Correlation between copy number variations of arm-level result and molecular subtypes
Breast Invasive Carcinoma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1W66HZ7
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1W66HZ7
Overview
Introduction

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

Summary

Testing the association between copy number variation 80 arm-level results and 10 molecular subtypes across 891 patients, 348 significant findings detected with Q value < 0.25.

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

  • 1q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • 3p gain cnv correlated to 'CN_CNMF'.

  • 3q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 4p gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'MIRSEQ_CNMF'.

  • 4q gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 5q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 6p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 6q gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 7p gain cnv correlated to 'CN_CNMF'.

  • 7q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 8q gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 9p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 9q gain cnv correlated to 'CN_CNMF'.

  • 10p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 10q gain cnv correlated to 'CN_CNMF'.

  • 12p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 12q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 13q gain cnv correlated to 'MRNASEQ_CNMF'.

  • 14q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 16p gain cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 17q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 18p gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 18q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 19q gain cnv correlated to 'CN_CNMF'.

  • 20p gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • 20q gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

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

  • 22q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Xq gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • 2q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

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

  • 3q loss cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • 4p 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'.

  • 4q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 5p 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'.

  • 5q 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'.

  • 6p loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 6q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 7p loss cnv correlated to 'CN_CNMF'.

  • 8p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • 9p loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • 9q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 10p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 11p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • 11q loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 12p loss cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

  • 12q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 14q 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'.

  • 15q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 16p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 16q 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'.

  • 17p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • 17q 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'.

  • 18p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 18q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 19p loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 19q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 20p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 20q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 21q loss cnv correlated to 'CN_CNMF'.

  • 22q 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'.

  • Xq loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level results and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 348 significant findings detected.

Molecular
subtypes 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Chi-square test Chi-square 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
2p gain 48 (5%) 843 7.76e-12
(5.74e-09) 		2.88e-11
(2.1e-08) 		2.47e-10
(1.76e-07) 		4.97e-05
(0.0267) 		2.71e-08
(1.84e-05) 		4.89e-08
(3.28e-05) 		1.06e-11
(7.86e-09) 		6.6e-13
(4.92e-10) 		1.36e-11
(1e-08) 		5.45e-10
(3.87e-07)
10p gain 109 (12%) 782 6.61e-09
(4.58e-06) 		7.19e-08
(4.79e-05) 		2.62e-18
(2.04e-15) 		1.21e-13
(9.12e-11) 		1.32e-05
(0.00764) 		1.1e-06
(0.000696) 		3.59e-15
(2.77e-12) 		1.14e-14
(8.71e-12) 		1.41e-14
(1.07e-11) 		4.47e-14
(3.38e-11)
4p loss 184 (21%) 707 2.69e-08
(1.83e-05) 		6.36e-13
(4.76e-10) 		8.63e-26
(6.84e-23) 		2e-14
(1.52e-11) 		0.000181
(0.0901) 		1.34e-05
(0.00771) 		5.08e-15
(3.9e-12) 		6.38e-15
(4.89e-12) 		1.99e-14
(1.51e-11) 		1.71e-10
(1.23e-07)
5p loss 72 (8%) 819 4.49e-05
(0.0242) 		5.98e-07
(0.000382) 		7.59e-21
(5.95e-18) 		7.3e-10
(5.16e-07) 		0.000141
(0.0715) 		4.19e-06
(0.00253) 		9.12e-09
(6.3e-06) 		2.39e-08
(1.64e-05) 		3.74e-15
(2.88e-12) 		1.78e-12
(1.32e-09)
5q loss 123 (14%) 768 1.82e-14
(1.39e-11) 		4.84e-15
(3.72e-12) 		5.85e-49
(4.68e-46) 		1.02e-31
(8.13e-29) 		2.75e-08
(1.87e-05) 		1.45e-10
(1.04e-07) 		3.31e-22
(2.61e-19) 		7.83e-24
(6.2e-21) 		1.31e-27
(1.04e-24) 		1.29e-30
(1.03e-27)
14q loss 131 (15%) 760 2.49e-07
(0.000162) 		4.23e-08
(2.84e-05) 		1.02e-21
(8.02e-19) 		2.89e-15
(2.23e-12) 		0.000103
(0.0534) 		4.06e-05
(0.0221) 		1.21e-10
(8.71e-08) 		5.59e-12
(4.15e-09) 		6.45e-13
(4.82e-10) 		8.25e-14
(6.23e-11)
16q loss 392 (44%) 499 2.06e-11
(1.51e-08) 		1.6e-13
(1.2e-10) 		1.41e-11
(1.03e-08) 		2.79e-14
(2.11e-11) 		7.03e-07
(0.000447) 		5.24e-11
(3.8e-08) 		7.21e-19
(5.62e-16) 		2.11e-20
(1.65e-17) 		1.96e-19
(1.53e-16) 		5.87e-20
(4.58e-17)
17q loss 141 (16%) 750 4.02e-08
(2.7e-05) 		1.03e-06
(0.000654) 		9.27e-14
(6.98e-11) 		1.12e-06
(0.000705) 		3.38e-10
(2.4e-07) 		5.84e-07
(0.000374) 		1.73e-10
(1.24e-07) 		1.06e-05
(0.00617) 		3.67e-09
(2.57e-06) 		1.09e-06
(0.000691)
22q loss 298 (33%) 593 3.08e-05
(0.017) 		5.42e-07
(0.000347) 		4.97e-08
(3.32e-05) 		9.12e-06
(0.00537) 		0.000358
(0.169) 		1.02e-05
(0.00595) 		1.54e-11
(1.13e-08) 		8.28e-10
(5.84e-07) 		1.65e-08
(1.13e-05) 		6.58e-07
(0.00042)
1p gain 89 (10%) 802 0.000412
(0.192) 		1.6e-06
(0.000997) 		2.83e-07
(0.000184) 		0.0191
(1.00) 		5.45e-05
(0.0292) 		0.000298
(0.144) 		7.78e-07
(0.000494) 		3.1e-05
(0.0171) 		2.8e-05
(0.0156) 		2.21e-05
(0.0124)
2q gain 25 (3%) 866 2.66e-07
(0.000173) 		1.85e-05
(0.0105) 		0.000334
(0.159) 		0.00612
(1.00) 		1.65e-07
(0.000108) 		0.000521
(0.237) 		3.15e-06
(0.00191) 		7.99e-06
(0.00474) 		0.000296
(0.143) 		0.000163
(0.0816)
6p gain 101 (11%) 790 2.87e-05
(0.016) 		2e-05
(0.0113) 		1.03e-14
(7.89e-12) 		4.26e-07
(0.000274) 		0.00415
(1.00) 		0.0509
(1.00) 		7.86e-09
(5.44e-06) 		2.67e-08
(1.82e-05) 		1.51e-11
(1.11e-08) 		1.13e-08
(7.79e-06)
9p gain 67 (8%) 824 0.000317
(0.152) 		7e-08
(4.67e-05) 		1.15e-09
(8.09e-07) 		0.000558
(0.252) 		0.0113
(1.00) 		0.000138
(0.0702) 		1.3e-07
(8.58e-05) 		2.63e-08
(1.8e-05) 		3.23e-06
(0.00196) 		3.9e-07
(0.000251)
1p loss 123 (14%) 768 0.000472
(0.216) 		3.78e-10
(2.68e-07) 		6.77e-22
(5.32e-19) 		2.35e-06
(0.00144) 		0.531
(1.00) 		0.282
(1.00) 		1.54e-11
(1.13e-08) 		2.27e-07
(0.000148) 		0.000167
(0.0833) 		0.000259
(0.127)
3p loss 90 (10%) 801 1.63e-07
(0.000107) 		0.000338
(0.16) 		1.19e-08
(8.22e-06) 		0.000132
(0.0675) 		0.00275
(1.00) 		6.62e-05
(0.0352) 		1.83e-05
(0.0105) 		0.00167
(0.696) 		1.82e-07
(0.000119) 		0.000131
(0.0671)
4q loss 154 (17%) 737 4.27e-05
(0.0231) 		5.71e-09
(3.97e-06) 		6.32e-22
(4.97e-19) 		7.78e-12
(5.75e-09) 		0.0157
(1.00) 		0.00193
(0.787) 		5.25e-11
(3.8e-08) 		4.7e-11
(3.41e-08) 		3.55e-08
(2.4e-05) 		7.55e-08
(5.02e-05)
6q gain 59 (7%) 832 0.000135
(0.0687) 		0.00513
(1.00) 		2.23e-15
(1.73e-12) 		0.00438
(1.00) 		0.000363
(0.171) 		0.0278
(1.00) 		6.43e-06
(0.00383) 		2.15e-06
(0.00133) 		3.22e-07
(0.000208) 		1.48e-06
(0.000925)
18p gain 86 (10%) 805 0.00719
(1.00) 		0.000172
(0.0859) 		1.77e-07
(0.000116) 		2.56e-06
(0.00157) 		0.00376
(1.00) 		0.00326
(1.00) 		3.05e-06
(0.00186) 		3.81e-08
(2.57e-05) 		2.19e-06
(0.00135) 		9.65e-06
(0.00566)
21q gain 101 (11%) 790 0.00199
(0.811) 		6.94e-05
(0.0369) 		5e-09
(3.48e-06) 		2.12e-06
(0.00131) 		0.113
(1.00) 		0.0127
(1.00) 		1.65e-10
(1.18e-07) 		6.63e-10
(4.7e-07) 		1.08e-05
(0.00627) 		1.97e-05
(0.0112)
6q loss 164 (18%) 727 0.00162
(0.682) 		3.04e-06
(0.00186) 		1.58e-13
(1.19e-10) 		2.9e-07
(0.000188) 		0.000711
(0.317) 		0.0076
(1.00) 		7.51e-09
(5.2e-06) 		7.66e-08
(5.09e-05) 		0.000236
(0.116) 		3.06e-06
(0.00187)
9q loss 142 (16%) 749 0.00486
(1.00) 		0.000138
(0.0702) 		6.57e-17
(5.1e-14) 		1.1e-08
(7.61e-06) 		0.0105
(1.00) 		0.17
(1.00) 		1.36e-08
(9.35e-06) 		0.000389
(0.183) 		7.84e-11
(5.66e-08) 		0.000162
(0.0812)
12q loss 52 (6%) 839 0.00314
(1.00) 		0.000187
(0.0927) 		4.08e-07
(0.000262) 		3.17e-08
(2.15e-05) 		0.006
(1.00) 		0.00346
(1.00) 		5.4e-08
(3.61e-05) 		1.31e-07
(8.61e-05) 		1.08e-05
(0.00629) 		1.98e-05
(0.0112)
8q gain 366 (41%) 525 0.00646
(1.00) 		4.37e-05
(0.0236) 		3.15e-23
(2.49e-20) 		4.66e-09
(3.25e-06) 		0.668
(1.00) 		0.559
(1.00) 		8.4e-08
(5.57e-05) 		4.63e-06
(0.00278) 		1.19e-10
(8.6e-08) 		0.00309
(1.00)
12p gain 110 (12%) 781 0.0024
(0.958) 		0.000563
(0.254) 		1.71e-14
(1.3e-11) 		0.000142
(0.0717) 		0.374
(1.00) 		0.0914
(1.00) 		7.38e-05
(0.0389) 		0.000397
(0.186) 		5.53e-06
(0.00331) 		0.000532
(0.242)
Xq gain 20 (2%) 871 3.9e-05
(0.0212) 		0.000889
(0.387) 		7e-05
(0.0371) 		0.0139
(1.00) 		0.0805
(1.00) 		0.0085
(1.00) 		0.000508
(0.232) 		7.97e-05
(0.042) 		9.25e-06
(0.00543) 		9.93e-05
(0.0518)
2p loss 71 (8%) 820 0.00222
(0.891) 		0.00031
(0.149) 		5.16e-12
(3.83e-09) 		2.2e-05
(0.0124) 		0.06
(1.00) 		0.0172
(1.00) 		1.23e-06
(0.000773) 		1.37e-06
(0.000856) 		2.22e-05
(0.0124) 		0.00571
(1.00)
6p loss 105 (12%) 786 0.00839
(1.00) 		0.000242
(0.119) 		2.19e-08
(1.5e-05) 		3.08e-05
(0.017) 		0.0168
(1.00) 		0.00506
(1.00) 		1.36e-06
(0.000853) 		6.98e-06
(0.00415) 		0.000147
(0.074) 		0.00304
(1.00)
15q loss 159 (18%) 732 0.00894
(1.00) 		0.000126
(0.0646) 		2.73e-18
(2.12e-15) 		2.03e-06
(0.00126) 		0.134
(1.00) 		0.00762
(1.00) 		3.13e-05
(0.0172) 		0.000971
(0.421) 		1.92e-07
(0.000125) 		6.58e-07
(0.00042)
3q gain 98 (11%) 793 0.0153
(1.00) 		0.0025
(0.991) 		1.91e-09
(1.34e-06) 		0.00054
(0.245) 		0.0266
(1.00) 		0.171
(1.00) 		0.00016
(0.0806) 		0.000409
(0.191) 		3.13e-05
(0.0172) 		0.00105
(0.455)
20q gain 272 (31%) 619 0.000311
(0.149) 		0.000843
(0.371) 		1.22e-33
(9.72e-31) 		2.77e-10
(1.97e-07) 		0.238
(1.00) 		0.752
(1.00) 		1.24e-05
(0.00716) 		0.00673
(1.00) 		3.78e-07
(0.000244) 		0.139
(1.00)
22q gain 42 (5%) 849 0.0128
(1.00) 		0.00478
(1.00) 		5.27e-11
(3.81e-08) 		0.0153
(1.00) 		0.133
(1.00) 		0.148
(1.00) 		3.02e-06
(0.00185) 		1.41e-05
(0.0081) 		0.000301
(0.145) 		6.32e-06
(0.00377)
9p loss 184 (21%) 707 0.00866
(1.00) 		0.000437
(0.203) 		3.99e-21
(3.13e-18) 		3.37e-11
(2.45e-08) 		0.0328
(1.00) 		0.747
(1.00) 		1.76e-06
(0.00109) 		0.0884
(1.00) 		8.43e-07
(0.000535) 		0.00669
(1.00)
11q loss 228 (26%) 663 3.85e-05
(0.021) 		0.00185
(0.76) 		6.26e-26
(4.96e-23) 		2.12e-10
(1.51e-07) 		0.173
(1.00) 		0.198
(1.00) 		3e-06
(0.00184) 		0.000346
(0.164) 		0.0024
(0.958) 		0.00472
(1.00)
13q loss 264 (30%) 627 0.0225
(1.00) 		0.000332
(0.159) 		2.45e-26
(1.95e-23) 		9.06e-08
(6e-05) 		0.838
(1.00) 		0.567
(1.00) 		0.000242
(0.119) 		0.00371
(1.00) 		3.09e-09
(2.16e-06) 		0.158
(1.00)
20q loss 29 (3%) 862 0.848
(1.00) 		0.102
(1.00) 		4.75e-06
(0.00285) 		8.43e-06
(0.00499) 		0.529
(1.00) 		0.162
(1.00) 		0.00418
(1.00) 		0.000217
(0.107) 		5.06e-05
(0.0272) 		2.76e-05
(0.0154)
7q gain 111 (12%) 780 0.159
(1.00) 		0.016
(1.00) 		1.52e-05
(0.00871) 		0.000437
(0.203) 		0.312
(1.00) 		0.199
(1.00) 		0.00574
(1.00) 		0.000438
(0.203) 		0.0773
(1.00) 		0.000295
(0.143)
17q gain 122 (14%) 769 0.0368
(1.00) 		0.00746
(1.00) 		2.3e-22
(1.82e-19) 		6.17e-05
(0.0329) 		0.37
(1.00) 		0.00944
(1.00) 		3.57e-05
(0.0195) 		4.62e-06
(0.00278) 		0.0914
(1.00) 		0.0185
(1.00)
18q gain 74 (8%) 817 0.176
(1.00) 		0.00206
(0.832) 		8.83e-06
(0.00521) 		0.0321
(1.00) 		0.208
(1.00) 		0.2
(1.00) 		0.000241
(0.119) 		9.8e-05
(0.0514) 		8.56e-05
(0.045) 		0.00603
(1.00)
20p gain 236 (26%) 655 1.41e-05
(0.00811) 		0.00184
(0.758) 		5.7e-26
(4.53e-23) 		2.61e-05
(0.0146) 		0.031
(1.00) 		0.108
(1.00) 		0.00159
(0.674) 		0.065
(1.00) 		1.98e-06
(0.00123) 		0.27
(1.00)
19q loss 51 (6%) 840 0.116
(1.00) 		3.12e-05
(0.0172) 		1.43e-11
(1.05e-08) 		1.15e-05
(0.00667) 		0.15
(1.00) 		0.125
(1.00) 		0.000133
(0.0677) 		0.00088
(0.384) 		0.0137
(1.00) 		0.258
(1.00)
20p loss 54 (6%) 837 0.554
(1.00) 		0.0157
(1.00) 		9.38e-08
(6.2e-05) 		0.000431
(0.201) 		0.362
(1.00) 		0.498
(1.00) 		0.00366
(1.00) 		0.000479
(0.219) 		5.09e-05
(0.0273) 		0.00325
(1.00)
4p gain 29 (3%) 862 0.116
(1.00) 		4.25e-05
(0.0231) 		1.67e-07
(0.00011) 		0.00156
(0.662) 		0.0447
(1.00) 		0.0399
(1.00) 		0.016
(1.00) 		0.00178
(0.736) 		0.000297
(0.144) 		0.258
(1.00)
5q gain 102 (11%) 789 0.0251
(1.00) 		0.00453
(1.00) 		1.36e-15
(1.05e-12) 		0.00349
(1.00) 		0.00134
(0.573) 		0.00226
(0.905) 		0.000577
(0.26) 		1.15e-05
(0.00666) 		0.00488
(1.00) 		2.18e-05
(0.0123)
8p gain 169 (19%) 722 0.134
(1.00) 		0.0134
(1.00) 		5.6e-13
(4.19e-10) 		0.00277
(1.00) 		0.143
(1.00) 		0.391
(1.00) 		0.000192
(0.0951) 		0.000113
(0.0583) 		0.00317
(1.00) 		0.893
(1.00)
16p gain 239 (27%) 652 0.00147
(0.623) 		0.00162
(0.682) 		0.00754
(1.00) 		8.8e-06
(0.0052) 		0.000697
(0.312) 		0.000608
(0.273) 		0.000156
(0.0787) 		3.64e-06
(0.0022) 		0.000713
(0.318) 		0.027
(1.00)
2q loss 87 (10%) 804 0.0761
(1.00) 		0.00326
(1.00) 		3.93e-11
(2.86e-08) 		2e-05
(0.0113) 		0.137
(1.00) 		0.0845
(1.00) 		0.00162
(0.682) 		0.00215
(0.865) 		3.61e-05
(0.0197) 		0.486
(1.00)
8p loss 274 (31%) 617 0.00989
(1.00) 		0.142
(1.00) 		1.98e-16
(1.53e-13) 		1.93e-06
(0.0012) 		0.62
(1.00) 		0.936
(1.00) 		0.000809
(0.357) 		0.142
(1.00) 		0.000464
(0.213) 		0.0402
(1.00)
10q loss 110 (12%) 781 0.00558
(1.00) 		0.00244
(0.97) 		3.69e-11
(2.69e-08) 		3.72e-06
(0.00225) 		0.00345
(1.00) 		0.0559
(1.00) 		7.57e-06
(0.0045) 		0.0299
(1.00) 		0.002
(0.812) 		0.0138
(1.00)
11p loss 148 (17%) 743 0.874
(1.00) 		0.218
(1.00) 		6.7e-12
(4.97e-09) 		2.78e-08
(1.88e-05) 		0.133
(1.00) 		0.0225
(1.00) 		0.0035
(1.00) 		0.0311
(1.00) 		9.9e-05
(0.0518) 		0.319
(1.00)
17p loss 367 (41%) 524 0.0376
(1.00) 		0.678
(1.00) 		2.04e-12
(1.52e-09) 		1.4e-07
(9.19e-05) 		0.00121
(0.519) 		0.152
(1.00) 		0.21
(1.00) 		0.914
(1.00) 		2.94e-05
(0.0163) 		0.0276
(1.00)
19p loss 65 (7%) 826 0.143
(1.00) 		0.000273
(0.133) 		8.83e-14
(6.66e-11) 		1.9e-09
(1.33e-06) 		0.538
(1.00) 		0.118
(1.00) 		0.000845
(0.371) 		0.0021
(0.848) 		0.000808
(0.357) 		0.165
(1.00)
1q gain 473 (53%) 418 0.163
(1.00) 		0.704
(1.00) 		1.12e-09
(7.89e-07) 		4.02e-14
(3.04e-11) 		0.12
(1.00) 		0.157
(1.00) 		0.105
(1.00) 		0.0172
(1.00) 		0.0248
(1.00) 		0.0261
(1.00)
4q gain 27 (3%) 864 0.236
(1.00) 		0.000438
(0.203) 		3.78e-09
(2.64e-06) 		0.00517
(1.00) 		0.0551
(1.00) 		0.0105
(1.00) 		0.0107
(1.00) 		0.00576
(1.00) 		0.0032
(1.00) 		0.113
(1.00)
12q gain 83 (9%) 808 0.0208
(1.00) 		0.0048
(1.00) 		1.21e-14
(9.23e-12) 		0.000357
(0.169) 		0.256
(1.00) 		0.514
(1.00) 		0.00165
(0.69) 		0.0394
(1.00) 		0.00756
(1.00) 		0.421
(1.00)
14q gain 77 (9%) 814 0.0764
(1.00) 		0.0214
(1.00) 		0.000121
(0.0624) 		0.00594
(1.00) 		0.949
(1.00) 		0.282
(1.00) 		1.94e-05
(0.011) 		0.00111
(0.481) 		0.000791
(0.35) 		0.11
(1.00)
19p gain 67 (8%) 824 0.0953
(1.00) 		0.0147
(1.00) 		0.000102
(0.0532) 		0.153
(1.00) 		0.0752
(1.00) 		0.103
(1.00) 		0.0139
(1.00) 		0.000444
(0.204) 		0.0205
(1.00) 		0.000877
(0.383)
3q loss 45 (5%) 846 2.89e-05
(0.0161) 		0.00412
(1.00) 		2.71e-05
(0.0151) 		0.0327
(1.00) 		0.206
(1.00) 		0.0798
(1.00) 		0.012
(1.00) 		0.126
(1.00) 		0.00114
(0.492) 		0.0866
(1.00)
10p loss 71 (8%) 820 0.0547
(1.00) 		0.0325
(1.00) 		1.52e-05
(0.00871) 		0.0108
(1.00) 		0.605
(1.00) 		0.399
(1.00) 		0.00029
(0.141) 		0.172
(1.00) 		0.00201
(0.814) 		0.2
(1.00)
12p loss 67 (8%) 824 0.052
(1.00) 		0.194
(1.00) 		0.00182
(0.752) 		9.21e-06
(0.00542) 		0.157
(1.00) 		0.333
(1.00) 		0.000112
(0.0583) 		0.00371
(1.00) 		0.00749
(1.00) 		0.0255
(1.00)
16p loss 56 (6%) 835 0.0699
(1.00) 		0.0224
(1.00) 		6.45e-05
(0.0344) 		0.000109
(0.0565) 		0.088
(1.00) 		0.186
(1.00) 		0.00166
(0.696) 		0.00394
(1.00) 		0.000864
(0.378) 		0.00188
(0.771)
18p loss 172 (19%) 719 0.0625
(1.00) 		0.0779
(1.00) 		3.2e-08
(2.16e-05) 		4.32e-06
(0.0026) 		0.987
(1.00) 		0.974
(1.00) 		0.0369
(1.00) 		0.559
(1.00) 		0.0452
(1.00) 		0.0275
(1.00)
18q loss 175 (20%) 716 0.00925
(1.00) 		0.122
(1.00) 		9.76e-11
(7.04e-08) 		4.04e-08
(2.72e-05) 		0.548
(1.00) 		0.795
(1.00) 		0.00357
(1.00) 		0.136
(1.00) 		0.0554
(1.00) 		0.188
(1.00)
Xq loss 30 (3%) 861 0.00415
(1.00) 		0.122
(1.00) 		0.000119
(0.0612) 		0.00143
(0.607) 		0.0356
(1.00) 		0.317
(1.00) 		0.00964
(1.00) 		0.0692
(1.00) 		7.21e-05
(0.0382) 		0.0278
(1.00)
3p gain 52 (6%) 839 0.835
(1.00) 		0.0381
(1.00) 		1.37e-06
(0.000856) 		0.181
(1.00) 		0.528
(1.00) 		0.216
(1.00) 		0.0432
(1.00) 		0.0466
(1.00) 		0.025
(1.00) 		0.17
(1.00)
5p gain 166 (19%) 725 0.514
(1.00) 		0.386
(1.00) 		2.4e-09
(1.68e-06) 		0.181
(1.00) 		0.541
(1.00) 		0.315
(1.00) 		0.707
(1.00) 		0.315
(1.00) 		0.0213
(1.00) 		0.632
(1.00)
7p gain 153 (17%) 738 0.392
(1.00) 		0.388
(1.00) 		0.000302
(0.145) 		0.00456
(1.00) 		0.986
(1.00) 		0.513
(1.00) 		0.0302
(1.00) 		0.115
(1.00) 		0.196
(1.00) 		0.0393
(1.00)
9q gain 54 (6%) 837 0.336
(1.00) 		0.0428
(1.00) 		9.79e-05
(0.0514) 		0.338
(1.00) 		0.968
(1.00) 		0.543
(1.00) 		0.0434
(1.00) 		0.00683
(1.00) 		0.0491
(1.00) 		0.243
(1.00)
10q gain 44 (5%) 847 0.00174
(0.724) 		0.0126
(1.00) 		1.23e-05
(0.00709) 		0.0219
(1.00) 		0.0822
(1.00) 		0.0515
(1.00) 		0.00391
(1.00) 		0.00266
(1.00) 		0.00114
(0.492) 		0.00801
(1.00)
13q gain 45 (5%) 846 0.0473
(1.00) 		0.0865
(1.00) 		0.0519
(1.00) 		0.0458
(1.00) 		0.0196
(1.00) 		0.134
(1.00) 		0.000424
(0.198) 		0.0405
(1.00) 		0.00693
(1.00) 		0.0081
(1.00)
19q gain 83 (9%) 808 0.467
(1.00) 		0.0384
(1.00) 		0.000114
(0.0587) 		0.0722
(1.00) 		0.199
(1.00) 		0.16
(1.00) 		0.0458
(1.00) 		0.00127
(0.545) 		0.0504
(1.00) 		0.00842
(1.00)
7p loss 47 (5%) 844 0.0926
(1.00) 		0.031
(1.00) 		4.07e-06
(0.00246) 		0.00415
(1.00) 		0.424
(1.00) 		0.443
(1.00) 		0.00174
(0.724) 		0.00955
(1.00) 		0.00848
(1.00) 		0.00808
(1.00)
21q loss 87 (10%) 804 0.235
(1.00) 		0.298
(1.00) 		1.31e-06
(0.000825) 		0.354
(1.00) 		0.978
(1.00) 		0.874
(1.00) 		0.324
(1.00) 		0.401
(1.00) 		0.0346
(1.00) 		0.145
(1.00)
11p gain 64 (7%) 827 0.613
(1.00) 		0.611
(1.00) 		0.0116
(1.00) 		0.232
(1.00) 		0.384
(1.00) 		0.163
(1.00) 		0.637
(1.00) 		0.819
(1.00) 		0.428
(1.00) 		0.304
(1.00)
11q gain 45 (5%) 846 0.174
(1.00) 		0.809
(1.00) 		0.000582
(0.261) 		0.286
(1.00) 		0.935
(1.00) 		0.687
(1.00) 		0.33
(1.00) 		0.433
(1.00) 		0.231
(1.00) 		0.094
(1.00)
15q gain 46 (5%) 845 0.604
(1.00) 		0.339
(1.00) 		0.29
(1.00) 		0.345
(1.00) 		0.918
(1.00) 		0.48
(1.00) 		0.216
(1.00) 		0.181
(1.00) 		0.245
(1.00) 		0.0964
(1.00)
16q gain 53 (6%) 838 0.505
(1.00) 		0.344
(1.00) 		0.00184
(0.757) 		0.168
(1.00) 		0.143
(1.00) 		0.775
(1.00) 		0.111
(1.00) 		0.109
(1.00) 		0.00793
(1.00) 		0.00351
(1.00)
17p gain 46 (5%) 845 0.0906
(1.00) 		0.309
(1.00) 		0.000766
(0.34) 		0.832
(1.00) 		0.178
(1.00) 		0.234
(1.00) 		0.575
(1.00) 		0.721
(1.00) 		0.474
(1.00) 		0.528
(1.00)
1q loss 21 (2%) 870 0.257
(1.00) 		0.067
(1.00) 		0.0421
(1.00) 		0.162
(1.00) 		0.406
(1.00) 		0.852
(1.00) 		0.0188
(1.00) 		0.461
(1.00) 		0.0225
(1.00) 		0.48
(1.00)
7q loss 63 (7%) 828 0.0382
(1.00) 		0.158
(1.00) 		0.00584
(1.00) 		0.125
(1.00) 		0.234
(1.00) 		0.421
(1.00) 		0.0434
(1.00) 		0.333
(1.00) 		0.02
(1.00) 		0.276
(1.00)
8q loss 45 (5%) 846 0.573
(1.00) 		0.549
(1.00) 		0.163
(1.00) 		0.148
(1.00) 		0.823
(1.00) 		0.856
(1.00) 		0.0255
(1.00) 		0.652
(1.00) 		0.0731
(1.00) 		1
(1.00)
'1p gain mutation analysis' versus 'MRNA_CNMF'

