Breast Invasive Carcinoma: Correlation between copy number variations of arm-level result and molecular subtypes
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
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 913 patients, 371 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 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_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_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_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

  • 5p gain cnv correlated to 'CN_CNMF'.

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

  • 7q gain cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

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

  • 8q gain cnv correlated to 'MRNA_CNMF',  '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'.

  • 11q 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'.

  • 14q gain cnv correlated to 'MRNASEQ_CNMF'.

  • 16p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

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

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

  • 19p gain cnv correlated to 'CN_CNMF'.

  • 19q gain cnv correlated to 'CN_CNMF'.

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

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

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

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

  • Xq gain cnv correlated to 'MRNA_CHIERARCHICAL',  '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', and 'MIRSEQ_CNMF'.

  • 1q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

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

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

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

  • 3q loss cnv correlated to 'MRNASEQ_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_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 7p loss cnv correlated to 'CN_CNMF'.

  • 7q loss cnv correlated to 'CN_CNMF'.

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

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

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

  • 10p loss cnv correlated to 'CN_CNMF'.

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

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

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

  • 16p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_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 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_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 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

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

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

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

  • 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 'MRNASEQ_CHIERARCHICAL' 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, 371 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 Chi-square test Fisher's exact test Chi-square test Chi-square test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test
2p gain 48 (5%) 865 1.06e-08
(7.24e-06) 		3.56e-11
(2.54e-08) 		3.7e-10
(2.6e-07) 		4.62e-05
(0.0237) 		1.97e-08
(1.33e-05) 		3.14e-08
(2.1e-05) 		2.5e-11
(1.8e-08) 		4.51e-15
(3.43e-12) 		9.66e-12
(7e-09) 		4.26e-10
(2.98e-07)
10p gain 110 (12%) 803 7.38e-11
(5.25e-08) 		9.62e-08
(6.29e-05) 		5.04e-15
(3.82e-12) 		3.37e-15
(2.57e-12) 		2.39e-05
(0.0127) 		1.42e-06
(0.00086) 		7.75e-18
(6e-15) 		6.2e-16
(4.77e-13) 		4.51e-14
(3.37e-11) 		2.89e-14
(2.16e-11)
4p loss 185 (20%) 728 4.5e-12
(3.27e-09) 		1.24e-12
(9.08e-10) 		9.98e-28
(7.92e-25) 		3.87e-14
(2.89e-11) 		0.00014
(0.0669) 		7.57e-06
(0.00429) 		2.98e-18
(2.32e-15) 		1.63e-19
(1.28e-16) 		5.21e-15
(3.95e-12) 		4.83e-11
(3.45e-08)
5p loss 73 (8%) 840 1.49e-08
(1.01e-05) 		4.14e-06
(0.0024) 		8.97e-21
(7.04e-18) 		4.03e-12
(2.93e-09) 		4.28e-05
(0.022) 		6.72e-06
(0.00383) 		1.77e-12
(1.3e-09) 		5.26e-10
(3.67e-07) 		6.17e-15
(4.66e-12) 		2.94e-12
(2.14e-09)
5q loss 124 (14%) 789 4.14e-19
(3.23e-16) 		9.95e-15
(7.5e-12) 		4.59e-45
(3.67e-42) 		1.21e-32
(9.64e-30) 		1.86e-09
(1.29e-06) 		6.93e-11
(4.93e-08) 		1.55e-34
(1.24e-31) 		4.74e-24
(3.75e-21) 		1.75e-27
(1.38e-24) 		2.27e-30
(1.8e-27)
14q loss 136 (15%) 777 1.09e-10
(7.74e-08) 		8.5e-08
(5.58e-05) 		2.6e-22
(2.04e-19) 		6.83e-16
(5.24e-13) 		0.000185
(0.0871) 		8.52e-05
(0.0424) 		3.58e-19
(2.79e-16) 		1.15e-11
(8.32e-09) 		1.06e-12
(7.8e-10) 		1.62e-13
(1.2e-10)
16q loss 390 (43%) 523 7.08e-08
(4.67e-05) 		1.75e-13
(1.3e-10) 		9.63e-12
(6.98e-09) 		6.1e-17
(4.7e-14) 		8.18e-06
(0.00462) 		1.02e-09
(7.06e-07) 		3.37e-19
(2.63e-16) 		3.58e-20
(2.81e-17) 		5.49e-17
(4.24e-14) 		3.27e-18
(2.53e-15)
17q loss 143 (16%) 770 1.08e-10
(7.67e-08) 		1.72e-06
(0.00103) 		8.88e-11
(6.3e-08) 		7.48e-05
(0.0375) 		9.69e-10
(6.72e-07) 		6.4e-07
(0.000396) 		9.87e-16
(7.56e-13) 		1.28e-08
(8.71e-06) 		4.97e-09
(3.41e-06) 		1.62e-06
(0.000977)
22q loss 306 (34%) 607 4.25e-05
(0.022) 		1.42e-07
(9.16e-05) 		2.97e-06
(0.00174) 		5.32e-07
(0.000331) 		0.000476
(0.208) 		1.64e-05
(0.00892) 		4.93e-06
(0.00285) 		6.75e-12
(4.9e-09) 		1.07e-08
(7.31e-06) 		5.27e-07
(0.000329)
1p gain 95 (10%) 818 1.33e-05
(0.00736) 		6.2e-07
(0.000384) 		3.78e-07
(0.000239) 		0.0198
(1.00) 		2.11e-05
(0.0114) 		0.000125
(0.0603) 		2.41e-06
(0.00143) 		5.53e-07
(0.000343) 		1.72e-05
(0.00932) 		4.52e-06
(0.00262)
6q loss 171 (19%) 742 4.71e-05
(0.0242) 		9.19e-07
(0.000562) 		1.2e-14
(9.01e-12) 		6.48e-08
(4.29e-05) 		0.00055
(0.237) 		0.0052
(1.00) 		1.21e-07
(7.84e-05) 		8.34e-08
(5.48e-05) 		0.000159
(0.0755) 		5.03e-06
(0.0029)
2q gain 25 (3%) 888 0.00458
(1.00) 		1.99e-05
(0.0107) 		0.000123
(0.0593) 		0.00625
(1.00) 		1.54e-07
(9.89e-05) 		0.000444
(0.196) 		0.000212
(0.099) 		1.22e-07
(7.89e-05) 		0.000282
(0.13) 		0.000132
(0.0637)
6p gain 104 (11%) 809 0.000185
(0.0871) 		4.92e-05
(0.0251) 		1e-14
(7.53e-12) 		6.04e-11
(4.3e-08) 		0.00785
(1.00) 		0.0427
(1.00) 		2.96e-07
(0.000187) 		2.12e-07
(0.000136) 		2.78e-11
(2e-08) 		1.93e-08
(1.3e-05)
9p gain 68 (7%) 845 1.38e-08
(9.34e-06) 		1.6e-08
(1.08e-05) 		1.79e-08
(1.21e-05) 		0.000842
(0.349) 		0.00881
(1.00) 		0.000106
(0.0519) 		3.38e-11
(2.42e-08) 		5.59e-09
(3.82e-06) 		2.51e-06
(0.00148) 		2.95e-07
(0.000187)
16p gain 254 (28%) 659 1.01e-05
(0.00561) 		8.07e-05
(0.0404) 		0.0119
(1.00) 		5.27e-07
(0.000329) 		0.000119
(0.0578) 		6.58e-05
(0.0333) 		7.12e-07
(0.000438) 		4.25e-05
(0.022) 		0.000186
(0.0876) 		0.00934
(1.00)
21q gain 104 (11%) 809 5.97e-05
(0.0303) 		0.00019
(0.0892) 		7.1e-10
(4.93e-07) 		4.67e-09
(3.2e-06) 		0.0684
(1.00) 		0.00554
(1.00) 		5.02e-07
(0.000315) 		1.77e-11
(1.27e-08) 		8.59e-06
(0.00484) 		1.59e-05
(0.00872)
4q loss 155 (17%) 758 1.79e-06
(0.00107) 		2.1e-08
(1.41e-05) 		7.17e-21
(5.64e-18) 		1.19e-10
(8.4e-08) 		0.0168
(1.00) 		0.00171
(0.66) 		3.35e-12
(2.44e-09) 		1.22e-15
(9.34e-13) 		3.33e-08
(2.22e-05) 		7.42e-08
(4.88e-05)
4p gain 29 (3%) 884 1.38e-06
(0.00084) 		2.66e-05
(0.014) 		1.12e-06
(0.000685) 		4.15e-05
(0.0215) 		0.0485
(1.00) 		0.0396
(1.00) 		2.53e-06
(0.00149) 		8.48e-05
(0.0423) 		0.000359
(0.163) 		0.285
(1.00)
8q gain 381 (42%) 532 2.29e-05
(0.0122) 		0.000315
(0.145) 		1.33e-23
(1.05e-20) 		8.16e-13
(6.02e-10) 		0.668
(1.00) 		0.503
(1.00) 		2.26e-13
(1.67e-10) 		7.04e-07
(0.000434) 		2.75e-11
(1.97e-08) 		0.00231
(0.868)
1p loss 123 (13%) 790 0.000228
(0.106) 		3.98e-10
(2.79e-07) 		2.44e-23
(1.93e-20) 		1.84e-06
(0.0011) 		0.702
(1.00) 		0.175
(1.00) 		5.14e-07
(0.000322) 		3.6e-18
(2.79e-15) 		0.000505
(0.22) 		0.00108
(0.436)
3p loss 92 (10%) 821 0.000694
(0.293) 		0.000914
(0.377) 		2.58e-09
(1.77e-06) 		3.42e-05
(0.0178) 		0.00233
(0.875) 		5.31e-05
(0.027) 		2.28e-05
(0.0122) 		0.000178
(0.084) 		1.46e-07
(9.39e-05) 		9.06e-05
(0.0448)
12q loss 52 (6%) 861 0.000708
(0.297) 		0.000244
(0.113) 		9.88e-05
(0.0486) 		4.1e-09
(2.82e-06) 		0.00486
(1.00) 		0.00265
(0.988) 		1.51e-08
(1.02e-05) 		1.31e-07
(8.5e-05) 		9.56e-06
(0.00535) 		1.65e-05
(0.00898)
4q gain 27 (3%) 886 1.38e-06
(0.00084) 		2.66e-05
(0.014) 		1.27e-08
(8.65e-06) 		0.000389
(0.174) 		0.0551
(1.00) 		0.0126
(1.00) 		5.15e-07
(0.000322) 		0.000471
(0.206) 		0.00346
(1.00) 		0.111
(1.00)
12p gain 115 (13%) 798 0.00691
(1.00) 		0.00154
(0.601) 		9e-14
(6.7e-11) 		4.76e-05
(0.0244) 		0.246
(1.00) 		0.0679
(1.00) 		3.57e-05
(0.0186) 		2.04e-05
(0.0109) 		3.71e-06
(0.00216) 		0.000406
(0.181)
18p gain 87 (10%) 826 0.00268
(0.998) 		0.00417
(1.00) 		2.57e-07
(0.000164) 		1.03e-07
(6.71e-05) 		0.0139
(1.00) 		0.0126
(1.00) 		5.06e-06
(0.00291) 		1.48e-05
(0.00813) 		4.68e-06
(0.0027) 		2.93e-05
(0.0153)
20q gain 276 (30%) 637 1.44e-05
(0.00795) 		0.00883
(1.00) 		3.32e-29
(2.64e-26) 		2.35e-14
(1.77e-11) 		0.199
(1.00) 		0.792
(1.00) 		6.82e-08
(4.51e-05) 		3.69e-06
(0.00215) 		3.09e-07
(0.000196) 		0.139
(1.00)
Xq gain 21 (2%) 892 0.000738
(0.309) 		0.000165
(0.0783) 		0.000166
(0.0788) 		0.0193
(1.00) 		0.0754
(1.00) 		0.00725
(1.00) 		0.000104
(0.0507) 		8.73e-06
(0.0049) 		8.71e-06
(0.00489) 		9.2e-05
(0.0455)
2p loss 75 (8%) 838 0.0116
(1.00) 		3.09e-05
(0.0162) 		2.58e-12
(1.89e-09) 		1.72e-07
(0.000111) 		0.0361
(1.00) 		0.00428
(1.00) 		0.0002
(0.0934) 		3.73e-08
(2.48e-05) 		6.92e-06
(0.00393) 		0.0037
(1.00)
6p loss 109 (12%) 804 0.0142
(1.00) 		9.32e-05
(0.046) 		1.09e-09
(7.52e-07) 		4.96e-05
(0.0253) 		0.0131
(1.00) 		0.00604
(1.00) 		3.46e-05
(0.018) 		1.44e-05
(0.00794) 		8.54e-05
(0.0424) 		0.0044
(1.00)
9p loss 190 (21%) 723 2.39e-05
(0.0127) 		0.00148
(0.578) 		5.07e-19
(3.95e-16) 		1.08e-13
(8.05e-11) 		0.0381
(1.00) 		0.858
(1.00) 		1.76e-07
(0.000113) 		5.28e-06
(0.00302) 		7.55e-07
(0.000464) 		0.00639
(1.00)
9q loss 147 (16%) 766 0.0075
(1.00) 		0.000614
(0.262) 		9.61e-16
(7.37e-13) 		1.74e-12
(1.28e-09) 		0.0135
(1.00) 		0.18
(1.00) 		2.88e-06
(0.00169) 		7.01e-06
(0.00397) 		1.36e-10
(9.59e-08) 		0.000119
(0.0578)
11q loss 229 (25%) 684 2.01e-07
(0.000129) 		0.000327
(0.15) 		2.04e-31
(1.62e-28) 		1.5e-11
(1.09e-08) 		0.208
(1.00) 		0.191
(1.00) 		1.88e-10
(1.33e-07) 		1.04e-06
(0.000633) 		0.00536
(1.00) 		0.00359
(1.00)
15q loss 162 (18%) 751 0.00701
(1.00) 		0.000121
(0.0586) 		3.85e-17
(2.98e-14) 		4.94e-07
(0.00031) 		0.117
(1.00) 		0.00548
(1.00) 		0.0056
(1.00) 		2.41e-06
(0.00143) 		1.01e-07
(6.61e-05) 		9.08e-07
(0.000557)
19p loss 67 (7%) 846 1.65e-05
(0.00898) 		0.000461
(0.203) 		7.77e-13
(5.73e-10) 		1.43e-08
(9.67e-06) 		0.424
(1.00) 		0.0741
(1.00) 		2.19e-06
(0.0013) 		3.82e-07
(0.000241) 		0.000705
(0.297) 		0.182
(1.00)
3q gain 99 (11%) 814 0.0146
(1.00) 		0.00685
(1.00) 		2.38e-09
(1.64e-06) 		0.000321
(0.148) 		0.0149
(1.00) 		0.11
(1.00) 		1.62e-05
(0.00886) 		2.26e-05
(0.0121) 		1.47e-05
(0.00808) 		0.00116
(0.465)
6q gain 61 (7%) 852 0.00194
(0.738) 		0.0048
(1.00) 		1.72e-14
(1.29e-11) 		0.00131
(0.524) 		0.000535
(0.231) 		0.0271
(1.00) 		0.00145
(0.571) 		6.89e-06
(0.00392) 		3.86e-06
(0.00224) 		2.41e-06
(0.00143)
17q gain 123 (13%) 790 4.01e-07
(0.000252) 		0.00782
(1.00) 		2.64e-18
(2.05e-15) 		3.27e-06
(0.00192) 		0.464
(1.00) 		0.00912
(1.00) 		2.44e-11
(1.76e-08) 		2.09e-07
(0.000133) 		0.064
(1.00) 		0.0212
(1.00)
20p gain 239 (26%) 674 3.66e-05
(0.019) 		0.0269
(1.00) 		3.08e-23
(2.43e-20) 		3.06e-08
(2.05e-05) 		0.0217
(1.00) 		0.133
(1.00) 		0.000325
(0.149) 		0.000675
(0.286) 		1.77e-06
(0.00106) 		0.256
(1.00)
2q loss 91 (10%) 822 0.112
(1.00) 		0.000444
(0.196) 		2.48e-12
(1.82e-09) 		4.01e-06
(0.00233) 		0.0688
(1.00) 		0.0281
(1.00) 		0.00709
(1.00) 		9.94e-06
(0.00555) 		1.58e-05
(0.0087) 		0.422
(1.00)
13q loss 267 (29%) 646 0.000134
(0.0642) 		0.000611
(0.262) 		1.62e-27
(1.28e-24) 		2.84e-10
(2e-07) 		0.727
(1.00) 		0.489
(1.00) 		0.00417
(1.00) 		2.63e-07
(0.000167) 		2.49e-09
(1.71e-06) 		0.157
(1.00)
17p loss 373 (41%) 540 8.23e-06
(0.00464) 		0.694
(1.00) 		6.2e-14
(4.62e-11) 		5.8e-08
(3.84e-05) 		0.00142
(0.561) 		0.123
(1.00) 		5.81e-10
(4.05e-07) 		0.0719
(1.00) 		1.77e-05
(0.00958) 		0.0277
(1.00)
19q loss 53 (6%) 860 7.41e-05
(0.0372) 		0.00138
(0.551) 		3.66e-10
(2.57e-07) 		1.62e-05
(0.00886) 		0.101
(1.00) 		0.0767
(1.00) 		5.18e-06
(0.00297) 		1.23e-07
(7.95e-05) 		0.0118
(1.00) 		0.289
(1.00)
20q loss 29 (3%) 884 0.0579
(1.00) 		0.1
(1.00) 		6.97e-05
(0.0352) 		2.82e-06
(0.00166) 		0.496
(1.00) 		0.172
(1.00) 		0.002
(0.759) 		0.000102
(0.0499) 		4.78e-05
(0.0244) 		2.24e-05
(0.012)
1q gain 487 (53%) 426 7.04e-05
(0.0355) 		0.714
(1.00) 		3.02e-08
(2.03e-05) 		2.87e-15
(2.19e-12) 		0.103
(1.00) 		0.186
(1.00) 		3.67e-07
(0.000232) 		0.15
(1.00) 		0.0435
(1.00) 		0.0499
(1.00)
22q gain 43 (5%) 870 0.0749
(1.00) 		0.00523
(1.00) 		3.75e-08
(2.5e-05) 		0.000999
(0.411) 		0.0685
(1.00) 		0.153
(1.00) 		0.00465
(1.00) 		8.33e-07
(0.000512) 		0.000348
(0.158) 		1.05e-05
(0.00584)
8p loss 270 (30%) 643 0.000103
(0.0506) 		0.178
(1.00) 		2.58e-15
(1.97e-12) 		9.84e-08
(6.42e-05) 		0.647
(1.00) 		0.909
(1.00) 		2.03e-07
(0.00013) 		0.00359
(1.00) 		0.000746
(0.312) 		0.028
(1.00)
10q loss 111 (12%) 802 0.000512
(0.223) 		0.00147
(0.576) 		4.34e-14
(3.24e-11) 		9.95e-07
(0.000608) 		0.00524
(1.00) 		0.112
(1.00) 		5.14e-06
(0.00295) 		0.00168
(0.653) 		0.00327
(1.00) 		0.0144
(1.00)
16p loss 55 (6%) 858 0.00385
(1.00) 		0.0204
(1.00) 		1.42e-05
(0.00785) 		2.47e-05
(0.0131) 		0.184
(1.00) 		0.286
(1.00) 		0.000751
(0.313) 		0.000424
(0.189) 		0.00052
(0.226) 		0.000626
(0.267)
18p loss 175 (19%) 738 0.000377
(0.17) 		0.645
(1.00) 		6.18e-10
(4.3e-07) 		3.32e-06
(0.00194) 		0.892
(1.00) 		0.962
(1.00) 		4.88e-08
(3.24e-05) 		0.0135
(1.00) 		0.0428
(1.00) 		0.0275
(1.00)
20p loss 53 (6%) 860 0.0561
(1.00) 		0.0463
(1.00) 		1.42e-06
(0.00086) 		2.42e-05
(0.0129) 		0.362
(1.00) 		0.43
(1.00) 		0.0136
(1.00) 		0.000148
(0.0708) 		2.75e-05
(0.0145) 		0.00208
(0.788)
8p gain 175 (19%) 738 0.0334
(1.00) 		0.0797
(1.00) 		5.71e-15
(4.33e-12) 		0.00037
(0.167) 		0.197
(1.00) 		0.457
(1.00) 		0.000381
(0.171) 		0.00144
(0.569) 		0.00361
(1.00) 		0.957
(1.00)
18q gain 77 (8%) 836 0.00117
(0.471) 		0.03
(1.00) 		6.69e-06
(0.00382) 		0.0127
(1.00) 		0.311
(1.00) 		0.274
(1.00) 		1.91e-05
(0.0103) 		0.00192
(0.734) 		0.000237
(0.11) 		0.0079
(1.00)
11p loss 144 (16%) 769 0.0342
(1.00) 		0.156
(1.00) 		8.5e-15
(6.41e-12) 		8.61e-08
(5.64e-05) 		0.0925
(1.00) 		0.0151
(1.00) 		0.00105
(0.426) 		0.00141
(0.561) 		0.000217
(0.101) 		0.387
(1.00)
18q loss 177 (19%) 736 0.00133
(0.529) 		0.644
(1.00) 		6.11e-13
(4.51e-10) 		7.01e-08
(4.63e-05) 		0.535
(1.00) 		0.828
(1.00) 		1.26e-06
(0.000765) 		0.0108
(1.00) 		0.0581
(1.00) 		0.181
(1.00)
5q gain 108 (12%) 805 0.00552
(1.00) 		0.00581
(1.00) 		7.31e-17
(5.63e-14) 		0.00965
(1.00) 		0.0042
(1.00) 		0.00691
(1.00) 		0.000627
(0.267) 		0.00109
(0.441) 		0.00674
(1.00) 		7.28e-05
(0.0366)
12q gain 87 (10%) 826 0.0372
(1.00) 		0.0631
(1.00) 		1.81e-15
(1.38e-12) 		8.74e-05
(0.0433) 		0.275
(1.00) 		0.4
(1.00) 		0.113
(1.00) 		0.00585
(1.00) 		0.00511
(1.00) 		0.385
(1.00)
12p loss 67 (7%) 846 0.305
(1.00) 		0.0978
(1.00) 		0.0158
(1.00) 		1.57e-06
(0.000947) 		0.149
(1.00) 		0.274
(1.00) 		0.0222
(1.00) 		0.000302
(0.139) 		0.007
(1.00) 		0.0222
(1.00)
Xq loss 31 (3%) 882 0.668
(1.00) 		0.0736
(1.00) 		0.000611
(0.262) 		0.00451
(1.00) 		0.0154
(1.00) 		0.2
(1.00) 		0.0281
(1.00) 		0.000433
(0.192) 		2.88e-05
(0.0151) 		0.0132
(1.00)
3p gain 57 (6%) 856 0.346
(1.00) 		0.153
(1.00) 		6.6e-07
(0.000408) 		0.532
(1.00) 		0.315
(1.00) 		0.151
(1.00) 		0.273
(1.00) 		0.0124
(1.00) 		0.0446
(1.00) 		0.212
(1.00)
5p gain 172 (19%) 741 0.156
(1.00) 		0.421
(1.00) 		4.56e-10
(3.18e-07) 		0.153
(1.00) 		0.593
(1.00) 		0.459
(1.00) 		0.372
(1.00) 		0.172
(1.00) 		0.0153
(1.00) 		0.605
(1.00)
7q gain 118 (13%) 795 0.00273
(1.00) 		0.0094
(1.00) 		0.00892
(1.00) 		0.00182
(0.701) 		0.404
(1.00) 		0.271
(1.00) 		0.0133
(1.00) 		0.00165
(0.641) 		0.104
(1.00) 		0.000358
(0.163)
9q gain 56 (6%) 857 0.455
(1.00) 		0.0805
(1.00) 		0.000148
(0.0708) 		0.161
(1.00) 		1
(1.00) 		0.488
(1.00) 		0.0631
(1.00) 		0.00573
(1.00) 		0.0491
(1.00) 		0.256
(1.00)
10q gain 45 (5%) 868 0.0114
(1.00) 		0.0144
(1.00) 		0.000533
(0.231) 		0.0159
(1.00) 		0.073
(1.00) 		0.0476
(1.00) 		0.00193
(0.737) 		0.00159
(0.62) 		0.00104
(0.424) 		0.00707
(1.00)
11q gain 46 (5%) 867 0.537
(1.00) 		0.77
(1.00) 		0.000131
(0.063) 		0.153
(1.00) 		0.909
(1.00) 		0.745
(1.00) 		0.652
(1.00) 		0.32
(1.00) 		0.174
(1.00) 		0.0922
(1.00)
14q gain 77 (8%) 836 0.000674
(0.286) 		0.012
(1.00) 		0.000978
(0.403) 		0.00684
(1.00) 		0.949
(1.00) 		0.316
(1.00) 		0.000442
(0.196) 		0.0077
(1.00) 		0.00123
(0.492) 		0.13
(1.00)
19p gain 69 (8%) 844 0.125
(1.00) 		0.0293
(1.00) 		0.000382
(0.171) 		0.141
(1.00) 		0.0373
(1.00) 		0.114
(1.00) 		0.00621
(1.00) 		0.000999
(0.411) 		0.0113
(1.00) 		0.00107
(0.433)
19q gain 86 (9%) 827 0.142
(1.00) 		0.0376
(1.00) 		0.000415
(0.185) 		0.111
(1.00) 		0.154
(1.00) 		0.251
(1.00) 		0.0237
(1.00) 		0.00263
(0.985) 		0.0361
(1.00) 		0.0129
(1.00)
1q loss 22 (2%) 891 0.243
(1.00) 		0.0336
(1.00) 		0.00419
(1.00) 		0.211
(1.00) 		0.272
(1.00) 		0.739
(1.00) 		0.121
(1.00) 		0.000357
(0.162) 		0.137
(1.00) 		0.323
(1.00)
3q loss 44 (5%) 869 0.0197
(1.00) 		0.00585
(1.00) 		0.00104
(0.424) 		0.00415
(1.00) 		0.185
(1.00) 		0.0657
(1.00) 		0.000579
(0.249) 		0.00832
(1.00) 		0.00192
(0.735) 		0.099
(1.00)
7p loss 48 (5%) 865 0.167
(1.00) 		0.024
(1.00) 		9.93e-06
(0.00555) 		0.0017
(0.657) 		0.371
(1.00) 		0.438
(1.00) 		0.00225
(0.849) 		0.000819
(0.341) 		0.00888
(1.00) 		0.00993
(1.00)
7q loss 64 (7%) 849 0.327
(1.00) 		0.0996
(1.00) 		0.000443
(0.196) 		0.206
(1.00) 		0.236
(1.00) 		0.421
(1.00) 		0.303
(1.00) 		0.00509
(1.00) 		0.0195
(1.00) 		0.254
(1.00)
10p loss 75 (8%) 838 0.025
(1.00) 		0.0119
(1.00) 		2.55e-06
(0.0015) 		0.0213
(1.00) 		0.716
(1.00) 		0.46
(1.00) 		0.0162
(1.00) 		0.0352
(1.00) 		0.0114
(1.00) 		0.258
(1.00)
21q loss 86 (9%) 827 0.0238
(1.00) 		0.269
(1.00) 		1.67e-06
(0.001) 		0.0576
(1.00) 		1
(1.00) 		0.812
(1.00) 		0.444
(1.00) 		0.316
(1.00) 		0.0344
(1.00) 		0.129
(1.00)
7p gain 158 (17%) 755 0.151
(1.00) 		0.257
(1.00) 		0.0621
(1.00) 		0.0146
(1.00) 		0.947
(1.00) 		0.52
(1.00) 		0.139
(1.00) 		0.169
(1.00) 		0.256
(1.00) 		0.0412
(1.00)
11p gain 67 (7%) 846 0.943
(1.00) 		0.606
(1.00) 		0.00507
(1.00) 		0.0342
(1.00) 		0.318
(1.00) 		0.155
(1.00) 		0.269
(1.00) 		0.468
(1.00) 		0.268
(1.00) 		0.287
(1.00)
13q gain 47 (5%) 866 0.525
(1.00) 		0.619
(1.00) 		0.0284
(1.00) 		0.0306
(1.00) 		0.0642
(1.00) 		0.258
(1.00) 		0.0668
(1.00) 		0.0308
(1.00) 		0.00732
(1.00) 		0.0112
(1.00)
15q gain 45 (5%) 868 0.727
(1.00) 		0.474
(1.00) 		0.682
(1.00) 		0.145
(1.00) 		0.817
(1.00) 		0.561
(1.00) 		0.498
(1.00) 		0.419
(1.00) 		0.473
(1.00) 		0.153
(1.00)
16q gain 56 (6%) 857 0.531
(1.00) 		0.215
(1.00) 		0.000841
(0.349) 		0.0705
(1.00) 		0.134
(1.00) 		0.775
(1.00) 		0.109
(1.00) 		0.00948
(1.00) 		0.00962
(1.00) 		0.00461
(1.00)
17p gain 47 (5%) 866 0.0217
(1.00) 		0.396
(1.00) 		0.00182
(0.701) 		0.619
(1.00) 		0.18
(1.00) 		0.2
(1.00) 		0.0226
(1.00) 		0.462
(1.00) 		0.417
(1.00) 		0.534
(1.00)
8q loss 46 (5%) 867 0.507
(1.00) 		0.526
(1.00) 		0.203
(1.00) 		0.103
(1.00) 		0.688
(1.00) 		0.566
(1.00) 		0.773
(1.00) 		0.369
(1.00) 		0.0649
(1.00) 		1
(1.00)
'1p gain mutation analysis' versus 'MRNA_CNMF'

