0.405
(0.548) 		0.267
(0.4) 		0.00046
(0.00229) 		0.449
(0.587) 		0.0724
(0.145) 		0.778
(0.898) 		0.789
(0.906) 		0.0111
(0.0332) 		0.685
(0.809) 		0.0342
(0.0794) 		0.606
(0.738) 		0.366
(0.509)
2q gain 79 (15%) 449 0.402
(0.548) 		0.268
(0.401) 		0.00122
(0.00532) 		0.623
(0.755) 		0.18
(0.297) 		0.669
(0.798) 		0.798
(0.913) 		0.018
(0.0498) 		0.638
(0.766) 		0.0048
(0.0171) 		0.728
(0.851) 		0.358
(0.5)
5q gain 210 (40%) 318 0.382
(0.525) 		0.626
(0.757) 		1e-05
(8.42e-05) 		0.689
(0.812) 		0.00742
(0.0238) 		0.329
(0.471) 		0.0885
(0.17) 		0.0523
(0.113) 		0.817
(0.929) 		0.427
(0.569) 		0.0333
(0.0783) 		0.79
(0.906)
10q gain 12 (2%) 516 0.11
(0.2) 		0.262
(0.396) 		0.0578
(0.122) 		0.0913
(0.174) 		0.00587
(0.0197) 		0.00183
(0.00741) 		0.0135
(0.0397) 		0.172
(0.287)
3q loss 102 (19%) 426 0.859
(0.97) 		0.22
(0.351) 		0.00021
(0.00115) 		0.353
(0.494) 		0.203
(0.329) 		0.0704
(0.143) 		0.0926
(0.175) 		0.00658
(0.0217) 		0.0138
(0.0403) 		0.938
(1.00) 		0.902
(1.00) 		0.199
(0.324)
9p gain 14 (3%) 514 0.00189
(0.00759) 		0.235
(0.368) 		0.444
(0.583) 		0.148
(0.255) 		0.566
(0.702) 		0.00982
(0.0307) 		0.449
(0.587) 		0.247
(0.382) 		1
(1.00) 		1
(1.00)
9q gain 13 (2%) 515 0.0215
(0.0565) 		0.687
(0.811) 		0.3
(0.438) 		0.0609
(0.128) 		0.916
(1.00) 		0.0157
(0.045) 		0.286
(0.422) 		0.212
(0.34) 		1
(1.00) 		1
(1.00)
15q gain 26 (5%) 502 1
(1.00) 		0.115
(0.209) 		0.00028
(0.0015) 		0.135
(0.236) 		0.0918
(0.174) 		0.00355
(0.0135) 		0.454
(0.592) 		0.105
(0.192) 		0.636
(0.765) 		0.315
(0.454) 		0.678
(0.802) 		0.285
(0.422)
22q gain 40 (8%) 488 0.42
(0.564) 		0.22
(0.351) 		0.0853
(0.165) 		0.258
(0.391) 		0.538
(0.676) 		0.293
(0.429) 		0.0826
(0.162) 		0.0159
(0.0456) 		0.0196
(0.0529) 		0.795
(0.911) 		0.914
(1.00) 		0.568
(0.702)
xq gain 31 (6%) 497 0.251
(0.387) 		0.7
(0.822) 		0.0111
(0.0332) 		0.628
(0.757) 		0.0225
(0.0585) 		0.0685
(0.139) 		0.224
(0.354) 		0.1
(0.187) 		0.549
(0.686) 		0.545
(0.682) 		0.43
(0.571) 		0.956
(1.00)
8q loss 65 (12%) 463 0.131
(0.23) 		0.125
(0.222) 		0.468
(0.604) 		0.00723
(0.0234) 		0.0214
(0.0564) 		0.435
(0.572) 		0.988
(1.00) 		0.199
(0.324) 		0.302
(0.441) 		0.545
(0.682) 		0.739
(0.863) 		0.331
(0.471)
11p loss 18 (3%) 510 0.571
(0.702) 		0.249
(0.385) 		0.437
(0.574) 		0.104
(0.192) 		0.0659
(0.135) 		0.0276
(0.0684) 		0.171
(0.285) 		0.0344
(0.0797) 		0.382
(0.525) 		0.569
(0.702)
16p loss 10 (2%) 518 0.483
(0.619) 		0.67
(0.798) 		0.126
(0.223) 		0.0493
(0.107) 		0.243
(0.377) 		0.0626
(0.131) 		0.258
(0.391) 		0.0425
(0.0947) 		0.152
(0.259) 		0.314
(0.454)
16q loss 16 (3%) 512 0.019
(0.0517) 		0.417
(0.56) 		0.295
(0.431) 		0.429
(0.571) 		0.0836
(0.163) 		0.0878
(0.169) 		0.189
(0.311) 		0.0317
(0.0761) 		0.15
(0.256) 		0.278
(0.413)
6p gain 11 (2%) 517 0.304
(0.443) 		0.643
(0.77) 		0.217
(0.347) 		0.952
(1.00) 		0.925
(1.00) 		0.983
(1.00) 		0.638
(0.766) 		0.0159
(0.0456) 		0.628
(0.757) 		0.576
(0.706)
11p gain 31 (6%) 497 0.255
(0.39) 		0.672
(0.798) 		0.134
(0.235) 		0.475
(0.612) 		0.0729
(0.146) 		0.509
(0.648) 		0.0345
(0.0797) 		0.237
(0.37) 		0.141
(0.244) 		0.564
(0.7) 		0.541
(0.679) 		0.927
(1.00)
18p gain 25 (5%) 503 0.403
(0.548) 		0.0768
(0.152) 		0.532
(0.672) 		0.0226
(0.0586) 		0.903
(1.00) 		0.523
(0.663) 		0.221
(0.351) 		0.421
(0.564) 		0.278
(0.413) 		0.345
(0.485) 		0.331
(0.471) 		0.0784
(0.155)
18q gain 25 (5%) 503 0.405
(0.548) 		0.0751
(0.149) 		0.763
(0.884) 		0.0298
(0.0728) 		0.763
(0.884) 		0.549
(0.686) 		0.47
(0.607) 		0.421
(0.564) 		0.552
(0.687) 		0.342
(0.483) 		0.328
(0.47) 		0.0806
(0.158)
12p loss 4 (1%) 524 0.00899
(0.0286) 		0.603
(0.736) 		0.467
(0.604) 		0.403
(0.548) 		0.0908
(0.174)
20p loss 8 (2%) 520 0.235
(0.367) 		1
(1.00) 		0.254
(0.39) 		0.495
(0.632) 		0.117
(0.21) 		0.233
(0.365) 		0.0237
(0.0606) 		0.204
(0.33)
6q gain 9 (2%) 519 0.0548
(0.118) 		0.671
(0.798) 		0.107
(0.196) 		0.809
(0.923) 		0.983
(1.00) 		0.913
(1.00) 		0.806
(0.921) 		0.0562
(0.12) 		0.628
(0.757) 		0.576
(0.706)
11q gain 29 (5%) 499 0.486
(0.621) 		0.906
(1.00) 		0.0853
(0.165) 		0.31
(0.45) 		0.139
(0.242) 		0.829
(0.941) 		0.118
(0.212) 		0.571
(0.702) 		0.563
(0.7) 		0.887
(0.994) 		0.754
(0.879) 		0.759
(0.882)
12q loss 4 (1%) 524 0.123
(0.219) 		0.214
(0.343) 		0.88
(0.989) 		0.317
(0.455) 		1
(1.00) 		0.568
(0.702) 		0.465
(0.603)
19q loss 4 (1%) 524 0.578
(0.706) 		0.263
(0.396) 		0.253
(0.389) 		0.635
(0.765) 		0.511
(0.65) 		0.317
(0.455) 		0.175
(0.29)
20q loss 3 (1%) 525 0.464
(0.603) 		0.307
(0.446) 		0.155
(0.263) 		0.175
(0.29) 		0.119
(0.212)
'1p gain' versus 'CN_CNMF'

P value = 0.00125 (Fisher's exact test), Q value = 0.0054

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
1P GAIN MUTATED 1 2 15 4 0 0
1P GAIN WILD-TYPE 60 78 141 78 80 69

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 0.004 (Fisher's exact test), Q value = 0.015

Table S2.  Gene #1: '1p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
1P GAIN MUTATED 0 6 5 0
1P GAIN WILD-TYPE 67 64 91 81

Figure S2.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p gain' versus 'MRNASEQ_CNMF'

P value = 0.0326 (Fisher's exact test), Q value = 0.078

Table S3.  Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
1P GAIN MUTATED 2 2 4 12 1
1P GAIN WILD-TYPE 79 168 77 141 39

Figure S3.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00514 (Fisher's exact test), Q value = 0.018

Table S4.  Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
1P GAIN MUTATED 1 1 4 11 4 0
1P GAIN WILD-TYPE 116 32 179 121 31 25

Figure S4.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00034

Table S5.  Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
1P GAIN MUTATED 0 2 3 15 2
1P GAIN WILD-TYPE 91 55 183 104 55

Figure S5.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0154 (Fisher's exact test), Q value = 0.044

Table S6.  Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
1P GAIN MUTATED 10 3 9
1P GAIN WILD-TYPE 163 206 119

Figure S6.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S7.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
1Q GAIN MUTATED 4 3 36 8 0 0
1Q GAIN WILD-TYPE 57 77 120 74 80 69

Figure S7.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 0.0336 (Fisher's exact test), Q value = 0.079

Table S8.  Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
1Q GAIN MUTATED 3 9 11 2
1Q GAIN WILD-TYPE 64 61 85 79

Figure S8.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0019

Table S9.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
1Q GAIN MUTATED 2 12 6 28 1
1Q GAIN WILD-TYPE 79 158 75 125 39

Figure S9.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00185 (Fisher's exact test), Q value = 0.0075

Table S10.  Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
1Q GAIN MUTATED 4 2 15 22 6 0
1Q GAIN WILD-TYPE 113 31 168 110 29 25

Figure S10.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CNMF'

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

Table S11.  Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
1Q GAIN MUTATED 2 8 12 24 3
1Q GAIN WILD-TYPE 89 49 174 95 54

Figure S11.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0023

Table S12.  Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
2P GAIN MUTATED 19 9 30 5 9 6
2P GAIN WILD-TYPE 42 71 126 77 71 63

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

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0111 (Fisher's exact test), Q value = 0.033

Table S13.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
2P GAIN MUTATED 13 2 30 29 3 0
2P GAIN WILD-TYPE 104 31 153 103 32 25

Figure S13.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0342 (Fisher's exact test), Q value = 0.079

Table S14.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
2P GAIN MUTATED 28 39 11
2P GAIN WILD-TYPE 145 170 117

Figure S14.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 0.00122 (Fisher's exact test), Q value = 0.0053

Table S15.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
2Q GAIN MUTATED 19 9 29 6 10 6
2Q GAIN WILD-TYPE 42 71 127 76 70 63

Figure S15.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.018 (Fisher's exact test), Q value = 0.05

Table S16.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
2Q GAIN MUTATED 13 2 32 28 4 0
2Q GAIN WILD-TYPE 104 31 151 104 31 25

Figure S16.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0048 (Fisher's exact test), Q value = 0.017

Table S17.  Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
2Q GAIN MUTATED 28 41 9
2Q GAIN WILD-TYPE 145 168 119

Figure S17.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00071

Table S18.  Gene #5: '3p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
3P GAIN MUTATED 1 3 11 3
3P GAIN WILD-TYPE 134 109 74 136

Figure S18.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 0.00177 (Fisher's exact test), Q value = 0.0073

Table S19.  Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
3P GAIN MUTATED 9 2 1 8 0
3P GAIN WILD-TYPE 72 168 80 145 40

Figure S19.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00069 (Fisher's exact test), Q value = 0.0033

Table S20.  Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
3P GAIN MUTATED 1 2 2 9 2 4
3P GAIN WILD-TYPE 116 31 181 123 33 21