P value = 0.000412 (Fisher's exact test), Q value = 0.19

Table S1.  Gene #1: '1p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
1P GAIN MUTATED 19 11 33
1P GAIN WILD-TYPE 237 81 126

Figure S1.  Get High-res Image Gene #1: '1p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'1p gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.6e-06 (Fisher's exact test), Q value = 0.001

Table S2.  Gene #1: '1p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
1P GAIN MUTATED 32 17 14
1P GAIN WILD-TYPE 89 235 120

Figure S2.  Get High-res Image Gene #1: '1p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'1p gain mutation analysis' versus 'CN_CNMF'

P value = 2.83e-07 (Chi-square test), Q value = 0.00018

Table S3.  Gene #1: '1p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
1P GAIN MUTATED 20 6 13 44 6
1P GAIN WILD-TYPE 326 70 185 171 50

Figure S3.  Get High-res Image Gene #1: '1p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'1p gain mutation analysis' versus 'RPPA_CNMF'

P value = 5.45e-05 (Fisher's exact test), Q value = 0.029

Table S4.  Gene #1: '1p gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
1P GAIN MUTATED 34 13 6
1P GAIN WILD-TYPE 112 116 109

Figure S4.  Get High-res Image Gene #1: '1p gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'1p gain mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.000298 (Fisher's exact test), Q value = 0.14

Table S5.  Gene #1: '1p gain mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
1P GAIN MUTATED 20 5 28
1P GAIN WILD-TYPE 136 103 98

Figure S5.  Get High-res Image Gene #1: '1p gain mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'1p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.78e-07 (Fisher's exact test), Q value = 0.00049

Table S6.  Gene #1: '1p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
1P GAIN MUTATED 46 12 27
1P GAIN WILD-TYPE 189 143 407

Figure S6.  Get High-res Image Gene #1: '1p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'1p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.1e-05 (Fisher's exact test), Q value = 0.017

Table S7.  Gene #1: '1p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
1P GAIN MUTATED 32 15 38
1P GAIN WILD-TYPE 381 201 157

Figure S7.  Get High-res Image Gene #1: '1p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'1p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.8e-05 (Fisher's exact test), Q value = 0.016

Table S8.  Gene #1: '1p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
1P GAIN MUTATED 13 30 44
1P GAIN WILD-TYPE 187 393 205

Figure S8.  Get High-res Image Gene #1: '1p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'1p gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.21e-05 (Fisher's exact test), Q value = 0.012

Table S9.  Gene #1: '1p gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
1P GAIN MUTATED 37 42 8
1P GAIN WILD-TYPE 167 567 51

Figure S9.  Get High-res Image Gene #1: '1p gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'1q gain mutation analysis' versus 'CN_CNMF'

P value = 1.12e-09 (Chi-square test), Q value = 7.9e-07

Table S10.  Gene #2: '1q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
1Q GAIN MUTATED 170 68 108 98 29
1Q GAIN WILD-TYPE 176 8 90 117 27