P value = 1.33e-05 (Chi-square test), Q value = 0.0074

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
1P GAIN MUTATED 11 2 1 27 11 4 4 5
1P GAIN WILD-TYPE 113 34 22 68 61 16 99 35

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 = 6.2e-07 (Fisher's exact test), Q value = 0.00038

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
1P GAIN MUTATED 14 34 17
1P GAIN WILD-TYPE 126 91 231

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 = 3.78e-07 (Chi-square test), Q value = 0.00024

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 347 222 72 223 49
1P GAIN MUTATED 21 15 7 46 6
1P GAIN WILD-TYPE 326 207 65 177 43

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 = 2.11e-05 (Fisher's exact test), Q value = 0.011

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
1P GAIN MUTATED 35 13 6
1P GAIN WILD-TYPE 112 120 111

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 = 0.000125 (Fisher's exact test), Q value = 0.06

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
1P GAIN MUTATED 20 5 29
1P GAIN WILD-TYPE 141 105 97

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 = 2.41e-06 (Chi-square test), Q value = 0.0014

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
1P GAIN MUTATED 35 6 4 14 11 2 13 2
1P GAIN WILD-TYPE 111 73 96 117 167 10 138 29

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 = 5.53e-07 (Fisher's exact test), Q value = 0.00034

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
1P GAIN MUTATED 21 43 23
1P GAIN WILD-TYPE 315 162 264

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 = 1.72e-05 (Fisher's exact test), Q value = 0.0093

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
1P GAIN MUTATED 14 30 45
1P GAIN WILD-TYPE 187 399 204

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 = 4.52e-06 (Fisher's exact test), Q value = 0.0026

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 616 59
1P GAIN MUTATED 39 42 8
1P GAIN WILD-TYPE 165 574 51

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

'1q gain mutation analysis' versus 'MRNA_CNMF'

P value = 7.04e-05 (Chi-square test), Q value = 0.035

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
1Q GAIN MUTATED 53 17 13 53 39 10 80 25
1Q GAIN WILD-TYPE 71 19 10 42 33 10 23 15

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

'1q gain mutation analysis' versus 'CN_CNMF'