Figure S20.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 6e-04

Table S21.  Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
3P GAIN MUTATED 3 1 1 14 1
3P GAIN WILD-TYPE 88 56 185 105 56

Figure S21.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00372 (Fisher's exact test), Q value = 0.014

Table S22.  Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
3P GAIN MUTATED 8 2 10
3P GAIN WILD-TYPE 165 207 118

Figure S22.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MRNA_CNMF'

P value = 0.0214 (Fisher's exact test), Q value = 0.056

Table S23.  Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 14
3Q GAIN MUTATED 1 7 2
3Q GAIN WILD-TYPE 30 18 12

Figure S23.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0305 (Fisher's exact test), Q value = 0.074

Table S24.  Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
3Q GAIN MUTATED 0 2 0 5 0 1 2
3Q GAIN WILD-TYPE 11 10 4 6 13 8 8

Figure S24.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.032

Table S25.  Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
3Q GAIN MUTATED 6 7 26 4 14 3
3Q GAIN WILD-TYPE 55 73 130 78 66 66

Figure S25.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00028

Table S26.  Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
3Q GAIN MUTATED 6 9 19 0
3Q GAIN WILD-TYPE 61 61 77 81

Figure S26.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S27.  Gene #6: '3q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
3Q GAIN MUTATED 16 4 24 4 7 0
3Q GAIN WILD-TYPE 72 82 66 78 85 33

Figure S27.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'3q gain' versus 'RPPA_CHIERARCHICAL'

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

Table S28.  Gene #6: '3q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
3Q GAIN MUTATED 9 12 25 9
3Q GAIN WILD-TYPE 126 100 60 130

Figure S28.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00028

Table S29.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
3Q GAIN MUTATED 15 8 7 29 1
3Q GAIN WILD-TYPE 66 162 74 124 39

Figure S29.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S30.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
3Q GAIN MUTATED 8 4 8 29 7 4
3Q GAIN WILD-TYPE 109 29 175 103 28 21

Figure S30.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S31.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
3Q GAIN MUTATED 7 9 8 31 4
3Q GAIN WILD-TYPE 84 48 178 88 53

Figure S31.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S32.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
3Q GAIN MUTATED 28 8 23
3Q GAIN WILD-TYPE 145 201 105

Figure S32.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0011

Table S33.  Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 44 38
3Q GAIN MUTATED 1 0 2 11
3Q GAIN WILD-TYPE 38 21 42 27

Figure S33.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p gain' versus 'CN_CNMF'

P value = 0.0481 (Fisher's exact test), Q value = 0.11

Table S34.  Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
4P GAIN MUTATED 2 2 4 0 0 5
4P GAIN WILD-TYPE 59 78 152 82 80 64

Figure S34.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'4p gain' versus 'RPPA_CNMF'

P value = 0.038 (Fisher's exact test), Q value = 0.086

Table S35.  Gene #7: '4p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
4P GAIN MUTATED 3 1 5 0 0 0
4P GAIN WILD-TYPE 85 85 85 82 92 33

Figure S35.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p gain' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00022

Table S36.  Gene #7: '4p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
4P GAIN MUTATED 0 2 7 0
4P GAIN WILD-TYPE 135 110 78 139

Figure S36.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.00377 (Fisher's exact test), Q value = 0.014

Table S37.  Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
4P GAIN MUTATED 5 0 3 2 2
4P GAIN WILD-TYPE 76 170 78 151 38

Figure S37.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00057 (Fisher's exact test), Q value = 0.0027

Table S38.  Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
4P GAIN MUTATED 3 0 0 5 0 4
4P GAIN WILD-TYPE 114 33 183 127 35 21

Figure S38.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CNMF'

P value = 0.00552 (Fisher's exact test), Q value = 0.019

Table S39.  Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
4P GAIN MUTATED 2 2 0 7 2
4P GAIN WILD-TYPE 89 55 186 112 55

Figure S39.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q gain' versus 'CN_CNMF'

P value = 0.0356 (Fisher's exact test), Q value = 0.082

Table S40.  Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
4Q GAIN MUTATED 2 1 5 0 0 5
4Q GAIN WILD-TYPE 59 79 151 82 80 64

Figure S40.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

'4q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0015 (Fisher's exact test), Q value = 0.0063

Table S41.  Gene #8: '4q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
4Q GAIN MUTATED 1 2 6 0
4Q GAIN WILD-TYPE 134 110 79 139

Figure S41.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 0.00372 (Fisher's exact test), Q value = 0.014

Table S42.  Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
4Q GAIN MUTATED 5 0 3 2 2
4Q GAIN WILD-TYPE 76 170 78 151 38

Figure S42.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00441 (Fisher's exact test), Q value = 0.016

Table S43.  Gene #8: '4q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
4Q GAIN MUTATED 3 0 1 4 0 4
4Q GAIN WILD-TYPE 114 33 182 128 35 21

Figure S43.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_CNMF'

P value = 0.00574 (Fisher's exact test), Q value = 0.019

Table S44.  Gene #8: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
4Q GAIN MUTATED 2 2 0 7 2
4Q GAIN WILD-TYPE 89 55 186 112 55

Figure S44.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S45.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
5P GAIN MUTATED 44 35 52 21 26 13
5P GAIN WILD-TYPE 17 45 104 61 54 56

Figure S45.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'RPPA_CNMF'

P value = 0.0265 (Fisher's exact test), Q value = 0.066

Table S46.  Gene #9: '5p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
5P GAIN MUTATED 32 19 39 36 36 10
5P GAIN WILD-TYPE 56 67 51 46 56 23

Figure S46.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.0171 (Fisher's exact test), Q value = 0.048

Table S47.  Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
5P GAIN MUTATED 21 57 25 71 15
5P GAIN WILD-TYPE 60 113 56 82 25

Figure S47.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0188 (Fisher's exact test), Q value = 0.052

Table S48.  Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
5P GAIN MUTATED 43 7 61 60 14 4
5P GAIN WILD-TYPE 74 26 122 72 21 21

Figure S48.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0209 (Fisher's exact test), Q value = 0.056

Table S49.  Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 44 38
5P GAIN MUTATED 13 4 16 22
5P GAIN WILD-TYPE 26 17 28 16

Figure S49.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S50.  Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
5Q GAIN MUTATED 47 35 55 30 29 14
5Q GAIN WILD-TYPE 14 45 101 52 51 55

Figure S50.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'RPPA_CNMF'

P value = 0.00742 (Fisher's exact test), Q value = 0.024

Table S51.  Gene #10: '5q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
5Q GAIN MUTATED 36 20 37 42 41 14
5Q GAIN WILD-TYPE 52 66 53 40 51 19

Figure S51.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'5q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0333 (Fisher's exact test), Q value = 0.078

Table S52.  Gene #10: '5q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 44 38
5Q GAIN MUTATED 12 4 17 21
5Q GAIN WILD-TYPE 27 17 27 17

Figure S52.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0159 (Fisher's exact test), Q value = 0.046

Table S53.  Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
6P GAIN MUTATED 2 9 0
6P GAIN WILD-TYPE 171 200 128

Figure S53.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S54.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
7P GAIN MUTATED 37 34 54 11 23 14
7P GAIN WILD-TYPE 24 46 102 71 57 55

Figure S54.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S55.  Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
7P GAIN MUTATED 32 22 51 23 22 5
7P GAIN WILD-TYPE 56 64 39 59 70 28

Figure S55.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S56.  Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
7P GAIN MUTATED 34 49 41 31
7P GAIN WILD-TYPE 101 63 44 108

Figure S56.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0015

Table S57.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
7P GAIN MUTATED 23 38 27 71 12
7P GAIN WILD-TYPE 58 132 54 82 28

Figure S57.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00802 (Fisher's exact test), Q value = 0.026

Table S58.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
7P GAIN MUTATED 38 9 46 60 12 6
7P GAIN WILD-TYPE 79 24 137 72 23 19

Figure S58.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.0381 (Fisher's exact test), Q value = 0.086

Table S59.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
7P GAIN MUTATED 26 26 56 48 14
7P GAIN WILD-TYPE 65 31 130 71 43

Figure S59.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S60.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
7Q GAIN MUTATED 39 34 54 11 22 13
7Q GAIN WILD-TYPE 22 46 102 71 58 56

Figure S60.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.0468 (Fisher's exact test), Q value = 0.1

Table S61.  Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
7Q GAIN MUTATED 12 23 35 20
7Q GAIN WILD-TYPE 55 47 61 61

Figure S61.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S62.  Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
7Q GAIN MUTATED 32 21 51 24 23 4
7Q GAIN WILD-TYPE 56 65 39 58 69 29

Figure S62.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S63.  Gene #14: '7q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
7Q GAIN MUTATED 35 50 41 29
7Q GAIN WILD-TYPE 100 62 44 110

Figure S63.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0011

Table S64.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
7Q GAIN MUTATED 25 37 27 70 12
7Q GAIN WILD-TYPE 56 133 54 83 28

Figure S64.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00439 (Fisher's exact test), Q value = 0.016

Table S65.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
7Q GAIN MUTATED 37 11 44 60 13 6
7Q GAIN WILD-TYPE 80 22 139 72 22 19

Figure S65.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.047

Table S66.  Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
7Q GAIN MUTATED 26 26 54 50 14
7Q GAIN WILD-TYPE 65 31 132 69 43

Figure S66.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.026 (Fisher's exact test), Q value = 0.066

Table S67.  Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
7Q GAIN MUTATED 60 57 53
7Q GAIN WILD-TYPE 113 152 75

Figure S67.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.00109 (Fisher's exact test), Q value = 0.0048

Table S68.  Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
8P GAIN MUTATED 2 4 15 1
8P GAIN WILD-TYPE 65 66 81 80

Figure S68.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p gain' versus 'RPPA_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0022

Table S69.  Gene #15: '8p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
8P GAIN MUTATED 3 2 16 4 4 0
8P GAIN WILD-TYPE 85 84 74 78 88 33

Figure S69.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S70.  Gene #15: '8p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
8P GAIN MUTATED 1 18 7 3
8P GAIN WILD-TYPE 134 94 78 136

Figure S70.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 6e-04

Table S71.  Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
8P GAIN MUTATED 4 1 5 19 2
8P GAIN WILD-TYPE 77 169 76 134 38

Figure S71.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00022

Table S72.  Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
8P GAIN MUTATED 6 2 1 19 2 1
8P GAIN WILD-TYPE 111 31 182 113 33 24

Figure S72.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00028

Table S73.  Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
8P GAIN MUTATED 4 4 2 18 3
8P GAIN WILD-TYPE 87 53 184 101 54

Figure S73.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00179 (Fisher's exact test), Q value = 0.0073

Table S74.  Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
8P GAIN MUTATED 15 4 12
8P GAIN WILD-TYPE 158 205 116

Figure S74.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0172 (Fisher's exact test), Q value = 0.048

Table S75.  Gene #15: '8p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 44 38
8P GAIN MUTATED 1 0 0 5
8P GAIN WILD-TYPE 38 21 44 33

Figure S75.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S76.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
8Q GAIN MUTATED 5 8 37 2 8 1
8Q GAIN WILD-TYPE 56 72 119 80 72 68

Figure S76.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S77.  Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
8Q GAIN MUTATED 2 13 23 2
8Q GAIN WILD-TYPE 65 57 73 79

Figure S77.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S78.  Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
8Q GAIN MUTATED 9 4 29 6 8 1
8Q GAIN WILD-TYPE 79 82 61 76 84 32

Figure S78.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S79.  Gene #16: '8q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
8Q GAIN MUTATED 5 29 16 7
8Q GAIN WILD-TYPE 130 83 69 132

Figure S79.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S80.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
8Q GAIN MUTATED 4 4 7 42 3
8Q GAIN WILD-TYPE 77 166 74 111 37

Figure S80.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S81.  Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
8Q GAIN MUTATED 8 2 4 41 4 1
8Q GAIN WILD-TYPE 109 31 179 91 31 24