Figure S10.  Get High-res Image Gene #2: '1q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'1q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.02e-14 (Chi-square test), Q value = 3e-11

Table S11.  Gene #2: '1q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
1Q GAIN MUTATED 43 110 51 52 16 24
1Q GAIN WILD-TYPE 53 32 29 71 20 66

Figure S11.  Get High-res Image Gene #2: '1q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'2p gain mutation analysis' versus 'MRNA_CNMF'

P value = 7.76e-12 (Fisher's exact test), Q value = 5.7e-09

Table S12.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
2P GAIN MUTATED 2 2 29
2P GAIN WILD-TYPE 254 90 130

Figure S12.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'2p gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 2.88e-11 (Fisher's exact test), Q value = 2.1e-08

Table S13.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
2P GAIN MUTATED 25 8 0
2P GAIN WILD-TYPE 96 244 134

Figure S13.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'2p gain mutation analysis' versus 'CN_CNMF'

P value = 2.47e-10 (Chi-square test), Q value = 1.8e-07

Table S14.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
2P GAIN MUTATED 3 1 10 31 3
2P GAIN WILD-TYPE 343 75 188 184 53

Figure S14.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'2p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.97e-05 (Chi-square test), Q value = 0.027

Table S15.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
2P GAIN MUTATED 14 1 4 5 1 2
2P GAIN WILD-TYPE 82 141 76 118 35 88

Figure S15.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'2p gain mutation analysis' versus 'RPPA_CNMF'

P value = 2.71e-08 (Fisher's exact test), Q value = 1.8e-05

Table S16.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
2P GAIN MUTATED 24 0 4
2P GAIN WILD-TYPE 122 129 111

Figure S16.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'2p gain mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 4.89e-08 (Fisher's exact test), Q value = 3.3e-05

Table S17.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
2P GAIN MUTATED 4 1 23
2P GAIN WILD-TYPE 152 107 103

Figure S17.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'2p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.06e-11 (Fisher's exact test), Q value = 7.9e-09

Table S18.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
2P GAIN MUTATED 35 0 12
2P GAIN WILD-TYPE 200 155 422

Figure S18.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'2p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.6e-13 (Fisher's exact test), Q value = 4.9e-10

Table S19.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
2P GAIN MUTATED 15 0 32
2P GAIN WILD-TYPE 398 216 163

Figure S19.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.36e-11 (Fisher's exact test), Q value = 1e-08

Table S20.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
2P GAIN MUTATED 1 8 33
2P GAIN WILD-TYPE 199 415 216

Figure S20.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'2p gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.45e-10 (Fisher's exact test), Q value = 3.9e-07

Table S21.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
2P GAIN MUTATED 27 10 5
2P GAIN WILD-TYPE 177 599 54

Figure S21.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain mutation analysis' versus 'MRNA_CNMF'

P value = 2.66e-07 (Fisher's exact test), Q value = 0.00017

Table S22.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
2Q GAIN MUTATED 1 1 17
2Q GAIN WILD-TYPE 255 91 142

Figure S22.  Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'2q gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.011

Table S23.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
2Q GAIN MUTATED 13 6 0
2Q GAIN WILD-TYPE 108 246 134

Figure S23.  Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'2q gain mutation analysis' versus 'CN_CNMF'

P value = 0.000334 (Chi-square test), Q value = 0.16

Table S24.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
2Q GAIN MUTATED 2 1 6 15 1
2Q GAIN WILD-TYPE 344 75 192 200 55

Figure S24.  Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'2q gain mutation analysis' versus 'RPPA_CNMF'

P value = 1.65e-07 (Fisher's exact test), Q value = 0.00011

Table S25.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
2Q GAIN MUTATED 16 0 0
2Q GAIN WILD-TYPE 130 129 115

Figure S25.  Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'2q gain mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.000521 (Fisher's exact test), Q value = 0.24

Table S26.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
2Q GAIN MUTATED 4 0 12
2Q GAIN WILD-TYPE 152 108 114

Figure S26.  Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'2q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.15e-06 (Fisher's exact test), Q value = 0.0019

Table S27.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
2Q GAIN MUTATED 18 0 6
2Q GAIN WILD-TYPE 217 155 428

Figure S27.  Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'2q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.99e-06 (Fisher's exact test), Q value = 0.0047

Table S28.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
2Q GAIN MUTATED 9 0 15
2Q GAIN WILD-TYPE 404 216 180

Figure S28.  Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000296 (Fisher's exact test), Q value = 0.14

Table S29.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
2Q GAIN MUTATED 1 5 14
2Q GAIN WILD-TYPE 199 418 235

Figure S29.  Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'2q gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000163 (Fisher's exact test), Q value = 0.082

Table S30.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
2Q GAIN MUTATED 13 6 1
2Q GAIN WILD-TYPE 191 603 58

Figure S30.  Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'3p gain mutation analysis' versus 'CN_CNMF'

P value = 1.37e-06 (Chi-square test), Q value = 0.00086

Table S31.  Gene #5: '3p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
3P GAIN MUTATED 3 11 16 15 7
3P GAIN WILD-TYPE 343 65 182 200 49

Figure S31.  Get High-res Image Gene #5: '3p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'3q gain mutation analysis' versus 'CN_CNMF'

P value = 1.91e-09 (Chi-square test), Q value = 1.3e-06

Table S32.  Gene #6: '3q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
3Q GAIN MUTATED 8 14 27 40 9
3Q GAIN WILD-TYPE 338 62 171 175 47

Figure S32.  Get High-res Image Gene #6: '3q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'3q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.00054 (Chi-square test), Q value = 0.24

Table S33.  Gene #6: '3q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
3Q GAIN MUTATED 17 5 10 12 2 2
3Q GAIN WILD-TYPE 79 137 70 111 34 88

Figure S33.  Get High-res Image Gene #6: '3q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'3q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.081

Table S34.  Gene #6: '3q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
3Q GAIN MUTATED 40 6 48
3Q GAIN WILD-TYPE 195 149 386

Figure S34.  Get High-res Image Gene #6: '3q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'3q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000409 (Fisher's exact test), Q value = 0.19

Table S35.  Gene #6: '3q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
3Q GAIN MUTATED 45 13 36
3Q GAIN WILD-TYPE 368 203 159

Figure S35.  Get High-res Image Gene #6: '3q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.13e-05 (Fisher's exact test), Q value = 0.017

Table S36.  Gene #6: '3q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
3Q GAIN MUTATED 10 40 45
3Q GAIN WILD-TYPE 190 383 204

Figure S36.  Get High-res Image Gene #6: '3q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'4p gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 4.25e-05 (Fisher's exact test), Q value = 0.023

Table S37.  Gene #7: '4p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
4P GAIN MUTATED 0 17 0
4P GAIN WILD-TYPE 121 235 134

Figure S37.  Get High-res Image Gene #7: '4p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'4p gain mutation analysis' versus 'CN_CNMF'

P value = 1.67e-07 (Chi-square test), Q value = 0.00011

Table S38.  Gene #7: '4p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
4P GAIN MUTATED 1 2 19 4 3
4P GAIN WILD-TYPE 345 74 179 211 53

Figure S38.  Get High-res Image Gene #7: '4p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'4p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000297 (Fisher's exact test), Q value = 0.14

Table S39.  Gene #7: '4p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
4P GAIN MUTATED 2 24 2
4P GAIN WILD-TYPE 198 399 247

Figure S39.  Get High-res Image Gene #7: '4p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'4q gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000438 (Fisher's exact test), Q value = 0.2

Table S40.  Gene #8: '4q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
4Q GAIN MUTATED 0 16 1
4Q GAIN WILD-TYPE 121 236 133

Figure S40.  Get High-res Image Gene #8: '4q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'4q gain mutation analysis' versus 'CN_CNMF'

P value = 3.78e-09 (Chi-square test), Q value = 2.6e-06

Table S41.  Gene #8: '4q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
4Q GAIN MUTATED 1 1 19 2 4
4Q GAIN WILD-TYPE 345 75 179 213 52

Figure S41.  Get High-res Image Gene #8: '4q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'5p gain mutation analysis' versus 'CN_CNMF'

P value = 2.4e-09 (Chi-square test), Q value = 1.7e-06

Table S42.  Gene #9: '5p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
5P GAIN MUTATED 33 26 58 38 11
5P GAIN WILD-TYPE 313 50 140 177 45

Figure S42.  Get High-res Image Gene #9: '5p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'5q gain mutation analysis' versus 'CN_CNMF'

P value = 1.36e-15 (Chi-square test), Q value = 1.1e-12

Table S43.  Gene #10: '5q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
5Q GAIN MUTATED 21 25 41 7 8
5Q GAIN WILD-TYPE 325 51 157 208 48

Figure S43.  Get High-res Image Gene #10: '5q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'5q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.15e-05 (Fisher's exact test), Q value = 0.0067

Table S44.  Gene #10: '5q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
5Q GAIN MUTATED 66 23 7
5Q GAIN WILD-TYPE 347 193 188

Figure S44.  Get High-res Image Gene #10: '5q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.18e-05 (Fisher's exact test), Q value = 0.012

Table S45.  Gene #10: '5q gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
5Q GAIN MUTATED 7 87 6
5Q GAIN WILD-TYPE 197 522 53

Figure S45.  Get High-res Image Gene #10: '5q gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'6p gain mutation analysis' versus 'MRNA_CNMF'

P value = 2.87e-05 (Fisher's exact test), Q value = 0.016

Table S46.  Gene #11: '6p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
6P GAIN MUTATED 19 5 34
6P GAIN WILD-TYPE 237 87 125

Figure S46.  Get High-res Image Gene #11: '6p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'6p gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S47.  Gene #11: '6p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
6P GAIN MUTATED 23 32 3
6P GAIN WILD-TYPE 98 220 131

Figure S47.  Get High-res Image Gene #11: '6p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'6p gain mutation analysis' versus 'CN_CNMF'

P value = 1.03e-14 (Chi-square test), Q value = 7.9e-12

Table S48.  Gene #11: '6p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
6P GAIN MUTATED 9 12 16 53 11
6P GAIN WILD-TYPE 337 64 182 162 45

Figure S48.  Get High-res Image Gene #11: '6p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'6p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.26e-07 (Chi-square test), Q value = 0.00027

Table S49.  Gene #11: '6p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
6P GAIN MUTATED 25 8 10 13 1 2
6P GAIN WILD-TYPE 71 134 70 110 35 88

Figure S49.  Get High-res Image Gene #11: '6p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'6p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.86e-09 (Fisher's exact test), Q value = 5.4e-06

Table S50.  Gene #11: '6p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
6P GAIN MUTATED 50 4 39
6P GAIN WILD-TYPE 185 151 395

Figure S50.  Get High-res Image Gene #11: '6p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'6p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.67e-08 (Fisher's exact test), Q value = 1.8e-05

Table S51.  Gene #11: '6p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
6P GAIN MUTATED 42 8 43
6P GAIN WILD-TYPE 371 208 152

Figure S51.  Get High-res Image Gene #11: '6p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'6p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.51e-11 (Fisher's exact test), Q value = 1.1e-08

Table S52.  Gene #11: '6p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
6P GAIN MUTATED 7 31 57
6P GAIN WILD-TYPE 193 392 192

Figure S52.  Get High-res Image Gene #11: '6p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'6p gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.13e-08 (Fisher's exact test), Q value = 7.8e-06

Table S53.  Gene #11: '6p gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
6P GAIN MUTATED 47 42 6
6P GAIN WILD-TYPE 157 567 53

Figure S53.  Get High-res Image Gene #11: '6p gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'6q gain mutation analysis' versus 'MRNA_CNMF'

P value = 0.000135 (Fisher's exact test), Q value = 0.069

Table S54.  Gene #12: '6q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
6Q GAIN MUTATED 11 3 24
6Q GAIN WILD-TYPE 245 89 135

Figure S54.  Get High-res Image Gene #12: '6q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'6q gain mutation analysis' versus 'CN_CNMF'

P value = 2.23e-15 (Chi-square test), Q value = 1.7e-12

Table S55.  Gene #12: '6q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
6Q GAIN MUTATED 4 8 6 40 1
6Q GAIN WILD-TYPE 342 68 192 175 55

Figure S55.  Get High-res Image Gene #12: '6q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'6q gain mutation analysis' versus 'RPPA_CNMF'

P value = 0.000363 (Fisher's exact test), Q value = 0.17

Table S56.  Gene #12: '6q gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
6Q GAIN MUTATED 21 7 2
6Q GAIN WILD-TYPE 125 122 113

Figure S56.  Get High-res Image Gene #12: '6q gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'6q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.43e-06 (Fisher's exact test), Q value = 0.0038

Table S57.  Gene #12: '6q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
6Q GAIN MUTATED 31 2 23
6Q GAIN WILD-TYPE 204 153 411

Figure S57.  Get High-res Image Gene #12: '6q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'6q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.15e-06 (Fisher's exact test), Q value = 0.0013

Table S58.  Gene #12: '6q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
6Q GAIN MUTATED 26 3 27
6Q GAIN WILD-TYPE 387 213 168

Figure S58.  Get High-res Image Gene #12: '6q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'6q gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.22e-07 (Fisher's exact test), Q value = 0.00021

Table S59.  Gene #12: '6q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
6Q GAIN MUTATED 4 17 34
6Q GAIN WILD-TYPE 196 406 215

Figure S59.  Get High-res Image Gene #12: '6q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'6q gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.48e-06 (Fisher's exact test), Q value = 0.00092

Table S60.  Gene #12: '6q gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
6Q GAIN MUTATED 28 21 6
6Q GAIN WILD-TYPE 176 588 53

Figure S60.  Get High-res Image Gene #12: '6q gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'7p gain mutation analysis' versus 'CN_CNMF'

P value = 0.000302 (Chi-square test), Q value = 0.15

Table S61.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
7P GAIN MUTATED 37 21 38 42 15
7P GAIN WILD-TYPE 309 55 160 173 41

Figure S61.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7q gain mutation analysis' versus 'CN_CNMF'

P value = 1.52e-05 (Chi-square test), Q value = 0.0087

Table S62.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
7Q GAIN MUTATED 22 18 23 38 10
7Q GAIN WILD-TYPE 324 58 175 177 46

Figure S62.  Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000437 (Chi-square test), Q value = 0.2

Table S63.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
7Q GAIN MUTATED 22 17 11 18 2 1
7Q GAIN WILD-TYPE 74 125 69 105 34 89

Figure S63.  Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'7q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000438 (Fisher's exact test), Q value = 0.2

Table S64.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
7Q GAIN MUTATED 46 18 41
7Q GAIN WILD-TYPE 367 198 154

Figure S64.  Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000295 (Fisher's exact test), Q value = 0.14

Table S65.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
7Q GAIN MUTATED 42 64 3
7Q GAIN WILD-TYPE 162 545 56

Figure S65.  Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'8p gain mutation analysis' versus 'CN_CNMF'

P value = 5.6e-13 (Chi-square test), Q value = 4.2e-10

Table S66.  Gene #15: '8p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
8P GAIN MUTATED 32 30 38 45 24
8P GAIN WILD-TYPE 314 46 160 170 32

Figure S66.  Get High-res Image Gene #15: '8p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'8p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000192 (Fisher's exact test), Q value = 0.095

Table S67.  Gene #15: '8p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
8P GAIN MUTATED 43 13 99
8P GAIN WILD-TYPE 192 142 335

Figure S67.  Get High-res Image Gene #15: '8p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'8p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000113 (Fisher's exact test), Q value = 0.058

Table S68.  Gene #15: '8p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
8P GAIN MUTATED 98 22 35
8P GAIN WILD-TYPE 315 194 160

Figure S68.  Get High-res Image Gene #15: '8p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 4.37e-05 (Fisher's exact test), Q value = 0.024

Table S69.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
8Q GAIN MUTATED 60 131 39
8Q GAIN WILD-TYPE 61 121 95

Figure S69.  Get High-res Image Gene #16: '8q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'8q gain mutation analysis' versus 'CN_CNMF'

P value = 3.15e-23 (Chi-square test), Q value = 2.5e-20

Table S70.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
8Q GAIN MUTATED 70 37 108 110 41
8Q GAIN WILD-TYPE 276 39 90 105 15

Figure S70.  Get High-res Image Gene #16: '8q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'8q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.66e-09 (Chi-square test), Q value = 3.2e-06