P value = 3.02e-08 (Chi-square test), Q value = 2e-05

Table S11.  Gene #2: '1q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
1Q GAIN MUTATED 171 124 63 104 25
1Q GAIN WILD-TYPE 176 98 9 119 24

Figure S11.  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 = 2.87e-15 (Chi-square test), Q value = 2.2e-12

Table S12.  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 101 139 93 137 40 97
1Q GAIN MUTATED 44 108 60 58 16 26
1Q GAIN WILD-TYPE 57 31 33 79 24 71

Figure S12.  Get High-res Image Gene #2: '1q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'1q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.67e-07 (Chi-square test), Q value = 0.00023

Table S13.  Gene #2: '1q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
1Q GAIN MUTATED 74 38 57 67 73 6 114 17
1Q GAIN WILD-TYPE 72 41 43 64 105 6 37 14

Figure S13.  Get High-res Image Gene #2: '1q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'2p gain mutation analysis' versus 'MRNA_CNMF'

P value = 1.06e-08 (Chi-square test), Q value = 7.2e-06

Table S14.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
2P GAIN MUTATED 3 0 0 18 11 0 1 0
2P GAIN WILD-TYPE 121 36 23 77 61 20 102 40

Figure S14.  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 = 3.56e-11 (Fisher's exact test), Q value = 2.5e-08

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
2P GAIN MUTATED 0 25 8
2P GAIN WILD-TYPE 140 100 240

Figure S15.  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 = 3.7e-10 (Chi-square test), Q value = 2.6e-07

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
2P GAIN MUTATED 2 11 3 31 1
2P GAIN WILD-TYPE 345 211 69 192 48

Figure S16.  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 = 4.62e-05 (Chi-square test), Q value = 0.024

Table S17.  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 101 139 93 137 40 97
2P GAIN MUTATED 14 1 4 5 1 2
2P GAIN WILD-TYPE 87 138 89 132 39 95

Figure S17.  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 = 1.97e-08 (Fisher's exact test), Q value = 1.3e-05

Table S18.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
2P GAIN MUTATED 24 0 4
2P GAIN WILD-TYPE 123 133 113

Figure S18.  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 = 3.14e-08 (Fisher's exact test), Q value = 2.1e-05

Table S19.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
2P GAIN MUTATED 4 1 23
2P GAIN WILD-TYPE 157 109 103

Figure S19.  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 = 2.5e-11 (Chi-square test), Q value = 1.8e-08

Table S20.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
2P GAIN MUTATED 24 0 1 16 4 1 1 0
2P GAIN WILD-TYPE 122 79 99 115 174 11 150 31

Figure S20.  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 = 4.51e-15 (Fisher's exact test), Q value = 3.4e-12

Table S21.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
2P GAIN MUTATED 13 34 0
2P GAIN WILD-TYPE 323 171 287

Figure S21.  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 = 9.66e-12 (Fisher's exact test), Q value = 7e-09

Table S22.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
2P GAIN MUTATED 1 8 33
2P GAIN WILD-TYPE 200 421 216

Figure S22.  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 = 4.26e-10 (Fisher's exact test), Q value = 3e-07

Table S23.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 616 59
2P GAIN MUTATED 27 10 5
2P GAIN WILD-TYPE 177 606 54

Figure S23.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.99e-05 (Fisher's exact test), Q value = 0.011

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
2Q GAIN MUTATED 0 13 6
2Q GAIN WILD-TYPE 140 112 242

Figure S24.  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 = 0.000123 (Chi-square test), Q value = 0.059

Table S25.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
2Q GAIN MUTATED 1 6 3 15 0
2Q GAIN WILD-TYPE 346 216 69 208 49

Figure S25.  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 = 1.54e-07 (Fisher's exact test), Q value = 9.9e-05

Table S26.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
2Q GAIN MUTATED 16 0 0
2Q GAIN WILD-TYPE 131 133 117

Figure S26.  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 = 0.000444 (Fisher's exact test), Q value = 0.2

Table S27.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
2Q GAIN MUTATED 4 0 12
2Q GAIN WILD-TYPE 157 110 114

Figure S27.  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 = 0.000212 (Chi-square test), Q value = 0.099

Table S28.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
2Q GAIN MUTATED 11 0 1 9 2 0 1 0
2Q GAIN WILD-TYPE 135 79 99 122 176 12 150 31

Figure S28.  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 = 1.22e-07 (Fisher's exact test), Q value = 7.9e-05

Table S29.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
2Q GAIN MUTATED 7 17 0
2Q GAIN WILD-TYPE 329 188 287

Figure S29.  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 = 0.000282 (Fisher's exact test), Q value = 0.13

Table S30.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
2Q GAIN MUTATED 1 5 14
2Q GAIN WILD-TYPE 200 424 235

Figure S30.  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 = 0.000132 (Fisher's exact test), Q value = 0.064

Table S31.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 616 59
2Q GAIN MUTATED 13 6 1
2Q GAIN WILD-TYPE 191 610 58

Figure S31.  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 = 6.6e-07 (Chi-square test), Q value = 0.00041

Table S32.  Gene #5: '3p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
3P GAIN MUTATED 5 19 11 14 8
3P GAIN WILD-TYPE 342 203 61 209 41

Figure S32.  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 = 2.38e-09 (Chi-square test), Q value = 1.6e-06

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
3Q GAIN MUTATED 9 26 13 42 9
3Q GAIN WILD-TYPE 338 196 59 181 40

Figure S33.  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 = 0.000321 (Chi-square test), Q value = 0.15

Table S34.  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 101 139 93 137 40 97
3Q GAIN MUTATED 18 5 11 13 2 2
3Q GAIN WILD-TYPE 83 134 82 124 38 95

Figure S34.  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 = 1.62e-05 (Chi-square test), Q value = 0.0089

Table S35.  Gene #6: '3q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
3Q GAIN MUTATED 33 1 11 20 17 1 9 2
3Q GAIN WILD-TYPE 113 78 89 111 161 11 142 29

Figure S35.  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 = 2.26e-05 (Fisher's exact test), Q value = 0.012

Table S36.  Gene #6: '3q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
3Q GAIN MUTATED 42 37 15
3Q GAIN WILD-TYPE 294 168 272

Figure S36.  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 = 1.47e-05 (Fisher's exact test), Q value = 0.0081

Table S37.  Gene #6: '3q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
3Q GAIN MUTATED 10 40 46
3Q GAIN WILD-TYPE 191 389 203

Figure S37.  Get High-res Image Gene #6: '3q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'4p gain mutation analysis' versus 'MRNA_CNMF'

P value = 1.38e-06 (Chi-square test), Q value = 0.00084

Table S38.  Gene #7: '4p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
4P GAIN MUTATED 15 0 0 0 1 0 1 0
4P GAIN WILD-TYPE 109 36 23 95 71 20 102 40

Figure S38.  Get High-res Image Gene #7: '4p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'4p gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 2.66e-05 (Fisher's exact test), Q value = 0.014

Table S39.  Gene #7: '4p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
4P GAIN MUTATED 0 0 17
4P GAIN WILD-TYPE 140 125 231

Figure S39.  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 = 1.12e-06 (Chi-square test), Q value = 0.00068

Table S40.  Gene #7: '4p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
4P GAIN MUTATED 1 19 2 4 3
4P GAIN WILD-TYPE 346 203 70 219 46

Figure S40.  Get High-res Image Gene #7: '4p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'4p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.15e-05 (Chi-square test), Q value = 0.022

Table S41.  Gene #7: '4p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
4P GAIN MUTATED 0 1 4 12 0 0
4P GAIN WILD-TYPE 101 138 89 125 40 97

Figure S41.  Get High-res Image Gene #7: '4p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'4p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.53e-06 (Chi-square test), Q value = 0.0015

Table S42.  Gene #7: '4p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
4P GAIN MUTATED 0 2 4 3 19 0 1 0
4P GAIN WILD-TYPE 146 77 96 128 159 12 150 31

Figure S42.  Get High-res Image Gene #7: '4p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'4p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.48e-05 (Fisher's exact test), Q value = 0.042

Table S43.  Gene #7: '4p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
4P GAIN MUTATED 23 3 3
4P GAIN WILD-TYPE 313 202 284

Figure S43.  Get High-res Image Gene #7: '4p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'4p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000359 (Fisher's exact test), Q value = 0.16

Table S44.  Gene #7: '4p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
4P GAIN MUTATED 2 24 2
4P GAIN WILD-TYPE 199 405 247

Figure S44.  Get High-res Image Gene #7: '4p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'4q gain mutation analysis' versus 'MRNA_CNMF'

P value = 1.38e-06 (Chi-square test), Q value = 0.00084

Table S45.  Gene #8: '4q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
4Q GAIN MUTATED 15 0 0 0 1 0 1 0
4Q GAIN WILD-TYPE 109 36 23 95 71 20 102 40

Figure S45.  Get High-res Image Gene #8: '4q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'4q gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 2.66e-05 (Fisher's exact test), Q value = 0.014

Table S46.  Gene #8: '4q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
4Q GAIN MUTATED 0 0 17
4Q GAIN WILD-TYPE 140 125 231

Figure S46.  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 = 1.27e-08 (Chi-square test), Q value = 8.6e-06

Table S47.  Gene #8: '4q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
4Q GAIN MUTATED 1 20 1 2 3
4Q GAIN WILD-TYPE 346 202 71 221 46

Figure S47.  Get High-res Image Gene #8: '4q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'4q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000389 (Chi-square test), Q value = 0.17

Table S48.  Gene #8: '4q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
4Q GAIN MUTATED 0 1 3 10 0 0
4Q GAIN WILD-TYPE 101 138 90 127 40 97

Figure S48.  Get High-res Image Gene #8: '4q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'4q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.15e-07 (Chi-square test), Q value = 0.00032

Table S49.  Gene #8: '4q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
4Q GAIN MUTATED 0 1 3 3 19 0 1 0
4Q GAIN WILD-TYPE 146 78 97 128 159 12 150 31

Figure S49.  Get High-res Image Gene #8: '4q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'4q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000471 (Fisher's exact test), Q value = 0.21

Table S50.  Gene #8: '4q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
4Q GAIN MUTATED 21 2 4
4Q GAIN WILD-TYPE 315 203 283

Figure S50.  Get High-res Image Gene #8: '4q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'5p gain mutation analysis' versus 'CN_CNMF'

P value = 4.56e-10 (Chi-square test), Q value = 3.2e-07

Table S51.  Gene #9: '5p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
5P GAIN MUTATED 30 61 26 43 12
5P GAIN WILD-TYPE 317 161 46 180 37

Figure S51.  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 = 7.31e-17 (Chi-square test), Q value = 5.6e-14

Table S52.  Gene #10: '5q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
5Q GAIN MUTATED 20 46 25 8 9
5Q GAIN WILD-TYPE 327 176 47 215 40

Figure S52.  Get High-res Image Gene #10: '5q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'5q gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.28e-05 (Fisher's exact test), Q value = 0.037

Table S53.  Gene #10: '5q gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 616 59
5Q GAIN MUTATED 8 88 6
5Q GAIN WILD-TYPE 196 528 53

Figure S53.  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 = 0.000185 (Chi-square test), Q value = 0.087

Table S54.  Gene #11: '6p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
6P GAIN MUTATED 11 0 0 20 12 5 10 0
6P GAIN WILD-TYPE 113 36 23 75 60 15 93 40

Figure S54.  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 = 4.92e-05 (Fisher's exact test), Q value = 0.025

Table S55.  Gene #11: '6p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
6P GAIN MUTATED 4 24 30
6P GAIN WILD-TYPE 136 101 218

Figure S55.  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 = 1e-14 (Chi-square test), Q value = 7.5e-12

Table S56.  Gene #11: '6p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
6P GAIN MUTATED 11 15 15 52 11
6P GAIN WILD-TYPE 336 207 57 171 38

Figure S56.  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 = 6.04e-11 (Chi-square test), Q value = 4.3e-08

Table S57.  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 101 139 93 137 40 97
6P GAIN MUTATED 31 8 14 14 1 1
6P GAIN WILD-TYPE 70 131 79 123 39 96

Figure S57.  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 = 2.96e-07 (Chi-square test), Q value = 0.00019

Table S58.  Gene #11: '6p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
6P GAIN MUTATED 35 3 10 19 13 3 9 0
6P GAIN WILD-TYPE 111 76 90 112 165 9 142 31

Figure S58.  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 = 2.12e-07 (Fisher's exact test), Q value = 0.00014

Table S59.  Gene #11: '6p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
6P GAIN MUTATED 37 42 13
6P GAIN WILD-TYPE 299 163 274

Figure S59.  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 = 2.78e-11 (Fisher's exact test), Q value = 2e-08

Table S60.  Gene #11: '6p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
6P GAIN MUTATED 7 31 56
6P GAIN WILD-TYPE 194 398 193

Figure S60.  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 = 1.93e-08 (Fisher's exact test), Q value = 1.3e-05

Table S61.  Gene #11: '6p gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 616 59
6P GAIN MUTATED 46 42 6
6P GAIN WILD-TYPE 158 574 53

Figure S61.  Get High-res Image Gene #11: '6p gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'6q gain mutation analysis' versus 'CN_CNMF'

P value = 1.72e-14 (Chi-square test), Q value = 1.3e-11

Table S62.  Gene #12: '6q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
6Q GAIN MUTATED 5 5 10 39 2
6Q GAIN WILD-TYPE 342 217 62 184 47

Figure S62.  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 = 0.000535 (Fisher's exact test), Q value = 0.23

Table S63.  Gene #12: '6q gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
6Q GAIN MUTATED 20 7 2
6Q GAIN WILD-TYPE 127 126 115

Figure S63.  Get High-res Image Gene #12: '6q gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'6q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.89e-06 (Fisher's exact test), Q value = 0.0039

Table S64.  Gene #12: '6q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
6Q GAIN MUTATED 25 25 5
6Q GAIN WILD-TYPE 311 180 282

Figure S64.  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 = 3.86e-06 (Fisher's exact test), Q value = 0.0022

Table S65.  Gene #12: '6q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
6Q GAIN MUTATED 5 17 32
6Q GAIN WILD-TYPE 196 412 217

Figure S65.  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 = 2.41e-06 (Fisher's exact test), Q value = 0.0014

Table S66.  Gene #12: '6q gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 616 59
6Q GAIN MUTATED 27 21 6
6Q GAIN WILD-TYPE 177 595 53

Figure S66.  Get High-res Image Gene #12: '6q gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'7q gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000358 (Fisher's exact test), Q value = 0.16

Table S67.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 616 59
7Q GAIN MUTATED 42 66 3
7Q GAIN WILD-TYPE 162 550 56

Figure S67.  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 = 5.71e-15 (Chi-square test), Q value = 4.3e-12

Table S68.  Gene #15: '8p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
8P GAIN MUTATED 33 42 30 46 24
8P GAIN WILD-TYPE 314 180 42 177 25

Figure S68.  Get High-res Image Gene #15: '8p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'8p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.00037 (Chi-square test), Q value = 0.17

Table S69.  Gene #15: '8p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 101 139 93 137 40 97
8P GAIN MUTATED 28 21 20 31 6 4
8P GAIN WILD-TYPE 73 118 73 106 34 93

Figure S69.  Get High-res Image Gene #15: '8p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'8p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000381 (Chi-square test), Q value = 0.17

Table S70.  Gene #15: '8p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
8P GAIN MUTATED 31 9 31 20 45 2 23 0
8P GAIN WILD-TYPE 115 70 69 111 133 10 128 31

Figure S70.  Get High-res Image Gene #15: '8p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'8q gain mutation analysis' versus 'MRNA_CNMF'

P value = 2.29e-05 (Chi-square test), Q value = 0.012

Table S71.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
8Q GAIN MUTATED 72 13 14 52 34 11 35 7
8Q GAIN WILD-TYPE 52 23 9 43 38 9 68 33

Figure S71.  Get High-res Image Gene #16: '8q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'8q gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000315 (Fisher's exact test), Q value = 0.14