Figure S81.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S82.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
8Q GAIN MUTATED 7 10 7 30 5
8Q GAIN WILD-TYPE 84 47 179 89 52

Figure S82.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00039

Table S83.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
8Q GAIN MUTATED 29 9 21
8Q GAIN WILD-TYPE 144 200 107

Figure S83.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S84.  Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 44 38
8Q GAIN MUTATED 3 0 0 11
8Q GAIN WILD-TYPE 36 21 44 27

Figure S84.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p gain' versus 'CN_CNMF'

P value = 0.00189 (Fisher's exact test), Q value = 0.0076

Table S85.  Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
9P GAIN MUTATED 1 2 1 0 3 7
9P GAIN WILD-TYPE 60 78 155 82 77 62

Figure S85.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00982 (Fisher's exact test), Q value = 0.031

Table S86.  Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
9P GAIN MUTATED 0 0 7 2 2 3
9P GAIN WILD-TYPE 117 33 176 130 33 22

Figure S86.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.056

Table S87.  Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
9Q GAIN MUTATED 1 3 1 0 3 5
9Q GAIN WILD-TYPE 60 77 155 82 77 64

Figure S87.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0157 (Fisher's exact test), Q value = 0.045

Table S88.  Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
9Q GAIN MUTATED 0 0 4 4 2 3
9Q GAIN WILD-TYPE 117 33 179 128 33 22

Figure S88.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 0.045 (Fisher's exact test), Q value = 0.099

Table S89.  Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
10P GAIN MUTATED 3 1 9 0 3 0
10P GAIN WILD-TYPE 58 79 147 82 77 69

Figure S89.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 0.00131 (Fisher's exact test), Q value = 0.0056

Table S90.  Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
10P GAIN MUTATED 3 0 2 11 0
10P GAIN WILD-TYPE 78 170 79 142 40

Figure S90.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.0024

Table S91.  Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
10P GAIN MUTATED 2 1 0 11 2 0
10P GAIN WILD-TYPE 115 32 183 121 33 25

Figure S91.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CNMF'

P value = 0.0342 (Fisher's exact test), Q value = 0.079

Table S92.  Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
10P GAIN MUTATED 3 1 2 9 1
10P GAIN WILD-TYPE 88 56 184 110 56

Figure S92.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0394 (Fisher's exact test), Q value = 0.089

Table S93.  Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
10P GAIN MUTATED 7 2 7
10P GAIN WILD-TYPE 166 207 121

Figure S93.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 0.00587 (Fisher's exact test), Q value = 0.02

Table S94.  Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
10Q GAIN MUTATED 2 0 1 9 0
10Q GAIN WILD-TYPE 79 170 80 144 40

Figure S94.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00183 (Fisher's exact test), Q value = 0.0074

Table S95.  Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
10Q GAIN MUTATED 1 1 0 9 1 0
10Q GAIN WILD-TYPE 116 32 183 123 34 25

Figure S95.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.04

Table S96.  Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
10Q GAIN MUTATED 1 1 1 8 1
10Q GAIN WILD-TYPE 90 56 185 111 56

Figure S96.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p gain' versus 'MRNASEQ_CNMF'

P value = 0.0345 (Fisher's exact test), Q value = 0.08

Table S97.  Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
11P GAIN MUTATED 7 3 7 12 2
11P GAIN WILD-TYPE 74 167 74 141 38

Figure S97.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNA_CNMF'

P value = 0.0219 (Fisher's exact test), Q value = 0.057

Table S98.  Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 14
12P GAIN MUTATED 3 10 2
12P GAIN WILD-TYPE 28 15 12

Figure S98.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'12p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0328 (Fisher's exact test), Q value = 0.078

Table S99.  Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
12P GAIN MUTATED 0 4 0 6 1 2 2
12P GAIN WILD-TYPE 11 8 4 5 12 7 8

Figure S99.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00028

Table S100.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
12P GAIN MUTATED 20 25 40 7 23 6
12P GAIN WILD-TYPE 41 55 116 75 57 63

Figure S100.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00092

Table S101.  Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
12P GAIN MUTATED 12 21 35 8
12P GAIN WILD-TYPE 55 49 61 73

Figure S101.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S102.  Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
12P GAIN MUTATED 16 3 47 20 19 2
12P GAIN WILD-TYPE 72 83 43 62 73 31

Figure S102.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'12p gain' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00022

Table S103.  Gene #23: '12p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
12P GAIN MUTATED 21 37 31 18
12P GAIN WILD-TYPE 114 75 54 121

Figure S103.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S104.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
12P GAIN MUTATED 18 14 15 67 6
12P GAIN WILD-TYPE 63 156 66 86 34

Figure S104.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S105.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
12P GAIN MUTATED 22 5 19 58 11 5
12P GAIN WILD-TYPE 95 28 164 74 24 20

Figure S105.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S106.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
12P GAIN MUTATED 16 18 22 49 14
12P GAIN WILD-TYPE 75 39 164 70 43

Figure S106.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S107.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
12P GAIN MUTATED 47 26 46
12P GAIN WILD-TYPE 126 183 82

Figure S107.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00176 (Fisher's exact test), Q value = 0.0073

Table S108.  Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 44 38
12P GAIN MUTATED 5 3 4 16
12P GAIN WILD-TYPE 34 18 40 22

Figure S108.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'MRNA_CNMF'

P value = 0.0211 (Fisher's exact test), Q value = 0.056

Table S109.  Gene #24: '12q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 14
12Q GAIN MUTATED 3 10 2
12Q GAIN WILD-TYPE 28 15 12

Figure S109.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'12q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0329 (Fisher's exact test), Q value = 0.078

Table S110.  Gene #24: '12q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
12Q GAIN MUTATED 0 4 0 6 1 2 2
12Q GAIN WILD-TYPE 11 8 4 5 12 7 8

Figure S110.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00022

Table S111.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
12Q GAIN MUTATED 20 24 41 7 23 7
12Q GAIN WILD-TYPE 41 56 115 75 57 62

Figure S111.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00081

Table S112.  Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
12Q GAIN MUTATED 12 20 36 8
12Q GAIN WILD-TYPE 55 50 60 73

Figure S112.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S113.  Gene #24: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
12Q GAIN MUTATED 16 3 49 20 18 2
12Q GAIN WILD-TYPE 72 83 41 62 74 31

Figure S113.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'12q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S114.  Gene #24: '12q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
12Q GAIN MUTATED 21 38 31 18
12Q GAIN WILD-TYPE 114 74 54 121

Figure S114.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S115.  Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
12Q GAIN MUTATED 19 14 14 68 6
12Q GAIN WILD-TYPE 62 156 67 85 34

Figure S115.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S116.  Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
12Q GAIN MUTATED 22 5 19 59 11 5
12Q GAIN WILD-TYPE 95 28 164 73 24 20

Figure S116.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S117.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
12Q GAIN MUTATED 15 19 22 49 15
12Q GAIN WILD-TYPE 76 38 164 70 42

Figure S117.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S118.  Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
12Q GAIN MUTATED 47 26 47
12Q GAIN WILD-TYPE 126 183 81

Figure S118.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00236 (Fisher's exact test), Q value = 0.0093

Table S119.  Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 44 38
12Q GAIN MUTATED 6 3 4 16
12Q GAIN WILD-TYPE 33 18 40 22

Figure S119.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.033

Table S120.  Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
13Q GAIN MUTATED 4 8 1 4 3 2
13Q GAIN WILD-TYPE 57 72 155 78 77 67

Figure S120.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.0367 (Fisher's exact test), Q value = 0.084

Table S121.  Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
13Q GAIN MUTATED 2 1 11 4
13Q GAIN WILD-TYPE 65 69 85 77

Figure S121.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 0.0488 (Fisher's exact test), Q value = 0.11

Table S122.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
13Q GAIN MUTATED 4 3 8 5 2
13Q GAIN WILD-TYPE 77 167 73 148 38

Figure S122.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 0.0279 (Fisher's exact test), Q value = 0.069

Table S123.  Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
13Q GAIN MUTATED 4 0 6 4 7
13Q GAIN WILD-TYPE 87 57 180 115 50

Figure S123.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q gain' versus 'RPPA_CNMF'

P value = 0.00179 (Fisher's exact test), Q value = 0.0073

Table S124.  Gene #26: '14q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
14Q GAIN MUTATED 5 0 7 1 0 0
14Q GAIN WILD-TYPE 83 86 83 81 92 33

Figure S124.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.034 (Fisher's exact test), Q value = 0.079

Table S125.  Gene #26: '14q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
14Q GAIN MUTATED 1 4 6 2
14Q GAIN WILD-TYPE 134 108 79 137

Figure S125.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.0392 (Fisher's exact test), Q value = 0.088

Table S126.  Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
14Q GAIN MUTATED 6 1 3 5 1
14Q GAIN WILD-TYPE 75 169 78 148 39

Figure S126.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0013

Table S127.  Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
14Q GAIN MUTATED 3 0 1 7 0 5
14Q GAIN WILD-TYPE 114 33 182 125 35 20

Figure S127.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.069

Table S128.  Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
14Q GAIN MUTATED 2 3 1 7 2
14Q GAIN WILD-TYPE 89 54 185 112 55

Figure S128.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0473 (Fisher's exact test), Q value = 0.1

Table S129.  Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
14Q GAIN MUTATED 6 2 7
14Q GAIN WILD-TYPE 167 207 121

Figure S129.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0015

Table S130.  Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
15Q GAIN MUTATED 7 4 3 0 10 2
15Q GAIN WILD-TYPE 54 76 153 82 70 67

Figure S130.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

'15q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00355 (Fisher's exact test), Q value = 0.013

Table S131.  Gene #27: '15q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
15Q GAIN MUTATED 0 7 6 9
15Q GAIN WILD-TYPE 135 105 79 130

Figure S131.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S132.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
16P GAIN MUTATED 25 21 30 6 19 6
16P GAIN WILD-TYPE 36 59 126 76 61 63

Figure S132.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'RPPA_CNMF'

P value = 0.0203 (Fisher's exact test), Q value = 0.055

Table S133.  Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
16P GAIN MUTATED 23 10 23 22 13 4
16P GAIN WILD-TYPE 65 76 67 60 79 29

Figure S133.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0018

Table S134.  Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
16P GAIN MUTATED 22 18 16 44 7
16P GAIN WILD-TYPE 59 152 65 109 33

Figure S134.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00459 (Fisher's exact test), Q value = 0.016

Table S135.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
16P GAIN MUTATED 26 13 23 34 6 5
16P GAIN WILD-TYPE 91 20 160 98 29 20

Figure S135.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00905 (Fisher's exact test), Q value = 0.029

Table S136.  Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
16P GAIN MUTATED 32 35 39
16P GAIN WILD-TYPE 141 174 89

Figure S136.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

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

Table S137.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
16Q GAIN MUTATED 22 21 26 5 19 6
16Q GAIN WILD-TYPE 39 59 130 77 61 63

Figure S137.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'RPPA_CNMF'

P value = 0.00559 (Fisher's exact test), Q value = 0.019

Table S138.  Gene #29: '16q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
16Q GAIN MUTATED 23 7 23 18 12 4
16Q GAIN WILD-TYPE 65 79 67 64 80 29

Figure S138.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0032

Table S139.  Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
16Q GAIN MUTATED 19 16 15 42 7
16Q GAIN WILD-TYPE 62 154 66 111 33

Figure S139.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0162 (Fisher's exact test), Q value = 0.046

Table S140.  Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
16Q GAIN MUTATED 23 11 22 33 6 4
16Q GAIN WILD-TYPE 94 22 161 99 29 21

Figure S140.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 0.0072 (Fisher's exact test), Q value = 0.023

Table S141.  Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
16Q GAIN MUTATED 18 17 22 30 11
16Q GAIN WILD-TYPE 73 40 164 89 46

Figure S141.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p gain' versus 'MRNA_CNMF'

P value = 0.023 (Fisher's exact test), Q value = 0.059

Table S142.  Gene #30: '17p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 14
17P GAIN MUTATED 1 0 3
17P GAIN WILD-TYPE 30 25 11