Table S71.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
8Q GAIN MUTATED 47 37 32 70 9 18
8Q GAIN WILD-TYPE 49 105 48 53 27 72

Figure S71.  Get High-res Image Gene #16: '8q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'8q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 8.4e-08 (Fisher's exact test), Q value = 5.6e-05

Table S72.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
8Q GAIN MUTATED 114 35 200
8Q GAIN WILD-TYPE 121 120 234

Figure S72.  Get High-res Image Gene #16: '8q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'8q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.63e-06 (Fisher's exact test), Q value = 0.0028

Table S73.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
8Q GAIN MUTATED 195 61 93
8Q GAIN WILD-TYPE 218 155 102

Figure S73.  Get High-res Image Gene #16: '8q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.19e-10 (Fisher's exact test), Q value = 8.6e-08

Table S74.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
8Q GAIN MUTATED 47 173 136
8Q GAIN WILD-TYPE 153 250 113

Figure S74.  Get High-res Image Gene #16: '8q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'9p gain mutation analysis' versus 'MRNA_CNMF'

P value = 0.000317 (Fisher's exact test), Q value = 0.15

Table S75.  Gene #17: '9p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
9P GAIN MUTATED 10 7 24
9P GAIN WILD-TYPE 246 85 135

Figure S75.  Get High-res Image Gene #17: '9p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'9p gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 7e-08 (Fisher's exact test), Q value = 4.7e-05

Table S76.  Gene #17: '9p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
9P GAIN MUTATED 26 9 6
9P GAIN WILD-TYPE 95 243 128

Figure S76.  Get High-res Image Gene #17: '9p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'9p gain mutation analysis' versus 'CN_CNMF'

P value = 1.15e-09 (Chi-square test), Q value = 8.1e-07

Table S77.  Gene #17: '9p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
9P GAIN MUTATED 9 13 6 33 6
9P GAIN WILD-TYPE 337 63 192 182 50

Figure S77.  Get High-res Image Gene #17: '9p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'9p gain mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.000138 (Fisher's exact test), Q value = 0.07

Table S78.  Gene #17: '9p gain mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
9P GAIN MUTATED 5 7 22
9P GAIN WILD-TYPE 151 101 104

Figure S78.  Get High-res Image Gene #17: '9p gain mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'9p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.3e-07 (Fisher's exact test), Q value = 8.6e-05

Table S79.  Gene #17: '9p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
9P GAIN MUTATED 38 7 17
9P GAIN WILD-TYPE 197 148 417

Figure S79.  Get High-res Image Gene #17: '9p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'9p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.63e-08 (Fisher's exact test), Q value = 1.8e-05

Table S80.  Gene #17: '9p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
9P GAIN MUTATED 20 7 35
9P GAIN WILD-TYPE 393 209 160

Figure S80.  Get High-res Image Gene #17: '9p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'9p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.23e-06 (Fisher's exact test), Q value = 0.002

Table S81.  Gene #17: '9p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
9P GAIN MUTATED 7 21 37
9P GAIN WILD-TYPE 193 402 212

Figure S81.  Get High-res Image Gene #17: '9p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'9p gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.9e-07 (Fisher's exact test), Q value = 0.00025

Table S82.  Gene #17: '9p gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
9P GAIN MUTATED 34 27 4
9P GAIN WILD-TYPE 170 582 55

Figure S82.  Get High-res Image Gene #17: '9p gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'9q gain mutation analysis' versus 'CN_CNMF'

P value = 9.79e-05 (Chi-square test), Q value = 0.051

Table S83.  Gene #18: '9q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
9Q GAIN MUTATED 10 12 9 20 3
9Q GAIN WILD-TYPE 336 64 189 195 53

Figure S83.  Get High-res Image Gene #18: '9q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'10p gain mutation analysis' versus 'MRNA_CNMF'

P value = 6.61e-09 (Fisher's exact test), Q value = 4.6e-06

Table S84.  Gene #19: '10p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
10P GAIN MUTATED 17 9 45
10P GAIN WILD-TYPE 239 83 114

Figure S84.  Get High-res Image Gene #19: '10p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'10p gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 7.19e-08 (Fisher's exact test), Q value = 4.8e-05

Table S85.  Gene #19: '10p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
10P GAIN MUTATED 37 25 9
10P GAIN WILD-TYPE 84 227 125

Figure S85.  Get High-res Image Gene #19: '10p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'10p gain mutation analysis' versus 'CN_CNMF'

P value = 2.62e-18 (Chi-square test), Q value = 2e-15

Table S86.  Gene #19: '10p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
10P GAIN MUTATED 8 10 20 62 9
10P GAIN WILD-TYPE 338 66 178 153 47

Figure S86.  Get High-res Image Gene #19: '10p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'10p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.21e-13 (Chi-square test), Q value = 9.1e-11

Table S87.  Gene #19: '10p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
10P GAIN MUTATED 32 4 11 12 0 3
10P GAIN WILD-TYPE 64 138 69 111 36 87

Figure S87.  Get High-res Image Gene #19: '10p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'10p gain mutation analysis' versus 'RPPA_CNMF'

P value = 1.32e-05 (Fisher's exact test), Q value = 0.0076

Table S88.  Gene #19: '10p gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
10P GAIN MUTATED 36 7 12
10P GAIN WILD-TYPE 110 122 103

Figure S88.  Get High-res Image Gene #19: '10p gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'10p gain mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 1.1e-06 (Fisher's exact test), Q value = 7e-04

Table S89.  Gene #19: '10p gain mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
10P GAIN MUTATED 10 10 35
10P GAIN WILD-TYPE 146 98 91

Figure S89.  Get High-res Image Gene #19: '10p gain mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'10p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.59e-15 (Fisher's exact test), Q value = 2.8e-12

Table S90.  Gene #19: '10p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
10P GAIN MUTATED 66 7 30
10P GAIN WILD-TYPE 169 148 404

Figure S90.  Get High-res Image Gene #19: '10p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'10p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.14e-14 (Fisher's exact test), Q value = 8.7e-12

Table S91.  Gene #19: '10p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
10P GAIN MUTATED 32 12 59
10P GAIN WILD-TYPE 381 204 136

Figure S91.  Get High-res Image Gene #19: '10p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'10p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.41e-14 (Fisher's exact test), Q value = 1.1e-11

Table S92.  Gene #19: '10p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
10P GAIN MUTATED 12 27 67
10P GAIN WILD-TYPE 188 396 182

Figure S92.  Get High-res Image Gene #19: '10p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'10p gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.47e-14 (Fisher's exact test), Q value = 3.4e-11

Table S93.  Gene #19: '10p gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
10P GAIN MUTATED 57 39 10
10P GAIN WILD-TYPE 147 570 49

Figure S93.  Get High-res Image Gene #19: '10p gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'10q gain mutation analysis' versus 'CN_CNMF'

P value = 1.23e-05 (Chi-square test), Q value = 0.0071

Table S94.  Gene #20: '10q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
10Q GAIN MUTATED 3 8 9 21 3
10Q GAIN WILD-TYPE 343 68 189 194 53

Figure S94.  Get High-res Image Gene #20: '10q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'12p gain mutation analysis' versus 'CN_CNMF'

P value = 1.71e-14 (Chi-square test), Q value = 1.3e-11

Table S95.  Gene #23: '12p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
12P GAIN MUTATED 3 16 40 43 8
12P GAIN WILD-TYPE 343 60 158 172 48

Figure S95.  Get High-res Image Gene #23: '12p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'12p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000142 (Chi-square test), Q value = 0.072

Table S96.  Gene #23: '12p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
12P GAIN MUTATED 18 9 11 22 1 2
12P GAIN WILD-TYPE 78 133 69 101 35 88

Figure S96.  Get High-res Image Gene #23: '12p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'12p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.38e-05 (Fisher's exact test), Q value = 0.039

Table S97.  Gene #23: '12p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
12P GAIN MUTATED 42 6 57
12P GAIN WILD-TYPE 193 149 377

Figure S97.  Get High-res Image Gene #23: '12p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'12p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000397 (Fisher's exact test), Q value = 0.19

Table S98.  Gene #23: '12p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
12P GAIN MUTATED 51 15 39
12P GAIN WILD-TYPE 362 201 156

Figure S98.  Get High-res Image Gene #23: '12p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 5.53e-06 (Fisher's exact test), Q value = 0.0033

Table S99.  Gene #23: '12p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
12P GAIN MUTATED 12 42 51
12P GAIN WILD-TYPE 188 381 198

Figure S99.  Get High-res Image Gene #23: '12p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'12p gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000532 (Fisher's exact test), Q value = 0.24

Table S100.  Gene #23: '12p gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
12P GAIN MUTATED 41 59 5
12P GAIN WILD-TYPE 163 550 54

Figure S100.  Get High-res Image Gene #23: '12p gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'12q gain mutation analysis' versus 'CN_CNMF'

P value = 1.21e-14 (Chi-square test), Q value = 9.2e-12

Table S101.  Gene #24: '12q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
12Q GAIN MUTATED 6 17 41 14 5
12Q GAIN WILD-TYPE 340 59 157 201 51

Figure S101.  Get High-res Image Gene #24: '12q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'12q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000357 (Chi-square test), Q value = 0.17

Table S102.  Gene #24: '12q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
12Q GAIN MUTATED 5 13 10 22 1 1
12Q GAIN WILD-TYPE 91 129 70 101 35 89

Figure S102.  Get High-res Image Gene #24: '12q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'13q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000424 (Fisher's exact test), Q value = 0.2

Table S103.  Gene #25: '13q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
13Q GAIN MUTATED 17 0 24
13Q GAIN WILD-TYPE 218 155 410

Figure S103.  Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'14q gain mutation analysis' versus 'CN_CNMF'

P value = 0.000121 (Chi-square test), Q value = 0.062

Table S104.  Gene #26: '14q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
14Q GAIN MUTATED 15 13 27 15 7
14Q GAIN WILD-TYPE 331 63 171 200 49

Figure S104.  Get High-res Image Gene #26: '14q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'14q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.94e-05 (Fisher's exact test), Q value = 0.011

Table S105.  Gene #26: '14q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
14Q GAIN MUTATED 15 3 56
14Q GAIN WILD-TYPE 220 152 378

Figure S105.  Get High-res Image Gene #26: '14q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'16p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.8e-06 (Chi-square test), Q value = 0.0052

Table S106.  Gene #28: '16p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
16P GAIN MUTATED 18 54 25 33 3 10
16P GAIN WILD-TYPE 78 88 55 90 33 80

Figure S106.  Get High-res Image Gene #28: '16p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'16p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000156 (Fisher's exact test), Q value = 0.079

Table S107.  Gene #28: '16p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
16P GAIN MUTATED 44 41 146
16P GAIN WILD-TYPE 191 114 288

Figure S107.  Get High-res Image Gene #28: '16p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'16p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.64e-06 (Fisher's exact test), Q value = 0.0022

Table S108.  Gene #28: '16p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
16P GAIN MUTATED 145 54 32
16P GAIN WILD-TYPE 268 162 163

Figure S108.  Get High-res Image Gene #28: '16p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain mutation analysis' versus 'CN_CNMF'

P value = 2.3e-22 (Chi-square test), Q value = 1.8e-19

Table S109.  Gene #31: '17q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
17Q GAIN MUTATED 21 10 68 10 13
17Q GAIN WILD-TYPE 325 66 130 205 43

Figure S109.  Get High-res Image Gene #31: '17q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'17q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.17e-05 (Chi-square test), Q value = 0.033

Table S110.  Gene #31: '17q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
17Q GAIN MUTATED 5 19 12 33 6 6
17Q GAIN WILD-TYPE 91 123 68 90 30 84

Figure S110.  Get High-res Image Gene #31: '17q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'17q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.57e-05 (Fisher's exact test), Q value = 0.02

Table S111.  Gene #31: '17q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
17Q GAIN MUTATED 16 20 83
17Q GAIN WILD-TYPE 219 135 351

Figure S111.  Get High-res Image Gene #31: '17q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'17q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.62e-06 (Fisher's exact test), Q value = 0.0028

Table S112.  Gene #31: '17q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
17Q GAIN MUTATED 80 29 10
17Q GAIN WILD-TYPE 333 187 185

Figure S112.  Get High-res Image Gene #31: '17q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000172 (Fisher's exact test), Q value = 0.086

Table S113.  Gene #32: '18p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
18P GAIN MUTATED 24 25 5
18P GAIN WILD-TYPE 97 227 129

Figure S113.  Get High-res Image Gene #32: '18p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'18p gain mutation analysis' versus 'CN_CNMF'

P value = 1.77e-07 (Chi-square test), Q value = 0.00012

Table S114.  Gene #32: '18p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
18P GAIN MUTATED 10 6 24 35 11
18P GAIN WILD-TYPE 336 70 174 180 45

Figure S114.  Get High-res Image Gene #32: '18p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'18p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.56e-06 (Chi-square test), Q value = 0.0016

Table S115.  Gene #32: '18p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
18P GAIN MUTATED 20 6 8 10 0 1
18P GAIN WILD-TYPE 76 136 72 113 36 89

Figure S115.  Get High-res Image Gene #32: '18p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'18p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.05e-06 (Fisher's exact test), Q value = 0.0019

Table S116.  Gene #32: '18p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
18P GAIN MUTATED 36 2 45
18P GAIN WILD-TYPE 199 153 389

Figure S116.  Get High-res Image Gene #32: '18p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'18p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.81e-08 (Fisher's exact test), Q value = 2.6e-05

Table S117.  Gene #32: '18p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
18P GAIN MUTATED 44 4 35
18P GAIN WILD-TYPE 369 212 160

Figure S117.  Get High-res Image Gene #32: '18p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.19e-06 (Fisher's exact test), Q value = 0.0014

Table S118.  Gene #32: '18p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
18P GAIN MUTATED 7 31 42
18P GAIN WILD-TYPE 193 392 207

Figure S118.  Get High-res Image Gene #32: '18p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'18p gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.65e-06 (Fisher's exact test), Q value = 0.0057

Table S119.  Gene #32: '18p gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
18P GAIN MUTATED 37 40 3
18P GAIN WILD-TYPE 167 569 56

Figure S119.  Get High-res Image Gene #32: '18p gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'18q gain mutation analysis' versus 'CN_CNMF'

P value = 8.83e-06 (Chi-square test), Q value = 0.0052

Table S120.  Gene #33: '18q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
18Q GAIN MUTATED 9 7 19 30 9
18Q GAIN WILD-TYPE 337 69 179 185 47

Figure S120.  Get High-res Image Gene #33: '18q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'18q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000241 (Fisher's exact test), Q value = 0.12

Table S121.  Gene #33: '18q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
18Q GAIN MUTATED 23 2 45
18Q GAIN WILD-TYPE 212 153 389

Figure S121.  Get High-res Image Gene #33: '18q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'18q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.8e-05 (Fisher's exact test), Q value = 0.051

Table S122.  Gene #33: '18q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
18Q GAIN MUTATED 41 5 24
18Q GAIN WILD-TYPE 372 211 171

Figure S122.  Get High-res Image Gene #33: '18q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 8.56e-05 (Fisher's exact test), Q value = 0.045

Table S123.  Gene #33: '18q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
18Q GAIN MUTATED 5 31 33
18Q GAIN WILD-TYPE 195 392 216

Figure S123.  Get High-res Image Gene #33: '18q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'19p gain mutation analysis' versus 'CN_CNMF'

P value = 0.000102 (Chi-square test), Q value = 0.053

Table S124.  Gene #34: '19p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
19P GAIN MUTATED 13 12 10 25 7
19P GAIN WILD-TYPE 333 64 188 190 49

Figure S124.  Get High-res Image Gene #34: '19p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'19p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000444 (Fisher's exact test), Q value = 0.2

Table S125.  Gene #34: '19p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
19P GAIN MUTATED 25 11 29
19P GAIN WILD-TYPE 388 205 166

Figure S125.  Get High-res Image Gene #34: '19p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain mutation analysis' versus 'CN_CNMF'

P value = 0.000114 (Chi-square test), Q value = 0.059

Table S126.  Gene #35: '19q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
19Q GAIN MUTATED 15 14 18 30 6
19Q GAIN WILD-TYPE 331 62 180 185 50

Figure S126.  Get High-res Image Gene #35: '19q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20p gain mutation analysis' versus 'MRNA_CNMF'