Table S72.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
8Q GAIN MUTATED 45 63 130
8Q GAIN WILD-TYPE 95 62 118

Figure S72.  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 = 1.33e-23 (Chi-square test), Q value = 1e-20

Table S73.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
8Q GAIN MUTATED 72 118 35 118 38
8Q GAIN WILD-TYPE 275 104 37 105 11

Figure S73.  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 = 8.16e-13 (Chi-square test), Q value = 6e-10

Table S74.  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 101 139 93 137 40 97
8Q GAIN MUTATED 54 29 37 79 10 20
8Q GAIN WILD-TYPE 47 110 56 58 30 77

Figure S74.  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 = 2.26e-13 (Chi-square test), Q value = 1.7e-10

Table S75.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
8Q GAIN MUTATED 80 20 55 53 104 7 35 6
8Q GAIN WILD-TYPE 66 59 45 78 74 5 116 25

Figure S75.  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 = 7.04e-07 (Fisher's exact test), Q value = 0.00043

Table S76.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
8Q GAIN MUTATED 170 101 89
8Q GAIN WILD-TYPE 166 104 198

Figure S76.  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 = 2.75e-11 (Fisher's exact test), Q value = 2e-08

Table S77.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
8Q GAIN MUTATED 49 180 141
8Q GAIN WILD-TYPE 152 249 108

Figure S77.  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 = 1.38e-08 (Chi-square test), Q value = 9.3e-06

Table S78.  Gene #17: '9p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
9P GAIN MUTATED 3 1 0 24 4 0 7 2
9P GAIN WILD-TYPE 121 35 23 71 68 20 96 38

Figure S78.  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 = 1.6e-08 (Fisher's exact test), Q value = 1.1e-05

Table S79.  Gene #17: '9p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
9P GAIN MUTATED 4 27 10
9P GAIN WILD-TYPE 136 98 238

Figure S79.  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 = 1.79e-08 (Chi-square test), Q value = 1.2e-05

Table S80.  Gene #17: '9p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
9P GAIN MUTATED 9 10 13 32 4
9P GAIN WILD-TYPE 338 212 59 191 45

Figure S80.  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 = 0.000106 (Fisher's exact test), Q value = 0.052

Table S81.  Gene #17: '9p gain mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
9P GAIN MUTATED 5 7 22
9P GAIN WILD-TYPE 156 103 104

Figure S81.  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 = 3.38e-11 (Chi-square test), Q value = 2.4e-08

Table S82.  Gene #17: '9p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
9P GAIN MUTATED 33 1 3 7 6 2 8 2
9P GAIN WILD-TYPE 113 78 97 124 172 10 143 29

Figure S82.  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 = 5.59e-09 (Fisher's exact test), Q value = 3.8e-06

Table S83.  Gene #17: '9p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
9P GAIN MUTATED 15 37 10
9P GAIN WILD-TYPE 321 168 277

Figure S83.  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 = 2.51e-06 (Fisher's exact test), Q value = 0.0015

Table S84.  Gene #17: '9p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
9P GAIN MUTATED 7 21 37
9P GAIN WILD-TYPE 194 408 212

Figure S84.  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 = 2.95e-07 (Fisher's exact test), Q value = 0.00019

Table S85.  Gene #17: '9p gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 616 59
9P GAIN MUTATED 34 27 4
9P GAIN WILD-TYPE 170 589 55

Figure S85.  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 = 0.000148 (Chi-square test), Q value = 0.071

Table S86.  Gene #18: '9q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
9Q GAIN MUTATED 10 12 12 19 3
9Q GAIN WILD-TYPE 337 210 60 204 46

Figure S86.  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 = 7.38e-11 (Chi-square test), Q value = 5.2e-08

Table S87.  Gene #19: '10p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
10P GAIN MUTATED 10 3 0 33 18 2 3 3
10P GAIN WILD-TYPE 114 33 23 62 54 18 100 37

Figure S87.  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 = 9.62e-08 (Fisher's exact test), Q value = 6.3e-05

Table S88.  Gene #19: '10p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
10P GAIN MUTATED 11 38 23
10P GAIN WILD-TYPE 129 87 225

Figure S88.  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 = 5.04e-15 (Chi-square test), Q value = 3.8e-12

Table S89.  Gene #19: '10p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
10P GAIN MUTATED 11 23 10 60 6
10P GAIN WILD-TYPE 336 199 62 163 43

Figure S89.  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 = 3.37e-15 (Chi-square test), Q value = 2.6e-12

Table S90.  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 101 139 93 137 40 97
10P GAIN MUTATED 34 4 11 14 0 2
10P GAIN WILD-TYPE 67 135 82 123 40 95

Figure S90.  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 = 2.39e-05 (Fisher's exact test), Q value = 0.013

Table S91.  Gene #19: '10p gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
10P GAIN MUTATED 36 8 12
10P GAIN WILD-TYPE 111 125 105

Figure S91.  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 = 1.42e-06 (Fisher's exact test), Q value = 0.00086

Table S92.  Gene #19: '10p gain mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
10P GAIN MUTATED 11 10 35
10P GAIN WILD-TYPE 150 100 91

Figure S92.  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 = 7.75e-18 (Chi-square test), Q value = 6e-15

Table S93.  Gene #19: '10p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
10P GAIN MUTATED 51 5 6 20 14 1 3 2
10P GAIN WILD-TYPE 95 74 94 111 164 11 148 29

Figure S93.  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 = 6.2e-16 (Fisher's exact test), Q value = 4.8e-13

Table S94.  Gene #19: '10p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
10P GAIN MUTATED 28 61 13
10P GAIN WILD-TYPE 308 144 274

Figure S94.  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 = 4.51e-14 (Fisher's exact test), Q value = 3.4e-11

Table S95.  Gene #19: '10p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
10P GAIN MUTATED 12 28 66
10P GAIN WILD-TYPE 189 401 183

Figure S95.  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 = 2.89e-14 (Fisher's exact test), Q value = 2.2e-11

Table S96.  Gene #19: '10p gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 616 59
10P GAIN MUTATED 57 39 10
10P GAIN WILD-TYPE 147 577 49

Figure S96.  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 = 0.000533 (Chi-square test), Q value = 0.23

Table S97.  Gene #20: '10q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
10Q GAIN MUTATED 5 10 7 19 4
10Q GAIN WILD-TYPE 342 212 65 204 45

Figure S97.  Get High-res Image Gene #20: '10q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'11q gain mutation analysis' versus 'CN_CNMF'

P value = 0.000131 (Chi-square test), Q value = 0.063

Table S98.  Gene #22: '11q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
11Q GAIN MUTATED 9 7 2 22 6
11Q GAIN WILD-TYPE 338 215 70 201 43

Figure S98.  Get High-res Image Gene #22: '11q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'12p gain mutation analysis' versus 'CN_CNMF'

P value = 9e-14 (Chi-square test), Q value = 6.7e-11

Table S99.  Gene #23: '12p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
12P GAIN MUTATED 4 44 15 44 8
12P GAIN WILD-TYPE 343 178 57 179 41

Figure S99.  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 = 4.76e-05 (Chi-square test), Q value = 0.024

Table S100.  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 101 139 93 137 40 97
12P GAIN MUTATED 19 9 11 25 1 2
12P GAIN WILD-TYPE 82 130 82 112 39 95

Figure S100.  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 = 3.57e-05 (Chi-square test), Q value = 0.019

Table S101.  Gene #23: '12p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
12P GAIN MUTATED 33 4 13 17 32 1 7 1
12P GAIN WILD-TYPE 113 75 87 114 146 11 144 30

Figure S101.  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 = 2.04e-05 (Fisher's exact test), Q value = 0.011

Table S102.  Gene #23: '12p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
12P GAIN MUTATED 50 40 18
12P GAIN WILD-TYPE 286 165 269

Figure S102.  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 = 3.71e-06 (Fisher's exact test), Q value = 0.0022

Table S103.  Gene #23: '12p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
12P GAIN MUTATED 12 44 52
12P GAIN WILD-TYPE 189 385 197

Figure S103.  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 = 0.000406 (Fisher's exact test), Q value = 0.18

Table S104.  Gene #23: '12p gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 616 59
12P GAIN MUTATED 42 61 5
12P GAIN WILD-TYPE 162 555 54

Figure S104.  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 = 1.81e-15 (Chi-square test), Q value = 1.4e-12

Table S105.  Gene #24: '12q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
12Q GAIN MUTATED 5 46 16 14 6
12Q GAIN WILD-TYPE 342 176 56 209 43

Figure S105.  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 = 8.74e-05 (Chi-square test), Q value = 0.043

Table S106.  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 101 139 93 137 40 97
12Q GAIN MUTATED 4 13 11 24 1 1
12Q GAIN WILD-TYPE 97 126 82 113 39 96

Figure S106.  Get High-res Image Gene #24: '12q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'14q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000442 (Chi-square test), Q value = 0.2

Table S107.  Gene #26: '14q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
14Q GAIN MUTATED 4 0 14 17 20 2 16 0
14Q GAIN WILD-TYPE 142 79 86 114 158 10 135 31

Figure S107.  Get High-res Image Gene #26: '14q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'16p gain mutation analysis' versus 'MRNA_CNMF'

P value = 1.01e-05 (Chi-square test), Q value = 0.0056

Table S108.  Gene #28: '16p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
16P GAIN MUTATED 41 6 8 18 15 5 53 10
16P GAIN WILD-TYPE 83 30 15 77 57 15 50 30

Figure S108.  Get High-res Image Gene #28: '16p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'16p gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 8.07e-05 (Fisher's exact test), Q value = 0.04

Table S109.  Gene #28: '16p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
16P GAIN MUTATED 38 22 96
16P GAIN WILD-TYPE 102 103 152

Figure S109.  Get High-res Image Gene #28: '16p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'16p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.27e-07 (Chi-square test), Q value = 0.00033

Table S110.  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 101 139 93 137 40 97
16P GAIN MUTATED 17 54 30 40 3 11
16P GAIN WILD-TYPE 84 85 63 97 37 86

Figure S110.  Get High-res Image Gene #28: '16p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'16p gain mutation analysis' versus 'RPPA_CNMF'

P value = 0.000119 (Fisher's exact test), Q value = 0.058

Table S111.  Gene #28: '16p gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
16P GAIN MUTATED 30 58 32
16P GAIN WILD-TYPE 117 75 85

Figure S111.  Get High-res Image Gene #28: '16p gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'16p gain mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 6.58e-05 (Fisher's exact test), Q value = 0.033

Table S112.  Gene #28: '16p gain mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
16P GAIN MUTATED 60 40 20
16P GAIN WILD-TYPE 101 70 106

Figure S112.  Get High-res Image Gene #28: '16p gain mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'16p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.12e-07 (Chi-square test), Q value = 0.00044

Table S113.  Gene #28: '16p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
16P GAIN MUTATED 26 17 50 30 50 2 57 9
16P GAIN WILD-TYPE 120 62 50 101 128 10 94 22

Figure S113.  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 = 4.25e-05 (Fisher's exact test), Q value = 0.022

Table S114.  Gene #28: '16p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
16P GAIN MUTATED 122 38 81
16P GAIN WILD-TYPE 214 167 206

Figure S114.  Get High-res Image Gene #28: '16p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000186 (Fisher's exact test), Q value = 0.088

Table S115.  Gene #28: '16p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
16P GAIN MUTATED 46 147 52
16P GAIN WILD-TYPE 155 282 197

Figure S115.  Get High-res Image Gene #28: '16p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'17q gain mutation analysis' versus 'MRNA_CNMF'

P value = 4.01e-07 (Chi-square test), Q value = 0.00025

Table S116.  Gene #31: '17q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
17Q GAIN MUTATED 35 6 2 6 4 2 4 5
17Q GAIN WILD-TYPE 89 30 21 89 68 18 99 35

Figure S116.  Get High-res Image Gene #31: '17q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'17q gain mutation analysis' versus 'CN_CNMF'

P value = 2.64e-18 (Chi-square test), Q value = 2.1e-15

Table S117.  Gene #31: '17q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
17Q GAIN MUTATED 23 70 8 13 9
17Q GAIN WILD-TYPE 324 152 64 210 40

Figure S117.  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 = 3.27e-06 (Chi-square test), Q value = 0.0019

Table S118.  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 101 139 93 137 40 97
17Q GAIN MUTATED 5 13 15 37 6 7
17Q GAIN WILD-TYPE 96 126 78 100 34 90

Figure S118.  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 = 2.44e-11 (Chi-square test), Q value = 1.8e-08

Table S119.  Gene #31: '17q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
17Q GAIN MUTATED 9 12 17 9 55 3 9 5
17Q GAIN WILD-TYPE 137 67 83 122 123 9 142 26

Figure S119.  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 = 2.09e-07 (Fisher's exact test), Q value = 0.00013

Table S120.  Gene #31: '17q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
17Q GAIN MUTATED 73 11 35
17Q GAIN WILD-TYPE 263 194 252

Figure S120.  Get High-res Image Gene #31: '17q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain mutation analysis' versus 'CN_CNMF'

P value = 2.57e-07 (Chi-square test), Q value = 0.00016

Table S121.  Gene #32: '18p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
18P GAIN MUTATED 12 25 4 35 11
18P GAIN WILD-TYPE 335 197 68 188 38

Figure S121.  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 = 1.03e-07 (Chi-square test), Q value = 6.7e-05

Table S122.  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 101 139 93 137 40 97
18P GAIN MUTATED 22 5 8 11 0 1
18P GAIN WILD-TYPE 79 134 85 126 40 96

Figure S122.  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 = 5.06e-06 (Chi-square test), Q value = 0.0029

Table S123.  Gene #32: '18p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
18P GAIN MUTATED 31 1 10 7 22 0 12 0
18P GAIN WILD-TYPE 115 78 90 124 156 12 139 31

Figure S123.  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 = 1.48e-05 (Fisher's exact test), Q value = 0.0081

Table S124.  Gene #32: '18p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
18P GAIN MUTATED 37 34 12
18P GAIN WILD-TYPE 299 171 275

Figure S124.  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 = 4.68e-06 (Fisher's exact test), Q value = 0.0027

Table S125.  Gene #32: '18p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
18P GAIN MUTATED 7 32 41
18P GAIN WILD-TYPE 194 397 208

Figure S125.  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 = 2.93e-05 (Fisher's exact test), Q value = 0.015

Table S126.  Gene #32: '18p gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 616 59
18P GAIN MUTATED 36 41 3
18P GAIN WILD-TYPE 168 575 56

Figure S126.  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 = 6.69e-06 (Chi-square test), Q value = 0.0038

Table S127.  Gene #33: '18q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
18Q GAIN MUTATED 11 21 5 30 10
18Q GAIN WILD-TYPE 336 201 67 193 39

Figure S127.  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 = 1.91e-05 (Chi-square test), Q value = 0.01

Table S128.  Gene #33: '18q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
18Q GAIN MUTATED 23 1 9 2 25 0 12 0
18Q GAIN WILD-TYPE 123 78 91 129 153 12 139 31

Figure S128.  Get High-res Image Gene #33: '18q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'18q gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000237 (Fisher's exact test), Q value = 0.11

Table S129.  Gene #33: '18q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
18Q GAIN MUTATED 6 32 33
18Q GAIN WILD-TYPE 195 397 216

Figure S129.  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 = 0.000382 (Chi-square test), Q value = 0.17

Table S130.  Gene #34: '19p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
19P GAIN MUTATED 15 11 11 27 5
19P GAIN WILD-TYPE 332 211 61 196 44

Figure S130.  Get High-res Image Gene #34: '19p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'19q gain mutation analysis' versus 'CN_CNMF'

P value = 0.000415 (Chi-square test), Q value = 0.18

Table S131.  Gene #35: '19q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
19Q GAIN MUTATED 17 19 13 30 7
19Q GAIN WILD-TYPE 330 203 59 193 42

Figure S131.  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 = 3.66e-05 (Chi-square test), Q value = 0.019