Figure S142.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00535 (Fisher's exact test), Q value = 0.019

Table S143.  Gene #30: '17p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
17P GAIN MUTATED 0 0 2 0 0 1 1
17P GAIN WILD-TYPE 11 12 2 11 13 8 9

Figure S143.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.0046

Table S144.  Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
17P GAIN MUTATED 11 4 1 10 0
17P GAIN WILD-TYPE 70 166 80 143 40

Figure S144.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00507 (Fisher's exact test), Q value = 0.018

Table S145.  Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
17P GAIN MUTATED 2 6 5 10 2 1
17P GAIN WILD-TYPE 115 27 178 122 33 24

Figure S145.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0262 (Fisher's exact test), Q value = 0.066

Table S146.  Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
17Q GAIN MUTATED 0 0 2 1 0 1 1
17Q GAIN WILD-TYPE 11 12 2 10 13 8 9

Figure S146.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00039

Table S147.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
17Q GAIN MUTATED 13 5 1 14 0
17Q GAIN WILD-TYPE 68 165 80 139 40

Figure S147.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0015 (Fisher's exact test), Q value = 0.0063

Table S148.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
17Q GAIN MUTATED 3 7 6 13 3 1
17Q GAIN WILD-TYPE 114 26 177 119 32 24

Figure S148.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 0.0184 (Fisher's exact test), Q value = 0.051

Table S149.  Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
17Q GAIN MUTATED 7 2 6 15 2
17Q GAIN WILD-TYPE 84 55 180 104 55

Figure S149.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00393 (Fisher's exact test), Q value = 0.015

Table S150.  Gene #31: '17q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 44 38
17Q GAIN MUTATED 1 0 0 6
17Q GAIN WILD-TYPE 38 21 44 32

Figure S150.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 0.0226 (Fisher's exact test), Q value = 0.059

Table S151.  Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
18P GAIN MUTATED 7 0 3 4
18P GAIN WILD-TYPE 60 70 93 77

Figure S151.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.073

Table S152.  Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
18Q GAIN MUTATED 7 0 4 4
18Q GAIN WILD-TYPE 60 70 92 77

Figure S152.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 0.00439 (Fisher's exact test), Q value = 0.016

Table S153.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
19P GAIN MUTATED 9 9 17 0 10 6
19P GAIN WILD-TYPE 52 71 139 82 70 63

Figure S153.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.00094 (Fisher's exact test), Q value = 0.0042

Table S154.  Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
19P GAIN MUTATED 9 3 19 3
19P GAIN WILD-TYPE 58 67 77 78

Figure S154.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'RPPA_CNMF'

P value = 0.0013 (Fisher's exact test), Q value = 0.0056

Table S155.  Gene #34: '19p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
19P GAIN MUTATED 13 3 17 7 6 0
19P GAIN WILD-TYPE 75 83 73 75 86 33

Figure S155.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'19p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0124 (Fisher's exact test), Q value = 0.037

Table S156.  Gene #34: '19p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
19P GAIN MUTATED 6 17 12 11
19P GAIN WILD-TYPE 129 95 73 128

Figure S156.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.00572 (Fisher's exact test), Q value = 0.019

Table S157.  Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
19P GAIN MUTATED 11 6 9 22 3
19P GAIN WILD-TYPE 70 164 72 131 37

Figure S157.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.0034

Table S158.  Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
19P GAIN MUTATED 10 2 8 24 2 5
19P GAIN WILD-TYPE 107 31 175 108 33 20

Figure S158.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 0.00145 (Fisher's exact test), Q value = 0.0062

Table S159.  Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
19P GAIN MUTATED 8 7 7 19 9
19P GAIN WILD-TYPE 83 50 179 100 48

Figure S159.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00081

Table S160.  Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
19Q GAIN MUTATED 9 3 22 3
19Q GAIN WILD-TYPE 58 67 74 78

Figure S160.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S161.  Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
19Q GAIN MUTATED 13 3 23 7 6 0
19Q GAIN WILD-TYPE 75 83 67 75 86 33

Figure S161.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'19q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.0037

Table S162.  Gene #35: '19q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
19Q GAIN MUTATED 6 20 15 11
19Q GAIN WILD-TYPE 129 92 70 128

Figure S162.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.0041

Table S163.  Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
19Q GAIN MUTATED 11 6 9 26 4
19Q GAIN WILD-TYPE 70 164 72 127 36

Figure S163.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00071

Table S164.  Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
19Q GAIN MUTATED 11 2 8 28 2 5
19Q GAIN WILD-TYPE 106 31 175 104 33 20

Figure S164.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00045

Table S165.  Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
19Q GAIN MUTATED 8 7 7 24 9
19Q GAIN WILD-TYPE 83 50 179 95 48

Figure S165.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S166.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
20P GAIN MUTATED 16 27 41 3 19 6
20P GAIN WILD-TYPE 45 53 115 79 61 63

Figure S166.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00051

Table S167.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
20P GAIN MUTATED 10 16 33 6
20P GAIN WILD-TYPE 57 54 63 75

Figure S167.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S168.  Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
20P GAIN MUTATED 19 5 45 11 19 2
20P GAIN WILD-TYPE 69 81 45 71 73 31

Figure S168.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S169.  Gene #36: '20p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
20P GAIN MUTATED 18 35 34 14
20P GAIN WILD-TYPE 117 77 51 125

Figure S169.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S170.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
20P GAIN MUTATED 18 9 20 60 5
20P GAIN WILD-TYPE 63 161 61 93 35

Figure S170.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S171.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
20P GAIN MUTATED 20 4 13 66 3 6
20P GAIN WILD-TYPE 97 29 170 66 32 19

Figure S171.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S172.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
20P GAIN MUTATED 18 13 16 48 16
20P GAIN WILD-TYPE 73 44 170 71 41

Figure S172.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S173.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
20P GAIN MUTATED 55 23 33
20P GAIN WILD-TYPE 118 186 95

Figure S173.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00028

Table S174.  Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 44 38
20P GAIN MUTATED 7 2 3 18
20P GAIN WILD-TYPE 32 19 41 20

Figure S174.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0361 (Fisher's exact test), Q value = 0.083

Table S175.  Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 52 28 22
20P GAIN MUTATED 8 17 4 1
20P GAIN WILD-TYPE 32 35 24 21

Figure S175.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S176.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
20Q GAIN MUTATED 16 26 44 4 19 6
20Q GAIN WILD-TYPE 45 54 112 78 61 63

Figure S176.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00039

Table S177.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
20Q GAIN MUTATED 10 16 33 6
20Q GAIN WILD-TYPE 57 54 63 75

Figure S177.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S178.  Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
20Q GAIN MUTATED 19 5 47 12 19 2
20Q GAIN WILD-TYPE 69 81 43 70 73 31

Figure S178.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S179.  Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
20Q GAIN MUTATED 18 38 34 14
20Q GAIN WILD-TYPE 117 74 51 125

Figure S179.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S180.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
20Q GAIN MUTATED 18 9 19 64 5
20Q GAIN WILD-TYPE 63 161 62 89 35

Figure S180.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S181.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
20Q GAIN MUTATED 20 4 13 69 3 6
20Q GAIN WILD-TYPE 97 29 170 63 32 19

Figure S181.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S182.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
20Q GAIN MUTATED 18 13 16 51 16
20Q GAIN WILD-TYPE 73 44 170 68 41

Figure S182.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S183.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
20Q GAIN MUTATED 57 23 34
20Q GAIN WILD-TYPE 116 186 94

Figure S183.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00022

Table S184.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 44 38
20Q GAIN MUTATED 7 2 3 19
20Q GAIN WILD-TYPE 32 19 41 19

Figure S184.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0209 (Fisher's exact test), Q value = 0.056

Table S185.  Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 52 28 22
20Q GAIN MUTATED 8 18 4 1
20Q GAIN WILD-TYPE 32 34 24 21

Figure S185.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.00337 (Fisher's exact test), Q value = 0.013

Table S186.  Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
21Q GAIN MUTATED 3 6 18 3
21Q GAIN WILD-TYPE 64 64 78 78

Figure S186.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.0047

Table S187.  Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
21Q GAIN MUTATED 6 8 6 28 2
21Q GAIN WILD-TYPE 75 162 75 125 38

Figure S187.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00314 (Fisher's exact test), Q value = 0.012

Table S188.  Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
21Q GAIN MUTATED 10 2 9 25 3 1
21Q GAIN WILD-TYPE 107 31 174 107 32 24

Figure S188.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 0.00802 (Fisher's exact test), Q value = 0.026

Table S189.  Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
21Q GAIN MUTATED 5 5 11 20 9
21Q GAIN WILD-TYPE 86 52 175 99 48

Figure S189.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0159 (Fisher's exact test), Q value = 0.046

Table S190.  Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
22Q GAIN MUTATED 5 1 10 17 2 5
22Q GAIN WILD-TYPE 112 32 173 115 33 20

Figure S190.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.053

Table S191.  Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
22Q GAIN MUTATED 8 3 7 17 4
22Q GAIN WILD-TYPE 83 54 179 102 53

Figure S191.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xp gain' versus 'CN_CNMF'

P value = 0.0421 (Fisher's exact test), Q value = 0.094

Table S192.  Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
XP GAIN MUTATED 9 5 10 1 3 4
XP GAIN WILD-TYPE 52 75 146 81 77 65

Figure S192.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

'xp gain' versus 'RPPA_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00056

Table S193.  Gene #40: 'xp gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
XP GAIN MUTATED 12 0 10 2 3 0
XP GAIN WILD-TYPE 76 86 80 80 89 33

Figure S193.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'xp gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00111 (Fisher's exact test), Q value = 0.0049

Table S194.  Gene #40: 'xp gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
XP GAIN MUTATED 5 6 13 3
XP GAIN WILD-TYPE 130 106 72 136

Figure S194.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 0.0355 (Fisher's exact test), Q value = 0.082

Table S195.  Gene #40: 'xp gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
XP GAIN MUTATED 7 5 3 16 1
XP GAIN WILD-TYPE 74 165 78 137 39

Figure S195.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xp gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00077 (Fisher's exact test), Q value = 0.0036

Table S196.  Gene #40: 'xp gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
XP GAIN MUTATED 3 4 6 18 1 0
XP GAIN WILD-TYPE 114 29 177 114 34 25

Figure S196.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_CNMF'

P value = 0.0472 (Fisher's exact test), Q value = 0.1

Table S197.  Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
XP GAIN MUTATED 6 4 6 14 2
XP GAIN WILD-TYPE 85 53 180 105 55

Figure S197.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.033

Table S198.  Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
XQ GAIN MUTATED 9 4 6 1 4 7
XQ GAIN WILD-TYPE 52 76 150 81 76 62

Figure S198.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'xq gain' versus 'RPPA_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.059

Table S199.  Gene #41: 'xq gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
XQ GAIN MUTATED 9 1 9 4 3 0
XQ GAIN WILD-TYPE 79 85 81 78 89 33

Figure S199.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'1p loss' versus 'MRNA_CNMF'

P value = 0.00363 (Fisher's exact test), Q value = 0.014

Table S200.  Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 14
1P LOSS MUTATED 2 4 7
1P LOSS WILD-TYPE 29 21 7

Figure S200.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00568 (Fisher's exact test), Q value = 0.019

Table S201.  Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
1P LOSS MUTATED 0 2 2 1 1 1 6
1P LOSS WILD-TYPE 11 10 2 10 12 8 4

Figure S201.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 0.00569 (Fisher's exact test), Q value = 0.019

Table S202.  Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
1P LOSS MUTATED 2 7 21 4 11 15
1P LOSS WILD-TYPE 59 73 135 78 69 54

Figure S202.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'RPPA_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.04

Table S203.  Gene #42: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
1P LOSS MUTATED 19 7 9 9 4 4
1P LOSS WILD-TYPE 69 79 81 73 88 29

Figure S203.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'1p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.033