P value = 1.41e-05 (Fisher's exact test), Q value = 0.0081

Table S127.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
20P GAIN MUTATED 67 15 68
20P GAIN WILD-TYPE 189 77 91

Figure S127.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'20p gain mutation analysis' versus 'CN_CNMF'

P value = 5.7e-26 (Chi-square test), Q value = 4.5e-23

Table S128.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
20P GAIN MUTATED 25 36 91 68 16
20P GAIN WILD-TYPE 321 40 107 147 40

Figure S128.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.61e-05 (Chi-square test), Q value = 0.015

Table S129.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
20P GAIN MUTATED 22 28 24 49 6 10
20P GAIN WILD-TYPE 74 114 56 74 30 80

Figure S129.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'20p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.98e-06 (Fisher's exact test), Q value = 0.0012

Table S130.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
20P GAIN MUTATED 27 121 83
20P GAIN WILD-TYPE 173 302 166

Figure S130.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'20q gain mutation analysis' versus 'MRNA_CNMF'

P value = 0.000311 (Fisher's exact test), Q value = 0.15

Table S131.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
20Q GAIN MUTATED 82 17 68
20Q GAIN WILD-TYPE 174 75 91

Figure S131.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'20q gain mutation analysis' versus 'CN_CNMF'

P value = 1.22e-33 (Chi-square test), Q value = 9.7e-31

Table S132.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
20Q GAIN MUTATED 29 34 115 74 20
20Q GAIN WILD-TYPE 317 42 83 141 36

Figure S132.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.77e-10 (Chi-square test), Q value = 2e-07

Table S133.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
20Q GAIN MUTATED 22 31 30 63 7 10
20Q GAIN WILD-TYPE 74 111 50 60 29 80

Figure S133.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'20q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.24e-05 (Fisher's exact test), Q value = 0.0072

Table S134.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
20Q GAIN MUTATED 70 28 165
20Q GAIN WILD-TYPE 165 127 269

Figure S134.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'20q gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.78e-07 (Fisher's exact test), Q value = 0.00024

Table S135.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
20Q GAIN MUTATED 32 143 93
20Q GAIN WILD-TYPE 168 280 156

Figure S135.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'21q gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 6.94e-05 (Fisher's exact test), Q value = 0.037

Table S136.  Gene #38: '21q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
21Q GAIN MUTATED 27 29 6
21Q GAIN WILD-TYPE 94 223 128

Figure S136.  Get High-res Image Gene #38: '21q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'21q gain mutation analysis' versus 'CN_CNMF'

P value = 5e-09 (Chi-square test), Q value = 3.5e-06

Table S137.  Gene #38: '21q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
21Q GAIN MUTATED 13 16 20 43 9
21Q GAIN WILD-TYPE 333 60 178 172 47

Figure S137.  Get High-res Image Gene #38: '21q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'21q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.12e-06 (Chi-square test), Q value = 0.0013

Table S138.  Gene #38: '21q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
21Q GAIN MUTATED 23 9 13 10 1 2
21Q GAIN WILD-TYPE 73 133 67 113 35 88

Figure S138.  Get High-res Image Gene #38: '21q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'21q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.65e-10 (Fisher's exact test), Q value = 1.2e-07

Table S139.  Gene #38: '21q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
21Q GAIN MUTATED 54 4 37
21Q GAIN WILD-TYPE 181 151 397

Figure S139.  Get High-res Image Gene #38: '21q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'21q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.63e-10 (Fisher's exact test), Q value = 4.7e-07

Table S140.  Gene #38: '21q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
21Q GAIN MUTATED 40 8 47
21Q GAIN WILD-TYPE 373 208 148

Figure S140.  Get High-res Image Gene #38: '21q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'21q gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.08e-05 (Fisher's exact test), Q value = 0.0063

Table S141.  Gene #38: '21q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
21Q GAIN MUTATED 15 34 49
21Q GAIN WILD-TYPE 185 389 200

Figure S141.  Get High-res Image Gene #38: '21q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'21q gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.97e-05 (Fisher's exact test), Q value = 0.011

Table S142.  Gene #38: '21q gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
21Q GAIN MUTATED 42 50 6
21Q GAIN WILD-TYPE 162 559 53

Figure S142.  Get High-res Image Gene #38: '21q gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain mutation analysis' versus 'CN_CNMF'

P value = 5.27e-11 (Chi-square test), Q value = 3.8e-08

Table S143.  Gene #39: '22q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
22Q GAIN MUTATED 3 0 6 29 4
22Q GAIN WILD-TYPE 343 76 192 186 52

Figure S143.  Get High-res Image Gene #39: '22q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'22q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.02e-06 (Fisher's exact test), Q value = 0.0019

Table S144.  Gene #39: '22q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
22Q GAIN MUTATED 23 0 14
22Q GAIN WILD-TYPE 212 155 420

Figure S144.  Get High-res Image Gene #39: '22q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'22q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.41e-05 (Fisher's exact test), Q value = 0.0081

Table S145.  Gene #39: '22q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
22Q GAIN MUTATED 17 1 19
22Q GAIN WILD-TYPE 396 215 176

Figure S145.  Get High-res Image Gene #39: '22q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000301 (Fisher's exact test), Q value = 0.15

Table S146.  Gene #39: '22q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
22Q GAIN MUTATED 3 15 23
22Q GAIN WILD-TYPE 197 408 226

Figure S146.  Get High-res Image Gene #39: '22q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'22q gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.32e-06 (Fisher's exact test), Q value = 0.0038

Table S147.  Gene #39: '22q gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
22Q GAIN MUTATED 23 15 3
22Q GAIN WILD-TYPE 181 594 56

Figure S147.  Get High-res Image Gene #39: '22q gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Xq gain mutation analysis' versus 'MRNA_CNMF'

P value = 3.9e-05 (Fisher's exact test), Q value = 0.021

Table S148.  Gene #40: 'Xq gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
XQ GAIN MUTATED 2 0 13
XQ GAIN WILD-TYPE 254 92 146

Figure S148.  Get High-res Image Gene #40: 'Xq gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Xq gain mutation analysis' versus 'CN_CNMF'

P value = 7e-05 (Chi-square test), Q value = 0.037

Table S149.  Gene #40: 'Xq gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
XQ GAIN MUTATED 2 1 3 14 0
XQ GAIN WILD-TYPE 344 75 195 201 56

Figure S149.  Get High-res Image Gene #40: 'Xq gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Xq gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000508 (Fisher's exact test), Q value = 0.23

Table S150.  Gene #40: 'Xq gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
XQ GAIN MUTATED 13 0 6
XQ GAIN WILD-TYPE 222 155 428

Figure S150.  Get High-res Image Gene #40: 'Xq gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Xq gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.97e-05 (Fisher's exact test), Q value = 0.042

Table S151.  Gene #40: 'Xq gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
XQ GAIN MUTATED 5 1 13
XQ GAIN WILD-TYPE 408 215 182

Figure S151.  Get High-res Image Gene #40: 'Xq gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Xq gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 9.25e-06 (Fisher's exact test), Q value = 0.0054

Table S152.  Gene #40: 'Xq gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
XQ GAIN MUTATED 0 4 15
XQ GAIN WILD-TYPE 200 419 234

Figure S152.  Get High-res Image Gene #40: 'Xq gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'Xq gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.93e-05 (Fisher's exact test), Q value = 0.052

Table S153.  Gene #40: 'Xq gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
XQ GAIN MUTATED 13 6 0
XQ GAIN WILD-TYPE 191 603 59

Figure S153.  Get High-res Image Gene #40: 'Xq gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss mutation analysis' versus 'MRNA_CNMF'

P value = 0.000472 (Fisher's exact test), Q value = 0.22

Table S154.  Gene #41: '1p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
1P LOSS MUTATED 47 3 19
1P LOSS WILD-TYPE 209 89 140

Figure S154.  Get High-res Image Gene #41: '1p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'1p loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.78e-10 (Fisher's exact test), Q value = 2.7e-07

Table S155.  Gene #41: '1p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
1P LOSS MUTATED 5 59 5
1P LOSS WILD-TYPE 116 193 129

Figure S155.  Get High-res Image Gene #41: '1p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'1p loss mutation analysis' versus 'CN_CNMF'

P value = 6.77e-22 (Chi-square test), Q value = 5.3e-19

Table S156.  Gene #41: '1p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
1P LOSS MUTATED 17 33 47 15 11
1P LOSS WILD-TYPE 329 43 151 200 45

Figure S156.  Get High-res Image Gene #41: '1p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'1p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.35e-06 (Chi-square test), Q value = 0.0014

Table S157.  Gene #41: '1p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
1P LOSS MUTATED 6 14 20 29 4 3
1P LOSS WILD-TYPE 90 128 60 94 32 87

Figure S157.  Get High-res Image Gene #41: '1p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'1p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.54e-11 (Fisher's exact test), Q value = 1.1e-08

Table S158.  Gene #41: '1p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
1P LOSS MUTATED 15 5 92
1P LOSS WILD-TYPE 220 150 342

Figure S158.  Get High-res Image Gene #41: '1p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'1p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.27e-07 (Fisher's exact test), Q value = 0.00015

Table S159.  Gene #41: '1p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
1P LOSS MUTATED 82 20 10
1P LOSS WILD-TYPE 331 196 185

Figure S159.  Get High-res Image Gene #41: '1p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000167 (Fisher's exact test), Q value = 0.083

Table S160.  Gene #41: '1p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
1P LOSS MUTATED 13 77 30
1P LOSS WILD-TYPE 187 346 219

Figure S160.  Get High-res Image Gene #41: '1p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'1p loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000259 (Fisher's exact test), Q value = 0.13

Table S161.  Gene #41: '1p loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
1P LOSS MUTATED 12 97 11
1P LOSS WILD-TYPE 192 512 48

Figure S161.  Get High-res Image Gene #41: '1p loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'2p loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.15

Table S162.  Gene #43: '2p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
2P LOSS MUTATED 3 33 6
2P LOSS WILD-TYPE 118 219 128

Figure S162.  Get High-res Image Gene #43: '2p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'2p loss mutation analysis' versus 'CN_CNMF'

P value = 5.16e-12 (Chi-square test), Q value = 3.8e-09

Table S163.  Gene #43: '2p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
2P LOSS MUTATED 5 15 33 11 7
2P LOSS WILD-TYPE 341 61 165 204 49

Figure S163.  Get High-res Image Gene #43: '2p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'2p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.2e-05 (Chi-square test), Q value = 0.012

Table S164.  Gene #43: '2p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
2P LOSS MUTATED 3 7 9 20 1 0
2P LOSS WILD-TYPE 93 135 71 103 35 90

Figure S164.  Get High-res Image Gene #43: '2p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'2p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.23e-06 (Fisher's exact test), Q value = 0.00077

Table S165.  Gene #43: '2p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
2P LOSS MUTATED 6 6 55
2P LOSS WILD-TYPE 229 149 379

Figure S165.  Get High-res Image Gene #43: '2p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'2p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.37e-06 (Fisher's exact test), Q value = 0.00086

Table S166.  Gene #43: '2p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
2P LOSS MUTATED 53 10 4
2P LOSS WILD-TYPE 360 206 191

Figure S166.  Get High-res Image Gene #43: '2p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.22e-05 (Fisher's exact test), Q value = 0.012

Table S167.  Gene #43: '2p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
2P LOSS MUTATED 5 50 12
2P LOSS WILD-TYPE 195 373 237

Figure S167.  Get High-res Image Gene #43: '2p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'2q loss mutation analysis' versus 'CN_CNMF'

P value = 3.93e-11 (Chi-square test), Q value = 2.9e-08

Table S168.  Gene #44: '2q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
2Q LOSS MUTATED 7 16 38 20 6
2Q LOSS WILD-TYPE 339 60 160 195 50

Figure S168.  Get High-res Image Gene #44: '2q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'2q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 2e-05 (Chi-square test), Q value = 0.011

Table S169.  Gene #44: '2q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
2Q LOSS MUTATED 9 7 10 23 1 0
2Q LOSS WILD-TYPE 87 135 70 100 35 90

Figure S169.  Get High-res Image Gene #44: '2q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'2q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.61e-05 (Fisher's exact test), Q value = 0.02

Table S170.  Gene #44: '2q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
2Q LOSS MUTATED 5 55 23
2Q LOSS WILD-TYPE 195 368 226

Figure S170.  Get High-res Image Gene #44: '2q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'3p loss mutation analysis' versus 'MRNA_CNMF'

P value = 1.63e-07 (Fisher's exact test), Q value = 0.00011

Table S171.  Gene #45: '3p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
3P LOSS MUTATED 15 3 35
3P LOSS WILD-TYPE 241 89 124

Figure S171.  Get High-res Image Gene #45: '3p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'3p loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000338 (Fisher's exact test), Q value = 0.16

Table S172.  Gene #45: '3p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
3P LOSS MUTATED 25 20 8
3P LOSS WILD-TYPE 96 232 126

Figure S172.  Get High-res Image Gene #45: '3p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'3p loss mutation analysis' versus 'CN_CNMF'

P value = 1.19e-08 (Chi-square test), Q value = 8.2e-06

Table S173.  Gene #45: '3p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
3P LOSS MUTATED 12 3 30 40 5
3P LOSS WILD-TYPE 334 73 168 175 51

Figure S173.  Get High-res Image Gene #45: '3p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'3p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000132 (Chi-square test), Q value = 0.068

Table S174.  Gene #45: '3p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
3P LOSS MUTATED 18 4 10 15 3 2
3P LOSS WILD-TYPE 78 138 70 108 33 88

Figure S174.  Get High-res Image Gene #45: '3p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'3p loss mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 6.62e-05 (Fisher's exact test), Q value = 0.035

Table S175.  Gene #45: '3p loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
3P LOSS MUTATED 14 4 27
3P LOSS WILD-TYPE 142 104 99

Figure S175.  Get High-res Image Gene #45: '3p loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'3p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.83e-05 (Fisher's exact test), Q value = 0.01

Table S176.  Gene #45: '3p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
3P LOSS MUTATED 43 8 34
3P LOSS WILD-TYPE 192 147 400

Figure S176.  Get High-res Image Gene #45: '3p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'3p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.82e-07 (Fisher's exact test), Q value = 0.00012

Table S177.  Gene #45: '3p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
3P LOSS MUTATED 9 31 48
3P LOSS WILD-TYPE 191 392 201

Figure S177.  Get High-res Image Gene #45: '3p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'3p loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000131 (Fisher's exact test), Q value = 0.067

Table S178.  Gene #45: '3p loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
3P LOSS MUTATED 34 44 10
3P LOSS WILD-TYPE 170 565 49

Figure S178.  Get High-res Image Gene #45: '3p loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'3q loss mutation analysis' versus 'MRNA_CNMF'

P value = 2.89e-05 (Fisher's exact test), Q value = 0.016

Table S179.  Gene #46: '3q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
3Q LOSS MUTATED 7 1 20
3Q LOSS WILD-TYPE 249 91 139

Figure S179.  Get High-res Image Gene #46: '3q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'3q loss mutation analysis' versus 'CN_CNMF'

P value = 2.71e-05 (Chi-square test), Q value = 0.015

Table S180.  Gene #46: '3q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
3Q LOSS MUTATED 4 1 18 19 3
3Q LOSS WILD-TYPE 342 75 180 196 53

Figure S180.  Get High-res Image Gene #46: '3q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'4p loss mutation analysis' versus 'MRNA_CNMF'

P value = 2.69e-08 (Fisher's exact test), Q value = 1.8e-05

Table S181.  Gene #47: '4p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
4P LOSS MUTATED 38 15 63
4P LOSS WILD-TYPE 218 77 96

Figure S181.  Get High-res Image Gene #47: '4p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'4p loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 6.36e-13 (Fisher's exact test), Q value = 4.8e-10

Table S182.  Gene #47: '4p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
4P LOSS MUTATED 54 54 8
4P LOSS WILD-TYPE 67 198 126

Figure S182.  Get High-res Image Gene #47: '4p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'4p loss mutation analysis' versus 'CN_CNMF'

P value = 8.63e-26 (Chi-square test), Q value = 6.8e-23

Table S183.  Gene #47: '4p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
4P LOSS MUTATED 18 27 40 91 8
4P LOSS WILD-TYPE 328 49 158 124 48

Figure S183.  Get High-res Image Gene #47: '4p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'4p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 2e-14 (Chi-square test), Q value = 1.5e-11