Table S132.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
20P GAIN MUTATED 42 6 6 26 32 13 21 6
20P GAIN WILD-TYPE 82 30 17 69 40 7 82 34

Figure S132.  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 = 3.08e-23 (Chi-square test), Q value = 2.4e-20

Table S133.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
20P GAIN MUTATED 27 95 34 69 14
20P GAIN WILD-TYPE 320 127 38 154 35

Figure S133.  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 = 3.06e-08 (Chi-square test), Q value = 2e-05

Table S134.  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 101 139 93 137 40 97
20P GAIN MUTATED 20 21 29 56 6 10
20P GAIN WILD-TYPE 81 118 64 81 34 87

Figure S134.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'20p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000325 (Chi-square test), Q value = 0.15

Table S135.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
20P GAIN MUTATED 35 14 34 49 60 5 30 3
20P GAIN WILD-TYPE 111 65 66 82 118 7 121 28

Figure S135.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'20p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.77e-06 (Fisher's exact test), Q value = 0.0011

Table S136.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
20P GAIN MUTATED 27 122 83
20P GAIN WILD-TYPE 174 307 166

Figure S136.  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 = 1.44e-05 (Chi-square test), Q value = 0.0079

Table S137.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
20Q GAIN MUTATED 56 7 5 26 33 12 21 10
20Q GAIN WILD-TYPE 68 29 18 69 39 8 82 30

Figure S137.  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 = 3.32e-29 (Chi-square test), Q value = 2.6e-26

Table S138.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
20Q GAIN MUTATED 31 118 32 78 17
20Q GAIN WILD-TYPE 316 104 40 145 32

Figure S138.  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 = 2.35e-14 (Chi-square test), Q value = 1.8e-11

Table S139.  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 101 139 93 137 40 97
20Q GAIN MUTATED 22 23 34 72 7 10
20Q GAIN WILD-TYPE 79 116 59 65 33 87

Figure S139.  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 = 6.82e-08 (Chi-square test), Q value = 4.5e-05

Table S140.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
20Q GAIN MUTATED 36 15 36 50 86 5 30 7
20Q GAIN WILD-TYPE 110 64 64 81 92 7 121 24

Figure S140.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'20q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.69e-06 (Fisher's exact test), Q value = 0.0022

Table S141.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
20Q GAIN MUTATED 140 57 68
20Q GAIN WILD-TYPE 196 148 219

Figure S141.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.09e-07 (Fisher's exact test), Q value = 2e-04

Table S142.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
20Q GAIN MUTATED 32 145 93
20Q GAIN WILD-TYPE 169 284 156

Figure S142.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'21q gain mutation analysis' versus 'MRNA_CNMF'

P value = 5.97e-05 (Chi-square test), Q value = 0.03

Table S143.  Gene #38: '21q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
21Q GAIN MUTATED 12 0 1 17 19 5 7 2
21Q GAIN WILD-TYPE 112 36 22 78 53 15 96 38

Figure S143.  Get High-res Image Gene #38: '21q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'21q gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.089

Table S144.  Gene #38: '21q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
21Q GAIN MUTATED 7 27 29
21Q GAIN WILD-TYPE 133 98 219

Figure S144.  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 = 7.1e-10 (Chi-square test), Q value = 4.9e-07

Table S145.  Gene #38: '21q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
21Q GAIN MUTATED 13 21 16 44 10
21Q GAIN WILD-TYPE 334 201 56 179 39

Figure S145.  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 = 4.67e-09 (Chi-square test), Q value = 3.2e-06

Table S146.  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 101 139 93 137 40 97
21Q GAIN MUTATED 26 7 17 10 1 2
21Q GAIN WILD-TYPE 75 132 76 127 39 95

Figure S146.  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 = 5.02e-07 (Chi-square test), Q value = 0.00031

Table S147.  Gene #38: '21q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
21Q GAIN MUTATED 31 2 6 28 16 2 10 1
21Q GAIN WILD-TYPE 115 77 94 103 162 10 141 30

Figure S147.  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 = 1.77e-11 (Fisher's exact test), Q value = 1.3e-08

Table S148.  Gene #38: '21q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
21Q GAIN MUTATED 39 48 9
21Q GAIN WILD-TYPE 297 157 278

Figure S148.  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 = 8.59e-06 (Fisher's exact test), Q value = 0.0048

Table S149.  Gene #38: '21q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
21Q GAIN MUTATED 15 34 49
21Q GAIN WILD-TYPE 186 395 200

Figure S149.  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 = 1.59e-05 (Fisher's exact test), Q value = 0.0087

Table S150.  Gene #38: '21q gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 616 59
21Q GAIN MUTATED 42 50 6
21Q GAIN WILD-TYPE 162 566 53

Figure S150.  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 = 3.75e-08 (Chi-square test), Q value = 2.5e-05

Table S151.  Gene #39: '22q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
22Q GAIN MUTATED 2 10 1 26 4
22Q GAIN WILD-TYPE 345 212 71 197 45

Figure S151.  Get High-res Image Gene #39: '22q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'22q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.33e-07 (Fisher's exact test), Q value = 0.00051

Table S152.  Gene #39: '22q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
22Q GAIN MUTATED 12 23 3
22Q GAIN WILD-TYPE 324 182 284

Figure S152.  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 = 0.000348 (Fisher's exact test), Q value = 0.16

Table S153.  Gene #39: '22q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
22Q GAIN MUTATED 3 16 23
22Q GAIN WILD-TYPE 198 413 226

Figure S153.  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 = 1.05e-05 (Fisher's exact test), Q value = 0.0058

Table S154.  Gene #39: '22q gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 616 59
22Q GAIN MUTATED 23 16 3
22Q GAIN WILD-TYPE 181 600 56

Figure S154.  Get High-res Image Gene #39: '22q gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Xq gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000165 (Fisher's exact test), Q value = 0.078

Table S155.  Gene #40: 'Xq gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
XQ GAIN MUTATED 1 11 3
XQ GAIN WILD-TYPE 139 114 245

Figure S155.  Get High-res Image Gene #40: 'Xq gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Xq gain mutation analysis' versus 'CN_CNMF'

P value = 0.000166 (Chi-square test), Q value = 0.079

Table S156.  Gene #40: 'Xq gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
XQ GAIN MUTATED 2 3 2 14 0
XQ GAIN WILD-TYPE 345 219 70 209 49

Figure S156.  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 = 0.000104 (Chi-square test), Q value = 0.051

Table S157.  Gene #40: 'Xq gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
XQ GAIN MUTATED 12 0 0 3 2 0 2 0
XQ GAIN WILD-TYPE 134 79 100 128 176 12 149 31

Figure S157.  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 = 8.73e-06 (Fisher's exact test), Q value = 0.0049

Table S158.  Gene #40: 'Xq gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
XQ GAIN MUTATED 4 14 1
XQ GAIN WILD-TYPE 332 191 286

Figure S158.  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 = 8.71e-06 (Fisher's exact test), Q value = 0.0049

Table S159.  Gene #40: 'Xq gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
XQ GAIN MUTATED 0 4 15
XQ GAIN WILD-TYPE 201 425 234

Figure S159.  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 = 9.2e-05 (Fisher's exact test), Q value = 0.045

Table S160.  Gene #40: 'Xq gain mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 616 59
XQ GAIN MUTATED 13 6 0
XQ GAIN WILD-TYPE 191 610 59

Figure S160.  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 = 0.000228 (Chi-square test), Q value = 0.11

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
1P LOSS MUTATED 24 3 1 4 19 0 15 3
1P LOSS WILD-TYPE 100 33 22 91 53 20 88 37

Figure S161.  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 = 3.98e-10 (Fisher's exact test), Q value = 2.8e-07

Table S162.  Gene #41: '1p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
1P LOSS MUTATED 7 4 58
1P LOSS WILD-TYPE 133 121 190

Figure S162.  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 = 2.44e-23 (Chi-square test), Q value = 1.9e-20

Table S163.  Gene #41: '1p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
1P LOSS MUTATED 13 57 30 17 6
1P LOSS WILD-TYPE 334 165 42 206 43

Figure S163.  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 = 1.84e-06 (Chi-square test), Q value = 0.0011

Table S164.  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 101 139 93 137 40 97
1P LOSS MUTATED 7 13 23 29 5 2
1P LOSS WILD-TYPE 94 126 70 108 35 95

Figure S164.  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 = 5.14e-07 (Chi-square test), Q value = 0.00032

Table S165.  Gene #41: '1p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
1P LOSS MUTATED 5 3 14 30 37 0 21 1
1P LOSS WILD-TYPE 141 76 86 101 141 12 130 30

Figure S165.  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 = 3.6e-18 (Fisher's exact test), Q value = 2.8e-15

Table S166.  Gene #41: '1p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
1P LOSS MUTATED 88 8 15
1P LOSS WILD-TYPE 248 197 272

Figure S166.  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 = 0.000505 (Fisher's exact test), Q value = 0.22

Table S167.  Gene #41: '1p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
1P LOSS MUTATED 14 76 29
1P LOSS WILD-TYPE 187 353 220

Figure S167.  Get High-res Image Gene #41: '1p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'1q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000357 (Fisher's exact test), Q value = 0.16

Table S168.  Gene #42: '1q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
1Q LOSS MUTATED 17 3 1
1Q LOSS WILD-TYPE 319 202 286

Figure S168.  Get High-res Image Gene #42: '1q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.09e-05 (Fisher's exact test), Q value = 0.016

Table S169.  Gene #43: '2p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
2P LOSS MUTATED 6 3 36
2P LOSS WILD-TYPE 134 122 212

Figure S169.  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 = 2.58e-12 (Chi-square test), Q value = 1.9e-09

Table S170.  Gene #43: '2p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
2P LOSS MUTATED 5 34 15 12 9
2P LOSS WILD-TYPE 342 188 57 211 40

Figure S170.  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 = 1.72e-07 (Chi-square test), Q value = 0.00011

Table S171.  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 101 139 93 137 40 97
2P LOSS MUTATED 1 7 9 24 1 0
2P LOSS WILD-TYPE 100 132 84 113 39 97

Figure S171.  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 = 2e-04 (Chi-square test), Q value = 0.093

Table S172.  Gene #43: '2p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
2P LOSS MUTATED 5 2 13 8 28 0 14 0
2P LOSS WILD-TYPE 141 77 87 123 150 12 137 31

Figure S172.  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 = 3.73e-08 (Fisher's exact test), Q value = 2.5e-05

Table S173.  Gene #43: '2p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
2P LOSS MUTATED 51 5 14
2P LOSS WILD-TYPE 285 200 273

Figure S173.  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 = 6.92e-06 (Fisher's exact test), Q value = 0.0039

Table S174.  Gene #43: '2p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
2P LOSS MUTATED 5 53 12
2P LOSS WILD-TYPE 196 376 237

Figure S174.  Get High-res Image Gene #43: '2p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'2q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

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

Table S175.  Gene #44: '2q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
2Q LOSS MUTATED 6 9 40
2Q LOSS WILD-TYPE 134 116 208

Figure S175.  Get High-res Image Gene #44: '2q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'2q loss mutation analysis' versus 'CN_CNMF'

P value = 2.48e-12 (Chi-square test), Q value = 1.8e-09

Table S176.  Gene #44: '2q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
2Q LOSS MUTATED 5 41 16 21 8
2Q LOSS WILD-TYPE 342 181 56 202 41

Figure S176.  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 = 4.01e-06 (Chi-square test), Q value = 0.0023

Table S177.  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 101 139 93 137 40 97
2Q LOSS MUTATED 8 7 11 26 1 0
2Q LOSS WILD-TYPE 93 132 82 111 39 97

Figure S177.  Get High-res Image Gene #44: '2q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'2q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.94e-06 (Fisher's exact test), Q value = 0.0055

Table S178.  Gene #44: '2q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
2Q LOSS MUTATED 55 15 15
2Q LOSS WILD-TYPE 281 190 272

Figure S178.  Get High-res Image Gene #44: '2q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.58e-05 (Fisher's exact test), Q value = 0.0087

Table S179.  Gene #44: '2q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
2Q LOSS MUTATED 5 58 23
2Q LOSS WILD-TYPE 196 371 226

Figure S179.  Get High-res Image Gene #44: '2q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'3p loss mutation analysis' versus 'CN_CNMF'

P value = 2.58e-09 (Chi-square test), Q value = 1.8e-06

Table S180.  Gene #45: '3p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
3P LOSS MUTATED 9 32 5 42 4
3P LOSS WILD-TYPE 338 190 67 181 45

Figure S180.  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 = 3.42e-05 (Chi-square test), Q value = 0.018

Table S181.  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 101 139 93 137 40 97
3P LOSS MUTATED 16 2 14 18 3 2
3P LOSS WILD-TYPE 85 137 79 119 37 95

Figure S181.  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 = 5.31e-05 (Fisher's exact test), Q value = 0.027

Table S182.  Gene #45: '3p loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
3P LOSS MUTATED 14 4 27
3P LOSS WILD-TYPE 147 106 99

Figure S182.  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 = 2.28e-05 (Chi-square test), Q value = 0.012

Table S183.  Gene #45: '3p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
3P LOSS MUTATED 26 5 9 23 17 1 3 0
3P LOSS WILD-TYPE 120 74 91 108 161 11 148 31

Figure S183.  Get High-res Image Gene #45: '3p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'3p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000178 (Fisher's exact test), Q value = 0.084

Table S184.  Gene #45: '3p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
3P LOSS MUTATED 31 36 17
3P LOSS WILD-TYPE 305 169 270

Figure S184.  Get High-res Image Gene #45: '3p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.46e-07 (Fisher's exact test), Q value = 9.4e-05

Table S185.  Gene #45: '3p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
3P LOSS MUTATED 9 31 48
3P LOSS WILD-TYPE 192 398 201

Figure S185.  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 = 9.06e-05 (Fisher's exact test), Q value = 0.045

Table S186.  Gene #45: '3p loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 616 59
3P LOSS MUTATED 33 44 11
3P LOSS WILD-TYPE 171 572 48

Figure S186.  Get High-res Image Gene #45: '3p loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'3q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000579 (Chi-square test), Q value = 0.25

Table S187.  Gene #46: '3q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
3Q LOSS MUTATED 9 3 4 16 9 0 0 0
3Q LOSS WILD-TYPE 137 76 96 115 169 12 151 31

Figure S187.  Get High-res Image Gene #46: '3q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'4p loss mutation analysis' versus 'MRNA_CNMF'

P value = 4.5e-12 (Chi-square test), Q value = 3.3e-09

Table S188.  Gene #47: '4p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
4P LOSS MUTATED 18 4 1 41 33 4 13 3
4P LOSS WILD-TYPE 106 32 22 54 39 16 90 37

Figure S188.  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 = 1.24e-12 (Fisher's exact test), Q value = 9.1e-10

Table S189.  Gene #47: '4p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
4P LOSS MUTATED 9 55 53
4P LOSS WILD-TYPE 131 70 195

Figure S189.  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 = 9.98e-28 (Chi-square test), Q value = 7.9e-25

Table S190.  Gene #47: '4p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
4P LOSS MUTATED 18 38 24 97 8
4P LOSS WILD-TYPE 329 184 48 126 41

Figure S190.  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 = 3.87e-14 (Chi-square test), Q value = 2.9e-11

Table S191.  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 101 139 93 137 40 97
4P LOSS MUTATED 44 19 22 14 4 3
4P LOSS WILD-TYPE 57 120 71 123 36 94

Figure S191.  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 = 0.00014 (Fisher's exact test), Q value = 0.067

Table S192.  Gene #47: '4p loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
4P LOSS MUTATED 52 25 17
4P LOSS WILD-TYPE 95 108 100

Figure S192.  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 = 7.57e-06 (Fisher's exact test), Q value = 0.0043

Table S193.  Gene #47: '4p loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
4P LOSS MUTATED 30 15 49
4P LOSS WILD-TYPE 131 95 77

Figure S193.  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 = 2.98e-18 (Chi-square test), Q value = 2.3e-15