Table S204.  Gene #42: '1p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
1P LOSS MUTATED 6 14 15 17
1P LOSS WILD-TYPE 129 98 70 122

Figure S204.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00022

Table S205.  Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
1P LOSS MUTATED 22 16 2 18 2
1P LOSS WILD-TYPE 59 154 79 135 38

Figure S205.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00039

Table S206.  Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
1P LOSS MUTATED 9 5 15 17 2 12
1P LOSS WILD-TYPE 108 28 168 115 33 13

Figure S206.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.00315 (Fisher's exact test), Q value = 0.012

Table S207.  Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
1P LOSS MUTATED 10 5 17 26 2
1P LOSS WILD-TYPE 81 52 169 93 55

Figure S207.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0249 (Fisher's exact test), Q value = 0.063

Table S208.  Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
1P LOSS MUTATED 16 20 24
1P LOSS WILD-TYPE 157 189 104

Figure S208.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'MRNA_CNMF'

P value = 0.0381 (Fisher's exact test), Q value = 0.086

Table S209.  Gene #43: '1q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 14
1Q LOSS MUTATED 2 2 5
1Q LOSS WILD-TYPE 29 23 9

Figure S209.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0115 (Fisher's exact test), Q value = 0.034

Table S210.  Gene #43: '1q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
1Q LOSS MUTATED 0 1 1 0 1 1 5
1Q LOSS WILD-TYPE 11 11 3 11 12 8 5

Figure S210.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00066

Table S211.  Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
1Q LOSS MUTATED 1 6 4 3 11 12
1Q LOSS WILD-TYPE 60 74 152 79 69 57

Figure S211.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.033

Table S212.  Gene #43: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
1Q LOSS MUTATED 9 1 8 2
1Q LOSS WILD-TYPE 58 69 88 79

Figure S212.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q loss' versus 'RPPA_CNMF'

P value = 0.0184 (Fisher's exact test), Q value = 0.051

Table S213.  Gene #43: '1q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
1Q LOSS MUTATED 13 4 8 3 2 2
1Q LOSS WILD-TYPE 75 82 82 79 90 31

Figure S213.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'1q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00419 (Fisher's exact test), Q value = 0.015

Table S214.  Gene #43: '1q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
1Q LOSS MUTATED 3 10 12 7
1Q LOSS WILD-TYPE 132 102 73 132

Figure S214.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S215.  Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
1Q LOSS MUTATED 17 8 0 11 1
1Q LOSS WILD-TYPE 64 162 81 142 39

Figure S215.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S216.  Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
1Q LOSS MUTATED 5 2 7 10 2 11
1Q LOSS WILD-TYPE 112 31 176 122 33 14

Figure S216.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CNMF'

P value = 0.0322 (Fisher's exact test), Q value = 0.077

Table S217.  Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
1Q LOSS MUTATED 6 3 8 17 3
1Q LOSS WILD-TYPE 85 54 178 102 54

Figure S217.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.032

Table S218.  Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
1Q LOSS MUTATED 11 9 17
1Q LOSS WILD-TYPE 162 200 111

Figure S218.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MRNA_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00051

Table S219.  Gene #44: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 14
2P LOSS MUTATED 0 1 6
2P LOSS WILD-TYPE 31 24 8

Figure S219.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0023

Table S220.  Gene #44: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
2P LOSS MUTATED 0 1 1 0 0 0 5
2P LOSS WILD-TYPE 11 11 3 11 13 9 5

Figure S220.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 0.0336 (Fisher's exact test), Q value = 0.079

Table S221.  Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
2P LOSS MUTATED 0 3 2 1 2 6
2P LOSS WILD-TYPE 61 77 154 81 78 63

Figure S221.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.058

Table S222.  Gene #44: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
2P LOSS MUTATED 4 0 2 0
2P LOSS WILD-TYPE 63 70 94 81

Figure S222.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p loss' versus 'RPPA_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.003

Table S223.  Gene #44: '2p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
2P LOSS MUTATED 7 0 2 0 0 0
2P LOSS WILD-TYPE 81 86 88 82 92 33

Figure S223.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'2p loss' versus 'RPPA_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.0011

Table S224.  Gene #44: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
2P LOSS MUTATED 0 1 7 1
2P LOSS WILD-TYPE 135 111 78 138

Figure S224.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S225.  Gene #44: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
2P LOSS MUTATED 12 0 0 2 0
2P LOSS WILD-TYPE 69 170 81 151 40

Figure S225.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S226.  Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
2P LOSS MUTATED 0 2 1 2 0 9
2P LOSS WILD-TYPE 117 31 182 130 35 16

Figure S226.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00045

Table S227.  Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
2P LOSS MUTATED 2 1 0 11 0
2P LOSS WILD-TYPE 89 56 186 108 57

Figure S227.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S228.  Gene #44: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
2P LOSS MUTATED 1 1 12
2P LOSS WILD-TYPE 172 208 116

Figure S228.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MRNA_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.002

Table S229.  Gene #45: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 14
2Q LOSS MUTATED 0 1 5
2Q LOSS WILD-TYPE 31 24 9

Figure S229.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00083 (Fisher's exact test), Q value = 0.0038

Table S230.  Gene #45: '2q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
2Q LOSS MUTATED 0 1 0 0 0 0 5
2Q LOSS WILD-TYPE 11 11 4 11 13 9 5

Figure S230.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.032

Table S231.  Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
2Q LOSS MUTATED 0 2 2 1 2 7
2Q LOSS WILD-TYPE 61 78 154 81 78 62

Figure S231.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 0.072

Table S232.  Gene #45: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
2Q LOSS MUTATED 4 0 3 0
2Q LOSS WILD-TYPE 63 70 93 81

Figure S232.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q loss' versus 'RPPA_CNMF'

P value = 0.00344 (Fisher's exact test), Q value = 0.013

Table S233.  Gene #45: '2q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
2Q LOSS MUTATED 6 0 3 0 0 0
2Q LOSS WILD-TYPE 82 86 87 82 92 33

Figure S233.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'2q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00097

Table S234.  Gene #45: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
2Q LOSS MUTATED 0 1 7 1
2Q LOSS WILD-TYPE 135 111 78 138

Figure S234.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S235.  Gene #45: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
2Q LOSS MUTATED 12 0 0 2 0
2Q LOSS WILD-TYPE 69 170 81 151 40

Figure S235.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S236.  Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
2Q LOSS MUTATED 0 1 1 3 0 9
2Q LOSS WILD-TYPE 117 32 182 129 35 16

Figure S236.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 6e-04

Table S237.  Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
2Q LOSS MUTATED 1 1 0 11 1
2Q LOSS WILD-TYPE 90 56 186 108 56

Figure S237.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S238.  Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
2Q LOSS MUTATED 1 0 13
2Q LOSS WILD-TYPE 172 209 115

Figure S238.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MRNA_CNMF'

P value = 0.00612 (Fisher's exact test), Q value = 0.02

Table S239.  Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 14
3P LOSS MUTATED 20 20 4
3P LOSS WILD-TYPE 11 5 10

Figure S239.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.032

Table S240.  Gene #46: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
3P LOSS MUTATED 8 9 1 10 7 7 2
3P LOSS WILD-TYPE 3 3 3 1 6 2 8

Figure S240.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S241.  Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
3P LOSS MUTATED 50 33 137 69 38 52
3P LOSS WILD-TYPE 11 47 19 13 42 17

Figure S241.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 0.00942 (Fisher's exact test), Q value = 0.03

Table S242.  Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
3P LOSS MUTATED 41 50 72 69
3P LOSS WILD-TYPE 26 20 24 12

Figure S242.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.034

Table S243.  Gene #46: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
3P LOSS MUTATED 52 70 63 65 62 26
3P LOSS WILD-TYPE 36 16 27 17 30 7

Figure S243.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00092

Table S244.  Gene #46: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
3P LOSS MUTATED 95 90 45 108
3P LOSS WILD-TYPE 40 22 40 31

Figure S244.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S245.  Gene #46: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
3P LOSS MUTATED 31 141 61 115 29
3P LOSS WILD-TYPE 50 29 20 38 11

Figure S245.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S246.  Gene #46: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
3P LOSS MUTATED 92 14 148 96 25 2
3P LOSS WILD-TYPE 25 19 35 36 10 23

Figure S246.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.043

Table S247.  Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
3P LOSS MUTATED 58 42 146 75 44
3P LOSS WILD-TYPE 33 15 40 44 13

Figure S247.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00419 (Fisher's exact test), Q value = 0.015

Table S248.  Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
3P LOSS MUTATED 114 166 85
3P LOSS WILD-TYPE 59 43 43

Figure S248.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0236 (Fisher's exact test), Q value = 0.061

Table S249.  Gene #46: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 44 38
3P LOSS MUTATED 26 10 36 22
3P LOSS WILD-TYPE 13 11 8 16

Figure S249.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3q loss' versus 'CN_CNMF'

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

Table S250.  Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
3Q LOSS MUTATED 16 14 34 24 3 11
3Q LOSS WILD-TYPE 45 66 122 58 77 58

Figure S250.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00658 (Fisher's exact test), Q value = 0.022

Table S251.  Gene #47: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
3Q LOSS MUTATED 35 5 28 29 4 1
3Q LOSS WILD-TYPE 82 28 155 103 31 24

Figure S251.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 0.0138 (Fisher's exact test), Q value = 0.04

Table S252.  Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
3Q LOSS MUTATED 14 9 30 25 21
3Q LOSS WILD-TYPE 77 48 156 94 36

Figure S252.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 0.00457 (Fisher's exact test), Q value = 0.016

Table S253.  Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
4P LOSS MUTATED 4 11 25 10
4P LOSS WILD-TYPE 63 59 71 71

Figure S253.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.002

Table S254.  Gene #48: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
4P LOSS MUTATED 6 11 26 10 15 1
4P LOSS WILD-TYPE 82 75 64 72 77 32

Figure S254.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00146 (Fisher's exact test), Q value = 0.0062

Table S255.  Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
4P LOSS MUTATED 16 1 19 31 4 0
4P LOSS WILD-TYPE 101 32 164 101 31 25

Figure S255.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.044 (Fisher's exact test), Q value = 0.098

Table S256.  Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 52 28 22
4P LOSS MUTATED 2 12 3 1
4P LOSS WILD-TYPE 38 40 25 21

Figure S256.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'METHLYATION_CNMF'

P value = 0.00387 (Fisher's exact test), Q value = 0.014

Table S257.  Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
4Q LOSS MUTATED 4 9 24 8
4Q LOSS WILD-TYPE 63 61 72 73

Figure S257.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'RPPA_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0017

Table S258.  Gene #49: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
4Q LOSS MUTATED 7 8 26 9 12 1
4Q LOSS WILD-TYPE 81 78 64 73 80 32

Figure S258.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0162 (Fisher's exact test), Q value = 0.046

Table S259.  Gene #49: '4q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
4Q LOSS MUTATED 12 21 17 13
4Q LOSS WILD-TYPE 123 91 68 126

Figure S259.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.00377 (Fisher's exact test), Q value = 0.014

Table S260.  Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
4Q LOSS MUTATED 4 13 13 28 7
4Q LOSS WILD-TYPE 77 157 68 125 33

Figure S260.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00034

Table S261.  Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
4Q LOSS MUTATED 15 0 14 32 4 0
4Q LOSS WILD-TYPE 102 33 169 100 31 25

Figure S261.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0262 (Fisher's exact test), Q value = 0.066

Table S262.  Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 52 28 22
4Q LOSS MUTATED 2 11 3 0
4Q LOSS WILD-TYPE 38 41 25 22

Figure S262.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'RPPA_CNMF'

P value = 0.00223 (Fisher's exact test), Q value = 0.0088

Table S263.  Gene #50: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
5P LOSS MUTATED 0 0 6 0 1 0
5P LOSS WILD-TYPE 88 86 84 82 91 33

Figure S263.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.026 (Fisher's exact test), Q value = 0.066