Table S184.  Gene #47: '4p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
4P LOSS MUTATED 42 17 23 12 4 3
4P LOSS WILD-TYPE 54 125 57 111 32 87

Figure S184.  Get High-res Image Gene #47: '4p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'4p loss mutation analysis' versus 'RPPA_CNMF'

P value = 0.000181 (Fisher's exact test), Q value = 0.09

Table S185.  Gene #47: '4p loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
4P LOSS MUTATED 52 25 17
4P LOSS WILD-TYPE 94 104 98

Figure S185.  Get High-res Image Gene #47: '4p loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'4p loss mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 1.34e-05 (Fisher's exact test), Q value = 0.0077

Table S186.  Gene #47: '4p loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
4P LOSS MUTATED 30 15 49
4P LOSS WILD-TYPE 126 93 77

Figure S186.  Get High-res Image Gene #47: '4p loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'4p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.08e-15 (Fisher's exact test), Q value = 3.9e-12

Table S187.  Gene #47: '4p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
4P LOSS MUTATED 89 9 76
4P LOSS WILD-TYPE 146 146 358

Figure S187.  Get High-res Image Gene #47: '4p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'4p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.38e-15 (Fisher's exact test), Q value = 4.9e-12

Table S188.  Gene #47: '4p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
4P LOSS MUTATED 75 19 80
4P LOSS WILD-TYPE 338 197 115

Figure S188.  Get High-res Image Gene #47: '4p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.99e-14 (Fisher's exact test), Q value = 1.5e-11

Table S189.  Gene #47: '4p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
4P LOSS MUTATED 16 70 92
4P LOSS WILD-TYPE 184 353 157

Figure S189.  Get High-res Image Gene #47: '4p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'4p loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.71e-10 (Fisher's exact test), Q value = 1.2e-07

Table S190.  Gene #47: '4p loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
4P LOSS MUTATED 72 87 19
4P LOSS WILD-TYPE 132 522 40

Figure S190.  Get High-res Image Gene #47: '4p loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss mutation analysis' versus 'MRNA_CNMF'

P value = 4.27e-05 (Fisher's exact test), Q value = 0.023

Table S191.  Gene #48: '4q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
4Q LOSS MUTATED 34 13 49
4Q LOSS WILD-TYPE 222 79 110

Figure S191.  Get High-res Image Gene #48: '4q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'4q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 5.71e-09 (Fisher's exact test), Q value = 4e-06

Table S192.  Gene #48: '4q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
4Q LOSS MUTATED 42 47 7
4Q LOSS WILD-TYPE 79 205 127

Figure S192.  Get High-res Image Gene #48: '4q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'4q loss mutation analysis' versus 'CN_CNMF'

P value = 6.32e-22 (Chi-square test), Q value = 5e-19

Table S193.  Gene #48: '4q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
4Q LOSS MUTATED 16 29 29 73 7
4Q LOSS WILD-TYPE 330 47 169 142 49

Figure S193.  Get High-res Image Gene #48: '4q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'4q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.78e-12 (Chi-square test), Q value = 5.8e-09

Table S194.  Gene #48: '4q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
4Q LOSS MUTATED 37 17 18 10 4 2
4Q LOSS WILD-TYPE 59 125 62 113 32 88

Figure S194.  Get High-res Image Gene #48: '4q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'4q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.25e-11 (Fisher's exact test), Q value = 3.8e-08

Table S195.  Gene #48: '4q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
4Q LOSS MUTATED 71 7 68
4Q LOSS WILD-TYPE 164 148 366

Figure S195.  Get High-res Image Gene #48: '4q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'4q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.7e-11 (Fisher's exact test), Q value = 3.4e-08

Table S196.  Gene #48: '4q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
4Q LOSS MUTATED 67 15 64
4Q LOSS WILD-TYPE 346 201 131

Figure S196.  Get High-res Image Gene #48: '4q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.55e-08 (Fisher's exact test), Q value = 2.4e-05

Table S197.  Gene #48: '4q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
4Q LOSS MUTATED 15 63 69
4Q LOSS WILD-TYPE 185 360 180

Figure S197.  Get High-res Image Gene #48: '4q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'4q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.55e-08 (Fisher's exact test), Q value = 5e-05

Table S198.  Gene #48: '4q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
4Q LOSS MUTATED 57 73 17
4Q LOSS WILD-TYPE 147 536 42

Figure S198.  Get High-res Image Gene #48: '4q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'5p loss mutation analysis' versus 'MRNA_CNMF'

P value = 4.49e-05 (Fisher's exact test), Q value = 0.024

Table S199.  Gene #49: '5p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
5P LOSS MUTATED 11 5 27
5P LOSS WILD-TYPE 245 87 132

Figure S199.  Get High-res Image Gene #49: '5p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'5p loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 5.98e-07 (Fisher's exact test), Q value = 0.00038

Table S200.  Gene #49: '5p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
5P LOSS MUTATED 24 17 2
5P LOSS WILD-TYPE 97 235 132

Figure S200.  Get High-res Image Gene #49: '5p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'5p loss mutation analysis' versus 'CN_CNMF'

P value = 7.59e-21 (Chi-square test), Q value = 5.9e-18

Table S201.  Gene #49: '5p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
5P LOSS MUTATED 2 3 11 51 5
5P LOSS WILD-TYPE 344 73 187 164 51

Figure S201.  Get High-res Image Gene #49: '5p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'5p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.3e-10 (Chi-square test), Q value = 5.2e-07

Table S202.  Gene #49: '5p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
5P LOSS MUTATED 22 2 6 9 0 1
5P LOSS WILD-TYPE 74 140 74 114 36 89

Figure S202.  Get High-res Image Gene #49: '5p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'5p loss mutation analysis' versus 'RPPA_CNMF'

P value = 0.000141 (Fisher's exact test), Q value = 0.072

Table S203.  Gene #49: '5p loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
5P LOSS MUTATED 26 5 6
5P LOSS WILD-TYPE 120 124 109

Figure S203.  Get High-res Image Gene #49: '5p loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'5p loss mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 4.19e-06 (Fisher's exact test), Q value = 0.0025

Table S204.  Gene #49: '5p loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
5P LOSS MUTATED 6 5 26
5P LOSS WILD-TYPE 150 103 100

Figure S204.  Get High-res Image Gene #49: '5p loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'5p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 9.12e-09 (Fisher's exact test), Q value = 6.3e-06

Table S205.  Gene #49: '5p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
5P LOSS MUTATED 38 1 26
5P LOSS WILD-TYPE 197 154 408

Figure S205.  Get High-res Image Gene #49: '5p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'5p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.39e-08 (Fisher's exact test), Q value = 1.6e-05

Table S206.  Gene #49: '5p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
5P LOSS MUTATED 25 5 35
5P LOSS WILD-TYPE 388 211 160

Figure S206.  Get High-res Image Gene #49: '5p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.74e-15 (Fisher's exact test), Q value = 2.9e-12

Table S207.  Gene #49: '5p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
5P LOSS MUTATED 4 15 51
5P LOSS WILD-TYPE 196 408 198

Figure S207.  Get High-res Image Gene #49: '5p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'5p loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.78e-12 (Fisher's exact test), Q value = 1.3e-09

Table S208.  Gene #49: '5p loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
5P LOSS MUTATED 40 21 9
5P LOSS WILD-TYPE 164 588 50

Figure S208.  Get High-res Image Gene #49: '5p loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss mutation analysis' versus 'MRNA_CNMF'

P value = 1.82e-14 (Fisher's exact test), Q value = 1.4e-11

Table S209.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
5Q LOSS MUTATED 13 9 54
5Q LOSS WILD-TYPE 243 83 105

Figure S209.  Get High-res Image Gene #50: '5q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'5q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 4.84e-15 (Fisher's exact test), Q value = 3.7e-12

Table S210.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
5Q LOSS MUTATED 47 24 5
5Q LOSS WILD-TYPE 74 228 129

Figure S210.  Get High-res Image Gene #50: '5q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'5q loss mutation analysis' versus 'CN_CNMF'

P value = 5.85e-49 (Chi-square test), Q value = 4.7e-46

Table S211.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
5Q LOSS MUTATED 2 3 14 95 9
5Q LOSS WILD-TYPE 344 73 184 120 47

Figure S211.  Get High-res Image Gene #50: '5q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'5q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.02e-31 (Chi-square test), Q value = 8.1e-29

Table S212.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
5Q LOSS MUTATED 48 2 6 13 0 2
5Q LOSS WILD-TYPE 48 140 74 110 36 88

Figure S212.  Get High-res Image Gene #50: '5q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'5q loss mutation analysis' versus 'RPPA_CNMF'

P value = 2.75e-08 (Fisher's exact test), Q value = 1.9e-05

Table S213.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
5Q LOSS MUTATED 45 7 13
5Q LOSS WILD-TYPE 101 122 102

Figure S213.  Get High-res Image Gene #50: '5q loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'5q loss mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 1.45e-10 (Fisher's exact test), Q value = 1e-07

Table S214.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
5Q LOSS MUTATED 11 9 45
5Q LOSS WILD-TYPE 145 99 81

Figure S214.  Get High-res Image Gene #50: '5q loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'5q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.31e-22 (Fisher's exact test), Q value = 2.6e-19

Table S215.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
5Q LOSS MUTATED 79 4 33
5Q LOSS WILD-TYPE 156 151 401

Figure S215.  Get High-res Image Gene #50: '5q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'5q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.83e-24 (Fisher's exact test), Q value = 6.2e-21

Table S216.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
5Q LOSS MUTATED 33 9 74
5Q LOSS WILD-TYPE 380 207 121

Figure S216.  Get High-res Image Gene #50: '5q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.31e-27 (Fisher's exact test), Q value = 1e-24

Table S217.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
5Q LOSS MUTATED 6 26 87
5Q LOSS WILD-TYPE 194 397 162

Figure S217.  Get High-res Image Gene #50: '5q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'5q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.29e-30 (Fisher's exact test), Q value = 1e-27

Table S218.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
5Q LOSS MUTATED 79 28 12
5Q LOSS WILD-TYPE 125 581 47

Figure S218.  Get High-res Image Gene #50: '5q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'6p loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000242 (Fisher's exact test), Q value = 0.12

Table S219.  Gene #51: '6p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
6P LOSS MUTATED 4 43 20
6P LOSS WILD-TYPE 117 209 114

Figure S219.  Get High-res Image Gene #51: '6p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'6p loss mutation analysis' versus 'CN_CNMF'

P value = 2.19e-08 (Chi-square test), Q value = 1.5e-05

Table S220.  Gene #51: '6p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
6P LOSS MUTATED 27 9 43 12 14
6P LOSS WILD-TYPE 319 67 155 203 42

Figure S220.  Get High-res Image Gene #51: '6p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'6p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.08e-05 (Chi-square test), Q value = 0.017

Table S221.  Gene #51: '6p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
6P LOSS MUTATED 4 13 10 28 1 5
6P LOSS WILD-TYPE 92 129 70 95 35 85

Figure S221.  Get High-res Image Gene #51: '6p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'6p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.36e-06 (Fisher's exact test), Q value = 0.00085

Table S222.  Gene #51: '6p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
6P LOSS MUTATED 11 14 76
6P LOSS WILD-TYPE 224 141 358

Figure S222.  Get High-res Image Gene #51: '6p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'6p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.98e-06 (Fisher's exact test), Q value = 0.0042

Table S223.  Gene #51: '6p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
6P LOSS MUTATED 68 26 7
6P LOSS WILD-TYPE 345 190 188

Figure S223.  Get High-res Image Gene #51: '6p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000147 (Fisher's exact test), Q value = 0.074

Table S224.  Gene #51: '6p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
6P LOSS MUTATED 12 69 21
6P LOSS WILD-TYPE 188 354 228

Figure S224.  Get High-res Image Gene #51: '6p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'6q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.04e-06 (Fisher's exact test), Q value = 0.0019

Table S225.  Gene #52: '6q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
6Q LOSS MUTATED 6 62 29
6Q LOSS WILD-TYPE 115 190 105

Figure S225.  Get High-res Image Gene #52: '6q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'6q loss mutation analysis' versus 'CN_CNMF'

P value = 1.58e-13 (Chi-square test), Q value = 1.2e-10

Table S226.  Gene #52: '6q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
6Q LOSS MUTATED 48 14 67 15 20
6Q LOSS WILD-TYPE 298 62 131 200 36

Figure S226.  Get High-res Image Gene #52: '6q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'6q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.9e-07 (Chi-square test), Q value = 0.00019

Table S227.  Gene #52: '6q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
6Q LOSS MUTATED 6 32 12 40 4 6
6Q LOSS WILD-TYPE 90 110 68 83 32 84

Figure S227.  Get High-res Image Gene #52: '6q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'6q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.51e-09 (Fisher's exact test), Q value = 5.2e-06

Table S228.  Gene #52: '6q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
6Q LOSS MUTATED 16 31 108
6Q LOSS WILD-TYPE 219 124 326

Figure S228.  Get High-res Image Gene #52: '6q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'6q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.66e-08 (Fisher's exact test), Q value = 5.1e-05

Table S229.  Gene #52: '6q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
6Q LOSS MUTATED 99 44 12
6Q LOSS WILD-TYPE 314 172 183

Figure S229.  Get High-res Image Gene #52: '6q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000236 (Fisher's exact test), Q value = 0.12

Table S230.  Gene #52: '6q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
6Q LOSS MUTATED 30 101 30
6Q LOSS WILD-TYPE 170 322 219

Figure S230.  Get High-res Image Gene #52: '6q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'6q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.06e-06 (Fisher's exact test), Q value = 0.0019

Table S231.  Gene #52: '6q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
6Q LOSS MUTATED 15 134 12
6Q LOSS WILD-TYPE 189 475 47

Figure S231.  Get High-res Image Gene #52: '6q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'7p loss mutation analysis' versus 'CN_CNMF'

P value = 4.07e-06 (Chi-square test), Q value = 0.0025

Table S232.  Gene #53: '7p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
7P LOSS MUTATED 4 3 15 24 1
7P LOSS WILD-TYPE 342 73 183 191 55

Figure S232.  Get High-res Image Gene #53: '7p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'8p loss mutation analysis' versus 'CN_CNMF'

P value = 1.98e-16 (Chi-square test), Q value = 1.5e-13

Table S233.  Gene #55: '8p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
8P LOSS MUTATED 58 11 92 88 25
8P LOSS WILD-TYPE 288 65 106 127 31

Figure S233.  Get High-res Image Gene #55: '8p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'8p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.93e-06 (Chi-square test), Q value = 0.0012

Table S234.  Gene #55: '8p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
8P LOSS MUTATED 32 28 29 56 7 14
8P LOSS WILD-TYPE 64 114 51 67 29 76

Figure S234.  Get High-res Image Gene #55: '8p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'8p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000464 (Fisher's exact test), Q value = 0.21

Table S235.  Gene #55: '8p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
8P LOSS MUTATED 41 137 92
8P LOSS WILD-TYPE 159 286 157

Figure S235.  Get High-res Image Gene #55: '8p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'9p loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000437 (Fisher's exact test), Q value = 0.2

Table S236.  Gene #57: '9p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
9P LOSS MUTATED 25 73 16
9P LOSS WILD-TYPE 96 179 118

Figure S236.  Get High-res Image Gene #57: '9p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'9p loss mutation analysis' versus 'CN_CNMF'

P value = 3.99e-21 (Chi-square test), Q value = 3.1e-18

Table S237.  Gene #57: '9p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
9P LOSS MUTATED 22 12 82 58 10
9P LOSS WILD-TYPE 324 64 116 157 46

Figure S237.  Get High-res Image Gene #57: '9p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'9p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.37e-11 (Chi-square test), Q value = 2.5e-08

Table S238.  Gene #57: '9p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
9P LOSS MUTATED 24 8 24 45 7 5
9P LOSS WILD-TYPE 72 134 56 78 29 85

Figure S238.  Get High-res Image Gene #57: '9p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'9p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.76e-06 (Fisher's exact test), Q value = 0.0011

Table S239.  Gene #57: '9p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
9P LOSS MUTATED 55 12 113
9P LOSS WILD-TYPE 180 143 321

Figure S239.  Get High-res Image Gene #57: '9p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'9p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 8.43e-07 (Fisher's exact test), Q value = 0.00053

Table S240.  Gene #57: '9p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
9P LOSS MUTATED 18 93 70
9P LOSS WILD-TYPE 182 330 179