Table S194.  Gene #47: '4p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
4P LOSS MUTATED 61 2 13 50 22 0 25 2
4P LOSS WILD-TYPE 85 77 87 81 156 12 126 29

Figure S194.  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 = 1.63e-19 (Fisher's exact test), Q value = 1.3e-16

Table S195.  Gene #47: '4p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
4P LOSS MUTATED 70 85 20
4P LOSS WILD-TYPE 266 120 267

Figure S195.  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 = 5.21e-15 (Fisher's exact test), Q value = 3.9e-12

Table S196.  Gene #47: '4p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
4P LOSS MUTATED 16 70 93
4P LOSS WILD-TYPE 185 359 156

Figure S196.  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 = 4.83e-11 (Fisher's exact test), Q value = 3.4e-08

Table S197.  Gene #47: '4p loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 616 59
4P LOSS MUTATED 73 87 19
4P LOSS WILD-TYPE 131 529 40

Figure S197.  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 = 1.79e-06 (Chi-square test), Q value = 0.0011

Table S198.  Gene #48: '4q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
4Q LOSS MUTATED 17 5 1 32 25 2 12 3
4Q LOSS WILD-TYPE 107 31 22 63 47 18 91 37

Figure S198.  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 = 2.1e-08 (Fisher's exact test), Q value = 1.4e-05

Table S199.  Gene #48: '4q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
4Q LOSS MUTATED 8 42 47
4Q LOSS WILD-TYPE 132 83 201

Figure S199.  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 = 7.17e-21 (Chi-square test), Q value = 5.6e-18

Table S200.  Gene #48: '4q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
4Q LOSS MUTATED 17 30 26 75 7
4Q LOSS WILD-TYPE 330 192 46 148 42

Figure S200.  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 = 1.19e-10 (Chi-square test), Q value = 8.4e-08

Table S201.  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 101 139 93 137 40 97
4Q LOSS MUTATED 37 20 16 12 4 2
4Q LOSS WILD-TYPE 64 119 77 125 36 95

Figure S201.  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 = 3.35e-12 (Chi-square test), Q value = 2.4e-09

Table S202.  Gene #48: '4q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
4Q LOSS MUTATED 49 3 8 40 21 0 25 1
4Q LOSS WILD-TYPE 97 76 92 91 157 12 126 30

Figure S202.  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 = 1.22e-15 (Fisher's exact test), Q value = 9.3e-13

Table S203.  Gene #48: '4q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
4Q LOSS MUTATED 64 68 15
4Q LOSS WILD-TYPE 272 137 272

Figure S203.  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 = 3.33e-08 (Fisher's exact test), Q value = 2.2e-05

Table S204.  Gene #48: '4q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
4Q LOSS MUTATED 15 64 69
4Q LOSS WILD-TYPE 186 365 180

Figure S204.  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 = 7.42e-08 (Fisher's exact test), Q value = 4.9e-05

Table S205.  Gene #48: '4q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 616 59
4Q LOSS MUTATED 57 74 17
4Q LOSS WILD-TYPE 147 542 42

Figure S205.  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 = 1.49e-08 (Chi-square test), Q value = 1e-05

Table S206.  Gene #49: '5p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
5P LOSS MUTATED 4 2 2 24 9 0 3 0
5P LOSS WILD-TYPE 120 34 21 71 63 20 100 40

Figure S206.  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 = 4.14e-06 (Fisher's exact test), Q value = 0.0024

Table S207.  Gene #49: '5p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
5P LOSS MUTATED 3 24 17
5P LOSS WILD-TYPE 137 101 231

Figure S207.  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 = 8.97e-21 (Chi-square test), Q value = 7e-18

Table S208.  Gene #49: '5p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
5P LOSS MUTATED 2 13 3 52 3
5P LOSS WILD-TYPE 345 209 69 171 46

Figure S208.  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 = 4.03e-12 (Chi-square test), Q value = 2.9e-09

Table S209.  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 101 139 93 137 40 97
5P LOSS MUTATED 25 2 5 11 0 1
5P LOSS WILD-TYPE 76 137 88 126 40 96

Figure S209.  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 = 4.28e-05 (Fisher's exact test), Q value = 0.022

Table S210.  Gene #49: '5p loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
5P LOSS MUTATED 27 5 6
5P LOSS WILD-TYPE 120 128 111

Figure S210.  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 = 6.72e-06 (Fisher's exact test), Q value = 0.0038

Table S211.  Gene #49: '5p loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
5P LOSS MUTATED 7 5 26
5P LOSS WILD-TYPE 154 105 100

Figure S211.  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 = 1.77e-12 (Chi-square test), Q value = 1.3e-09

Table S212.  Gene #49: '5p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
5P LOSS MUTATED 35 1 4 12 10 1 3 0
5P LOSS WILD-TYPE 111 78 96 119 168 11 148 31

Figure S212.  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 = 5.26e-10 (Fisher's exact test), Q value = 3.7e-07

Table S213.  Gene #49: '5p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
5P LOSS MUTATED 27 35 4
5P LOSS WILD-TYPE 309 170 283

Figure S213.  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 = 6.17e-15 (Fisher's exact test), Q value = 4.7e-12

Table S214.  Gene #49: '5p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
5P LOSS MUTATED 4 16 51
5P LOSS WILD-TYPE 197 413 198

Figure S214.  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 = 2.94e-12 (Fisher's exact test), Q value = 2.1e-09

Table S215.  Gene #49: '5p loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 616 59
5P LOSS MUTATED 40 22 9
5P LOSS WILD-TYPE 164 594 50

Figure S215.  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 = 4.14e-19 (Chi-square test), Q value = 3.2e-16

Table S216.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
5Q LOSS MUTATED 9 3 3 44 13 0 3 1
5Q LOSS WILD-TYPE 115 33 20 51 59 20 100 39

Figure S216.  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 = 9.95e-15 (Fisher's exact test), Q value = 7.5e-12

Table S217.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
5Q LOSS MUTATED 5 47 24
5Q LOSS WILD-TYPE 135 78 224

Figure S217.  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 = 4.59e-45 (Chi-square test), Q value = 3.7e-42

Table S218.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
5Q LOSS MUTATED 4 15 4 94 7
5Q LOSS WILD-TYPE 343 207 68 129 42

Figure S218.  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 = 1.21e-32 (Chi-square test), Q value = 9.6e-30

Table S219.  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 101 139 93 137 40 97
5Q LOSS MUTATED 50 3 5 16 0 2
5Q LOSS WILD-TYPE 51 136 88 121 40 95

Figure S219.  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 = 1.86e-09 (Fisher's exact test), Q value = 1.3e-06

Table S220.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
5Q LOSS MUTATED 46 6 13
5Q LOSS WILD-TYPE 101 127 104

Figure S220.  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 = 6.93e-11 (Fisher's exact test), Q value = 4.9e-08

Table S221.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
5Q LOSS MUTATED 12 8 45
5Q LOSS WILD-TYPE 149 102 81

Figure S221.  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 = 1.55e-34 (Chi-square test), Q value = 1.2e-31

Table S222.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
5Q LOSS MUTATED 70 3 6 17 16 1 3 1
5Q LOSS WILD-TYPE 76 76 94 114 162 11 148 30

Figure S222.  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 = 4.74e-24 (Fisher's exact test), Q value = 3.8e-21

Table S223.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
5Q LOSS MUTATED 32 75 10
5Q LOSS WILD-TYPE 304 130 277

Figure S223.  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 = 1.75e-27 (Fisher's exact test), Q value = 1.4e-24

Table S224.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
5Q LOSS MUTATED 6 27 87
5Q LOSS WILD-TYPE 195 402 162

Figure S224.  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 = 2.27e-30 (Fisher's exact test), Q value = 1.8e-27

Table S225.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 616 59
5Q LOSS MUTATED 79 29 12
5Q LOSS WILD-TYPE 125 587 47

Figure S225.  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 = 9.32e-05 (Fisher's exact test), Q value = 0.046

Table S226.  Gene #51: '6p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
6P LOSS MUTATED 21 4 44
6P LOSS WILD-TYPE 119 121 204

Figure S226.  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 = 1.09e-09 (Chi-square test), Q value = 7.5e-07

Table S227.  Gene #51: '6p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
6P LOSS MUTATED 21 52 10 16 10
6P LOSS WILD-TYPE 326 170 62 207 39

Figure S227.  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 = 4.96e-05 (Chi-square test), Q value = 0.025

Table S228.  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 101 139 93 137 40 97
6P LOSS MUTATED 4 13 11 29 2 4
6P LOSS WILD-TYPE 97 126 82 108 38 93

Figure S228.  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 = 3.46e-05 (Chi-square test), Q value = 0.018

Table S229.  Gene #51: '6p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
6P LOSS MUTATED 9 6 12 11 42 0 22 2
6P LOSS WILD-TYPE 137 73 88 120 136 12 129 29

Figure S229.  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 = 1.44e-05 (Fisher's exact test), Q value = 0.0079

Table S230.  Gene #51: '6p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
6P LOSS MUTATED 61 10 33
6P LOSS WILD-TYPE 275 195 254

Figure S230.  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 = 8.54e-05 (Fisher's exact test), Q value = 0.042

Table S231.  Gene #51: '6p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
6P LOSS MUTATED 12 72 22
6P LOSS WILD-TYPE 189 357 227

Figure S231.  Get High-res Image Gene #51: '6p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'6q loss mutation analysis' versus 'MRNA_CNMF'

P value = 4.71e-05 (Chi-square test), Q value = 0.024

Table S232.  Gene #52: '6q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
6Q LOSS MUTATED 40 10 4 6 9 1 19 11
6Q LOSS WILD-TYPE 84 26 19 89 63 19 84 29

Figure S232.  Get High-res Image Gene #52: '6q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'6q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 9.19e-07 (Fisher's exact test), Q value = 0.00056

Table S233.  Gene #52: '6q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
6Q LOSS MUTATED 32 6 62
6Q LOSS WILD-TYPE 108 119 186

Figure S233.  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 = 1.2e-14 (Chi-square test), Q value = 9e-12

Table S234.  Gene #52: '6q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
6Q LOSS MUTATED 44 79 13 19 16
6Q LOSS WILD-TYPE 303 143 59 204 33

Figure S234.  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 = 6.48e-08 (Chi-square test), Q value = 4.3e-05

Table S235.  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 101 139 93 137 40 97
6Q LOSS MUTATED 6 30 18 44 5 5
6Q LOSS WILD-TYPE 95 109 75 93 35 92

Figure S235.  Get High-res Image Gene #52: '6q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'6q loss mutation analysis' versus 'RPPA_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.24

Table S236.  Gene #52: '6q loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
6Q LOSS MUTATED 14 33 29
6Q LOSS WILD-TYPE 133 100 88

Figure S236.  Get High-res Image Gene #52: '6q loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'6q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.21e-07 (Chi-square test), Q value = 7.8e-05

Table S237.  Gene #52: '6q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
6Q LOSS MUTATED 12 14 22 14 61 1 30 5
6Q LOSS WILD-TYPE 134 65 78 117 117 11 121 26

Figure S237.  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 = 8.34e-08 (Fisher's exact test), Q value = 5.5e-05

Table S238.  Gene #52: '6q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
6Q LOSS MUTATED 88 15 56
6Q LOSS WILD-TYPE 248 190 231

Figure S238.  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 = 0.000159 (Fisher's exact test), Q value = 0.076

Table S239.  Gene #52: '6q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
6Q LOSS MUTATED 30 105 31
6Q LOSS WILD-TYPE 171 324 218

Figure S239.  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 = 5.03e-06 (Fisher's exact test), Q value = 0.0029

Table S240.  Gene #52: '6q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 616 59
6Q LOSS MUTATED 16 138 12
6Q LOSS WILD-TYPE 188 478 47

Figure S240.  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 = 9.93e-06 (Chi-square test), Q value = 0.0055

Table S241.  Gene #53: '7p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
7P LOSS MUTATED 3 17 4 23 1
7P LOSS WILD-TYPE 344 205 68 200 48

Figure S241.  Get High-res Image Gene #53: '7p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7q loss mutation analysis' versus 'CN_CNMF'

P value = 0.000443 (Chi-square test), Q value = 0.2

Table S242.  Gene #54: '7q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
7Q LOSS MUTATED 11 21 8 24 0
7Q LOSS WILD-TYPE 336 201 64 199 49

Figure S242.  Get High-res Image Gene #54: '7q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'8p loss mutation analysis' versus 'MRNA_CNMF'

P value = 0.000103 (Chi-square test), Q value = 0.051

Table S243.  Gene #55: '8p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
8P LOSS MUTATED 54 9 4 24 29 4 16 15
8P LOSS WILD-TYPE 70 27 19 71 43 16 87 25

Figure S243.  Get High-res Image Gene #55: '8p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'8p loss mutation analysis' versus 'CN_CNMF'

P value = 2.58e-15 (Chi-square test), Q value = 2e-12

Table S244.  Gene #55: '8p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
8P LOSS MUTATED 56 97 10 92 15
8P LOSS WILD-TYPE 291 125 62 131 34

Figure S244.  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 = 9.84e-08 (Chi-square test), Q value = 6.4e-05

Table S245.  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 101 139 93 137 40 97
8P LOSS MUTATED 34 23 32 61 8 14
8P LOSS WILD-TYPE 67 116 61 76 32 83

Figure S245.  Get High-res Image Gene #55: '8p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'8p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.03e-07 (Chi-square test), Q value = 0.00013

Table S246.  Gene #55: '8p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
8P LOSS MUTATED 42 14 30 54 76 4 22 10
8P LOSS WILD-TYPE 104 65 70 77 102 8 129 21

Figure S246.  Get High-res Image Gene #55: '8p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'9p loss mutation analysis' versus 'MRNA_CNMF'

P value = 2.39e-05 (Chi-square test), Q value = 0.013

Table S247.  Gene #57: '9p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
9P LOSS MUTATED 42 8 5 17 26 5 11 2
9P LOSS WILD-TYPE 82 28 18 78 46 15 92 38

Figure S247.  Get High-res Image Gene #57: '9p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'9p loss mutation analysis' versus 'CN_CNMF'

P value = 5.07e-19 (Chi-square test), Q value = 4e-16

Table S248.  Gene #57: '9p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
9P LOSS MUTATED 22 82 9 65 12
9P LOSS WILD-TYPE 325 140 63 158 37

Figure S248.  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 = 1.08e-13 (Chi-square test), Q value = 8.1e-11

Table S249.  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 101 139 93 137 40 97
9P LOSS MUTATED 23 5 29 48 8 3
9P LOSS WILD-TYPE 78 134 64 89 32 94

Figure S249.  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-07 (Chi-square test), Q value = 0.00011

Table S250.  Gene #57: '9p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
9P LOSS MUTATED 30 8 24 41 58 2 14 2
9P LOSS WILD-TYPE 116 71 76 90 120 10 137 29

Figure S250.  Get High-res Image Gene #57: '9p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'9p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.28e-06 (Fisher's exact test), Q value = 0.003

Table S251.  Gene #57: '9p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
9P LOSS MUTATED 95 48 36
9P LOSS WILD-TYPE 241 157 251

Figure S251.  Get High-res Image Gene #57: '9p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 7.55e-07 (Fisher's exact test), Q value = 0.00046

Table S252.  Gene #57: '9p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
9P LOSS MUTATED 18 94 70
9P LOSS WILD-TYPE 183 335 179

Figure S252.  Get High-res Image Gene #57: '9p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'9q loss mutation analysis' versus 'CN_CNMF'

P value = 9.61e-16 (Chi-square test), Q value = 7.4e-13

Table S253.  Gene #58: '9q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
9Q LOSS MUTATED 12 57 8 56 14
9Q LOSS WILD-TYPE 335 165 64 167 35

Figure S253.  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 = 1.74e-12 (Chi-square test), Q value = 1.3e-09

Table S254.  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 101 139 93 137 40 97
9Q LOSS MUTATED 30 3 17 36 3 2
9Q LOSS WILD-TYPE 71 136 76 101 37 95