Table S264.  Gene #50: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
5P LOSS MUTATED 1 2 4 0
5P LOSS WILD-TYPE 134 110 81 139

Figure S264.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0052 (Fisher's exact test), Q value = 0.018

Table S265.  Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
5P LOSS MUTATED 0 0 0 6 1 1
5P LOSS WILD-TYPE 117 33 183 126 34 24

Figure S265.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 0.0236 (Fisher's exact test), Q value = 0.061

Table S266.  Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
5P LOSS MUTATED 2 1 0 5 0
5P LOSS WILD-TYPE 89 56 186 114 57

Figure S266.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0274 (Fisher's exact test), Q value = 0.068

Table S267.  Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
5P LOSS MUTATED 5 0 3
5P LOSS WILD-TYPE 168 209 125

Figure S267.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'RPPA_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.032

Table S268.  Gene #51: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
5Q LOSS MUTATED 0 0 5 0 1 0
5Q LOSS WILD-TYPE 88 86 85 82 91 33

Figure S268.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00632 (Fisher's exact test), Q value = 0.021

Table S269.  Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
5Q LOSS MUTATED 0 0 0 6 0 1
5Q LOSS WILD-TYPE 117 33 183 126 35 24

Figure S269.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

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

Table S270.  Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
5Q LOSS MUTATED 2 1 0 4 0
5Q LOSS WILD-TYPE 89 56 186 115 57

Figure S270.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0317 (Fisher's exact test), Q value = 0.076

Table S271.  Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
5Q LOSS MUTATED 5 0 2
5Q LOSS WILD-TYPE 168 209 126

Figure S271.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MRNA_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.076

Table S272.  Gene #52: '6p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 14
6P LOSS MUTATED 4 10 6
6P LOSS WILD-TYPE 27 15 8

Figure S272.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0142 (Fisher's exact test), Q value = 0.041

Table S273.  Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
6P LOSS MUTATED 2 7 0 3 1 1 6
6P LOSS WILD-TYPE 9 5 4 8 12 8 4

Figure S273.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S274.  Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
6P LOSS MUTATED 7 10 61 0 14 8
6P LOSS WILD-TYPE 54 70 95 82 66 61

Figure S274.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.00315 (Fisher's exact test), Q value = 0.012

Table S275.  Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
6P LOSS MUTATED 9 13 25 5
6P LOSS WILD-TYPE 58 57 71 76

Figure S275.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S276.  Gene #52: '6p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
6P LOSS MUTATED 16 9 37 17 7 4
6P LOSS WILD-TYPE 72 77 53 65 85 29

Figure S276.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'6p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S277.  Gene #52: '6p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
6P LOSS MUTATED 10 40 27 13
6P LOSS WILD-TYPE 125 72 58 126

Figure S277.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S278.  Gene #52: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
6P LOSS MUTATED 16 15 9 53 5
6P LOSS WILD-TYPE 65 155 72 100 35

Figure S278.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S279.  Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
6P LOSS MUTATED 19 1 12 51 6 9
6P LOSS WILD-TYPE 98 32 171 81 29 16

Figure S279.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S280.  Gene #52: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
6P LOSS MUTATED 15 15 15 40 11
6P LOSS WILD-TYPE 76 42 171 79 46

Figure S280.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S281.  Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
6P LOSS MUTATED 44 14 38
6P LOSS WILD-TYPE 129 195 90

Figure S281.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0304 (Fisher's exact test), Q value = 0.074

Table S282.  Gene #52: '6p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 52 28 22
6P LOSS MUTATED 5 13 3 0
6P LOSS WILD-TYPE 35 39 25 22

Figure S282.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S283.  Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
6Q LOSS MUTATED 7 10 85 0 16 10
6Q LOSS WILD-TYPE 54 70 71 82 64 59

Figure S283.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S284.  Gene #53: '6q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
6Q LOSS MUTATED 18 21 39 25 7 5
6Q LOSS WILD-TYPE 70 65 51 57 85 28

Figure S284.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'6q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S285.  Gene #53: '6q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
6Q LOSS MUTATED 13 45 29 28
6Q LOSS WILD-TYPE 122 67 56 111

Figure S285.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00039

Table S286.  Gene #53: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
6Q LOSS MUTATED 19 33 11 58 5
6Q LOSS WILD-TYPE 62 137 70 95 35

Figure S286.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S287.  Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
6Q LOSS MUTATED 22 5 29 53 8 9
6Q LOSS WILD-TYPE 95 28 154 79 27 16

Figure S287.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 0.00172 (Fisher's exact test), Q value = 0.0071

Table S288.  Gene #53: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
6Q LOSS MUTATED 20 17 31 44 12
6Q LOSS WILD-TYPE 71 40 155 75 45

Figure S288.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 6e-04

Table S289.  Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
6Q LOSS MUTATED 50 31 43
6Q LOSS WILD-TYPE 123 178 85

Figure S289.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.031 (Fisher's exact test), Q value = 0.075

Table S290.  Gene #53: '6q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 52 28 22
6Q LOSS MUTATED 6 17 5 1
6Q LOSS WILD-TYPE 34 35 23 21

Figure S290.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 0.0491 (Fisher's exact test), Q value = 0.11

Table S291.  Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
8P LOSS MUTATED 14 22 53 14 15 19
8P LOSS WILD-TYPE 47 58 103 68 65 50

Figure S291.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.032 (Fisher's exact test), Q value = 0.077

Table S292.  Gene #54: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
8P LOSS MUTATED 15 40 16 53 12
8P LOSS WILD-TYPE 66 130 65 100 28

Figure S292.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00125 (Fisher's exact test), Q value = 0.0054

Table S293.  Gene #54: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
8P LOSS MUTATED 28 3 47 50 4 4
8P LOSS WILD-TYPE 89 30 136 82 31 21

Figure S293.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0179 (Fisher's exact test), Q value = 0.05

Table S294.  Gene #54: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
8P LOSS MUTATED 59 46 29
8P LOSS WILD-TYPE 114 163 99

Figure S294.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'METHLYATION_CNMF'

P value = 0.00723 (Fisher's exact test), Q value = 0.023

Table S295.  Gene #55: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
8Q LOSS MUTATED 11 1 14 10
8Q LOSS WILD-TYPE 56 69 82 71

Figure S295.  Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q loss' versus 'RPPA_CNMF'

P value = 0.0214 (Fisher's exact test), Q value = 0.056

Table S296.  Gene #55: '8q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
8Q LOSS MUTATED 13 3 13 16 9 5
8Q LOSS WILD-TYPE 75 83 77 66 83 28

Figure S296.  Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9p loss' versus 'MRNA_CNMF'

P value = 0.00706 (Fisher's exact test), Q value = 0.023

Table S297.  Gene #56: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 14
9P LOSS MUTATED 5 12 1
9P LOSS WILD-TYPE 26 13 13

Figure S297.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0362 (Fisher's exact test), Q value = 0.083

Table S298.  Gene #56: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
9P LOSS MUTATED 2 7 0 5 1 2 1
9P LOSS WILD-TYPE 9 5 4 6 12 7 9

Figure S298.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S299.  Gene #56: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
9P LOSS MUTATED 6 21 85 17 20 0
9P LOSS WILD-TYPE 55 59 71 65 60 69

Figure S299.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S300.  Gene #56: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
9P LOSS MUTATED 9 24 56 4
9P LOSS WILD-TYPE 58 46 40 77

Figure S300.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S301.  Gene #56: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
9P LOSS MUTATED 16 15 54 22 25 6
9P LOSS WILD-TYPE 72 71 36 60 67 27

Figure S301.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S302.  Gene #56: '9p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
9P LOSS MUTATED 25 52 36 25
9P LOSS WILD-TYPE 110 60 49 114

Figure S302.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S303.  Gene #56: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
9P LOSS MUTATED 14 16 23 88 7
9P LOSS WILD-TYPE 67 154 58 65 33

Figure S303.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S304.  Gene #56: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
9P LOSS MUTATED 31 2 16 82 13 4
9P LOSS WILD-TYPE 86 31 167 50 22 21

Figure S304.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S305.  Gene #56: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
9P LOSS MUTATED 21 23 27 60 13
9P LOSS WILD-TYPE 70 34 159 59 44

Figure S305.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S306.  Gene #56: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
9P LOSS MUTATED 70 25 49
9P LOSS WILD-TYPE 103 184 79

Figure S306.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.033

Table S307.  Gene #56: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 44 38
9P LOSS MUTATED 8 4 4 15
9P LOSS WILD-TYPE 31 17 40 23

Figure S307.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MRNA_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.052

Table S308.  Gene #57: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 14
9Q LOSS MUTATED 5 12 2
9Q LOSS WILD-TYPE 26 13 12

Figure S308.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S309.  Gene #57: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
9Q LOSS MUTATED 6 20 86 18 21 0
9Q LOSS WILD-TYPE 55 60 70 64 59 69

Figure S309.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S310.  Gene #57: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
9Q LOSS MUTATED 9 25 54 3
9Q LOSS WILD-TYPE 58 45 42 78

Figure S310.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S311.  Gene #57: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
9Q LOSS MUTATED 18 14 52 24 26 6
9Q LOSS WILD-TYPE 70 72 38 58 66 27

Figure S311.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S312.  Gene #57: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
9Q LOSS MUTATED 26 52 36 26
9Q LOSS WILD-TYPE 109 60 49 113

Figure S312.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S313.  Gene #57: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
9Q LOSS MUTATED 15 17 23 88 7
9Q LOSS WILD-TYPE 66 153 58 65 33

Figure S313.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S314.  Gene #57: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
9Q LOSS MUTATED 32 3 16 82 13 4
9Q LOSS WILD-TYPE 85 30 167 50 22 21

Figure S314.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S315.  Gene #57: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
9Q LOSS MUTATED 20 23 26 62 14
9Q LOSS WILD-TYPE 71 34 160 57 43

Figure S315.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S316.  Gene #57: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
9Q LOSS MUTATED 69 25 51
9Q LOSS WILD-TYPE 104 184 77

Figure S316.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00256 (Fisher's exact test), Q value = 0.01

Table S317.  Gene #57: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 44 38
9Q LOSS MUTATED 6 4 5 17
9Q LOSS WILD-TYPE 33 17 39 21

Figure S317.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0177 (Fisher's exact test), Q value = 0.049

Table S318.  Gene #58: '10p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
10P LOSS MUTATED 9 18 17 16
10P LOSS WILD-TYPE 126 94 68 123

Figure S318.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.0027

Table S319.  Gene #58: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
10P LOSS MUTATED 16 3 13 25 2 9
10P LOSS WILD-TYPE 101 30 170 107 33 16

Figure S319.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.00739 (Fisher's exact test), Q value = 0.024

Table S320.  Gene #58: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
10P LOSS MUTATED 11 4 16 27 8
10P LOSS WILD-TYPE 80 53 170 92 49

Figure S320.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0309 (Fisher's exact test), Q value = 0.075

Table S321.  Gene #58: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
10P LOSS MUTATED 25 18 23
10P LOSS WILD-TYPE 148 191 105

Figure S321.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 0.0293 (Fisher's exact test), Q value = 0.072

Table S322.  Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
10Q LOSS MUTATED 6 11 35 7 14 16
10Q LOSS WILD-TYPE 55 69 121 75 66 53

Figure S322.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0213 (Fisher's exact test), Q value = 0.056

Table S323.  Gene #59: '10q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
10Q LOSS MUTATED 14 24 21 22
10Q LOSS WILD-TYPE 121 88 64 117

Figure S323.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00193 (Fisher's exact test), Q value = 0.0077

Table S324.  Gene #59: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
10Q LOSS MUTATED 22 3 20 32 3 9
10Q LOSS WILD-TYPE 95 30 163 100 32 16

Figure S324.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.00261 (Fisher's exact test), Q value = 0.01

Table S325.  Gene #59: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
10Q LOSS MUTATED 14 4 24 33 12
10Q LOSS WILD-TYPE 77 53 162 86 45