Figure S240.  Get High-res Image Gene #57: '9p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'9q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000138 (Fisher's exact test), Q value = 0.07

Table S241.  Gene #58: '9q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
9Q LOSS MUTATED 24 57 9
9Q LOSS WILD-TYPE 97 195 125

Figure S241.  Get High-res Image Gene #58: '9q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'9q loss mutation analysis' versus 'CN_CNMF'

P value = 6.57e-17 (Chi-square test), Q value = 5.1e-14

Table S242.  Gene #58: '9q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
9Q LOSS MUTATED 9 11 54 54 14
9Q LOSS WILD-TYPE 337 65 144 161 42

Figure S242.  Get High-res Image Gene #58: '9q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'9q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.1e-08 (Chi-square test), Q value = 7.6e-06

Table S243.  Gene #58: '9q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
9Q LOSS MUTATED 27 7 14 31 3 3
9Q LOSS WILD-TYPE 69 135 66 92 33 87

Figure S243.  Get High-res Image Gene #58: '9q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'9q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.36e-08 (Fisher's exact test), Q value = 9.3e-06

Table S244.  Gene #58: '9q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
9Q LOSS MUTATED 51 4 81
9Q LOSS WILD-TYPE 184 151 353

Figure S244.  Get High-res Image Gene #58: '9q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'9q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000389 (Fisher's exact test), Q value = 0.18

Table S245.  Gene #58: '9q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
9Q LOSS MUTATED 79 18 39
9Q LOSS WILD-TYPE 334 198 156

Figure S245.  Get High-res Image Gene #58: '9q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 7.84e-11 (Fisher's exact test), Q value = 5.7e-08

Table S246.  Gene #58: '9q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
9Q LOSS MUTATED 8 64 66
9Q LOSS WILD-TYPE 192 359 183

Figure S246.  Get High-res Image Gene #58: '9q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'9q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000162 (Fisher's exact test), Q value = 0.081

Table S247.  Gene #58: '9q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
9Q LOSS MUTATED 51 76 11
9Q LOSS WILD-TYPE 153 533 48

Figure S247.  Get High-res Image Gene #58: '9q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss mutation analysis' versus 'CN_CNMF'

P value = 1.52e-05 (Chi-square test), Q value = 0.0087

Table S248.  Gene #59: '10p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
10P LOSS MUTATED 7 8 24 26 6
10P LOSS WILD-TYPE 339 68 174 189 50

Figure S248.  Get High-res Image Gene #59: '10p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'10p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.14

Table S249.  Gene #59: '10p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
10P LOSS MUTATED 23 2 44
10P LOSS WILD-TYPE 212 153 390

Figure S249.  Get High-res Image Gene #59: '10p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'10q loss mutation analysis' versus 'CN_CNMF'

P value = 3.69e-11 (Chi-square test), Q value = 2.7e-08

Table S250.  Gene #60: '10q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
10Q LOSS MUTATED 10 9 34 49 8
10Q LOSS WILD-TYPE 336 67 164 166 48

Figure S250.  Get High-res Image Gene #60: '10q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'10q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.72e-06 (Chi-square test), Q value = 0.0023

Table S251.  Gene #60: '10q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
10Q LOSS MUTATED 20 6 15 21 3 1
10Q LOSS WILD-TYPE 76 136 65 102 33 89

Figure S251.  Get High-res Image Gene #60: '10q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'10q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.57e-06 (Fisher's exact test), Q value = 0.0045

Table S252.  Gene #60: '10q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
10Q LOSS MUTATED 40 4 60
10Q LOSS WILD-TYPE 195 151 374

Figure S252.  Get High-res Image Gene #60: '10q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'11p loss mutation analysis' versus 'CN_CNMF'

P value = 6.7e-12 (Chi-square test), Q value = 5e-09

Table S253.  Gene #61: '11p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
11P LOSS MUTATED 20 12 58 49 9
11P LOSS WILD-TYPE 326 64 140 166 47

Figure S253.  Get High-res Image Gene #61: '11p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'11p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.78e-08 (Chi-square test), Q value = 1.9e-05

Table S254.  Gene #61: '11p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
11P LOSS MUTATED 19 10 23 30 3 1
11P LOSS WILD-TYPE 77 132 57 93 33 89

Figure S254.  Get High-res Image Gene #61: '11p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'11p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 9.9e-05 (Fisher's exact test), Q value = 0.052

Table S255.  Gene #61: '11p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
11P LOSS MUTATED 16 74 56
11P LOSS WILD-TYPE 184 349 193

Figure S255.  Get High-res Image Gene #61: '11p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'11q loss mutation analysis' versus 'MRNA_CNMF'

P value = 3.85e-05 (Fisher's exact test), Q value = 0.021

Table S256.  Gene #62: '11q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
11Q LOSS MUTATED 95 18 30
11Q LOSS WILD-TYPE 161 74 129

Figure S256.  Get High-res Image Gene #62: '11q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'11q loss mutation analysis' versus 'CN_CNMF'

P value = 6.26e-26 (Chi-square test), Q value = 5e-23

Table S257.  Gene #62: '11q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
11Q LOSS MUTATED 47 22 109 41 9
11Q LOSS WILD-TYPE 299 54 89 174 47

Figure S257.  Get High-res Image Gene #62: '11q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'11q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.12e-10 (Chi-square test), Q value = 1.5e-07

Table S258.  Gene #62: '11q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
11Q LOSS MUTATED 15 30 30 54 8 5
11Q LOSS WILD-TYPE 81 112 50 69 28 85

Figure S258.  Get High-res Image Gene #62: '11q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'11q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3e-06 (Fisher's exact test), Q value = 0.0018

Table S259.  Gene #62: '11q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
11Q LOSS MUTATED 38 35 145
11Q LOSS WILD-TYPE 197 120 289

Figure S259.  Get High-res Image Gene #62: '11q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'11q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000346 (Fisher's exact test), Q value = 0.16

Table S260.  Gene #62: '11q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
11Q LOSS MUTATED 126 61 31
11Q LOSS WILD-TYPE 287 155 164

Figure S260.  Get High-res Image Gene #62: '11q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'12p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.21e-06 (Chi-square test), Q value = 0.0054

Table S261.  Gene #63: '12p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
12P LOSS MUTATED 17 7 2 9 7 1
12P LOSS WILD-TYPE 79 135 78 114 29 89

Figure S261.  Get High-res Image Gene #63: '12p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'12p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000112 (Fisher's exact test), Q value = 0.058

Table S262.  Gene #63: '12p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
12P LOSS MUTATED 33 8 21
12P LOSS WILD-TYPE 202 147 413

Figure S262.  Get High-res Image Gene #63: '12p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'12q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000187 (Fisher's exact test), Q value = 0.093

Table S263.  Gene #64: '12q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
12Q LOSS MUTATED 18 12 3
12Q LOSS WILD-TYPE 103 240 131

Figure S263.  Get High-res Image Gene #64: '12q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'12q loss mutation analysis' versus 'CN_CNMF'

P value = 4.08e-07 (Chi-square test), Q value = 0.00026

Table S264.  Gene #64: '12q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
12Q LOSS MUTATED 8 3 8 30 3
12Q LOSS WILD-TYPE 338 73 190 185 53

Figure S264.  Get High-res Image Gene #64: '12q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'12q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.17e-08 (Chi-square test), Q value = 2.1e-05

Table S265.  Gene #64: '12q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
12Q LOSS MUTATED 19 2 2 8 2 1
12Q LOSS WILD-TYPE 77 140 78 115 34 89

Figure S265.  Get High-res Image Gene #64: '12q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'12q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.4e-08 (Fisher's exact test), Q value = 3.6e-05

Table S266.  Gene #64: '12q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
12Q LOSS MUTATED 31 2 13
12Q LOSS WILD-TYPE 204 153 421

Figure S266.  Get High-res Image Gene #64: '12q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'12q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.31e-07 (Fisher's exact test), Q value = 8.6e-05

Table S267.  Gene #64: '12q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
12Q LOSS MUTATED 12 6 28
12Q LOSS WILD-TYPE 401 210 167

Figure S267.  Get High-res Image Gene #64: '12q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.08e-05 (Fisher's exact test), Q value = 0.0063

Table S268.  Gene #64: '12q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
12Q LOSS MUTATED 6 14 30
12Q LOSS WILD-TYPE 194 409 219

Figure S268.  Get High-res Image Gene #64: '12q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'12q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.98e-05 (Fisher's exact test), Q value = 0.011

Table S269.  Gene #64: '12q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
12Q LOSS MUTATED 26 21 3
12Q LOSS WILD-TYPE 178 588 56

Figure S269.  Get High-res Image Gene #64: '12q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000332 (Fisher's exact test), Q value = 0.16

Table S270.  Gene #65: '13q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
13Q LOSS MUTATED 42 92 24
13Q LOSS WILD-TYPE 79 160 110

Figure S270.  Get High-res Image Gene #65: '13q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'13q loss mutation analysis' versus 'CN_CNMF'

P value = 2.45e-26 (Chi-square test), Q value = 1.9e-23

Table S271.  Gene #65: '13q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
13Q LOSS MUTATED 31 34 91 77 31
13Q LOSS WILD-TYPE 315 42 107 138 25

Figure S271.  Get High-res Image Gene #65: '13q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'13q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.06e-08 (Chi-square test), Q value = 6e-05

Table S272.  Gene #65: '13q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
13Q LOSS MUTATED 34 36 40 42 3 11
13Q LOSS WILD-TYPE 62 106 40 81 33 79

Figure S272.  Get High-res Image Gene #65: '13q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'13q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000242 (Fisher's exact test), Q value = 0.12

Table S273.  Gene #65: '13q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
13Q LOSS MUTATED 79 27 146
13Q LOSS WILD-TYPE 156 128 288

Figure S273.  Get High-res Image Gene #65: '13q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'13q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.09e-09 (Fisher's exact test), Q value = 2.2e-06

Table S274.  Gene #65: '13q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
13Q LOSS MUTATED 26 142 91
13Q LOSS WILD-TYPE 174 281 158

Figure S274.  Get High-res Image Gene #65: '13q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'14q loss mutation analysis' versus 'MRNA_CNMF'

P value = 2.49e-07 (Fisher's exact test), Q value = 0.00016

Table S275.  Gene #66: '14q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
14Q LOSS MUTATED 25 7 46
14Q LOSS WILD-TYPE 231 85 113

Figure S275.  Get High-res Image Gene #66: '14q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'14q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 4.23e-08 (Fisher's exact test), Q value = 2.8e-05

Table S276.  Gene #66: '14q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
14Q LOSS MUTATED 38 33 7
14Q LOSS WILD-TYPE 83 219 127

Figure S276.  Get High-res Image Gene #66: '14q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'14q loss mutation analysis' versus 'CN_CNMF'

P value = 1.02e-21 (Chi-square test), Q value = 8e-19

Table S277.  Gene #66: '14q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
14Q LOSS MUTATED 10 9 26 72 14
14Q LOSS WILD-TYPE 336 67 172 143 42

Figure S277.  Get High-res Image Gene #66: '14q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'14q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.89e-15 (Chi-square test), Q value = 2.2e-12

Table S278.  Gene #66: '14q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
14Q LOSS MUTATED 37 5 13 16 0 4
14Q LOSS WILD-TYPE 59 137 67 107 36 86

Figure S278.  Get High-res Image Gene #66: '14q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'14q loss mutation analysis' versus 'RPPA_CNMF'

P value = 0.000103 (Fisher's exact test), Q value = 0.053

Table S279.  Gene #66: '14q loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
14Q LOSS MUTATED 39 12 12
14Q LOSS WILD-TYPE 107 117 103

Figure S279.  Get High-res Image Gene #66: '14q loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'14q loss mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 4.06e-05 (Fisher's exact test), Q value = 0.022

Table S280.  Gene #66: '14q loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
14Q LOSS MUTATED 18 9 36
14Q LOSS WILD-TYPE 138 99 90

Figure S280.  Get High-res Image Gene #66: '14q loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'14q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.21e-10 (Fisher's exact test), Q value = 8.7e-08

Table S281.  Gene #66: '14q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
14Q LOSS MUTATED 65 7 51
14Q LOSS WILD-TYPE 170 148 383

Figure S281.  Get High-res Image Gene #66: '14q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'14q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.59e-12 (Fisher's exact test), Q value = 4.1e-09

Table S282.  Gene #66: '14q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
14Q LOSS MUTATED 53 11 59
14Q LOSS WILD-TYPE 360 205 136

Figure S282.  Get High-res Image Gene #66: '14q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 6.45e-13 (Fisher's exact test), Q value = 4.8e-10

Table S283.  Gene #66: '14q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
14Q LOSS MUTATED 13 40 72
14Q LOSS WILD-TYPE 187 383 177

Figure S283.  Get High-res Image Gene #66: '14q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'14q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.25e-14 (Fisher's exact test), Q value = 6.2e-11

Table S284.  Gene #66: '14q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
14Q LOSS MUTATED 65 52 8
14Q LOSS WILD-TYPE 139 557 51

Figure S284.  Get High-res Image Gene #66: '14q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000126 (Fisher's exact test), Q value = 0.065

Table S285.  Gene #67: '15q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
15Q LOSS MUTATED 37 50 13
15Q LOSS WILD-TYPE 84 202 121

Figure S285.  Get High-res Image Gene #67: '15q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'15q loss mutation analysis' versus 'CN_CNMF'

P value = 2.73e-18 (Chi-square test), Q value = 2.1e-15

Table S286.  Gene #67: '15q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
15Q LOSS MUTATED 19 30 32 68 10
15Q LOSS WILD-TYPE 327 46 166 147 46

Figure S286.  Get High-res Image Gene #67: '15q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'15q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.03e-06 (Chi-square test), Q value = 0.0013

Table S287.  Gene #67: '15q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
15Q LOSS MUTATED 33 15 18 19 3 7
15Q LOSS WILD-TYPE 63 127 62 104 33 83

Figure S287.  Get High-res Image Gene #67: '15q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'15q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.13e-05 (Fisher's exact test), Q value = 0.017

Table S288.  Gene #67: '15q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
15Q LOSS MUTATED 61 13 74
15Q LOSS WILD-TYPE 174 142 360

Figure S288.  Get High-res Image Gene #67: '15q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'15q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.92e-07 (Fisher's exact test), Q value = 0.00013

Table S289.  Gene #67: '15q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
15Q LOSS MUTATED 16 70 69
15Q LOSS WILD-TYPE 184 353 180

Figure S289.  Get High-res Image Gene #67: '15q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'15q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.58e-07 (Fisher's exact test), Q value = 0.00042

Table S290.  Gene #67: '15q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
15Q LOSS MUTATED 51 82 22
15Q LOSS WILD-TYPE 153 527 37

Figure S290.  Get High-res Image Gene #67: '15q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'16p loss mutation analysis' versus 'CN_CNMF'

P value = 6.45e-05 (Chi-square test), Q value = 0.034

Table S291.  Gene #68: '16p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
16P LOSS MUTATED 8 2 16 26 4
16P LOSS WILD-TYPE 338 74 182 189 52

Figure S291.  Get High-res Image Gene #68: '16p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'16p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000109 (Chi-square test), Q value = 0.057

Table S292.  Gene #68: '16p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
16P LOSS MUTATED 13 1 7 4 1 2
16P LOSS WILD-TYPE 83 141 73 119 35 88

Figure S292.  Get High-res Image Gene #68: '16p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'16q loss mutation analysis' versus 'MRNA_CNMF'

P value = 2.06e-11 (Fisher's exact test), Q value = 1.5e-08

Table S293.  Gene #69: '16q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
16Q LOSS MUTATED 157 37 43
16Q LOSS WILD-TYPE 99 55 116

Figure S293.  Get High-res Image Gene #69: '16q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'16q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.6e-13 (Fisher's exact test), Q value = 1.2e-10

Table S294.  Gene #69: '16q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
16Q LOSS MUTATED 21 141 75
16Q LOSS WILD-TYPE 100 111 59

Figure S294.  Get High-res Image Gene #69: '16q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'16q loss mutation analysis' versus 'CN_CNMF'

P value = 1.41e-11 (Chi-square test), Q value = 1e-08

Table S295.  Gene #69: '16q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
16Q LOSS MUTATED 167 52 93 52 28
16Q LOSS WILD-TYPE 179 24 105 163 28

Figure S295.  Get High-res Image Gene #69: '16q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'16q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.79e-14 (Chi-square test), Q value = 2.1e-11