Figure S254.  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 = 2.88e-06 (Chi-square test), Q value = 0.0017

Table S255.  Gene #58: '9q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
9Q LOSS MUTATED 35 2 21 16 43 2 14 1
9Q LOSS WILD-TYPE 111 77 79 115 135 10 137 30

Figure S255.  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 = 7.01e-06 (Fisher's exact test), Q value = 0.004

Table S256.  Gene #58: '9q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
9Q LOSS MUTATED 70 41 23
9Q LOSS WILD-TYPE 266 164 264

Figure S256.  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 = 1.36e-10 (Fisher's exact test), Q value = 9.6e-08

Table S257.  Gene #58: '9q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
9Q LOSS MUTATED 8 65 65
9Q LOSS WILD-TYPE 193 364 184

Figure S257.  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 = 0.000119 (Fisher's exact test), Q value = 0.058

Table S258.  Gene #58: '9q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 616 59
9Q LOSS MUTATED 51 76 11
9Q LOSS WILD-TYPE 153 540 48

Figure S258.  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 = 2.55e-06 (Chi-square test), Q value = 0.0015

Table S259.  Gene #59: '10p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
10P LOSS MUTATED 6 28 8 27 6
10P LOSS WILD-TYPE 341 194 64 196 43

Figure S259.  Get High-res Image Gene #59: '10p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'10q loss mutation analysis' versus 'MRNA_CNMF'

P value = 0.000512 (Chi-square test), Q value = 0.22

Table S260.  Gene #60: '10q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
10Q LOSS MUTATED 25 2 7 17 9 2 6 0
10Q LOSS WILD-TYPE 99 34 16 78 63 18 97 40

Figure S260.  Get High-res Image Gene #60: '10q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'10q loss mutation analysis' versus 'CN_CNMF'

P value = 4.34e-14 (Chi-square test), Q value = 3.2e-11

Table S261.  Gene #60: '10q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
10Q LOSS MUTATED 6 38 8 53 6
10Q LOSS WILD-TYPE 341 184 64 170 43

Figure S261.  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 = 9.95e-07 (Chi-square test), Q value = 0.00061

Table S262.  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 101 139 93 137 40 97
10Q LOSS MUTATED 23 6 15 23 3 1
10Q LOSS WILD-TYPE 78 133 78 114 37 96

Figure S262.  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 = 5.14e-06 (Chi-square test), Q value = 0.003

Table S263.  Gene #60: '10q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
10Q LOSS MUTATED 26 1 13 23 35 0 8 0
10Q LOSS WILD-TYPE 120 78 87 108 143 12 143 31

Figure S263.  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 = 8.5e-15 (Chi-square test), Q value = 6.4e-12

Table S264.  Gene #61: '11p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
11P LOSS MUTATED 12 58 15 54 5
11P LOSS WILD-TYPE 335 164 57 169 44

Figure S264.  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 = 8.61e-08 (Chi-square test), Q value = 5.6e-05

Table S265.  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 101 139 93 137 40 97
11P LOSS MUTATED 21 9 22 32 3 1
11P LOSS WILD-TYPE 80 130 71 105 37 96

Figure S265.  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 = 0.000217 (Fisher's exact test), Q value = 0.1

Table S266.  Gene #61: '11p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
11P LOSS MUTATED 16 71 54
11P LOSS WILD-TYPE 185 358 195

Figure S266.  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 = 2.01e-07 (Chi-square test), Q value = 0.00013

Table S267.  Gene #62: '11q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
11Q LOSS MUTATED 60 13 4 14 18 3 19 9
11Q LOSS WILD-TYPE 64 23 19 81 54 17 84 31

Figure S267.  Get High-res Image Gene #62: '11q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'11q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000327 (Fisher's exact test), Q value = 0.15

Table S268.  Gene #62: '11q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
11Q LOSS MUTATED 36 19 85
11Q LOSS WILD-TYPE 104 106 163

Figure S268.  Get High-res Image Gene #62: '11q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'11q loss mutation analysis' versus 'CN_CNMF'

P value = 2.04e-31 (Chi-square test), Q value = 1.6e-28

Table S269.  Gene #62: '11q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
11Q LOSS MUTATED 34 120 23 45 7
11Q LOSS WILD-TYPE 313 102 49 178 42

Figure S269.  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 = 1.5e-11 (Chi-square test), Q value = 1.1e-08

Table S270.  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 101 139 93 137 40 97
11Q LOSS MUTATED 16 27 34 58 8 4
11Q LOSS WILD-TYPE 85 112 59 79 32 93

Figure S270.  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 = 1.88e-10 (Chi-square test), Q value = 1.3e-07

Table S271.  Gene #62: '11q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
11Q LOSS MUTATED 20 23 21 33 83 1 31 4
11Q LOSS WILD-TYPE 126 56 79 98 95 11 120 27

Figure S271.  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 = 1.04e-06 (Fisher's exact test), Q value = 0.00063

Table S272.  Gene #62: '11q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
11Q LOSS MUTATED 116 30 70
11Q LOSS WILD-TYPE 220 175 217

Figure S272.  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 = 1.57e-06 (Chi-square test), Q value = 0.00095

Table S273.  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 101 139 93 137 40 97
12P LOSS MUTATED 18 7 1 10 7 1
12P LOSS WILD-TYPE 83 132 92 127 33 96

Figure S273.  Get High-res Image Gene #63: '12p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'12p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000302 (Fisher's exact test), Q value = 0.14

Table S274.  Gene #63: '12p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
12P LOSS MUTATED 23 28 11
12P LOSS WILD-TYPE 313 177 276

Figure S274.  Get High-res Image Gene #63: '12p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000244 (Fisher's exact test), Q value = 0.11

Table S275.  Gene #64: '12q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
12Q LOSS MUTATED 3 18 12
12Q LOSS WILD-TYPE 137 107 236

Figure S275.  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 = 9.88e-05 (Chi-square test), Q value = 0.049

Table S276.  Gene #64: '12q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
12Q LOSS MUTATED 10 9 4 27 2
12Q LOSS WILD-TYPE 337 213 68 196 47

Figure S276.  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 = 4.1e-09 (Chi-square test), Q value = 2.8e-06

Table S277.  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 101 139 93 137 40 97
12Q LOSS MUTATED 20 2 2 8 2 1
12Q LOSS WILD-TYPE 81 137 91 129 38 96

Figure S277.  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 = 1.51e-08 (Chi-square test), Q value = 1e-05

Table S278.  Gene #64: '12q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
12Q LOSS MUTATED 25 1 3 8 7 0 2 0
12Q LOSS WILD-TYPE 121 78 97 123 171 12 149 31

Figure S278.  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 = 8.5e-05

Table S279.  Gene #64: '12q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
12Q LOSS MUTATED 13 28 5
12Q LOSS WILD-TYPE 323 177 282

Figure S279.  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 = 9.56e-06 (Fisher's exact test), Q value = 0.0054

Table S280.  Gene #64: '12q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
12Q LOSS MUTATED 6 14 30
12Q LOSS WILD-TYPE 195 415 219

Figure S280.  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 = 1.65e-05 (Fisher's exact test), Q value = 0.009

Table S281.  Gene #64: '12q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 616 59
12Q LOSS MUTATED 26 21 3
12Q LOSS WILD-TYPE 178 595 56

Figure S281.  Get High-res Image Gene #64: '12q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss mutation analysis' versus 'MRNA_CNMF'

P value = 0.000134 (Chi-square test), Q value = 0.064

Table S282.  Gene #65: '13q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
13Q LOSS MUTATED 58 10 4 31 25 4 22 5
13Q LOSS WILD-TYPE 66 26 19 64 47 16 81 35

Figure S282.  Get High-res Image Gene #65: '13q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'13q loss mutation analysis' versus 'CN_CNMF'

P value = 1.62e-27 (Chi-square test), Q value = 1.3e-24

Table S283.  Gene #65: '13q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
13Q LOSS MUTATED 28 100 31 80 28
13Q LOSS WILD-TYPE 319 122 41 143 21

Figure S283.  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 = 2.84e-10 (Chi-square test), Q value = 2e-07

Table S284.  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 101 139 93 137 40 97
13Q LOSS MUTATED 36 26 44 51 3 11
13Q LOSS WILD-TYPE 65 113 49 86 37 86

Figure S284.  Get High-res Image Gene #65: '13q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'13q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.63e-07 (Fisher's exact test), Q value = 0.00017

Table S285.  Gene #65: '13q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
13Q LOSS MUTATED 131 67 55
13Q LOSS WILD-TYPE 205 138 232

Figure S285.  Get High-res Image Gene #65: '13q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.49e-09 (Fisher's exact test), Q value = 1.7e-06

Table S286.  Gene #65: '13q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
13Q LOSS MUTATED 26 144 91
13Q LOSS WILD-TYPE 175 285 158

Figure S286.  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 = 1.09e-10 (Chi-square test), Q value = 7.7e-08

Table S287.  Gene #66: '14q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
14Q LOSS MUTATED 25 1 2 36 8 3 5 0
14Q LOSS WILD-TYPE 99 35 21 59 64 17 98 40

Figure S287.  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 = 8.5e-08 (Fisher's exact test), Q value = 5.6e-05

Table S288.  Gene #66: '14q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
14Q LOSS MUTATED 7 38 35
14Q LOSS WILD-TYPE 133 87 213

Figure S288.  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 = 2.6e-22 (Chi-square test), Q value = 2e-19

Table S289.  Gene #66: '14q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
14Q LOSS MUTATED 10 29 9 75 13
14Q LOSS WILD-TYPE 337 193 63 148 36

Figure S289.  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 = 6.83e-16 (Chi-square test), Q value = 5.2e-13

Table S290.  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 101 139 93 137 40 97
14Q LOSS MUTATED 39 5 16 18 1 3
14Q LOSS WILD-TYPE 62 134 77 119 39 94

Figure S290.  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 = 0.000185 (Fisher's exact test), Q value = 0.087

Table S291.  Gene #66: '14q loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
14Q LOSS MUTATED 39 12 14
14Q LOSS WILD-TYPE 108 121 103

Figure S291.  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 = 8.52e-05 (Fisher's exact test), Q value = 0.042

Table S292.  Gene #66: '14q loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
14Q LOSS MUTATED 18 11 36
14Q LOSS WILD-TYPE 143 99 90

Figure S292.  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 = 3.58e-19 (Chi-square test), Q value = 2.8e-16

Table S293.  Gene #66: '14q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
14Q LOSS MUTATED 57 2 11 15 33 1 5 0
14Q LOSS WILD-TYPE 89 77 89 116 145 11 146 31

Figure S293.  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 = 1.15e-11 (Fisher's exact test), Q value = 8.3e-09

Table S294.  Gene #66: '14q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
14Q LOSS MUTATED 47 60 17
14Q LOSS WILD-TYPE 289 145 270

Figure S294.  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 = 1.06e-12 (Fisher's exact test), Q value = 7.8e-10

Table S295.  Gene #66: '14q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
14Q LOSS MUTATED 13 42 72
14Q LOSS WILD-TYPE 188 387 177

Figure S295.  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 = 1.62e-13 (Fisher's exact test), Q value = 1.2e-10

Table S296.  Gene #66: '14q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 616 59
14Q LOSS MUTATED 65 54 8
14Q LOSS WILD-TYPE 139 562 51

Figure S296.  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 = 0.000121 (Fisher's exact test), Q value = 0.059

Table S297.  Gene #67: '15q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
15Q LOSS MUTATED 13 37 49
15Q LOSS WILD-TYPE 127 88 199

Figure S297.  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 = 3.85e-17 (Chi-square test), Q value = 3e-14

Table S298.  Gene #67: '15q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
15Q LOSS MUTATED 19 37 28 68 10
15Q LOSS WILD-TYPE 328 185 44 155 39

Figure S298.  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 = 4.94e-07 (Chi-square test), Q value = 0.00031

Table S299.  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 101 139 93 137 40 97
15Q LOSS MUTATED 36 15 19 22 3 8
15Q LOSS WILD-TYPE 65 124 74 115 37 89

Figure S299.  Get High-res Image Gene #67: '15q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'15q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.41e-06 (Fisher's exact test), Q value = 0.0014

Table S300.  Gene #67: '15q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
15Q LOSS MUTATED 69 53 27
15Q LOSS WILD-TYPE 267 152 260

Figure S300.  Get High-res Image Gene #67: '15q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.01e-07 (Fisher's exact test), Q value = 6.6e-05

Table S301.  Gene #67: '15q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
15Q LOSS MUTATED 16 71 70
15Q LOSS WILD-TYPE 185 358 179

Figure S301.  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 = 9.08e-07 (Fisher's exact test), Q value = 0.00056

Table S302.  Gene #67: '15q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 616 59
15Q LOSS MUTATED 51 84 22
15Q LOSS WILD-TYPE 153 532 37

Figure S302.  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 = 1.42e-05 (Chi-square test), Q value = 0.0078

Table S303.  Gene #68: '16p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
16P LOSS MUTATED 5 19 2 25 4
16P LOSS WILD-TYPE 342 203 70 198 45

Figure S303.  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 = 2.47e-05 (Chi-square test), Q value = 0.013

Table S304.  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 101 139 93 137 40 97
16P LOSS MUTATED 14 1 7 5 0 2
16P LOSS WILD-TYPE 87 138 86 132 40 95

Figure S304.  Get High-res Image Gene #68: '16p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'16p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000424 (Fisher's exact test), Q value = 0.19

Table S305.  Gene #68: '16p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
16P LOSS MUTATED 25 20 6
16P LOSS WILD-TYPE 311 185 281

Figure S305.  Get High-res Image Gene #68: '16p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'16p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.23

Table S306.  Gene #68: '16p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
16P LOSS MUTATED 4 22 26
16P LOSS WILD-TYPE 197 407 223

Figure S306.  Get High-res Image Gene #68: '16p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'16q loss mutation analysis' versus 'MRNA_CNMF'

P value = 7.08e-08 (Chi-square test), Q value = 4.7e-05

Table S307.  Gene #69: '16q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
16Q LOSS MUTATED 59 20 13 16 33 7 62 23
16Q LOSS WILD-TYPE 65 16 10 79 39 13 41 17

Figure S307.  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 = 1.75e-13 (Fisher's exact test), Q value = 1.3e-10

Table S308.  Gene #69: '16q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
16Q LOSS MUTATED 76 21 136
16Q LOSS WILD-TYPE 64 104 112

Figure S308.  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 = 9.63e-12 (Chi-square test), Q value = 7e-09

Table S309.  Gene #69: '16q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
16Q LOSS MUTATED 161 107 46 50 26
16Q LOSS WILD-TYPE 186 115 26 173 23

Figure S309.  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 = 6.1e-17 (Chi-square test), Q value = 4.7e-14

Table S310.  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 101 139 93 137 40 97
16Q LOSS MUTATED 18 95 45 58 13 20
16Q LOSS WILD-TYPE 83 44 48 79 27 77

Figure S310.  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 = 8.18e-06 (Fisher's exact test), Q value = 0.0046

Table S311.  Gene #69: '16q loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
16Q LOSS MUTATED 40 73 54
16Q LOSS WILD-TYPE 107 60 63

Figure S311.  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 = 1.02e-09 (Fisher's exact test), Q value = 7.1e-07

Table S312.  Gene #69: '16q loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
16Q LOSS MUTATED 90 52 25
16Q LOSS WILD-TYPE 71 58 101

Figure S312.  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 = 3.37e-19 (Chi-square test), Q value = 2.6e-16

Table S313.  Gene #69: '16q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
16Q LOSS MUTATED 24 37 63 47 73 0 99 15
16Q LOSS WILD-TYPE 122 42 37 84 105 12 52 16

Figure S313.  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 = 3.58e-20 (Fisher's exact test), Q value = 2.8e-17

Table S314.  Gene #69: '16q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
16Q LOSS MUTATED 170 33 155
16Q LOSS WILD-TYPE 166 172 132