Figure S325.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00572 (Fisher's exact test), Q value = 0.019

Table S326.  Gene #59: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
10Q LOSS MUTATED 34 23 30
10Q LOSS WILD-TYPE 139 186 98

Figure S326.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0276 (Fisher's exact test), Q value = 0.068

Table S327.  Gene #60: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
11P LOSS MUTATED 3 1 2 11 1 0
11P LOSS WILD-TYPE 114 32 181 121 34 25

Figure S327.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0344 (Fisher's exact test), Q value = 0.08

Table S328.  Gene #60: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
11P LOSS MUTATED 11 3 4
11P LOSS WILD-TYPE 162 206 124

Figure S328.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.032

Table S329.  Gene #61: '11q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
11Q LOSS MUTATED 2 10 6 3
11Q LOSS WILD-TYPE 133 102 79 136

Figure S329.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.00624 (Fisher's exact test), Q value = 0.021

Table S330.  Gene #61: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
11Q LOSS MUTATED 6 3 1 13 0
11Q LOSS WILD-TYPE 75 167 80 140 40

Figure S330.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.0019

Table S331.  Gene #61: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
11Q LOSS MUTATED 3 1 2 16 1 0
11Q LOSS WILD-TYPE 114 32 181 116 34 25

Figure S331.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.046

Table S332.  Gene #61: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
11Q LOSS MUTATED 7 0 4 10 2
11Q LOSS WILD-TYPE 84 57 182 109 55

Figure S332.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00976 (Fisher's exact test), Q value = 0.031

Table S333.  Gene #61: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
11Q LOSS MUTATED 13 3 7
11Q LOSS WILD-TYPE 160 206 121

Figure S333.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 0.00899 (Fisher's exact test), Q value = 0.029

Table S334.  Gene #62: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
12P LOSS MUTATED 0 0 0 0 1 3
12P LOSS WILD-TYPE 61 80 156 82 79 66

Figure S334.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'MRNA_CNMF'

P value = 0.00662 (Fisher's exact test), Q value = 0.022

Table S335.  Gene #64: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 14
13Q LOSS MUTATED 0 6 3
13Q LOSS WILD-TYPE 31 19 11

Figure S335.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0462 (Fisher's exact test), Q value = 0.1

Table S336.  Gene #64: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
13Q LOSS MUTATED 0 3 0 3 0 0 3
13Q LOSS WILD-TYPE 11 9 4 8 13 9 7

Figure S336.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 0.024 (Fisher's exact test), Q value = 0.061

Table S337.  Gene #64: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
13Q LOSS MUTATED 3 10 29 6 15 7
13Q LOSS WILD-TYPE 58 70 127 76 65 62

Figure S337.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.00094 (Fisher's exact test), Q value = 0.0042

Table S338.  Gene #64: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
13Q LOSS MUTATED 7 16 19 3
13Q LOSS WILD-TYPE 60 54 77 78

Figure S338.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S339.  Gene #64: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
13Q LOSS MUTATED 11 2 30 9 9 1
13Q LOSS WILD-TYPE 77 84 60 73 83 32

Figure S339.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

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

Table S340.  Gene #64: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
13Q LOSS MUTATED 8 22 22 10
13Q LOSS WILD-TYPE 127 90 63 129

Figure S340.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S341.  Gene #64: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
13Q LOSS MUTATED 13 11 6 40 0
13Q LOSS WILD-TYPE 68 159 75 113 40

Figure S341.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S342.  Gene #64: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
13Q LOSS MUTATED 6 2 9 40 6 7
13Q LOSS WILD-TYPE 111 31 174 92 29 18

Figure S342.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S343.  Gene #64: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
13Q LOSS MUTATED 9 9 10 35 5
13Q LOSS WILD-TYPE 82 48 176 84 52

Figure S343.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S344.  Gene #64: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
13Q LOSS MUTATED 30 9 29
13Q LOSS WILD-TYPE 143 200 99

Figure S344.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S345.  Gene #65: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 14
14Q LOSS MUTATED 8 20 2
14Q LOSS WILD-TYPE 23 5 12

Figure S345.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00039

Table S346.  Gene #65: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
14Q LOSS MUTATED 4 7 1 11 5 0 2
14Q LOSS WILD-TYPE 7 5 3 0 8 9 8

Figure S346.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S347.  Gene #65: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
14Q LOSS MUTATED 22 32 98 25 34 5
14Q LOSS WILD-TYPE 39 48 58 57 46 64

Figure S347.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S348.  Gene #65: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
14Q LOSS MUTATED 16 34 59 14
14Q LOSS WILD-TYPE 51 36 37 67

Figure S348.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S349.  Gene #65: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
14Q LOSS MUTATED 29 22 57 53 31 6
14Q LOSS WILD-TYPE 59 64 33 29 61 27

Figure S349.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 0.039

Table S350.  Gene #65: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
14Q LOSS MUTATED 45 54 45 54
14Q LOSS WILD-TYPE 90 58 40 85

Figure S350.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S351.  Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
14Q LOSS MUTATED 19 54 22 109 9
14Q LOSS WILD-TYPE 62 116 59 44 31

Figure S351.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S352.  Gene #65: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
14Q LOSS MUTATED 41 7 52 79 32 2
14Q LOSS WILD-TYPE 76 26 131 53 3 23

Figure S352.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S353.  Gene #65: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
14Q LOSS MUTATED 27 34 61 76 12
14Q LOSS WILD-TYPE 64 23 125 43 45

Figure S353.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S354.  Gene #65: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
14Q LOSS MUTATED 72 64 74
14Q LOSS WILD-TYPE 101 145 54

Figure S354.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0441 (Fisher's exact test), Q value = 0.098

Table S355.  Gene #65: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 52 28 22
14Q LOSS MUTATED 12 20 14 3
14Q LOSS WILD-TYPE 28 32 14 19

Figure S355.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 0.005 (Fisher's exact test), Q value = 0.018

Table S356.  Gene #66: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
15Q LOSS MUTATED 2 2 21 4 5 1
15Q LOSS WILD-TYPE 59 78 135 78 75 68

Figure S356.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'RPPA_CNMF'

P value = 0.0292 (Fisher's exact test), Q value = 0.072

Table S357.  Gene #66: '15q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
15Q LOSS MUTATED 7 2 14 4 5 2
15Q LOSS WILD-TYPE 81 84 76 78 87 31

Figure S357.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'15q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.016 (Fisher's exact test), Q value = 0.046

Table S358.  Gene #66: '15q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
15Q LOSS MUTATED 5 14 9 6
15Q LOSS WILD-TYPE 130 98 76 133

Figure S358.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00045

Table S359.  Gene #66: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
15Q LOSS MUTATED 2 4 6 23 0
15Q LOSS WILD-TYPE 79 166 75 130 40

Figure S359.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S360.  Gene #66: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
15Q LOSS MUTATED 5 0 4 24 2 0
15Q LOSS WILD-TYPE 112 33 179 108 33 25

Figure S360.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.00701 (Fisher's exact test), Q value = 0.023

Table S361.  Gene #66: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
15Q LOSS MUTATED 5 6 6 16 2
15Q LOSS WILD-TYPE 86 51 180 103 55

Figure S361.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00654 (Fisher's exact test), Q value = 0.022

Table S362.  Gene #66: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
15Q LOSS MUTATED 18 6 11
15Q LOSS WILD-TYPE 155 203 117

Figure S362.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0493 (Fisher's exact test), Q value = 0.11

Table S363.  Gene #67: '16p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
16P LOSS MUTATED 0 3 4 2
16P LOSS WILD-TYPE 135 109 81 137

Figure S363.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0425 (Fisher's exact test), Q value = 0.095

Table S364.  Gene #67: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
16P LOSS MUTATED 7 1 2
16P LOSS WILD-TYPE 166 208 126

Figure S364.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 0.019 (Fisher's exact test), Q value = 0.052

Table S365.  Gene #68: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
16Q LOSS MUTATED 0 3 10 3 0 0
16Q LOSS WILD-TYPE 61 77 146 79 80 69

Figure S365.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0317 (Fisher's exact test), Q value = 0.076

Table S366.  Gene #68: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
16Q LOSS MUTATED 10 3 2
16Q LOSS WILD-TYPE 163 206 126

Figure S366.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

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

Table S367.  Gene #69: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 14
17P LOSS MUTATED 0 5 6
17P LOSS WILD-TYPE 31 20 8

Figure S367.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00097

Table S368.  Gene #69: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
17P LOSS MUTATED 0 5 1 0 0 0 5
17P LOSS WILD-TYPE 11 7 3 11 13 9 5

Figure S368.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 0.0243 (Fisher's exact test), Q value = 0.062

Table S369.  Gene #69: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
17P LOSS MUTATED 3 6 20 1 9 7
17P LOSS WILD-TYPE 58 74 136 81 71 62

Figure S369.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'RPPA_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0027

Table S370.  Gene #69: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
17P LOSS MUTATED 13 2 16 3 5 1
17P LOSS WILD-TYPE 75 84 74 79 87 32

Figure S370.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'17p loss' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00022

Table S371.  Gene #69: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
17P LOSS MUTATED 6 11 19 4
17P LOSS WILD-TYPE 129 101 66 135

Figure S371.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17p loss' versus 'MRNASEQ_CNMF'

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

Table S372.  Gene #69: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
17P LOSS MUTATED 14 2 7 21 2
17P LOSS WILD-TYPE 67 168 74 132 38

Figure S372.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S373.  Gene #69: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
17P LOSS MUTATED 6 3 3 23 2 9
17P LOSS WILD-TYPE 111 30 180 109 33 16

Figure S373.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

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

Table S374.  Gene #69: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
17P LOSS MUTATED 6 5 4 24 7
17P LOSS WILD-TYPE 85 52 182 95 50

Figure S374.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00056

Table S375.  Gene #69: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
17P LOSS MUTATED 21 6 19
17P LOSS WILD-TYPE 152 203 109

Figure S375.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MRNA_CNMF'

P value = 0.00151 (Fisher's exact test), Q value = 0.0063

Table S376.  Gene #70: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 14
17Q LOSS MUTATED 0 4 5
17Q LOSS WILD-TYPE 31 21 9

Figure S376.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0026

Table S377.  Gene #70: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
17Q LOSS MUTATED 0 4 0 0 0 0 5
17Q LOSS WILD-TYPE 11 8 4 11 13 9 5

Figure S377.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00273 (Fisher's exact test), Q value = 0.011

Table S378.  Gene #70: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
17Q LOSS MUTATED 3 5 11 3
17Q LOSS WILD-TYPE 132 107 74 136

Figure S378.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 6e-04

Table S379.  Gene #70: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
17Q LOSS MUTATED 11 1 3 12 1
17Q LOSS WILD-TYPE 70 169 78 141 39

Figure S379.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S380.  Gene #70: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
17Q LOSS MUTATED 4 1 2 11 1 9
17Q LOSS WILD-TYPE 113 32 181 121 34 16

Figure S380.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0016

Table S381.  Gene #70: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
17Q LOSS MUTATED 4 2 2 14 6
17Q LOSS WILD-TYPE 87 55 184 105 51

Figure S381.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00496 (Fisher's exact test), Q value = 0.018

Table S382.  Gene #70: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
17Q LOSS MUTATED 9 5 14
17Q LOSS WILD-TYPE 164 204 114

Figure S382.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0027

Table S383.  Gene #71: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
18P LOSS MUTATED 9 16 43 5 13 7
18P LOSS WILD-TYPE 52 64 113 77 67 62

Figure S383.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S384.  Gene #71: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
18P LOSS MUTATED 8 20 27 2
18P LOSS WILD-TYPE 59 50 69 79

Figure S384.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S385.  Gene #71: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
18P LOSS MUTATED 13 4 37 15 11 3
18P LOSS WILD-TYPE 75 82 53 67 81 30