Table S296.  Gene #69: '16q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
16Q LOSS MUTATED 21 99 40 49 13 23
16Q LOSS WILD-TYPE 75 43 40 74 23 67

Figure S296.  Get High-res Image Gene #69: '16q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'16q loss mutation analysis' versus 'RPPA_CNMF'

P value = 7.03e-07 (Fisher's exact test), Q value = 0.00045

Table S297.  Gene #69: '16q loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
16Q LOSS MUTATED 40 75 56
16Q LOSS WILD-TYPE 106 54 59

Figure S297.  Get High-res Image Gene #69: '16q loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'16q loss mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 5.24e-11 (Fisher's exact test), Q value = 3.8e-08

Table S298.  Gene #69: '16q loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
16Q LOSS MUTATED 91 55 25
16Q LOSS WILD-TYPE 65 53 101

Figure S298.  Get High-res Image Gene #69: '16q loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'16q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.21e-19 (Fisher's exact test), Q value = 5.6e-16

Table S299.  Gene #69: '16q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
16Q LOSS MUTATED 47 78 239
16Q LOSS WILD-TYPE 188 77 195

Figure S299.  Get High-res Image Gene #69: '16q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'16q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.11e-20 (Fisher's exact test), Q value = 1.7e-17

Table S300.  Gene #69: '16q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
16Q LOSS MUTATED 230 102 32
16Q LOSS WILD-TYPE 183 114 163

Figure S300.  Get High-res Image Gene #69: '16q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.96e-19 (Fisher's exact test), Q value = 1.5e-16

Table S301.  Gene #69: '16q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
16Q LOSS MUTATED 77 249 58
16Q LOSS WILD-TYPE 123 174 191

Figure S301.  Get High-res Image Gene #69: '16q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'16q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.87e-20 (Fisher's exact test), Q value = 4.6e-17

Table S302.  Gene #69: '16q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
16Q LOSS MUTATED 37 328 19
16Q LOSS WILD-TYPE 167 281 40

Figure S302.  Get High-res Image Gene #69: '16q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'17p loss mutation analysis' versus 'CN_CNMF'

P value = 2.04e-12 (Chi-square test), Q value = 1.5e-09

Table S303.  Gene #70: '17p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
17P LOSS MUTATED 93 25 108 116 25
17P LOSS WILD-TYPE 253 51 90 99 31

Figure S303.  Get High-res Image Gene #70: '17p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'17p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.4e-07 (Chi-square test), Q value = 9.2e-05

Table S304.  Gene #70: '17p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
17P LOSS MUTATED 39 47 47 67 13 18
17P LOSS WILD-TYPE 57 95 33 56 23 72

Figure S304.  Get High-res Image Gene #70: '17p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'17p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.94e-05 (Fisher's exact test), Q value = 0.016

Table S305.  Gene #70: '17p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
17P LOSS MUTATED 57 179 123
17P LOSS WILD-TYPE 143 244 126

Figure S305.  Get High-res Image Gene #70: '17p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'17q loss mutation analysis' versus 'MRNA_CNMF'

P value = 4.02e-08 (Fisher's exact test), Q value = 2.7e-05

Table S306.  Gene #71: '17q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
17Q LOSS MUTATED 25 14 52
17Q LOSS WILD-TYPE 231 78 107

Figure S306.  Get High-res Image Gene #71: '17q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'17q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.03e-06 (Fisher's exact test), Q value = 0.00065

Table S307.  Gene #71: '17q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
17Q LOSS MUTATED 41 38 12
17Q LOSS WILD-TYPE 80 214 122

Figure S307.  Get High-res Image Gene #71: '17q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'17q loss mutation analysis' versus 'CN_CNMF'

P value = 9.27e-14 (Chi-square test), Q value = 7e-11

Table S308.  Gene #71: '17q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
17Q LOSS MUTATED 22 9 33 69 8
17Q LOSS WILD-TYPE 324 67 165 146 48

Figure S308.  Get High-res Image Gene #71: '17q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'17q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.12e-06 (Chi-square test), Q value = 7e-04

Table S309.  Gene #71: '17q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
17Q LOSS MUTATED 26 4 14 21 2 8
17Q LOSS WILD-TYPE 70 138 66 102 34 82

Figure S309.  Get High-res Image Gene #71: '17q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'17q loss mutation analysis' versus 'RPPA_CNMF'

P value = 3.38e-10 (Fisher's exact test), Q value = 2.4e-07

Table S310.  Gene #71: '17q loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
17Q LOSS MUTATED 51 6 19
17Q LOSS WILD-TYPE 95 123 96

Figure S310.  Get High-res Image Gene #71: '17q loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'17q loss mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 5.84e-07 (Fisher's exact test), Q value = 0.00037

Table S311.  Gene #71: '17q loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
17Q LOSS MUTATED 15 17 44
17Q LOSS WILD-TYPE 141 91 82

Figure S311.  Get High-res Image Gene #71: '17q loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'17q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.73e-10 (Fisher's exact test), Q value = 1.2e-07

Table S312.  Gene #71: '17q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
17Q LOSS MUTATED 71 13 49
17Q LOSS WILD-TYPE 164 142 385

Figure S312.  Get High-res Image Gene #71: '17q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'17q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.06e-05 (Fisher's exact test), Q value = 0.0062

Table S313.  Gene #71: '17q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
17Q LOSS MUTATED 52 27 54
17Q LOSS WILD-TYPE 361 189 141

Figure S313.  Get High-res Image Gene #71: '17q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.67e-09 (Fisher's exact test), Q value = 2.6e-06

Table S314.  Gene #71: '17q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
17Q LOSS MUTATED 18 48 70
17Q LOSS WILD-TYPE 182 375 179

Figure S314.  Get High-res Image Gene #71: '17q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'17q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.09e-06 (Fisher's exact test), Q value = 0.00069

Table S315.  Gene #71: '17q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
17Q LOSS MUTATED 54 69 13
17Q LOSS WILD-TYPE 150 540 46

Figure S315.  Get High-res Image Gene #71: '17q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss mutation analysis' versus 'CN_CNMF'

P value = 3.2e-08 (Chi-square test), Q value = 2.2e-05

Table S316.  Gene #72: '18p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
18P LOSS MUTATED 33 23 58 47 11
18P LOSS WILD-TYPE 313 53 140 168 45

Figure S316.  Get High-res Image Gene #72: '18p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'18p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.32e-06 (Chi-square test), Q value = 0.0026

Table S317.  Gene #72: '18p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
18P LOSS MUTATED 10 18 28 33 3 11
18P LOSS WILD-TYPE 86 124 52 90 33 79

Figure S317.  Get High-res Image Gene #72: '18p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'18q loss mutation analysis' versus 'CN_CNMF'

P value = 9.76e-11 (Chi-square test), Q value = 7e-08

Table S318.  Gene #73: '18q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
18Q LOSS MUTATED 30 25 61 50 9
18Q LOSS WILD-TYPE 316 51 137 165 47

Figure S318.  Get High-res Image Gene #73: '18q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'18q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.04e-08 (Chi-square test), Q value = 2.7e-05

Table S319.  Gene #73: '18q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
18Q LOSS MUTATED 17 18 32 33 2 7
18Q LOSS WILD-TYPE 79 124 48 90 34 83

Figure S319.  Get High-res Image Gene #73: '18q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'19p loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000273 (Fisher's exact test), Q value = 0.13

Table S320.  Gene #74: '19p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
19P LOSS MUTATED 8 31 2
19P LOSS WILD-TYPE 113 221 132

Figure S320.  Get High-res Image Gene #74: '19p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'19p loss mutation analysis' versus 'CN_CNMF'

P value = 8.83e-14 (Chi-square test), Q value = 6.7e-11

Table S321.  Gene #74: '19p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
19P LOSS MUTATED 3 1 37 16 8
19P LOSS WILD-TYPE 343 75 161 199 48

Figure S321.  Get High-res Image Gene #74: '19p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'19p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.9e-09 (Chi-square test), Q value = 1.3e-06

Table S322.  Gene #74: '19p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
19P LOSS MUTATED 7 0 7 23 0 0
19P LOSS WILD-TYPE 89 142 73 100 36 90

Figure S322.  Get High-res Image Gene #74: '19p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'19q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.12e-05 (Fisher's exact test), Q value = 0.017

Table S323.  Gene #75: '19q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
19Q LOSS MUTATED 7 26 0
19Q LOSS WILD-TYPE 114 226 134

Figure S323.  Get High-res Image Gene #75: '19q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'19q loss mutation analysis' versus 'CN_CNMF'

P value = 1.43e-11 (Chi-square test), Q value = 1e-08

Table S324.  Gene #75: '19q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
19Q LOSS MUTATED 3 0 29 11 8
19Q LOSS WILD-TYPE 343 76 169 204 48

Figure S324.  Get High-res Image Gene #75: '19q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'19q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.15e-05 (Chi-square test), Q value = 0.0067

Table S325.  Gene #75: '19q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
19Q LOSS MUTATED 6 0 7 15 0 0
19Q LOSS WILD-TYPE 90 142 73 108 36 90

Figure S325.  Get High-res Image Gene #75: '19q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'19q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000133 (Fisher's exact test), Q value = 0.068

Table S326.  Gene #75: '19q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
19Q LOSS MUTATED 18 0 31
19Q LOSS WILD-TYPE 217 155 403

Figure S326.  Get High-res Image Gene #75: '19q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'20p loss mutation analysis' versus 'CN_CNMF'

P value = 9.38e-08 (Chi-square test), Q value = 6.2e-05

Table S327.  Gene #76: '20p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
20P LOSS MUTATED 3 1 18 25 7
20P LOSS WILD-TYPE 343 75 180 190 49

Figure S327.  Get High-res Image Gene #76: '20p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000431 (Chi-square test), Q value = 0.2

Table S328.  Gene #76: '20p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
20P LOSS MUTATED 14 3 5 7 1 1
20P LOSS WILD-TYPE 82 139 75 116 35 89

Figure S328.  Get High-res Image Gene #76: '20p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'20p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000479 (Fisher's exact test), Q value = 0.22

Table S329.  Gene #76: '20p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
20P LOSS MUTATED 23 4 21
20P LOSS WILD-TYPE 390 212 174

Figure S329.  Get High-res Image Gene #76: '20p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 5.09e-05 (Fisher's exact test), Q value = 0.027

Table S330.  Gene #76: '20p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
20P LOSS MUTATED 5 17 29
20P LOSS WILD-TYPE 195 406 220

Figure S330.  Get High-res Image Gene #76: '20p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'20q loss mutation analysis' versus 'CN_CNMF'

P value = 4.75e-06 (Chi-square test), Q value = 0.0028

Table S331.  Gene #77: '20q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
20Q LOSS MUTATED 0 1 7 17 4
20Q LOSS WILD-TYPE 346 75 191 198 52

Figure S331.  Get High-res Image Gene #77: '20q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.43e-06 (Chi-square test), Q value = 0.005

Table S332.  Gene #77: '20q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
20Q LOSS MUTATED 10 0 1 2 0 1
20Q LOSS WILD-TYPE 86 142 79 121 36 89

Figure S332.  Get High-res Image Gene #77: '20q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'20q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000217 (Fisher's exact test), Q value = 0.11

Table S333.  Gene #77: '20q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
20Q LOSS MUTATED 9 1 14
20Q LOSS WILD-TYPE 404 215 181

Figure S333.  Get High-res Image Gene #77: '20q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'20q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 5.06e-05 (Fisher's exact test), Q value = 0.027

Table S334.  Gene #77: '20q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
20Q LOSS MUTATED 2 7 19
20Q LOSS WILD-TYPE 198 416 230

Figure S334.  Get High-res Image Gene #77: '20q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'20q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.76e-05 (Fisher's exact test), Q value = 0.015

Table S335.  Gene #77: '20q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
20Q LOSS MUTATED 17 9 2
20Q LOSS WILD-TYPE 187 600 57

Figure S335.  Get High-res Image Gene #77: '20q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss mutation analysis' versus 'CN_CNMF'

P value = 1.31e-06 (Chi-square test), Q value = 0.00083

Table S336.  Gene #78: '21q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
21Q LOSS MUTATED 10 9 31 27 10
21Q LOSS WILD-TYPE 336 67 167 188 46

Figure S336.  Get High-res Image Gene #78: '21q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'22q loss mutation analysis' versus 'MRNA_CNMF'

P value = 3.08e-05 (Fisher's exact test), Q value = 0.017

Table S337.  Gene #79: '22q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 256 92 159
22Q LOSS MUTATED 110 31 34
22Q LOSS WILD-TYPE 146 61 125

Figure S337.  Get High-res Image Gene #79: '22q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'22q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 5.42e-07 (Fisher's exact test), Q value = 0.00035

Table S338.  Gene #79: '22q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 252 134
22Q LOSS MUTATED 19 108 48
22Q LOSS WILD-TYPE 102 144 86

Figure S338.  Get High-res Image Gene #79: '22q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'22q loss mutation analysis' versus 'CN_CNMF'

P value = 4.97e-08 (Chi-square test), Q value = 3.3e-05

Table S339.  Gene #79: '22q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
22Q LOSS MUTATED 87 40 87 59 25
22Q LOSS WILD-TYPE 259 36 111 156 31

Figure S339.  Get High-res Image Gene #79: '22q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'22q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.12e-06 (Chi-square test), Q value = 0.0054

Table S340.  Gene #79: '22q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 96 142 80 123 36 90
22Q LOSS MUTATED 27 43 34 60 7 16
22Q LOSS WILD-TYPE 69 99 46 63 29 74

Figure S340.  Get High-res Image Gene #79: '22q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'22q loss mutation analysis' versus 'RPPA_CNMF'

P value = 0.000358 (Fisher's exact test), Q value = 0.17

Table S341.  Gene #79: '22q loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 129 115
22Q LOSS MUTATED 37 62 37
22Q LOSS WILD-TYPE 109 67 78

Figure S341.  Get High-res Image Gene #79: '22q loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'22q loss mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 1.02e-05 (Fisher's exact test), Q value = 0.0059

Table S342.  Gene #79: '22q loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 108 126
22Q LOSS MUTATED 73 38 25
22Q LOSS WILD-TYPE 83 70 101

Figure S342.  Get High-res Image Gene #79: '22q loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'22q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.54e-11 (Fisher's exact test), Q value = 1.1e-08

Table S343.  Gene #79: '22q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 235 155 434
22Q LOSS MUTATED 43 43 191
22Q LOSS WILD-TYPE 192 112 243

Figure S343.  Get High-res Image Gene #79: '22q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'22q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.28e-10 (Fisher's exact test), Q value = 5.8e-07

Table S344.  Gene #79: '22q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 413 216 195
22Q LOSS MUTATED 171 75 31
22Q LOSS WILD-TYPE 242 141 164

Figure S344.  Get High-res Image Gene #79: '22q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.65e-08 (Fisher's exact test), Q value = 1.1e-05

Table S345.  Gene #79: '22q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
22Q LOSS MUTATED 45 182 63
22Q LOSS WILD-TYPE 155 241 186

Figure S345.  Get High-res Image Gene #79: '22q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'22q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.58e-07 (Fisher's exact test), Q value = 0.00042

Table S346.  Gene #79: '22q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 609 59
22Q LOSS MUTATED 39 235 16
22Q LOSS WILD-TYPE 165 374 43

Figure S346.  Get High-res Image Gene #79: '22q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Xq loss mutation analysis' versus 'CN_CNMF'

P value = 0.000119 (Chi-square test), Q value = 0.061

Table S347.  Gene #80: 'Xq loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 346 76 198 215 56
XQ LOSS MUTATED 0 2 12 14 2
XQ LOSS WILD-TYPE 346 74 186 201 54

Figure S347.  Get High-res Image Gene #80: 'Xq loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Xq loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 7.21e-05 (Fisher's exact test), Q value = 0.038

Table S348.  Gene #80: 'Xq loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 200 423 249
XQ LOSS MUTATED 0 12 17
XQ LOSS WILD-TYPE 200 411 232

Figure S348.  Get High-res Image Gene #80: 'Xq loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

Methods & Data
Input

  • Mutation data file = broad_values_by_arm.mutsig.cluster.txt

  • Molecular subtypes file = BRCA-TP.transferedmergedcluster.txt

  • Number of patients = 891

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 10

  • 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] 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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