Figure S314.  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 = 5.49e-17 (Fisher's exact test), Q value = 4.2e-14

Table S315.  Gene #69: '16q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
16Q LOSS MUTATED 77 242 58
16Q LOSS WILD-TYPE 124 187 191

Figure S315.  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 = 3.27e-18 (Fisher's exact test), Q value = 2.5e-15

Table S316.  Gene #69: '16q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 616 59
16Q LOSS MUTATED 37 321 19
16Q LOSS WILD-TYPE 167 295 40

Figure S316.  Get High-res Image Gene #69: '16q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'17p loss mutation analysis' versus 'MRNA_CNMF'

P value = 8.23e-06 (Chi-square test), Q value = 0.0046

Table S317.  Gene #70: '17p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
17P LOSS MUTATED 58 19 11 40 47 3 27 15
17P LOSS WILD-TYPE 66 17 12 55 25 17 76 25

Figure S317.  Get High-res Image Gene #70: '17p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'17p loss mutation analysis' versus 'CN_CNMF'

P value = 6.2e-14 (Chi-square test), Q value = 4.6e-11

Table S318.  Gene #70: '17p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
17P LOSS MUTATED 87 122 25 117 22
17P LOSS WILD-TYPE 260 100 47 106 27

Figure S318.  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 = 5.8e-08 (Chi-square test), Q value = 3.8e-05

Table S319.  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 101 139 93 137 40 97
17P LOSS MUTATED 38 47 47 75 14 16
17P LOSS WILD-TYPE 63 92 46 62 26 81

Figure S319.  Get High-res Image Gene #70: '17p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'17p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.81e-10 (Chi-square test), Q value = 4e-07

Table S320.  Gene #70: '17p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
17P LOSS MUTATED 58 31 42 81 88 2 32 10
17P LOSS WILD-TYPE 88 48 58 50 90 10 119 21

Figure S320.  Get High-res Image Gene #70: '17p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'17p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.77e-05 (Fisher's exact test), Q value = 0.0096

Table S321.  Gene #70: '17p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
17P LOSS MUTATED 57 181 124
17P LOSS WILD-TYPE 144 248 125

Figure S321.  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 = 1.08e-10 (Chi-square test), Q value = 7.7e-08

Table S322.  Gene #71: '17q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
17Q LOSS MUTATED 17 2 2 29 30 0 5 7
17Q LOSS WILD-TYPE 107 34 21 66 42 20 98 33

Figure S322.  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 = 1.72e-06 (Fisher's exact test), Q value = 0.001

Table S323.  Gene #71: '17q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
17Q LOSS MUTATED 12 41 39
17Q LOSS WILD-TYPE 128 84 209

Figure S323.  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 = 8.88e-11 (Chi-square test), Q value = 6.3e-08

Table S324.  Gene #71: '17q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
17Q LOSS MUTATED 24 34 11 66 8
17Q LOSS WILD-TYPE 323 188 61 157 41

Figure S324.  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 = 7.48e-05 (Chi-square test), Q value = 0.037

Table S325.  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 101 139 93 137 40 97
17Q LOSS MUTATED 25 7 13 23 2 8
17Q LOSS WILD-TYPE 76 132 80 114 38 89

Figure S325.  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 = 9.69e-10 (Fisher's exact test), Q value = 6.7e-07

Table S326.  Gene #71: '17q loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
17Q LOSS MUTATED 51 7 19
17Q LOSS WILD-TYPE 96 126 98

Figure S326.  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 = 6.4e-07 (Fisher's exact test), Q value = 4e-04

Table S327.  Gene #71: '17q loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
17Q LOSS MUTATED 16 17 44
17Q LOSS WILD-TYPE 145 93 82

Figure S327.  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 = 9.87e-16 (Chi-square test), Q value = 7.6e-13

Table S328.  Gene #71: '17q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
17Q LOSS MUTATED 41 3 4 47 25 1 9 4
17Q LOSS WILD-TYPE 105 76 96 84 153 11 142 27

Figure S328.  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 = 1.28e-08 (Fisher's exact test), Q value = 8.7e-06

Table S329.  Gene #71: '17q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
17Q LOSS MUTATED 49 60 25
17Q LOSS WILD-TYPE 287 145 262

Figure S329.  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 = 4.97e-09 (Fisher's exact test), Q value = 3.4e-06

Table S330.  Gene #71: '17q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
17Q LOSS MUTATED 18 50 70
17Q LOSS WILD-TYPE 183 379 179

Figure S330.  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 = 1.62e-06 (Fisher's exact test), Q value = 0.00098

Table S331.  Gene #71: '17q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 616 59
17Q LOSS MUTATED 54 71 13
17Q LOSS WILD-TYPE 150 545 46

Figure S331.  Get High-res Image Gene #71: '17q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss mutation analysis' versus 'MRNA_CNMF'

P value = 0.000377 (Chi-square test), Q value = 0.17

Table S332.  Gene #72: '18p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
18P LOSS MUTATED 27 5 4 13 30 5 14 9
18P LOSS WILD-TYPE 97 31 19 82 42 15 89 31

Figure S332.  Get High-res Image Gene #72: '18p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'18p loss mutation analysis' versus 'CN_CNMF'

P value = 6.18e-10 (Chi-square test), Q value = 4.3e-07

Table S333.  Gene #72: '18p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
18P LOSS MUTATED 28 57 24 57 9
18P LOSS WILD-TYPE 319 165 48 166 40

Figure S333.  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 = 3.32e-06 (Chi-square test), Q value = 0.0019

Table S334.  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 101 139 93 137 40 97
18P LOSS MUTATED 13 14 30 36 3 11
18P LOSS WILD-TYPE 88 125 63 101 37 86

Figure S334.  Get High-res Image Gene #72: '18p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'18p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.88e-08 (Chi-square test), Q value = 3.2e-05

Table S335.  Gene #72: '18p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
18P LOSS MUTATED 17 7 19 51 35 4 22 5
18P LOSS WILD-TYPE 129 72 81 80 143 8 129 26

Figure S335.  Get High-res Image Gene #72: '18p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'18q loss mutation analysis' versus 'CN_CNMF'

P value = 6.11e-13 (Chi-square test), Q value = 4.5e-10

Table S336.  Gene #73: '18q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
18Q LOSS MUTATED 24 58 26 61 8
18Q LOSS WILD-TYPE 323 164 46 162 41

Figure S336.  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 = 7.01e-08 (Chi-square test), Q value = 4.6e-05

Table S337.  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 101 139 93 137 40 97
18Q LOSS MUTATED 21 15 33 36 2 7
18Q LOSS WILD-TYPE 80 124 60 101 38 90

Figure S337.  Get High-res Image Gene #73: '18q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'18q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.26e-06 (Chi-square test), Q value = 0.00076

Table S338.  Gene #73: '18q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
18Q LOSS MUTATED 21 8 17 50 34 3 24 3
18Q LOSS WILD-TYPE 125 71 83 81 144 9 127 28

Figure S338.  Get High-res Image Gene #73: '18q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'19p loss mutation analysis' versus 'MRNA_CNMF'

P value = 1.65e-05 (Chi-square test), Q value = 0.009

Table S339.  Gene #74: '19p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
19P LOSS MUTATED 17 4 0 5 15 1 1 0
19P LOSS WILD-TYPE 107 32 23 90 57 19 102 40

Figure S339.  Get High-res Image Gene #74: '19p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'19p loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000461 (Fisher's exact test), Q value = 0.2

Table S340.  Gene #74: '19p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
19P LOSS MUTATED 3 8 32
19P LOSS WILD-TYPE 137 117 216

Figure S340.  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 = 7.77e-13 (Chi-square test), Q value = 5.7e-10

Table S341.  Gene #74: '19p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
19P LOSS MUTATED 1 38 2 19 7
19P LOSS WILD-TYPE 346 184 70 204 42

Figure S341.  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 = 1.43e-08 (Chi-square test), Q value = 9.7e-06

Table S342.  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 101 139 93 137 40 97
19P LOSS MUTATED 8 0 7 23 0 0
19P LOSS WILD-TYPE 93 139 86 114 40 97

Figure S342.  Get High-res Image Gene #74: '19p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'19p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.19e-06 (Chi-square test), Q value = 0.0013

Table S343.  Gene #74: '19p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
19P LOSS MUTATED 10 4 4 20 26 0 1 0
19P LOSS WILD-TYPE 136 75 96 111 152 12 150 31

Figure S343.  Get High-res Image Gene #74: '19p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'19p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.82e-07 (Fisher's exact test), Q value = 0.00024

Table S344.  Gene #74: '19p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
19P LOSS MUTATED 42 18 5
19P LOSS WILD-TYPE 294 187 282

Figure S344.  Get High-res Image Gene #74: '19p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss mutation analysis' versus 'MRNA_CNMF'

P value = 7.41e-05 (Chi-square test), Q value = 0.037

Table S345.  Gene #75: '19q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
19Q LOSS MUTATED 14 3 0 3 13 1 1 0
19Q LOSS WILD-TYPE 110 33 23 92 59 19 102 40

Figure S345.  Get High-res Image Gene #75: '19q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'19q loss mutation analysis' versus 'CN_CNMF'

P value = 3.66e-10 (Chi-square test), Q value = 2.6e-07

Table S346.  Gene #75: '19q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
19Q LOSS MUTATED 2 30 0 15 6
19Q LOSS WILD-TYPE 345 192 72 208 43

Figure S346.  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 = 1.62e-05 (Chi-square test), Q value = 0.0089

Table S347.  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 101 139 93 137 40 97
19Q LOSS MUTATED 7 0 6 16 0 0
19Q LOSS WILD-TYPE 94 139 87 121 40 97

Figure S347.  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 = 5.18e-06 (Chi-square test), Q value = 0.003

Table S348.  Gene #75: '19q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
19Q LOSS MUTATED 7 2 3 19 19 0 1 0
19Q LOSS WILD-TYPE 139 77 97 112 159 12 150 31

Figure S348.  Get High-res Image Gene #75: '19q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'19q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.23e-07 (Fisher's exact test), Q value = 7.9e-05

Table S349.  Gene #75: '19q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
19Q LOSS MUTATED 35 14 2
19Q LOSS WILD-TYPE 301 191 285

Figure S349.  Get High-res Image Gene #75: '19q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss mutation analysis' versus 'CN_CNMF'

P value = 1.42e-06 (Chi-square test), Q value = 0.00086

Table S350.  Gene #76: '20p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
20P LOSS MUTATED 3 20 2 21 7
20P LOSS WILD-TYPE 344 202 70 202 42

Figure S350.  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 = 2.42e-05 (Chi-square test), Q value = 0.013

Table S351.  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 101 139 93 137 40 97
20P LOSS MUTATED 15 1 5 9 1 1
20P LOSS WILD-TYPE 86 138 88 128 39 96

Figure S351.  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 = 0.000148 (Fisher's exact test), Q value = 0.071

Table S352.  Gene #76: '20p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
20P LOSS MUTATED 21 21 5
20P LOSS WILD-TYPE 315 184 282

Figure S352.  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 = 2.75e-05 (Fisher's exact test), Q value = 0.014

Table S353.  Gene #76: '20p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
20P LOSS MUTATED 5 16 29
20P LOSS WILD-TYPE 196 413 220

Figure S353.  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 = 6.97e-05 (Chi-square test), Q value = 0.035

Table S354.  Gene #77: '20q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
20Q LOSS MUTATED 1 7 2 14 5
20Q LOSS WILD-TYPE 346 215 70 209 44

Figure S354.  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 = 2.82e-06 (Chi-square test), Q value = 0.0017

Table S355.  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 101 139 93 137 40 97
20Q LOSS MUTATED 11 0 1 3 0 1
20Q LOSS WILD-TYPE 90 139 92 134 40 96

Figure S355.  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 = 0.000102 (Fisher's exact test), Q value = 0.05

Table S356.  Gene #77: '20q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
20Q LOSS MUTATED 9 14 1
20Q LOSS WILD-TYPE 327 191 286

Figure S356.  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 = 4.78e-05 (Fisher's exact test), Q value = 0.024

Table S357.  Gene #77: '20q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
20Q LOSS MUTATED 2 7 19
20Q LOSS WILD-TYPE 199 422 230

Figure S357.  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 = 2.24e-05 (Fisher's exact test), Q value = 0.012

Table S358.  Gene #77: '20q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 616 59
20Q LOSS MUTATED 17 9 2
20Q LOSS WILD-TYPE 187 607 57

Figure S358.  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 = 1.67e-06 (Chi-square test), Q value = 0.001

Table S359.  Gene #78: '21q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
21Q LOSS MUTATED 9 31 9 28 9
21Q LOSS WILD-TYPE 338 191 63 195 40

Figure S359.  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 = 4.25e-05 (Chi-square test), Q value = 0.022

Table S360.  Gene #79: '22q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 124 36 23 95 72 20 103 40
22Q LOSS MUTATED 63 17 7 17 19 5 37 13
22Q LOSS WILD-TYPE 61 19 16 78 53 15 66 27

Figure S360.  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 = 1.42e-07 (Fisher's exact test), Q value = 9.2e-05

Table S361.  Gene #79: '22q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 125 248
22Q LOSS MUTATED 52 19 107
22Q LOSS WILD-TYPE 88 106 141

Figure S361.  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 = 2.97e-06 (Chi-square test), Q value = 0.0017

Table S362.  Gene #79: '22q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 347 222 72 223 49
22Q LOSS MUTATED 90 93 34 64 25
22Q LOSS WILD-TYPE 257 129 38 159 24

Figure S362.  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 = 5.32e-07 (Chi-square test), Q value = 0.00033

Table S363.  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 101 139 93 137 40 97
22Q LOSS MUTATED 26 46 38 67 8 15
22Q LOSS WILD-TYPE 75 93 55 70 32 82

Figure S363.  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 = 0.000476 (Fisher's exact test), Q value = 0.21

Table S364.  Gene #79: '22q loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
22Q LOSS MUTATED 37 63 39
22Q LOSS WILD-TYPE 110 70 78

Figure S364.  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 = 1.64e-05 (Fisher's exact test), Q value = 0.0089

Table S365.  Gene #79: '22q loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
22Q LOSS MUTATED 74 40 25
22Q LOSS WILD-TYPE 87 70 101

Figure S365.  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 = 4.93e-06 (Chi-square test), Q value = 0.0028

Table S366.  Gene #79: '22q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 146 79 100 131 178 12 151 31
22Q LOSS MUTATED 29 23 45 38 81 1 54 7
22Q LOSS WILD-TYPE 117 56 55 93 97 11 97 24

Figure S366.  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 = 6.75e-12 (Fisher's exact test), Q value = 4.9e-09

Table S367.  Gene #79: '22q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
22Q LOSS MUTATED 148 31 99
22Q LOSS WILD-TYPE 188 174 188

Figure S367.  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 = 1.07e-08 (Fisher's exact test), Q value = 7.3e-06

Table S368.  Gene #79: '22q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
22Q LOSS MUTATED 45 185 63
22Q LOSS WILD-TYPE 156 244 186

Figure S368.  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 = 5.27e-07 (Fisher's exact test), Q value = 0.00033

Table S369.  Gene #79: '22q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 204 616 59
22Q LOSS MUTATED 39 238 16
22Q LOSS WILD-TYPE 165 378 43

Figure S369.  Get High-res Image Gene #79: '22q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Xq loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000433 (Fisher's exact test), Q value = 0.19

Table S370.  Gene #80: 'Xq loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 336 205 287
XQ LOSS MUTATED 15 14 2
XQ LOSS WILD-TYPE 321 191 285

Figure S370.  Get High-res Image Gene #80: 'Xq loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Xq loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.88e-05 (Fisher's exact test), Q value = 0.015

Table S371.  Gene #80: 'Xq loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 201 429 249
XQ LOSS MUTATED 0 12 18
XQ LOSS WILD-TYPE 201 417 231

Figure S371.  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 = 913

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

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

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[2] 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)
[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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