Figure S385.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S386.  Gene #71: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
18P LOSS MUTATED 10 33 25 15
18P LOSS WILD-TYPE 125 79 60 124

Figure S386.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S387.  Gene #71: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
18P LOSS MUTATED 11 7 12 60 2
18P LOSS WILD-TYPE 70 163 69 93 38

Figure S387.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S388.  Gene #71: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
18P LOSS MUTATED 10 5 9 55 10 3
18P LOSS WILD-TYPE 107 28 174 77 25 22

Figure S388.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S389.  Gene #71: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
18P LOSS MUTATED 18 17 9 43 6
18P LOSS WILD-TYPE 73 40 177 76 51

Figure S389.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S390.  Gene #71: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
18P LOSS MUTATED 43 12 38
18P LOSS WILD-TYPE 130 197 90

Figure S390.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.0038

Table S391.  Gene #71: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 44 38
18P LOSS MUTATED 7 4 0 10
18P LOSS WILD-TYPE 32 17 44 28

Figure S391.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00667 (Fisher's exact test), Q value = 0.022

Table S392.  Gene #71: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 52 28 22
18P LOSS MUTATED 7 13 1 0
18P LOSS WILD-TYPE 33 39 27 22

Figure S392.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0018

Table S393.  Gene #72: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
18Q LOSS MUTATED 9 15 44 5 15 7
18Q LOSS WILD-TYPE 52 65 112 77 65 62

Figure S393.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00039

Table S394.  Gene #72: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
18Q LOSS MUTATED 8 20 25 4
18Q LOSS WILD-TYPE 59 50 71 77

Figure S394.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S395.  Gene #72: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
18Q LOSS MUTATED 14 6 37 14 12 3
18Q LOSS WILD-TYPE 74 80 53 68 80 30

Figure S395.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18q loss' versus 'RPPA_CHIERARCHICAL'

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

Table S396.  Gene #72: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
18Q LOSS MUTATED 12 33 25 16
18Q LOSS WILD-TYPE 123 79 60 123

Figure S396.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S397.  Gene #72: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
18Q LOSS MUTATED 13 8 13 59 1
18Q LOSS WILD-TYPE 68 162 68 94 39

Figure S397.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S398.  Gene #72: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
18Q LOSS MUTATED 10 6 10 55 10 3
18Q LOSS WILD-TYPE 107 27 173 77 25 22

Figure S398.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S399.  Gene #72: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
18Q LOSS MUTATED 18 18 10 42 7
18Q LOSS WILD-TYPE 73 39 176 77 50

Figure S399.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S400.  Gene #72: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
18Q LOSS MUTATED 44 13 38
18Q LOSS WILD-TYPE 129 196 90

Figure S400.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00927 (Fisher's exact test), Q value = 0.029

Table S401.  Gene #72: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 44 38
18Q LOSS MUTATED 7 3 1 10
18Q LOSS WILD-TYPE 32 18 43 28

Figure S401.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0322 (Fisher's exact test), Q value = 0.077

Table S402.  Gene #72: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 52 28 22
18Q LOSS MUTATED 7 12 2 0
18Q LOSS WILD-TYPE 33 40 26 22

Figure S402.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'RPPA_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0012

Table S403.  Gene #73: '19p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
19P LOSS MUTATED 0 0 8 2 0 0
19P LOSS WILD-TYPE 88 86 82 80 92 33

Figure S403.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'19p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00193 (Fisher's exact test), Q value = 0.0077

Table S404.  Gene #73: '19p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
19P LOSS MUTATED 0 3 6 1
19P LOSS WILD-TYPE 135 109 79 138

Figure S404.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.034

Table S405.  Gene #73: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
19P LOSS MUTATED 1 0 1 9 0 0
19P LOSS WILD-TYPE 116 33 182 123 35 25

Figure S405.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 0.027 (Fisher's exact test), Q value = 0.067

Table S406.  Gene #73: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
19P LOSS MUTATED 2 0 1 7 1
19P LOSS WILD-TYPE 89 57 185 112 56

Figure S406.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00537 (Fisher's exact test), Q value = 0.019

Table S407.  Gene #73: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
19P LOSS MUTATED 7 0 4
19P LOSS WILD-TYPE 166 209 124

Figure S407.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.061

Table S408.  Gene #75: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
20P LOSS MUTATED 2 1 0 5 0
20P LOSS WILD-TYPE 89 56 186 114 57

Figure S408.  Get High-res Image Gene #75: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q loss' versus 'MRNA_CNMF'

P value = 0.0328 (Fisher's exact test), Q value = 0.078

Table S409.  Gene #77: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 14
21Q LOSS MUTATED 1 2 4
21Q LOSS WILD-TYPE 30 23 10

Figure S409.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0033

Table S410.  Gene #77: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
21Q LOSS MUTATED 2 15 18 1 9 10
21Q LOSS WILD-TYPE 59 65 138 81 71 59

Figure S410.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'RPPA_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0037

Table S411.  Gene #77: '21q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
21Q LOSS MUTATED 11 7 19 8 3 0
21Q LOSS WILD-TYPE 77 79 71 74 89 33

Figure S411.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'21q loss' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00022

Table S412.  Gene #77: '21q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
21Q LOSS MUTATED 4 12 21 11
21Q LOSS WILD-TYPE 131 100 64 128

Figure S412.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0037

Table S413.  Gene #77: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
21Q LOSS MUTATED 19 10 4 17 3
21Q LOSS WILD-TYPE 62 160 77 136 37

Figure S413.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00081

Table S414.  Gene #77: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
21Q LOSS MUTATED 10 4 10 17 2 10
21Q LOSS WILD-TYPE 107 29 173 115 33 15

Figure S414.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0023

Table S415.  Gene #77: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
21Q LOSS MUTATED 7 7 14 25 1
21Q LOSS WILD-TYPE 84 50 172 94 56

Figure S415.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0049 (Fisher's exact test), Q value = 0.017

Table S416.  Gene #77: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
21Q LOSS MUTATED 21 12 21
21Q LOSS WILD-TYPE 152 197 107

Figure S416.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MRNA_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.056

Table S417.  Gene #78: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 14
22Q LOSS MUTATED 0 5 2
22Q LOSS WILD-TYPE 31 20 12

Figure S417.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0013 (Fisher's exact test), Q value = 0.0056

Table S418.  Gene #78: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
22Q LOSS MUTATED 0 0 2 4 0 0 1
22Q LOSS WILD-TYPE 11 12 2 7 13 9 9

Figure S418.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.049

Table S419.  Gene #78: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
22Q LOSS MUTATED 2 9 19 5 3 1
22Q LOSS WILD-TYPE 59 71 137 77 77 68

Figure S419.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 0.00998 (Fisher's exact test), Q value = 0.031

Table S420.  Gene #78: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
22Q LOSS MUTATED 2 6 14 2
22Q LOSS WILD-TYPE 65 64 82 79

Figure S420.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0021

Table S421.  Gene #78: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 88 86 90 82 92 33
22Q LOSS MUTATED 6 4 19 3 4 1
22Q LOSS WILD-TYPE 82 82 71 79 88 32

Figure S421.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0211 (Fisher's exact test), Q value = 0.056

Table S422.  Gene #78: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
22Q LOSS MUTATED 5 15 9 8
22Q LOSS WILD-TYPE 130 97 76 131

Figure S422.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S423.  Gene #78: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
22Q LOSS MUTATED 7 2 2 27 1
22Q LOSS WILD-TYPE 74 168 79 126 39

Figure S423.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S424.  Gene #78: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
22Q LOSS MUTATED 6 6 3 21 3 0
22Q LOSS WILD-TYPE 111 27 180 111 32 25

Figure S424.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00034

Table S425.  Gene #78: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
22Q LOSS MUTATED 3 7 6 21 2
22Q LOSS WILD-TYPE 88 50 180 98 55

Figure S425.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00108 (Fisher's exact test), Q value = 0.0048

Table S426.  Gene #78: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
22Q LOSS MUTATED 17 6 16
22Q LOSS WILD-TYPE 156 203 112

Figure S426.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0384 (Fisher's exact test), Q value = 0.087

Table S427.  Gene #78: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 44 38
22Q LOSS MUTATED 0 0 2 5
22Q LOSS WILD-TYPE 39 21 42 33

Figure S427.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'MRNA_CNMF'

P value = 0.0261 (Fisher's exact test), Q value = 0.066

Table S428.  Gene #79: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 14
XP LOSS MUTATED 3 1 5
XP LOSS WILD-TYPE 28 24 9

Figure S428.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0192 (Fisher's exact test), Q value = 0.052

Table S429.  Gene #79: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
XP LOSS MUTATED 2 1 0 0 1 0 5
XP LOSS WILD-TYPE 9 11 4 11 12 9 5

Figure S429.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

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

Table S430.  Gene #79: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
XP LOSS MUTATED 0 1 22 6 6 10
XP LOSS WILD-TYPE 61 79 134 76 74 59

Figure S430.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.059

Table S431.  Gene #79: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
XP LOSS MUTATED 6 3 15 3
XP LOSS WILD-TYPE 61 67 81 78

Figure S431.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 0.00447 (Fisher's exact test), Q value = 0.016

Table S432.  Gene #79: 'xp loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
XP LOSS MUTATED 15 11 2 12 5
XP LOSS WILD-TYPE 66 159 79 141 35

Figure S432.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0214 (Fisher's exact test), Q value = 0.056

Table S433.  Gene #79: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
XP LOSS MUTATED 9 1 12 11 5 7
XP LOSS WILD-TYPE 108 32 171 121 30 18

Figure S433.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00101 (Fisher's exact test), Q value = 0.0045

Table S434.  Gene #79: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
XP LOSS MUTATED 10 12 22
XP LOSS WILD-TYPE 163 197 106

Figure S434.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MRNA_CNMF'

P value = 0.0408 (Fisher's exact test), Q value = 0.092

Table S435.  Gene #80: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 14
XQ LOSS MUTATED 2 3 5
XQ LOSS WILD-TYPE 29 22 9

Figure S435.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xq loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0187 (Fisher's exact test), Q value = 0.051

Table S436.  Gene #80: 'xq loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
XQ LOSS MUTATED 1 3 0 0 1 0 5
XQ LOSS WILD-TYPE 10 9 4 11 12 9 5

Figure S436.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0011

Table S437.  Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 61 80 156 82 80 69
XQ LOSS MUTATED 0 2 26 6 4 7
XQ LOSS WILD-TYPE 61 78 130 76 76 62

Figure S437.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.00328 (Fisher's exact test), Q value = 0.013

Table S438.  Gene #80: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 67 70 96 81
XQ LOSS MUTATED 4 3 16 2
XQ LOSS WILD-TYPE 63 67 80 79

Figure S438.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.033 (Fisher's exact test), Q value = 0.078

Table S439.  Gene #80: 'xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 85 139
XQ LOSS MUTATED 8 12 13 7
XQ LOSS WILD-TYPE 127 100 72 132

Figure S439.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.041

Table S440.  Gene #80: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 170 81 153 40
XQ LOSS MUTATED 14 9 3 15 4
XQ LOSS WILD-TYPE 67 161 78 138 36

Figure S440.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0418 (Fisher's exact test), Q value = 0.094

Table S441.  Gene #80: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
XQ LOSS MUTATED 8 2 10 15 4 6
XQ LOSS WILD-TYPE 109 31 173 117 31 19

Figure S441.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.042

Table S442.  Gene #80: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 57 186 119 57
XQ LOSS MUTATED 6 5 10 20 3
XQ LOSS WILD-TYPE 85 52 176 99 54

Figure S442.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00163 (Fisher's exact test), Q value = 0.0068

Table S443.  Gene #80: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 173 209 128
XQ LOSS MUTATED 13 10 21
XQ LOSS WILD-TYPE 160 199 107

Figure S443.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRC-TP/22531285/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRC-TP/22555002/KIRC-TP.transferedmergedcluster.txt

  • Number of patients = 528

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have mutations, 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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